Imperial College 2006

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|width="40%" style="background:#2171B8"| <font face="arial" font style="color: #FFFFFF" > <center><big><u>'''Project Summary'''</u></big></center> <br> 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. <br><br>
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'''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. </font>
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<center><big><u>'''Project Summary'''</u></big></center>
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|width="40%" style="background:#2171B8" | <font face="arial" font style="color: #FFFFFF" > <center><big><u>'''Achievements'''</u></big></center> <br>
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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.
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*We have used the traditional engineering approach to build a stable and flexible molecular oscillator
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*Our original design relies on population dynamics and was inspired by the Lotka-Volterra predation model
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*Every step of the development cycle (Specifications, Design, Modelling, Implementation, Testing/Validation) has been fully documented on our OWW site</font>
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<center><big><u>'''Achievements'''</u></big></center>
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<br>
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*Derivation of the complete dynamical model, describing the main biochemical reactions driving our oscillator
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*Full theoretical analysis and detailed computer simulations, validating our design with regard to our specifications
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*Successful building and characterization of functional parts, providing the building blocks for the final oscillator
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Revision as of 00:30, 1 November 2006


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


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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





Main Project

Oscillator Icon.PNG
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.

[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System 1) Specifications: ]

  • Stable and robust oscillations
  • Controllable frequency/amplitude
  • Generic and modular

[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Design 2) Design: ]

  • Mimics predator-prey dynamics based on the Lotka-Volterra model

[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Modelling 3) Modelling: ]

  • [http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/Theoretical_Analyses Full theoretical analysis]
  • Modelling of the full system

[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Implementation 4) Implementation: ]

  • All parts designed and modelled
  • 4 functional & 5 intermediate submitted to the Registry

[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/TestingValidation 5) Testing/ Validation: ]

  • Successful characterization of sub-components.

ArrowCurvedRight.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]Click on picture for more info ArrowCurvedDown.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]Click on picture for more info
IGEM IMPERIAL DevCycle FullSystem.png
[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]Click on picture for more info
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[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]Click on picture for more info ArrowLeft.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]Click on picture for more info

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 (!) Favorite Part
J37015.PNG Final Prey Cell (!) J37015 YES YES Pending YES YES
J37027.png Cre/Lox Prey Control (!) J37027 YES YES YES YES YES
Test Constructs
J37016.PNG Final Polycistronic Predator Cell Test Construct (!) J37016 YES YES YES YES YES
J37020.png Predator Cell, pLux Transfer Function (two promoters) J37020 YES YES NO NO YES
Intermediate Parts
J37019.PNG AHL induced LuxR generator (for predator cell) J37019 YES N/A N/A YES YES
J37033.PNG RBS + LuxR J37033 YES N/A N/A YES YES
J37034.PNG Prey Cell Intermediate J37034 YES N/A N/A YES YES
J37032.png LuxR + GFP J37032 YES N/A N/A YES YES

Our Open Documentation

  • 300+ Pages of documentation on OWW, 100's of Photographs, Extensive Modelling, Lab Notebook and much more!
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006 iGEM@imperial]
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser Oscillator project]
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/popsblocker PoPs Blocker project]
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Bio_elec_interface AHL Biosensor project]


  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/LabCalendar Lab Notebook]
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Protocols Protocols]
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Journal_Club Journal Club]
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Lecture_Notes Lecture Notes]
  • [http://openwetware.org/wiki/BioSysBio:abstracts/2007/iGEM2006_Imperial_College BioSysBio Conference, UK]
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/Methodology Description of our Methodology]
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Calendar/2006-7-26 UK iGEM Teams Meeting]
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Photos Photos]
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Instructors_Feedbacks Feedbacks on our experience]

The Team and Acknowledgements

Undergrads

  • [http://openwetware.org/wiki/User:Cys Christin Sander]
  • [http://openwetware.org/wiki/User:da104 Deepti Aswani]
  • [http://openwetware.org/wiki/User:Farah Farah Vohra]
  • [http://openwetware.org/wiki/User:Baijiongjun Jiongjun Bai]
  • [http://openwetware.org/wiki/User:Johnsy John Sy]
  • [http://openwetware.org/wiki/User:JohnChattaway John Chattaway]
  • [http://openwetware.org/wiki/User:Jonny Jonathan Wells]
  • [http://openwetware.org/wiki/User:Tom Tom Hinson]
The Imperial College iGEM team and advisors on the terrace of the Biochemistry building

Advisors

  • [http://www3.imperial.ac.uk/people/r.kitney Prof. Richard Kitney]
  • [http://www3.imperial.ac.uk/people/p.freemont Prof. Paul Freemont]
  • [http://www3.imperial.ac.uk/people/d.mann Dr. David Mann]
  • Kirsten Jensen
  • [http://openwetware.org/wiki/User:Vincent Vincent Rouilly]
  • [http://openwetware.org/wiki/User:chuehloo Chueh-Loo Poh]
  • [http://openwetware.org/wiki/User:SxE00 Matthieu Bultelle]

Funding

  • European Commission
  • Imperial College Deputy Rector's Fund
  • Imperial College Faculty of Engineering
  • Imperial College Faculty of Natural Sciences

Retrieved from "http://2006.igem.org/wiki/index.php/Imperial_College_2006"
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