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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


The Team and Acknowledgements

Undergrads

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

Advisors

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
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