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<div class="row"><div class="col-xs-12"> | <div class="row"><div class="col-xs-12"> | ||
− | <p><table> | + | <div style="text-align:center;"><object class="highlighted-image" data="https://static.igem.org/mediawiki/2017/archive/f/fd/20171030103312%21T--SDU-Denmark--modelling-graph-dormancy_variation.svg" type="image/svg+xml" style="width:100%;"></object></div><br> |
− | + | <div style="text-align:center;"><object class="highlighted-image" data="https://static.igem.org/mediawiki/2017/4/47/T--SDU-Denmark--Flow-celle2.svg" type="image/svg+xml" style="width:100%;"></object></div> | |
+ | |||
+ | <p> | ||
+ | <table> | ||
+ | <tr> | ||
<th>Constant</th> | <th>Constant</th> | ||
<th>Identifier</th> | <th>Identifier</th> | ||
<th>Units</th> | <th>Units</th> | ||
<th>Value</th> | <th>Value</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>mrna transcription rate<span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span></th> | ||
+ | <td>α<sub>0</sub></th> | ||
+ | <td>1/min</th> | ||
+ | <td>154.665</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>mrna half life<span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span></th> | ||
+ | <td>τ<sub>m</sub></th> | ||
+ | <td>min</th> | ||
+ | <td>7.2</th> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
− | <td> | + | <td>RelB half life<span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span><span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812701/">Overgaard M., Borch J., Gerdes K. RelB and RelE of Escherichia coli form a tight complex that represses transcription via the ribbon-helix-helix motif in RelB. J. Mol. Biol. 2009;394:183–196. doi: 10.1016/j.jmb.2009.09.006</a></span></span></th> |
− | <td>& | + | <td>τ<sub>B</sub></th> |
− | <td> | + | <td>min</th> |
− | <td> | + | <td>4.3</th> |
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>RelE half life<span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span></th> | ||
+ | <td>τ<sub>E</sub></th> | ||
+ | <td>min</th> | ||
+ | <td>43 (growing)<br> 2000 (dormant)</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Bound RelB half life<span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span><span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812701/">Overgaard M., Borch J., Gerdes K. RelB and RelE of Escherichia coli form a tight complex that represses transcription via the ribbon-helix-helix motif in RelB. J. Mol. Biol. 2009;394:183–196. doi: 10.1016/j.jmb.2009.09.006</a></span></span></th> | ||
+ | <td>τ<sub>c</sub></th> | ||
+ | <td>min</th> | ||
+ | <td>17</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>RelB transcription rate<span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span></th> | ||
+ | <td><i>trans</i><sub>B</sub></th> | ||
+ | <td>1/min</th> | ||
+ | <td>15</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>RelE transcription rate<span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span></th> | ||
+ | <td><i>trans</i><sub>E</sub></th> | ||
+ | <td>1/min</th> | ||
+ | <td>0.3</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Binding rate<span class="reference"><span class="referencetext">Sneppen K, Zocchi G. Physics in Molecular Biology. Cambridge, UK: Cambridge University Press; 2005.</span></span></th> | ||
+ | <td>k <sub>b</sub></th> | ||
+ | <td>1/min</th> | ||
+ | <td>3.8</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Dissociation rate B<sub>2</sub>E<span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pubmed/18532983">Overgaard, M., Borch, J., Jørgensen, M. G. and Gerdes, K. (2008), Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Molecular Microbiology, 69: 841–857. doi:10.1111/j.1365-2958.2008.06313.x</a></span></span></th> | ||
+ | <td>K<sub>D</sub> (B<sub>2</sub>E)</th> | ||
+ | <td>molecules</th> | ||
+ | <td>0.3</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Dissociation rate B<sub>2</sub>E<sub>2</sub><span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pubmed/18532983">Overgaard, M., Borch, J., Jørgensen, M. G. and Gerdes, K. (2008), Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity. Molecular Microbiology, 69: 841–857. doi:10.1111/j.1365-2958.2008.06313.x</a></span></span></th> | ||
+ | <td> K<sub>D</sub>(B<sub>2</sub>E<sub>2</sub>)</th> | ||
+ | <td>molecules</th> | ||
+ | <td>0.3</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Dissociation rate O.B<sub>f</sub><span class="reference"><span class="referencetext"><a target="blank" href="http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.1998.00993.x/abstract">Gotfredsen, M. and Gerdes, K. (1998), The Escherichia coli relBE genes belong to a new toxin–antitoxin gene family. Molecular Microbiology, 29: 1065–1076. doi:10.1046/j.1365-2958.1998.00993.x</a></span></span><span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span></th> | ||
+ | <td>K<sub>D1</sub></th> | ||
+ | <td>molecules</th> | ||
+ | <td>10</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Dissociation rate O.B<sub>2</sub>E<span class="reference"><span class="referencetext"><a target="blank" href="http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.1998.00993.x/abstract">Gotfredsen, M. and Gerdes, K. (1998), The Escherichia coli relBE genes belong to a new toxin–antitoxin gene family. Molecular Microbiology, 29: 1065–1076. doi:10.1046/j.1365-2958.1998.00993.x</a></span></span><span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span></th> | ||
+ | <td> K<sub>D2</sub></th> | ||
+ | <td>molecules</th> | ||
+ | <td>0.04</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Dissociation rate O.(B<sub>2</sub>E)<sub>2</sub><span class="reference"><span class="referencetext"><a target="blank" href="http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.1998.00993.x/abstract">Gotfredsen, M. and Gerdes, K. (1998), The Escherichia coli relBE genes belong to a new toxin–antitoxin gene family. Molecular Microbiology, 29: 1065–1076. doi:10.1046/j.1365-2958.1998.00993.x</a></span></span><span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span></th> | ||
+ | <td> K<sub>D3</sub></th> | ||
+ | <td>molecules</th> | ||
+ | <td>30</th> | ||
+ | </tr> | ||
+ | |||
+ | <tr> | ||
+ | <td>Cleavage rate<span class="reference"><span class="referencetext"><a target="blank" href="http://www.sciencedirect.com/science/article/pii/S0092867402012485?">Pedersen K, et al. The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell. 2003;112:131–140. doi: 10.1016/S0092-8674(02)01248-5</a></span></span> | ||
+ | <span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span></th> | ||
+ | <td> k<sub>c</sub></th> | ||
+ | <td>1/min 1/molecules</th> | ||
+ | <td>2.0</th> | ||
</tr> | </tr> | ||
</table> | </table> | ||
+ | |||
</p><br> | </p><br> | ||
<p> In order to find the best way to implement the toxin-antitoxin system, we resort to modelling. We use the <span class="btn-link btn-lg" data-toggle="modal" data-target="#gillespie-algorithm">gillespie algorithm</span> to model the interactions of the <span class="btn-link btn-lg" data-toggle="modal" data-target="#toxin-antitoxin-system">toxin antitoxin system</span>.<br> | <p> In order to find the best way to implement the toxin-antitoxin system, we resort to modelling. We use the <span class="btn-link btn-lg" data-toggle="modal" data-target="#gillespie-algorithm">gillespie algorithm</span> to model the interactions of the <span class="btn-link btn-lg" data-toggle="modal" data-target="#toxin-antitoxin-system">toxin antitoxin system</span>.<br> | ||
+ | <span class="btn-link btn-lg" data-target="#https://static.igem.org/mediawiki/2017/1/1e/Matlab-scripts_SDU.zip">toxin antitoxin system</span>.<br> | ||
<object class="highlighted-image" data="https://static.igem.org/mediawiki/2017/6/61/T--SDU-Denmark--modelling-figure-2-rele-relb.svg" type="image/svg+xml" style="width:100%;"></object> | <object class="highlighted-image" data="https://static.igem.org/mediawiki/2017/6/61/T--SDU-Denmark--modelling-figure-2-rele-relb.svg" type="image/svg+xml" style="width:100%;"></object> | ||
We find that when we implement enhanced relE production as a tool to make the bacteria dormant, an additional implementation of relB to ensure don’t stay dormant when in light again. | We find that when we implement enhanced relE production as a tool to make the bacteria dormant, an additional implementation of relB to ensure don’t stay dormant when in light again. | ||
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</ol> | </ol> | ||
<p>For each time step two things are calculated, using the random number generator: The time before next reaction and which reaction occurs. | <p>For each time step two things are calculated, using the random number generator: The time before next reaction and which reaction occurs. | ||
− | The time before next step is given by <br> | + | The time before next step is given by </p><br> |
− | < | + | |
+ | <div style="text-align:center;"><p> Hello Emil</p></div><br> | ||
+ | |||
+ | <p> | ||
Where S is the sum of the reaction rates and r1 is a random number between 0 and 1. This gives the time as if the system was one reaction with reaction rate S, using the random number to give a statistic distribution. | Where S is the sum of the reaction rates and r1 is a random number between 0 and 1. This gives the time as if the system was one reaction with reaction rate S, using the random number to give a statistic distribution. | ||
The reaction is chosen proportionally to each individual reaction rate, using another random number. This way, reaction with high rates compared to other reactions will happen the most. | The reaction is chosen proportionally to each individual reaction rate, using another random number. This way, reaction with high rates compared to other reactions will happen the most. | ||
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<span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span>. | <span class="reference"><span class="referencetext"><a target="blank" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3413109/">Cataudella I., Trusina A., Sneppen K., Gerdes K., Mitarai N. Conditional cooperativity in toxin-antitoxin regulation prevents random toxin activation and promotes fast translational recovery. Nucleic Acids Res. 2012;40:6424–6434. doi: 10.1093/nar/gks297</a></span></span>. | ||
</p><br> | </p><br> | ||
− | <object class="highlighted-image" data="https://static.igem.org/mediawiki/2017/ | + | <object class="highlighted-image" data="https://static.igem.org/mediawiki/2017/c/c5/T--SDU-Denmark--Flow-celle1.svg" type="image/svg+xml" style="width:100%;"></object> |
Latest revision as of 23:01, 1 November 2017