Time-dependent simulations of the dynamic switch between acidogenesis and solventogenesis based on the metabolic network and pH-dependent regulation of the enzymes.
SEEK ID: https://fairdomhub.org/assays/122
Biological problem addressed: Metabolic Network
Created: 8th Nov 2010 at 18:07
Last updated: 8th Nov 2017 at 15:21
I am a Birmingham and MRC Fellow in mathematical biology. Specialising in the modelling of gene regulation networks using both numerical and analytical approaches, my work spans a range of biological applications, from drug development to bioenergy to understanding bacterial behaviour. My MRC fellowship gave me the opportunity to gain experimental training in order to generate the complementary data required to adopt a truly interdisciplinary approach to mathematical modelling in biology.
Snapshots: No snapshots
Studies: Effect of pH on the metabolome, Effect of pH on the proteome, Effect of pH upon the transcriptome, Identification of clusters of co-regulated and anti-regulated genes, Modelling the effect of pH on the metabolic shift
Assays: Comparison of the proteome between pH 5.7 (acidogenesis) and pH 4.5 (sol..., Comparison of the transcriptome between pH 5.7 (acidogenesis) and pH 4.5..., Comparison of the transcriptome between pH 5.8 (acidogenesis) and pH 4.5..., Identification of dynamically similar transcript profiles, Steady state study of the effect of gene regulation on yields of end-pro..., Study of the end products of the acidogenesis and solventogenesis pathways, Time-dependent simulations
Mathematical modelling of the dynamic shift experiments and the effect of pH upon gene regulation.
Person responsible: Sara Jabbari
Snapshots: No snapshots
An ODE model representing the metabolic network governing acid and solvent production by Clostridium acetobutylicum, incorporating the effect of pH upon gene regulation and subsequent end-product levels.
The zip file containes 4 models (in SBML), each representing slightly different experimental conditions.
Contributor: The JERM Harvester
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Not specified
Organism: Clostridium acetobutylicum
Investigations: The effect of pH upon the metabolic shift in Cl...
Modelling analyses: Steady state study of the effect of gene regula..., Time-dependent simulations