Team:NTNU-Trondheim/Model

From 2013.igem.org

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(→Results)
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A deterministic simulation of the system was run on [http://cain.sourceforge.net/ Cain software] with the parameters as viewed in figure 2.
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A deterministic simulation of the system was run on [http://cain.sourceforge.net/ Cain software] with the parameters as viewed in figure 2. Only the number/consentration of the inducer was varieted.
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<center>[[file:cainpic.jpg|1000px]]</center>
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<center>[[file:cainpic.jpg|1200px]]</center>
<center>Figure 2: Overview of parameters applied in the [http://cain.sourceforge.net/ Cain program]. 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.</center>
<center>Figure 2: Overview of parameters applied in the [http://cain.sourceforge.net/ Cain program]. 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.</center>
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===Results===
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===<center>Results</center>===
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The result of varies starter consentration, 0, 0.06, 0.3, 0.6, 1.2 and 6 &micro;M of the inducer gave the result as indicated  in figure 3 below.
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Varies starter consentration, 0, 0.06, 0.3, 0.6, 1.2 and 6 &micro;M of the inducer gave the result as indicated  in figure 3 below.
<center>[[file:model123.jpg|600px]]</center>
<center>[[file:model123.jpg|600px]]</center>
<center>Figure 3: Different consentrations of inducer (0 to 6 uM) was applyed in the deterministic simulations, yeilding different amounts of RFP.</center>
<center>Figure 3: Different consentrations of inducer (0 to 6 uM) was applyed in the deterministic simulations, yeilding different amounts of RFP.</center>
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Revision as of 10:17, 3 October 2013

iGEM 2013
NTNU Trondheim
iGEM NTNU 2013



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Modelling of the Pm/Xyls Promotor system

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) and 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.

Modelpic.jpg
Figure 1 Overview of how the Pm/Xyls Promotor system funtions. Production of recombinant protein is dependent on access to the indicer m-toluic acid [http://www.vectronbiosolutions.com/info.php?id=13 (1)].


The reaction equations in the Pm/Xyls promotor system are listed below

Modeleq.jpg


A deterministic simulation of the system was run on [http://cain.sourceforge.net/ Cain software] with the parameters as viewed in figure 2. Only the number/consentration of the inducer was varieted.

Cainpic.jpg
Figure 2: Overview of parameters applied in the [http://cain.sourceforge.net/ Cain program]. 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.


Results

Varies starter consentration, 0, 0.06, 0.3, 0.6, 1.2 and 6 µM of the inducer gave the result as indicated in figure 3 below.

Model123.jpg
Figure 3: Different consentrations of inducer (0 to 6 uM) was applyed in the deterministic simulations, yeilding different amounts of RFP.






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