Oscillation Counter
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Back to [[ETH Zurich]] main page. | 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= | ||
| Line 5: | Line 9: | ||
=Principle= | =Principle= | ||
| - | The first part of the module | + | 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== | |
| - | ==The | + | One could assign the system four different states as opposed to only two: |
| - | + | ||
_ _ _ | _ _ _ | ||
| Line 15: | Line 33: | ||
States: 0 1 2 3 0 1 | 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>---==============-- | | |
| - | gene3 --<iSi>- | + | ,- - - - - - - - - - - - - - | |
| + | v , - - - - - | ||
| + | gene1 --<iSi>-AND-<ig0i>---==============-- | | | ||
| + | ,- - - - - - - - - - - - - - | ||
| + | v , - - - - - | | ||
| + | gene2 --<xSx>-AND-<ig1i>---==============-- | | ||
| + | ,- - - - - - - - - - - - - - | | ||
| + | v , - - - - - - - - - - -> Reporter gene (e.g. GFP) | ||
| + | gene3 --<iSi>-AND-<ig2i>---==============-- | ||
| + | |||
legend: | legend: | ||
| - | === : gene | + | === : gene |
| + | --- : DNA | ||
| + | - - : Regulatory pathway | ||
<iGi> : promoter region induced by G | <iGi> : promoter region induced by G | ||
<xGx> : promoter region repressed 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= | =Challenges= | ||
| + | * bootstrapping? | ||
* how does noise accumulate and propagate? | * how does noise accumulate and propagate? | ||
* what about delays and timescale? | * what about delays and timescale? | ||
| Line 38: | Line 68: | ||
=References= | =References= | ||
| - | = | + | =Discussion= |
| - | + | >> for comments, questions and temporary remarks go to the [[Talk:Oscillation_Counter]] | |
Back to [[ETH Zurich]] main page. | 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.
