Spatio-temporal complexity of gene expression in non-synchronized infections of cell cultures

Research in molecular biology commonly relies on experiments that measure the expression of specific genes to investigate a variety of phenomena like viral infections, metabolic pathways or regulatory networks. For in vitro experiments it is often assumed that the gene expression is synchronized over all the cells, however for viral infections this is difficult to achieve. The aim of this work is to identify those experimental conditions under which the error of gene expression measurements is still acceptable, and investigate whether it is possible to correct for the effect of asynchronicity. You’ll investigate the effects of non-synchronized infections on in silico experiments performed by a spatially extended agent-based model of quantitative temporal gene expression. This model enables to investigate spatio-temporal asynchronicity, in contrast to traditional models where either the spatial or the temporal dimension is missing. You’ll study the effect of different infection dynamics on the resulting gene expression, for which you’ll quantify the error induced by assuming ideal synchronicity.