Difference between revisions of "Team:Aalto-Helsinki/Modeling"

m (texts)
(switched to the micelle pic with amphiphilic proteins visible)
 
(12 intermediate revisions by 4 users not shown)
Line 1: Line 1:
 
{{Aalto-Helsinki/CSS}}
 
{{Aalto-Helsinki/CSS}}
 
<html>
 
<html>
 +
 +
<style type="text/css">
 +
/* Navbar, text color changes if you are on this page */
 +
#modelingnav:visited {
 +
  color: gray;
 +
}
 +
 +
/* Background pic */
 +
.compscreens {
 +
    background-repeat: repeat-y;
 +
    background-image: url("https://static.igem.org/mediawiki/2015/1/11/Aalto-Helsinki_modeling_background.png");
 +
    background-size: 100%;
 +
}
 +
</style>
  
 
<!-- Closing divs for ready wiki things, still one more to add?-->
 
<!-- Closing divs for ready wiki things, still one more to add?-->
 
</p></div>
 
</p></div>
  
 +
<div class="compscreens">
 
<div class="inner-container">
 
<div class="inner-container">
  
Line 10: Line 25:
 
<!-- Our text below, the above is left for now if someone wants to have those as reference -->
 
<!-- Our text below, the above is left for now if someone wants to have those as reference -->
 
<!-- Introduction -->
 
<!-- Introduction -->
−
<p style="margin-top: 40px"> Modeling is an important part of synthetic biology. With good models, one can gain insight of the reaction before doing anything in the lab. By having a better understanding of the ideas that govern our project, we could see the influence of each compound in the reaction pathway and have a basis to make decisions that would have a long term impact in our results. Our project consisted of a few quite different parts, and that gave us a natural way to divide our modeling to four parts. </p>
+
 
 +
<h1>Modeling</h1>
 +
 
 +
<p style="margin-top: 40px"> Modeling is an important part of synthetic biology. With good models, one can gain insight of the biological phenomena before doing anything in the lab. Understanding the biological system allows us to make better decisions as we modify the system for our purposes. Our project consisted of quite a few different parts, and that gave us a natural way to divide our modeling to four parts. </p>
  
 
<!-- Introduction of our models -->
 
<!-- Introduction of our models -->
Line 16: Line 34:
 
<h2>Models of propane pathway</h2>
 
<h2>Models of propane pathway</h2>
  
−
<p>The main thing of our project was the production of propane with <span style="font-style:italic;">e. coli</span>, so the main task in modeling was to gain insight to the propane pathway. We made a model based on Michaelis-Menten enzyme kinetics and calculated numerical results from it with <a href="http://www.copasi.org/tiki-view_articles.php">Copasi</a> and <a href="http://se.mathworks.com/">Matlab</a>. With these tools we found the bottlenecks and most sensitive parts of our reaction. We also have some idea of how much propane will be produced in our system. For more information, see our page of <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_propane">modeling propane pathway</a>.</p>
+
<p>The main goal of our project was the production of propane with <span style="font-style:italic;">E. coli</span>, so the main task in modeling was to gain insight to the propane pathway. We made a model based on Michaelis-Menten enzyme kinetics and calculated numerical results from it with <a href="http://copasi.org/" target="_blank">Copasi</a> and <a href="http://se.mathworks.com/" target="_blank">Matlab</a>. With these tools we found the bottlenecks and most sensitive parts of our reaction. We also got some ideas on how much propane will be produced in our system. For more information, see our page of <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_propane">modeling propane pathway</a>.</p>
  
 
<!-- Synergy -->
 
<!-- Synergy -->
Line 22: Line 40:
  
 
<figure style="float:right;margin-left:20px;">
 
<figure style="float:right;margin-left:20px;">
−
   <img src="https://static.igem.org/mediawiki/2015/d/da/Aalto-Helsinki_Micelle_structure.png" style="width:200px;"/>
+
   <img src="https://static.igem.org/mediawiki/2015/e/e4/Aalto-Helsinki_micelle_circle_approach_2.png" style="width:200px;"/>
 
</figure>
 
</figure>
  
−
<p>One big concern in our project was the efficiency of propane production. To solve this problem we wanted to use micelles to hold enzymes together and speed up the reactions. We thought that this approach would be especially suitable for the two last enzymes in our pathway, Car and Ado, who have toxic butyraldehyde as a substrate in between them. Since there are many butyraldehyde-eating enzymes in a cell, the speed up we could get would be even better. We did a <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_synergy">stochastic model of synergy with python</a> to confirm if this approach would really work as we hope.</p>
+
<p>One big concern in our project was the efficiency of propane production. To solve this problem we wanted to use micelles to hold enzymes together and speed up the reactions. We thought that this approach would be especially suitable for the of the last enzymes in our pathway, CAR and ADO, who have toxic butyraldehyde as a substrate between them. Since there are many butyraldehyde-consuming enzymes in a cell, the speed up we could get would be even better. We did a <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_synergy">stochastic model of synergy with python</a> to confirm if this approach would really work as we hope.</p>
  
  
Line 31: Line 49:
 
<h2>Modeling micelle formation</h2>
 
<h2>Modeling micelle formation</h2>
  
−
<p>As mentioned above we wanted to make propane production more efficient by having enzymes together in a micelle. While we modeled the efficiency of this solution, we also wanted to know if the solution was possible in the first place. That is why we made a geometrical model about <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_micelle">micelle structure</a>.</p>
+
<p>As mentioned above we wanted to make propane production more efficient by having enzymes together in a micelle. While we modeled the efficiency of having the enzymes close together, we also wanted to know if it was possible to form the micelles with our enzymes in the first place. That is why we made a geometrical model about <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_micelle">micelle structure</a>.</p>
  
 
<!-- Cellulose -->
 
<!-- Cellulose -->
 
<h2>Cellulose pathway</h2>
 
<h2>Cellulose pathway</h2>
  
−
<p>In our project we produce propane from cellulose, so our modeling team also <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_cellulose">took a look into cellulose pathway</a>.</p>
+
<p style="padding-bottom:8%;margin-bottom:0;">Our project involves creating renewable propane from cellulose, which is why we wanted to model the pathway responsible for hydrolysing cellulose. The pathway consists of three different genes that cut the cellulose to glucose which the cell can then use as an energy source for propane production. While building a beneficial model of this wasn't possible for us, see our page of <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_cellulose">modeling cellulose pathway</a> to see what thoughts our modeling team had on this.</p>
  
 +
<!--<p>In our project we produce propane from cellulose, so our modeling team also <a href="https://2015.igem.org/Team:Aalto-Helsinki/Modeling_cellulose">took a look into cellulose pathway</a>.</p>-->
  
  
 +
</div>
 
</div>
 
</div>
 
</div></div></div> <!--These are the closing tags for div id="mainContainer" and div id="contentContainer". The corresponding opening tags appear in the template that is {{included}} at the top of this page.-->
 
</div></div></div> <!--These are the closing tags for div id="mainContainer" and div id="contentContainer". The corresponding opening tags appear in the template that is {{included}} at the top of this page.-->
−
 
+
<p style="margin-bottom:0;"> <!-- there is a closing /p at the footer we can't access, this prevents a gap in the background at the bottom of the page -->
−
</body>
+
−
</html>
+

Latest revision as of 21:27, 18 September 2015

Modeling

Modeling is an important part of synthetic biology. With good models, one can gain insight of the biological phenomena before doing anything in the lab. Understanding the biological system allows us to make better decisions as we modify the system for our purposes. Our project consisted of quite a few different parts, and that gave us a natural way to divide our modeling to four parts.

Models of propane pathway

The main goal of our project was the production of propane with E. coli, so the main task in modeling was to gain insight to the propane pathway. We made a model based on Michaelis-Menten enzyme kinetics and calculated numerical results from it with Copasi and Matlab. With these tools we found the bottlenecks and most sensitive parts of our reaction. We also got some ideas on how much propane will be produced in our system. For more information, see our page of modeling propane pathway.

Modeling synergy

One big concern in our project was the efficiency of propane production. To solve this problem we wanted to use micelles to hold enzymes together and speed up the reactions. We thought that this approach would be especially suitable for the of the last enzymes in our pathway, CAR and ADO, who have toxic butyraldehyde as a substrate between them. Since there are many butyraldehyde-consuming enzymes in a cell, the speed up we could get would be even better. We did a stochastic model of synergy with python to confirm if this approach would really work as we hope.

Modeling micelle formation

As mentioned above we wanted to make propane production more efficient by having enzymes together in a micelle. While we modeled the efficiency of having the enzymes close together, we also wanted to know if it was possible to form the micelles with our enzymes in the first place. That is why we made a geometrical model about micelle structure.

Cellulose pathway

Our project involves creating renewable propane from cellulose, which is why we wanted to model the pathway responsible for hydrolysing cellulose. The pathway consists of three different genes that cut the cellulose to glucose which the cell can then use as an energy source for propane production. While building a beneficial model of this wasn't possible for us, see our page of modeling cellulose pathway to see what thoughts our modeling team had on this.