Section: New Results

Qualitative modeling of gene regulatory networks in food-borne pathogens

Bacteria are able to respond to a variety of environmental stresses, which poses food safety problems when these bacteria are food-borne pathogens. Addition of salt, one of the most ancient and common way of preserving food, subjects the bacteria to an osmotic stress to which some may survive. However, the molecular mechanisms of adaptation in food-born pathogens are largely unknown. As a first step towards better understanding these adaptation processes on the molecular level, Delphine Ropers and Aline Métris from the Institute for Food Research in Norwich (UK), invited researcher in IBIS this year, have developed a qualitative model of the osmotic stress response in the model bacterium Escherichia coli for which more information is available in the literature. The model has allowed to reproduce the behavior of E. coli cells adapting to an osmotic stress by including the regulatory mechanisms involved in the process. This work has been published in the International Journal of Food Microbiology [15] and in Data in Brief [16]. It paves the way to modelling stress responses of other foodborne pathogens like Salmonella to stresses relevant for the food industry, for which much less is known.

The tool used for the qualitative modeling and simulation of the regulatory mechanism underlying osmotic stress is Genetic Network Analyzer (GNA) . This tool describes the dynamics of gene regulatory networks by means of PLDE models, as described in Section 5.1. GNA has been integrated with the other bioinformatics tools distributed by Genostar (http://www.genostar.com/). Version 8.7.2 of GNA was released by IBIS and Genostar this year and has been deposited at the Agence pour la Protection des Programmes (APP). Some bugs have been corrected in the new version and the program has been adapted to the latest versions of Java and the software platform of Genostar. Version 8.7.2 supports the SBML standard and is also capable of exporting its models to the newly-developed standard for qualitative models, SBML Qual. This standard has been elaborated by the community of developers of logical and related modeling tools (CoLoMoTo), in which the GNA developers participate.