In Silico Cells


Expressing genes in a bacterial cell is noisy and random. A colony of bacteria grown from a single cell can show remarkable differences in the copy numbers per cell of a given protein after only a few generations. In a recent study, the Luthey-Schulten group and their collaborators at the Max Planck Institute of Biochemistry used computer simulations to study the variation in how individual cells in a population express a set of genes in response to an environmental signal. The modeled system was the lac genetic switch that Escherichia coli uses to find, collect, and process lactose sugar from the environment. The noise inherent in the genetic circuit controlling the cell's response determines how similar the cells are to each other and the authors studied how the different components of the circuit affected this noise. Furthermore, an estimated 30-50\% of the cell volume is taken up by a wide variety of large biomolecules. To study the response of the circuit caused by crowding, they simulated the circuit inside a three-dimensional model of an E. coli cell built using data from cryoelectron tomography reconstructions of a single cell and proteomics studies. The authors report that correctly including random effects of molecular crowding will be critical to developing fully dynamic models of living cells.

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