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Team:NYMU-Taipei/ymim1
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<p>Before designing our experiment, we would like to do a simple simulation to estimate the efficiency and productivity of nitrogen for our modified bacteria.</p> | <p>Before designing our experiment, we would like to do a simple simulation to estimate the efficiency and productivity of nitrogen for our modified bacteria.</p> | ||
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<p>In order to produce nitrogen from nitrate, we needed to use Michaelis-Menten’s equation to help us simulate the substrate concentration in a single cell. </p> | <p>In order to produce nitrogen from nitrate, we needed to use Michaelis-Menten’s equation to help us simulate the substrate concentration in a single cell. </p> | ||
| - | <p><img src=" | + | <p><img src="https://static.igem.org/mediawiki/2012/e/e1/M1_clip_image002.png" alt="" width="232" height="41" /><br /> |
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Where v=reaction rate, [P]=product concentration, Vmax=max reaction rate, [S]=substrate concentration, Km= equilibrium constant of enzyme, Kcat=turnover number. </p> | Where v=reaction rate, [P]=product concentration, Vmax=max reaction rate, [S]=substrate concentration, Km= equilibrium constant of enzyme, Kcat=turnover number. </p> | ||
<p>Our pathway looked like this</p><div class=out style='text-align:center'> | <p>Our pathway looked like this</p><div class=out style='text-align:center'> | ||
| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/2012/8/8f/Ymim1.gif" alt="" width="554" height="291" /></div></p> |
<p>Reaction 2, 3, 4 were already in the E.coli before we engineered the bacteria. Reaction 1, 5, 6, 7 are the new pathways that we engineered.</p> | <p>Reaction 2, 3, 4 were already in the E.coli before we engineered the bacteria. Reaction 1, 5, 6, 7 are the new pathways that we engineered.</p> | ||
| - | <p>For reaction 2, 3, 4, we used the equation <img src=" | + | <p>For reaction 2, 3, 4, we used the equation <img src="https://static.igem.org/mediawiki/2012/9/93/M1_clip_image002_0000.png" alt="" width="71" height="30" />. <br /> |
| - | As for the rest, we used <img src=" | + | As for the rest, we used <img src="https://static.igem.org/mediawiki/2012/b/ba/M1_clip_image004.png" alt="" width="82" height="31" /> instead. <br /> |
<br /> | <br /> | ||
To determine the enzyme concentration for our new pathways, we needed another two equations. </p> | To determine the enzyme concentration for our new pathways, we needed another two equations. </p> | ||
| - | <p><img width="287" height="40" src=" | + | <p><img width="287" height="40" src="https://static.igem.org/mediawiki/2012/2/25/M1_clip_image002_0002.png" /> <br /> |
| - | <img width="307" height="37" src=" | + | <img width="307" height="37" src="https://static.igem.org/mediawiki/2012/b/b0/M1_clip_image004_0001.png" /><br /> |
</p> | </p> | ||
<p>Where nplasmid= plasmid copy number in E.coli, P=promoter strength, NA= Avogadaros' Number, VEcoli= cell volume of E.coli, deltamrna=degradation rate of mRNA, alpha= translation rate of mRNA, gammaEnzyme=degradation rate or Enzyme</p> | <p>Where nplasmid= plasmid copy number in E.coli, P=promoter strength, NA= Avogadaros' Number, VEcoli= cell volume of E.coli, deltamrna=degradation rate of mRNA, alpha= translation rate of mRNA, gammaEnzyme=degradation rate or Enzyme</p> | ||
<p>Combined the two equations, we got the relationship between enzyme concentration and time.<br /> | <p>Combined the two equations, we got the relationship between enzyme concentration and time.<br /> | ||
<br /> | <br /> | ||
| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/2012/9/99/M1_clip_image002_0003.png" alt="" width="576" height="87" /> |
</p> | </p> | ||
<p>Then we combined the equation above with Michaelis-Menten’s equation.</p> | <p>Then we combined the equation above with Michaelis-Menten’s equation.</p> | ||
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| - | <p><img src=" | + | <p><img src="https://static.igem.org/mediawiki/2012/4/44/M1_clip_image002_0004.png" alt="" width="422" height="43" /> <br /> |
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| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/2012/d/d9/M1_clip_image004_0002.png" alt="" width="576" height="86" /> <br /> |
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| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/2012/d/d0/M1_clip_image006.png" alt="" width="362" height="43" /> <br /> |
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| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/2012/0/03/M1_clip_image008.png" alt="" width="425" height="43" /> <br /> |
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| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/2012/e/e8/M1_clip_image010.png" alt="" width="422" height="43" /> <br /> |
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| - | <img src=" | + | <img src="https://static.igem.org/mediawiki/2012/e/e9/M1_clip_image012.png" alt="" width="219" height="43" /></p> |
<p> </p> | <p> </p> | ||
<p> </p> | <p> </p> | ||
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| - | <li><a title="Description" href="https://2012.igem.org/Team:NYMU-Taipei/ymim1 | + | <li><a title="Description" href="https://2012.igem.org/Team:NYMU-Taipei/ymim1">Description</a></li> |
| - | <li><a title=" | + | <li><a title="Results & Conclusion" href="https://2012.igem.org/Team:NYMU-Taipei/ymim2">Results & Conclusion<br /> |
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</a></li> | </a></li> | ||
Latest revision as of 17:28, 26 October 2012
Modeling
Objective
Before designing our experiment, we would like to do a simple simulation to estimate the efficiency and productivity of nitrogen for our modified bacteria.
Description
In order to produce nitrogen from nitrate, we needed to use Michaelis-Menten’s equation to help us simulate the substrate concentration in a single cell.
Where v=reaction rate, [P]=product concentration, Vmax=max reaction rate, [S]=substrate concentration, Km= equilibrium constant of enzyme, Kcat=turnover number.
Our pathway looked like this
Reaction 2, 3, 4 were already in the E.coli before we engineered the bacteria. Reaction 1, 5, 6, 7 are the new pathways that we engineered.
For reaction 2, 3, 4, we used the equation 
.
As for the rest, we used 
instead.
To determine the enzyme concentration for our new pathways, we needed another two equations.
Where nplasmid= plasmid copy number in E.coli, P=promoter strength, NA= Avogadaros' Number, VEcoli= cell volume of E.coli, deltamrna=degradation rate of mRNA, alpha= translation rate of mRNA, gammaEnzyme=degradation rate or Enzyme
Combined the two equations, we got the relationship between enzyme concentration and time.
Then we combined the equation above with Michaelis-Menten’s equation.
-
Modeling
