Team:KULeuven/Zandbak/Global


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  Home   The Team Research Labs and Groups Students Instructors</a> Advisors</a> Pictures</a> </li>  The Project</a> Summary</a> Components</a> Input</a> Output</a> Filter</a> Invertimer</a> Reset</a> Cell Death</a> Memory</a> End Evaluation</a> Literature</a> Brainstorm</a> </li> <li> <a>Ethics</a>

</li> <li> <a>Submitted Parts</a> <a href="http://2008.igem.org/Team:KULeuven/Parts">Listing</a> <a href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2008&group=KULeuven">Sandbox</a> </li> <li> <a>Modeling</a> <a href="http://2008.igem.org/Team:KULeuven/Model/Overview">Overview</a> <a href="http://2008.igem.org/Team:KULeuven/Model/KineticConstants">Kinetic Constants</a> <a>Components</a> <a href="http://2008.igem.org/Team:KULeuven/Model/Output">Output</a> <a href="http://2008.igem.org/Team:KULeuven/Model/Filter">Filter</a> <a href="http://2008.igem.org/Team:KULeuven/Model/Inverter">Invertimer</a> <a href="http://2008.igem.org/Team:KULeuven/Model/Reset">Reset</a> <a href="http://2008.igem.org/Team:KULeuven/Model/CellDeath">Cell Death</a> <a href="http://2008.igem.org/Team:KULeuven/Model/Memory">Memory</a> <a href="http://2008.igem.org/Team:KULeuven/Model/FullModel">Full Model</a> <a href="http://2008.igem.org/Team:KULeuven/Model/Sensitivity">Sensitivity Analysis</a> <a href="http://2008.igem.org/Team:KULeuven/Model/MultiCell">Multi-cell Model</a> <a href="http://2008.igem.org/Team:KULeuven/Model/Diffusion">Diffusion</a> </li> <li> <a>Data Analysis</a> <a href="http://2008.igem.org/Team:KULeuven/Data/Overview">Overview</a> <a>New Parts</a> <a href="http://2008.igem.org/Team:KULeuven/Data/GFP">GFP (LVA-tag)</a> <a href="http://2008.igem.org/Team:KULeuven/Data/T7">T7 (UmuD-tag)</a> <a href="http://2008.igem.org/Team:KULeuven/Data/Antisense">Antisense LuxI</a> <a href="http://2008.igem.org/Team:KULeuven/Data/ccdB">Celldeath (ccdB)</a> <a href="http://2008.igem.org/Team:KULeuven/Data/HybridProm">Hybrid Promotor</a> <a>Components</a> <a href="http://2008.igem.org/Team:KULeuven/Data/Input">Input</a> <a href="http://2008.igem.org/Team:KULeuven/Data/Output">Output</a> <a href="http://2008.igem.org/Team:KULeuven/Data/Filter">Filter</a> <a href="http://2008.igem.org/Team:KULeuven/Data/Inverter">Invertimer</a> <a href="http://2008.igem.org/Team:KULeuven/Data/Reset">Reset</a> <a href="http://2008.igem.org/Team:KULeuven/Data/CellDeath">Cell Death</a> <a href="http://2008.igem.org/Team:KULeuven/Data/Memory">Memory</a> <a href="http://2008.igem.org/Team:KULeuven/Data/FullModel">Full Model</a> </li> <li> <a>Software</a> <a href="http://2008.igem.org/Team:KULeuven/Software/MultiCell">Multi-cell Toolbox</a> <a href="http://2008.igem.org/Team:KULeuven/Software/Simbiology2LaTeX">Simbiology2LaTeX Toolbox</a> </li> <li> <a>Notebook</a> <a href="http://2008.igem.org/Team:KULeuven/Meeting_Calendar">Calendar</a> <a href="http://2008.igem.org/Team:KULeuven/SummerHolidays">Summer Holidays</a> <a>Reports</a> <a href="http://2008.igem.org/Team:KULeuven/Meeting Reports">Daily</a> <a href="http://2008.igem.org/Team:KULeuven/Weekly Meetings">Weekly</a> <a>Lab Data</a> <a href="http://2008.igem.org/Team:KULeuven/Freezer">Freezer</a> <a href="http://2008.igem.org/Team:KULeuven/Primers">Primers</a> <a href="http://2008.igem.org/Team:KULeuven/Ligation">Ligation</a> <a href="http://2008.igem.org/Team:KULeuven/Tools">Tools</a> <a href="http://2008.igem.org/Team:KULeuven/Press">Press</a> <a href="http://2008.igem.org/Team:KULeuven/Guestbook">Guestbook</a> </li> </ul>



Input
Searching for an input signal that was easily turned on and off, we chose to use the light-sensing device BBa_M30109. This device has already been used by a number of teams, but for the sake of completeness, we describe it here again. We also gave it our own (working) number: BBa_K145011.

Components
The first step is to produce ho1 (heme oxigenase 1) that converts heme to biliverdin IXalpha. This enzyme is encoded by BBa_I15008. The second step is to produce PcyA (phycocyanobilin:ferredoxin oxidoreductase) that converts the biliverdin IXalpha to phycocyanobilin. This enzyme is encoded by BBa_I15009. This phycocyanobilin associates with the light receptive domain Cph1 of a Cph1/EnvZ fusion protein, encoded by BBa_I15010.

An extra need for the input mechanism is the presence of the TetR repressor. This molecule is encoded by part BBa_C0040, and contains an LVA tag for rapid degradation. testing environment

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Action
The ho1 and PcyA coding parts are placed under a Pbad promoter (BBa_I13453). As the AraC repressor is present in the cell, phycocyanobilin will only be made upon activation with arabinose. The coding part for the Cph1/EnvZ fusion protein is placed under control of a pTet promoter (BBa_R0040). This means that, as TetR (BBa_C0040), the Tet repressor, is present, the fusion protein will only be produced when aTc is added to the medium. This gives us the possibility to test the system with an exogenous memory instead of the endogenous one, which will then be added later on in the project (see here).

Test
The Cph1 part of the Cph1/EnvZ fusion protein acts as the light sensor, the EnvZ part is a kinase. Upon radiation with 660nm (red) light, the fusion protein gets dephosphorylated. This renders the kinase in an inactive state. The active kinase phosphorylates the molecule OmpR. A high concentration of the phosphorylated ompR represses the OmpF promoter (BBa_R0084). A lower concentration activates it. So when 660nm light is irradiated on the input mechanism, the concentration of phosphorylated OmpR drops and the OmpF promoter is turned on.