The model describes the behaviour of E. coli in a stationary chemostat with different oxygen availability.
SEEK ID: https://fairdomhub.org/assays/210
Biological problem addressed: Metabolic Network
Organisms: Escherichia coli : MG1655 (del LAM;del rph-1 / pyrimidine starvation ) (chemostat)
- A Mathematical Model of Metabolism and Regulation Provides a Systems-Level View of the Oxygen Response of E...
Created: 19th Dec 2012 at 15:53
Last updated: 8th Nov 2017 at 15:21
I'm interested in the application and development of methods of systems theory in biology (systems biology). In particulary I work on the following topics:
Thermodynamic constraints on biochemical network; Model reduction; Modeling and Analysis of metabolic regulation.
"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
Snapshots: No snapshots
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
Person responsible: Michael Ederer
Snapshots: No snapshots
Investigation: Steady state studies for different oxygen avail...
Assays: ArcA phosphorylation at different aerobiosis levels (steady states), 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), 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
Contributor: Not available
Provider Name: Yale CGSC
Provider's strain ID: CGSC#: 6300
Organism: Escherichia coli
Genotypes: del LAM;del rph-1
Phenotypes: pyrimidine starvation
Comment: This culture was grown from lyophil Oct. 2003 and it tested Fnr+. The previous working culture was mixed fnr-/fnr+.
The abscissa of the plots shows the percentage of aerobiosis that is a physiological measure for oxygen availability (http://www.ncbi.nlm.nih.gov/pubmed/11844770).
1) Grey Boxes: Enzymes & Reactions
blue lines/symbols: flux in mmol per gramm dry cell weight an hour
red lines/symbols: mRNA levels
2) White Boxes: Intracellular and extracellular metabolites
blue lines/symbols: concentration of the metabolites (extracellular: mM, intracellular: AU)
3) Yellow Boxes:
Aggregated Quantities as yield,
This is the csv version of the file: 091016 quinones complete data magdeburg
This document contains data for quinone concentrations and ratios of ubichinon and menachinon.These data have been generated for analysis of MG1655 at steady-state conditions in Infors-Multifors-Bioreactors. All measurements have been done in Amsterdam at the group of Prof. Joost Teixeira de Mattos.
Duplicates of samples for quinones were taken after 20 hours of steady state conditions. Chemostat experiments were carried
Contributor: The JERM Harvester
Relationship type: Construction data
The model describes the catabolism of Escherichia coli and its regulation. The metabolic reactions are modeled by the thermokinetic model formalism. The model is simplified by assuming rapid equilibrium of many reactions. Regulation is modeled by phenomenological laws describing the activation or repression of enzymes and genes in dependence of metabolic signals. The model is intended to describe the behavior of E. coli in a chemostat culture in depedence on the oxygen supply.
The model is described
Contributor: Michael Ederer
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Environment: Not specified
Organism: Escherichia coli
Investigations: Steady state studies for different oxygen avail...
Modelling analyses: Steady State Oxygen Response of E. coli WT and ...