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Real-Time Optogenetics System for Controlling Gene Expression Using a Model-Based Design.

Author(s): Soffer G, Perry JM, Shih SCC

Optimization of engineered biological systems requires precise control over the rates and timing of gene expression. Optogenetics is used to dynamically control gene expression as an alternative to conventional chemical-based methods since it provides a mor...

Article GUID: 33543619
One Cell, One Drop, One Click: Hybrid Microfluidics for Mammalian Single Cell Isolation.

Author(s): Samlali K, Ahmadi F, Quach ABV, Soffer G, Shih SCC

Small. 2020 Jul 23;:e2002400 Authors: Samlali K, Ahmadi F, Quach ABV, Soffer G, Shih SCC

Article GUID: 32705796
Integration of World-to-Chip Interfaces with Digital Microfluidics for Bacterial Transformation and Enzymatic Assays.

Author(s): Moazami E, Perry JM, Soffer G, Husser MC, Shih SCC

Anal Chem. 2019 Apr 16;91(8):5159-5168 Authors: Moazami E, Perry JM, Soffer G, Husser MC, Shih SCC

Article GUID: 30945840
Title:Real-Time Optogenetics System for Controlling Gene Expression Using a Model-Based Design.
Authors:Soffer G,  Perry JM,  Shih SCC
Link:https://www.ncbi.nlm.nih.gov/pubmed/33543619
DOI:10.1021/acs.analchem.0c04594
Category:Anal Chem
PMID:33543619
Dept Affiliation: BIOLOGY
1 Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd West, Montréal, Québec H3G1M8, Canada.
2 Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada.
3 Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada.

Description:

Real-Time Optogenetics System for Controlling Gene Expression Using a Model-Based Design.

Anal Chem. 2021 Feb 05; :

Authors: Soffer G, Perry JM, Shih SCC

Abstract

Optimization of engineered biological systems requires precise control over the rates and timing of gene expression. Optogenetics is used to dynamically control gene expression as an alternative to conventional chemical-based methods since it provides a more convenient interface between digital control software and microbial culture. Here, we describe the construction of a real-time optogenetics platform, which performs closed-loop control over the CcaR-CcaS two-plasmid system in Escherichia coli. We showed the first model-based design approach by constructing a nonlinear representation of the CcaR-CcaS system, tuned the model through open-loop experimentation to capture the experimental behavior, and applied the model in silico to inform the necessary changes to build a closed-loop optogenetic control system. Our system periodically induces and represses the CcaR-CcaS system while recording optical density and fluorescence using image processing techniques. We highlight the facile nature of constructing our system and how our model-based design approach will potentially be used to model other systems requiring closed-loop optogenetic control.

PMID: 33543619 [PubMed - as supplied by publisher]