Computer aided Control of Gene Expression – COGEX

Biology is undergoing a historical revolution with the development of systems and synthetic approaches. Signaling pathways, transcriptional network and other cellular processes involve a large number of molecular actors with multiple interactions. While such processes are often well described mechanistically as lists of molecular reactions, not much is known on their quantitative and dynamical properties. Time-lapse fluorescent imaging of cells exposed to time-varying stimulus can be used to probe the dynamical behavior of gene circuits. Indeed, cells can be seen as complex machines, which response functions can be measured by time varying stimulations, as it is classically done in electrical and mechanical engineering. Several recent studies have used such methods to constrain the modeling of gene networks and signaling pathways. We are, however, far from being able to construct models of biological processes which are as predictive and robust as it is usually the case in physics and engineering. One of the main difficulties is the limited knowledge of the cell state that can be obtained simultaneously through fluorescence imaging and the existence of noise associated with gene transcription and translation. In turn, this strongly limits our ability to drive cellular processes, such as gene expression, over long time periods and with a quantitative accuracy. Recent developments in microfluidics, synthetic biology and optogenetics allow interrogating cellular processes in space and time at the single cell level. Having a mean to externally control, in real time, the expression level of a gene of interest, and use this to generate time-varying perturbations of the internal component of a regulatory network, would be a major step towards a quantitative understanding of how a cell functions. This would also have important consequences for applied biotechnology. As a matter of fact, a major challenge of synthetic biology is to engineer cells that can robustly perform a program in a broad range of environmental conditions and despite the stochastic nature of gene expression. However, given the complex, noisy nature of gene expression, an external control is usually needed to generate accurate time-varying perturbation of complex gene circuit for the interrogation of their behavior. The principle of controlling a dynamical system with a feedback-loop has been used extensively in engineering and is a key feature of most electromechanical devices of our everyday life. The basic idea is simple: monitor the readout and operate a change on the system to adjust it in real time so that it follows a given target profile. This permits to compensate for environmental fluctuations and un-modeled dynamics. We recently made a first step towards the construction of such a computer based control of gene expression in population of yeast cells.

In this context, the CoGEx project aims at developing the experimental and theoretical tools for the computer-based remote-control of live cells and to use such a system to interrogate cellular processes at the single cell level. More specifically, our research project aims at (1) creating a versatile, open platform for the control of gene expression at the single cell level in yeast; (2) study the performance of real time control and (3) apply this method to find optimal conditions for the production of a biomolecule in an industrial fermentor. These research directions will be the basis for a larger, long term project that will aim at developing technologically and conceptually cell-machine interfaces based on genetics using advanced microfluidics, optogenetics, microscopy, control theory, modeling and synthetic biology.