IGEM:IMPERIAL/2006/project/Oscillator/project browser/Prey Construct/Design: Difference between revisions
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!height="25pt" width="80pt"| Super Parts | !height="25pt" width="80pt"| Super Parts | ||
!colspan=" | !colspan="3" | [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Full_System | Molecular Prey-Predator Oscillator]] | ||
|- | |- | ||
!height="25pt" width="80pt"|Actual Part | !height="25pt" width="80pt"|Actual Part | ||
!colspan=" | !colspan="3"| [[Image:J37015page.JPG]] | ||
|- | |- | ||
!height="25pt" width="80pt"|Sub Parts | !height="25pt" width="80pt"|Sub Parts | ||
! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Test_Sensing_Prey_Construct| Test Sensing Prey Construct]] | ! [[IGEM:IMPERIAL/2006/project/Oscillator/project browser/Test_Sensing_Prey_Construct| Test Sensing Prey Construct]] | ||
! | ! <bbpart>C0261</bbpart> | ||
! <bbpart>I13401</bbpart> | |||
|} | |} | ||
<div class="tabs-blue"> | <div class="tabs-blue"> | ||
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<br style="clear:both"> | <br style="clear:both"> | ||
*Design | ==Registry== | ||
* | |||
*Design | *The prey part: [http://parts.mit.edu/registry/index.php/Part:BBa_J37015 J37015 @ MIT Parts Registry] | ||
[[Image:J37015page.JPG]] | |||
==Design Choices== | |||
*Design must fulfil the [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/Oscillator/project_browser/Prey_Construct specifications for the prey construct]. | |||
*Part design will be based on Quorum-sensing/quenching and the availability of BioBricks. | |||
::*Research into the registry directed us to use AHL as our prey molecule. | |||
*Design allows for an exponential increase of AHL (to fulfil the [[IGEM:IMPERIAL/2006/project/Oscillator/Theoretical_Analyses/2D_Model1|Lotka-Volterra model]]) via a positive feedback loop. | |||
*The prey part can be decoupled into a prey sensing part and a prey producing part. | |||
*Initiation of positive feedback loop depends on leaky expression of the tetR promoter which is a constitutive promoter. | |||
** This leaky expression produces LuxR which can form a dimer with AHL already withing the cell. | |||
** LuxR, AHL and promoter control the expression of LuxI which produces AHL. | |||
*Design allows for assesment of status of positive feedback loop via: | |||
**GFP Production - Linked to LuxI expression | |||
**AHL Production - Can be indirectly assessed according to [http://openwetware.org/wiki/IGEM:IMPERIAL/2006/Protocols/J37015 J37015 protocol]. | |||
{| border="1" width="100%" | |||
|- style="background:lightgreen" | |||
! INPUTS !! biological component !! comments | |||
|- | |||
|AHL||LuxR & pLuxR|| To initiate the positive feedback loop, LuxR is produced via leaky expression of the tetR promoter. | |||
|- style="background:orange" | |||
! OUTPUTS !! biological component !! comments | |||
|- | |||
|AHL||LuxI||LuxR, AHL and pLuxR form a complex, activating production of LuxI expression which causes enzymatic generation of AHL | |||
|} | |||
==Open Issues== | |||
*We need to consider methods of controlling the positive feedback loop while cells are growing to ensure AHL concentration stays at zero. Possible suggestions are: | |||
::*Periodic dilution of culture to allow degradation of LuxI | |||
::*Riboswitch | |||
::*[http://openwetware.org/wiki/IGEM:IMPERIAL/2006/project/popsblocker Pops blocker] | |||
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Latest revision as of 09:40, 30 October 2006
Super Parts | Molecular Prey-Predator Oscillator | ||
---|---|---|---|
Actual Part | |||
Sub Parts | Test Sensing Prey Construct | <bbpart>C0261</bbpart> | <bbpart>I13401</bbpart> |
Registry
- The prey part: J37015 @ MIT Parts Registry
Design Choices
- Design must fulfil the specifications for the prey construct.
- Part design will be based on Quorum-sensing/quenching and the availability of BioBricks.
- Research into the registry directed us to use AHL as our prey molecule.
- Design allows for an exponential increase of AHL (to fulfil the Lotka-Volterra model) via a positive feedback loop.
- The prey part can be decoupled into a prey sensing part and a prey producing part.
- Initiation of positive feedback loop depends on leaky expression of the tetR promoter which is a constitutive promoter.
- This leaky expression produces LuxR which can form a dimer with AHL already withing the cell.
- LuxR, AHL and promoter control the expression of LuxI which produces AHL.
- Design allows for assesment of status of positive feedback loop via:
- GFP Production - Linked to LuxI expression
- AHL Production - Can be indirectly assessed according to J37015 protocol.
INPUTS | biological component | comments |
---|---|---|
AHL | LuxR & pLuxR | To initiate the positive feedback loop, LuxR is produced via leaky expression of the tetR promoter. |
OUTPUTS | biological component | comments |
AHL | LuxI | LuxR, AHL and pLuxR form a complex, activating production of LuxI expression which causes enzymatic generation of AHL |
Open Issues
- We need to consider methods of controlling the positive feedback loop while cells are growing to ensure AHL concentration stays at zero. Possible suggestions are:
- Periodic dilution of culture to allow degradation of LuxI
- Riboswitch
- Pops blocker
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