Oberhänsli, S. | bioRxiv Science

bioRxiv2022

OpenGenomeBrowser: A versatile, dataset-independent and scalable web platform for genome data management and comparative genomics

OpenGenomeBrowser is a self-hostable open-source platform that manages access to genomic data and drastically simplifies comparative genomics analyses. It enables users to interactively generate phylogenetic trees, compare gene loci, browse biochemical pathways, perform gene trait matching, create dot plots, execute BLAST searches, and access the data. It features a flexible user management system, and its modular folder structure enables the organization of genomic data and metadata, and to automate analyses. We tested OpenGenomeBrowser with bacterial, archaeal and yeast genomes. The largest instance currently contains over 1,400 bacterial genomes. Source code, documentation, tutorials and a demo server are available at opengenomebrowser.github.io.

bioinformatics↗

bioRxiv2020

Repetitive Transcranial Magnetic Stimulation Activates Glial Cells and Inhibits Neurogenesis after Pneumococcal Meningitis

Pneumococcal meningitis (PM) causes damage to the hippocampus, a brain structure critically involved in learning and memory. Hippocampal injury - which compromises neurofunctional outcome - occurs as apoptosis of progenitor cells and immature neurons of the hippocampal dentate granule cell layer thereby impairing the regenerative capacity of the hippocampal stem cell niche. Repetitive transcranial magnetic stimulation (rTMS) harbours the potential to modulate the proliferative activity of this neuronal stem cell niche. In this study, specific rTMS protocols - namely continuous and intermittent theta burst stimulation (cTBS and iTBS) - were applied on infant rats microbiologically cured from PM by five days of antibiotic treatment. Following two days of exposure to TBS, differential gene expression was analysed by whole transcriptome analysis using RNAseq. cTBS provoked a prominent effect in inducing differential gene expression in the cortex and the hippocampus, whereas iTBS only affect gene expression in the cortex. TBS induced polarisation of microglia and astrocytes towards an inflammatory phenotype, while reducing neurogenesis, neuroplasticity and regeneration. cTBS was further found to induce the release of pro-inflammatory cytokines in vitro. We conclude that cTBS intensified neuroinflammation after PM, which translated into increased release of pro-inflammatory mediators thereby inhibiting neuroregeneration.

neuroscience↗