A Mathematical Model of Metabolism and Regulation Provides a Systems-Level View of the Oxygen Response of Escherichia coli Version 5
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 in Ederer M, Steinsiek S, Stagge S, Rolfe M, Ter Beek A, Knies D, de Mattos JT, Sauter T, Green J, Poole R, Bettenbrock K and Sawodny O (2014) A mathematical model of metabolism and regulation provides a systems-level view of how Escherichia coli responds to oxygen. Front. Microbiol. 5:124. doi: 10.3389/fmicb.2014.00124
Instructions: Unpack the tgz file (tar zxvf ecoli.tgz). The file README in the folder "ecoli" contains further instructions. The model is tested with Linux (Ubunutu) and Cygwin under Windows.
SEEK ID: https://fairdomhub.org/models/23?version=5
1 item is associated with this Model:-
ecoli.tgz (Tar archive (gzip-compressed) - 552 KB)
Organism: Escherichia coli
Model type: Ordinary differential equations (ODE)
Model format: Mathematica
Execution or visualisation environment: Not specified
Model image: No image specified
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Created: 26th Oct 2009 at 14:48
Last updated: 18th Mar 2014 at 12:34
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Version 5 (latest) Created 18th Mar 2014 at 12:22 by Michael Ederer
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. Instructions: Unpack the tgz file (tar zxvf ecoli.tgz). The file README in the folder "ecoli" contains further instructions. The model is tested with Linux (Ubunutu) and Cygwin under Windows.
Related items
Projects: SUMO
Institutions: University of Stuttgart
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.
Projects: SUMO
Institutions: University of Stuttgart
I recently joined the Institute for System Dynamics as a PhD student. I'm currently working on a dynamic model of nitrate respiration in E. coli.
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 ...
Projects: BaCell-SysMO, COSMIC, SUMO, KOSMOBAC, SysMO-LAB, PSYSMO, SCaRAB, MOSES, TRANSLUCENT, STREAM, SulfoSys, SysMO DB, SysMO Funders, SilicoTryp, Noisy-Strep
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 ...
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=55
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
Submitter: Michael Ederer
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
The model describes the behaviour of E. coli in a stationary chemostat with different oxygen availability.
Submitter: Michael Ederer
Biological problem addressed: Metabolic Network
Investigation: Steady state studies for different oxygen avail...
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Date Published: 27th Mar 2014
Publication Type: Not specified
