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Team:Evry/Model3
From 2013.igem.org
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<p> | <p> | ||
Variables:<br/> | Variables:<br/> | ||
| - | < | + | <ul> |
| - | [Fe] : Iron concentration inside the bacteria | + | <li>[Fe] : Iron concentration inside the bacteria</li> |
| - | [Fur] : FUR concentration inside the bacteria | + | <li>[Fur] : FUR concentration inside the bacteria</li> |
| - | [FeFur] : Iron-FUR complex concentration inside the bacteria | + | <li>[FeFur] : Iron-FUR complex concentration inside the bacteria</li> |
| - | LacI : Number of inhibited LacI | + | <li>LacI : Number of inhibited LacI</li> |
| - | LacO : Number of non-inhibited LacO | + | <li>LacO : Number of non-inhibited LacO</li> |
| - | [mRNA]: mRNA (from LacO) concentration | + | <li>[mRNA]: mRNA (from LacO) concentration</li> |
| - | [Enz] : Enzyme concentration : EntA,-B,-C,-D,-E,-F | + | <li>[Enz] : Enzyme concentration : EntA,-B,-C,-D,-E,-F</li> |
| - | + | </ul> | |
All those concentrations are expressed in mmol/L</p> | All those concentrations are expressed in mmol/L</p> | ||
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Fe, FUR and FeFUR:<br/> | Fe, FUR and FeFUR:<br/> | ||
The iron-FUR complex is simply formed that way:<br/> | The iron-FUR complex is simply formed that way:<br/> | ||
| - | <img src= | + | <img src=”https://static.igem.org/mediawiki/2013/7/72/Reg1.png”/><br/> |
| - | + | ||
We reduced this equation to:<br/> | We reduced this equation to:<br/> | ||
| - | <img src= | + | <img src=”https://static.igem.org/mediawiki/2013/e/e8/Reg2.png”/><br/> |
| - | + | ||
Which is not annoying, since we just have to divide our [FeFur] by to to get the real complex concentration.<br/> | Which is not annoying, since we just have to divide our [FeFur] by to to get the real complex concentration.<br/> | ||
We can easily write down both the formation (v) and the dissociation (v') speed:<br/> | We can easily write down both the formation (v) and the dissociation (v') speed:<br/> | ||
| - | <img src= | + | <img src=”https://static.igem.org/mediawiki/2013/f/fe/Reg3.png”/><br/> |
| - | + | <img src=”https://static.igem.org/mediawiki/2013/8/84/Reg4.png”/><br/> | |
| - | + | ||
We chose to model the iron input in the bacteria using a linear function of the external iron concentration <i>Ferext</i>, the factor <i>p</i> being the cell-wall permeability for iron.<br/> | We chose to model the iron input in the bacteria using a linear function of the external iron concentration <i>Ferext</i>, the factor <i>p</i> being the cell-wall permeability for iron.<br/> | ||
The FUR on the other hand, is produced by the bacteria. It's evolution can also be considered linerar, using a mean production rate <i>Fur0</i>.<br/> | The FUR on the other hand, is produced by the bacteria. It's evolution can also be considered linerar, using a mean production rate <i>Fur0</i>.<br/> | ||
| - | <img src= | + | <img src=”https://static.igem.org/mediawiki/2013/5/51/Regfer.png”/><br/> |
| - | + | <img src=”https://static.igem.org/mediawiki/2013/6/68/Regfur.png”/><br/> | |
| - | + | ||
In this model, we only track the free Fe-FUR and not those which are attached to a FUR Binding Site. As <i>LacI</i> 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.<br/> | In this model, we only track the free Fe-FUR and not those which are attached to a FUR Binding Site. As <i>LacI</i> 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.<br/> | ||
| - | <img src= | + | <img src=”https://static.igem.org/mediawiki/2013/6/6d/Regfefur.png”/> |
| - | + | ||
</p> | </p> | ||
Revision as of 16:01, 4 October 2013
Metabolic model
Overview
Assumptions
Model Description
Results
Conclusion
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.
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
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.
References:
