Team:Aberdeen Scotland/Modeling/QS

From 2014.igem.org

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<div class="center"><img src="https://static.igem.org/mediawiki/2014/7/7e/Qs_field.png"></div>
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<p>Fig.3: Concentration potential in medium with many senders</p>
<p>Fig.3: Concentration potential in medium with many senders</p>
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<p>From Fig.3 you can see that the overall "background" concentration in the medium is very uniform regardless of cell distribution. This quick observation made us investigate further and calculate precisely if Receiver cells will be able to tell the difference between local high concentration and simply a lot of Senders far away in the medium.</p>
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<ul>
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<li>Consider the following situation:
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<ul>
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<li>Medium of 1 ml volume</li>
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<li>A spherical shell of radius 150 μm (roughly 100 cell radii) of cells concentrated in the middle of that volume</li>
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<li>Assume the concentrated shell has 3 orders of magnitude higher concentration of cells per volume</li>
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$$\frac{V_{shell}}{V_{volume}}=10^{3}$$
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</ul>
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</li>
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</ul>
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<!-- REFERENCES -->
<h3>References</h3>
<h3>References</h3>
<p><a href="http://www.uni-leipzig.de/diffusion/journal/pdf/volume2/diff_fund_2(2005)1.pdf">[1] Jean Philibert, One and a Half Century of Diffusion: Fick, Einstein,
<p><a href="http://www.uni-leipzig.de/diffusion/journal/pdf/volume2/diff_fund_2(2005)1.pdf">[1] Jean Philibert, One and a Half Century of Diffusion: Fick, Einstein,

Revision as of 17:12, 17 October 2014

Team:Aberdeen Scotland/Modelling - 2014.ogem.org



Quorum Sensing Model


Our goal with this model was to analyse our system in detail so that we learn more about its spacial features. Namely we wanted to see if co-localised cells will be able to distinguish each other from far away cells through quorum sensing and if so under what conditions. This was essential to our design as initially we envisioned that cells will communicate and create an AND-gate type of response in presence of according stimuli.

Since Quorum Sensing(QS) occurs due to diffusion of molecules in the medium, we naturally decided to employ the diffusion equation.

Diffusion Equation (more precisely Fick's 2nd Law)1

$$\frac{\partial{C}}{\partial{t}}=D\nabla^2{C}$$ $$C - concentration$$ $$D - diffusion\:constant$$

However, in our system there is a dedicated Sender and Receiver cells, which is different from natural QS. Sender cells can only produce and diffuse AHLs into the medium without the ability to react to it and Receiver cells can only react to AHLs without the ability to produce it. This arrangement made our system particularly interesting as we will find further down.

  • Initial Assumptions

    • Constant Production of AHL from Sender cells
    • Receivers react to the AHL concentration around them
    • E. Coli cell-shape symmetry is taken into account

Initially we wanted to solve the equation in a particular case, so that we gain some intuition for the situation. Thus, in a big enough medium after some time T we can say that

$$\frac{\partial{C}}{\partial{t}}=0 \implies D\nabla^2{C}=0$$

Finally, assuming spherical coordinates we get: $$C(R)=\frac{K}{R}$$ for some constant K.

Now if we look at the Gaussian around a Sender cell, we find: $$\phi=-D\nabla{C}$$ which directly leads to a solution of the form $$C(R)=\frac{Q}{4\pi{}DR}$$ where Q is the production of AHLs by the Sender per unit time.

Knowing this we were able to simulate Senders and look at the resulting AHL concentration in the medium

Fig.1: Concentration potential around single sender (top view)

Fig.2: Concentration potential around single sender (side view)

Fig.3: Concentration potential in medium with many senders

From Fig.3 you can see that the overall "background" concentration in the medium is very uniform regardless of cell distribution. This quick observation made us investigate further and calculate precisely if Receiver cells will be able to tell the difference between local high concentration and simply a lot of Senders far away in the medium.

  • Consider the following situation:
    • Medium of 1 ml volume
    • A spherical shell of radius 150 μm (roughly 100 cell radii) of cells concentrated in the middle of that volume
    • Assume the concentrated shell has 3 orders of magnitude higher concentration of cells per volume
    • $$\frac{V_{shell}}{V_{volume}}=10^{3}$$

References

[1] Jean Philibert, One and a Half Century of Diffusion: Fick, Einstein, before and beyond, Diffusion Fundamentals 2, 2005 1.1–1.10