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Imperial College London iGEM 2006

   

Full Documentation of the project on OWW

Project Summary: Oscillators are a fundamental building block in many engineering fields and are a widespread phenomenon in biology. Building a biological oscillator is thus a crucial step forward in the field of Synthetic Biology. Engineering a Molecular Predation Oscillator, the iGEM project 2006 of Imperial College London, provides a new approach to create a stable biological oscillator: It follows an engineering-based cycle of specification, design, modelling, implementation and testing/validation. The innovative design of the oscillator relies on predator-prey dynamics based on the Lotka-Volterra model.

Achievements: Following the design of the oscillator, a full theoretical analysis of the Lotka-Volterra properties was carried out, which promised the successful outcome of oscillations. Additionally, all components as well as the overall oscillator were modelled such that the behaviour of the system could be predicted. Our team successfully built functional parts, thus providing the building block for the final oscillator. All parts created were experimentally tested and their characterization could be used to feedback information into the modelling.

Main Project

	Our Approach: Engineering a Molecular Predation Oscillator For building our biological oscillator, the engineering cycle below was followed. Click on each of the stages of the engineering cycle below in order to find out about the different stages & aspects of the project.
1) Specifications: Building a stable biological oscillator with controllable oscillations in a modular design 2) Design: Mimics predator-prey dynamics based on the Lotka-Volterra model 3) Modelling: Full theoretical analysis Modelling of the full system 4) Implementation: 4 functional & 5 intermediate parts successfully submitted to the Registry 5) Testing/Validation: Testing of different components of the oscillator, thus characterizing the parts

Secondary Projects

PoPs Blocker

Biological to Electrical Interface

As a method of controlling the activation of the positive-feedback loop in our predator-prey based oscillator, we successfully created this part, which can be used as a general Pops Blocker: This part is placed downstream of a promoter and prevents any Pops from the promoter passing through this part When an accompanying Cre Recombinase plasmid becomes activated, the enzyme produced will permanently cut a section of DNA from the plasmid containing this part Only then, the polymerase can pass through this part and transcribe downstream genes.

We also worked on a Biosensor for measuring AHL concentrations in order to establish a Biological to Electrical Interface this summer. Using an enzyme to hydrolize the lactone AHL would result in a local change in pH Measuring the change in pH gives a measurement of how much AHL is present

Our Contributions to the Registry

Part Logo	Description	Link to registry	Built	Tested	Characterized	Sequenced	Sent
Final Constructs
	Final Prey Cell	<bbpart>J37015</bbpart>	YES	YES	Pending	YES	YES
	Cre/Lox Prey Control	<bbpart>J37027</bbpart>	YES	YES	YES	YES	YES
Test Constructs
	Final Polycistronic Predator Cell Test Construct	<bbpart>J37016</bbpart>	YES	YES	YES	YES	YES
	Predator Cell, pLux Transfer Function (two promoters)	<bbpart>J37020</bbpart>	YES	YES	NO	NO	YES
Intermediate Parts
	AHL induced LuxR generator (for predator cell)	<bbpart>J37019</bbpart>	YES	N/A	N/A	YES	YES
	RBS + LuxR	<bbpart>J37033</bbpart>	YES	N/A	N/A	YES	YES
	Prey Cell Intermediate	<bbpart>J37034</bbpart>	YES	N/A	N/A	YES	YES
	LuxR + GFP	<bbpart>J37032</bbpart>	YES	N/A	N/A	YES	YES

Our Open Documentation

Lab Notebook Protocols	Journal Club<br\> Lecture Notes<br\>	BioSysBio Conference, UK	UK iGEM Teams Meeting	Photos

The Team and Acknowledgements

The Imperial College iGEM team and instructors on the terrace of the Biochemistry building

Undergrads Christin Sander Deepti Aswani Farah Vohra Jiongjun Bai John Sy John Chattaway Jonathan Wells Tom Hinson	Advisors Prof. Richard Kitney Prof. Paul Freemont Dr. David Mann Kirsten Jensen Vincent Rouilly Chueh-Loo Poh Matthieu Bultelle	Acknowledgements Prof. Tony Cass Dr. Anna Radomska Dr. Rupert Fray Dr. David Leak Dr. Mauricio Barahona Dr. Danny O'Hare Dr. Geoff Baldwin Dr. Ian Smith Susan E. Wryter David Featherbe Ciaran Mckeown James Mansfield	Funding European Commission Imperial College Deputy Rector's Fund Imperial College Faculty of Engineering Imperial College Faculty of Natural Sciences