http://2009.igem.org/wiki/index.php?title=Team:Paris/Transduction_modeling&feed=atom&action=historyTeam:Paris/Transduction modeling - Revision history2024-03-28T18:39:29ZRevision history for this page on the wikiMediaWiki 1.16.5http://2009.igem.org/wiki/index.php?title=Team:Paris/Transduction_modeling&diff=159413&oldid=prevChristophe.R: /* The chemical equations */2009-10-21T23:22:19Z<p><span class="autocomment">The chemical equations</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The rest of the signal transduction pathway is described through a series of reactions listed below and shown on the diagram. To get more details on this description, please see our [https://2009.igem.org/Team:Paris/Transduction_modeling_The_Fec_Operon_as_used_in_our_system_:_chemical_equations_and_kinetics#bottom chemical equations description] page.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The rest of the signal transduction pathway is described through a series of reactions listed below and shown on the diagram. To get more details on this description, please see our [https://2009.igem.org/Team:Paris/Transduction_modeling_The_Fec_Operon_as_used_in_our_system_:_chemical_equations_and_kinetics#bottom chemical equations description] page.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Fec general.png|600px|center]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Fec general.png|600px|center]]</div></td></tr>
</table>Christophe.Rhttp://2009.igem.org/wiki/index.php?title=Team:Paris/Transduction_modeling&diff=156728&oldid=prevCChabbert: /* The chemical equations */2009-10-21T21:58:56Z<p><span class="autocomment">The chemical equations</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The rest of the signal transduction pathway is described through a series of reactions listed below and shown on the diagram. To get more details on this description, please see our [https://2009.igem.org/Team:Paris/Transduction_modeling_The_Fec_Operon_as_used_in_our_system_:_chemical_equations_and_kinetics#<del class="diffchange diffchange-inline">Kinetics_Equations </del>chemical equations description] page.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The rest of the signal transduction pathway is described through a series of reactions listed below and shown on the diagram. To get more details on this description, please see our [https://2009.igem.org/Team:Paris/Transduction_modeling_The_Fec_Operon_as_used_in_our_system_:_chemical_equations_and_kinetics#<ins class="diffchange diffchange-inline">bottom </ins>chemical equations description] page.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Fec general.png|600px|center]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Fec general.png|600px|center]]</div></td></tr>
</table>CChabberthttp://2009.igem.org/wiki/index.php?title=Team:Paris/Transduction_modeling&diff=156464&oldid=prevCChabbert at 21:49, 21 October 20092009-10-21T21:49:54Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li> [[Team:Paris/Transduction_modeling#1 | ^]]Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems H.Li & L.Petzold 2006 - [http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]</li></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><li> [[Team:Paris/Transduction_modeling#1 | ^]]Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems H.Li & L.Petzold 2006 - [http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]</li></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;"></del></div></td><td colspan="2"> </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;">==draft==</del></div></td><td colspan="2"> </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;">Our reception system uses the fec operon in order to transmit the signal received on the outer membrane via the vesicules into the cytoplasm to induce a response of the reception cells.</del></div></td><td colspan="2"> </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;">Once the vesicule has fusioned with the cell, the FecA molecule present on the previous vesicule wall activates the FecR molecule on the inner membrane ; then, the FecI molecule is activated and the pFec promoter is ON and transcription can start.</del></div></td><td colspan="2"> </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 plasmid of this reception cell was designed to produce a positive reaction once the signal is received so that, even with a very faint signal (very very few FecA molecules inside the vesicules), the reception population will be activated. To this end, we have placed the of FecR and the FecI coding downstream th epfec promoter. This way, once the first FecR and FecI molecules are produced, they take part in the activation of the pfec promoter thus creating a positive retroaction.</del></div></td><td colspan="2"> </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;">Our modelling study focussed on the description and analysis of this trancriptional cascade in order to caracterize the ability of the system to receive a signal. To this end, we tried to describe the system with elementary chemical equations allowing both deterministic and stochastic simulation runs.</del></div></td><td colspan="2"> </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;">To get more information on this study, please visit the following sections :</del></div></td><td colspan="2"> </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;">* [[Team:Paris/Transduction_modeling_The Fec Operon as used in our system : chemical equations and kinetics#Overview |The Fec Operon in our system ]] to read more about the chemical equations chosen to describe the system and the kinetics equations associated</del></div></td><td colspan="2"> </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;">* [[Team:Paris/Transduction_modeling_Deterministic and Stochastic Simulations#Overview |Deterministic and Stochastic Simulations]] to read more about the different simulations.</del></div></td><td colspan="2"> </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;">* [[Team:Paris/Transduction_modeling_Results and discussion#Overview | Results and discussion]] to learn more about the results of this study.</del></div></td><td colspan="2"> </td></tr>
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</table>CChabberthttp://2009.igem.org/wiki/index.php?title=Team:Paris/Transduction_modeling&diff=156440&oldid=prevCChabbert at 21:49, 21 October 20092009-10-21T21:49:02Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_modeling#bottom"> Introduction </a>|</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_modeling#bottom"> Introduction </a>|</div></td></tr>
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</table>CChabberthttp://2009.igem.org/wiki/index.php?title=Team:Paris/Transduction_modeling&diff=156352&oldid=prevCChabbert: /* Modeling the reception system: Fec operon */2009-10-21T21:45:53Z<p><span class="autocomment">Modeling the reception system: Fec operon</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As the number of molecules at stake can be very low at the beginning of the reception, we performed '''stochastic simulations''' based on the '''Gillespie algorithm''' to study the properties of our system <sup>[[https://2009.igem.org/Team:Paris/Transduction_modeling#References 1]]</sup><sup>[[https://2009.igem.org/Team:Paris/Transduction_modeling#References 2]]</sup><sup>[[https://2009.igem.org/Team:Paris/Transduction_modeling#References 3]]</sup></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>As the number of molecules at stake can be very low at the beginning of the reception, we performed '''stochastic simulations''' based on the '''Gillespie algorithm''' to study the properties of our system <sup>[[https://2009.igem.org/Team:Paris/Transduction_modeling#References 1]]</sup><sup>[[https://2009.igem.org/Team:Paris/Transduction_modeling#References 2]]</sup><sup>[[https://2009.igem.org/Team:Paris/Transduction_modeling#References 3]]</sup></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Stochastic simulations===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Stochastic simulations===</div></td></tr>
</table>CChabberthttp://2009.igem.org/wiki/index.php?title=Team:Paris/Transduction_modeling&diff=156336&oldid=prevCChabbert: /* Stochastic simulations */2009-10-21T21:45:25Z<p><span class="autocomment">Stochastic simulations</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>These values confirmed the significant variability of response times.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>These values confirmed the significant variability of response times.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Getting a robust reception===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Getting a robust reception===</div></td></tr>
</table>CChabberthttp://2009.igem.org/wiki/index.php?title=Team:Paris/Transduction_modeling&diff=156316&oldid=prevCChabbert: /* Getting a robust reception */2009-10-21T21:45:04Z<p><span class="autocomment">Getting a robust reception</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Therefore, our advice to the biologist would be to express FecR protein in receiving cells to ensure a robust and reliable reception of signal.'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Therefore, our advice to the biologist would be to express FecR protein in receiving cells to ensure a robust and reliable reception of signal.'''</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;"><a href="https://2009.igem.org/Team:Paris/Transduction_modeling#bottom"><img style="width:40px; height:40px;" src="https://static.igem.org/mediawiki/2009/1/10/Paris_Up.png"/></a></ins></div></td></tr>
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</table>CChabberthttp://2009.igem.org/wiki/index.php?title=Team:Paris/Transduction_modeling&diff=156254&oldid=prevCChabbert at 21:43, 21 October 20092009-10-21T21:43:16Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_modeling#bottom"> Introduction </a>|</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_modeling#bottom"> Introduction </a>|</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><a class="menu_sub"href="https://2009.igem.org/Team:Paris/<del class="diffchange diffchange-inline">Transduction_modeling_The Fec Operon as used in our system : chemical equations and kinetics</del>#<del class="diffchange diffchange-inline">bottom</del>"> Fec Operon</a>|</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><a class="menu_sub"href="https://2009.igem.org/Team:Paris/<ins class="diffchange diffchange-inline">Transduction_modeling</ins>#<ins class="diffchange diffchange-inline">Modeling_the_reception_system:_Fec_operon</ins>"> Fec Operon</a>|</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_modeling_Deterministic and Stochastic Simulations#bottom"> Deterministic and stochastic simulations</a>|</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_modeling_Deterministic and Stochastic Simulations#bottom"> Deterministic and stochastic simulations</a>|</div></td></tr>
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</table>CChabberthttp://2009.igem.org/wiki/index.php?title=Team:Paris/Transduction_modeling&diff=155600&oldid=prevCChabbert: /* The chemical equations */2009-10-21T21:22:13Z<p><span class="autocomment">The chemical equations</span></p>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The rest of the signal transduction pathway is described through a series of reactions listed below and shown on the diagram. To get more details on this description, please see our <del class="diffchange diffchange-inline">[</del>[https://2009.igem.org/Team:Paris/Transduction_modeling_The_Fec_Operon_as_used_in_our_system_:_chemical_equations_and_kinetics#Kinetics_Equations <del class="diffchange diffchange-inline">| </del>chemical equations description<del class="diffchange diffchange-inline">]</del>] page.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The rest of the signal transduction pathway is described through a series of reactions listed below and shown on the diagram. To get more details on this description, please see our [https://2009.igem.org/Team:Paris/Transduction_modeling_The_Fec_Operon_as_used_in_our_system_:_chemical_equations_and_kinetics#Kinetics_Equations chemical equations description] page.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Fec general.png|600px|center]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Fec general.png|600px|center]]</div></td></tr>
</table>CChabberthttp://2009.igem.org/wiki/index.php?title=Team:Paris/Transduction_modeling&diff=155579&oldid=prevCChabbert: /* The chemical equations */2009-10-21T21:21:21Z<p><span class="autocomment">The chemical equations</span></p>
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<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 rest of the signal transduction pathway is described through a series of reactions listed below and shown on the diagram. To get more details on this description, please see our <del class="diffchange diffchange-inline">????? </del>page.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The rest of the signal transduction pathway is described through a series of reactions listed below and shown on the diagram. To get more details on this description, please see our <ins class="diffchange diffchange-inline">[[https://2009.igem.org/Team:Paris/Transduction_modeling_The_Fec_Operon_as_used_in_our_system_:_chemical_equations_and_kinetics#Kinetics_Equations | chemical equations description]] </ins>page.</div></td></tr>
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</table>CChabbert