Imperial College 2006

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== Welcome to '''''Imperial College''''' iGEM team! ==
+
__NOTOC__
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== Team Members ==
+
__NOTOC__
-
*Christin Sander
+
<center>[[Image:Banner.png|800px]]</center>
-
*Deepti Aswani
+
-
*Farah Vohra
+
-
*Jiongjun Bai
+
-
*John Sy
+
-
*John Chattaway
+
-
*Jonathan Wells
+
-
*Thomas Hinson
+
-
== Instructors ==
 
-
*Prof. Richard Kitney
+
<center><font size="4">'''[http://openwetware.org/wiki/IGEM:IMPERIAL/2006 Full Documentation of the project on OpenWetWare]'''</font></center>
-
*Prof. Paul Freemont
+
<center><font size="3">'''[[Media:IGEM_Imperial_2006_presentation.pdf |Presentation ]]'''</font></center>
-
*Dr. David Mann
+
<center><font size="3">'''[[Media:IGEM_Imperial_2006_Poster.pdf |Poster]]'''</font></center>
-
*Vincent Rouilly
+
-
*Chueh-Loo Poh
+
-
== Schedule ==
 
-
Start Date: '''3 July 2006'''
 
-
We have just finished forming the team. Now it is the examination period. Soon after that we will have a more detailed planning schedule.
+
{| border="0" width="100%" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;"
 +
|-
 +
|width="20%" style="background:#2171B8"|[[Image:LogoFinal2.png|210px|center]]
 +
|width="40%" style="background:#2171B8"| <font face="arial" font style="color: #FFFFFF" >
 +
<center><big><u>'''Project Summary'''</u></big></center>
 +
 
 +
 
 +
*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</font>
 +
|width="40%" style="background:#2171B8" | <font face="arial" font style="color: #FFFFFF" >
 +
 
 +
 
 +
<center><big><u>'''Achievements'''</u></big></center>
 +
<br>
 +
*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
 +
<br>
 +
<br>
 +
<br>
 +
</font>
 +
|}
 +
 
 +
 
 +
 
 +
==Main Project==
 +
{| border="0" width="100%" align="center" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;"
 +
| width="20%" style="background:#2171B8"| <center>[[Image:Oscillator Icon.PNG|100px|center]] </center>
 +
| style="background:#2171B8" colspan="3"| <font face="arial" font style="color: yellow"> <center><big>'''Engineering a Molecular Predation Oscillator'''</big><br>
 +
<font face="arial" font style="color: #ffffff">For building our biological oscillator, the engineering cycle below was followed.<br>
 +
'''<font style="color: orange">Click</font> on <font style="color: orange">each</font> of the stages of the <font style="color: orange">engineering cycle</font> below in order to find out about the different stages & aspects of the project. '''</font></center>
 +
|-
 +
| style="background:#2171B8" width="200pt" rowspan="4" |
 +
[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System <font face="arial" font style="color: yellow"> '''1) Specifications: '''</font>]
 +
<font face="arial" font style="color: #ffffff">
 +
*Stable and robust oscillations
 +
*Controllable frequency/amplitude
 +
*Generic and modular</font>
 +
[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Design <font face="arial" font style="color: yellow">'''2) Design: '''</font>]
 +
<font face="arial" font style="color: #ffffff">
 +
*Mimics predator-prey dynamics based on the Lotka-Volterra model
 +
</font>
 +
[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Modelling <font face="arial" font style="color: yellow">'''3) Modelling: '''</font>]
 +
<font face="arial" font style="color: #ffffff">
 +
*[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/Theoretical_Analyses <font face="arial" font style="color: #FFFFFF">Full theoretical analysis</font>]
 +
*Modelling of the full system
 +
</font>
 +
[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Implementation <font face="arial" font style="color: yellow"> '''4) Implementation: '''</font>]
 +
<font face="arial" font style="color: #ffffff">
 +
*All parts designed and modelled
 +
*4 functional & 5 intermediate submitted to the Registry
 +
</font>
 +
[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/TestingValidation <font face="arial" font style="color: yellow">'''5) Testing/ Validation: '''</font>]
 +
<font face="arial" font style="color: #ffffff">
 +
*Successful characterization of sub-components.
 +
</font>
 +
| align="right"|[[Image:ArrowCurvedRight.png|110px]]
 +
| align="center" |[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]<font style="color:red"><br>Click on picture for more info</font>
 +
| align="left"|[[Image:ArrowCurvedDown.PNG|120px]]
 +
|-
 +
| align="center"|[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]<font style="color:red"><br>Click on picture for more info</font>
 +
| align="center" rowspan="2"|[[Image:IGEM_IMPERIAL_DevCycle_FullSystem.png |206px|center]]
 +
| align="center"|[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]<font style="color:red"><br>Click on picture for more info</font>
 +
|-
 +
| align="center"|[[Image:ArrowUp.png|20px]]
 +
| align="center"|[[Image:ArrowDown.png|20px]]
 +
|-
 +
| align="center"|[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]<font style="color:red"><br>Click on picture for more info</font>
 +
| align="center"|[[Image:ArrowLeft.png|150px]]
 +
| align="center"|[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]<font style="color:red"><br>Click on picture for more info</font>
 +
|}
 +
 
 +
==Secondary Projects==
 +
{| border="0"  width="100%" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;"  width="100%"
 +
|-
 +
!  width="50%" | <big>'''[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/popsblocker <font face="arial" font style="color: #2171B8">PoPs Blocker</font>]  '''</big>!! width="50%"| <big>'''[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Bio_elec_interface <font face="arial" font style="color: #2171B8">Biological to Electrical Interface]</font>'''</big>
 +
|-
 +
| style="background:#2171B8" width="50%" |
 +
<font face="arial" font style="color: #FFFFFF"> 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.
 +
</font>
 +
| style="background:#2171B8" width="50%" |
 +
<font face="arial" font style="color: #FFFFFF">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.
 +
<br>
 +
<br>
 +
<br>
 +
<br>
 +
</font>
 +
|}
 +
 
 +
==Our Contributions to the Registry==
 +
{|border="0" width="100%" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;"
 +
! style="background:#2171B8" | <font face="arial" font style="color: #FFFFFF">Part Logo !! style="background:#2171B8" |<font face="arial" font style="color: #FFFFFF">Description</font> !! style="background:#2171B8" |<font face="arial" font style="color: #FFFFFF">Link to registry</font> !! style="background:#2171B8" |<font face="arial" font style="color: #FFFFFF">Built</font> !! style="background:#2171B8" |<font face="arial" font style="color: #FFFFFF">Tested </font>!! style="background:#2171B8" |<font face="arial" font style="color: #FFFFFF">Characterized </font>!! style="background:#2171B8" |<font face="arial" font style="color: #FFFFFF">Sequenced</font> !! style="background:#2171B8" |<font face="arial" font style="color: #FFFFFF">Sent</font>
 +
|-
 +
!style="background:#008080" |<font face="arial" font style="color: #FFFFFF">Final Constructs</font>
 +
!style="background:#008080"|<font face="arial" font style="color: orange">(!) Favorite Part</font>
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
|-
 +
![[Image:J37015.PNG|250px]]!! Final Prey Cell <font face="arial" font style="color: orange">(!) </font> !! <bbpart>J37015</bbpart> !! YES !! YES !! Pending !! YES !! YES
 +
|-
 +
! [[Image:J37027.png|120px]] !! Cre/Lox Prey Control <font face="arial" font style="color: orange">(!) </font>!! <bbpart>J37027</bbpart> !! YES !! YES !! YES !! YES !!YES
 +
|-
 +
!style="background:#008080" |<font face="arial" font style="color: #FFFFFF">Test Constructs</font>
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
|-
 +
![[Image:J37016.PNG|150px]]!! Final Polycistronic Predator Cell Test Construct <font face="arial" font style="color: orange">(!) </font>!! <bbpart>J37016</bbpart> !! YES !! YES !! YES !! YES!! YES
 +
|-
 +
! [[Image:J37020.png|170px]] !! Predator Cell, pLux Transfer Function (two promoters)  !! <bbpart>J37020</bbpart> !! YES !! YES !! NO !! NO !! YES
 +
|-
 +
!style="background:#008080" |<font face="arial" font style="color: #FFFFFF">Intermediate Parts</font>
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
!style="background:#008080"|
 +
|-
 +
! [[Image:J37019.PNG|80px]] !! AHL induced LuxR generator (for predator cell) !! <bbpart>J37019</bbpart> !! YES !! N/A !! N/A!! YES !!YES
 +
|-
 +
! [[Image:J37033.PNG|65px]] !! RBS + LuxR !! <bbpart>J37033</bbpart> !! YES !! N/A !! N/A!! YES !!YES
 +
|-
 +
! [[Image:J37034.PNG|90px]] !! Prey Cell Intermediate!! <bbpart>J37034</bbpart> !! YES !! N/A !! N/A!! YES !!YES
 +
|-
 +
! [[Image:J37032.png|90px]] !! LuxR + GFP !! <bbpart>J37032</bbpart> !! YES !! N/A !! N/A!! YES !!YES
 +
|}
 +
 
 +
==Our Open Documentation==
 +
 
 +
*'''<font face="arial" font style="color: #2171B8">300+ Pages of documentation on OWW, 100's of Photographs, Extensive Modelling, Lab Notebook and much more!</font>'''
 +
__NOTOC__
 +
{| class="wikitable" border="0" cellpadding="10" cellspacing="1" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;text-align:center"
 +
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
 +
 
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006 <font face="arial" font style="color: #FFFFFF">iGEM@imperial</font>]
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser <font face="arial" font style="color: #FFFFFF">Oscillator project</font>]
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/popsblocker <font face="arial" font style="color: #FFFFFF">PoPs Blocker project</font>]
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Bio_elec_interface <font face="arial" font style="color: #FFFFFF">AHL Biosensor project</font>]
 +
 
 +
 
 +
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/LabCalendar <font face="arial" font style="color: #FFFFFF">Lab Notebook</font>]
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Protocols <font face="arial" font style="color: #FFFFFF">Protocols</font>]
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Journal_Club<font face="arial" font style="color: #FFFFFF"> Journal Club</font>]<br\>
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Lecture_Notes <font face="arial" font style="color: #FFFFFF">Lecture Notes</font>]<br\>
 +
 
 +
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
 +
*[http://openwetware.org/wiki/BioSysBio:abstracts/2007/iGEM2006_Imperial_College <font face="arial" font style="color: #FFFFFF">BioSysBio Conference, UK</font>]
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/Methodology <font face="arial" font style="color: #FFFFFF">Description of our Methodology</font>]
 +
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Calendar/2006-7-26 <font face="arial" font style="color: #FFFFFF">UK iGEM Teams Meeting</font>]
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Photos <font face="arial" font style="color: #FFFFFF">Photos</font>]
 +
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Instructors_Feedbacks <font face="arial" font style="color: #FFFFFF">Feedbacks on our experience</font>]
 +
|}
 +
 
 +
==The Team and Acknowledgements==
 +
 
 +
{| class="wikitable" border="0" width="100%" cellpadding="10" cellspacing="1" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;text-align:center"
 +
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
 +
<center>
 +
 
 +
==<font face="arial" font style="color: #FFFFFF">Undergrads</font>==
 +
</center>
 +
*[http://openwetware.org/wiki/User:Cys <font face="arial" font style="color: #FFFFFF">Christin Sander</font>]
 +
*[http://openwetware.org/wiki/User:da104 <font face="arial" font style="color: #FFFFFF">Deepti Aswani</font>]
 +
*[http://openwetware.org/wiki/User:Farah <font face="arial" font style="color: #FFFFFF">Farah Vohra</font>]
 +
*[http://openwetware.org/wiki/User:Baijiongjun<font face="arial" font style="color: #FFFFFF"> Jiongjun Bai</font>]
 +
*[http://openwetware.org/wiki/User:Johnsy <font face="arial" font style="color: #FFFFFF">John Sy</font>]
 +
*[http://openwetware.org/wiki/User:JohnChattaway <font face="arial" font style="color: #FFFFFF">John Chattaway</font>]
 +
*[http://openwetware.org/wiki/User:Jonny<font face="arial" font style="color: #FFFFFF"> Jonathan Wells</font>]
 +
*[http://openwetware.org/wiki/User:Tom <font face="arial" font style="color: #FFFFFF">Tom Hinson</font>]
 +
 
 +
!width="25%" align="left" valign="top"  color:black"|
 +
 
 +
[[Image:IGEM GroupPhotos0015.JPG|thumb|center|200px|The Imperial College iGEM team and advisors on the terrace of the Biochemistry building]]
 +
 
 +
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
 +
<center>
 +
 
 +
==<font face="arial" font style="color: #FFFFFF">Advisors</font>==
 +
</center>
 +
*[http://www3.imperial.ac.uk/people/r.kitney <font face="arial" font style="color: #FFFFFF">Prof. Richard Kitney</font>]
 +
*[http://www3.imperial.ac.uk/people/p.freemont <font face="arial" font style="color: #FFFFFF">Prof. Paul Freemont</font>]
 +
*[http://www3.imperial.ac.uk/people/d.mann <font face="arial" font style="color: #FFFFFF">Dr. David Mann</font>]
 +
*<font face="arial" font style="color: #FFFFFF">Kirsten Jensen</font>
 +
*[http://openwetware.org/wiki/User:Vincent <font face="arial" font style="color: #FFFFFF">Vincent Rouilly</font>]
 +
*[http://openwetware.org/wiki/User:chuehloo <font face="arial" font style="color: #FFFFFF">Chueh-Loo Poh</font>]
 +
*[http://openwetware.org/wiki/User:SxE00 <font face="arial" font style="color: #FFFFFF">Matthieu Bultelle</font>]
 +
 
 +
!width="20%" align="left" valign="top" style="background:#2171B8; color:white"|
 +
 
 +
<center>
 +
 
 +
==<font face="arial" font style="color: #FFFFFF">Funding</font>==
 +
</center>
 +
*European Commission
 +
*Imperial College Deputy Rector's Fund
 +
*Imperial College Faculty of Engineering
 +
*Imperial College Faculty of Natural Sciences
 +
|}
 +
 
 +
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Latest revision as of 16:42, 10 November 2006


Banner.png


Full Documentation of the project on OpenWetWare
Presentation
Poster


LogoFinal2.png
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.

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:

4) Implementation:

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

5) Testing/ Validation:

  • Successful characterization of sub-components.

ArrowCurvedRight.png http://openwetware.org/images/f/fd/IGEM_IMPERIAL_DevCycle_Specifications.png
Click on picture for more info
ArrowCurvedDown.PNG
http://openwetware.org/images/2/20/IGEM_IMPERIAL_DevCycle_Validation.png
Click on picture for more info
IGEM IMPERIAL DevCycle FullSystem.png
http://openwetware.org/images/c/ce/IGEM_IMPERIAL_DevCycle_Design.png
Click on picture for more info
ArrowUp.png ArrowDown.png
http://openwetware.org/images/0/04/IGEM_IMPERIAL_DevCycle_Implementation.png
Click on picture for more info
ArrowLeft.png http://openwetware.org/images/5/5f/IGEM_IMPERIAL_DevCycle_Modelling.png
Click on picture for more info

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 (!) 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!


The Team and Acknowledgements

Undergrads

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

Advisors

Funding

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

Personal tools
Past/present/future years