http://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&feed=atom&action=historyTeam:Colombia/Deterministic - Revision history2024-03-28T09:27:37ZRevision history for this page on the wikiMediaWiki 1.16.5http://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&diff=393895&oldid=prevPablocarderam at 03:05, 18 October 20142014-10-18T03:05:36Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to get this behavior, we needed to find the right set of parameters. You can check the [https://2014.igem.org/Team:Colombia/Parameters Parameters Section] to understand how we did it. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to get this behavior, we needed to find the right set of parameters. You can check the [https://2014.igem.org/Team:Colombia/Parameters Parameters Section] to understand how we did it. </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div class="button-fill orange" ><div class="button-text"> Back to modeling</div><div class="button-inside"><div class="inside-text"><a style="text-decoration: none; background-color: none; color: red;" href="https://2014.igem.org/Team:Colombia/Modeling">Go! </a></div></div></div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div class="button-fill orange" ><div class="button-text"> Back to modeling</div><div class="button-inside"><div class="inside-text"><a style="text-decoration: none; background-color: none; color: red;" href="https://2014.igem.org/Team:Colombia/Modeling">Go! </a></div></div></div></div></td></tr>
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</table>Pablocarderamhttp://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&diff=393813&oldid=prevPablocarderam at 03:05, 18 October 20142014-10-18T03:05:01Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to get this behavior, we needed to find the right set of parameters. You can check the [https://2014.igem.org/Team:Colombia/Parameters Parameters Section] to understand how we did it. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to get this behavior, we needed to find the right set of parameters. You can check the [https://2014.igem.org/Team:Colombia/Parameters Parameters Section] to understand how we did it. </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div class="button-fill orange" ><div class="button-text"> Back to modeling</div><div class="button-inside"><div class="inside-text"><a style="text-decoration: none; background-color: none; color: red;" href="https://2014.igem.org/Team:Colombia/Modeling">Go! </a></div></div></div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><div class="button-fill orange" ><div class="button-text"> Back to modeling</div><div class="button-inside"><div class="inside-text"><a style="text-decoration: none; background-color: none; color: red;" href="https://2014.igem.org/Team:Colombia/Modeling">Go! </a></div></div></div></div></td></tr>
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</table>Pablocarderamhttp://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&diff=393720&oldid=prevPablocarderam at 03:04, 18 October 20142014-10-18T03:04:24Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to get this behavior, we needed to find the right set of parameters. You can check the [https://2014.igem.org/Team:Colombia/Parameters Parameters Section] to understand how we did it. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>In order to get this behavior, we needed to find the right set of parameters. You can check the [https://2014.igem.org/Team:Colombia/Parameters Parameters Section] to understand how we did it. </div></td></tr>
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</table>Pablocarderamhttp://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&diff=392876&oldid=prevPablocarderam at 02:58, 18 October 20142014-10-18T02:58:12Z<p></p>
<a href="http://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&diff=392876&oldid=147676">Show changes</a>Pablocarderamhttp://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&diff=147676&oldid=prevD.olivera1320 at 15:36, 30 September 20142014-09-30T15:36:54Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test8.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test8.png|center|600px]]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">In order to get this behaviour we needed to find the right set of parameters. You can check the [https://2014.igem.org/Team:Colombia/Parameters Parameters Section] to understand how we did it. </ins></div></td></tr>
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</table>D.olivera1320http://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&diff=147659&oldid=prevD.olivera1320 at 15:31, 30 September 20142014-09-30T15:31:48Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As soon as the CAI molecule is present the CqsS concentration is instantly decreased, and CqsS* (which stands for the CAI bound with the Cqss protein) increases. After half an hour the concentration of CqsS starts to decrease because it is consume by LuxU,just the way it’s supposed to.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As soon as the CAI molecule is present the CqsS concentration is instantly decreased, and CqsS* (which stands for the CAI bound with the Cqss protein) increases. After half an hour the concentration of CqsS starts to decrease because it is consume by LuxU,just the way it’s supposed to.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The next step is to check what happens with LuxU and its phosphorylated version <del class="diffchange diffchange-inline">now </del>that we know that Cqss is modeled properly we want to check the phosphorylation/ phosphate cascade. As with CqsS this molecule was already modelled by Lelu et al (2012).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The next step is to check what happens with LuxU and its phosphorylated version<ins class="diffchange diffchange-inline">. Now </ins>that we know that Cqss is modeled properly we want to check the phosphorylation/ phosphate cascade. As with CqsS this molecule was already modelled by Lelu et al (2012).</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The first time we modelled the system, LuxO response was a slower than we want. So we changed the hill constant coefficient, proposed by Lelu et al in order to make the response faster and last longer. This change compensates the lack of the negative feedback caused by miRNA that is present in <i>V. cholera </i> but not in <i> <del class="diffchange diffchange-inline">S. </del>coli</i>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The first time we modelled the system, LuxO response was a slower than we want. So we changed the hill constant coefficient, proposed by Lelu et al in order to make the response faster and last longer. This change compensates the lack of the negative feedback caused by miRNA that is present in <i>V. cholera </i> but not in <ins class="diffchange diffchange-inline">our </ins><i> <ins class="diffchange diffchange-inline">Sherlock </ins>coli</i>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>With this modification we can see that the systems takes 20 hours to react and after 30h the production of LuxO is completely on and LuxO* is almost zero, which is desirable, because we do not want any LuxO phosphorylated to turn on the Pqrr4 promoter. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>With this modification we can see that the systems takes 20 hours to react and after 30h the production of LuxO is completely on and LuxO* is almost zero, which is desirable, because we do not want any LuxO phosphorylated to turn on the Pqrr4 promoter. </div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>When CAI is present in the media TetR production turns off, which can be seen as a small change in TetR concentration; even tough the change is small it is enough to decrease the dimer concentration by 10 times. Now is time to see if this decrease is enough to turn on the production of the signal. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>When CAI is present in the media TetR production turns off, which can be seen as a small change in TetR concentration; even tough the change is small it is enough to decrease the dimer concentration by 10 times. </div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Now is time to see if this decrease is enough to turn on the production of the signal. <ins class="diffchange diffchange-inline">When TetR is produced it dimerises and blocks the production of pTet promoter; downstream this promoter, in our system is the chromoprotein. Using the Hill equation for repression we have that the response equation is:</ins></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">The first model we try was given by the equation: </del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ1.png|center|680px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ1.png|center|680px]]</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Where the production term is given by the Hill equation for repression. </del>After running the model we got the figure below:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>After running the model we got the figure below:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test6.png|center|400px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test6.png|center|400px]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Even tough chromoprotein increases in 500%, the maximum concentration is less than 10uM, which makes it difficult to see without microscope. So we decided to change the model and add a positive feedback. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Even tough chromoprotein increases in 500%, the maximum concentration is less than 10uM, which makes it difficult to see without microscope. So we decided to change the model and add a positive feedback. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>At first we thought of using the same promoter <b> pTet </b> which has an activator protein <b> TetA </b>. In this case the promoter and the activator <del class="diffchange diffchange-inline">will </del>compete for the DNA binding site, so the expression for the system <del class="diffchange diffchange-inline">would be</del>: </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>At first we thought of using the same promoter <b> pTet </b> which has an activator protein <b> TetA </b>. In this case the promoter and the activator compete for the DNA binding site, so the expression for the system <ins class="diffchange diffchange-inline">is</ins>: </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ.png|center|650px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ.png|center|650px]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In order to have more options we also tried the system with another positive feedback: <b> Psp3 </b> with <b> pag </b> promoter from the [https://2009.igem.org/Team:Cambridge Cambridge 2009 Team]. In this case the activator and repressor have different DNA binding sites, so the expression for the change in the response trough time <del class="diffchange diffchange-inline">would be</del>: </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to have more options we also tried the system with another positive feedback: <b> Psp3 </b> with <b> pag </b> promoter from the [https://2009.igem.org/Team:Cambridge Cambridge 2009 Team]. In this case the activator and repressor have different DNA binding sites, so the expression for the change in the response trough time <ins class="diffchange diffchange-inline">is</ins>: </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ2.png|center|650px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ2.png|center|650px]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The Figure below shows how the system will behave if the positive feedback is added to the circuit. On the left is the response of <i> Sherlock coli </i> if the Psp3 protein is used as an activator. <del class="diffchange diffchange-inline">The </del>chromoprotein concentration will be adequate for the system, but <del class="diffchange diffchange-inline">the increase </del>is <del class="diffchange diffchange-inline">only about 100%</del>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The Figure below shows how the system will behave if the positive feedback is added to the circuit. On the left is the response of <i> Sherlock coli </i> if the Psp3 protein is used as an activator. <ins class="diffchange diffchange-inline">We can see that the </ins>chromoprotein concentration will be adequate for the system, but <ins class="diffchange diffchange-inline">basal production </ins>is <ins class="diffchange diffchange-inline">high compared with the maximum production</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>On the other hand the response with TetA has a higher chromoprotein concentration and the increase when CAI is in the media is 12 times greater the <del class="diffchange diffchange-inline">initial </del>concentration. This is exactly what we wanted!!! </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>On the other hand the response with TetA has a higher chromoprotein concentration and the increase when CAI is in the media is 12 times greater <ins class="diffchange diffchange-inline">than </ins>the <ins class="diffchange diffchange-inline">basal </ins>concentration. This is exactly what we wanted!!! </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test7.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test7.png|center|600px]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>We <del class="diffchange diffchange-inline">can see </del>that the system takes about 20h to start producing the chromoprotein and 72h to reach its maximum expression. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>We <ins class="diffchange diffchange-inline">chose the system with a positive feedback </ins>that <ins class="diffchange diffchange-inline">includes the TetA activator. The Figure below shows how </ins>the system <ins class="diffchange diffchange-inline">behaves with the two impulses. We can see that <i> Sherlock coli </i> </ins>takes about 20h to start producing the chromoprotein and 72h to reach its maximum expression. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test8.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test8.png|center|600px]]</div></td></tr>
</table>D.olivera1320http://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&diff=146014&oldid=prevD.olivera1320 at 02:06, 30 September 20142014-09-30T02:06:42Z<p></p>
<table style="background-color: white; color:black;">
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test7.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test7.png|center|600px]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">We can see that the system takes about 20h to start producing the chromoprotein and 72h to reach its maximum expression. </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test8.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test8.png|center|600px]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">And now the response is up, now this might be enough or it might not, there’s still much tweaking we can do to increase the response signal but if this is enough we can use this. When the part is ready at the lab we will know.</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
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</table>D.olivera1320http://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&diff=146005&oldid=prevD.olivera1320 at 02:01, 30 September 20142014-09-30T02:01:25Z<p></p>
<table style="background-color: white; color:black;">
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<td colspan='2' style="background-color: white; color:black;">Revision as of 02:01, 30 September 2014</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ2.png|center|650px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ2.png|center|650px]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The Figure below <del class="diffchange diffchange-inline">show</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The Figure below <ins class="diffchange diffchange-inline">shows how the system will behave if the positive feedback is added to the circuit. On the left is the response of <i> Sherlock coli </i> if the Psp3 protein is used as an activator. The chromoprotein concentration will be adequate for the system, but the increase is only about 100%. </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">On the other hand the response with TetA has a higher chromoprotein concentration and the increase when CAI is in the media is 12 times greater the initial concentration. This is exactly what we wanted!!! </ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test7.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test7.png|center|600px]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Now that we can see that the activator is actually being produced lets check how the response goes with this feedback.</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test8.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test8.png|center|600px]]</div></td></tr>
</table>D.olivera1320http://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&diff=145999&oldid=prevD.olivera1320 at 01:52, 30 September 20142014-09-30T01:52:59Z<p></p>
<table style="background-color: white; color:black;">
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<td colspan='2' style="background-color: white; color:black;">Revision as of 01:52, 30 September 2014</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>With this modification we can see that the systems takes 20 hours to react and after 30h the production of LuxO is completely on and LuxO* is almost zero, which is desirable, because we do not want any LuxO phosphorylated to turn on the Pqrr4 promoter. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>With this modification we can see that the systems takes 20 hours to react and after 30h the production of LuxO is completely on and LuxO* is almost zero, which is desirable, because we do not want any LuxO phosphorylated to turn on the Pqrr4 promoter. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>So far the model is working great, and all this part correspond to the parts registered by[ https://2011.igem.org/Team:Peking_S Peking 2011 Team]. But we are really interested in the response signal and we want to see if <i>S. coli </i> would be able to shows us when <i> V. cholerae </i> is in the media. Given that when CAI is in the media de Pqrr4 promoter turns off, we need an NOT logical gate to invert the transduction, so we used the pTet and TetR system. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>So far the model is working great, and all this part correspond to the parts registered by [https://2011.igem.org/Team:Peking_S Peking 2011 Team]. But we are really interested in the response signal and we want to see if <i>S. coli </i> would be able to shows us when <i> V. cholerae </i> is in the media. Given that when CAI is in the media de Pqrr4 promoter turns off, we need an NOT logical gate to invert the transduction, so we used the pTet and TetR system. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test5.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test5.png|center|600px]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ.png|center|650px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ.png|center|650px]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In order to have more options we also tried the system with another positive feedback: <b> Psp3 </b> with <b> pag </b> promoter from the [https://2009.igem.org/Team:Cambridge Cambridge 2009 Team]. In this case the activator and repressor have different DNA binding sites so the expression for the change in the response trough time would be: </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to have more options we also tried the system with another positive feedback: <b> Psp3 </b> with <b> pag </b> promoter from the [https://2009.igem.org/Team:Cambridge Cambridge 2009 Team]. In this case the activator and repressor have different DNA binding sites<ins class="diffchange diffchange-inline">, </ins>so the expression for the change in the response trough time would be: </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ2.png|center|650px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: EqJ2.png|center|650px]]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The Figure below show</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test7.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test7.png|center|600px]]</div></td></tr>
</table>D.olivera1320http://2014.igem.org/wiki/index.php?title=Team:Colombia/Deterministic&diff=145998&oldid=prevD.olivera1320 at 01:51, 30 September 20142014-09-30T01:51:52Z<p></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
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<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 01:51, 30 September 2014</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 113:</td>
<td colspan="2" class="diff-lineno">Line 113:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>With this modification we can see that the systems takes 20 hours to react and after 30h the production of LuxO is completely on and LuxO* is almost zero, which is desirable, because we do not want any LuxO phosphorylated to turn on the Pqrr4 promoter. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>With this modification we can see that the systems takes 20 hours to react and after 30h the production of LuxO is completely on and LuxO* is almost zero, which is desirable, because we do not want any LuxO phosphorylated to turn on the Pqrr4 promoter. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>So far the model is working great, and all this part correspond to the parts registered by Peking 2011 Team. But we are really interested in the response signal and we want to see if <i>S. coli </i> would be able to shows us when <i> V. cholerae </i> is in the media. Given that when CAI is in the media de Pqrr4 promoter turns off, we need an NOT logical gate to invert the transduction, so we used the pTet and TetR system. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>So far the model is working great, and all this part correspond to the parts registered by<ins class="diffchange diffchange-inline">[ https://2011.igem.org/Team:Peking_S </ins>Peking 2011 Team<ins class="diffchange diffchange-inline">]</ins>. But we are really interested in the response signal and we want to see if <i>S. coli </i> would be able to shows us when <i> V. cholerae </i> is in the media. Given that when CAI is in the media de Pqrr4 promoter turns off, we need an NOT logical gate to invert the transduction, so we used the pTet and TetR system. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test5.png|center|600px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File: Colombia_Test5.png|center|600px]]</div></td></tr>
</table>D.olivera1320