Team:NTNU-Trondheim/Model
From 2013.igem.org
Line 67: | Line 67: | ||
<p> | <p> | ||
- | + | The Pm/Xyls promotor system is a positive regulator system where the regulator molcule, Xyls, is constitutivly produced. When Xyls binds to the inducer m-toluic acid this complex binds to the Pm promotor(see figure 1). Binding to the promotor facilitates binding of RNA polymerase (RNAp) making it active (RNApA). This starts production of mRNA in an elongation step. The mRNA will be translated into the recombinant protein, or in our case, RFP. Over time mRNA and RFP will be degraded to som extent.</p> <br><br> | |
- | + | <div class="col4" style="background-color:white;><a href="https://static.igem.org/mediawiki/2013/d/d1/Modelpic.jpg"> <img src="https://static.igem.org/mediawiki/2013/d/d1/Modelpic.jpg" width="303"> | |
+ | <p style="text-align:center; color:black; "> Figure: Overview of how the Pm/Xyls Promotor system funtions. Production of recombinant protein is dependent on access to the indicer m-toluic acid.</p> </div> | ||
+ | <br> | ||
+ | </p> | ||
+ | <div class ="row-end"> </div> | ||
+ | </div> | ||
- | |||
- | |||
- | The reaction equations in the Pm/Xyls promotor system are listed below. The degradation of mRNA and RFP will inhibit an exponential production of these and after time the levels of mRNA and RFP will stabilize around a steady state. | + | <p>The reaction equations in the Pm/Xyls promotor system are listed below. The degradation of mRNA and RFP will inhibit an exponential production of these and after time the levels of mRNA and RFP will stabilize around a steady state.</p><br><br> |
- | < | + | <div class="col4" style="background-color:white;><a href="https://static.igem.org/mediawiki/2013/c/c6/Modeleq.jpg"> <img src="https://static.igem.org/mediawiki/2013/c/c6/Modeleq.jpg" width="303"> |
+ | <p style="text-align:center; color:black; "> Figure:</p> </div> | ||
+ | <br> | ||
+ | </p> | ||
+ | <div class ="row-end"> </div> | ||
+ | </div> | ||
- | |||
- | |||
- | + | A deterministic simulation of the system was run on <a href="http://cain.sourceforge.net/">Cain software</a> with the parameters as viewed in figure 2. Only the number/consentration of the inducer was varieted. A .zip file with all of the modeling files can be downloaded [[Media:NTNU_Trondheim_modelingfiles.zip|here]]. The csv files are named according to the number of inducer that was applied in the deterministic simulation.<br><br> | |
+ | <div class="col4" style="background-color:white;><a href="https://static.igem.org/mediawiki/2013/0/08/Cainpic.jpg"> <img src="https://static.igem.org/mediawiki/2013/0/08/Cainpic.jpg" width="303"> | ||
+ | <p style="text-align:center; color:black; ">Figure 2: Overview of parameters applied in the <a href="http://cain.sourceforge.net/">Cain program</a> </p> </div> | ||
+ | <br> | ||
+ | </p> | ||
+ | <div class ="row-end"> </div> | ||
+ | </div> | ||
+ | |||
+ | The labels of the species (reaction molecules) are as follow: XLS = Xyls, inducer = m-toluic acid, XLSinducer = complex of XylS and m-toluic acid, DNA = plasmic DNA, XDNA = Binding of XLSindicer to the DNA, RNAp = RNA polymerase, RNApa = active RNA polymerase, E = elongation, RFP = red fluorescent protein. | ||
+ | </p> | ||
+ | <div class ="row-end"> </div> | ||
+ | </div> | ||
+ | |||
+ | |||
+ | <div class="row"> | ||
+ | <div class="col12-2"> | ||
+ | <div class="col8" align = "justify" style="background-color:#7352B0;> | ||
+ | <p style="text-align:center; color:#1A1719; "> Results </p> </div> | ||
+ | <br><br> | ||
+ | <p> | ||
- | |||
Varies starter consentration of inducer (0, 0.06, 0.3, 0.6, 1.2 and 6 µM) gave the result as indicated in figure 3 and the table below. | Varies starter consentration of inducer (0, 0.06, 0.3, 0.6, 1.2 and 6 µM) gave the result as indicated in figure 3 and the table below. | ||
- | < | + | <div class="col4" style="background-color:white;><a href="https://static.igem.org/mediawiki/2013/9/98/Model123.jpg"> <img src="https://static.igem.org/mediawiki/2013/9/98/Model123.jpg" width="303"> |
+ | <p style="text-align:center; color:black; "> Figure 3: Different consentrations of inducer (0 to 6 uM) was applyed in the deterministic simulations, yeilding different amounts of RFP.</p> </div> | ||
+ | <br> | ||
+ | </p> | ||
+ | <div class ="row-end"> </div> | ||
+ | </div> | ||
+ | |||
+ | |||
- | <center> | + | <center></center> |
Revision as of 12:43, 3 October 2013
The Pm/Xyls promotor system is a positive regulator system where the regulator molcule, Xyls, is constitutivly produced. When Xyls binds to the inducer m-toluic acid this complex binds to the Pm promotor(see figure 1). Binding to the promotor facilitates binding of RNA polymerase (RNAp) making it active (RNApA). This starts production of mRNA in an elongation step. The mRNA will be translated into the recombinant protein, or in our case, RFP. Over time mRNA and RFP will be degraded to som extent.
Figure: Overview of how the Pm/Xyls Promotor system funtions. Production of recombinant protein is dependent on access to the indicer m-toluic acid.
The reaction equations in the Pm/Xyls promotor system are listed below. The degradation of mRNA and RFP will inhibit an exponential production of these and after time the levels of mRNA and RFP will stabilize around a steady state.
Figure:
Figure 2: Overview of parameters applied in the Cain program
Varies starter consentration of inducer (0, 0.06, 0.3, 0.6, 1.2 and 6 µM) gave the result as indicated in figure 3 and the table below.
Figure 3: Different consentrations of inducer (0 to 6 uM) was applyed in the deterministic simulations, yeilding different amounts of RFP.