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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!

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.
 * 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:

Feedback Loop promoters
Here are a list of articles that outline promoters (not in ecoli) that are both activated and repressed. Cheers, Simon

Title: Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein. Author: Smits, Wiep Klaas

Title: The transcriptional regulators NorG and MgrA resistance to both quinolones and beta-lactams in Staphylococcus aureas. Author: Troung-Bolduc, Que Chi

Title: Antagonistic interplay of Swi1 and Tup1 on filamentous growth of Candida albicans. Author: Mao, Xuming

Title: The tyrosine degradation gene hppD is transcriptionally activated by HpdA and repressed by HpdR in Streptomyces coelicolor, while hpdA is negatively autoregulated and repressed by HpdR. Author: Yang,Haihua

Title: Different proteins bind to the butyrolactone receptor protein ARE sequence located upstream of the regulatory ccaR gene of Streptomyces clavuligerus. Author: Santamarta,Irene

Title: Positive control of tylosin biosynthesis: pivotal role of TylR. Author: Stratigopoulos,George

Title: Identification of DNA-binding proteins involved in regulation of expression of the Streptomyces aureofaciens whiH gene encoding a sporulation transcription factor. Author: Homerova,D

Title: Identification of DNA-binding proteins involved in regulation of expression of the Streptomyces aureofaciens sigF gene, which encodes sporulation sigma factor sigma(F). Author: Homerova,D