Oscillation Counter

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Back to [[ETH Zurich]] main page.
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  '''This page is not updated any more; for current state, please have a look at [[Oscillator_based]]'''
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=Intro=
=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.
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=
=Principle=
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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 developped 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.
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The first part of the module discretizes the analogue oscillation of concentrations of a substance A into two states - ON and OFF - and can be seen as an alternating toggle switch or as the clock of the system.
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=Design=
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Based on this basic clock, a counter module based on a cascade reaction or even layers of such modules could be added.
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==The Discretizer==
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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?
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=Implementation=
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==The Clock Design==
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This part takes as input the concentration of the oscillating substance and leads to the all-or-none response '''S'''.
                     _  _  _
                     _  _  _
  /\/\/\/\/\/\  -> _| |_| |_|
  /\/\/\/\/\/\  -> _| |_| |_|
                    
                    
-
           States: 0 1 2 3 0 1
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           States: 0 1 0 1 0 1
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        (see below)
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          (0 = OFF, 1 = ON)
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==The Divider==
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Could this be done through strong cooperativity?
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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.
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gene0    --<x'''S'''x>---<i'''g3'''i>---==============--
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==The Counter/Display Design==
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gene1    --<i'''S'''i>---<i'''g0'''i>---==============--
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One could assign the system four different states as opposed to only two:
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gene2    --<x'''S'''x>---<i'''g1'''i>---==============--
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gene3    --<i'''S'''i>---<i'''g2'''i>---==============--
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                    _  _  _
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/\/\/\/\/\/\  -> _| |_| |_|
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          States: 0 1 2 3 0 1
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The counter would keep track of the succession of those four states, i.e. count alternations of S up to four. It would response during - and only during! - state 0 and finally flash at state 3:
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                            ,- - - - - - - - - - - - - - - -
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                          v                , - - - - -    \
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  gene0    --<xSx>-AND-<ig3i>---==============--      | 
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                            ,- - - - - - - - - - - - - -      |
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                          v                , - - - - -   
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  gene1    --<iSi>-AND-<ig0i>---==============--      |    |
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                            ,- - - - - - - - - - - - - - 
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                          v                , - - - - -      |
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  gene2    --<xSx>-AND-<ig1i>---==============--      | 
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                            ,- - - - - - - - - - - - - -      |
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                          v                , - - - - - - - - - - -> Reporter gene (e.g. GFP)
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  gene3    --<iSi>-AND-<ig2i>---==============-- 
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   legend:
   legend:
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     === : gene
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     ===   : gene
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     <i'''G'''i> : promoter region induced by G
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    ---  : DNA
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     <x'''G'''x> : promoter region repressed by G
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    - -  : Regulatory pathway
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     <iGi> : promoter region induced by G
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     <xGx> : promoter region repressed by G
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All genes 0 to 3 need to induce strong responses while being quite instable themselves to insure rapid degradation time.
=Challenges=
=Challenges=
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* bootstrapping?
* how does noise accumulate and propagate?
* how does noise accumulate and propagate?
* what about delays and timescale?
* what about delays and timescale?
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=References=
=References=
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=Comments=
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=Discussion=
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Please add any comments and critics here or directly in the corpus above.
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>> for comments, questions and temporary remarks go to the [[Talk:Oscillation_Counter]]
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Back to [[ETH Zurich]] main page.

Latest revision as of 15:46, 9 August 2005

Back to ETH Zurich main page. 


 This page is not updated any more; for current state, please have a look at Oscillator_based


Contents

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 discretizes the analogue oscillation of concentrations of a substance A into two states - ON and OFF - and can be seen as an alternating toggle switch or as the clock of the system.

Based on this basic clock, a counter module based on a cascade reaction or even layers of such modules could be added.

Implementation

The Clock Design

This part takes as input the concentration of the oscillating substance and leads to the all-or-none response S. 

                   _   _   _
/\/\/\/\/\/\  -> _| |_| |_|
                 
         States: 0 1 0 1 0 1
         (0 = OFF, 1 = ON)


Could this be done through strong cooperativity?

The Counter/Display Design

One could assign the system four different states as opposed to only two: 

                   _   _   _
/\/\/\/\/\/\  -> _| |_| |_|
                 
         States: 0 1 2 3 0 1


The counter would keep track of the succession of those four states, i.e. count alternations of S up to four. It would response during - and only during! - state 0 and finally flash at state 3: 

                           ,- - - - - - - - - - - - - - - - 
                          v                 , - - - - -     \ 
  gene0    --<xSx>-AND-<ig3i>---==============--       |  
                           ,- - - - - - - - - - - - - -      |
                          v                 , - - - - -    
  gene1    --<iSi>-AND-<ig0i>---==============--       |     |
                           ,- - - - - - - - - - - - - -   
                          v                 , - - - - -      |
  gene2    --<xSx>-AND-<ig1i>---==============--       |  
                           ,- - - - - - - - - - - - - -      |
                          v                 , - - - - - - - - - - -> Reporter gene (e.g. GFP)
  gene3    --<iSi>-AND-<ig2i>---==============--  
 
  
  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

Back to ETH Zurich main page.

Retrieved from "http://2006.igem.org/wiki/index.php/Oscillation_Counter"
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