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Revision as of 08:54, 4 August 2005

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Intro

The Oscillation Counter is a genetic circuit module that activates the production of a gene every other peak. The ultimate goal is to combine such modules to count to an arbitrary number. Therefore, this project is cool, and every effort should be put to bring it to reality.

Principle

The first part of the module discretize the oscillation into two states -- on and off, and can be seen as a reversible switch. This part can be seen as the elementary counter. The second part is the divider and should be ultimately developed into a cascade of such units. But let's not get carried away. We shall first focus on the implementation of a single divider, a large enough endeavor if you ask me.

Design

The Discretizer

This part takes as input the concentration of the oscillating object and leads to the all-or-none response S. That could be done through strong cooperativity?

                   _   _   _
/\/\/\/\/\/\  -> _| |_| |_|
                 
         States: 0 1 2 3 0 1
       (see below)

The Divider

The divider should have response during -- and only during! -- state 1. A design idea here is to use four genes that keep track of all four states.

                           ,- - - - - - - - - - - - - - - - 
                          v                 , - - - - -     \ 
  gene0    --<xSx>-AND-<ig3i>---==============--       |  
                           ,- - - - - - - - - - - - - -      |
                          v                 , - - - - -    
  gene1    --<iSi>-AND-<ig0i>---==============--       |     |
                           ,- - - - - - - - - - - - - -   
                          v                 , - - - - -      |
  gene2    --<xSx>-AND-<ig1i>---==============--       |  
                           ,- - - - - - - - - - - - - -      |
                          v                                 ,
  gene3    --<iSi>-AND-<ig2i>---==============--      - - - - -> Reporter gene (e.g. GFP)
 
  
  legend:
    ===   : gene
    ---   : DNA
    - -   : Regulatory pathway
    <iGi> : promoter region induced by G
    <xGx> : promoter region repressed by G
    

All genes 0 to 3 need to induce strong responses while being quite instable themselves to insure rapid degradation time.

Challenges

• bootstrapping?
• how does noise accumulate and propagate?
• what about delays and timescale?
• do we have a reliable oscillator at all to start with?

References

Discussion

>> for comments, questions and temporary remarks go to the Talk:Oscillation_Counter

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