Imperial College 2006

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[http://openwetware.org/wiki/IGEM:IMPERIAL/2006 Full Documentation of the project on OWW]

Project Summary
Oscillators are a fundamental building block in many fields of engineering and are a widespread phenomenon in biology. Building a biological oscillator is thus a critical 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 creating 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 and detailed computer modelling of the Lotka-Volterra dynamics was carried out. These studies showed that it is theoretically possible to provide a stable oscillator. Because all components as well as the overall oscillator were modelled, its behaviour could be accurately predicted. Our team successfully built the functional parts, thus providing the building blocks for the final oscillator. All parts created were experimentally tested and their characterization could be used to feedback information into the modelling.

Main Project

	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: Stable and robust oscillations Controllable frequency/amplitude Generic and modular 2) Design: Mimics predator-prey dynamics based on the Lotka-Volterra model 3) Modelling: Full theoretical analysis [http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/Theoretical_Analyses] Modelling of the full system 4) Implementation: All parts designed 4 functional & 5 intermediate submitted to the Registry 5) Testing/Validation: Successful characterization of sub-components.		[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Design http://openwetware.org/images/c/ce/IGEM_IMPERIAL_DevCycle_Design.png]
	[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System http://openwetware.org/images/f/fd/IGEM_IMPERIAL_DevCycle_Specifications.png]		[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Modelling http://openwetware.org/images/5/5f/IGEM_IMPERIAL_DevCycle_Modelling.png]

	[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/TestingValidation http://openwetware.org/images/2/20/IGEM_IMPERIAL_DevCycle_Validation.png]		[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Implementation http://openwetware.org/images/0/04/IGEM_IMPERIAL_DevCycle_Implementation.png]

Secondary Projects

[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/popsblocker PoPs Blocker]

[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Bio_elec_interface 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	J37015	YES	YES	Pending	YES	YES
	Cre/Lox Prey Control	J37027	YES	YES	YES	YES	YES
Test Constructs
	Final Polycistronic Predator Cell Test Construct	J37016	YES	YES	YES	YES	YES
	Predator Cell, pLux Transfer Function (two promoters)	J37020	YES	YES	NO	NO	YES
Intermediate Parts
	AHL induced LuxR generator (for predator cell)	J37019	YES	N/A	N/A	YES	YES
	RBS + LuxR	J37033	YES	N/A	N/A	YES	YES
	Prey Cell Intermediate	J37034	YES	N/A	N/A	YES	YES
	LuxR + GFP	J37032	YES	N/A	N/A	YES	YES