New Publication: Evolution of resource and energy management in biologically realistic gene regulatory network models

Today sees the publication of a new article:

Stekel, D.J. and Jenkins, D.J. 2012. Evolution of resource and energy management in biologically realistic gene regulatory network models. Advances in Experimental Medicine and Biology 751: 301-328.

This is, in fact, a chapter in the book Evolutionary Systems Biology that has been edited by Orkun Soyer and contains many interesting articles.

Our own article is a review of research work carried out mostly by Dafyd during his PhD. The abstract is:

We describe the use of computational models of evolution of artificial gene regulatory networks to understand the topologies of biological gene regulatory networks. We summarize results from three complementary approaches that explicitly represent biological processes of transcription, translation, metabolism and gene regulation: a fine-grained model that allows detailed molecular interactions, a coarse-grained model that allows rapid evolution of many generations, and a fixed-architecture model that allows for comparison of different hypotheses. In the first two cases, we are able to evolve networks towards the biological fitness objectives of survival and reproduction. A theme that emerges is that the control of cell energy and resources is a major driver of gene network topology and function. This is demonstrated in the fine-grained model with the emergence of biologically realistic mRNA and protein turnover rates that optimize energy usage and cell division time, and the evolution of basic repressor activities; in the fixed architecture model with a negative self-regulating gene evolving major efficiencies in mRNA usage; and in the coarse-grained model by the need for the inclusion of basal gene expression to obtain biologically plausible networks and the emergence of global regulators keeping all cellular systems under negative control. In summary, we demonstrate the value of biologically realistic computer evolution techniques, and the importance of energy and resource management in driving the topology and function of gene regulatory networks.

We are excited by this article as it brings together an important and emergent theme from four of our previous research articles.


Three Posters at Biometals 2012 in Brussels

Together with Hiroki Takahashi, Jon Hobman and Selina Clayton we are attending the Biometals 2012 conference in Brussels. We have three posters between us:

Crossland, R.C., Hobman, J.L. and Stekel, D.J. Mathematical Modelling of Mercury Resistance.

Takahashi, H., Oshima, T., Clayton, S.R., Hobman, J.L., Tobe, T., Kanaya, S., Ogasawara, N. and Stekel, D.J. Mathematical modelling towards understanding of zinc homeostasis in Escherichia coli.

Clayton, S.R., Patel, M.D., Constantinidou, C., Oshima, T., Takahashi, H., Heurlier, K., Stekel, D.J., Hobman, J.L. The role of zinc uptake regulator, Zur, in pathogenic and non-pathogenic Escherichia coli.

These are posters 53, 54 and 55 so if you are in the area or at the conference please do look us up.