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Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines.
Microb Genom
January 2025
GMT Science 75 route de Lyons-La-Foret, Rouen F-76000, France.
Microbiome profiling tools rely on reference catalogues, which significantly affect their performance. Comparing them is, however, challenging, mainly due to differences in their native catalogues. In this study, we present a novel standardized benchmarking framework that makes such comparisons more accurate.
View Article and Find Full Text PDFsp. nov., a novel yeast species isolated from plant leaves in China.
Int J Syst Evol Microbiol
January 2025
School of Life Science, Nanyang Normal University, Nanyang 473061, PR China.
Two novel yeast strains, NYNU 236247 and NYNU 23523, were isolated from the leaves of Hance, collected in the Tianchi Mountain National Forest Park, Henan Province, central China. Phylogenetic analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer (ITS) region revealed the closest relatives of the strains are three described species: , and . The novel species differed from the type strains of these three species by 12 to 22 nucleotide substitutions and 1 gap (~2.
View Article and Find Full Text PDFRobust single-nucleus RNA sequencing reveals depot-specific cell population dynamics in adipose tissue remodeling during obesity.
Elife
January 2025
Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, United States.
Single-nucleus RNA sequencing (snRNA-seq), an alternative to single-cell RNA sequencing (scRNA-seq), encounters technical challenges in obtaining high-quality nuclei and RNA, persistently hindering its applications. Here, we present a robust technique for isolating nuclei across various tissue types, remarkably enhancing snRNA-seq data quality. Employing this approach, we comprehensively characterize the depot-dependent cellular dynamics of various cell types underlying mouse adipose tissue remodeling during obesity.
View Article and Find Full Text PDFsp. nov., sp. nov., sp. nov. and gen. nov., sp. nov., isolated from human faeces.
Int J Syst Evol Microbiol
January 2025
Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
Small, obligately anaerobic strains 13CB8C, 13CB11C, 13CB18C and 13GAM1G were isolated from a faecal sample in a patient with Parkinson's disease with a history of duodenal resection. After conducting a comprehensive polyphasic taxonomic analysis including genomic analysis, we propose the establishment of one new genus and four new species. The novel bacteria are sp.
View Article and Find Full Text PDFIdentification of differentially expressed non-coding RNAs in the plasma of women with preterm birth.
RNA Biol
December 2025
Biorepository and Omics Research Group, Department of Pediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan.
This study aimed to identify differentially expressed non-coding RNAs (ncRNAs) associated with preterm birth (PTB) and determine biological pathways being influenced in the context of PTB. We processed cell-free RNA sequencing data and identified seventeen differentially expressed (DE) ncRNAs that could be involved in the onset of PTB. Per the validation via customized RT-qPCR, the recorded variations in expressions of eleven ncRNAs were concordant with the analyses.
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