Bright, C. | bioRxiv Science

bioRxiv2024

ArchMap: A web-based platform for reference-based analysis of single-cell datasets

Leveraging single cell reference atlases to analyse new data has brought about a paradigm shift in single cell data science akin to the first reference genome in genomics. However methods to perform this mapping require computational expertise as well as sometimes considerable compute power, and thus may exclude the researchers from this innovation who may benefit the most from it. ArchMap, a no-code query-to-reference mapping tool, removes this barrier by providing all-in-one automated mapping, cell type annotation, and collaborative features to analyse single-cell datasets from a wide range of integrated, often published, reference atlases and allows extension of atlases with the growing Human Cell Atlas and related efforts. This paves the way for a democratisation of reference mapping capabilities.

bioinformatics↗

bioRxiv2021

The Application of Countercurrent Chromatography for the study of Bacteriophages

1.Bacteriophages (phages) are viruses that target bacteria, with the ability to lyse and kill host bacterial cells. Due to this, they have been of some interest as a therapeutic since their discovery in the early 1900s, but with the recent increase in antibiotic resistance, phages have seen a resurgence in attention. Current methods of isolation and purification of phages can be long and tedious, with caesium chloride concentration gradients the gold standard for purifying a phage fraction. Isolation of novel phages requires centrifugation and ultrafiltration of mixed samples, such as water sources, effluent or faecal samples etc, to prepare phage filtrates for further testing. We propose countercurrent chromatography as a novel and alternative approach to use when studying phages, as a scalable and high-yield method for obtaining phage fractions. However, the full extent of the usefulness and resolution of separation with this technique has not been researched; it requires optimisation and ample testing before this can be revealed. Here we present an initial study to determine survivability of two phages, T4 and {phi}X174, using only water as a mobile phase in a Spectrum Series 20 HPCCC. Both phages were found to remain active once eluted from the column. Phages do not fully elute from the column and sodium hydroxide is necessary to flush the column between runs to deactivate remaining phages.

microbiology↗