Team:Grenoble/Projet/Design

From 2011.igem.org

(Difference between revisions)
Line 14: Line 14:
  <h2>Table of content</h2>  
  <h2>Table of content</h2>  
    <p>
    <p>
-
  Our synthetic biology constructions feature tens of parameters and at this scale human brains can only guess how the whole system would work. We of course needed mathematical modelling in order to check the effectiveness of the genetic circuit.<br/><br/>
+
  Our device is oriented in this problematic, Mercuro-Coli is a mercury biosensor which allows detecting and quantifying this molecule contained into polluted water. Intended to fieldwork studies, the device should be very easy to use.
 +
</p>
 +
<p>
 +
We think to create a plate, with bacteria fixed on. Each bacteria have the same Regulating network, which is composed by a choice way (Toggle Switch), a specific communication inter bacterial (Quorum Sensing)and a coloration way depending of Quorum Sensing. all of these compounds are regulated by a post-transcriptional regulator (Rsma system).
 +
<br>
 +
overall our fixed bacteria have a regulatory network, with ability to detect two different molecules (mercury and IPTG), and the concentration ratio between both engaged definitively bacteria in one way and turn off the second. This activated pathway contain one of the two protein required for a functional Quorum Sensing (CinI (sender) and CinR (receptor)).
 +
</br>
 +
So one bacteria can just have one active way and one Quorum Sensing protein. one bacterium can't lead to the last step of our network, she need other bacteria which have activate the other way.  Clearly the senders bacteria emit Quorum sensing molecule synthesize by CinI to receptor cells (expressing CinR). Now the AHL (quorum sensing molecule) can be complexed with the receptor and activate the synthesis of a red pigment.
 +
</p>
 +
<p>
 +
The finality of our project is to use our bacteria on a plate containing an IPTG gradient, we the water sample to test(homogeneous concentration). the ratio of concentration lead all bacteria in the right way depending the IPTG gradient. The plate is separate in two group of differentiate cells (senders and receptors). the bacteria communicate in short distance, so the two Quorum Sensing elements are present both exclusively at he interface of the two cell populations. Finally it's only here that the pigment is activated. and generate a red band on our plate, locate in function of tested molecule concentration. 
-
  In the particular case of our circuit and final use of the bacteria, the modelling team also had to give the specificities (size, number of bacteria, IPTG gradient specificities) of the measuring device we intend to produce.<br/><br/>
 
-
  In the next pages we expose which algorithms we used for both deterministic modelling and stochastic modelling, explain our MATLAB scripts (available <a href="http://igemgrenoble-files.perso.sfr.fr/2011/MATLAB_Archives/">here</a>) and finally give the results of our simulations.<br/><br/>
+
</p>
   
   
  <a href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Deterministic" ><img class="icon" src="https://static.igem.org/mediawiki/2011/b/b4/Icon_deterministic.png"/></a>
  <a href="https://2011.igem.org/Team:Grenoble/Projet/Modelling/Deterministic" ><img class="icon" src="https://static.igem.org/mediawiki/2011/b/b4/Icon_deterministic.png"/></a>

Revision as of 16:45, 18 September 2011

Grenoble 2011, Mercuro-Coli iGEM


Modelling

Table of content

Our device is oriented in this problematic, Mercuro-Coli is a mercury biosensor which allows detecting and quantifying this molecule contained into polluted water. Intended to fieldwork studies, the device should be very easy to use.

We think to create a plate, with bacteria fixed on. Each bacteria have the same Regulating network, which is composed by a choice way (Toggle Switch), a specific communication inter bacterial (Quorum Sensing)and a coloration way depending of Quorum Sensing. all of these compounds are regulated by a post-transcriptional regulator (Rsma system).
overall our fixed bacteria have a regulatory network, with ability to detect two different molecules (mercury and IPTG), and the concentration ratio between both engaged definitively bacteria in one way and turn off the second. This activated pathway contain one of the two protein required for a functional Quorum Sensing (CinI (sender) and CinR (receptor)).
So one bacteria can just have one active way and one Quorum Sensing protein. one bacterium can't lead to the last step of our network, she need other bacteria which have activate the other way. Clearly the senders bacteria emit Quorum sensing molecule synthesize by CinI to receptor cells (expressing CinR). Now the AHL (quorum sensing molecule) can be complexed with the receptor and activate the synthesis of a red pigment.

The finality of our project is to use our bacteria on a plate containing an IPTG gradient, we the water sample to test(homogeneous concentration). the ratio of concentration lead all bacteria in the right way depending the IPTG gradient. The plate is separate in two group of differentiate cells (senders and receptors). the bacteria communicate in short distance, so the two Quorum Sensing elements are present both exclusively at he interface of the two cell populations. Finally it's only here that the pigment is activated. and generate a red band on our plate, locate in function of tested molecule concentration.

Deterministic Modelling :
Our equations and how we obtained them.
Our algorithms
Isoclines and Hysteresis

Stochastic Modelling :
Geoffrey
Gillespie algorithm
Mean, standard deviation and statistical properties


Parameters



Results :
Validation of our genetical network
Device

Retrieved from "http://2011.igem.org/Team:Grenoble/Projet/Design"