Team:Northwestern/MathModel

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Introduction
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<DIV style="font-size:20px">Modelling Overview</DIV><DIV style="font:15px Helvetica;">
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In our mathematical model we developed a system to characterize each of the two (las and rhl) plasmids. Simple detection is fairly straightforward. The engineered E. coli cells will be saturated with R-proteins (LasR and RhlR) due to constitutive production. In the presence of PAI-1 and PAI-2, the R-proteins and the autoinducers will dimerize which results in the induction of the induced promoter. Upon induction the induced promoters will express the reporter genes.
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On the other hand, quorum sensing is somewhat unusual. The las system is independent of all other cell signaling systems; however, the rhl system is not. PAI-1 can competitively bind to the RhlR/PAI-2 induced promoter, deactivating the induced promoter. Therefore, at quorum, the rhl system is regulated, while simultaneously induced owing to the presence of both PAI-1 and PAI-2. Our modeling approach will express the concentration of the relevant molecules as a system of first-order, nonlinear, ordinary differential equations using the variable specified in the table below.
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<html><div align="center"><img src="https://static.igem.org/mediawiki/2011/a/ab/Tableofvariables.gif" style="opacity:1;filter:alpha(opacity=100);" width="250" height="500px" alt="fig1"/ border="0"></div></html>
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<DIV style="font-size:20px">The Las Plasmid System</DIV>
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The first system of differential equations is centered on the las plasmid. This entails the production of LasR from the plasmid, diffusion of the autoinducer into the cell, and finally, the transcriptional activation and fluorescent reporting. A graphical representation of the biochemical system can be found below in Figure 1.
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<caption align="bottom"></html>'''Figure 1:''' The Las plasmid system <html></caption>
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<tr><td><img src="https://static.igem.org/mediawiki/2011/9/93/LasR_system.jpg" style="opacity:1;filter:alpha(opacity=100);" width="400px" height="250px" alt="fig1"/ border="0"></td></tr>
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Our first assumption is that LasR/PAI-1 dimer (D<sub>L</sub>) is produced at a rate r1 and degrades at rate r2. Additionally, D<sub>L</sub> can act as a transcriptional factor and bind to the induced promoter (LasP), which induces the expression of the reporter at the rate r6,
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<html><div align="center"><img src="https://static.igem.org/mediawiki/2011/5/59/DL.gif" style="opacity:1;filter:alpha(opacity=100);" width="398px" height="52px" alt="fig1"/ border="0"></div></html>
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LasR is produced by the translation of the LasR mRNA (LRmRNA) at a rate r5 and degrades at the rate r10. Moreover, LasR can forward dimerize at the rate r1 and reverse at rate r2. LRmRNA is transcribed at the rate r3 by the constitutive promoter (CP) and degrades at the rate r4,
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<html><div align="center"><img src="https://static.igem.org/mediawiki/2011/1/12/LR_LRmRNA.gif" style="opacity:1;filter:alpha(opacity=100);" width="397" height="104px" alt="fig1"/ border="0"></div></html>
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Upon the binding of DL to LasP at the rate r6, GFP mRNA (GmRNA) is transcribed. GmRNA degrades at the rate r9 and is translated to GFP at the rate r7. GFP degrades at the rate r8,
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<html><div align="center"><img src="https://static.igem.org/mediawiki/2011/5/50/GmRNA_GFP.gif" style="opacity:1;filter:alpha(opacity=100);" width="368" height="109px" alt="fig1"/ border="0"></div></html>
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The autoinducer PAI-1 diffuses passively into the cell as a result of the concentration gradient, cell volume, surface area and membrane thickness which establish the equation mass transfer1. The intracellular (A1i) and extracellular (A1e) PAI-1 degrade at the rate r11 and r12,
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<html><div align="center"><img src="https://static.igem.org/mediawiki/2011/2/2d/A1i_A1e.gif" style="opacity:1;filter:alpha(opacity=100);" width="498" height="104px" alt="fig1"/ border="0"></div></html>
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Revision as of 01:37, 26 September 2011

RETURN TO IGEM 2010



Modelling Overview

In our mathematical model we developed a system to characterize each of the two (las and rhl) plasmids. Simple detection is fairly straightforward. The engineered E. coli cells will be saturated with R-proteins (LasR and RhlR) due to constitutive production. In the presence of PAI-1 and PAI-2, the R-proteins and the autoinducers will dimerize which results in the induction of the induced promoter. Upon induction the induced promoters will express the reporter genes.


On the other hand, quorum sensing is somewhat unusual. The las system is independent of all other cell signaling systems; however, the rhl system is not. PAI-1 can competitively bind to the RhlR/PAI-2 induced promoter, deactivating the induced promoter. Therefore, at quorum, the rhl system is regulated, while simultaneously induced owing to the presence of both PAI-1 and PAI-2. Our modeling approach will express the concentration of the relevant molecules as a system of first-order, nonlinear, ordinary differential equations using the variable specified in the table below.

fig1

The Las Plasmid System

The first system of differential equations is centered on the las plasmid. This entails the production of LasR from the plasmid, diffusion of the autoinducer into the cell, and finally, the transcriptional activation and fluorescent reporting. A graphical representation of the biochemical system can be found below in Figure 1.



Figure 1: The Las plasmid system
fig1


Our first assumption is that LasR/PAI-1 dimer (DL) is produced at a rate r1 and degrades at rate r2. Additionally, DL can act as a transcriptional factor and bind to the induced promoter (LasP), which induces the expression of the reporter at the rate r6,

fig1

LasR is produced by the translation of the LasR mRNA (LRmRNA) at a rate r5 and degrades at the rate r10. Moreover, LasR can forward dimerize at the rate r1 and reverse at rate r2. LRmRNA is transcribed at the rate r3 by the constitutive promoter (CP) and degrades at the rate r4,

fig1

Upon the binding of DL to LasP at the rate r6, GFP mRNA (GmRNA) is transcribed. GmRNA degrades at the rate r9 and is translated to GFP at the rate r7. GFP degrades at the rate r8,

fig1

The autoinducer PAI-1 diffuses passively into the cell as a result of the concentration gradient, cell volume, surface area and membrane thickness which establish the equation mass transfer1. The intracellular (A1i) and extracellular (A1e) PAI-1 degrade at the rate r11 and r12,

fig1

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