Shephard, F. | bioRxiv Science

bioRxiv2024

PIMMS-Dash: Accessible analysis, interrogation, and visualisation of high-throughput transposon insertion sequencing (TIS) data

MotivationCurrent methods for visualising and interrogating high-throughput transposon insertion mutagenesis sequencing (TIS) data requires a significant time investment in learning bioinformatics, often producing static figures that do not facilitate real time analysis. SummaryWe have created an accessible web-based browser tool for visualisation and downstream analysis of high-throughput TIS data. This includes multiple interactive and sortable tables to aid the user to identify genes of interest, enabling the user to gain a greater understanding of the genes contributing to fitness in their experimental work. PIMMS-Dash permits researchers, with any level of bioinformatics knowledge, to interrogate data sets and generate publication quality figures. AvailabilityPIMMS-Dash is freely available and is accessible online at https://pimms-dashboard-uon.azurewebsites.net

bioinformatics↗

bioRxiv2020

The effect of E-liquid exposure on Caenorhabditis elegans.

E-cigarettes are being promoted as a less harmful alternative to smoking tobacco. However, vaping is a new phenomenon and safety profiles have not been fully established. Model organisms can be used to examine the cellular processes that may be changed by exposure to the E-liquids used for vaping. Mitochondria are essential in eukaryotic cells for production of ATP, protein biogenesis, metabolic pathways, cellular signalling, stress responses and apoptosis. Mitochondrial health can be used as a proxy for many aspects of healthy cellular physiology. Mutations in the PINK1 gene can lead to mitochondria-specific autophagy deficiency. We exposed two strains of Caenorhabditis elegans, CB5600 control and CC46 pink1, with 10% concentrations of nine different flavoured E liquids. We measured lifespan, movement, body size, brood size, and we examined their mitochondrial networks to investigate the effect of the E-liquids. We show that the CC46 (pink1) strain is affected by the E-liquids, even the flavours without nicotine, and that they have reduced lifespan, movement ability and mitochondrial organisation. We found that some E-liquids can dramatically shorten lifespan in this strain. Our data emphasise a need to carefully ascertain the potential harm that may be caused by the use of E-liquids.

cell biology↗