From Genomes to Mathematical Models for Systems Biology

Systems biology is a discipline which has mainly been developed in biotechnology for enhancing yields of production of bacterial by-products or synthetic biology. As a consequence, models have been developed with organisms used in biotechnology, such as Escherichia coli and Saccharomyces cerevisiae, and in environmental conditions that are not necessarily relevant to the food industry. We propose that existing modelling methods could be used in the food industry to design novel strategies for antimicrobial intervention in the food chain. However, the models have to be extrapolated to foodborne pathogens and genomic sequences provide insufficient information; condition specific data are also essential to build meaningful models.

In the first part, we will illustrate how a metabolic model of Campylobacter jejuni was derived from an existing model of Helicobacter pilori. Metabolic networks can be analysed mathematically with constrained-based analysis. How this method may be exploited in the food industry will be illustrated in the subsequent talk, so the method will not be detailed but the steps involved in the conversion of the genome annotation into a mathematical model will be explained.

In the second part, we will introduce a qualitative method to model the response of bacteria to osmotic stress and show the challenges of inferring a model for Salmonella from E. coli. We will also prove that potential regulatory interactions deduced from bioinformatics analyses are not sufficient to explain regulation as they are condition specific.