"
Team:Freiburg Bioware/Modelling
From 2010.igem.org
(Difference between revisions)
| Line 18: | Line 18: | ||
<h3>Reaction Scheme</h3> | <h3>Reaction Scheme</h3> | ||
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> | 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> | ||
| - | The plasmids are transported into the nucleus where gene expression is initiated. Processed mRNA is transported into the cytoplasm and proteins 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 single stranded DNA (<i>ssDNA</i>) is encapsidated into the preformed capsids forming infectious viral particles (<i>V</i>).<br> | + | 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> |
| - | + | Finally the recombinant viruses are released into the extracellular matrix and can be harvested for transduction.<br> | |
| - | + | ||
| - | + | ||
| - | + | ||
Revision as of 16:22, 21 October 2010
Modeling
For the modeling part we considered three main parts:- the virus production
- the infection of a target cell
- the therapy
Model for Virus Production
Reaction Scheme
Reducing the complexity of virus production we divide the cell into three compartments: the extracellular matrix (all quantities with the index ext), the cytoplasm (cyt) and the nucleus (nuc). Four plasmids are transfected - the plasmid coding for the helper proteins (helper), the gene of interest (goi) and two types of plasmids coding for the capsid proteins (capwt [wild type], capmod [modified]).The plasmids are transported into the nucleus where gene expression is initiated. Processed mRNA is transported into the cytoplasm and proteins (phelper, pcapwt, pcapmod) 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 single stranded DNA (ssDNA) is encapsidated into the preformed capsids (capsid) forming infectious viral particles (V).
Finally the recombinant viruses are released into the extracellular matrix and can be harvested for transduction.
Reduced Reaction Scheme
Differential Equations
Model for Virus Infection
Reaction Scheme
Reduced Reaction Scheme
Differential Equations
