Team:Grenoble/Projet/Modelling/Parameters

From 2011.igem.org

(Difference between revisions)
 
(3 intermediate revisions not shown)
Line 20: Line 20:
<div class="left">
<div class="left">
 +
    <div class="blocbackground">
    <h1>Modelling - Parameters</h1>
    <h1>Modelling - Parameters</h1>
 +
    </div>
<div  class="blocbackground" id="Parameters">
<div  class="blocbackground" id="Parameters">
    <h2>Parameters</h2>
    <h2>Parameters</h2>
Line 134: Line 136:
      </tr>
      </tr>
    </table>
    </table>
-
 
+
-
+
<p>
-
 
+
Working with the aTc/TetR parameters, we needed to now if our system could work with mercury.
 +
In order to see if it's <a href="https://2011.igem.org/Team:Grenoble/Projet/Results/Sensitivity#Mercury">applicable to mercury</a>,
 +
we realized a <a href="https://2011.igem.org/Team:Grenoble/Projet/Results/Sensitivity#Robustness">sensitivity to parameters study</a>.
 +
</p>
Line 165: Line 170:
       
       
</div>
</div>
-
<div  class="blocbackground" id="Sensitivity">
 
-
    <h2>Parameters sensitivity</h2>
 
-
    <p>
 
-
      In order to know if an error on the parameters would induce a completely different behaviour of our system,
 
-
      we studied the sensitivity of our system to changes in the parameter values.
 
-
    </p>
 
-
    <p>
 
-
      This study was performed by increasing or decreasing our parameters values by a range of percentages (from -66% to +300% for each parameter).
 
-
      Then we studied the change on the output of our system, the ratio of IPTG over aTc that induces the coloration.
 
-
    </p>
 
-
    <p>
 
-
      On the following figure one can see the influence on the output of our system (the ratio of IPTG over aTc on the interface)
 
-
      for several aTc concentrations. For these concentrations the switch is still efficient, even though the resulting
 
-
      variation on the output will induce an error on our measure.
 
-
    </p>
 
-
    <table class="nobordure">
 
-
<tr>
 
-
<td>
 
-
<center>
 
-
<a href= "https://static.igem.org/mediawiki/2011/4/41/Parameters_sensitivity1.png"><img src="https://static.igem.org/mediawiki/2011/4/41/Parameters_sensitivity1.png" style="width: 600px;" class="centerwide"/></a>
 
-
<div class="legend"><strong>Figure 1: </strong>Parameters sensitivity for 2.8e-07 M of aTc</div>
 
-
</center>
 
-
</td>
 
-
<td>
 
-
<p><strong>Note:</strong> On the next two figures the parameters are the following<br/>
 
-
<table style="border: 1px;">
 
-
  <tr>
 
-
    <td><strong>1</strong></td>
 
-
    <td>k<SUB>plac</SUB></td>
 
-
  </tr>
 
-
  <tr>
+
-
    <td><strong>2</strong></td>
+
-
    <td>V<SUB>cell</SUB></td>
+
-
  </tr>
+
-
  <tr>
 
-
    <td><strong>3</strong></td>
 
-
    <td>k<SUB>pTet <br/></td>
 
-
  </tr>
 
-
  <tr>
 
-
    <td><strong>4</strong></td>
 
-
    <td>K<SUB>pLac - LacI</SUB></td>
 
-
  </tr>
 
-
 
-
  <tr>
 
-
    <td><strong>5</strong></td>
 
-
    <td>K<SUB>pTet - TerR</SUB></td>
 
-
  </tr>
 
-
 
-
  <tr>
 
-
    <td><strong>6</strong></td>
 
-
    <td>K<SUB>LacI - IPTG</SUB></td>
 
-
  </tr>
 
-
 
-
  <tr>
 
-
    <td><strong>7</strong></td>
 
-
    <td>K<SUB>TetR - aTc</SUB></td>
 
-
  </tr>
 
-
 
-
  <tr>
 
-
    <td><strong>8</strong></td>
 
-
    <td>n<SUB>plac</SUB></td>
 
-
  </tr>
 
-
 
-
  <tr>
 
-
    <td><strong>9</strong></td>
 
-
    <td>n<SUB>pTet</SUB></td>
 
-
  </tr>
 
-
 
-
  <tr>
 
-
    <td><strong>10</strong></td>
 
-
    <td>δ<SUB>TetR</SUB></td>
 
-
  </tr>
 
-
 
-
  <tr>
 
-
    <td><strong>11</strong></td>
 
-
    <td>δ<SUB>LacI</SUB></td>
 
-
  </tr>
 
-
 
-
 
-
</table>
 
-
</td>
 
-
</tr>
 
-
    </table>
 
-
    <table class="nobordure">
 
-
    <tr>
 
-
      <td>
 
-
<a href="https://static.igem.org/mediawiki/2011/5/5b/Parameters_sensitivity2.png"><img src="https://static.igem.org/mediawiki/2011/5/5b/Parameters_sensitivity2.png" class ="centerwide" style="width: 600px;"/></a>
 
-
<div class="legend"><strong>Figure 2: </strong>Parameters sensitivity for 6.3e-06 M of aTc</div>
 
-
      </td>
 
-
      <td> 
 
-
<p>Variations from 1 to 13 : </p>
 
-
<table>
 
-
    <tr>
 
-
      <td><strong>1</strong></td>
 
-
      <td>-66%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>2</strong></td>
 
-
      <td>-50%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>3</strong></td>
 
-
      <td>-20%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>4</strong></td>
 
-
      <td>-10%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>5</strong></td>
 
-
      <td>-5%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>6</strong></td>
 
-
      <td>+0%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>7</strong></td>
 
-
      <td>+5%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>8</strong></td>
 
-
      <td>+10%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>9</strong></td>
 
-
      <td>+20%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>10</strong></td>
 
-
      <td>+50%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>11</strong></td>
 
-
      <td>+100%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>11</strong></td>
 
-
      <td>+200%</td>
 
-
    </tr>
 
-
 
-
    <tr>
 
-
      <td><strong>11</strong></td>
 
-
      <td>+300%</td>
 
-
    </tr>
 
-
</table>
 
-
    </td>
 
-
    </tr>
 
-
    </table>
 
-
   
 
-
    <p>For low values of aTc concentration the error is too minor to perturb the mechanism of our system. However,
 
-
    it becomes impossible to predict the system output if the error is superior to -50% or +100% for parameters such
 
-
    as K<SUB>pLac - LacI</SUB> or K<SUB>pTet - TetR</SUB>. In such a case a characterization of the responsible
 
-
    parameter would be necessary.
 
-
    </p>
 
-
    <p>
 
-
    For higher aTc concentrations however, the level of IPTG at which the switch occurs is very high. Errors on the parameters
 
-
    prevents the system to switch for the chosen IPTG gradient. In this case, the IPTG maximal necessary valuefor quantification
 
-
    would be too high for a living cell. The only problem being a decrease of the maximum value we can quantify.
 
-
    </p>
 
-
    <center>
 
-
    <a href="https://static.igem.org/mediawiki/2011/0/01/Parameters_sensitivity3.png"><img src="https://static.igem.org/mediawiki/2011/0/01/Parameters_sensitivity3.png" class="centerwide"/></a>
 
-
    <div class="legend"><strong>Figure 2: </strong>Parameters sensitivity for 6.2e-04 M of aTc</div>
 
-
    </center>
 
-
 
 
-
</div>
 
-
<div id="selector">
+
<center>
<form method="get" >
<form method="get" >
  <input type="button" value="< PREVIOUS <" onclick="document.location = '/Team:Grenoble/Projet/Modelling/Stochastic';" />
  <input type="button" value="< PREVIOUS <" onclick="document.location = '/Team:Grenoble/Projet/Modelling/Stochastic';" />
Line 359: Line 188:
    </optgroup>
    </optgroup>
-
    <optgroup label="Deterministic Modelling" >
+
    <optgroup label="Construction of the model" >
                                  
                                  
-
                                     <option value="/Deterministic#Our_EquationsTS" >Our equations - Toggle switch</option>
+
                                     <option value="/Deterministic#Our_EquationsTS" >Establishment of the equation - Toggle switch</option>
-
                                     <option value="/Deterministic#Our_EquationsQS" >Our equations - Quorum sensing</option>
+
                                     <option value="/Deterministic#Our_EquationsQS" >Establishment of the equation - Quorum sensing</option>
                                  
                                  
                                     <option value="/Deterministic#Our_algorithms" >Our algorithms</option>
                                     <option value="/Deterministic#Our_algorithms" >Our algorithms</option>
-
                               
 
-
                                    <option value="/Deterministic#Isoclines">Isoclines and Hysteresis</option>
 
                                  
                                  
                                      
                                      
Line 374: Line 201:
                             <optgroup label="Stochastic Modelling">
                             <optgroup label="Stochastic Modelling">
                                  
                                  
-
                                     <option value="/Stochastic#Geof" >Geof's</option>
+
                                     <option value="/Stochastic#Geof">Sensitivity to noise</option>
                                  
                                  
                                     <option value="/Stochastic#Gillespie_algorithm">Gillespie algorithm</option>
                                     <option value="/Stochastic#Gillespie_algorithm">Gillespie algorithm</option>
Line 384: Line 211:
                             <optgroup label="Parameters">
                             <optgroup label="Parameters">
                              
                              
-
    <option value="/Parameters" selected="selected">Our parameters</option>
+
    <option value="/Parameters" selected="selected">Table of parameters</option>
-
   
+
-
    <option value="/Parameters#Sensitivity">Parameters sensitivity</option>
+
    </optgroup>
    </optgroup>
 +
                    </select>
 +
                    <input type="hidden" name="id2" value="0" />
 +
                    <input type="submit" value="Go!" />
 +
  <input type="button" value="> NEXT >" onclick="document.location = '/Team:Grenoble/Projet/Modelling/Parameters';" />
 +
               
 +
            </form>
 +
            </center>
-
                            <optgroup label="Results">
 
-
    <option value="/Results#Validation">Validation of our Network</option>
 
-
    <option value="/Results#Device">Device specificities</option>
 
-
    </optgroup>
 
-
                    </select>
 
-
                    <input type="hidden" name="id2" value="0" />
 
-
                    <input type="submit" value="Go!" />
 
-
  <input type="button" value="> NEXT >" onclick="document.location = '/Team:Grenoble/Projet/Modelling/Results';" />
 
-
            </form>
 
-
            </div>
 
</div>
</div>
</div>
</div>
</html>
</html>
{{:Team:Grenoble/Design/pied}}
{{:Team:Grenoble/Design/pied}}

Latest revision as of 03:02, 29 October 2011

Grenoble 2011, Mercuro-Coli iGEM


Modelling - Parameters

Parameters

PDF file (detailed explanation on parameters and how we deduced them) for Toggle Switch
kplac pLac production rate 600 proteins/min [1]
kpTet pTet production rate 600 proteins/min [1]
kpMer pMer production rate 600 proteins/min [1]
δLacI LacI degradation rate 4.6E-2 min−1 PDF file
δTetR TetR degradation rate 4.6E-2 min−1 PDF file
δMerR MerR degradation rate 4.6E-2 min−1 PDF file
KpLac - LacI plac - LacI dissociation constant 5.45E-7 M Kyoto 10
KpMer - MerR pMer - MerR dissociation constant 1.00E-8 M [2]
KpTet - TerR pTet - TetR dissociation constant 5.00E-8 M [3]
KLacI - IPTG LacI - IPTG dissociation constant 2.96E-5 M [4]
KTetR - aTc aTc - TetR dissociation constant 1.5E-8 M [5]
KHg2+ - MerR Hg2+ - MerR dissociation constant 1E-7 M [2]
nplac plac cooperativity number 2,3 [4]
npMer pMer cooperativity number 2,5 [6]
npTet pTet cooperativity number 3 [7]

Working with the aTc/TetR parameters, we needed to now if our system could work with mercury. In order to see if it's applicable to mercury, we realized a sensitivity to parameters study.

References

[1] Nature. 2000 Jan 20;403(6767):335-8. A synthetic oscillatory network of transcriptional regulators. Elowitz MB, Leibler S.

[2] Mol Gen Genet. 1999 Aug;262(1):154-62. Purification and characterization of MerR, the regulator of the broad-spectrum mercury resistance genes in Streptomyces lividans 1326. Rother D, Mattes R, Altenbuchner J.

[3] David Braun et al. Parameter estimation for two synthetic gene networks: A case study. IEEE 2005.

[4] Nature 403, 339-342 (20 January 2000) Construction of a genetic toggle switch in Escherichia coli. Timothy S. Gardner Charles R. Cantor & James J. Collins

[5] O. Scholz, P. Schubert, M. Kintrup and W. Hillen, Tet repressor induction without Mg2+, Biochemistry 39 (2000), pp. 10914–10920

[6] Ultrasensitivity and heavy-metal selectivity of the allosterically modulated MerR transcription complex. D M Ralston and T V O'Halloran

[7] Systems analysis of a quorum sensing network: design constraints imposed by the functional requirements, network topology and kinetic constants. Goryachev AB, Toh DJ, Lee T.

logo iGEM
iGEM 2011 Main Page


Contact Us:

Clic here !

Retrieved from "http://2011.igem.org/Team:Grenoble/Projet/Modelling/Parameters"