Team:Evry/auxin detection

From 2012.igem.org

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<h2> Hypotheses </h2>
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<h2> Assumptions </h2>
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<p>The same promoter is used for the creation of GFP and TIR, so the efficiency  Gamma for the creation of GFP and TIR1 will be identical.
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<p>
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In these reactions, we assimilate the complex Auxin-TIR to an enzyme that is able to degrade the GFP. Auxin would then be its activator.
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<br>
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The degradation rate of GFP is negligible; indeed a molecule of GFP takes 72 hours to degrade normally, whereas during auxin detection the complex auxin-TIR degrades it in less than an hour.
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<h2> Descritpion of the model </h2>
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<h2> Model Description </h2>
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Chemical equations corresponding to:
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Chemical equations:
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<ul>
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<li> Creation of auxin-TIR1 complex : <center><img src="https://static.igem.org/mediawiki/2012/8/81/Reaction1_degradation.png" width="200px"></center>
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</li>
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<li> Degradation of GFP by this complex: <center><img src="https://static.igem.org/mediawiki/2012/c/c1/Reaction2_degradation.png" width="200px"></center>
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<br>
<br>
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After adding to these equations creation rates of TIR1 and GFP and desintegration rates of each actor whe obtain the system of equations:<center><img src="https://static.igem.org/mediawiki/2012/8/83/System_equations_degrad.png" width="500px" ></center>
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After adding to these equations the creation rate of GFP and desintegration rate of auxin whe obtain the system of equations:<center><img src="https://static.igem.org/mediawiki/2012/2/25/Eqs.png" width="200px"></center>
Where:
Where:
<ul>
<ul>
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   <li> A stands for auxin</li>
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   <li> [A] stands for auxin concentration</li>
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   <li> T stands for TIR1</li>  
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   <li> [T] stands for TIR concentration</li>  
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   <li> AT stands for the complex auxin-TIR1</li>
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   <li> [AT] stands for the complex auxin-TIR concentration</li>
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   <li> G stands for GFP</li>
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   <li> [G] stands for GFP concentration</li>
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  <li>P<sub>X</sub> is the quantity of X in the cell</li>
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   <li>&#404; is the strength of the promoter used to create GFP</li>
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   <li>&#404;<sub>X</sub> is the "efficiency" of the promoter used to create X</li>
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   <li>f<sub>e<sub>aux</sub></sub>(t) is the quantity of auxin that enters in the cell at time t</li>
   <li>f<sub>e<sub>aux</sub></sub>(t) is the quantity of auxin that enters in the cell at time t</li>
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   <li>K<sub>1</sub> is the reaction constant of the creation of the auxin-TIR1 complex</li>
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   <li>K<sub>A</sub> is the reaction constant of the creation of the auxin-TIR1 complex</li>
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   <li>K<sub>2</sub> is the reaction constant of the degradation o f GFP</li>   
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   <li>K<sub>G</sub> is the reaction constant of the degradation o f GFP</li>   
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   <li>d<sub>X</sub> is the degradation rate of X</li>
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   <li>&delta; is the degradation rate of auxin</li>
</ul>
</ul>
<h2> Model's calibration </h2>
<h2> Model's calibration </h2>

Revision as of 00:03, 27 September 2012

Auxin detection

Overview

Now that we’ve managed to model auxin creation and transport, you may be asking yourself ; great, those guys have done all those models, but how can we link it to what we see ? That’s the aim of this model that will link the quantity of auxin transported into the cell to GFP degradation that we can observe in our tadpole’s cells. As for us, this model will also help our biologists to find the conditions upon which the reception can work and the help them guess the reasons of possible dysfunction in the auxin reception. This is what's happening during auxin detection:




Thus, once TIR 1 ang GFP are produced and auxin has entered the cell, it binds with TIR1 and then this complex degrades GFP. This is what we're going to model.

Assumptions

In these reactions, we assimilate the complex Auxin-TIR to an enzyme that is able to degrade the GFP. Auxin would then be its activator.
The degradation rate of GFP is negligible; indeed a molecule of GFP takes 72 hours to degrade normally, whereas during auxin detection the complex auxin-TIR degrades it in less than an hour.

Model Description

Chemical equations:
After adding to these equations the creation rate of GFP and desintegration rate of auxin whe obtain the system of equations:
Where:
  • [A] stands for auxin concentration
  • [T] stands for TIR concentration
  • [AT] stands for the complex auxin-TIR concentration
  • [G] stands for GFP concentration
  • Ɣ is the strength of the promoter used to create GFP
  • feaux(t) is the quantity of auxin that enters in the cell at time t
  • KA is the reaction constant of the creation of the auxin-TIR1 complex
  • KG is the reaction constant of the degradation o f GFP
  • δ is the degradation rate of auxin

Model's calibration

Results

Criticisms

Confrontation with experiences

Conclusion

References