Imperial College 2006/Sandbox

From 2006.igem.org

(Difference between revisions)
Jump to: navigation, search
 
(19 intermediate revisions not shown)
Line 7: Line 7:
-
{| border="0" width="100%" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;"
+
{| 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="20%" style="background:#2171B8"|[[Image:LogoFinal2.png|210px|center]]  
-
|width="40%" style="background:#2171B8" | <font face="century gothic" font style="color: #FFFFFF"> <center><u>'''Project Summary:'''</u></center> <br>
+
|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>
-
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>
-
|width="40%" style="background:#2171B8" | <font face="century gothic" font style="color: #FFFFFF"> <center><u>'''Achievements:'''</u></center> <br>
+
|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.
 +
<br>
 +
<br>
 +
<br>
</font>
</font>
|}
|}
Line 23: Line 25:
{| border="0" width="100%" align="center" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;"
{| 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>
| width="20%" style="background:#2171B8"| <center>[[Image:Oscillator Icon.PNG|100px|center]] </center>
-
| style="background:#2171B8" colspan="3"| <font face="century gothic" font style="color: #FFFFFF"> <center><big>'''Engineering a Molecular Predation Oscillator'''</big><br>
+
| style="background:#2171B8" colspan="3"| <font face="arial" font style="color: #FFFFFF"> <center><big>'''Engineering a Molecular Predation Oscillator'''</big><br>
-
For building our biological oscillator, the engineering cycle below was followed.<br> '''Click on each of the stages of the engineering cycle below in order to find out about the different stages & aspects of the project. '''</center></font>
+
For building our biological oscillator, the engineering cycle below was followed.<br>  
 +
'''Click on each of the stages of the engineering cycle below in order to find out about the different stages & aspects of the project. '''</center>
|-
|-
| style="background:#2171B8" width="200pt" rowspan="4" |  
| style="background:#2171B8" width="200pt" rowspan="4" |  
-
<font face="century gothic" font style="color: #FFFFFF"> '''1) Specifications: '''
+
<font face="arial" font style="color: #FFFFFF"> '''1) Specifications: '''
*Stable and robust oscillations
*Stable and robust oscillations
*Controllable frequency/amplitude
*Controllable frequency/amplitude
Line 34: Line 37:
*Mimics predator-prey dynamics based on the Lotka-Volterra model
*Mimics predator-prey dynamics based on the Lotka-Volterra model
'''3) Modelling: '''
'''3) Modelling: '''
-
*Full theoretical analysis
+
*Full theoretical analysis [http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/Theoretical_Analyses]
*Modelling of the full system
*Modelling of the full system
'''4) Implementation: '''
'''4) Implementation: '''
Line 45: Line 48:
| align="left"|[[Image:ArrowCurvedDown.PNG|120px]]
| align="left"|[[Image:ArrowCurvedDown.PNG|120px]]
|-
|-
-
| align="center"|[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]
+
| 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]
| align="center" rowspan="2"|[[Image:IGEM_IMPERIAL_DevCycle_FullSystem.png |206px|center]]
| 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/Modelling http://openwetware.org/images/5/5f/IGEM_IMPERIAL_DevCycle_Modelling.png]
| 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]
Line 52: Line 55:
| align="center"|[[Image:ArrowDown.png|20px]]
| align="center"|[[Image:ArrowDown.png|20px]]
|-
|-
-
| align="center"|[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]
+
| 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]
| align="center"|[[Image:ArrowLeft.png|150px]]
| align="center"|[[Image:ArrowLeft.png|150px]]
| 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]
| 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]
Line 60: Line 63:
{| border="0"  width="100%" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;"  width="100%"  
{| 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="century gothic" font style="color: #2171B8">PoPs Blocker</font>]  '''</big>!! width="50%"| <big>'''[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Bio_elec_interface <font face="century gothic" font style="color: #2171B8">Biological to Electrical Interface]</font>'''</big>
+
!  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%" |  
| style="background:#2171B8" width="50%" |  
-
<font face="century gothic" 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:
+
<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
*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
*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>
+
*Only then, the polymerase can pass through this part and transcribe downstream genes.  
-
| style="background:#2171B8" width="50%"|  
+
</font>
-
<font face="century gothic" 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.  
+
| 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
*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.</font>
+
*Measuring the change in pH gives a measurement of how much AHL is present.
 +
<br>
 +
<br>
 +
<br>
 +
<br>
 +
</font>
|}
|}
==Our Contributions to the Registry==
==Our Contributions to the Registry==
{|border="0" width="100%" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;"
{|border="0" width="100%" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;"
-
! style="background:#2171B8" | <font face="century gothic" font style="color: #FFFFFF">Part Logo !! style="background:#2171B8" |<font face="century gothic" font style="color: #FFFFFF">Description</font> !! style="background:#2171B8" |<font face="century gothic" font style="color: #FFFFFF">Link to registry</font> !! style="background:#2171B8" |<font face="century gothic" font style="color: #FFFFFF">Built</font> !! style="background:#2171B8" |<font face="century gothic" font style="color: #FFFFFF">Tested </font>!! style="background:#2171B8" |<font face="century gothic" font style="color: #FFFFFF">Characterized </font>!! style="background:#2171B8" |<font face="century gothic" font style="color: #FFFFFF">Sequenced</font> !! style="background:#2171B8" |<font face="century gothic" font style="color: #FFFFFF">Sent</font>
+
! 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="century gothic" 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="century gothic" font style="color: #FFFFFF">Final Constructs</font>
+
!style="background:#008080" |<font face="arial" font style="color: #FFFFFF">Final Constructs</font>
!style="background:#008080"|
!style="background:#008080"|
!style="background:#008080"|
!style="background:#008080"|
Line 90: Line 99:
! [[Image:J37027.png|120px]] !! Cre/Lox Prey Control !! <bbpart>J37027</bbpart> !! YES !! YES !! YES !! YES !!YES
! [[Image:J37027.png|120px]] !! Cre/Lox Prey Control !! <bbpart>J37027</bbpart> !! YES !! YES !! YES !! YES !!YES
|-
|-
-
!style="background:#008080" |<font face="century gothic" font style="color: #FFFFFF">Test Constructs</font>
+
!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"|
Line 103: Line 112:
! [[Image:J37020.png|170px]] !! Predator Cell, pLux Transfer Function (two promoters)  !! <bbpart>J37020</bbpart> !! YES !! YES !! NO !! NO !! 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="century gothic" font style="color: #FFFFFF">Intermediate Parts</font>
+
!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"|
Line 122: Line 131:
==Our Open Documentation==
==Our Open Documentation==
 +
 +
*Full Documentation, 100's of Photographs, Extensive Modelling, Lab Notebook and much more!
 +
__NOTOC__
__NOTOC__
{| class="wikitable" border="0" cellpadding="10" cellspacing="1" style="padding: 5px; background-color: #ffffff; border: 2px solid #2171B8;text-align:center"  
{| 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"|
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
-
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/LabCalendar <font face="century gothic" font style="color: #FFFFFF">Lab Notebook</font>]
+
*[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="century gothic" font style="color: #FFFFFF">Protocols</font>]
+
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Protocols <font face="arial" font style="color: #FFFFFF">Protocols</font>]
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
-
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Journal_Club<font face="century gothic" font style="color: #FFFFFF"> Journal Club</font>]<br\>
+
*[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="century gothic" font style="color: #FFFFFF">Lecture Notes</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"|
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
-
*[http://openwetware.org/wiki/BioSysBio:abstracts/2007/iGEM2006_Imperial_College <font face="century gothic" font style="color: #FFFFFF">BioSysBio Conference, UK</font>]
+
*[http://openwetware.org/wiki/BioSysBio:abstracts/2007/iGEM2006_Imperial_College <font face="arial" font style="color: #FFFFFF">BioSysBio Conference, UK</font>]
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
-
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Calendar/2006-7-26 <font face="century gothic" font style="color: #FFFFFF">UK iGEM Teams Meeting</font>]
+
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Calendar/2006-7-26 <font face="arial" font style="color: #FFFFFF">UK iGEM Teams Meeting</font>]
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
-
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Photos <font face="century gothic" font style="color: #FFFFFF">Photos</font>]
+
*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Photos <font face="arial" font style="color: #FFFFFF">Photos</font>]
|}
|}
-
 
==The Team and Acknowledgements==
==The Team and Acknowledgements==
Line 149: Line 160:
<center>
<center>
-
==<font face="century gothic" font style="color: #FFFFFF">Undergrads</font>==
+
==<font face="arial" font style="color: #FFFFFF">Undergrads</font>==
</center>
</center>
-
*[http://openwetware.org/wiki/User:Cys <font face="century gothic" font style="color: #FFFFFF">Christin Sander</font>]
+
*[http://openwetware.org/wiki/User:Cys <font face="arial" font style="color: #FFFFFF">Christin Sander</font>]
-
*[http://openwetware.org/wiki/User:da104 <font face="century gothic" font style="color: #FFFFFF">Deepti Aswani</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="century gothic" font style="color: #FFFFFF">Farah Vohra</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="century gothic" font style="color: #FFFFFF"> Jiongjun Bai</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="century gothic" font style="color: #FFFFFF">John Sy</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="century gothic" font style="color: #FFFFFF">John Chattaway</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="century gothic" font style="color: #FFFFFF"> Jonathan Wells</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="century gothic" font style="color: #FFFFFF">Tom Hinson</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"|
!width="25%" align="left" valign="top"  color:black"|
Line 167: Line 178:
<center>
<center>
-
==<font face="century gothic" font style="color: #FFFFFF">Advisors</font>==
+
==<font face="arial" font style="color: #FFFFFF">Advisors</font>==
</center>
</center>
-
*[http://www3.imperial.ac.uk/people/r.kitney <font face="century gothic" font style="color: #FFFFFF">Prof. Richard Kitney</font>]
+
*[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="century gothic" font style="color: #FFFFFF">Prof. Paul Freemont</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="century gothic" font style="color: #FFFFFF">Dr. David Mann</font>]
+
*[http://www3.imperial.ac.uk/people/d.mann <font face="arial" font style="color: #FFFFFF">Dr. David Mann</font>]
-
*<font face="century gothic" font style="color: #FFFFFF">Kirsten Jensen</font>
+
*<font face="arial" font style="color: #FFFFFF">Kirsten Jensen</font>
-
*[http://openwetware.org/wiki/User:Vincent <font face="century gothic" font style="color: #FFFFFF">Vincent Rouilly</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="century gothic" font style="color: #FFFFFF">Chueh-Loo Poh</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="century gothic" font style="color: #FFFFFF">Matthieu Bultelle</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"|
!width="20%" align="left" valign="top" style="background:#2171B8; color:white"|
<center>
<center>
-
==<font face="century gothic" font style="color: #FFFFFF">Funding</font>==
+
 
 +
==<font face="arial" font style="color: #FFFFFF">Funding</font>==
</center>
</center>
*European Commission
*European Commission

Latest revision as of 12:57, 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 [http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/Theoretical_Analyses]
  • 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 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]
ArrowUp.png ArrowDown.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] 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

Retrieved from "http://2006.igem.org/wiki/index.php/Imperial_College_2006/Sandbox"
Personal tools
Past/present/future years