Imperial College 2006

From 2006.igem.org

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Latest revision as of 16:42, 10 November 2006

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

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

	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.		[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
	[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		[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

	[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		[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
	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!

[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

@@ Line 2: / Line 2: @@
 __NOTOC__
-<center>{{Click||image=Banner.png|link=IGEM:IMPERIAL/2006|width=800px|height=100px}}</center>
+<center>[[Image:Banner.png|800px]]</center>
-<center><big>'''[http://openwetware.org/wiki/IGEM:IMPERIAL/2006 Full Documentation of the project on OWW]'''</big></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>
@@ Line 10: / Line 14: @@
 |-
 |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> <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>
+|width="40%" style="background:#2171B8"| <font face="arial" font style="color: #FFFFFF" >
-'''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>
+<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>
-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.
+*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>
@@ Line 25: / Line 40: @@
 {| 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: #FFFFFF"> <center><big>'''Engineering a Molecular Predation Oscillator'''</big><br>
+| 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" |
-[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System <font face="arial" font style="color: #FFFFFF"> '''1) Specifications: '''</font>]
+[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
+*Generic and modular</font>
-[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Design <font face="arial" font style="color: #FFFFFF">'''2) Design: '''</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
-[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Modelling <font face="arial" font style="color: #FFFFFF">'''3) Modelling: '''</font>]
+</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
-[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Implementation <font face="arial" font style="color: #FFFFFF"> '''4) Implementation: '''</font>]
+</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
-[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Full_System/Validation <font face="arial" font style="color: #FFFFFF">'''5) Testing/ Validation: '''</font>]
+</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="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]
+| 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 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/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/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/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/TestingValidation 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/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/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/Modelling http://openwetware.org/images/5/5f/IGEM_IMPERIAL_DevCycle_Modelling.png]<font style="color:red"><br>Click on picture for more info</font>
 |}
@@ Line 87: / Line 111: @@
 |-
 !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"|
@@ Line 95: / Line 119: @@
 !style="background:#008080"|
 |-
-![[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
 |-
 !style="background:#008080" |<font face="arial" font style="color: #FFFFFF">Test Constructs</font>
@@ Line 108: / Line 132: @@
 !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
@@ Line 132: / Line 156: @@
 ==Our Open Documentation==
-*Full Documentation, 100's of Photographs, Extensive Modelling, Lab Notebook and much more!
+*'''<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>]
-!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
 *[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\>
@@ Line 145: / Line 175: @@
 !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>]
-!width="20%" align="left" valign="top" style="background:#2171B8; color:black"|
 *[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>]
 |}

Imperial College 2006

From 2006.igem.org

Latest revision as of 16:42, 10 November 2006

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