The task of this assay is to determine the impact of oxygen availability on the concentrations of metabolites from different central metabolic pathways. The focus lies on metabolites connected to glycolysis, tri-carbon-acid-cycle and energy metabolism. All strains have been cultured and analysed according to the SOPs listed below
SEEK ID: https://fairdomhub.org/assays/33
Assay type: Metabolomics
Technology type: Liquid Chromatography Mass Spectrometry
Organisms: Escherichia coli (chemostat)
Created: 13th Apr 2010 at 16:52
Last updated: 8th Nov 2017 at 15:21
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SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".
The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.
Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...
Web page: http://sysmo.net/
"Systems Understanding of Microbial Oxygen responses" (SUMO) investigates how Escherichia coli senses oxygen, or the associated changes in oxidation/reduction balance, via the Fnr and ArcA proteins, how these systems interact with other regulatory systems, and how the redox response of an E. coli population is generated from the responses of single cells. There are five sub-projects to determine system properties and behaviour and three sub-projects to employ different and complementary modelling ...
Changing the oxygen availability leads to an adaptation of Escherichia coli at different biological levels. After pertubation of oxygen in chemostat experiments the microorganism(s) will come back to another steady state. This investigation deals with these stationary responses of Escherichia coli within the aerobiosis scale. The change for different biological variables, in different areas of the organism like the electron transport chain, the TCA cycle or globally is investigated by wildtype ...
Submitter: Michael Ederer
Studies: Basic regulatory principles of Escherichia coli’s electron transport cha..., Determination of the impact of specific enzyme reactions and regulatory ..., Quantitative analysis of catabolic carbon and electron fluxes in E. coli..., The Escherichia coli steady state response to oxygen: from molecular int...
Assays: Analysis of by-product formation rates in MG1655, Analysis of gene expression rates at different aerobiosis levels via RT-PCR, ArcA phosphorylation at different aerobiosis levels (steady states), Characterization of E. coli MG1655 and ∆sdhC and ∆frdA isogenic mutant s..., Determination of intracellular metabolite concentrations, Determination of intracellular redox state by means of NAD/NADH ratio, Determination of intracellular redox state by means of ubiquinones (oxd/..., FNR activity at different aerobiosis levels (steady state), Kinetic modelling of Escherichia coli's electron transport chain, Kinetic modelling of Escherichia coli's electron transport chain coupled..., Literature Data from Alexeeva et al., J. Bacteriol., 2000, 2002, 2003, Measurement of cytochrome numbers, Physiological measurements from Sheffield chemostat, Steady State Oxygen Response of E. coli WT and two Electron Transport Ch..., Transcriptional profiling of steady states at different aerobiosis levels
Snapshots: No snapshots
Mutant strains which carry deletions of important metabolic enzymes, as well as mutant strains with altered regulation, need to adapt by changing fluxes or gene expression to compensate with the absence/differed concentration of these key enzymes. This may give new insights in the regulation of these pathways/enzymes.
Submitter: Sonja Steinsiek
Investigation: Steady state studies for different oxygen avail...
Assays: Analysis of by-product formation rates in MG1655, Analysis of gene expression rates at different aerobiosis levels via RT-PCR, Characterization of E. coli MG1655 and ∆sdhC and ∆frdA isogenic mutant s..., Determination of intracellular metabolite concentrations
Snapshots: No snapshots
This method describes how one can quench metabolism of Escherichia coli and extract metabolites from many kinds of metabolite classes like: nucleotides, sugar-phosphates, organic acids ....
Creator: Martijn Bekker
Submitter: The JERM Harvester
Investigations: Steady state studies for different oxygen avail...
Assays: Analysis of by-product formation rates in MG1655, Determination of intracellular metabolite conce..., Determination of intracellular redox state by m..., FNR activity at different aerobiosis levels (st..., Physiological measurements from Sheffield chemo...
This document describes the chemostat conditions to run comparable experiments in different bioreactors in different labs.
Investigations: Analysis of Escherichia coli with linear electr..., Analysis of the glucose transport in Escherichi..., Dynamical studies for different oxygen availabi..., Steady state studies for different oxygen avail...
Studies: Analysis of Escherichia coli strains with linea..., Characterization of mutant strains with defects..., Determination of the impact of specific enzyme ..., The Escherichia coli dynamical response to oxyg..., The Escherichia coli steady state response to o...
Assays: Analysis of by-product formation rates in MG1655, Analysis of gene expression rates at different ..., ArcA phosphorylation at different aerobiosis le..., Characterization of MG1655 and mutant strains u..., Determination of by-product formation and gluco..., Determination of intracellular metabolite conce..., Determination of intracellular redox state by m..., Gene expression analysis of mutants with linear..., Physiological measurements from Sheffield chemo..., Transcriptional profiling of E. coli during ana...
Date Published: 27th Mar 2014
Publication Type: Not specified
PubMed ID: 24723921