Genetic Network Models of Biodegradation

Abstract

The dynamical model of bacterial degradation of organic compounds which is discussed here provides a description of the degrading behaviour in terms of interacting genes which may switch from active to inactive state, thus providing a generalization of the well known Kauffman model of random boolean networks, which is well suited for single cells, to the multi-cell case. This generalization requires that the variables describing gene activation be real, instead of boolean. Moreover, the vast majority of the cell’s genes, which provide the standard metabolic machinery of the cell, are treated in a way different from the relatively few genes which are directly involved in biodegradation: the latter ones are carefully described, while the effects of the former ones are described by an aggregate variable. Two different examples of specific models, which are both consistent with the overall framework, are introduced, and their dynamical behaviour is studied, in the particular case where all the genes are arranged on a 2-D regular square topology, with connections among neighbouring sites. Thus, the model is an example of a cellular-automata like model, and a continuum generalization of random boolean networks.