Team:Grenoble/Modeling/Amplification

From 2012.igem.org

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<h1> Overview</h1>
<h1> Overview</h1>
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What do we want?
 
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<span style="text-decoration:underline;">Remark:</span>
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We want to create a detector which is:
 
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-As sensitive as possible
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As we designed a biosensor, when the molecule to detect is detected by our bacterium, our bacterium will send us a signal. This signal is a green light. Our bacterium activates the production of a protein, called Gfp, which makes it become green. In our system the production of Gfp begins when the production of an other protein, the adenylate cyclase (Ca) begins. Indeed, they are under the control of the same promotor, pBad, and thus they have exatly the same behavior:
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-Which enables us to get a signal.
 
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-With an answer as fast as possible.
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<center><img src="https://static.igem.org/mediawiki/2012/7/74/Overview_grenoble_1.png" alt="" /></center>
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We wanted to create a detector, thus we could have designed it like following:
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The protein Gfp is only the protein that enables us to control the behavior of the adenylate cyclase. Thus, in the development, I won’t speak about the gfp, but always about the adenylate cyclase, and we will consider that the adenylate cyclase gives us the signal.
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<center><img src="https://static.igem.org/mediawiki/2012/a/a2/X_z_grenoble.png" alt="" /></center>
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<b>Why an amplification module?</b>
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When one bacterium detects the dipeptide, it will become green. However, if only one bacterium becomes green, we won’t be able to get the signal. That is why we decided to use the communication between the bacteria, called the quorum sensing: if one bacterium becomes green, the surrounding bacteria will become green too, and thus we will be able to get the signal.
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Where X is the molecule to detect, and Z the fluorescent signal. However, with this design, the communication between the bacteria (quorum sensing) wouldn’t have worked really well, we would have needed an important quantity of X at the initial time to be able to obtain an important diffusion that we could actually see. Indeed, the evolution of X would have been like following:
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The question became: How to do this?
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First, we had to choose a molecule, which would enable the communication between the bacteria. We chose the cyclic AMP, which production is catalyzed by the adenylate cyclase. Thus, we designed:
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Thus, the next idea was to amplify X:
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Like this, as soon as it would be detected, by a bacterium, the bacterium would re-create some X, and the quorum sensing would work, as we would have this evolution of X:
 
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Thanks to the quorum sensing if we detect X, we can easily measure it.
 
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Now, we had a last problem: the false positives. Indeed, we have a detector, so we don’t want to have a signal if there is nothing to detect. Thus, we decided to add a classic feed forward loop, because it is known to reduce the false positives. Finally, we got our system:
 
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X is a molecule that has the ability to be transmitted from bacterium to an other. It is a quorum-sensing molecule.
 
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Y, and Z are 2 genes. X is the transcription factor of Y.  Thus when it is introduced, the gene Y is expressed. Then, the molecule X and the protein Y together will be the transcription factor of Z. When Z is expressed it creates more X.
 
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<span class="gras">Conclusion:</span>
 
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Now that we designed our system, we wanted to really study the behavior of this topology before going further in this project.
 
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Revision as of 12:53, 22 September 2012

iGEM Grenoble 2012

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Introduction


In this part we will model the amplification module. Our work in this module is subdivided in three main parts: a deterministic model of the reactions at the local scale, another version of the former taking into account some random noise/perturbations, and a model of the signal's diffusion in space.

In the deterministic model, we check the sensitivity of our system and we give the link with the signaling module. Then, in the diffusion part we check if our system has a fast answer. Eventually, in the random perturbations model, we check that it is robust to perturbations.


Overview



Remark:

As we designed a biosensor, when the molecule to detect is detected by our bacterium, our bacterium will send us a signal. This signal is a green light. Our bacterium activates the production of a protein, called Gfp, which makes it become green. In our system the production of Gfp begins when the production of an other protein, the adenylate cyclase (Ca) begins. Indeed, they are under the control of the same promotor, pBad, and thus they have exatly the same behavior:



The protein Gfp is only the protein that enables us to control the behavior of the adenylate cyclase. Thus, in the development, I won’t speak about the gfp, but always about the adenylate cyclase, and we will consider that the adenylate cyclase gives us the signal.

Why an amplification module?

When one bacterium detects the dipeptide, it will become green. However, if only one bacterium becomes green, we won’t be able to get the signal. That is why we decided to use the communication between the bacteria, called the quorum sensing: if one bacterium becomes green, the surrounding bacteria will become green too, and thus we will be able to get the signal.

The question became: How to do this?

First, we had to choose a molecule, which would enable the communication between the bacteria. We chose the cyclic AMP, which production is catalyzed by the adenylate cyclase. Thus, we designed:



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