Imperial College 2006

From IGEM

Full Documentation of the project on OpenWetWare

Presentation

Poster

Project Summary

We have used the traditional engineering approach to build a stable and flexible molecular oscillator

Our original design relies on population dynamics and was inspired by the Lotka-Volterra predation model

Every step of the development cycle (Specifications, Design, Modelling, Implementation, Testing/Validation) has been fully documented on our OWW site

Achievements

Derivation of the complete dynamical model, describing the main biochemical reactions driving our oscillator
Full theoretical analysis and detailed computer simulations, validating our design with regard to our specifications
Successful building and characterization of functional parts, providing the building blocks for the final oscillator

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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 Modelling of the full system 4) Implementation: All parts designed and modelled 4 functional & 5 intermediate submitted to the Registry 5) Testing/ Validation: Successful characterization of sub-components.		Click on picture for more info
	Click on picture for more info		Click on picture for more info

	Click on picture for more info		Click on picture for more info

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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.

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.

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Our Contributions to the Registry

Part Logo	Description	Link to registry	Built	Tested	Characterized	Sequenced	Sent
Final Constructs	(!) Favorite Part
	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