Team:Evry/Model3

From 2013.igem.org

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<img src="https://static.igem.org/mediawiki/2013/6/6d/Regfefur.png"/>
<img src="https://static.igem.org/mediawiki/2013/6/6d/Regfefur.png"/>
</p>
</p>
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<u>Parameters:</u><br/>
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<table width="100%" border="1">
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<tr width="100%">
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<th>Name</th>
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<th>Value</th>
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<th>Unite</th>
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<th>Description</th>
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<th>Reference</th>
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</tr>
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<tr width="100%">
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<td>p</td>
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<td>0.1</td>
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<td>min^-1</td>
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<td>Permeability of cell wall</td>
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<td>-</td>
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</tr>
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<tr width="100%">
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<td>KfeFUR</td>
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<td>0.01</td>
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<td>M^-1.s^-1</td>
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<td>Formation constant of FeFur complex</td>
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<td>-</td>
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</tr>
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<tr width="100%">
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<td>Dff</td>
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<td>0.001</td>
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<td>min^-1</td>
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<td>-</td>
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<td>-</td>
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</tr>
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<tr width="100%">
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<td>Kp</td>
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<td>0.5</td>
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<td>min^-1</td>
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<td>translation rate</td>
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<td>-</td>
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</tr>
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<tr width="100%">
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<td>milliNa</td>
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<td>6.02.10^20</td>
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<td>mol^-1</td>
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<td>Avogadro's constant</td>
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<td>[1]</td>
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</tr>
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<tr width="100%">
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<td>V</td>
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<td>6.5.10^-16</td>
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<td>m^3</td>
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<td>Volume of a call</td>
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<td>-</td>
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</tr>
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<tr width="100%">
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<td>p</td>
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<td>0.005</td>
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<td>Value at zero of the activator</td>
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<td>-</td>
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</tr>
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<tr width="100%">
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<td>Dmrna</td>
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<td>0.001</td>
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<td>min^-1</td>
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<td>mRNA degradation rate</td>
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<td>-</td>
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</tr>
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<tr width="100%">
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<td>Denz</td>
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<td>0.001</td>
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<td>min^-1</td>
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<td>Enzyme degradation rate</td>
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<td>-</td>
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</tr>
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<tr width="100%">
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<td>d</td>
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<td>10^-9</td>
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<td>Activator threshold</td>
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<td>[2]</td>
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</tr>
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</table>
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<h2>Results</h2>
<h2>Results</h2>

Revision as of 00:37, 5 October 2013

Iron coli project

Metabolic model

Overview

Enzymes regulation:
This regulation is based on two consecutives inhibitions, which, in the end, is an activator with a certain delay. The model will follow this principle.

Assumptions

Model Description

Variables:

  • [Fe] : Iron concentration inside the bacteria
  • [Fur] : FUR concentration inside the bacteria
  • [FeFur] : Iron-FUR complex concentration inside the bacteria
  • LacI : Number of inhibited LacI
  • LacO : Number of non-inhibited LacO
  • [mRNA]: mRNA (from LacO) concentration
  • [Enz] : Enzyme concentration : EntA,-B,-C,-D,-E,-F
All those concentrations are expressed in mmol/L

Parameters table:

Fe, FUR and FeFUR:
The iron-FUR complex is simply formed that way:
 
We reduced this equation to:

Which is not annoying, since we just have to divide our [FeFur] by to to get the real complex concentration.
We can easily write down both the formation (v) and the dissociation (v') speed:

We chose to model the iron input in the bacteria using a linear function of the external iron concentration Ferext, the factor p being the cell-wall permeability for iron.
The FUR on the other hand, is produced by the bacteria. It's evolution can also be considered linerar, using a mean production rate Fur0.


In this model, we only track the free Fe-FUR and not those which are attached to a FUR Binding Site. As LacI is the number of inhibited LacI, we can use this number to express how much Fe-FUR does bind to a FBS per unit of time.

Parameters:
Name Value Unite Description Reference
p 0.1 min^-1 Permeability of cell wall -
KfeFUR 0.01 M^-1.s^-1 Formation constant of FeFur complex -
Dff 0.001 min^-1 - -
Kp 0.5 min^-1 translation rate -
milliNa 6.02.10^20 mol^-1 Avogadro's constant [1]
V 6.5.10^-16 m^3 Volume of a call -
p 0.005 Value at zero of the activator -
Dmrna 0.001 min^-1 mRNA degradation rate -
Denz 0.001 min^-1 Enzyme degradation rate -
d 10^-9 Activator threshold [2]

Results

Conclusion

References:

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