Difference between revisions of "Team:IIT Delhi/modelling"

Line 658: Line 658:
 
   <div class="container con">
 
   <div class="container con">
 
    <table>
 
    <table>
−
<tr id="mathematical">
+
<tr id="introduction">
 
<td class="det" align="left" style="vertical-align:top;">
 
<td class="det" align="left" style="vertical-align:top;">
 
<h1 style="font-family:'Trebuchet MS', 'Lucida Grande', 'Lucida Sans Unicode', 'Lucida Sans', Tahoma, sans-serif;color:white;font-size:250%;padding-top:18px;">Mathematical Model</h1>
 
<h1 style="font-family:'Trebuchet MS', 'Lucida Grande', 'Lucida Sans Unicode', 'Lucida Sans', Tahoma, sans-serif;color:white;font-size:250%;padding-top:18px;">Mathematical Model</h1>
 
<h2 style="font-family: 'Roboto', sans-serif;color:white;font-size:150%;vertical-align:text-top;">
 
<h2 style="font-family: 'Roboto', sans-serif;color:white;font-size:150%;vertical-align:text-top;">
−
Synthetic Biology targets to design and create original biological systems. But the genetic systems involved are very intricate. Before going to lab and start working,  one should first have a reasonable estimate of what they expect to do. And here mathematical modeling is useful.
+
Three of the proteins required in the project are cytochrome c proteins (haem proteins). Hence, the heme biosynthesis pathway needs to be modelled.
−
<br><br>
+
Pathway of heme production in E. coli (C-5 pathway from glutamate)
−
Mathematical Model <br><br>
+
−
The following assumptions were taken for modeling the system:
+
−
    <li> All the cells behaves the same way in our system</li>
+
−
    <li> Our consideration of the concentrations of mRNA and Protein starts from t=0, and there concentration is zero at t=0</li>
+
−
    <li> We have assumed the mRNA concentration to be "x" and protein concentration to be "y"</li>
+
−
 
+
−
<br>
+
−
We chose a constitutive promoter so the input gene expression function do not involve any repression or activation term, So formulated the following set of differential equations of transcription and translation.
+
 
      
 
      
 
</h2>
 
</h2>
Line 679: Line 671:
 
      </table>
 
      </table>
 
      </table>
 
      </table>
 +
<table>
 +
  <tr id="mathematical">
 +
    <td><img class="team" src="https://static.igem.org/mediawiki/2015/8/89/IITDhp8.jpeg" height="200px" width="200px"></td>
 +
<td class="det">
 +
<h1 style="font-family:'Trebuchet MS', 'Lucida Grande', 'Lucida Sans Unicode', 'Lucida Sans', Tahoma, sans-serif;color:white;font-size:250%;padding-top:18px;">Surveys (August 2015)</h1>
 +
<h2 style="font-family: 'Roboto', sans-serif;color:white;font-size:150%;vertical-align:text-top;">
 +
Also,d-Aminolevulinate (ALA) produced as an intermediate in the above reactions. -Aminolevulinate Synthase (ALA Synthase) is the committed step of the heme synthesis pathway, and is usually rate-limiting for the overall pathway. Regulation occurs through control of gene transcription. Heme functions as a feedback inhibitor, repressing transcription of the gene for -Aminolevulinate Synthase.
 +
 +
</h2>
 +
<br />
 +
                                        <br />
 +
</td>
 +
</tr>
 +
</table>
 +
 +
<table>
 +
<tr id="">
 +
<td class="det" align="left" style="vertical-align:top;">
 +
<h1 style="font-family:'Trebuchet MS', 'Lucida Grande', 'Lucida Sans Unicode', 'Lucida Sans', Tahoma, sans-serif;color:white;font-size:250%;padding-top:18px;">Mathematical Model</h1>
 +
<h2 style="font-family: 'Roboto', sans-serif;color:white;font-size:150%;vertical-align:text-top;">
 +
A non-competitive irreversible feedback inhibition model is assumed for this step with a ki value of 0.02 mM. Hence, the following equation governs the conversion to ALA:
 +
   
 +
</h2>
 +
        </td>
 +
<td><img class="team" src="https://static.igem.org/mediawiki/2015/0/07/Igem-iitd-modeling-1.jpg" height="400px" width="200px"></td>
 +
</tr>
 +
      </table>
  
 
         </div>
 
         </div>

Revision as of 11:03, 18 September 2015

Mathematical Model

Three of the proteins required in the project are cytochrome c proteins (haem proteins). Hence, the heme biosynthesis pathway needs to be modelled. Pathway of heme production in E. coli (C-5 pathway from glutamate)

Surveys (August 2015)

Also,d-Aminolevulinate (ALA) produced as an intermediate in the above reactions. -Aminolevulinate Synthase (ALA Synthase) is the committed step of the heme synthesis pathway, and is usually rate-limiting for the overall pathway. Regulation occurs through control of gene transcription. Heme functions as a feedback inhibitor, repressing transcription of the gene for -Aminolevulinate Synthase.



Mathematical Model

A non-competitive irreversible feedback inhibition model is assumed for this step with a ki value of 0.02 mM. Hence, the following equation governs the conversion to ALA: