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Design and construction of clock based synthetic oscillators

Primary Supervisor: Dr Bruno Martins, School of Life Sciences

Secondary supervisor: Declan Bates

PhD project title: Design and construction of clock based synthetic oscillators

University of Registration: University of Warwick

Project outline:

Background:
The rational design of oscillators has been a pursuit of synthetic biology since its inception (1), but evolution has already endowed natural systems with reliable and robust oscillators – circadian clocks, regulatory networks that oscillate with 24-h periods and drive expression of other genes. Existing synthetic oscillators do not typically share the clock’s robustness and this prevents construction of complex synthetic circuits. In electronics, clocks are essential elements of integrated circuits, allowing different parts to be linked and synchronised. If we can understand how to modulate the frequency of the cyanobacterial clock, and how to systematically integrate it with other pathways, clock based oscillators can play a similar role in synthetic biology and enable the construction of complex circuits.

General aims and methodology: In previous work (2), our lab identified a gene circuit that generates frequency doubling of clock outputs in the cyanobacterium S. elongatus, i.e. it converts oscillations that peak once per day into oscillations that peak twice per day. This project will build upon that work in order to understand how to harness the cyanobacterial clock to produce specific (non-circadian) frequencies and to construct a suite of clock-based oscillators. Owing to cell-to-cell heterogeneity, which can mask underlying behaviours, circuit dynamics will be characterised primarily through single-cell time-lapse microscopy. Guided by mathematical simulations, clock mutants will be used to provide a baseline of starting frequencies, which will then be coupled to transcriptional modules to generate harmonics. Our final aim is to transplant this suite of oscillators into other systems, following up on recent work that demonstrated the feasibility of this undertaking (3).

References:

  1. O. Purcell, N. J. Savery, C. S. Grierson, M. di Bernardo, A comparative analysis of synthetic genetic oscillators. J R Soc Interface 7, 1503–1524 (2010).
  2. B. M. Martins, A. K. Das, L. Antunes, J. C. Locke, Frequency doubling in the cyanobacterial circadian clock. Molecular Systems Biology 12, 896 (2016).
  3. A. H. Chen, D. Lubkowicz, V. Yeong, R. L. Chang, P. A. Silver, Transplantability of a circadian clock to a noncircadian organism. Science Advances 1, e1500358 (2015).

BBSRC Strategic Research Priority: Understanding the rules of life: Microbiology

Techniques undertaken during the project:

  • Single-cell time-lapse microscopy
  • Mathematical models
  • Computational work including quantitative image analysis, time-series analysis and writing short routines for automated microscopy acquisition
  • Microbiology and molecular genetics

Contact: Dr Bruno Martins, University of Warwick