IGEM:Melbourne/2008/BioClock/Feedback loops: Difference between revisions

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[[IGEM:Melbourne/2008|Return to Melbourne Homepage]]
[[IGEM:Melbourne/2008|Return to Melbourne Homepage]]
==Screened Registry==
1*. [http://parts.mit.edu/registry/index.php/Part:BBa_I13211 LuxI -> HSL -> LuxR -> R0062 -> LuxI]
2. [http://parts.mit.edu/registry/index.php/Part:BBa_J64713 3OC12 + LasR -> more 3OC12 HSL]
3. [http://parts.mit.edu/registry/index.php/Part:BBa_J64714 C4 HSL + RHLR -> more C4 HSL]
4. [http://parts.mit.edu/registry/index.php?title=Part:BBa_R0062 LuxPr + OHHL -> LuxR -> LuxR upregulates LuxPr]
5. [http://parts.mit.edu/registry/index.php/Part:BBa_J13030 Amplifier, Don't quite know how it works yet]
6. [http://parts.mit.edu/registry/index.php/Part:BBa_J37015 tetR constituitively -> LuxR -> (LuxR-AHL-LuxPr) -> LuxI -> AHL -> (LuxR-AHL-LuxPr)] Note: AHL is also an inter-cellular signaling molecule
==Paper==
[http://www.openwetware.org/images/c/ce/OnnBrandman.pdf Interlinked Fast and Slow Positive Feedback Loops Drive Reliable Cell Decisions] <font color = "red"><-- A very nice paper, has many examples of +ve feedback loops, and testing for fast and slow loops' qualities.</font>
[http://www.openwetware.org/images/7/7d/Drubin_2007.pdf Tetra-cycline responsive positive feedback] <-- A Nice loop
[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRW-45B5X0J-4&_user=559483&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000028178&_version=1&_urlVersion=0&_userid=559483&md5=96a95a151f8be5f9f58acbf221401536 Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability]
==Simon's proposal==
Hi guys, I thought of an idea for a feedback loop that should effectively work in bacteria without the concern of its sloppy repression inadvertantly turning it on.
Here it is:
[[Image:on_off_loop.gif]]
Basically, It is composed of two feedback loops. The purpose of having two loops is because each represents a state i.e. on or off. It is necessary to have these states because one state needs to repress the other state because of bacteria's inherent sloppiness.
For example. If we only had one loop for 'on' then it could easily turn on by itself. However, in this system, the off loop is constantly repressing the on loop therefore it doesnt turn on by itself. Also vica vera, the on loop represses the off loop.
As you can see from the diagram, the way to change the state is to express the activator for the next state with the repressor of the current state.
I hope you guys like it!
*I thought that's what we had in our binary model version 2 diagram. That's what the Tr0' and Off loops are doing to each other in the diagrams:
http://www.openwetware.org/images/0/00/BinaryClockV2.ppt
The On signal is equal to On0, the blue On loop is the Tr0 loop, the red Off loop is the same as the Off loop in the slides, the Off signal is equivalent to the signal sent out by the Off loop, which is co-activated by B1 and On1.

Latest revision as of 20:08, 16 March 2008

Return to Melbourne Homepage

Screened Registry

1*. LuxI -> HSL -> LuxR -> R0062 -> LuxI

2. 3OC12 + LasR -> more 3OC12 HSL

3. C4 HSL + RHLR -> more C4 HSL

4. LuxPr + OHHL -> LuxR -> LuxR upregulates LuxPr

5. Amplifier, Don't quite know how it works yet

6. tetR constituitively -> LuxR -> (LuxR-AHL-LuxPr) -> LuxI -> AHL -> (LuxR-AHL-LuxPr) Note: AHL is also an inter-cellular signaling molecule

Paper

Interlinked Fast and Slow Positive Feedback Loops Drive Reliable Cell Decisions <-- A very nice paper, has many examples of +ve feedback loops, and testing for fast and slow loops' qualities.

Tetra-cycline responsive positive feedback <-- A Nice loop

Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability


Simon's proposal

Hi guys, I thought of an idea for a feedback loop that should effectively work in bacteria without the concern of its sloppy repression inadvertantly turning it on.

Here it is:

Basically, It is composed of two feedback loops. The purpose of having two loops is because each represents a state i.e. on or off. It is necessary to have these states because one state needs to repress the other state because of bacteria's inherent sloppiness.

For example. If we only had one loop for 'on' then it could easily turn on by itself. However, in this system, the off loop is constantly repressing the on loop therefore it doesnt turn on by itself. Also vica vera, the on loop represses the off loop.

As you can see from the diagram, the way to change the state is to express the activator for the next state with the repressor of the current state.

I hope you guys like it!

  • I thought that's what we had in our binary model version 2 diagram. That's what the Tr0' and Off loops are doing to each other in the diagrams:

http://www.openwetware.org/images/0/00/BinaryClockV2.ppt The On signal is equal to On0, the blue On loop is the Tr0 loop, the red Off loop is the same as the Off loop in the slides, the Off signal is equivalent to the signal sent out by the Off loop, which is co-activated by B1 and On1.