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Biology subjects

Soderholm, N.

Publications and source records attributed to Soderholm, N..

2 recordsLinked to original sources

Extracellular ATP is a signalling molecule in bacteria

In animals and plants extracellular ATP (eATP) functions as signal and regulates the immune response. During inflammation intestinal bacteria are exposed to elevated eATP originating from the mucosa. However, whether bacteria respond to eATP is unclear. Here we show that non-pathogenic Escherichia coli responds to eATP by modifying its transcriptional and metabolic landscapes. A genome-scale promoter library showed that the response is time-, concentration-, and medium-dependent and ATP-specific. The second messenger cAMP and genes related to metabolism, quorum sensing, and envelope stress were regulated downstream of eATP. Metabolomics confirmed that eATP triggers enrichment of compounds with bioactive properties on the host or bacteria. Combined genome-scale modelling revealed global metabolic and biomass building blocks modifications. Consequently, eATP altered the sensitivity to antibiotics and antimicrobial peptides. Finally, in pathogens eATP controlled virulence factor expression. Our results indicate that eATP is an environmental cue in prokaryotes which broadly regulates physiology, antimicrobial resistance, and virulence.

microbiology↗

DSeg: A dynamic image segmentation program to extract backbone patterns for filamentous bacteria and hyphae structures

MotivationQuantitative image analysis of growing filamentous fungi and prokaryotes are important to detect and evaluate morphological effects of growth conditions, compounds and mutations. However, analysis of time-series image data is often limited by the ability of the algorithms to accurately segment structures that are complicated or if an organism is within a crowded population. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data as well as single images to find multiple filamentous structures e.g., filamentous prokaryotes, yeasts and molds using a dynamic segmentation approach. DSeg automatically segments and analyzes objects, includes drift correction, and outputs statistical data such as persistence length, growth rate and growth direction.\n\nAvailability and implementationDSeg is a free open-source program written in MATLAB. DSeg can be downloaded as a package from https://sourceforge.net/projects/dseg-software.\n\nContactmagnus.andersson@umu.se and hanqing.zhang@umu.se\n\nSupplementary informationSupplementary data are available at online.

bioinformatics↗