Team:TU-Delft/Modeling

From 2013.igem.org

(Difference between revisions)
 
(40 intermediate revisions not shown)
Line 1: Line 1:
{{:Team:TU-Delft/Templates/Navigation}}
{{:Team:TU-Delft/Templates/Navigation}}
{{:Team:TU-Delft/Templates/Style}}
{{:Team:TU-Delft/Templates/Style}}
-
{{:Team:TU-Delft/Templates/Counter}}
+
{{:Team:TU-Delft/Templates/Frog}}
-
{{:Team:TU-Delft/Templates/Facebook}}
+
{{:Team:TU-Delft/Templates/Logo}}
-
 
+
<html>
<html>
 +
<div id="tmp">
 +
<div style="margin-left:30px;margin-right:30px; width:900px;float:left;"> 
 +
<h2 align="center"><br> Modeling</h2>
 +
</div>
 +
</div>
-
<h2 align="center">Modeling</h2>
 
-
<div style="margin-left:50px;margin-right:50px;float:left;display:inline-block;"> 
 
-
<br>
 
-
<p align="justify">Modeling will play an important role in the iGEM project. Our total system is rather complex and requires careful tuning in order for it to work. This tuning cannot be done in the lab due to time constraints, so the modeling will be used to derive conditions on strengths of promoters and binding sites in order for the system to work. This way the correct implementation can be done in the lab, saving effort and time.
 
-
The modeling will first focus on the timer, then the SUMO fusion and finally the kill switch. These parts will be introduced below and details on these parts will be added later on in the project.
 
-
</p>
 
-
<br>
 
-
<b><font color="#330000" size="3">Timer</font></b>
 
-
<p align="justify" margin: 20px >The most important aspect here is the modeling of the ‘time delay’: What is the difference in time between inducing and the output. In our case we have two outputs, a small delay must also be present between those two.
 
-
<br>
 
-
<center>
+
<div id="img">
-
<img src="https://static.igem.org/mediawiki/2013/1/1a/Timer_simple.png" height=300px>
+
        <div style="margin-top:10px;margin-left:40px;float:left;display:inline-block;">  
-
</center>
+
<img src="https://static.igem.org/mediawiki/2013/e/e5/Systems_biology_pic.jpg" height="260" width="400" >
 +
</div>
 +
</div>
 +
<br><br>
 +
<div id="img">
 +
<div style="margin-left:10px;margin-right:0px;width:450px;float:left;display:inline-block;"> 
 +
<p align="justify">
 +
Modeling is the bridge between science and engineering in this project; using the scientific knowledge on our system, we can describe how the system will act and interact. Furthermore, using the quantitative relations derived from the models the circuit has been adjusted and redesigned. This description is used for predicting what will happen in the lab, but also if the project can be applied in reality in a 'band-aid' product. Next to giving a preliminary design of the band-aid, new peptides are designed to give us the properties we want for this application.</p>
 +
</div>
 +
</div>
-
<br>
+
<br><br><br><br><br><br><br><br><br><br><br><br>
-
At the moment only one output is currently modeled, the ULP-1 protease.  Results of this simulation are shown in Figure 1, here the time delay is about …  minutes. Next to add is the interaction with the peptide tagged with SUMO and the ULP-1 protease. The second output will be added later (the kill switch cassette).  
+
<div id="tmp">
 +
<div style="margin-left:30px;margin-right:30px; width:900px;float:left;"> 
 +
<h2 align="center">Circuit modeling</h2>
 +
<p align = "justify">
 +
By modelling the behavior of the circuit, we are finding answers for the following questions:
 +
  <ol>
 +
<li>How many minutes does the cell lysis take from the point of induction?</li>
 +
<li>How much peptides are produced by the circuit?</li>
 +
<li>How much peptides are still uncleaved by the SUMO at the point of cell lysis?</li>
 +
</ol>
 +
</p>
 +
<p align = "justify">In order to simplify this modeling, we split it up into three different modules which were used as building blocks for the final model. In this way the feasibility of the total model is more easily validated, as the building blocks can be validated independently. The three building blocks are:
 +
<ul style="list-style-type: circle">
 +
  <li> <a href="https://2013.igem.org/Team:TU-Delft/Timer_Plus_Sumo" style="text-decoration: none"" target="_blank"><font color="#0080FF" size="3">Timer plus SUMO</font></a> </li>
 +
<li> <a href="https://2013.igem.org/Team:TU-Delft/KillSwitch" style="text-decoration: none"" target="_blank"><font color="#0080FF" size="3">Kill Switch</font></a> </li>
 +
<li> <a href="https://2013.igem.org/Team:TU-Delft/Timer-Sumo-KillSwitch" style="text-decoration: none"" target="_blank"><font
 +
color="#0080FF" size="3">Timer-SUMO-KillSwitch (total circuit)</font></a> </li>
 +
</ul>
 +
</p>
 +
<p align = "justify">
 +
In the total circuit model the questions stated above are answered. Moreover, to indicate the validity of these answers, we perform a sensitivity analysis to investigate which parameters most influence the results. This gives an indication of the validity as some parameters are quite well known well others are less sure.  
</p>
</p>
-
<br>
 
-
<b><font color="#330000" size="3">SUMO fusion</font></b>
 
-
<p align="justify" margin: 20px >The peptide is expressed with a SUMO tag added to it, expressing the protease will cleave of the SUMO. It is important to accurately know this cleavage rate in order to describe the rate of ‘free’ peptide production.
 
-
<br>
 
-
<b><font color="#330000" size="3">Kill switch</font></b>
 
-
<p align="justify" margin: 20px >
 
-
The kill switch contains two important parts the expression of holin and the antiholin. These two are important tuning parameters to make the system stable and robust. It will be essential to make sure that the ‘free’ peptide reaches a steady state before lysis of the cell. Making sure of this yields the most efficient system, lysis before the cleavage is done yields less active peptides. The tuning parameters will be the respective RBS and the const. promoter, a thorough sensitivity analysis will be performed on this model to derive the optimal conditions and robustness.
 
-
<br>
+
<h2 align="center">Application modeling (band-aid)</h2>
 +
<p align = "justify">
 +
One of the most important parts of the project is to indicate the final application. For that reason, band aid modelling was performed. To be more specific, the idea of the final application is related to placing our engineered organism into a  band aid.The band aid will be located on the wound. In that way, MRSA will be detected and the peptides will be produced and released through the band aid. By modelling the band aid, we are trying to answer questions like:
 +
  <ol>
 +
<li>If the MRSA is detected, is the amount of the produced peptide enough to kill it ?</li>
 +
<li>How many pores are necessary in order to be possible for the peptide to be released?</li>
 +
</ol>
 +
</p>
 +
<h2 align="center">Peptide synthesis</h2>
 +
<p align="justify">
 +
We also decided to design
 +
<a href="https://2013.igem.org/Team:TU-Delft/NovelPeptides" style="text-decoration: none"" target="_blank"><font
 +
color="#0080FF" size="3">novel peptides</font></a>
 +
which meet our specific needs: very toxic for <i>S.aureus</i> (very low MIC), not toxic for humans and <i>E.coli</i>. These properties we also had in mind by choosing from the existing peptides, but the matching peptides did not met the requirements that well.
 +
In order to manage this, we performed data analysis and feature extraction of the existing experimentally validated datasets combined with association rule mining.
 +
</p>
 +
 +
</p>
 +
</div>
 +
</div>
</html>
</html>

Latest revision as of 17:23, 4 October 2013


Modeling



Modeling is the bridge between science and engineering in this project; using the scientific knowledge on our system, we can describe how the system will act and interact. Furthermore, using the quantitative relations derived from the models the circuit has been adjusted and redesigned. This description is used for predicting what will happen in the lab, but also if the project can be applied in reality in a 'band-aid' product. Next to giving a preliminary design of the band-aid, new peptides are designed to give us the properties we want for this application.













Circuit modeling

By modelling the behavior of the circuit, we are finding answers for the following questions:

  1. How many minutes does the cell lysis take from the point of induction?
  2. How much peptides are produced by the circuit?
  3. How much peptides are still uncleaved by the SUMO at the point of cell lysis?

In order to simplify this modeling, we split it up into three different modules which were used as building blocks for the final model. In this way the feasibility of the total model is more easily validated, as the building blocks can be validated independently. The three building blocks are:

In the total circuit model the questions stated above are answered. Moreover, to indicate the validity of these answers, we perform a sensitivity analysis to investigate which parameters most influence the results. This gives an indication of the validity as some parameters are quite well known well others are less sure.

Application modeling (band-aid)

One of the most important parts of the project is to indicate the final application. For that reason, band aid modelling was performed. To be more specific, the idea of the final application is related to placing our engineered organism into a band aid.The band aid will be located on the wound. In that way, MRSA will be detected and the peptides will be produced and released through the band aid. By modelling the band aid, we are trying to answer questions like:

  1. If the MRSA is detected, is the amount of the produced peptide enough to kill it ?
  2. How many pores are necessary in order to be possible for the peptide to be released?

Peptide synthesis

We also decided to design novel peptides which meet our specific needs: very toxic for S.aureus (very low MIC), not toxic for humans and E.coli. These properties we also had in mind by choosing from the existing peptides, but the matching peptides did not met the requirements that well. In order to manage this, we performed data analysis and feature extraction of the existing experimentally validated datasets combined with association rule mining.

Retrieved from "http://2013.igem.org/Team:TU-Delft/Modeling"