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Strain details
Name | Provider name | Provider's strain ID | Genotypes | Phenotypes | Synonym | Comments | Based on |
---|---|---|---|---|---|---|---|
ATCC824 | Not specified | Not specified | wild-type | wild-type | Not specified | None | Not specified |
NCIMB8052 | Not specified | Not specified | wild-type | wild-type | Not specified | None | Not specified |
Related items
Systems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves
Programme: SysMO
Public web page: http://www.sysmo.net/index.php?index=54
Organisms: Clostridium acetobutylicum
Measurements of acetone, butanol, acetate, butyrate and ethanol taken during dynamic shift (pH 5.8, 5.5, 5.3, 5.1, 4.9, 4.7, 4.5) and at steady state (pH 5.7, 5.5, 5.3, 5.1, 4.9, 4.7, 4.5).
Contributor: Sara Jabbari
Assay type: Metabolomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: The effect of pH upon the metabolic shift in Cl...
Study: Effect of pH on the metabolome
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: End products of Clostridium acetobutylicum grow..., End products of Clostridium acetobutylicum grow...
Investigation of all steady state pH-values between pH 5.7 and 4.5 (pH 5.5, 5.3, 5.1, 4.9, 4.7).
Contributor: Sara Jabbari
Assay type: Proteomics
Technology type: Technology Type
Snapshots: No snapshots
Investigation: The effect of pH upon the metabolic shift in Cl...
Study: Effect of pH on the proteome
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: Standard operating procedure to analyze the int...
Data files: Proteome Reference maps of Clostridium acetobuy..., Proteome of Clostridium acetobutylicum growing ...
Investigation of the dynamic switch at pH values between 5.8 and 4.5 (pH 5.5, 5.3, 5.1, 4.9, 4.7 and 4.5).
Investigation: The effect of pH upon the metabolic shift in Cl...
Study: Effect of pH upon the transcriptome
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: No Data files
Comparison of the transcriptome at steady state in acidogenesis and at steady state in solventogenesis.
Investigation: The effect of pH upon the metabolic shift in Cl...
Study: Effect of pH upon the transcriptome
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: Transcriptome data of Clostridium acetobutylicu..., Transcriptome data of Clostridium acetobutylicu...
Contributor: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Snapshots: No snapshots
Investigation: Investigation on the effect of pulsed metabolit...
Study: Effect of acid pulses during acidogenesis and s...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: Chemostat Fermentation B, Chemostat Fermentation C
Contributor: Sebastian Curth
Assay type: Metabolite Profiling
Technology type: Liquid Chromatography-tandom Mass Spectrometry
Snapshots: No snapshots
Investigation: Investigation on the effect of pulsed metabolit...
Study: Effect of acid pulses during acidogenesis and s...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: Chemostat Fermentation B, Chemostat Fermentation C, Fermentation D, Fermentation E, Fermentation F, Fermentation G
Contributor: Sebastian Curth
Assay type: Transcriptional Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Investigation on the effect of pulsed metabolit...
Study: Effect of acid pulses during acidogenesis and s...
Organisms: Clostridium acetobutylicum : ATCC824 (wild-type / wild-type) (chemostat)
SOPs: No SOPs
Data files: No Data files
Contributor: Sebastian Curth
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Clostridium acetobutylicum
Genotypes: wild-type
Phenotypes: wild-type
Comment: Not specified
Contributor: Not available
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Clostridium acetobutylicum
Genotypes: wild-type
Phenotypes: wild-type
Comment: Not specified
Here, we use hyperbolic tangents to fit experimental data of AB fermentation in C. acetobutylicum in continous culture at steady state for different external pHs. The estimated parameters are used to define acidogenic and solventogenic phase. Furthermore, an transition phase is identified which cannot be assigned to acidogenesis or solventogenesis.
Several plots compare the fits to the experimental data.
Creator: Thomas Millat
Contributor: Thomas Millat
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Organism: Clostridium acetobutylicum
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
This function estimates the parameters of growth functions of the acid-forming and solvent-forming population observed in 'forward'-shift experiments of phosphate-limited continuous cultures of C. acetobutylicum. The parameters are used in the 'Two-Populations'-Model of the pH-induced metabolic shift.
It assumed that the found behaviour of the optical density during these experiments results from a phenotypic switch caused by the changing pH level.
Creator: Thomas Millat
Contributor: Thomas Millat
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Organism: Clostridium acetobutylicum
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
This model assumes a phenotypic switch between an acid- and solvent-forming population caused by the changing pH levels. The two phenotypes differ in their transcriptomic, proteomic, and ,thus, their metabolomic profile. Because the growth rates of these phenotypes depends on the extracellular pH, the initiation of the pH-shift results in a significant decline of the acidogenic population. Simultaneously, the solvent-forming population rises and establishes an new steady state.
The model is build
...
Creators: Thomas Millat, Graeme Thorn, Olaf Wolkenhauer, John King
Contributor: Thomas Millat
Model type: Ordinary differential equations (ODE)
Model format: Matlab package
Environment: Matlab
Organism: Clostridium acetobutylicum
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
The fitted function describes the pH-drop during 'forward'-shift experiments and the increase of the pH during 'reverse'-shift experiments. The estimated parameters are used to compute the changing pH level in the models of the pH.induced metabolic shift in continuous cultures under phosphate limitation of C. acetobutylicum. Furthermore, the parameters can be applied to join different independent experiments into a single data set.
To fit the changing pH level, an exponential function and a
...
Creator: Thomas Millat
Contributor: Thomas Millat
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Organism: Clostridium acetobutylicum
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum (Haus et al. BMC Systems Biology 2011, 5:10), incorporating the effect of pH upon gene regulation and subsequent end-product levels. This model describes the third of four experiments in which the pH of the culture was shifted. For this experiment acidogenesis at pH 5.7 was maintained for 121 hours, after which the pH control was stopped, allowing the natural metabolic shift to the
...
Creators: Sara Jabbari, Sylvia Haus
Contributor: Franco Du Preez
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
Organism: Clostridium acetobutylicum
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum (Haus et al. BMC Systems Biology 2011, 5:10), incorporating the effect of pH upon gene regulation and subsequent end-product levels. This model describes the last of four experiments in which the pH of the culture was shifted. For this experiment the pH shift was reversed compared to the first three (shift from pH 4.5 to 5.7), with the pH control switched off after 129 hours.
...
Creators: Sara Jabbari, Sylvia Haus
Contributor: Franco Du Preez
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
Organism: Clostridium acetobutylicum
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses
An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum (Haus et al. BMC Systems Biology 2011, 5:10), incorporating the effect of pH upon gene regulation and subsequent end-product levels. This model describes the second of four experiments in which the pH of the culture was shifted. For this experiment acidogenesis at pH 5.7 was maintained for 137.5 hours, after which the pH control was stopped, allowing the natural metabolic shift to
...
Creators: Sara Jabbari, Sylvia Haus
Contributor: Franco Du Preez
Model type: Ordinary differential equations (ODE)
Model format: Not specified
Environment: JWS Online
Organism: Clostridium acetobutylicum
Investigations: No Investigations
Studies: No Studies
Modelling analyses: No Modelling analyses