Qualitative Simulation of the Carbon Starvation Response in Escherichia coli
INRIA Rhône-Alpes –
The adaptation of living organisms to their environment is controlled at the molecular level by large and complex networks of genes, mRNAs, proteins, metabolites, and their mutual interactions. In order to understand the overall behavior of an organism, we must complement molecular biology with the dynamic analysis of cellular interaction networks, by constructing mathematical models derived from experimental data, and using simulation tools to predict the behavior of the system under a variety of conditions. Following this methodology, we have started the analysis of the network of global transcription regulators controlling the adaptation of the bacterium Escherichia coli to environmental stress conditions. Even though E. coli is one of the best studied organisms, it is currently little understood how a stress signal is sensed and propagated throughout the network of global regulators, so as to enable the cell to respond in an adequate way. Using a qualitative method that is able to overcome the current lack of quantitative data on kinetic parameters and molecular concentrations, we have modeled the carbon starvation response network and simulated the response of E. coli cells to carbon deprivation. This has allowed us to identify essential features of the transition between exponential and stationary phase and to make new predictions on the qualitative system behavior following a carbon upshift. The model predictions have been tested experimentally by means of gene reporter systems.
Date: 2007-May-30 Time: 17:30:00 Room: Anfiteatro QA1.1 – Torre de Química/IST
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Workshop “Metabolism and mathematical models: Two for a tango” – 2nd Edition
Title: Workshop Metabolism and mathematical models: Two for a tango – 2nd Edition
Dates: October 25-26, 2022
Location: This workshop will be held in a virtual way
The topic of this workshop is metabolism in general, with a special focus, although not exclusive, on parasitology. Besides an exploration of the biological, biochemical and biomedical aspects, the workshop will also aim at presenting some of the mathematical modelling, algorithmic theory and software development that have become crucial to explore such aspects.
This workshop is being organised in the context of two projects, both with the Inria European Team Erable. One of the projects involves a partnership with the University of São Paulo (USP), in São Paulo, Brazil, more specifically the Institute of Mathematics and Statistics (IME) and the Institute of Biomedical Sciences – Inria Associated Team Capoeira – and the other involves the Inesc-ID/IST in Portugal, ETH in Zürich and EMBL in Heidelberg – H2020 Twinning Project Olissipo.
The workshop is open to all members of these two projects but also, importantly, to the community in general.
The program and more details are available here.