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Design and analysis of a tunable synchronized oscillator

Brendan M Ryback1, Dorett I Odoni1, Ruben GA van Heck1, Youri van Nuland1, Matthijn C Hesselman1, Vítor AP Martins dos Santos1*, Mark WJ van Passel14 and Floor Hugenholtz23

Author Affiliations

1 Systems and Synthetic Biology, Wageningen University, Wageningen, Netherlands

2 Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands

3 Netherlands Consortium for Systems Biology, University of Amsterdam, Amsterdam, Netherlands

4 Centre for Zoonoses and Environmental Microbiology, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands

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Journal of Biological Engineering 2013, 7:26  doi:10.1186/1754-1611-7-26

Published: 18 November 2013

Abstract

Background

The use of in silico simulations as a basis for designing artificial biological systems (and experiments to characterize them) is one of the tangible differences between Synthetic Biology and “classical” Genetic Engineering. To this end, synthetic biologists have adopted approaches originating from the traditionally non-biological fields of Nonlinear Dynamics and Systems & Control Theory. However, due to the complex molecular interactions affecting the emergent properties of biological systems, mechanistic descriptions of even the simplest genetic circuits (transcriptional feedback oscillators, bi-stable switches) produced by these methods tend to be either oversimplified, or numerically intractable. More comprehensive and realistic models can be approximated by constructing “toy” genetic circuits that provide the experimenter with some degree of control over the transcriptional dynamics, and allow for experimental set-ups that generate reliable data reflecting the intracellular biochemical state in real time. To this end, we designed two genetic circuits (basic and tunable) capable of exhibiting synchronized oscillatory green fluorescent protein (GFP) expression in small populations of Escherichia coli cells. The functionality of the basic circuit was verified microscopically. High-level visualizations of computational simulations were analyzed to determine whether the reliability and utility of a synchronized transcriptional oscillator could be enhanced by the introduction of chemically inducible repressors.

Results

Synchronized oscillations in GFP expression were repeatedly observed in chemically linked sub-populations of cells. Computational simulations predicted that the introduction of independently inducible repressors substantially broaden the range of conditions under which oscillations could occur, in addition to allowing the frequency of the oscillation to be tuned.

Conclusions

The genetic circuits described here may prove to be valuable research tools for the study of synchronized transcriptional feedback loops under a variety of conditions and experimental set-ups. We further demonstrate the benefit of using abstract visualizations to discover subtle non-linear trends in complex dynamic models with large parameter spaces.

Keywords:
Synchronized tunable oscillator; Genetic circuit; Transcriptional feedback; Delay differential equation