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| - | <html>
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| - | <head>
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| | | | |
| - | <!-- affichage des maths -->
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| - | <script type="text/javascript"
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| - | src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
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| - | </script>
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| - |
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| - | <script type="text/x-mathjax-config">
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| - | MathJax.Hub.Config({
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| - | tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']]}
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| - | });
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| - | </script>
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| - | <script type="text/javascript" src="path-to-mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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| - |
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| - |
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| - | <style>
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| - |
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| - | #menubar .left-menu noprint{
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| - | color: white;
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| - | }
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| - |
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| - | .right-menu{
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| - | background: none;
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| - | }
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| - |
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| - |
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| - | #content {
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| - | background: none;
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| - | padding:0;
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| - | width:100%;
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| - | border:0;
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| - | margin-top:Opx;
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| - | }
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| - |
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| - |
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| - |
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| - | #p-logo {
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| - | display:none;
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| - | }
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| - |
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| - |
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| - | #top-section {
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| - | border:none;
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| - | margin: 0 auto;
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| - | height:0px ! important;
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| - | width:100%;
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| - | }
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| - |
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| - | img.bg_team {
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| - | /* Set rules to fill background */
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| - | min-height: 100%;
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| - | min-width: 1024px;
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| - |
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| - | /* Set up proportionate scaling */
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| - | width: 100%;
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| - | height: auto;
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| - |
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| - | /* Set up positioning */
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| - | position: fixed;
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| - | top: 0;
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| - | left: 0;
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| - | z-index:-1;
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| - | }
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| - |
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| - |
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| - |
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| - | #catlinks{
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| - | width:0px;
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| - | height:0px;
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| - | display:none;
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| - | }
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| - | #footer-box{
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| - | width:0px;
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| - | height:0px;
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| - | display:none;
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| - | }
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| - | #search-controls {
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| - | display:none;
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| - | }
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| - |
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| - | #globalWrapper{
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| - | margin:0;
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| - | padding:0;
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| - | border:0;
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| - | }
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| - | #top-section {
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| - | border:none;
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| - | margin: 0 auto;
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| - | height:0px ! important;
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| - | width:100%;
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| - | }
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| - | .firstHeading {
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| - | display:none;
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| - | }
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| - |
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| - |
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| - |
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| - |
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| - | body
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| - | {
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| - | background-image: url("https://static.igem.org/mediawiki/2011/0/04/Fondt.png");
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| - | background-repeat: repeat-x;
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| - |
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| - | background-color: #b4b4b4;
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| - | }
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| - |
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| - |
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| - | #header
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| - | {
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| - | background-image: url("https://static.igem.org/mediawiki/2011/1/11/Haut.png");
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| - | width:985px;
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| - | height:170px;
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| - | margin: auto;
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| - | padding-top: 10px;
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| - | margin-top: 0px;
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| - | }
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| - | #main
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| - | {
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| - | width:980px;
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| - | height:900px;/* A faire varier pour que la barre rouge soit au bonne endroit */
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| - | margin: auto;
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| - | padding-left: 5px;
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| - | }
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| - |
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| - | #maintext
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| - | {
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| - | float: left;
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| - | width:980px;
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| - | }
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| - |
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| - | #menu a{
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| - | color: red;
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| - | }
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| - |
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| - | #hmaint
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| - | {
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| - | color: white;
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| - | font-weight: bolder;
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| - | float: left;
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| - | background-image: url("https://static.igem.org/mediawiki/2011/e/e1/Ulbmaintext.png");
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| - | background-repeat:no-repeat;
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| - | width:985px;
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| - | height: 16px;
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| - | padding-left: 4px;
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| - | }
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| - |
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| - | #maint
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| - | {
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| - | float: left;
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| - | padding: 4px;
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| - | width:980px;
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| - | /* Valeur du height de maintext -16px */
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| - | border: 2px inset #27303e;
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| - | text-align: justify;
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| - | background-color: white;
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| - | }
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| - |
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| - | #facebook{
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| - | margin-left: 707px;
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| - | height:200px;
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| - | }
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| - | #joinus{
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| - | background-repeat: no-repeat;
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| - | padding-left: 4px;
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| - | color: white;
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| - | font-weight: bolder;
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| - | width:274px;
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| - | height:16px;
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| - | background-image: url("https://static.igem.org/mediawiki/2011/6/6d/Ulbfacebook.png");
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| - | }
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| - |
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| - | #module{
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| - | background-color: white;
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| - | width:270px;
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| - | height:400px;
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| - | border: 2px inset #27303e;
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| - | clear:float;
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| - | }
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| - |
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| - | #footer{
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| - | width: 980px;
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| - | height: 201px;
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| - | margin:auto;
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| - | text-align: left;
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| - | padding-left: 5px;
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| - |
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| - | }
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| - |
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| - | #sponsor{
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| - | width: 440px;
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| - | height: 201px;
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| - | float: left;
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| - | }
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| - |
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| - | #sponsort{
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| - | background-repeat: no-repeat;
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| - | padding-left:4px;
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| - | color: white;
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| - | font-weight: bolder;
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| - | width:440px;
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| - | height:16px;
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| - | background-image: url("https://static.igem.org/mediawiki/2011/1/11/Ulbsponsor.png");
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| - | }
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| - |
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| - | #sponsori{
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| - | font-weight: bolder;
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| - | background-image:url("https://static.igem.org/mediawiki/2011/e/ed/Logosponsors.png");
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| - | padding: 4px;
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| - | color: #690115;
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| - | background-color: white;
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| - | width:428px;
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| - | height:175px;
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| - | border: 2px inset #27303e;
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| - | text-align:center;
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| - | }
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| - |
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| - | #photo{
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| - | padding-top: 8px;
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| - | background-color: black;
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| - | background-repeat: no-repeat;
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| - | float: left;
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| - | width:245px;
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| - | height: 195px;
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| - | margin-left: 10px;
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| - | }
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| - |
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| - | #photot
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| - | {
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| - | width:247px;
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| - | height: 16px;
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| - | background-image: url("https://static.igem.org/mediawiki/2011/0/0b/Ulbphoto.png");
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| - | }
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| - |
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| - | #photoi
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| - | {
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| - | width:247px;
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| - | height: 187px;
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| - | background-color: black;
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| - | }
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| - |
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| - | #event{
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| - | float: left;
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| - | margin-left: 10px;
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| - | width: 274px;
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| - | height: 201px;
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| - | }
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| - |
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| - | #nextevent{
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| - | background-repeat: no-repeat;
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| - | padding-left: 4px;
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| - | color: white;
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| - | font-weight: bolder;
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| - | width:274px;
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| - | height:16px;
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| - | background-image: url("https://static.igem.org/mediawiki/2011/a/a8/Ulbnextevent.png");
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| - | }
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| - |
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| - | #eventi{
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| - | padding: 4px;
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| - | color: white
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| - | width:266px;
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| - | height: 175px;
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| - | border: 2px inset #27303e;
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| - | background-color: #690115;
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| - | }
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| - |
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| - | #bas{
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| - | margin-top: 4px;
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| - | background-image: url("https://static.igem.org/mediawiki/2011/3/34/Ulbbas.png");
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| - | background-repeat: repeat-x;
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| - | height: 30px;
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| - | margin: auto;
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| - | }
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| - |
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| - | #basi{
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| - | padding-top: 5px;
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| - | color: white;
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| - | text-align: center;
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| - | font-size: 11px;
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| - | }
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| - |
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| - | #basi a{
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| - | color: white;
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| - | }
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| - |
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| - |
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| - | /*code justine */
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| - |
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| - | #menu a /* pour changer les laids liens bleu soulignÈs*/
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| - | {
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| - | position:relative;
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| - | color: white;
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| - | text-decoration: none;
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| - | text-align: center;
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| - | }
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| - |
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| - | #menu
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| - | {
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| - | position:relative;
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| - | top:126px;
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| - | font-size: 14px;
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| - | color:white;
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| - | font-weight: bolder;
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| - | widht: 900px;
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| - |
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| - |
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| - | }
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| - |
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| - | #menu1 /* mise en forme menu1, plein de choses ‡ virer sur la version dÈfinitive*/
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| - | {
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| - | width:800px; /* version dÈfinitive:virer ca*/
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| - | height: 20px; /* version dÈfinitive:virer ca*/
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| - | font-size: 14px;
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| - | text-align:center;
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| - | }
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| - |
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| - | #home
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| - | {
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| - | float:left;
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| - | position: absolute;
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| - | width: 50px;
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| - | height: 20px;
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| - | text-align:center;
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| - |
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| - | }
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| - |
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| - | #project
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| - | {
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| - | float:left;
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| - | position: relative;
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| - | left: 70px;
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| - | width: 70px;
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| - | height: 15px;
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| - | text-align:center;
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| - |
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| - | }
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| - |
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| - | #modeling
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| - | {
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| - | float:left;
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| - | text-align:center;
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| - | position: relative;
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| - | width: 90px;
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| - | height: 20px;
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| - | left:80px;
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| - | }
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| - |
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| - | #results
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| - | {
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| - | float:left;
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| - | position: relative;
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| - | width: 70px;
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| - | height: 20px;
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| - | left:90px;
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| - | text-align:center;
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| - | }
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| - |
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| - | #parts
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| - | {
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| - | float:left;
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| - | position: relative;
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| - | width: 55px;
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| - | height: 20px;
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| - | left:100px;
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| - | text-align:center;
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| - | }
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| - |
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| - | #human
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| - | {
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| - | float:left;
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| - | position: relative;
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| - | width: 130px;
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| - | height: 20px;
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| - | left:110px;
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| - | text-align:center;
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| - | }
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| - |
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| - | #team
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| - | {
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| - | float:left;
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| - | position: relative;
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| - | width: 85px;
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| - | height: 20px;
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| - | left:110px;
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| - | text-align:center;
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| - | margin : auto;
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| - | }
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| - |
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| - | #team td
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| - | {
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| - | text-align:center;
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| - | }
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| - |
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| - | #sponsors
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| - | {
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| - | float:left;
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| - | position: relative;
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| - | width: 90px;
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| - | height: 20px;
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| - | left:110px;
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| - | text-align:center;
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| - | }
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| - |
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| - | .select
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| - | {
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| - | height:21px; /* si tu modifies hauteur du menu1, il faut modifier ca aussi. Il ne s'adapte pas automatiquement, parce qu'il fait en fonctiond ela taille du texte */
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| - | background-color:rgb(105,1,21);
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| - | }
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| - |
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| - | #menu2
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| - | {
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| - | width:985px;
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| - | height:18px;
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| - | font-size: 12px;
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| - | padding-top: 1px;
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| - | }
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| - |
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| - | #menu2project /* juste pour dÈcaler l'Ècriture des sous-menus. plus facile que de repositionner chaque sous-menu, surtout quand c'ets les mÍmes pour modeling et results*/
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| - | {
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| - | position:relative;
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| - | left: 61px;
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| - | width:807px; /* version dÈfinitive:virer ca*/
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| - | height:18px; /* version dÈfinitive:virer ca*/
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| - | }
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| - |
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| - |
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| - | #menu2results /* juste pour dÈcaler l'Ècriture des sous-menus. plus facile que de repositionner chaque sous-menu, surtout quand c'ets les mÍmes pour modeling et results*/
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| - | {
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| - | position:relative;
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| - | left: 220px;
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| - | width:807px; /* version dÈfinitive:virer ca*/
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| - | height:18px; /* version dÈfinitive:virer ca*/
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| - | }
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| - |
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| - | #menu2modeling
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| - | {
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| - | position:relative;
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| - | left:132px;
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| - | width:888px; /* version dÈfinitive:virer ca*/
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| - | height:18px; /* version dÈfinitive:virer ca*/
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| - | }
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| - |
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| - | #souspindel /* mise en forme du sous-menu "pindel", aussi bien pour modeling que result*/
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| - | {
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| - | position:absolute;
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| - | left:50px;
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| - | height:18px;
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| - | text-align:center;
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| - | width:50px;
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| - | }
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| - |
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| - | #soushelper /* mise en forme du sous-menu "plasmide helper", aussi bien pour modeling que result*/
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| - | {
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| - | position:absolute;
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| - | left:111px;
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| - | height:18px;
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| - | text-align:center;
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| - | width:80px;
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| - | top:0px;
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| - | }
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| - |
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| - | #sousproof /* mise en forme du sous-menu "proof of concept", aussi bien pour modeling que result*/
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| - | {
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| - | position:absolute;
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| - | left:193px;
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| - | height:18px;
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| - | text-align:center;
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| - | width:120px;
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| - | top:0px;
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| - | }
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| - |
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| - |
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| - | .left-menu, .left-menu a {
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| - | color: white;
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| - | left: 0px;
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| - | text-align: left;
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| - | color:transparent;
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| - | text-transform: lowercase;
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| - |
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| - | }
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| - | .left-menu a:hover {
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| - | }
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| - | .left-menu:hover {
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| - | color: white;
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| - | background:none;
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| - | }
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| - | .right-menu, .right-menu a {
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| - | right: 0px;
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| - | text-align: right;
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| - | color: white;
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| - |
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| - | }
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| - | #menubar ul {
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| - | color: white;
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| - | list-style: none;
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| - | }
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| - | #menubar li {
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| - | display: inline;
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| - | position: relative;
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| - | cursor: pointer;
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| - | padding-left: 0px;
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| - | padding-right: 0px;
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| - | }
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| - | .left-menu li a {
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| - | padding: 0px 10px 0px 0px;
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| - | }
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| - | .left-menu .selected {
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| - | # color:white;
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| - | }
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| - | #.left-menu .selected:hover {
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| - | # color:white;
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| - | #}
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| - |
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| - | .left-menu:hover a {
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| - | color: white;
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| - | }
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| - | .right-menu li {
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| - | # background: none;
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| - | }
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| - | .right-menu li a {
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| - | padding: 0px 15px 0px 0px;
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| - | color: white;
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| - | background: none;
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| - | }
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| - | .right-menu li a:hover {
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| - | color: white;
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| - | }
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| - |
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| - | #menu a
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| - | {
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| - | margin-left:20px; /*espace entre les lien*/
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| - | display:block; /*Pour que le lien soit un vrai bloc*/
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| - | float:left; /*Pour que les blocs soient alignés horizontalement (essayez de l'enlever pour voir)*/
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| - | height:30px; /*La même hauteur que notre menu*/
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| - | border:none; /*On enlève les bordures (enfin, on ne les met pas, même s'il n'y en avait pas)*/
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| - | }
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| - |
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| - | #couleur
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| - | {
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| - | padding-left: 5px;
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| - | padding-right:5px;
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| - | background-color: #690115;
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| - | }
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| - |
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| - | #sousm
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| - | {
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| - | clear:left;
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| - | position:relative;
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| - | top:112px;
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| - | margin-left: 135px; /*tu change ici pour le bouger horizontalement*/
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| - | color:white;
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| - | widht: 900px;
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| - | }
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| - | #sousm a
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| - | {
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| - | position:relative;
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| - | color: white;
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| - | text-decoration: none;
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| - | text-align: center;
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| - | margin-left:20px; /*espace entre les lien*/
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| - | display:block; /*Pour que le lien soit un vrai bloc*/
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| - | float:left; /*Pour que les blocs soient alignés horizontalement (essayez de l'enlever pour voir)*/
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| - | height:30px; /*La même hauteur que notre menu*/
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| - | border:none; /*On enlève les bordures (enfin, on ne les met pas, même s'il n'y en avait pas)*/
| |
| - | }
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| - |
| |
| - | </style>
| |
| - |
| |
| - | </head>
| |
| - |
| |
| - | <div id="header"> <!-- Images de logo -->
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| - | <div id="menu">
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| - | <a href="https://2011.igem.org/Team:ULB-Brussels/modeling/introduction">Introduction</a>
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| - | <a href="https://2011.igem.org/Team:ULB-Brussels/modeling/30">Phase at 30°C</a>
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| - | <a href="https://2011.igem.org/Team:ULB-Brussels/modeling/42">Phase at 42°C</a>
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| - | <a href="https://2011.igem.org/Team:ULB-Brussels/modeling/comparison">Comparison with the Wet Lab work </a>
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| - | <a href="https://2011.igem.org/Team:ULB-Brussels/modeling/conclusion">Conclusion</a>
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| - | Modeling : introduction </div>
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| - | <div id="maint">
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| - | We will consider a population of <em>Escherichia Coli</em>, that possesses the Pindel plasmid, inserted beforehand by electroporation. The replication origin (ORI) of this plasmid is activated by RepA101, produced by the plasmid itself; at $42^\circ$C, this protein (RepA101) becomes rapidly inactive. Also, the plasmid includes a three-genes sequence coding proteins (Red recombinase) inducing the insertion, in the DNA, of a gene "X" (at which we added, as a control, a resistance gene to chloramphenicol). The promotor of this three-genes sequence, Pbad, is activated by arabinose. Pindel includes in addition a coding sequence for flippase, whose promotor is blocked by a thermo-sensible repressor (at $42^\circ$C, the promotor isn't repressed at all, whereas at $30^\circ$C it is almost completely repressed, to $\ldots\%$). Those two sequences follow each other, but are encrypted in opposite directions, which eventually leads to an interference phenomenal. Furthermore, flippase, originally coming from yeast, is entirely active at $30^\circ$C, but is disabled at $42^\circ$C. Red recombinase recognizes the gene sequence to insert (the "X" gene followed by the resistance gene) and insert them in the bacteria's genome, while flippase excise the resistance to chloramphenicol package.
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| - | </p>
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| - | <p>
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| - | At start, we place bacteria possessing Pindel at $30^\circ$C on arabinose. The Red recombinase genes are then expressed because of the presence of arabinose. In parallel, a small amount of flippase is produced: in section (2.1), we will study, by a computer simulation, the interference that occurs during the transcription of those two opposite-oriented genes, which will give us an idea of the probability that the flippase sequence eventually is transcribed. Nevertheless, we do expect that the amount of flippase produced stays low. After a while, those bacteria are electroporated in order to insert the X gene.
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| - | </p>
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| - | <p>
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| - | By testing the resistance to chloramphenicol, we can determine which colony's integrated the X gene, coupled with the resistance gene. We take some of those bacteria and place them at $42^\circ$C on glucose. Flippase is then fully produced, and is able to excise the chloramphenicol-resistance package. At the same time, the RepA101-enzyme, allowing the Pindel plasmid to reproduce is strongly suppressed, and becomes fast completely inactive. In consequence, the total number of plasmids remains constant; and the increase in population will dilute that amount of plasmids among the bacteria, leaving most of them without any plasmid. In the same way, flippase stops being produced, and therefore, by natural degradation, disappears. We thus obtain a population possessing the X gene, but devoid of the chloramphenicol resistance nor the Pindel plasmid.
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| - | </p>
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| - | <p>
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| - | It is this whole process that we will try to modelise here. In our model, we considered a few different parameters, of which we will estimate the values, based on biological considerations. Afterwards, we will analyze the coherence of our predictions together with the results of the experiments, or if necessary, adapt the model itself.
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| - | </p>
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| - | <p>
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| - | Let us begin with a proper definition of the different biological functions we are to study:
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| - | <ul>
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| - | <li>$N$ : total amount of bacteria in the considered population;</li>
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| - | <li>$P$ : average amount of Pindel plasmids per bacterium;</li>
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| - | <li>$E_{tot}$ : average amount of RepA101 enzymes per bacterium;</li>
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| - | <li>$E$ : average amount of RepA101 enzymes active per bacterium;</li>
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| - | <li>$F$ : average amount of flippase per bacterium;</li>
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| - | <li>$G_i (i=1,2,3)$ : average amount of the protein $i$ for the Red recombinase, per bacterium.</li>
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| - | </ul>
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| - | iGEM ULB Brussels Team - <a href="mailto:sgerard@ulb.ac.be">Contact us</a>
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| - | ==
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| - |
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| - | == Headline text ==
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