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Project Overview: Synchronizing the Repressilator

Background

A sinusoidal wave demonstrates a circadian rhythm

Although typically used to describe physical phenomena, oscillations are also observed in a range of biological processes such as circadian rhythms, pacemaker cells, neuronal communication and nephron function. [http://www.aph.caltech.edu/people/elowitz_m.html Elowitz] and Leibler ([http://www.aph.caltech.edu/people/Repressilator.pdf 2000]) have designed a genetic system called the Repressilator, composed of three genes (λcI, TetR, LacI) tied in negative feedback loops, which generates oscillations in protein expression within Escherichia coli.

In a Nutshell

Unlike oscillating cells in the human body, the Repressilator does not allow for the synchronization of oscillations in a population of cells. We attempt to bring oscillating cells into phase with eachother by coupling via the "autoinducer" molecule AI. Our 2-gene construct may also be used in future genetic systems, making it a system of choice in a highly modular synthetic biology framework.

Relevance and inspiration

While it may be presumptuous to call the synchronization of Elowitz's Repressilator the proverbial '[http://en.wikipedia.org/wiki/Holy_Grail Holy Grail]' of modern bioengineering, parallels can be drawn between these two that tempt the leap to association. Synchronization is a crucial stepping stone towards the understanding of natural oscillatory systems and towards creating a synthetic system that can accurately emulate this natural phenomenon. Innumerable past, present and future bioengineering projects in iGEM and the scientific community focus and revolve around this concept and its applications. By exploring the fundamental theory through mathematical models and empirical observation, we hope to understand the nature of these systems and develop future synthetic applications. •

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-== '''Project Overview: Elucidating an Experimentally Viable Repressilator''' ==
+== '''Project Overview: Synchronizing the Repressilator''' ==
 ===Background===
-[[Image:mcgill_osc.jpg||thumb|left|300px | A sinusoidal wave demonstrates a circadian rhythm]]Although typically used to describe physical phenomena, oscillations are also observed in a range of biological processes such as the circadian rhythm, neuronal communication and nephron function. [http://www.aph.caltech.edu/people/elowitz_m.html Elowitz] and Leibler ([http://www.aph.caltech.edu/people/Repressilator.pdf 2000]) postulated that a relaxation oscillator system called the Repressilator, composed of three genes (&lambda;cI, TetR, LacI) tied in negative feedback loops, would generate oscillations in protein expression within ''Escherichia coli''. Using one of these genes (TetR) linked with a Yellow Fluorescent Protein (YFP) gene to create a reporter plasmid, we expect to see the cells blinking over time as the concentration of the relevant proteins in the cell fluctuate.
+[[Image:Osc-rep.jpg||thumb|right|300px | A sinusoidal wave demonstrates a circadian rhythm]]Although typically used to describe physical phenomena, oscillations are also observed in a range of biological processes such as circadian rhythms, pacemaker cells, neuronal communication and nephron function. [http://www.aph.caltech.edu/people/elowitz_m.html Elowitz] and Leibler ([http://www.aph.caltech.edu/people/Repressilator.pdf 2000]) have designed a genetic system called the Repressilator, composed of three genes (&lambda;cI, TetR, LacI) tied in negative feedback loops, which generates oscillations in protein expression within ''Escherichia coli''.
-<br><br>
-===McGill iGEM Projects 2006 & 2007===
-The two-gene intercellular oscillatory system ([http://www.utm.utoronto.ca/~mcmillen/ McMillen] [http://www.pnas.org/cgi/reprint/99/2/679.pdf 2002]) examined in past projects developed irregular, triangular-shaped oscillation curves over extended periods of time. In an effort to improve the consistency and regularity of the oscillations, the Repressilator will be used. The system in theory should have better long-term fidelity in oscillation patterns and develop a more natural sinusoidal oscillatory pattern. Despite the foreseeable advantages of Elowitz's theoretical system, the repressilator has yet to be reproduced empirically; in addition, theoretical models indicate that, in general, these synthetic oscillatory systems in bacteria degrade and become irregular, unlike the natural physiological oscillations of larger lifeforms.
-<br><br>
-===iGEM Project 2008===
-[[Image:mcgill_quorum.jpg||thumb|left|300px | Quorum sensing at work in e. coli bacteria]]Building on previous years of research, the McGill University iGEM team intends to construct a set of Biobricks that will mimic the repressilator behavior and maintain synchronous oscillations in a large population of cells. If accomplished, our theorists and experimentalists will cooperate to refine this system using various modifications to further our understanding of biological clocks and their functioning.
-<br><br><br><br><br><br><br>
-==Relevance and inspiration==
+===In a Nutshell===
-While it may be presumptuous to call Elowitz's Repressilator the proverbial '[http://en.wikipedia.org/wiki/Holy_Grail Holy Grail]' of modern bioengineering, parallels can be drawn between these two that tempt the leap to association. The Repressilator, often theorized about but never reproduced in a laboratory, is a crucial stepping stone towards a true understanding of synthetic oscillatory systems and the road towards creating a synthetic system that emulate the natural. Innumerable past, present and future bioengineering projects in iGEM and the real scientific community focus and revolve around this concept and its applications. By exploring the fundamental theory through mathematical models and empirical observation, we hope to understand the nature of these systems and develop future synthetic applications.
+Unlike oscillating cells in the human body, the Repressilator does not allow for the synchronization of oscillations in a population of cells. We attempt to bring oscillating cells into phase with eachother by coupling via the "autoinducer" molecule AI. Our 2-gene construct may also be used in future genetic systems, making it a system of choice in a highly modular synthetic biology framework.
+===Relevance and inspiration===
+While it may be presumptuous to call the synchronization of Elowitz's Repressilator the proverbial '[http://en.wikipedia.org/wiki/Holy_Grail Holy Grail]' of modern bioengineering, parallels can be drawn between these two that tempt the leap to association. Synchronization is a crucial stepping stone towards the understanding of natural oscillatory systems and towards creating a synthetic system that can accurately emulate this natural phenomenon. Innumerable past, present and future bioengineering projects in iGEM and the scientific community focus and revolve around this concept and its applications. By exploring the fundamental theory through mathematical models and empirical observation, we hope to understand the nature of these systems and develop future synthetic applications.
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 [[Image:mcgillwinterpng.png|800px|center|McGill in winter]]