IGEM:IMPERIAL/2009/M2/Modelling/Analysis

From OpenWetWare
Jump to navigationJump to search

<html> <style type="text/css"> /*----------------------------------------------------------------------------*/ /* Structure */ /*----------------------------------------------------------------------------*/

  1. II09_mainWrapper{
   width: 800px;
   align: center;
   border: none;
   margin: 0px auto;
   padding: 0px;

}

/*----------------------------------------------------------------------------*/ /* Content */ /*----------------------------------------------------------------------------*/

  1. II09_content_wrapper {
   width: 550px;
   float: left;
   margin-top: 5px;
   margin-bottom: 5px;
   position:relative;

}

  1. II09_content_boxtop {
   width: 550px;
   height: 10px;
   background:url(http://2009.igem.org/wiki/images/c/c8/II09_content_top.png) no-repeat bottom left;
   position: relative;
   float: left;

}

  1. II09_content_boxbottom {
   width: 550px;
   height: 10px;
   background:url(http://2009.igem.org/wiki/images/b/b4/II09_content_bottom.png) no-repeat top left;
   position: relative;
   float: left;

}

  1. II09_content {
   width: 550px;
   padding: 10px;
   background-color:#ffffff;
   border-left: 1px solid #ccc;
   border-right: 1px solid #ccc;
   position: relative;
   float: left;
   font-size: 9pt;
   text-align: justify;

}

/*----------------------------------------------------------------------------*/ /* Tabs */ /*----------------------------------------------------------------------------*/

.II09_Tabs_Blue { 

 float:left;
 width:100%;
 background:#CCCCFF url("http://openwetware.org/images/b/bb/SDbg.gif") repeat-x bottom;
 font-size:93%;
 line-height:normal;
 margin: 0;
 padding: 0;

}

.II09_Tabs_Blue ul { 

 margin:0;
 padding:10px 10px 0;
 list-style:none;

} .II09_Tabs_Blue li { 

 float:left;
 background:url("http://openwetware.org/images/b/b7/SDleft.gif") no-repeat left top;
 margin:0;
 padding:0 0 0 9px;

}

.II09_Tabs_Blue b { 

 float:left;
 display:block;
 background:url("http://openwetware.org/images/f/f8/SDright.gif") no-repeat right top;
 padding:5px 15px 4px 6px;
 text-decoration:none;
 font-weight:bold;
 color:#765;

} </style> </html>

<html> <body> </html> <html>

<head> <style type="text/css">

  1. II09_Header{
 border-top: 1px solid #7b7b7b;
 border-left: 1px solid #7b7b7b;
 border-right: 1px solid #7b7b7b;
 border-bottom: none;

 background: url(http://2009.igem.org/wiki/images/3/39/II09_Banner.jpg);
 background-position: right -75px;
 width: 783px;
 height: 150px;
 
 margin-left:15px;
 align: right;

} </style> </head>

<body>

The E.ncapsulator: the disease killer

</body> </html> <html> <head> <style type="text/css">

  1. II09_Breadcrumb{
  backgrounewd: #7b7b7b;
  background: url(http://2008.igem.org/wiki/images/c/c8/Tudelft_menu_header_bg_1.gif);
  border-top: none;
  border-left: 1px #7b7b7b solid;
  border-right: 1px #7b7b7b solid;
  border-bottom: 1px #7b7b7b solid;
  
  filter:alpha(opacity=100);
  -moz-opacity:1.00;
  opacity:1.0;
  text-color: #000000;
  padding-left: 10px;
  margin-left: 15px;
  width: 773px;

} </style> </head>

<body>

<script type="text/javascript">

var address = document.location.href; var addressSplit = address.split("/");

document.write('<a href="http://2009.igem.org/' +addressSplit[3]+ '">Home (' +addressSplit[3]+ ')</a>');

for (i=4;i<8;i++){ 

  if (addressSplit[i]!=undefined){
     document.write(' | ');
     document.write('<a href="' +addressSplit[i]+ '">' +addressSplit[i]+ '</a>');
  }

} 

  document.write('');

</script>

</body> </html> <html> <style type="text/css"> /*----------------------------------------------------------------------------*/ /* Menu */ /*----------------------------------------------------------------------------*/

  1. menu {
   width: 200px;
   margin: 5px 15px 0 15px;
   position: relative;
   float: left;

}

  1. menu ul {
   padding: 0;
   margin: 0 0 10px 0;
   list-style: none;

}

  1. menu li {
   margin:0;

}

  1. menu a {
   display: block;
   width: 185px;
   height: 19px;
   margin-top: 1px;
   margin-left:15px;
   background: url(http://openwetware.org/images/4/46/II09_Menu_ItemHover.png) no-repeat right top;
   padding: 2px 4px;
   text-decoration: none;
   color: #fff;

}

  1. menu a:hover {
   display: block;
   width: 185px;
   height: 19px;
   margin-top: 1px;
   margin-left:15px;
   background: url(http://openwetware.org/images/b/bf/II09_Menu_Item.png) no-repeat right top;
   padding: 2px 4px;
   color: #000;

}

  1. menu .selflink {
   /*font-weight:bold;
   width: 200px;
   border: 1px solid #bbb;
   background: url(http://2008.igem.org/wiki/images/c/c8/Tudelft_menu_header_bg_1.gif) repeat-x bottom;
   color: #111;
   padding: 2px 4px;*/

   display: block;
   width: 200px;
   height: 30px;
   margin-top: 1px;
   border: 1px solid #bbb;
   background: url(http://2008.igem.org/wiki/images/c/c8/Tudelft_menu_header_bg_1.gif) repeat-x left bottom;
   padding: 2px 4px;
   color: #000;

}

  1. menu a.external {
   margin: 0;
   padding: 0;
   width: 156px;

}

.menu_header { 

   font-weight:bold;
   width: 200px;
   border: 1px solid #bbb;
   background: url(http://2008.igem.org/wiki/images/c/c8/Tudelft_menu_header_bg_1.gif) repeat-x bottom;
   color: #111;
   padding: 2px 4px;
   text-align:left;

} </style>

</html> <html>


<img src="http://2008.igem.org/wiki/images/a/a1/Tudelft_content_top.png" width="572">


<script type="text/javascript"> var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www."); document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E")); </script> <script type="text/javascript"> try { var pageTracker = _gat._getTracker("UA-11206997-1"); pageTracker._trackPageview(); } catch(err) {}</script>

</html>



Preliminary Model 1: Genetic circuit

Hypothesis

  • When glucose concentrations are above threshold, there would not be any activation of production of colanic acid or trehalose.
  • When glucose concentrations decrease below threshold, there will be strong activation of M2 and there will be an increase in protein production in the system.
  • For decreased concentration of glucose, there will be increased amounts of colanic acid and trehalose produced.

Equations

[math]\displaystyle{ \begin{alignat}{2} \frac{d[m_i]}{dt} = \frac{km_i^{n_i}}{{[g]}^{n_i}+ km_i^{n_i}} - dm_i*[m_i] \qquad (1)\\ \frac{d[p_i]}{dt} = [m_i]*kp_i - dp_i*[p_i] \qquad (2)\\ where\ i = 1, 2, 3, 4, 5 \end{alignat} }[/math]

Legend

Term Variable/Parameter Meaning/description
1 - RcsB
2 - B3023
3 - Waal Ligase
4 - OtsA
5 - OtsB
g Variable Concentration of glucose
mi Variable Concentration of ith mRNA
pi Variable Concentration of ith protein
ni Parameter Hill coefficient of ith mRNA


Explanation of equations

  • In equation (1), we have used a repressing hill function of glucose. This is because glucose, represses CRP, which activates our system. A decrease in [glucose] below threshold will activate M2 strongly.
  • The genes are produced in parallel, hence the repressing hill function will appear in the mRNA equations, for all our proteins.


Simulations

Simulation 1: Effects of increasing glucose concentrations on production of protein

Explanations

  • When there is a decrease in glucose concentration beyond threshold, there is a great increase in amount and rate of protein production.
  • A short time delay is seen as transcription and translation takes time.

Data Fitting

Matlab files

References

<html>

<img src="http://2008.igem.org/wiki/images/8/89/Tudelft_content_bottom.png" width="572">

</body> </html>







































<html> <style type="text/css">

  1. II09_Footer{
 width:763px;
 margin-left: 15px;
 background: url(http://2008.igem.org/wiki/images/c/c8/Tudelft_menu_header_bg_1.gif) repeat-x;
 background-position: bottom;
 padding: 10px;
 border-top: 1px #7b7b7b solid;
 border-left: 1px #7b7b7b solid;
 border-right: 1px #7b7b7b solid;
 border-bottom: 1px #7b7b7b solid;
 position:relative;
 float: left;

} </style>

<body>

</body> </html>

Retrieved from "https://openwetware.org/mediawiki/index.php?title=IGEM:IMPERIAL/2009/M2/Modelling/Analysis&oldid=346788"