Team:NYMU-Taipei/ymim1

From 2012.igem.org

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   <p>In order to  produce nitrogen from nitrate, we needed to use Michaelis-Menten&rsquo;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&rsquo;s equation to  help us simulate the substrate concentration in a single cell. </p>
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   <p><img src="m1_clip_image002.png" alt="" width="232" height="41" /><br />
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   <p><img src="http://2012.igem.org/wiki/images/e/e1/M1_clip_image002.png" alt="" width="232" height="41" /><br />
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     <br />
     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'>
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<img src="images/m1.gif" alt="" width="554" height="291" /></div></p>
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<img src="http://2012.igem.org/wiki/images/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>
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<p>For reaction 2,  3, 4, we used the equation <img src="m1_clip_image002_0001.png" alt="" width="71" height="30" />.  <br />
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<p>For reaction 2,  3, 4, we used the equation <img src="http://2012.igem.org/wiki/images/9/93/M1_clip_image002_0000.png" alt="" width="71" height="30" />.  <br />
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   As for the rest, we used <img src="m1_clip_image004_0000.png" alt="" width="82" height="31" /> instead. <br />
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   As for the rest, we used <img src="http://2012.igem.org/wiki/images/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>
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<p><img width="287" height="40" src="m1_clip_image002_0002.png" /> <br />
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<p><img width="287" height="40" src="http://2012.igem.org/wiki/images/2/25/M1_clip_image002_0002.png" /> <br />
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   <img width="307" height="37" src="m1_clip_image004_0001.png" /><br />
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   <img width="307" height="37" src="http://2012.igem.org/wiki/images/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 />
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   <br />
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<img src="m1_clip_image002_0003.png" alt="" width="576" height="87" />
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<img src="http://2012.igem.org/wiki/images/9/99/M1_clip_image002_0003.png" alt="" width="576" height="87" />
</p>
</p>
<p>Then we combined  the equation above with Michaelis-Menten&rsquo;s equation.</p>
<p>Then we combined  the equation above with Michaelis-Menten&rsquo;s equation.</p>
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<p><img src="m1_clip_image002_0004.png" alt="" width="422" height="43" /> <br />
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<p><img src="http://2012.igem.org/wiki/images/4/44/M1_clip_image002_0004.png" alt="" width="422" height="43" /> <br />
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   <img src="m1_clip_image004_0002.png" alt="" width="576" height="86" /> <br />
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   <img src="http://2012.igem.org/wiki/images/d/d9/M1_clip_image004_0002.png" alt="" width="576" height="86" /> <br />
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   <img src="m1_clip_image006.png" alt="" width="362" height="43" /> <br />
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   <img src="http://2012.igem.org/wiki/images/d/d0/M1_clip_image006.png" alt="" width="362" height="43" /> <br />
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   <img src="m1_clip_image008.png" alt="" width="425" height="43" /> <br />
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   <img src="http://2012.igem.org/wiki/images/0/03/M1_clip_image008.png" alt="" width="425" height="43" /> <br />
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   <img src="m1_clip_image010.png" alt="" width="422" height="43" /> <br />
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   <img src="http://2012.igem.org/wiki/images/e/e8/M1_clip_image010.png" alt="" width="422" height="43" /> <br />
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   <img src="m1_clip_image012.png" alt="" width="219" height="43" /></p>
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   <img src="http://2012.igem.org/File:M1_clip_image012.png" alt="" width="219" height="43" /></p>
<p>&nbsp; </p>
<p>&nbsp; </p>
<p>&nbsp; </p>
<p>&nbsp; </p>

Revision as of 02:40, 27 September 2012

NYMU iGEM

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.