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| - | {{:Team:Freiburg_Bioware/Head}}
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| - | {{:Team:Freiburg_Bioware/menu_modelling}}
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| - | <html>
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| - | <h1>Modeling</h1>
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| - | For the modeling part we considered three main parts:
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| - | <ul>
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| - | <li>the virus production
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| - | <li>the infection of a target cell
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| - | <li>the therapy
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| - | </ul>
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| - | For the first two models we assumed reactions according to the law of mass action to create a model of ordinary differential equations (ODE).
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| - | <br><br>
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| - | <h2>Model for Virus Production</h2>
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| - | <br>
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| - | <h3>Reaction Scheme</h3>
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| - | Reducing the complexity of virus production we divide the cell into three compartments: the <b>extracellular matrix</b> (all quantities with the index <i>ext</i>), the <b>cytoplasm</b> (<i>cyt</i>) and the <b>nucleus</b> (<i>nuc</i>). Four plasmids are transfected - the plasmid coding for the <b>helper proteins</b> (<i>helper</i>), the <b>gene of interest</b> (<i>goi</i>) and two types of plasmids coding for the <b>capsid proteins</b> (<i>capwt</i> [wild type], <i>capmod</i> [modified]).<br>
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| - | The plasmids are transported into the nucleus where gene expression is initiated. Processed mRNA is transported into the cytoplasm and <b>proteins</b> (<i>phelper</i>, <i>pcapwt</i>, <i>pcapmod</i>) are produced. Containing a nuclear localization sequence proteins are relocated into the nucleus where capsid assembly occurs. The gene of interest is replicated by cellular polymerases and <b>single stranded DNA</b> (<i>ssDNA</i>) is encapsidated into the preformed <b>capsids</b> (<i>capsid</i>) forming infectious viral particles (<i>V</i>).<br>
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| - | Finally the recombinant viruses are released into the extracellular matrix and can be harvested for transduction.<br>
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| - | <center>
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| - | <img width="733" height="966" src="https://static.igem.org/mediawiki/2010/b/b8/Freiburg10_VirusProduction01.png" alt="Reaction scheme for the virus production" />
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| - | </center>
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| - | <br><br>
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| - | <h3>Reduced Reaction Scheme</h3>
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| - | <center>
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| - | <img width="733" height="643" src="https://static.igem.org/mediawiki/2010/6/68/Freiburg10_VirusProduction02.png" alt="reduced reaction scheme for the virus production" />
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| - | </center>
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| - | <br><br>
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| - | <h3>Differential Equations</h3>
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| - | <center>
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| - | <img width="739" height="899" src="https://static.igem.org/mediawiki/2010/2/24/Freiburg10_VirusProduction03.png" alt="Reaction scheme for the virus production" />
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| - | </center>
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| - |
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| - | <br><br>
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| - | <h2>Model for Virus Infection</h2>
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| - | <br><br>
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| - | <h3>Reaction Scheme</h3>
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| - | <center>
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| - | <img width="359" height="335" src="https://static.igem.org/mediawiki/2010/9/90/Freiburg10_VirusInfection01.png" alt="Reaction scheme for the virus production" />
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| - | </center>
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| - | <br><br>
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| - | <h3>Reduced Reaction Scheme</h3>
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| - | <center>
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| - | <img width="359" height="227" src="https://static.igem.org/mediawiki/2010/8/83/Freiburg10_VirusInfection02.png" alt="Reaction scheme for the virus production" />
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| - | </center>
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| - | <br><br>
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| - | <center>
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| - | <img width="429" height="134" src="https://static.igem.org/mediawiki/2010/3/3f/Freiburg10_VirusInfection03.png" alt="Reaction scheme for the virus production" />
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| - | </center>
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| - | <br><br>
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| - |
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| - | <h3>Differential Equations</h3>
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| - | <center>
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| - | <img width="655" height="314" src="https://static.igem.org/mediawiki/2010/8/85/Freiburg10_VirusInfection04.png" alt="Reaction scheme for the virus production" />
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| - | </center>
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| - | <br><br>
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| - | <center>
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| - | <img width="800" height="285" src="https://static.igem.org/mediawiki/2010/8/84/Freiburg10_VirusInfection05.png" alt="Reaction scheme for the virus production" />
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| - | </center>
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| - |
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| - | </html>
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| - | {{:Team:Freiburg_Bioware/Footer}}
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