Imperial College 2006/Sandbox

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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>
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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>
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>
'''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>
'''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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|width="40%" style="background:#2171B8" | <font face="arial" font style="color: #FFFFFF" > <center><big><u>'''Achievements:'''</u></big></center> <br>
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|width="40%" style="background:#2171B8" | <font face="arial" font style="color: #FFFFFF" > <center><big><u>'''Achievements'''</u></big></center> <br>
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.
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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Revision as of 12:11, 30 October 2006


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


LogoFinal2.png
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

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.

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
  • 4 functional & 5 intermediate submitted to the Registry

5) Testing/Validation:

  • Successful characterization of sub-components.
ArrowCurvedRight.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] ArrowCurvedDown.PNG
[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Specifications http://openwetware.org/images/f/fd/IGEM_IMPERIAL_DevCycle_Specifications.png]
IGEM IMPERIAL DevCycle FullSystem.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]
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[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Validation http://openwetware.org/images/2/20/IGEM_IMPERIAL_DevCycle_Validation.png] ArrowLeft.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
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

  • Full Documentation, 100's of Photographs, Extensive Modelling, Lab Notebook and much more!


  • [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/2006/Calendar/2006-7-26 UK iGEM Teams Meeting]
  • [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Photos Photos]

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

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