Control strategies for mitigating the effect for external perturbations on gene regulatory networks

Mathias Foo, Iulia Gherman, Katherine Denby, Declan Bates

Research output: Chapter in Book/Report/Conference proceedingConference proceeding

1 Citation (Scopus)
29 Downloads (Pure)

Abstract

External perturbations affecting gene regulatory networks, such as pathogen/virus attacks, can lead to adverse effects on the phenotype of the biological system. In this paper, we propose a systematic approach to mitigate the effect of such perturbations that can be implemented using the tools of synthetic biology. We use system identification techniques to build accurate models of an example gene regulatory network from time-series data, and proceed to identify the kernel architecture of the network, which is defined as the minimal set of interactions needed to reproduce the wild type temporal behaviour. The kernel architecture reveals four key pathways in the network which allow us to investigate a number of different mitigation strategies in the event of external perturbations. We show that while network reoptimisation can reduce the impact of perturbations, combining network rewiring with a synthetic feedback control loop allows the effect of the perturbation to be completely eliminated. The proposed approach highlights the potential of combining feedback control theory with synthetic biology for developing more resilient biological systems.
Original languageEnglish
Title of host publicationIFAC World Congress
PublisherIFAC-Papers OnLine
Pages12647-12652
Number of pages6
Volume50
Edition1
DOIs
Publication statusPublished - 9 Jul 2017
EventThe 20th World Congress of the International Federation of Automatic Control - Toulouse, France
Duration: 9 Jul 201714 Jul 2017
https://www.ifac2017.org/

Conference

ConferenceThe 20th World Congress of the International Federation of Automatic Control
Abbreviated titleIFAC 2017
CountryFrance
CityToulouse
Period9/07/1714/07/17
Internet address

Fingerprint

Biological systems
Feedback control
Genes
Pathogens
Control theory
Viruses
Time series
Identification (control systems)
Synthetic Biology

Bibliographical note

NOTICE: this is the author’s version of a work that was accepted for publication in IFAC-Papers OnLine. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in IFAC-Papers OnLine, Vol 50, (2017)] DOI: 10.1016/j.ifacol.2017.08.2237

© 2017, Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/

Cite this

Foo, M., Gherman, I., Denby, K., & Bates, D. (2017). Control strategies for mitigating the effect for external perturbations on gene regulatory networks. In IFAC World Congress (1 ed., Vol. 50, pp. 12647-12652). IFAC-Papers OnLine. https://doi.org/10.1016/j.ifacol.2017.08.2237

Control strategies for mitigating the effect for external perturbations on gene regulatory networks. / Foo, Mathias; Gherman, Iulia; Denby, Katherine; Bates, Declan.

IFAC World Congress. Vol. 50 1. ed. IFAC-Papers OnLine, 2017. p. 12647-12652.

Research output: Chapter in Book/Report/Conference proceedingConference proceeding

Foo, M, Gherman, I, Denby, K & Bates, D 2017, Control strategies for mitigating the effect for external perturbations on gene regulatory networks. in IFAC World Congress. 1 edn, vol. 50, IFAC-Papers OnLine, pp. 12647-12652, The 20th World Congress of the International Federation of Automatic Control, Toulouse, France, 9/07/17. https://doi.org/10.1016/j.ifacol.2017.08.2237
Foo M, Gherman I, Denby K, Bates D. Control strategies for mitigating the effect for external perturbations on gene regulatory networks. In IFAC World Congress. 1 ed. Vol. 50. IFAC-Papers OnLine. 2017. p. 12647-12652 https://doi.org/10.1016/j.ifacol.2017.08.2237
Foo, Mathias ; Gherman, Iulia ; Denby, Katherine ; Bates, Declan. / Control strategies for mitigating the effect for external perturbations on gene regulatory networks. IFAC World Congress. Vol. 50 1. ed. IFAC-Papers OnLine, 2017. pp. 12647-12652
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