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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid40501993,
year = {2025},
author = {Hanna, AR and Shepherd, SJ and Datto, GA and Navarro, IB and Ricciardi, AS and Padilla, MS and Srikumar, N and Zhang, S and Yamagata, HM and Meng, NY and Buser, JR and Mitchell, MJ and Issadore, DA},
title = {Automated and parallelized microfluidic generation of large and precisely-defined lipid nanoparticle libraries.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.26.656157},
pmid = {40501993},
issn = {2692-8205},
abstract = {Building on the success of lipid nanoparticles (LNPs) in vaccines, LNPs are being developed for a broad set of therapeutic applications by changing both the structures of the lipids used to formulate each LNP and their relative proportions. Because lipid synthesis and in vivo screening have been parallelized using combinatorial chemistry and LNP barcoding respectively, the manual and sequential microfluidic formulation of LNPs has become the rate-limiting step in the discovery process. In this work, we present a high-throughput, automated microfluidic platform capable of generating large, precisely-defined LNP libraries in parallel at a rate of one distinct formulation every three seconds. Each formulation is defined by varying the reagent flow ratios into one of eight microscale mixers using litho-graphically encoded fluidic resistors and dynamically controlled external pressure supplies. The microfluidic chip is integrated with custom frobotic plate handling for the rapid collection of each distinct formulation. Using this platform, we produce a library of 96 formulations, which we profile physicochemically and evaluate in terms of both in vitro and in vivo transfection.},
}

@article {pmid40501638,
year = {2025},
author = {Goldstein, I and Hale, JJ and Ehrenreich, IM},
title = {Global epistasis in budding yeast driven by many natural variants whose effects scale with fitness.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40501638},
issn = {2692-8205},
abstract = {Global epistasis is a phenomenon in which the effects of genetic perturbations depend on the fitness of the individuals in which they occur. In populations with natural genetic variation, global epistasis arises from interactions between perturbations and polymorphic loci that are mediated by fitness. To investigate the prevalence and characteristics of loci involved in these interactions in the budding yeast Saccharomyces cerevisiae, we used combinatorial DNA barcode sequencing to measure the fitness of 169 cross progeny (segregants) subjected to 8,126 CRISPRi perturbations across two environments. Global epistasis was evident in these data, with more fit segregants within each environment exhibiting greater sensitivity to genetic perturbations than less fit segregants. We dissected the genetic basis of this global epistasis by scanning the genome for loci whose effects covary with CRISPRi-induced reductions in population fitness. This approach identified 58 loci that interact with fitness, most of which exhibited larger effects in the absence of genetic perturbations. In aggregate, these loci explained the observed global epistasis in each environment and demonstrated that the loci contributing to global epistasis largely overlap with those influencing fitness in unperturbed conditions.},
}

@article {pmid40501448,
year = {2025},
author = {Taylor, KE and Saunders, GW},
title = {First report of articuliths (free-living geniculate corallines, Corallinales, Rhodophyta) in the northern hemisphere revealed during diversity surveys of Haida Gwaii, British Columbia, Canada.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70049},
pmid = {40501448},
issn = {1529-8817},
support = {//Canada Foundation for Innovation/ ; //New Brunswick Innovation Foundation/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {Free-living coralline beds are typically composed of rhodoliths, or unattached non-geniculate coralline algae. In 2017, the first beds comprised primarily of free-living geniculate coralline algae, termed articuliths, were documented in Arraial do Cabo Bay in southeastern Brazil. During routine barcode surveys of the Haida Gwaii, British Columbia, Canada flora, 16 rhodolith-like specimens were collected from a rhodolith bed that DNA sequences assigned to the geniculate taxa Calliarthron tuberculosum and Bossiella sp. 1heteroforma. To our knowledge, articuliths have not been documented outside of Brazil; this discovery thus documents the first instance of northern hemisphere articuliths. Despite disparate gross morphologies to attached conspecific populations, anatomical observations revealed internal anatomies consistent with those of attached forms but with a significant reduction in the number of genicula and increased uniformity in intergenicular shape.},
}

@article {pmid40500871,
year = {2025},
author = {Gómez, GF and Laurito, M and Correa, MM},
title = {Molecular analysis supports at least two putative species within Anopheles pseudopunctipennis s.l. on the American mainland.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.12815},
pmid = {40500871},
issn = {1365-2915},
support = {2023-66350//Escuela de Microbiología, Universidad de Antioquia/ ; },
abstract = {Anopheles (Anopheles) pseudopunctipennis, involved in seasonal malaria transmission in the Andean foothills and American coastal areas, was previously proposed as a species complex based on cross-mating experiments and population genetic analyses. In this work, a fragment of the mitochondrial gene cytochrome c oxidase subunit I or COI barcode region, and the nuclear second internal transcribed spacer (ITS2) were analysed in Colombian An. pseudopunctipennis s.l. specimens; the obtained sequences were compared to publicly available data using phylogeny and distance-based species delimitation approaches. Assemble Species by Automatic Partitioning (ASAP) and coalescent-based approaches provided strong evidence of at least two putative species on the American mainland, here designated as the North-Central and Southern lineages. The North-Central lineage is primarily found in southern/southwestern United States, Central America (Mexico and Honduras) and northwestern Colombia, while the Southern lineage is mainly detected in the Colombian Pacific and Argentina; there were some co-occurrences of these lineages in the Colombian regions. The definition of these putative species is crucial for understanding their bionomy, ecology and potential role in malaria transmission. Further research, including a more comprehensive sampling and population genetic analysis, is needed to fully elucidate their evolutionary history and demographic dynamics.},
}

@article {pmid40500336,
year = {2025},
author = {Moraes Zenker, M and Portella, TP and Pessoa, FAC and Bengtsson-Palme, J and Galetti, PM},
title = {Correction: Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20045},
doi = {10.1038/s41598-025-02631-6},
pmid = {40500336},
issn = {2045-2322},
}

@article {pmid40498465,
year = {2025},
author = {Samimi, A and Hengoju, S and Martin, K and Rosenbaum, MA},
title = {Advancing droplet-based microbiological assays: optofluidic detection meets multiplexed droplet generation.},
journal = {The Analyst},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5an00130g},
pmid = {40498465},
issn = {1364-5528},
abstract = {Microbiological assays are crucial in understanding microbial ecology and developing new bioproducts. Given the significance of these assays, there is a growing interest in developing high throughput experimentation methods capable of assay multiplexing to enhance the accuracy and efficiency. In this study, we integrate a multiplexed droplet generation set-up into an optofluidic detection chip to facilitate rapid and high throughput analysis of microbiological assays. The optofluidic detection set-up at the same time enables fast and sensitive assessment of droplet condition and content, providing analysis scalability in a high throughput manner. Employing the integration, we produced unique fluorescence barcoded droplets containing defined concentrations of various carbon sources, allowing the simultaneous investigation of microbial growth and metabolic capacity under different experimental conditions. We successfully validated the robustness of the established setup in analyzing and distinguishing different fluorescence barcodes. Our findings highlight the potential of the integrated platform for a broader range of applications in high throughput drug screening, environmental monitoring, and microbiology research.},
}

@article {pmid40494311,
year = {2025},
author = {van Galen, LG and Corrales, A and Truong, C and van den Hoogen, J and Kumar, S and Manley, BF and Stewart, JD and Kohout, P and Baldrian, P and Větrovský, T and Crowther, TW and Kiers, ET and Van Nuland, ME},
title = {The biogeography and conservation of Earth's 'dark' ectomycorrhizal fungi.},
journal = {Current biology : CB},
volume = {35},
number = {11},
pages = {R563-R574},
doi = {10.1016/j.cub.2025.03.079},
pmid = {40494311},
issn = {1879-0445},
mesh = {*Mycorrhizae/physiology/classification/genetics ; *Biodiversity ; *Conservation of Natural Resources ; *Soil Microbiology ; Mycobiome ; Phylogeography ; Earth, Planet ; Symbiosis ; },
abstract = {Breakthroughs in DNA sequencing have upended our understanding of fungal diversity. Only ∼155,000 of the 2-3 million fungal species on the planet have been formally described and named, and 'dark taxa' - species known only from sequences - represent the vast majority of species within the fungal kingdom. The International Code of Nomenclature requires physical type specimens to officially recognize new fungal species, making it difficult to name dark taxa. This is a significant problem for conservation because, without names, species cannot be recognized for environmental and legal protection. Symbiotic ectomycorrhizal (EcM) fungi play a particularly important role in forest carbon drawdown, but at present we have little understanding of how many EcM fungal species exist, or where to prioritize research activities to survey and describe EcM fungal lineages. In this review, we use global soil metabarcoding databases (GlobalFungi and the Global Soil Mycobiome consortium) to evaluate current estimates of the total number of EcM fungal species on Earth, outline the current state of undescribed EcM dark taxa, and identify priority regions for future dark taxa exploration. The metabarcoding databases include up to 219,730 EcM fungal operational taxonomic units (OTUs) detected from almost 39,500 samples. Using Chao richness estimates corrected for extrapolating species numbers from metabarcoding datasets, we predict that the global diversity of EcM fungi could be ∼25,500-55,500 species. Dark taxa - those that do not match species-level identities - account for 79-83% of OTUs. Oceania contains the highest percentage of dark taxa (87%), and Europe the lowest (78%). Priority 'darkspots' for future research occur predominantly in tropical regions, but also in selected temperate forests at both southern and northern latitudes. We propose concrete steps to reduce the prevalence of EcM darkspots, including performing targeted field surveys, barcoding fungaria voucher specimens, and developing new ways to describe and conserve fungal taxa from DNA alone.},
}

*Mycorrhizae/physiology/classification/genetics
*Biodiversity
*Conservation of Natural Resources
*Soil Microbiology
Mycobiome
Phylogeography
Earth, Planet
Symbiosis

@article {pmid40493884,
year = {2025},
author = {Loke, J and Kim, PG and Nguyen, TTP and Boileau, M and McConkey, M and Miller, AP and Shin, W and Hergott, CB and Ericsson, M and Nordstrom, A and Montero-Llopis, P and Armstrong, SA and Mancias, JD and Ebert, BL},
title = {An in vivo barcoded CRISPR-Cas9 screen identifies Ncoa4-mediated ferritinophagy as a dependence in Tet2-deficient hematopoiesis.},
journal = {Blood},
volume = {},
number = {},
pages = {},
doi = {10.1182/blood.2024028033},
pmid = {40493884},
issn = {1528-0020},
abstract = {TET2 is among the most commonly mutated genes in both clonal hematopoiesis and myeloid malignancies, thus, the ability to identify selective dependencies in TET2 deficient cells has broad translational significance. Here, we identify regulators of Tet2 knockout (KO) hematopoietic stem and progenitor cell (HSPC) expansion using an in vivo CRISPR-Cas9 KO screen, in which nucleotide barcoding enabled large-scale clonal tracing of Tet2 deficient HSPCs in a physiological setting. Our screen identified candidate genes, including Ncoa4, that are selectively required for Tet2 KO clonal outgrowth compared to wild-type (WT). Ncoa4 targets ferritin for lysosomal degradation (ferritinophagy), maintaining intracellular iron homeostasis by releasing labile iron (Fe2+) in response to cellular demands. In Tet2-deficient HSPCs, increased mitochondrial ATP production correlates with increased cellular iron requirements, and in turn, promotes Ncoa4-dependent ferritinophagy. Restricting iron availability reduces Tet2 KO stem cell numbers, revealing a dependency in TET2-mutated myeloid neoplasms.},
}

@article {pmid40492465,
year = {2025},
author = {Verbruggen, H and Uthanumallian, K and Powrie, F and Jalali, T and Cremen, C and Preuss, M and Duchene, S and Diaz-Tapia, P},
title = {Scaling Up Species Delimitation From DNA Barcodes to Whole Organelle Genomes: Strong Evidence for Discordance Among Genes and Methods for the Red Alga Dasyclonium.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14132},
doi = {10.1111/1755-0998.14132},
pmid = {40492465},
issn = {1755-0998},
support = {4-G046WSD//Australian Biological Resources Study/ ; CEECIND:2023.06155//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {Molecular sequence data have become a ubiquitous tool for delimiting species and are particularly important in organisms where morphological traits are not informative about species boundaries. A range of statistical methods have been developed to derive species limits from molecular data, for example, by quantifying changes in branching patterns in phylogenetic trees. We aim to investigate how such methods scale up from single genes to whole organelle genomes. We gathered chloroplast genome data from 38 samples of the red algal genus Dascyclonium and analysed them with the popular species delimitation methods Assemble Species by Automatic Partitioning (ASAP), General Mixed Yule Coalescent (GMYC), and Poisson Tree Processes (PTP). We show extensive variation in inferred species boundaries depending on the method and dataset used. Genome-scale analyses differed substantially between methods, with ASAP predicting the fewest species, PTP intermediate, and GMYC inferring many species. Based on a series of simulations, we identify a tendency of GMYC to overestimate species numbers as alignments increase in length, while the other two methods are not sensitive to this scaling. Gene-by-gene analyses show strong differences in predicted species limits, which is unexpected seeing that all genes are on a single uniparentally inherited chromosome, and highlight that choosing a particular gene as a DNA barcode has significant consequences for species diversity estimates. We show extensive cryptic diversity in the genus Dasyclonium and propose a consensus solution for species limits based on our combined results, enriched with biogeographic and morphological interpretations. Finally, we make recommendations for interpreting the results and improving the inferences drawn from species delimitation methods.},
}

@article {pmid40492407,
year = {2025},
author = {Shibata, D},
title = {Human brain ancestral barcodes.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {40492407},
issn = {2050-084X},
support = {P01 CA196569/CA/NCI NIH HHS/United States ; R01 CA271237/CA/NCI NIH HHS/United States ; P01CA196569/NH/NIH HHS/United States ; CA271237/NH/NIH HHS/United States ; },
mesh = {Humans ; *Brain/cytology/metabolism ; Male ; *DNA Methylation ; Neurons ; CpG Islands ; Single-Cell Analysis ; Chromosomes, Human, X/genetics ; },
abstract = {Dynamic CpG methylation 'barcodes' were read from 15,000-21,000 single cells from three human male brains. To overcome sparse sequencing coverage, the barcode had ~31,000 rapidly fluctuating X-chromosome CpG sites (fCpGs), with at least 500 covered sites per cell and at least 30 common sites between cell pairs (average of ~48). Barcodes appear to start methylated and record mitotic ages because excitatory neurons and glial cells that emerge later in development were less methylated. Barcodes are different between most cells, with average pairwise differences (PWDs) of ~0.5 between cells. About 10 cell pairs per million were more closely related with PWDs <0.05. Barcodes appear to record ancestry and reconstruct trees where more related cells had similar phenotypes, albeit some pairs had phenotypic differences. Inhibitory neurons showed more evidence of tangential migration than excitatory neurons, with related cells in different cortical regions. fCpG barcodes become polymorphic during development and can distinguish between thousands of human cells.},
}

Humans
*Brain/cytology/metabolism
Male
*DNA Methylation
Neurons
CpG Islands
Single-Cell Analysis
Chromosomes, Human, X/genetics

@article {pmid40492230,
year = {2025},
author = {Song, WL and Jiang, ZQ and Li, M and Leontyev, D and Gao, Y and Chen, SL},
title = {Comprehensive revision of Lycogala (Myxomycetes) in subtropical China: morphological and phylogenetic insights and ten new species.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e147535},
pmid = {40492230},
issn = {2210-6340},
abstract = {In recent years, significant advancements have been made in the taxonomy and phylogenetics of Lycogala, leading to the description of numerous new species. However, Lycogala in China has never been systematically revised, and only eight species have been recorded. In this study, specimens of Lycogala from 22 sites in 11 provinces or cities of subtropical China were studied in terms of morphology, two-gene phylogenetic analysis (nuclear 18S rDNA and cytochrome oxidase subunit I), and ASAP species delimitation. We provide a checklist, which includes 21 species of Lycogala collected in subtropical China. These species include (1) seven species already known from the country, for which we report new localities, (2) four species, new to China (Lycogalaalisaulianovae, L.fossiculatum, L.skovorodaense, and L.succineum) and (3) ten species new to science, including L.annulatum sp. nov., L.chinense sp. nov., L.convexum sp. nov., L.fasciculovesiculiferum sp. nov., L.helvolum sp. nov., L.indirubinum sp. nov., L.nigrum sp. nov., L.planovesiculiferum sp. nov., L.projectum sp. nov., and L.uviforme sp. nov. A comprehensive morphological description, detailed illustrations, molecular barcoding data, and putative position in phylogenies are provided for the newly described taxa.},
}

@article {pmid40492207,
year = {2025},
author = {Pimvichai, P and Enghoff, H and Breugelmans, K and Segers, B and Backeljau, T},
title = {Morphological and DNA sequence data uncover a new millipede species in the Thyropygus opinatus subgroup and assign T. peninsularis to this subgroup (Diplopoda: Spirostreptida: Harpagophoridae).},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19277},
pmid = {40492207},
issn = {2167-8359},
mesh = {Animals ; Thailand ; Phylogeny ; *Arthropods/genetics/classification/anatomy & histology ; Male ; Sequence Analysis, DNA ; Female ; Species Specificity ; },
abstract = {The millipede genus Thyropygus Pocock, 1894 is one of the most diverse genera within the family Harpagophoridae in Southeast Asia. The Thyropygus opinatus subgroup, belonging to the T. allevatus group, is distinguished by the presence of an additional projection on the anterior coxal fold. Here, we describe a new species of the T. opinatus subgroup, Thyropygus payamense sp. nov., from Payam Island, Ranong Province, Thailand, based on morphological and DNA sequence data. The mean interspecific COI divergence between the new species and other Thyropygus species is 0.13 ± 0.02 (range: 0.07-0.16). The new species is distinguished by (1) a small, slender, pointed spine at base of femoral spine, (2) a short, triangular mesal process of the anterior coxal fold, and (3) a short, slender, slightly mesad-curving tibial spine. Additionally, T. peninsularis Hoffman, 1982 is confirmed as a member of the T. opinatus subgroup, because it shares key gonopodal characters with other species in this subgroup, while COI and 16S rRNA sequence data firmly support this new classification, with a mean interspecific COI sequence divergence of 0.13 ± 0.03 (range: 0.07-0.17) from other species in the T. allevatus group. An identification key for all 29 species in the T. opinatus subgroup is provided. Further research is needed to assess the taxonomic status of, and phylogenetic relationships within, this subgroup, which, except for two species, may tentatively represent an endemic species radiation in the peninsular area of Thailand, Malaysia and Myanmar.},
}

Animals
Thailand
Phylogeny
*Arthropods/genetics/classification/anatomy & histology
Male
Sequence Analysis, DNA
Female
Species Specificity

@article {pmid40491537,
year = {2025},
author = {Haque, MA and Hadi, SB and Sumona, AA and Rashid, J and Khan, MGQ and Alam, MS},
title = {Morpho-Molecular Identification of Common Freshwater Loaches Collected From Different Ecosystems of Bangladesh.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71559},
pmid = {40491537},
issn = {2045-7758},
abstract = {The biodiversity of hill stream fishes, especially loaches, in Bangladesh is declining, despite limited exploration. Conservation strategies can flourish through the effective identification of species. Ambiguous loaches were collected to resolve taxonomic confusion. Morphology was analyzed through morphometric and meristic traits, with mitochondrial COI and nuclear RAG1 genes as molecular markers. Sixteen morphotypes are found in 60 specimens, and the molecular study confirmed the existence of seven species. Furthermore, the species delimitation method ASAP suggests seven species according to the best partition. A low level of intraspecific diversity is found in the RAG1 gene analysis compared with the COI gene. The lowest interspecific genetic divergence (3.7%) was observed between Botia lohachata and Botia rostrata , whereas Canthophrys gongota showed the highest interspecific genetic divergence (24.45%) with B. lohachata. A potential barcoding gap of 2.52% in the COI gene is typically the threshold for distinguishing intra-species from inter-species comparisons. In the maximum likelihood phylogenetic tree of both COI and RAG1 gene sequences, the species are divided into distinct clades with high bootstrap support, and specimens within the same species do not converge. Morphology, along with the molecular data of this study, will strengthen conservation efforts for loaches.},
}

@article {pmid40491322,
year = {2025},
author = {Cao, J and Guo, Z and Xu, X and Li, P and Fang, Y and Deng, S},
title = {Advances in CRISPR-Cas9 in lineage tracing of model animals.},
journal = {Animal models and experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/ame2.70033},
pmid = {40491322},
issn = {2576-2095},
support = {22SH19//Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Collaborative Innovation Program of the Chinese Academy of Sciences/ ; 2023-PT180-01//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; },
abstract = {Cell lineage tracing is a key technology for describing the developmental history of individual progenitor cells and assembling them to form a lineage development tree. However, traditional methods have limitations of poor stability and insufficient resolution. As an efficient and flexible gene editing tool, CRISPR-Cas9 system has been widely used in biological research. Furthermore, CRISPR-Cas9 gene editing-based tracing methods can introduce fluorescent proteins, reporter genes, or DNA barcodes for high-throughput sequencing, enabling precise lineage analysis, significantly improving precision and resolution, and expanding its application range. In this review, we summarize applications of CRISPR-Cas9 system in cell lineage tracing, with special emphasis on its successful applications in traditional model animals (e.g., zebrafish and mice), large animal models (pigs), and human cells or organoids. We also discussed its potential prospects and challenges in xenotransplantation and regenerative medicine.},
}

@article {pmid40490500,
year = {2025},
author = {Robinson, CM and Carreño, D and Weber, T and Chen, Y and Riglar, DT},
title = {A discovery platform for identification of host-induced bacterial biosensors from diverse sources.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {40490500},
issn = {1744-4292},
support = {211230/Z/18/Z//Wellcome Trust (WT)/ ; President's PhD Scholarship//Imperial College London (ICL)/ ; },
abstract = {Synthetic biology approaches such as whole-cell biosensing and 'sense-and-respond' therapeutics aim to enlist the vast sensing repertoire of gut microbes to drive cutting-edge clinical and research applications. However, well-characterised circuit components that sense health- and disease-relevant conditions within the gut remain limited. Here, we extend the flexibility and power of a biosensor screening platform using bacterial memory circuits. We construct libraries of sensory components sourced from diverse gut bacteria using a bespoke two-component system identification and cloning pipeline. Tagging unique strains using a hypervariable DNA barcode enables parallel tracking of thousands of unique clones, corresponding to ~150 putative biosensors, in a single experiment. Evaluating sensor activity and performance heterogeneity across various in vitro and in vivo conditions using mouse models, we identify several biosensors of interest. Validated hits include biosensors with relevance for autonomous control of synthetic functions within the mammalian gut and for non-invasive monitoring of inflammatory disease using faecal sampling. This approach will promote rapid biosensor engineering to advance the development of synthetic biology tools for deployment within complex environments.},
}

@article {pmid40490497,
year = {2025},
author = {Löbbert, A and Lorz, N and Matthees, ESF and Rößler, P and Hoffmann, C and Gossert, AD},
title = {GPCR kinases phosphorylate GPCR C-terminal peptides in a hierarchical manner.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {899},
pmid = {40490497},
issn = {2399-3642},
support = {31-208029//Swiss National Science Foundation | National Center of Competence in Research Affective Sciences - Emotions in Individual Behaviour and Social Processes (National Centre of Competence in Research Affective Sciences)/ ; ETH-37 19-2//Eidgenössische Technische Hochschule Zürich (Federal Institute of Technology Zurich)/ ; },
mesh = {Phosphorylation ; Humans ; *Receptors, G-Protein-Coupled/metabolism/chemistry ; *G-Protein-Coupled Receptor Kinase 2/metabolism ; *G-Protein-Coupled Receptor Kinases/metabolism ; *Peptides/metabolism/chemistry ; *G-Protein-Coupled Receptor Kinase 1/metabolism ; Rhodopsin/metabolism/chemistry ; Receptors, Adrenergic, beta-2/metabolism ; },
abstract = {Responses from G protein-coupled receptors (GPCRs) are downregulated in a precisely orchestrated process called desensitization. This process consists of two major steps: phosphorylation of the receptor by GPCR kinases (GRKs), predominantly on its C-terminus, and recruitment of arrestin, resulting in different signaling outcomes. Yet, it remains unclear how the phosphorylation pattern on the receptor is determined. We carried out an NMR-based study of the phosphorylation patterns generated by GRK1 and GRK2 on C-terminal peptides of selected receptors (rhodopsin for GRK1, and β1- and β2-adrenergic receptors (ARs) for GRK2). Our data reveal that the kinases are promiscuous with respect to the substrate peptide, but produce clearly defined phosphorylation patterns on each substrate. We found pronounced differences in the rates at which certain residues are phosphorylated, in particular in the PXPP motifs in rhodopsin and β1AR. These results show that GRKs produce well-defined phosphorylation patterns in absence of further modulators like the full receptor or Gβγ, and that the time profile of the phosphorylation barcode seems to be largely encoded in the minimal pair of C-terminal peptide and GRK. The data further suggest that arrestin might encounter different phosphorylation barcodes over time, hinting at the possibility of time-dependent arrestin responses.},
}

Phosphorylation
Humans
*Receptors, G-Protein-Coupled/metabolism/chemistry
*G-Protein-Coupled Receptor Kinase 2/metabolism
*G-Protein-Coupled Receptor Kinases/metabolism
*Peptides/metabolism/chemistry
*G-Protein-Coupled Receptor Kinase 1/metabolism
Rhodopsin/metabolism/chemistry
Receptors, Adrenergic, beta-2/metabolism

@article {pmid40489934,
year = {2025},
author = {Arnela, M and Vidaña-Vila, E and Fantinelli, A and Moñux-Bernal, A and Vaquerizo-Serrano, J and Socoró, JC},
title = {Generation of ultrasonic and audible sound waves for the automatic classification of packaging waste in reverse vending machines.},
journal = {Waste management (New York, N.Y.)},
volume = {204},
number = {},
pages = {114934},
doi = {10.1016/j.wasman.2025.114934},
pmid = {40489934},
issn = {1879-2456},
abstract = {Reverse vending machines (RVMs) are essential for promoting waste sorting at the source by offering incentives for recycling. However, current RVMs, which primarily rely on expensive sensors such as barcode scanners and computer vision systems, face limitations including unreadable barcodes, high computational demands, and sensitivity to environmental conditions like lighting. This paper presents an alternative approach using acoustic sensors for waste classification. The proposed method consists of emitting ultrasonic and audible sound waves towards the recyclable object and, by analyzing the variations in the acoustic field, an artificial intelligence system classifies the material. For doing so, the system uses the ultrasonic and audible impulse response of each item, measured using the exponential sine sweep (ESS) technique. To validate this approach, a proof-of-concept has been developed and tested in a controlled environment using a scaled replica of a reverberation chamber, designed to achieve ideal acoustic conditions. Acoustic impulse responses have been captured using ESS emitted by an omnidirectional parametric loudspeaker (OPL), which generates both ultrasonic and audible sound waves via the parametric acoustic array (PAA) effect. This setup allows for simultaneous collection of ultrasonic and audible impulse responses for each recyclable item. The collected acoustic data has then been used to train classical machine learning and deep learning models to classify the introduced material, specifically plastic, glass, cardboard, and metallic cans. The results demonstrate a promising classification accuracy of more than 90%, highlighting the potential of this acoustic technology for waste sorting and supporting further research into its application in RVMs.},
}

@article {pmid40489257,
year = {2025},
author = {Feng, Y and Chen, D and Applegate, C and Gonzalez Medina, N and Kuo, CW and Arogundade, OH and Wright, CL and Xu, F and Drnevich, J and Smith, AM},
title = {Nanocoding: Lipid Nanoparticle Barcoding for Multiplexed Single-Cell RNA Sequencing.},
journal = {ACS nano},
volume = {19},
number = {24},
pages = {22079-22092},
doi = {10.1021/acsnano.5c02111},
pmid = {40489257},
issn = {1936-086X},
mesh = {*Single-Cell Analysis/methods ; *Nanoparticles/chemistry ; *Lipids/chemistry ; Animals ; Mice ; *Sequence Analysis, RNA/methods ; Humans ; Liposomes ; },
abstract = {Sample multiplexing is an emerging method in single-cell RNA sequencing (scRNA-seq) that addresses high costs and batch effects. Current multiplexing schemes use DNA labels to barcode cell samples but are limited in their stability and extent of labeling of heterogeneous cell populations. Here, we describe nanocoding, a technology that applies lipid nanoparticles (LNPs) for high barcode labeling density in multiplexed scRNA-seq. LNPs reduce dependencies on cell surface labeling mechanisms due to multiple controllable means of cell uptake, amplifying barcode loading 10-100-fold and allowing both protection and efficient release by upon cell lysis. In cultured cell lines and heterogeneous cells from tissue digests, nanocoding occurs in 40 min with stability after sample mixing and requires only commercially available reagents without complex chemical modifications. In spleen digests, 6-plex barcoded samples show minimal unlabeled cells, with all barcodes giving bimodal count distributions. Challenging samples from adipose tissue of obese rodents containing lipid-rich debris and heterogeneous cells show more than 95% labeling with all known subtypes identified. Using nanocoding, we investigate gene expression changes related to aging in adipose tissue, profiling cells that could not be readily identified with current direct conjugate methods using lipid or antibody conjugates. The ease of generating and tuning these constructs may afford efficient and robust sample multiplexing with minimal crosstalk.},
}

*Single-Cell Analysis/methods
*Nanoparticles/chemistry
*Lipids/chemistry
Animals
Mice
*Sequence Analysis, RNA/methods
Humans
Liposomes

@article {pmid40488904,
year = {2025},
author = {Kwasnoski, L and Brown, J and Taylor, J and Watson, JL and Oleyar, D and Ellis, VA},
title = {Avian haemosporidian parasite prevalence and diversity in two populations of the American kestrel (Falco sparverius).},
journal = {Parasitology research},
volume = {124},
number = {6},
pages = {60},
pmid = {40488904},
issn = {1432-1955},
support = {DEL00774, DEL00854, NE1943, NE2443//USDA Hatch/ ; },
mesh = {Animals ; *Falconiformes/parasitology ; *Haemosporida/genetics/isolation & purification/classification ; *Bird Diseases/parasitology/epidemiology ; *Genetic Variation ; Prevalence ; Utah/epidemiology ; Cytochromes b/genetics ; *Protozoan Infections, Animal/epidemiology/parasitology ; Delaware/epidemiology ; Phylogeny ; },
abstract = {Parasite communities vary among host species and across space. However, little is known about differences in parasite communities between geographically and genetically distinct populations of the same host species. American kestrels (Falco sparverius) are small falcons with regionally distinct genetic populations across North America. We sampled kestrels from Delaware and Utah for avian haemosporidian parasites (genera: Haemoproteus, Plasmodium, and Leucocytozoon) and used molecular barcoding of the parasite cytochrome b gene (cyt b) to quantify parasite genetic lineage diversity. We identified four lineages of Haemoproteus parasites and one Leucocytozoon lineage infecting kestrels. A comparison with previous studies suggests that most of these lineages are largely restricted to kestrels. We found similar infection prevalence and lineage composition between the sites. All kestrels sampled in Utah were adults (i.e., sampled after hatch year), but in Delaware, we found adult birds had a higher infection prevalence than juveniles (i.e., hatch-year birds). Despite harboring largely the same parasite lineages, kestrels are unlikely to disperse between Utah and Delaware. The similarity in parasite lineages in the two kestrel populations could be due to a number of factors including broadly distributed vector species (of which little is known), movement of alternative and undetected host species, or transmission during migration or on overwintering grounds. Alternatively, the cyt b gene might not capture recent genetic differentiation among the parasites. Future studies should explore these various possibilities to understand the mechanisms underpinning parasite distributions across genetically structured host populations.},
}

Animals
*Falconiformes/parasitology
*Haemosporida/genetics/isolation & purification/classification
*Bird Diseases/parasitology/epidemiology
*Genetic Variation
Prevalence
Utah/epidemiology
Cytochromes b/genetics
*Protozoan Infections, Animal/epidemiology/parasitology
Delaware/epidemiology
Phylogeny

@article {pmid40487348,
year = {2025},
author = {Inumaru, M and Itokawa, K and Matsumura, R and Sawabe, K and Watanabe, M and Isawa, H and Kasai, S and Higa, Y},
title = {COI barcoding can distinguish bisexual and parthenogenetic populations of Haemaphysalis longicornis in Japan: Revisiting methods with SNP analysis as another possible method.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {27},
number = {},
pages = {101083},
pmid = {40487348},
issn = {2213-2244},
abstract = {Haemaphysalis longicornis, the Asian long-horned tick, is an important vector for various infectious diseases, such as severe fever with thrombocytopenia syndrome (SFTS) and Japanese spotted fever. In this species, a triploid parthenogenetic reproductive form occurs along with a diploid bisexual form. Several approaches have been used to distinguish these two groups, including the presence/absence of males in the population, karyotyping, flow cytometry, and most recently, mitochondrial phylogeny. Mitochondrial gene (COI) barcoding has also been casually used, although its validity has not been investigated. In the present study, the validity of COI barcoding, genotyping nuclear markers (SNPs), and morphometrics was evaluated for distinguishing the reproductive forms of H. longicornis in Japan. Ticks were collected using the flagging method at two locations in Hyogo, Japan. DNA was extracted from ticks after photography, which was used for morphometric measurements. The DNA was used for COI barcoding by direct sequencing and genotyping SNPs in the nuclear genome. The resulting COI haplotypes were clustered into two distinct haplogroups, which represented different ploidy levels, corresponding to the different reproductive groups. Genotypes of nuclear SNPs supported that the individuals from each mitochondrial haplogroup belonged to distinct reproductive populations with different ploidy levels. Meanwhile, although significant differences were observed in multiple morphometric characteristics between these reproductive groups, large overlaps were generally evident in the distribution, indicating that morphological identification is not sufficient to distinguish the reproductive groups. This study suggested for the first time that COI barcoding and SNP genotyping are both convenient and reliable methods to distinguish the two reproductive forms of H. longicornis in Japan.},
}

@article {pmid40486261,
year = {2024},
author = {Barmaki, A and Rassi, Y and Absavaran, A and Akhavan, AA and Moradi-Asl, E and Zahraei-Ramazani, A and Rafizadeh, S},
title = {Discrimination of Phlebotomus perfiliewi transcaucasicus, Ph. major sensu lato and Ph. tobbi (Diptera: Psychodidae) Using Morphometric and DNA Barcoding Methods in the Endemic Foci of Visceral Leishmaniasis in Ardabil Province, North West of Iran.},
journal = {Journal of arthropod-borne diseases},
volume = {18},
number = {3},
pages = {197-217},
pmid = {40486261},
issn = {2322-1984},
abstract = {BACKGROUND: Visceral leishmaniasis, commonly known as kala-azar, and prevalent in more than 70 countries and several regions of Iran. It is one of the main diseases transmitted by sand flies. In this work, geometric morphometrics and DNA barcoding were employed as novel techniques to enhance the diagnostic tools used in this study.

METHODS: Phlebotomus perfiliewi transcaucasicus, Phlebotomus major s.l., and Phlebotomus tobbi caught from three districts in the Ardabil Province, northwest of Iran. The right wings of 286 female sand flies were analyzed using geometric morphometric (GM) tools. Additionally, the COI gene was isolated from each of the three species, amplified using universal primers, and sequenced through the DNA barcoding method for classification. This sequencing data was then formatted to generate morphometric analyses.

RESULTS: The landmarks with the most variations were found in sets 10, 12, 13, and 14, whereas the first set's landmarks at 1 and 11, along with those from the second set at positions 2, 3, and 5 exhibited the greatest variations. Analysis of the size and shape variations in the wings indicates the presence of distinct populations (P< 0.05). Furthermore, the DNA barcoding results not only confirmed the findings from the geometric morphometric analysis but also revealed both interspecific and intraspecific distances.

CONCLUSION: This study was the first attempt to assess whether wing geometry morphometrics, combined with DNA barcode techniques, can effectively distinguish the three mentioned species in the studied areas. Furthermore, the identification of Phlebotomus neglectus in this area prompted recommendations for additional research.},
}

@article {pmid40485605,
year = {2025},
author = {Zhou, Z and Kang, T and Chen, J and Doctor, Y and Camposagrado, JG and Makris, Y and Pertsemlidis, A and Bleris, L},
title = {Biosecurity Primitive: Polymerase X-based Genetic Physical Unclonable Functions.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e15820},
doi = {10.1002/advs.202415820},
pmid = {40485605},
issn = {2198-3844},
support = {2300340//National Science Foundation/ ; 2029121//National Science Foundation/ ; 2114192//National Science Foundation/ ; HG012884//National Institutes of Health/NHGRI/ ; },
abstract = {A Physical Unclonable Function (PUF) is a security primitive that exploits inherent variations in manufacturing protocols to generate unique, random-like identifiers. These identifiers are used for authentication and encryption purposes in hardware security applications in the semiconductor industry. Inspired by the success of silicon PUFs, herein it is leverage Terminal deoxynucleotidyl Transferase (TdT), a template-independent polymerase belonging to the X-family of DNA polymerases, to augment the intrinsic entropy generated during DNA lesion repair and rapidly produce genetic PUFs that satisfy the following properties: robustness (i.e., they repeatedly produce the same output), uniqueness (i.e., they do not coincide with any other identically produced PUF), and unclonability (i.e., they are virtually impossible to replicate). Furthermore, a post-sequencing feature selection methodology based on logistic regression to facilitate PUF classification is developed. This experimental and computational pipeline drastically reduces production time and cost compared to conventional genetic barcoding without compromising the stringent PUF criteria of uniqueness and unclonability. This results provide novel insights into the function of TdT and represent a major step toward utilization of PUFs as a biosecurity primitive for cell line authentication and provenance attestation.},
}

@article {pmid40483279,
year = {2025},
author = {Weng, J and Wu, X and Li, C and Li, Y and Li, Q and Dou, F and Wang, T and Li, J and Wang, Y and Zhang, L},
title = {Comprehensive Dataset for Polychaetes in the IPC: Species Distribution, DNA Barcodes, and Functional Traits.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {956},
pmid = {40483279},
issn = {2052-4463},
mesh = {Animals ; *Polychaeta/genetics/classification/physiology ; *DNA Barcoding, Taxonomic ; Biodiversity ; Genome, Mitochondrial ; Ecosystem ; },
abstract = {The Indo Pacific Convergence Zone (IPC) is recognized as an area of highest taxonomic and functional diversity. The polychaetes have garnered attention as their enormous functional trait diversity and their significant role in biomonitoring ecosystems. Here, we developed a comprehensive dataset for polychaetes in the IPC, encompassing information on species distribution, DNA barcodes, and functional traits. The species distribution data were collected from 39,310 occurrence records, with over 13% newly contributed from museum collections and 350 scientific papers. This dataset also provides 29% known species coverage in the IPC, 154 mitochondrial genomes (35.1% are new contributions), and 7,052 COI/18S/16S sequences (4.6% are new contributions). Our functional traits subdatabase comprises approximately 12,000 records and 2,831 species, belonging to 696 genera and 75 families, with 90% of which are new additions. The functional trait data were categorized into 13 traits spanning morphology, life history, physiology, and behavior. The datasetbase provide an unprecedented and original contribution for conservation and for studying the biogeography, evolution processes, and ecology of tropic organisms.},
}

Animals
*Polychaeta/genetics/classification/physiology
*DNA Barcoding, Taxonomic
Biodiversity
Genome, Mitochondrial
Ecosystem

@article {pmid40480178,
year = {2025},
author = {Kochergina, A and Schnittler, M},
title = {Epiphytic and fimicolous myxomycetes on the island Hiddensee (Germany): rare species, new genotypes and unexpected ecological preferences.},
journal = {European journal of protistology},
volume = {99},
number = {},
pages = {126153},
doi = {10.1016/j.ejop.2025.126153},
pmid = {40480178},
issn = {1618-0429},
mesh = {*Myxomycetes/genetics/classification/physiology/isolation & purification ; Germany ; Islands ; Phylogeny ; *Genotype ; Species Specificity ; DNA Barcoding, Taxonomic ; Ecosystem ; },
abstract = {Hiddensee, a small island in the Baltic Sea, is characterized by a rather dry, windy, and sunny climate, resembling a periodic desert. We studied epiphytic and fimicolous myxomycetes on the island using the moist chamber method for 101 substrate samples. A total of 37 myxomycete species were identified from 124 records, including 4 species newly recorded in Germany. Molecular barcoding revealed that 67 % of the obtained DNA sequences were new, differing by more than 1 % from their closest matches in the GenBank database. We obtained the first molecular data for Didymium megalosporum (found to be related to the aethaloid species D. spongiosum and D. yulii) and C. elegans var. microspora (new data for both the species and the variety). For Trichia rapa, described in 2023 based on a single barcoded collection, we found three different ribotypes, including one already known. Presumably undescribed taxa within the morphospecies Comatricha nigra, Didymium squamulosum, Enerthenema papillatum, and Trichia contorta were identified by molecular barcoding. Substrate preferences of myxomycetes, categorized into four substrate types (bark of living trees, leaf litter, twigs, and dung), showed distinct patterns of occurrence, with each substrate type associated with a characteristic assemblage of myxomycetes. The species composition on the bark of living trees showed a well-known dependence on bark pH and hardness, with differing pH optima and tolerance ranges among the studied species. Echinostelium minutum occurred across a broad pH spectrum (6.1-8.0; 11 records), whereas Didymium leptotrichum was restricted to a narrow pH range (7.9-8.1; 7 records). Trichia munda preferred relatively acidic substrates (6.4-7.2; 9 records), while Perichaena luteola (7.4-8.0, 5 records) was more commonly found in slightly alkaline conditions.},
}

*Myxomycetes/genetics/classification/physiology/isolation & purification
Germany
Islands
Phylogeny
*Genotype
Species Specificity
DNA Barcoding, Taxonomic
Ecosystem

@article {pmid40476221,
year = {2025},
author = {Piraonapicha, K and Kaewtongkum, N and Chomphuphuang, N and Kimsawat, P and Kumtanom, K and Samung, Y},
title = {Mukariasakaeratensis sp. nov. (Hemiptera, Cicadellidae, Deltocephalinae), a new species of bamboo leafhopper from Sakaerat Biosphere Reserve, Thailand.},
journal = {ZooKeys},
volume = {1239},
number = {},
pages = {305-320},
pmid = {40476221},
issn = {1313-2989},
abstract = {Mukariasakaeratensis Piraonapicha & Chomphuphuang, sp. nov. is described based on male and female specimens recently collected in Nakhon Ratchasima, Thailand. The new species is herein described by an integrative approach combining morphological and molecular evidence. Genetic distance analyses revealed a potential barcoding gap (K2P) of 0.20-12.07% for COI in Mukaria. Species delimitation methods ABGD and ASAP demonstrated promising results for the COI gene. This species clearly differs from all its congeners in the aedeagal shaft abruptly narrowed and curved inward in the distal half, and with a pair of spines pointed anteriorly. Mukariasakaeratensis sp. nov. has been found on the bamboo Vietnamosasapusilla (A. Chev. & A. Camus) T.Q. Nguyen. This finding constitutes the first recorded instance of a specialized member of the tribe Mukariini (Hemiptera: Cicadellidae: Deltocephalinae) feeding exclusively on bamboo from the genus Vietnamosasa. The holotype has been deposited in the Entomology Section, Queen Sirikit Botanic Garden, The Botanical Garden Organization, Thailand.},
}

@article {pmid40476220,
year = {2025},
author = {Morinha, F and Ernest, J and Archer-Taveira, A and Rocha, AM and Iwamasa, RT},
title = {Molecular and morphological data support the synonymy of Muricanthusradix Gmelin, 1791 and Muricanthusambiguus Reeve, 1845 (Gastropoda, Muricidae).},
journal = {ZooKeys},
volume = {1239},
number = {},
pages = {281-303},
pmid = {40476220},
issn = {1313-2989},
abstract = {The Muricanthusradix/ambiguus/nigritus complex includes species with a great diversity of shell shapes and shared habitats in various regions, which has raised questions and doubts about the current taxonomic classification of these species. Muricanthusnigritus, M.radix, and M.ambiguus are three similar-looking black and white murex found commonly on the west coast of North and South America. The wide variety of morphological patterns within and between these species makes the classification of specimens difficult by visual observation. To this day, controversy persists over whether M.radix and M.ambiguus are one or two distinct species. Molecular genetic data have helped clarify the taxonomic classification of many mollusk species in recent decades, contributing to a more accurate understanding of biodiversity and ecosystems. In this study, DNA barcoding and double digest restriction-site associated DNA sequencing (ddRAD-seq) methodologies were applied to complement morphological data, establishing for the first time the phylogenetic relationships between M.nigritus, M.ambiguus and M.radix. The classic mitochondrial and nuclear barcodes obtained from 80 specimens collected from three different geographic locations differentiated only two phylogenetic clades (M.nigritus and M.radix/ambiguus from Mexico differentiated from M.radix/ambiguus from Mexico and Panama). High levels of mitochondrial DNA introgression have been observed between M.nigritus and M.radix/ambiguus. The deep-level approach performed using 3692 loci obtained from ddRAD-seq also differentiated only two genetic clusters (M.nigritus and M.radix/ambiguus). Our results clearly support the proposal that M.ambiguus should be synonymized with M.radix.},
}

@article {pmid40475874,
year = {2025},
author = {Zhang, C and Hu, S and Lin, X and Huang, H and Liu, S},
title = {Crustaceans as Key Prey: Insights Into the Dietary Partitioning of Four Carnivorous Fishes in the Nansha Islands, South China Sea.},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71497},
pmid = {40475874},
issn = {2045-7758},
abstract = {Small carnivorous fishes serve as important mesopredators in coral reef ecosystems. However, the habitat and prey availability degradation within these ecosystems has intensified the trend of body size miniaturization and interspecific competition among these species. To better understand the food selection and resource partitioning strategies of mesopredators, we conducted a comprehensive study on the feeding habits of four small carnivorous fish species collected from the coral reefs of the Nansha Islands. This study employed a combination of morphological analysis and molecular identification of gut contents, along with stable isotope analysis. Similar food items, mostly semi-digested/undigested body remains/fragments from crustaceans, fish, and mollusk were detected in the guts of the analyzed fishes. High-throughput sequencing based on DNA barcoding identified approximately 24 taxa belonging to Arthropoda, Chordata, and Mollusca, with Arthropoda being the most abundant prey group, accounting for 82.2%-92% of the total sequences across the four fish species. Stable isotope analysis further revealed that the trophic levels of the four species ranged from 3.4 to 3.6. The results of food overlap analysis based on stable isotopes contrasted with those obtained from high-throughput sequencing, highlighting the distinct characteristics and complementary strengths of these methods. This study broadens the current understanding of the feeding ecology of four carnivorous fish species. The findings reveal that crustaceans are the primary food source for carnivorous fishes in the Nansha Islands, differing from previous assumptions that their diets were predominantly fish-based. Additionally, the differentiated utilization of crustacean resources among these species suggests that marine benthic invertebrates may play a crucial role in supporting mesopredators within degraded coral reef ecosystems, potentially helping to mitigate the environmental stress they face.},
}

@article {pmid40475247,
year = {2025},
author = {Rammouz, S and Reichstein, A and Riehle, J and Ferner, A and Fischer, M and Schäfers, C},
title = {Authenticity in bakery products: Detection of pistachio fraud using NGS metabarcoding.},
journal = {Food chemistry. Molecular sciences},
volume = {10},
number = {},
pages = {100260},
pmid = {40475247},
issn = {2666-5662},
abstract = {Ensuring the authenticity of food ingredients is a key aspect of food safety and quality control. High-quality raw materials are often replaced by cheaper ones and not declared. In fine bakery products such as baklava, pistachios are illegally replaced by cheaper nuts. In this study we introduce a Next-generation sequencing (NGS)-based DNA metabarcoding approach as a sensitive, reliable, and semi-quantitative method that enables a successfully detection of such adulterations, even in complex and highly processed food matrices. NGS offers increased depth, efficiency and further applications compared to conventional Sanger sequencing. In the present study, the mini-rbcL region of the chloroplast genome was used and sequencing was performed on an Illumina MiSeq® instrument. The method enabled the identification of six common pistachio adulterants, including nuts, seeds, and legumes. By preparing analytical control samples, matrix effects could be observed and included in the semi-quantitative analysis. We successfully applied the method and demonstrated the high potential of NGS technologies for routine food authentication, offering a cost- and time-efficient solution for high-throughput sample analysis.},
}

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

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

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

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

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

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

@article {pmid40459854,
year = {2025},
author = {Devitt, G and Hanrahan, N and Ramírez Moreno, M and Mudher, A and Mahajan, S},
title = {A Novel Spectral Barcoding and Classification Approach for Complex Biological Samples Using Multiexcitation Raman Spectroscopy (MX-Raman).},
journal = {Analytical chemistry},
volume = {97},
number = {23},
pages = {12189-12197},
pmid = {40459854},
issn = {1520-6882},
mesh = {*Spectrum Analysis, Raman/methods ; Humans ; *Neurodegenerative Diseases/diagnosis ; Discriminant Analysis ; Brain/pathology/metabolism ; },
abstract = {We report the development and application of a novel spectral barcoding approach that exploits our multiexcitation (MX) Raman spectroscopy-based methodology for improved label-free detection and classification of complex biological samples. To develop our improved MX-Raman methodology, we utilized post-mortem brain tissue from several neurodegenerative diseases (NDDs) that have considerable clinical overlap. For improving our methodology we used three sources of spectral information arising from distinct physical phenomena to assess which was most important for NDD classification. Spectral measurements utilized combinations of data from multiple, distinct excitation laser wavelengths and polarization states to differentially probe molecular vibrations and autofluorescence signals. We demonstrate that the more informative MX-Raman (532 nm-785 nm) spectra are classified with 96.7% accuracy on average, compared to conventional single-excitation Raman spectroscopy that resulted in 78.5% accuracy (532 nm) or 85.6% accuracy (785 nm) using linear discriminant analysis (LDA) on 5 NDD classes. By combining information from distinct laser polarizations we observed a nonsignificant increase in classification accuracy without the need of a second laser (785 nm-785 nm polarized), whereas combining Raman spectra with autofluorescence signals did not increase classification accuracy. Finally, by filtering out spectral features that were redundant for classification or not descriptive of disease class, we engineered spectral barcodes consisting of a minimal subset of highly disease-specific MX-Raman features that improved the unsupervised and cross-validated clustering of MX-Raman spectra. The results demonstrate that increasing spectral information content using our optical MX-Raman methodology enables enhanced identification and distinction of complex biological samples but only when that information is independent and descriptive of class. The future translation of such technology to biofluids could support diagnosis and stratification of patients living with dementia and potentially other clinical conditions such as cancer and infectious disease.},
}

*Spectrum Analysis, Raman/methods
Humans
*Neurodegenerative Diseases/diagnosis
Discriminant Analysis
Brain/pathology/metabolism

@article {pmid40458985,
year = {2025},
author = {Carné, A and Vieites, DR and van den Burg, MP},
title = {In Vouchers We (Hope to) Trust: Unveiling Hidden Errors in GenBank's Tetrapod Taxonomic Foundations.},
journal = {Molecular ecology},
volume = {34},
number = {13},
pages = {e17812},
pmid = {40458985},
issn = {1365-294X},
support = {10.13039/501100011033//Ministerio de Ciencia, Innovación y Universidades, Agencia Estatal de Investigación./ ; },
mesh = {Animals ; *Databases, Nucleic Acid/standards ; Sequence Analysis, DNA ; Phylogeny ; DNA Barcoding, Taxonomic ; },
abstract = {Genetic repositories are invaluable resources foundational to various biological disciplines. While their data and metadata reliability are essential for robust research outcomes, numerous studies have highlighted data quality and consistency issues. Here, we detect and quantify errors at the most fundamental level by analysing the congruence of sequences derived from the same genetic marker and specimen voucher across tetrapods. Our analysis reveals that 32% of re-sequenced vouchers (with identical field or museum numbers) yield unequal sequences, ranging from a few mutations to significant divergences (0.06%-33.95%). These divergences may result from sample misidentification, labelling errors, fidelity disparities between sequencing methods, or contamination at various stages of the research process. Our findings demonstrate errors within GenBank at its most basal level and suggest that, although undetectable, a similar error rate likely exists in non-re-sequenced data. These previously overlooked errors are concerning because they arise from replicated experiments, which are uncommon, and raise serious questions about the reliability of non-re-sequenced specimens. Such errors can compromise the accuracy of biodiversity assessments (e.g., taxonomic assessment, eDNA and barcoding), phylogenetic analyses and conservation planning by artificially inflating the intraspecific divergence or misidentifying (to-be-described) species. Additionally, the accuracy of large-scale biological studies that rely on such data can be compromised. Our concerning results call for protocols ensuring sample traceability to the specimens or tissues during the whole process of data generation, analysis and deposition in a database. We propose a third-party annotation system for individual GenBank records that would allow flagging common errors and alert both the original submitter and all users to potential problems without modifying the original records.},
}

Animals
*Databases, Nucleic Acid/standards
Sequence Analysis, DNA
Phylogeny
DNA Barcoding, Taxonomic

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

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

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

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

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

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

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

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

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

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

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

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

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

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

*Composting/methods
*Fungi/physiology
*Phytophthora/physiology
*Oomycetes/physiology
*Soil Microbiology
Fagaceae/microbiology

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

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

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

*Genome, Chloroplast
*Salvia/genetics/classification
*Phylogeny
Iran
*Genomics/methods
Genetic Markers
Base Composition
Evolution, Molecular

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

@article {pmid40447231,
year = {2025},
author = {Rochwarger, A and Kaufmann, L and Zhao, J and Makky, A and Nguyen, NA and Lehmann, N and Samusik, N and Beschorner, C and Manmadhan, SS and Greif, K and Schürch, CM},
title = {A Validation Workflow for Novel Oligonucleotide Sequences to Expand the Multiplexing Capacity of the CO-Detection by indEXing (CODEX) Platform.},
journal = {Laboratory investigation; a journal of technical methods and pathology},
volume = {105},
number = {10},
pages = {104200},
doi = {10.1016/j.labinv.2025.104200},
pmid = {40447231},
issn = {1530-0307},
abstract = {Antibody-based multiplexed tissue imaging has the potential to provide critical advances in biological discoveries and their translation for clinical applications. With the increasing introduction of markers and modalities for spatial analysis, there is an according demand for the expansion of multiplexing capacities of such imaging platforms. CO-Detection by indEXing (CODEX) is a widely used multiplexed tissue imaging platform that utilizes DNA-conjugated antibodies for imaging. The multiplexing capacity of CODEX is limited by the availability of unique DNA-oligonucleotide sequences for antibody barcoding. In this study, we demonstrate a workflow for the validation and the introduction of novel sets of candidate DNA-oligonucleotide sequences for CODEX. Through cross-validation multicycle experiments with the already published library of DNA barcodes, we here present a set of 27 novel oligonucleotide sequences for CODEX, increasing the potential multiplexing capacity to 85+ markers. We confirmed the utility of the new barcodes using a 74-plex antibody panel on a multitumor tissue microarray of paraffin-embedded tissues. The workflow presented here provides a reproducible method for extending the plexity of the CODEX platform, facilitating a deeper understanding of tissue microenvironments.},
}

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

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

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

@article {pmid40443187,
year = {2025},
author = {Jiang, C and Wang, Q and Shi, Z and Liu, S and Chen, G and Liang, B and Li, D and Ye, X},
title = {Controlled fabrication of novel magneto-fluorescent encoded microspheres with host-guest structures for simultaneous detection of thyroxine and thyroid stimulating hormone.},
journal = {Analytical methods : advancing methods and applications},
volume = {17},
number = {23},
pages = {4734-4744},
doi = {10.1039/d5ay00554j},
pmid = {40443187},
issn = {1759-9679},
mesh = {*Thyrotropin/blood ; *Thyroxine/blood ; *Microspheres ; Humans ; Limit of Detection ; Quantum Dots/chemistry ; Fluorescent Dyes/chemistry ; },
abstract = {Simultaneous detection of serum thyroxine (T4) and thyroid stimulating hormone (TSH) is essential for diagnosis and monitoring of congenital hypothyroidism (CH). Here, we reported a novel suspension array platform based on host-guest-structured magneto-fluorescent encoded beads (HGBs) for concurrent T4 and TSH detection. The foundation of HGBs lays in low-density polystyrene microsphere templates, ingeniously transformed into micron-scale host beads through the sequential deposition of iron oxide nanoparticles, quantum dots, and silica layers, resulting in good magnetism, satisfactory suspension ability and fluorescence stability. By combining micron-scale host beads exhibiting distinct red fluorescence intensities with nano-scale guest beads displaying varying green fluorescence intensities, we could repeatedly and accurately prepare 24 discriminable HGBs easily. Then, two representative HGBs were selected to construct a suspension arrays system for concurrent T4 and TSH detection. Under the optimal detection conditions, the suspension arrays we tested on T4 and TSH could be assayed in the ranges of 4 to 400 ng mL[-1], and 0.032 to 100 mIU L[-1] with limits of detection of 1.2 ng mL[-1], and 0.014 mIU L[-1], respectively. This innovative methodology not only exhibits commendable accuracy and precision but also demonstrates strong concordance with established chemiluminescence immunoassay results. Consequently, the suspension arrays based on HGB barcodes hold immense promise for enhancing the diagnostic efficiency in the realm of CH management.},
}

*Thyrotropin/blood
*Thyroxine/blood
*Microspheres
Humans
Limit of Detection
Quantum Dots/chemistry
Fluorescent Dyes/chemistry

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

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

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

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

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

Animals
*Ceratopogonidae/parasitology/genetics/classification
Thailand
*DNA Barcoding, Taxonomic
*Leishmania/isolation & purification/genetics/classification
Female
*Insect Vectors/parasitology/genetics/classification
Phylogeny
*Trypanosomatina/isolation & purification/genetics/classification

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

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

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

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

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

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

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

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

@article {pmid40433188,
year = {2024},
author = {Mahmud, BU and Hong, GY and Sharmin, A and Asher, ZD and Hoyle, JD},
title = {Accurate Medical Vial Identification Through Mixed Reality: A HoloLens 2 Implementation.},
journal = {Electronics},
volume = {13},
number = {22},
pages = {4420},
pmid = {40433188},
issn = {2079-9292},
support = {R18 HS029283/HS/AHRQ HHS/United States ; },
abstract = {The accurate identification of medicine vials is crucial for emergency medical services, especially for vials that resemble one another but have different labels, volumes, and concentrations. This study introduces a method to detect vials in real-time using mixed reality technology through Microsoft HoloLens 2. The system is also equipped with an SQL server to manage barcode and vial information. We conducted a comparative analysis of the barcode detection capabilities of the HoloLens 2 camera and an external scanner. The HoloLens 2 effectively identified larger barcodes when they were 20-25 cm away in normal lighting conditions. However, it faced difficulties in detecting smaller barcodes that were consistently detected by the external scanner. The frame rate investigation revealed performance fluctuations: an average of 10.54 frames per second (fps) under standard lighting conditions, decreasing to 10.10 fps in low light and further reducing to 10.05 fps when faced with high barcode density. Resolution tests demonstrated that a screen resolution of 1920 × 1080 yielded the best level of accuracy, with a precision rate of 98%. On the other hand, a resolution of 1280 × 720 achieved a good balance between accuracy 93% and speed. The HoloLens 2 demonstrates satisfactory performance under ideal circumstances; however, enhancements in detecting algorithms and camera resolution are required to accommodate diverse surroundings. This approach seeks to help paramedics make quick and accurate decisions during critical situations and tackle common obstacles such as reliance on networks and human mistakes. Our new approach of a hybrid method that integrates an external Bluetooth scanner with the MR device gives optimal results compared to the scanner-only approach.},
}

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

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

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

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