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Controlling for contaminant sequences in microbiome experiments involving low-biomass samples is a highly challenging task which still lacks of standardized protocols. Here we propose a simple sequence-based filtering method for 16S rRNA gene microbial profiling approaches, and validate its efficiency using mock community dilution series and environmental samples collected in a clinical setting.
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http://dx.doi.org/10.1016/j.mimet.2020.106060 | DOI Listing |
Sci Rep
August 2025
Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, 313001, India.
The current study explores the impact of gamma radiation on the in vitro morphogenesis of Moringa concanensis. In vitro regenerated shoots were exposed to Barium and Cobalt gamma radiation sources for varying lengths of time (3, 6, 9, and 15 min). All the treated shoots survived with 100% regeneration frequency.
View Article and Find Full Text PDFMicrobiol Spectr
August 2025
Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan.
Unlabelled: Bacterial species cultured from sputum change during treatment or observation for non-tuberculous mycobacterial pulmonary disease; however, strain-level changes remain unrecognized. Variable number tandem repeat typing is a standard technique for strain identification; nonetheless, its labor-intensive and time-consuming nature limits routine clinical use. Therefore, we aimed to elucidate species-subspecies and strain dynamics in non-tuberculous mycobacteria and develop a simple sequence-based strain-level determination method.
View Article and Find Full Text PDFPLoS One
August 2025
Clinical Informatics Research Unit, Cancer Sciences, Department of Medicine, University of Southampton, Southampton, United Kingdom.
Inferring protein function is a fundamental and long-standing problem in biology. Laboratory experiments in this field are often expensive, and therefore large-scale computational protein inference from readily available amino acid sequences is needed to understand in more detail the mechanisms underlying biological processes in living organisms. Recently, studies have utilised mathematical ideas from natural language processing and self-supervised learning, to derive features based on protein sequence information.
View Article and Find Full Text PDFAnal Sci
August 2025
Department of Forensic Medicine, Chongqing Medical University, Chongqing, 400016, China.
MicroRNAs (miRNAs) are pivotal regulators of cellular processes, with dysregulation linked to diverse diseases, particularly cancer. Current methods, while effective, are often expensive, complex, and require sophisticated equipment. To address these limitations, we developed a label-free, one-pot miRNA detection platform integrating toehold-mediated strand displacement (TMSD) with nucleic acid sequence-based amplification (NASBA).
View Article and Find Full Text PDFBMC Bioinformatics
August 2025
Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine & Health, The University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK.
Background: Cellular development and differentiation in Eukaryotes depends upon sequential gene regulatory decisions that allow a single genome to encode many hundreds of distinct cellular phenotypes. Decisions are stored in the regulatory state of each cell, an important part of which is the epi-genome-the collection of proteins, RNA and their specific associations with the genome. Additionally, further cellular responses are, in part, determined by this regulatory state.
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