Imperial College 2006
From 2006.igem.org
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__NOTOC__ | __NOTOC__ | ||
- | <center> | + | <center>[[Image:Banner.png|800px]]</center> |
- | <center>< | + | |
+ | |||
+ | <center><font size="4">'''[http://openwetware.org/wiki/IGEM:IMPERIAL/2006 Full Documentation of the project on OpenWetWare]'''</font></center> | ||
+ | <center><font size="3">'''[[Media:IGEM_Imperial_2006_presentation.pdf |Presentation ]]'''</font></center> | ||
+ | <center><font size="3">'''[[Media:IGEM_Imperial_2006_Poster.pdf |Poster]]'''</font></center> | ||
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|- | |- | ||
|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="arial" font style="color: #FFFFFF" > <center><big><u>'''Project Summary'''</u></big></center> | + | |width="40%" style="background:#2171B8"| <font face="arial" font style="color: #FFFFFF" > |
- | + | <center><big><u>'''Project Summary'''</u></big></center> | |
- | |width="40%" style="background:#2171B8" | <font face="arial" font style="color: #FFFFFF" > <center><big><u>'''Achievements'''</u></big></center> <br> | + | |
- | + | ||
+ | *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> | <br> | ||
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{| 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="arial" font style="color: | + | | style="background:#2171B8" colspan="3"| <font face="arial" font style="color: yellow"> <center><big>'''Engineering a Molecular Predation Oscillator'''</big><br> |
- | For building our biological oscillator, the engineering cycle below was followed.<br> | + | <font face="arial" font style="color: #ffffff">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 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" | | | style="background:#2171B8" width="200pt" rowspan="4" | | ||
- | <font face="arial" font style="color: | + | [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 | *Stable and robust oscillations | ||
*Controllable frequency/amplitude | *Controllable frequency/amplitude | ||
- | *Generic and modular | + | *Generic and modular</font> |
- | '''2) Design: ''' | + | [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 | *Mimics predator-prey dynamics based on the Lotka-Volterra model | ||
- | '''3) Modelling: ''' | + | </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 | *Modelling of the full system | ||
- | '''4) Implementation: ''' | + | </font> |
- | *All parts designed | + | [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 | *4 functional & 5 intermediate submitted to the Registry | ||
- | '''5) Testing/Validation: ''' | + | </font> |
- | *Successful characterization of sub-components.</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="right"|[[Image:ArrowCurvedRight.png|110px]] | ||
- | | align="center" |[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System | + | | 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="left"|[[Image:ArrowCurvedDown.PNG|120px]] | ||
|- | |- | ||
- | | align="center"|[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System http://openwetware.org/images/ | + | | 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" 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/ | + | | 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:ArrowUp.png|20px]] | ||
| 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/ | + | | 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"|[[Image:ArrowLeft.png|150px]] | ||
- | | align="center"|[http://www.openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/ | + | | 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> |
|} | |} | ||
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==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="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=" | + | ! 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: #FFFFFF">Final Constructs</font> | ||
- | !style="background:#008080"| | + | !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"| | ||
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|- | |- | ||
- | ![[Image:J37015.PNG|250px]]!! Final Prey Cell !! <bbpart>J37015</bbpart> !! YES !! YES !! Pending !! YES !! YES | + | ![[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 !! <bbpart>J37027</bbpart> !! YES !! YES !! YES !! 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 |
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!style="background:#008080" |<font face="arial" font style="color: #FFFFFF">Test Constructs</font> | !style="background:#008080" |<font face="arial" font style="color: #FFFFFF">Test Constructs</font> | ||
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!style="background:#008080"| | !style="background:#008080"| | ||
|- | |- | ||
- | ![[Image:J37016.PNG|150px]]!! Final Polycistronic Predator Cell Test Construct !! <bbpart>J37016</bbpart> !! YES !! YES !! YES !! YES!! YES | + | ![[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 | ! [[Image:J37020.png|170px]] !! Predator Cell, pLux Transfer Function (two promoters) !! <bbpart>J37020</bbpart> !! YES !! YES !! NO !! NO !! YES | ||
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==Our Open Documentation== | ==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__ | __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"| | ||
+ | |||
+ | *[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"| | !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/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/Protocols <font face="arial" font style="color: #FFFFFF">Protocols</font>] | ||
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*[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/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\> | *[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Lecture_Notes <font face="arial" font style="color: #FFFFFF">Lecture Notes</font>]<br\> | ||
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!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="arial" 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>] | ||
- | + | *[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"| | !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/Calendar/2006-7-26 <font face="arial" font style="color: #FFFFFF">UK iGEM Teams Meeting</font>] | ||
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*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Photos <font face="arial" font style="color: #FFFFFF">Photos</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>] | ||
|} | |} | ||
Latest revision as of 16:42, 10 November 2006
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Main Project
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] |
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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:
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We also worked on a Biosensor for measuring AHL concentrations in order to establish a Biological to Electrical Interface this summer.
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Our Contributions to the Registry
Part Logo | Description | Link to registry | Built | Tested | Characterized | Sequenced | Sent |
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Final Constructs | (!) Favorite Part | ||||||
Final Prey Cell (!) | J37015 | YES | YES | Pending | YES | YES | |
Cre/Lox Prey Control (!) | J37027 | YES | YES | YES | YES | YES | |
Test Constructs | |||||||
Final Polycistronic Predator Cell Test Construct (!) | J37016 | YES | YES | YES | YES | YES | |
Predator Cell, pLux Transfer Function (two promoters) | J37020 | YES | YES | NO | NO | YES | |
Intermediate Parts | |||||||
AHL induced LuxR generator (for predator cell) | J37019 | YES | N/A | N/A | YES | YES | |
RBS + LuxR | J37033 | YES | N/A | N/A | YES | YES | |
Prey Cell Intermediate | J37034 | YES | N/A | N/A | YES | YES | |
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!
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The Team and Acknowledgements
Undergrads
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Advisors
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Funding
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