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Rapid Multi-Well Evaluation of Assorted Materials for Hydrogel-Assisted Giant Unilamellar Vesicle Production: Empowering Bottom-Up Synthetic Biology.
Gels
January 2025
Institute of Synthetic Bioarchitectures, Department of Bionanosciences, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, Level 2, 1190 Vienna, Austria.
Giant unilamellar vesicles (GUVs) are versatile cell models in biomedical and environmental research. Of the various GUV production methods, hydrogel-assisted GUV production is most easily implemented in a typical biological laboratory. To date, agarose, polyvinyl alcohol, cross-linked dextran-PEG, polyacrylamide, and starch hydrogels have been used to produce GUVs.
View Article and Find Full Text PDFDeep Learning for Biomarker Discovery in Cancer Genomes.
bioRxiv
January 2025
Else Kroener Fresenius Center for Digital Health, University of Technology Dresden, Dresden, Germany.
Background: Genomic data is essential for clinical decision-making in precision oncology. Bioinformatic algorithms are widely used to analyze next-generation sequencing (NGS) data, but they face two major challenges. First, these pipelines are highly complex, involving multiple steps and the integration of various tools.
View Article and Find Full Text PDFThe (in)dependence of single-cell data inferences on model constructs.
Forensic Sci Int Genet
January 2025
Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA; Department of Computer Science, Rutgers University, Camden, NJ 08102, USA.
Recent developments in single-cell analysis have revolutionized basic research and have garnered the attention of the forensic domain. Though single-cell analysis is not new to forensics, the ways in which these data can be generated and interpreted are. Modern interpretation strategies report likelihood ratios that rely on a model of the world that is a simplification of it.
View Article and Find Full Text PDFMedication use is associated with distinct microbial features in anxiety and depression.
Mol Psychiatry
January 2025
Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
This study investigated the relationship between gut microbiota and neuropsychiatric disorders (NPDs), specifically anxiety disorder (ANXD) and/or major depressive disorder (MDD), as defined by Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV or V criteria. The study also examined the influence of medication use, particularly antidepressants and/or anxiolytics, classified through the Anatomical Therapeutic Chemical (ATC) Classification System, on the gut microbiota. Both 16S rRNA gene amplicon sequencing (16S) and shallow shotgun sequencing (WGS) were performed on DNA extracted from 666 fecal samples from the Tulsa-1000 and Neurocomputational Mechanisms of Affiliation and Personality Study Center for Biomedical Research Excellence (NeuroMAP CoBRE) cohorts.
View Article and Find Full Text PDFHighly accurate Korean draft genomes reveal structural variation highlighting human telomere evolution.
Nucleic Acids Res
January 2025
Korea Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, 125, Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
Given the presence of highly repetitive genomic regions such as subtelomeric regions, understanding human genomic evolution remains challenging. Recently, long-read sequencing technology has facilitated the identification of complex genetic variants, including structural variants (SVs), at the single-nucleotide level. Here, we resolved SVs and their underlying DNA damage-repair mechanisms in subtelomeric regions, which are among the most uncharted genomic regions.
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