http://2013.igem.org/wiki/index.php?title=Team:TU-Delft/Timer-Sumo-KillSwitch&feed=atom&action=historyTeam:TU-Delft/Timer-Sumo-KillSwitch - Revision history2024-03-29T15:01:45ZRevision history for this page on the wikiMediaWiki 1.16.5http://2013.igem.org/wiki/index.php?title=Team:TU-Delft/Timer-Sumo-KillSwitch&diff=280089&oldid=prevJfkooijman at 17:48, 3 October 20132013-10-03T17:48:12Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Figure 1: Simulation Results</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Figure 1: Simulation Results</p></div></td></tr>
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</table>Jfkooijmanhttp://2013.igem.org/wiki/index.php?title=Team:TU-Delft/Timer-Sumo-KillSwitch&diff=278733&oldid=prevJfkooijman at 16:31, 3 October 20132013-10-03T16:31:47Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Figure 1: Circuit of the kill switch</p></div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Figure 1: Circuit of the kill switch</p></div></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>By this model, we are finding answers for the following questions:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>By this model, we are finding answers for the following questions:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Differential Equations</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Differential Equations</h2></div></td></tr>
</table>Jfkooijmanhttp://2013.igem.org/wiki/index.php?title=Team:TU-Delft/Timer-Sumo-KillSwitch&diff=278708&oldid=prevJfkooijman at 16:30, 3 October 20132013-10-03T16:30:41Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Figure 1: Circuit of the kill switch</p></div></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Figure 1: Circuit of the kill switch</p></div></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><ins style="color: red; font-weight: bold; text-decoration: none;">By this model, we are finding answers for the following questions:</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;"> <ol></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;"><li>How many minutes does the cell lysis take from the point of induction?</li></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;"><li>How much peptides are produced by the circuit?</li></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;"><li>How much peptides are still uncleaved by the SUMO at the point of cell lysis?</li></ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Differential Equations</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Differential Equations</h2></div></td></tr>
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</table>Jfkooijmanhttp://2013.igem.org/wiki/index.php?title=Team:TU-Delft/Timer-Sumo-KillSwitch&diff=265563&oldid=prevJfkooijman at 09:30, 2 October 20132013-10-02T09:30:07Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>So, for the three answers the sensitivity analysis is done, yielding the follow results and conclusions:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>So, for the three answers the sensitivity analysis is done, yielding the follow results and conclusions:</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li>The lysis time is not significantly affected by most parameters, only two are important. The degradation rate of cI has the most influence, the relative sensitivity is around 80&#37;. This is logical, because this is of major influence on the timer, as the timer is determined by the time cI takes to degrade. In the same way, the CcI, the expression rate of the cI promotor also influences the lysis time. The cpconst also has a significant influence, a relative sensitivity of around &#37;, which is explained by the fact that the expression rate changes the speed of the production of anti-holin and thus the lysis time. What is interesting is that the dimerization parameters do not hold a major influence, as well as the degradation rates of holin and anti-holin.</li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li>The lysis time is not significantly affected by most parameters, only two are important. The degradation rate of cI has the most influence, the relative sensitivity is around 80&#37;. This is logical, because this is of major influence on the timer, as the timer is determined by the time cI takes to degrade. In the same way, the CcI, the expression rate of the cI promotor also influences the lysis time. The cpconst also has a significant influence, a relative sensitivity of around <ins class="diffchange diffchange-inline">40</ins>&#37;, which is explained by the fact that the expression rate changes the speed of the production of anti-holin and thus the lysis time. What is interesting is that the dimerization parameters do not hold a major influence, as well as the degradation rates of holin and anti-holin.</li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>The total amount of produced peptide is influenced by almost every parameter. The most significant ones are the expression strength of the T7 promoter and the degradation rate of the mRNA, both having a relative sensitivity of over 100&#37;. The T7 promoter strength directly influences the amount of produced SUMO-peptides, thereby the amount of peptides. The mRNA degradation rate influences all the degradations in the system, also the SUMO-peptide production. Furthermore, the parameters found in the previous item, affecting the lysis time, also have a firm influence, over 50&#37;. This is explained by the fact that if the lysis time increases, the circuit has more time to produce the peptides.</li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>The total amount of produced peptide is influenced by almost every parameter. The most significant ones are the expression strength of the T7 promoter and the degradation rate of the mRNA, both having a relative sensitivity of over 100&#37;. The T7 promoter strength directly influences the amount of produced SUMO-peptides, thereby the amount of peptides. The mRNA degradation rate influences all the degradations in the system, also the SUMO-peptide production. Furthermore, the parameters found in the previous item, affecting the lysis time, also have a firm influence, over 50&#37;. This is explained by the fact that if the lysis time increases, the circuit has more time to produce the peptides.</li></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>The amount of uncleaved peptide is also influenced by a lot of parameters, however the relative sensitivity is always below 200&#37;. This might seem a lot, but the concentration is virtually zero thus these influences can be neglected. It is safe to say that except for very large changes, the conclusion will hold that there is almost no uncleaved peptide.</li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>The amount of uncleaved peptide is also influenced by a lot of parameters, however the relative sensitivity is always below 200&#37;. This might seem a lot, but the concentration is virtually zero thus these influences can be neglected. It is safe to say that except for very large changes, the conclusion will hold that there is almost no uncleaved peptide.</li></div></td></tr>
</table>Jfkooijmanhttp://2013.igem.org/wiki/index.php?title=Team:TU-Delft/Timer-Sumo-KillSwitch&diff=133149&oldid=prevDimitra at 09:51, 18 September 20132013-09-18T09:51:07Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Variables</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Variables</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The variables used are the same as in the separated modules(<a href="https://2013.igem.org/Team:TU-Delft/Timer_Plus_Sumo#variables" target="blank" >TimerPlusSumo</a>).The one added in the combined model can be seen below: </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The variables used are the same as in the separated modules(<a href="https://2013.igem.org/Team:TU-Delft/Timer_Plus_Sumo#variables" target="blank" >TimerPlusSumo</a><ins class="diffchange diffchange-inline">,<a href="https://2013.igem.org/Team:TU-Delft/KillSwitch#variables2" target="blank">KillSwitch</a> </ins>).The one added in the combined model can be seen below: </div></td></tr>
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</table>Dimitrahttp://2013.igem.org/wiki/index.php?title=Team:TU-Delft/Timer-Sumo-KillSwitch&diff=133136&oldid=prevDimitra at 09:45, 18 September 20132013-09-18T09:45:59Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Timer-SUMO-KillSwitch</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Timer-SUMO-KillSwitch</h2></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><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align="justify">The separate modules: <a href="https://2013.igem.org/Timer_Plus_Sumo">Timer plus SUMO </a> and <a href="https://2013.igem.org/KillSwitch">Kill Switch</a> are combined to form the complete model of the system: Timer - SUMO - Kill Switch. For the final model, the kill switch module is converted in such a way so as the holin and antiholin to be activated by the Pci promoter.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p align="justify">The separate modules: <a href="https://2013.igem.org/Timer_Plus_Sumo">Timer plus SUMO </a> and <a href="https://2013.igem.org/KillSwitch">Kill Switch</a> are combined to form the complete model of the system: Timer - SUMO - Kill Switch. For the final model, the kill switch module is converted in such a way so as the holin and antiholin to be activated by the Pci promoter.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Variables</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Variables</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The variables used are the same as in the separated modules.The one added in the combined model can be seen below: </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The variables used are the same as in the separated modules<ins class="diffchange diffchange-inline">(<a href="https://2013.igem.org/Team:TU-Delft/Timer_Plus_Sumo#variables" target="blank" >TimerPlusSumo</a>)</ins>.The one added in the combined model can be seen below: </div></td></tr>
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</table>Dimitrahttp://2013.igem.org/wiki/index.php?title=Team:TU-Delft/Timer-Sumo-KillSwitch&diff=133066&oldid=prevDimitra at 09:12, 18 September 20132013-09-18T09:12:37Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Variables</h2></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><h2 align="center">Variables</h2></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The variables used are the same as in the separated modules.The one added in the combined model can be seen below </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The variables used are the same as in the separated modules.The one added in the combined model can be seen below<ins class="diffchange diffchange-inline">: </ins></div></td></tr>
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</table>Dimitrahttp://2013.igem.org/wiki/index.php?title=Team:TU-Delft/Timer-Sumo-KillSwitch&diff=133065&oldid=prevDimitra at 09:11, 18 September 20132013-09-18T09:11:57Z<p></p>
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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">br</del>></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><<ins class="diffchange diffchange-inline">html</ins>></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><ins class="diffchange diffchange-inline"><h2 align="center">Variables</h2></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 class="diffchange diffchange-inline">The variables used are the same as in the separated modules.The one added in the combined model can be seen below </ins></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><ins class="diffchange diffchange-inline">|'''Variable'''</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 class="diffchange diffchange-inline">|'''Description'''</ins></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><ins class="diffchange diffchange-inline">|Pep<sub>m</sub></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 class="diffchange diffchange-inline">|concentration of translated peptide</ins></div></td></tr>
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</table>Dimitrahttp://2013.igem.org/wiki/index.php?title=Team:TU-Delft/Timer-Sumo-KillSwitch&diff=133045&oldid=prevJfkooijman at 08:57, 18 September 20132013-09-18T08:57:31Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To asses the validity of the found answers a sensitivity analysis is performed. In this case the numerical derivative of the solution is taken with respect to the parameters of the model. This derivative represents the change of the solution upon changing the specific parameter. If this change is large, the solution is very sensitive for this parameter. Also, since the solution is highly non-linear this numerical derivative is taken in both directions, as they differ greatly in this model. To compare the found values of the derivative, they are normalized by the nominal value (the solution, e.g. the lyse time). In this way a percentual change is found. Mathematically this can be expressed as:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>To asses the validity of the found answers a sensitivity analysis is performed. In this case the numerical derivative of the solution is taken with respect to the parameters of the model. This derivative represents the change of the solution upon changing the specific parameter. If this change is large, the solution is very sensitive for this parameter. Also, since the solution is highly non-linear this numerical derivative is taken in both directions, as they differ greatly in this model. To compare the found values of the derivative, they are normalized by the nominal value (the solution, e.g. the lyse time). In this way a percentual change is found. Mathematically this can be expressed as:</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><ins style="color: red; font-weight: bold; text-decoration: none;"><p>Figure 2: Equation of the relative sensitivity of s with respect to the parameter pi, note that sn is the nominal value of s. As an example the equation of the lysis time is written out.</p></ins></div></td></tr>
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</table>Jfkooijmanhttp://2013.igem.org/wiki/index.php?title=Team:TU-Delft/Timer-Sumo-KillSwitch&diff=133026&oldid=prevJfkooijman at 08:45, 18 September 20132013-09-18T08:45:44Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>The lysis time is not significantly affected by most parameters, only two are important. The degradation rate of cI has the most influence, the relative sensitivity is around 80&#37;. This is logical, because this is of major influence on the timer, as the timer is determined by the time cI takes to degrade. In the same way, the CcI, the expression rate of the cI promotor also influences the lysis time. The cpconst also has a significant influence, a relative sensitivity of around &#37;, which is explained by the fact that the expression rate changes the speed of the production of anti-holin and thus the lysis time. What is interesting is that the dimerization parameters do not hold a major influence, as well as the degradation rates of holin and anti-holin.</li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li>The lysis time is not significantly affected by most parameters, only two are important. The degradation rate of cI has the most influence, the relative sensitivity is around 80&#37;. This is logical, because this is of major influence on the timer, as the timer is determined by the time cI takes to degrade. In the same way, the CcI, the expression rate of the cI promotor also influences the lysis time. The cpconst also has a significant influence, a relative sensitivity of around &#37;, which is explained by the fact that the expression rate changes the speed of the production of anti-holin and thus the lysis time. What is interesting is that the dimerization parameters do not hold a major influence, as well as the degradation rates of holin and anti-holin.</li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li>The total amount of produced peptide is influenced by almost every parameter. The most significant ones are the expression strength of the T7 promoter and the degradation rate of the mRNA, both having a relative sensitivity of over 100&#37;. </li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li>The total amount of produced peptide is influenced by almost every parameter. The most significant ones are the expression strength of the T7 promoter and the degradation rate of the mRNA, both having a relative sensitivity of over 100&#37;<ins class="diffchange diffchange-inline">. The T7 promoter strength directly influences the amount of produced SUMO-peptides, thereby the amount of peptides. The mRNA degradation rate influences all the degradations in the system, also the SUMO-peptide production. Furthermore, the parameters found in the previous item, affecting the lysis time, also have a firm influence, over 50&#37;. This is explained by the fact that if the lysis time increases, the circuit has more time to produce the peptides</ins>.</li></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><li>The amount of uncleaved peptide is also influenced by a lot of parameters, however the relative sensitivity is always below 200&#37;. This might seem a lot, but the concentration is virtually zero thus these influences can be neglected. It is safe to say that except for very large changes, the conclusion will hold that there is almost no uncleaved peptide. <del class="diffchange diffchange-inline"> </del></li></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><li>The amount of uncleaved peptide is also influenced by a lot of parameters, however the relative sensitivity is always below 200&#37;. This might seem a lot, but the concentration is virtually zero thus these influences can be neglected. It is safe to say that except for very large changes, the conclusion will hold that there is almost no uncleaved peptide.</li></div></td></tr>
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