Wednesday 27 Nov 2013Entrainment, Synchronization and Control of transcriptional networks

Professor Mario diBernardo - Universities of Naples and Bristol

Harrison 170 11:00-12:00

This talk is concerned with the modeling, analysis and control of synthetic transcriptional networks using nonlinear ODEs [1], [2]. The problem will be discussed of how the insight gained from modeling and in-silico experiments can be effectively used to design in-vivo control strategies to steer the network behaviour in a desired way. Specifically, we will describe the in-vivo implementation of a feedback control based on hybrid systems theory that can be used to achieve both regulation and tracking control of a biological network of interest [6]. Entrainment and synchronization of cell populations will also be discussed. It will be shown that revisiting a classical tool in the theory of nonlinear systems, contraction theory, can yield an effective methodology to give conditions on the biochemical parameters of the networks of interest that guarantee entrainment [7] or synchronization [8]. A novel synthetic biological network recently developed at the Telethon Institute for Genetics and Medicine in collaboration with the University of Naples Federico II will be used as a case of study [3]. The synthetic network, named IRMA, was built in the yeast Saccharomyces Cerevisiae to provide for In-vivo benchmarking of Reverse-engineering and Modelling Approaches.

References

[1] A. Polynikis, S.J. Hogan, M. di Bernardo, Comparing different ODE modelling approaches for gene regulatory networks, Journal of Theoretical Biology, 261, 4, 511-530, 2009

[2] O. Purcell, N.J. Savery, C.G. Grierson, M. di Bernardo, A comparative analysis of synthetic genetic oscillators, Journal Royal Society Interface, 7, 1503-1524, 2010

[3] Irene Cantone, L. Marucci, Francesco Iorio, Mukesh Bansal, Vincenzo Belcastro, Maria Aurelia Ricci, S. Santini, M. di Bernardo, Diego di Bernardo, Maria Pia Cosma, A Yeast Synthetic Network for In Vivo Assessment of Reverse-Engineering and Modeling Approaches, Cell, 137, 1-10, 2009

[4] L. Marucci, S. Santini, M. di Bernardo, Diego di Bernardo, Derivation, identification and validation of a computational model of a novel synthetic regulatory network in yeast, Journal of Mathematical Biology, doi: 10.1007/s00285-010-0350-z, 2010

[5] L. Marucci, David A.W. Barton, Irene Cantone, Maria Aurelia Ricci, Maria Pia Cosma, S. Santini, di Bernardo D., M. di Bernardo, How to turn a genetic circuit into a synthetic tunable oscillator, or a bistable switch, PloS One, 4, 12, 1-10, 2009

[6] F. Menolascina, di Bernardo D., di Bernardo, M, Analysis, Design and Implementation of a novel scheme for in-vivo control of synthetic biological networks, 47, 1265-1270, Automatica, 2011

[7] G. Russo, M. di Bernardo, Eduardo D. Sontag, Global entrainment of transcriptional systems to periodic inputs, PLoS Computational Biology, 6, 4, e1000739, 2010

[8] G. Russo, M. di Bernardo, How to synchronize Biological Clocks, Journal of Computational Biology, 16, 379-393, 2009

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