Team:UANL Mty-Mexico/Modeling/Biosensor

From 2012.igem.org

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<p><br><h3>Parameters</h3><br></p>
<p><br><h3>Parameters</h3><br></p>
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<br><hr align="center" width="33%"/></br>
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<br><p><b>Parameter table</b></p>
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<br>
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<center>
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<table border="1" cellspacing="1" cellpadding="1">
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  <tbody>
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    <tr  style="background-color:#99CCFF">
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      <td valign="top">
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        <p>Parameter</p>
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      </td>
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      <td valign="top">
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        <p>Description</p>
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      </td>
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      <td valign="top">
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        <p>Value</p>
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      </td>
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      <td valign="top">
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        <p>References</p>
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      </td>
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    </tr>
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  <tr  border="1" style="background-color:#CCCCCC">
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      <td valign="top">
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        <p>α<sub>mArsR</sub></p>
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      </td>
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      <td valign="top">
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        <p>Maximal transcription rate of ArsR</p>
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      </td>
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      <td valign="top">
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        <p>3.74 nM/min</p>
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      </td>
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      <td valign="top">
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        <p>Assumptions</p>
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      </td>
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    </tr>
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  <tr  border="1" style="background-color:#CCCCCC">
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      <td valign="top">
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        <p>α<sub>mFluc</sub></p>
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      </td>
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      <td valign="top">
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        <p>Maximal transcription rate of Fluc</p>
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      </td>
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      <td valign="top">
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        <p>1.40 nM/min</p>
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      </td>
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      <td valign="top">
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        <p>Assumptions</p>
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      </td>
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    </tr>
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  <tr  border="1" style="background-color:#CCCCCC">
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      <td valign="top">
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        <p>α<sub>pArsR</sub></p>
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      </td>
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      <td valign="top">
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        <p>Maximal translation rate of ArsR</p>
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      </td>
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      <td valign="top">
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        <p>9.74 nM/min</p>
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      </td>
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      <td valign="top">
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        <p>Assumptions</p>
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      </td>
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    </tr>
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  <tr  border="1" style="background-color:#CCCCCC">
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      <td valign="top">
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        <p>α<sub>pFluc</sub></p>
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      </td>
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      <td valign="top">
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        <p>Maximal translation rate of Fluc</p>
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      </td>
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      <td valign="top">
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        <p>2.06 nM/min</p>
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      </td>
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      <td valign="top">
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        <p>Assumptions</p>
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      </td>
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    </tr>
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  <tr  border="1" style="background-color:#CCCCCC">
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      <td valign="top">
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        <p>δ<sub>mRNAArsR</sub></p>
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      </td>
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      <td valign="top">
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        <p>Degradation rate of ArsR mRNA</p>
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      </td>
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      <td valign="top">
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        <p>2.16x10<sup>-1</sup> min<sup>-1</sup></p>
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      </td>
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      <td valign="top">
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        <p>Assumptions, <a href="http://subtiwiki.uni-goettingen.de/wiki/index.php/GlpP">GlpP, SubtiWiki.</p>
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      </td>
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    </tr>
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  <tr  border="1" style="background-color:#CCCCCC">
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      <td valign="top">
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        <p>δ<sub>mRNAFluc</sub></p>
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      </td>
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      <td valign="top">
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        <p>Degradation rate of Fluc mRNA</p>
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      </td>
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      <td valign="top">
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        <p>3.37x10<sup>-2</sup> min<sup>-1</sup></p>
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      </td>
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      <td valign="top">
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        <p>Assumptions, <a href="http://www.sciencemag.org/content/suppl/2011/03/16/science.1198817.DC1/Suter.SOM.pdf">Suter, <i>et al.,</i> (2011), <a href="http://jgv.sgmjournals.org/content/88/1/286.full">Karetnivok and Lehto (2006).</p>
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      </td>
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    </tr>
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  <tr  border="1" style="background-color:#CCCCCC">
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      <td valign="top">
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        <p>δ<sub>ArsR</sub></p>
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      </td>
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      <td valign="top">
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        <p>Degradation rate of ArsR</p>
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      </td>
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      <td valign="top">
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        <p>2.31x10<sup>-2</sup> min<sup>-1</sup></p>
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      </td>
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      <td valign="top">
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        <p>Assumptions</p>
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      </td>
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    </tr>
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  <tr  border="1" style="background-color:#CCCCCC">
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      <td valign="top">
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        <p>δ<sub>Fluc</sub></p>
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      </td>
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      <td valign="top">
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        <p>Degradation rate of Fluc</p>
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      </td>
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      <td valign="top">
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        <p>2.60x10<sup>-2</sup> min<sup>-1</sup></p>
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      </td>
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      <td valign="top">
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        <p>Assumptions, <a href="http://www.pnas.org/content/early/2009/02/10/0813345106.full.pdf">Auld, <i>et al.,</i> (2008)</p>
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      </td>
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    </tr>
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<tr  border="1" style="background-color:#CCCCCC">
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      <td valign="top">
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        <p>pro<sub>ars</sub></p>
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      </td>
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      <td valign="top">
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        <p>Concentration of ars promoter</p>
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      </td>
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      <td valign="top">
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        <p>aprox. 1*plasmid copy (nM)</p>
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      </td>
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      <td valign="top">
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        <p>Assumptions</p>
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      </td>
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    </tr>
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  </tbody>
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</table>
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</center>
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<p><br><h2>Simulations</h2><br></p>
<p><br><h2>Simulations</h2><br></p>

Revision as of 01:43, 26 September 2012

iGEM UANL 2012


Biosensor


Our biosensor model is a continuation of the previously exposed transport and accumulation model with the addition of the production of luciferase as a function of ArsR|As concentration. In this way, we can relate the concentration of extracellular As to the production of luciferase.


ODEs



Parameters





Parameter table


Parameter

Description

Value

References

αmArsR

Maximal transcription rate of ArsR

3.74 nM/min

Assumptions

αmFluc

Maximal transcription rate of Fluc

1.40 nM/min

Assumptions

αpArsR

Maximal translation rate of ArsR

9.74 nM/min

Assumptions

αpFluc

Maximal translation rate of Fluc

2.06 nM/min

Assumptions

δmRNAArsR

Degradation rate of ArsR mRNA

2.16x10-1 min-1

Assumptions, GlpP, SubtiWiki.

δmRNAFluc

Degradation rate of Fluc mRNA

3.37x10-2 min-1

Assumptions, Suter, et al., (2011), Karetnivok and Lehto (2006).

δArsR

Degradation rate of ArsR

2.31x10-2 min-1

Assumptions

δFluc

Degradation rate of Fluc

2.60x10-2 min-1

Assumptions, Auld, et al., (2008)

proars

Concentration of ars promoter

aprox. 1*plasmid copy (nM)

Assumptions


Simulations


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