Difference between revisions of "Team:INSA-UPS France/test"

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     <div class="main_title">
 
       <div>
 
       <div>
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         <p>Model overview</p>
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         <p>SBGN overview</p>
 
       </div>
 
       </div>
 
       <img src="https://static.igem.org/mediawiki/2017/d/db/T--INSA-UPS_France--Model_croco.png" alt="">
 
       <img src="https://static.igem.org/mediawiki/2017/d/db/T--INSA-UPS_France--Model_croco.png" alt="">
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     <section>
 
     <section>
  
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     <h1>Aims of the model</h1>
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     <h1>SBGN: a way to normalize the models of systems biology</h1>
 
       <p>
 
       <p>
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         Our strategy was based on an input with a quorum sensing molecule production, a molecular communication between two organisms, and an output with the antimicrobial peptides effect. We needed to use a model to simulate this biological system and analyze if this communication was feasible:
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         <quote>“Systems biology is based on the understanding that the whole is greater than the sum of the parts.”</quote>(1)
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      </p>
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Systems biology is a new approach to understand and to manipulate biological material. It proposes to represent biological systems such as networks transforming inputs into outputs that could be modeled mathematically, similarly to technological and electronical devices.(1) It requires communication between biochemists, mathematicians and computer scientists. The SBGN (Systems Biology Graphical Notation) project has been launched in 2005 to facilitate this communication. It proposes a standard notation to represent biochemical and cellular processes, and to easily share biological systems to the community.(2) The standard notation can be found there.</p>
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      <img src="https://static.igem.org/mediawiki/2017/8/8d/T--INSA-UPS_France--Model_fig1.png" alt="">
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<p>
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      <p>
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Our system is constituted of microorganisms interacting by responding to stimulations (inputs) and producing a molecular response (outputs). We had a perfect example of a systematic use of biological material, at the scale of both a unique microorganisms and a microbial consortium.
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        Would the quorum sensing molecule (CAI-1) induce a sufficient answer to activate the sensor (<i>Vibrio harveyi</i>)? Would the receptor be able to produce enough molecular message (diacetyl) to communicate with the effector <i>Pichia pastoris</i>? Would the effector produce enough antimicrobial peptides to deliver the guessed output, which is the lysis of <i>V. cholerae</i> to reach a non-toxic concentration?
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      </p>
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      <p>
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        A model was also crucial regarding the entrepreneurship and the integrated human practices parts of our project: we needed to show to clients and investors, but also to citizens, how our system would work, how we will dimensionate our device, and how long do you have to wait before drinking a non-contaminated water.
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      </p>
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      <p>
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        To sum up, the goals of our model could be sum up into four objectives:
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       </p>
 
       </p>
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       <ul>
 
       <ul>
 
         <li>Demonstrate the feasibility</li>
 
         <li>Demonstrate the feasibility</li>
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     <section>
 
     <section>
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       <h1>Approaches</h1>
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       <h1>Our SBGN representation</h1>
 +
<p>Abbreviations:</p>
 +
<ul>
 +
        <li>cqsA: cqsA gene</li>
 +
        <li>CqsS*: engineered CqsS receptor protein</li>
 +
        <li>als/ALS: acetolactate synthase</li>
 +
        <li>S: substrate for diacetyl production</li>
 +
<li>dac: diacetyl</li>
 +
<li>Odr10: Odr10 receptor protein</li>
 +
<li>AMP: antimicrobial peptide</li>
 +
<li>V: velocity</li>
 +
<li>deg: degradation</li>
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<li>diff: diffusion</li>
 +
      </ul>
 
       <p>
 
       <p>
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        Two complementary approaches have been used to represent our model. Working with a complex biological system involving three microorganisms and several molecules, the Systemic Biology Graphical Notation (SBGN) was a perfect way to ordinate the system and represent the interactions between organisms and the molecules involved.
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The SBGN representation is an easy way to visualize and inventory all the elements we had to consider to modelize our synthetic system with Ordinary Differential Equations (ODEs). It is also a way to present our system to different interlocutors (biologist, bioinformatician, mathematician), and to make it reusable and adaptable.
 
       </p>
 
       </p>
 
       <p>
 
       <p>
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        The SBGN representation was convenient to elaborate the Ordinary Differential Equations (ODEs) system, which is our second approach. Starting with a complex system, choices have been made to simplify some molecular cascades or some interactions to reduce it to a system of 12 differential equations.
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To simplify our system, some assumptions were made such as the one that the substrate does not interact with <i>Vibrio cholerae</i> and <i>Pichia pastoris</i>.</p>
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      </p>
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−
      <img src="https://static.igem.org/mediawiki/2017/archive/e/e4/20170924215505%21T--INSA-UPS_France--Model_fig2.png" alt="">
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     </section>
 
     </section>
 
     <!-- fin section -->     
 
     <!-- fin section -->     

Revision as of 21:26, 28 September 2017

Croc'n Cholera
iGEM UPS-INSA Toulouse 2017

SBGN overview

SBGN: a way to normalize the models of systems biology

“Systems biology is based on the understanding that the whole is greater than the sum of the parts.”(1) Systems biology is a new approach to understand and to manipulate biological material. It proposes to represent biological systems such as networks transforming inputs into outputs that could be modeled mathematically, similarly to technological and electronical devices.(1) It requires communication between biochemists, mathematicians and computer scientists. The SBGN (Systems Biology Graphical Notation) project has been launched in 2005 to facilitate this communication. It proposes a standard notation to represent biochemical and cellular processes, and to easily share biological systems to the community.(2) The standard notation can be found there.

Our system is constituted of microorganisms interacting by responding to stimulations (inputs) and producing a molecular response (outputs). We had a perfect example of a systematic use of biological material, at the scale of both a unique microorganisms and a microbial consortium.

  • Demonstrate the feasibility
  • Confirm our wet lab strategy
  • Dimensionate
  • Estimate the waiting time

Our SBGN representation

Abbreviations:

  • cqsA: cqsA gene
  • CqsS*: engineered CqsS receptor protein
  • als/ALS: acetolactate synthase
  • S: substrate for diacetyl production
  • dac: diacetyl
  • Odr10: Odr10 receptor protein
  • AMP: antimicrobial peptide
  • V: velocity
  • deg: degradation
  • diff: diffusion

The SBGN representation is an easy way to visualize and inventory all the elements we had to consider to modelize our synthetic system with Ordinary Differential Equations (ODEs). It is also a way to present our system to different interlocutors (biologist, bioinformatician, mathematician), and to make it reusable and adaptable.

To simplify our system, some assumptions were made such as the one that the substrate does not interact with Vibrio cholerae and Pichia pastoris.