Team:UANL Mty-Mexico/Project/Circuit

From 2011.igem.org

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{{:Team:UANL_Mty-Mexico/Templates/Banner-blueprints}}
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{{:Team:UANL_Mty-Mexico/Templates/Menu-template}}
<html>
<html>
<head>
<head>
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/-->
/-->
-
        <!-- Include jQuery first. -->
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<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
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<script type="text/javascript" src="http://www.genobiotec2011.org/iGEMwiki/jquery-1.3.2.min.js"></script>
+
  <title>Team: UANL_Mty-Mexico</title>
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-
        <!-- Include the below script, Copyright 2010, Brandon Aaron (http://brandonaaron.net/) for scrollwheel support. -->
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<script type="text/javascript" src="http://www.genobiotec2011.org/iGEMwiki/jquery-mousewheel/jquery.mousewheel.min.js"></script>
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<link rel="stylesheet" type="text/css" href="http://www.genobiotec2011.org/iGEMwiki/slidedeck.skin.css" media="screen" />
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        <!-- Styles for the skin that only load for Internet Explorer -->
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        <!--[if lte IE 8]>
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        <link rel="stylesheet" type="text/css" href="http://www.genobiotec2011.org/iGEMwiki/slidedeck.skin.ie.css" media="screen,handheld" />
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        <![endif]-->
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-
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        <!-- Include the SlideDeck jQuery script. -->
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<script type="text/javascript" src="http://www.genobiotec2011.org/iGEMwiki/slidedeck.jquery.lite.pack.js"></script>
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-
       
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        <style type="text/css">
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            #slidedeck_frame {
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width: 665px;
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height: 200px;
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-
            }       
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        </style>
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<style>
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#botonera {
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}
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.lateral-button {
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font-family: Verdana, Geneva, sans-serif;
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font-size: 12px;
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font-weight: bold;
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color: #036;
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text-decoration: none;
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padding-top: 10px;
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padding-bottom: 10px;
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padding-left: 10px;
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padding-right: 10px;
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margin: 2px;
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-webkit-border-radius: 5px;
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-moz-border-radius: 5px;
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  border-radius: 5px;
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  cursor: pointer;
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  text-align: center;
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}
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.lateral-button:hover {
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font-family: Verdana, Geneva, sans-serif;
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font-size: 12px;
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font-weight: bolder;
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color: #036;
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text-decoration:underline;
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background-color:#CCC;
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color:#000;
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padding-top: 10px;
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padding-bottom: 10px;
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padding-left: 10px;
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padding-right: 10px;
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margin: 2px;
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-webkit-border-radius: 5px;
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  border-radius: 5px;
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  cursor: pointer;
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.lateral-button a {
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font-family: Verdana, Geneva, sans-serif;
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font-size: 12px;
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font-weight: bold;
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color: #036;
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text-decoration: none;
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padding-top: 10px;
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padding-bottom: 10px;
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padding-left: 10px;
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padding-right: 10px;
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margin: 2px;
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-webkit-border-radius: 5px;
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  border-radius: 5px;
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  cursor: pointer;
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font-family: Verdana, Geneva, sans-serif;
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font-size: 12px;
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font-weight: bolder;
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color: #036;
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text-decoration:underline;
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background-color:#CCC;
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color:#000;
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padding-top: 10px;
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padding-bottom: 10px;
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padding-left: 10px;
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padding-right: 10px;
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margin: 2px;
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-webkit-border-radius: 5px;
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-moz-border-radius: 5px;
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  border-radius: 5px;
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  cursor: pointer;
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.style5.top-menu {
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  background: transparent;
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  margin: auto;
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  width: 950px;
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  margin-top: -35px;
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}
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<META NAME="keywords" CONTENT="UANL,iGEM,Universidad,Autonoma,Nuevo,Leon,Biphasic,switch,Lambda,Genetic,Regulation,Quorum,Sensing,pRM,OL,Green Light,Red Light">
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.style5 ul.top-menu-main {
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<META NAME="description" CONTENT="iGEM-UANL is the representative team from Universidad Autonoma de Nuevo León, at Monterrey, México. This team is composed of ten students who spent their summer in the lab, having fun with transformations, constructions and plasmidic DNA extractions. This">
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  margin: auto;
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<META NAME="abstract" CONTENT="Information processing through living things remains a challenge to science. Genetic logic-gates and">
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<META NAME="author" CONTENT="iGEM-UANL">
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  font-family: Georgia, Tahoma, Arial;
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<META NAME="robots" CONTENT="FOLLOW,INDEX">
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  background: #000;
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  border-right: 1px solid #afafaf;
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<link href="http://www.asebiogen.org/igemuanl/mainStyle.css" rel="stylesheet" type="text/css">
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  border-right: none;
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}
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.style5 ul.top-menu-main > li:hover .menu-item-text  
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{color: #cfcfcf; text-shadow: 0 1px 0 #0C131C;}
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<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/jquery-1.3.2.min.js"></script>
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  background: #333 transparent;
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  color: #fff;
 
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  text-decoration: none;
 
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}
 
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  color: #fff;
 
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}
 
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.style5 ul.top-menu-main > li > a {
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<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/jquery-1.3.2.min.js"></script>
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  padding: 10px 10px;
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}
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.style5 ul.top-submenu {
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<script type='text/javascript' src='http://www.asebiogen.org/igemuanl/jquery.easing.1.3.js'></script>
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  -moz-box-shadow: 0 0 8px #333;
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<script type='text/javascript' src='http://www.asebiogen.org/igemuanl/jquery.slideup.menu.1.0.min.js'></script>
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  -webkit-box-shadow: 0 0 8px #333;
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  /*box-shadow: 0 0 8px #333;*/
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  box-shadow: 0 0 8px #fff;
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}
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<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/jquery.scroll-follow.js"></script>
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<script type="text/javascript" src="http://www.asebiogen.org/igemuanl/Scripts/slimbox2/js/slimbox2.js"></script>
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  margin: 0px;
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  padding: 5px 10px;
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.style5 ul.top-submenu > li a {
 
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/* Wiki Hacks - START */
 
-
/* Author: Pieter van Boheemen */
 
-
/* Team: TU Delft */
 
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#globalWrapper { background-color: transparent; border: none; margin: 0; padding: 0; width: 100%; height:100%;}
 
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#content { background-color: transparent; border: none; padding: 0; margin: 0; width: 100%; overflow: hidden; height:100%;}
 
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#p-logo { height:1px; overflow:hidden; display: none;}
 
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#search-controls { overflow:hidden; display:block; background: none; position: absolute; top: 100px; right: 40px;}
 
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/*
 
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.left-menu { width: 500px !important; display:block; margin-top:-80px; border: none; text-align: right;}
 
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.left-menu ul { border: none; }
 
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#menubar.right-menu { width:300px; display:block; float:left; margin-top:-80px; border: none;}
 
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#footer-box { background-image: url(http://www.genobiotec2011.org/iGEMwiki/images/back.jpg); background-color: #000000; width: 100%; margin: -10px; padding: 20px 0; display: none;}
 
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.visualClear { display: none; }
 
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#search-controls { display:none; }
 
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h3#siteSub { display: none;}
 
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//p:first-child { display: none;}
 
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#footer { border: none; width: 965px; margin: 0 auto; padding: 0;}
 
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.firstHeading { display: none;}
 
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#f-list a { color: #333; font-size: 10px;}
 
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#f-list a:hover { color: #666; height: 100px;}
 
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#footer ul { margin: 0; padding: 0;}
 
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#footer ul li { margin-top: 0; margin-bottom: 0; margin-left: 10px; margin-right: 10px; padding: 0;}
 
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/* Wiki Hacks - END */
 
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body {
 
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margin: 0;
 
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padding: 0;
 
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color: #333;
 
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font-family: tahoma, arial;
 
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font-size: 10px;
 
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background-color: #333;
 
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background-image: url(http://www.genobiotec2011.org/iGEMwiki/images/back.jpg);
 
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a {
 
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color: #fff;
 
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text-decoration: none;
 
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font-size: 10px;
 
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/* float clearing for IE6 */
 
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* html .clearfix{
 
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/* float clearing for IE7 */
 
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*+html .clearfix{
 
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content: ".";
 
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width: 964px;
 
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margin: auto;
 
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background-color: #FFF;
 
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font-size: 12px;
 
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z-index: 10;
 
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text-align: center;
 
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padding-right: 10px;
 
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padding-bottom: 10px;
 
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color: #ffffff;
 
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text-decoration:underline;
 
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font-weight:bolder;
 
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text-align:center;
 
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}
 
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#leftColumn1 {
 
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}
 
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#ColorHeader {
 
-
background-color:#FFF;
 
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color: #333;
 
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padding-top: 5;
 
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padding-bottom: 5;
 
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padding-left: 5;
 
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font-family: "Arial Black";
 
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font-size: 30px;
 
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}
 
-
 
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#project-column p {
 
-
background-color:#FFF;
 
-
color:#000;
 
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font: Tahoma;
 
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font-size: 14px;
 
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}
 
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#project-column {
 
-
width:340px;
 
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padding-top: 15;
 
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padding-right: 15;
 
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padding-bottom: 5;
 
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padding-left: 0;
 
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float: left;
 
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}
 
-
 
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#header-project-column {
 
-
background-color:#036;
 
-
color: #FFF;
 
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padding-top: 5;
 
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padding-right: 5;
 
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padding-bottom: 5;
 
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padding-left: 10px;
 
-
font-family: "Arial Black";
 
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font-size: 18px;
 
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text-align:left;
 
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-
 
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#header-navigation {
 
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color: #333;
 
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font-family: "Arial Black";
 
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font-size: 14px;
 
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text-align:center;
 
-
text-decoration:underline;
 
-
text-transform:uppercase;
 
-
 
-
}
 
-
 
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-
 
-
}
 
-
 
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#About-column {
 
-
float:left;
 
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width:320px;
 
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padding-top: 15;
 
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<div class="br"></div><div class="br"></div>
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-
<div class="br2"></div><div class="br2"></div><div class="br2"></div><div class="br2"></div> <div class="br2"></div>           
+
<div class="br2"></div>
-
          <a name="circuit"></a>The Whole Genetic Circuit
+
<div class="br2"></div>
-
<div class="br2"></div><div class="br2"></div><div class="br2"></div><div class="br2"></div> <div class="br2"></div>         
+
<div class="br2"></div>  
 +
        <a name="circuit"></a>The Whole Genetic Circuit
 +
<div class="br2"></div>
 +
<div class="br2"></div>
 +
<div class="br2"></div>        
       </div>
       </div>
<p>
<p>
Once explained the <span class="content-link"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Mechanism" title="Mechanism Description">mechanism</a> </span> through which the community processes the information, it is time to have a look at the whole genetic circuit. A brief description of each figure is provided in sake of clarity.</p>
Once explained the <span class="content-link"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Mechanism" title="Mechanism Description">mechanism</a> </span> through which the community processes the information, it is time to have a look at the whole genetic circuit. A brief description of each figure is provided in sake of clarity.</p>
-
<p>Most of the circuit is made up of biobricks, listed at the bottom of the page. However, some of the parts are yet to be submitted to the registry of biological parts. </p>
+
<p>Most of the circuit is made up of biobricks, listed at the bottom of the page. However, some of the parts are yet to be submitted to the registry of biological parts. The genetic light induction system is described in the <span class="content-link"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Contributions/Photochassis" title="Mechanism Description">Photochassis</a></span> section.</p>
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 +
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 +
<div class="br2"></div>        
         <a name="one"></a>Cell One
         <a name="one"></a>Cell One
-
        <div class = "goBackToTop">
+
<div class="br2"></div>
-
        <a href="#top">Go back to top</a>
+
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<p> <b>Red light induced, green light repressed.</b> Red light induces cI's expression as well as PAI auntoinducer synthetase (QS1 producer) from pTetMnt and pMnt, respectively. cI can activate rather pRM or pRM434, depending on its concentration. pRM transcribes GFP and cI434, the latter repressing pRM434. The community then enters state 1. As [cI] increases, pRM gets repressed and pRM434 is allowed to be activated by cI; YFP is then transcribed from pRM434. That would mean state 2. </p><p>
+
<p> <b>Red light induced, green light repressed.</b> Red light induces cI's expression as well as PAI auntoinducer synthetase (QS1 producer) from pTetMnt and pMnt, respectively. cI can activate rather pRM or pRM434, depending on its concentration. pRM transcribes GFP and cI434, the latter repressing pRM434. The community then enters <b>state 1</b>. As [cI] increases, pRM gets repressed and pRM434 is allowed to be activated by cI; YFP is then transcribed from pRM434. That would mean <b>state 2</b>. </p><p>
-
In the dotted box, green light-activated HSL auntoinducer synthetase from cell two which produces HSL molecules (QS2). RhIR is constitutively produced in cell one. When QS2 molecules reach cell one, they bind to RhIR and the complex activates transcription of TetR and cI434 from pRhIR/HSL. TetR represses pTetMnt inhibiting cI's further transcription; cI434 represses pRM434 enforcing cell's one off state. Note that aisPAI does not get repressed by green light. The λ operators OL and OR, spaced ∼2.4 kb apart, allow DNA looping required for the <span class="content-link"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Mechanism#Molecularly" title="Why DNA looping?">biphasic switch</a> </span>.
+
In the dotted box, green light-activated HHL auntoinducer synthetase from cell two which produces HHL molecules (QS2). RhIR is constitutively produced in cell one. When QS2 molecules reach cell one, they bind to RhIR and the complex activates transcription of TetR and cI434 from pRhIR/HHL. TetR represses pTetMnt inhibiting cI's further transcription; cI434 represses pRM434 enforcing cell's one off state. Note that aisPAI does not get repressed by green light. The λ operators OL and OR, spaced ∼2.4 kb apart, allow DNA looping required for the <span class="content-link"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Mechanism#Molecularly" title="Why DNA looping?">biphasic switch</a> </span>.
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+
<div class = "img-holder" style="width:686px"> <a href="https://static.igem.org/mediawiki/2011/f/fe/Circuit.jpg" rel="lightbox" title="<b>Red light induced, green light repressed.</b> Red light induces cI's expression as well as PAI auntoinducer synthetase (QS1 producer) from pTetMnt and pMnt, respectively. cI can activate rather pRM or pRM434, depending on its concentration. pRM transcribes GFP and cI434, the latter repressing pRM434. The community then enters <b>state 1</b>. As [cI] increases, pRM gets repressed and pRM434 is allowed to be activated by cI; YFP is then transcribed from pRM434. That would mean <b>state 2</b>. </p><p>
-
<img src="http://www.genobiotec2011.org/iGEMwiki/images/circuit.jpg"width="686px" height="346px" alt="Circuit Cell One" align="center">
+
In the dotted box, green light-activated HHL auntoinducer synthetase from cell two which produces HHL molecules (QS2). RhIR is constitutively produced in cell one. When QS2 molecules reach cell one, they bind to RhIR and the complex activates transcription of TetR and cI434 from pRhIR/HHL. TetR represses pTetMnt inhibiting cI's further transcription; cI434 represses pRM434 enforcing cell's one off state. Note that aisPAI does not get repressed by green light. The λ operators OL and OR, spaced ∼2.4 kb apart, allow DNA looping required for the biphasic switch."><img src="https://static.igem.org/mediawiki/2011/f/fe/Circuit.jpg"width="686px" height="346px" alt="Circuit Cell One" align="center"></a>
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         <a name="two"></a>Cell Two
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    </div>
+
<div class="br2"></div>               
<div class="br2"></div>               
       </div>
       </div>
-
<p><b>Green light induced, red light repressed.</b> Remember cells one and two share a very similar mechanism. Green light induces cI's expression as well as HSL auntoinducer synthetase (QS2 producer) from pCpcG2/TetR and pCpcG2, respectively. cI can activate rather pRM or pRM434, depending on its concentration. pRM transcribes RFP and cI434, the latter repressing pRM434. The community then enters state 3. As [cI] increases, pRM gets repressed and pRM434 is allowed to be activated by cI; BFP is then transcribed from pRM434. That would be state 4.</p><p>In the dotted box, red light-activated HSL auntoinducer synthetase from cell one which produces PAI molecules (QS1). LasR is constitutively produced in cell two. When QS1 molecules reach cell two, they bind to LasR and the complex activates transcription of TetR and cI434 from pLasR/PAI. TetR represses pCpcG2/tetR inhibiting cI's further transcription; cI434 represses pRM434 enforcing cell's two off state. Note that aisHSL does not get repressed by red light. The λ operators OL and OR, spaced ∼2.4 kb apart, allow DNA looping required for the <span class="content-link"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Mechanism#Molecularly" title="Why DNA looping?">biphasic switch</a> </span>.  
+
<p><b>Green light induced, red light repressed.</b> Remember cells one and two share a very similar mechanism. Green light induces cI's expression as well as HHL auntoinducer synthetase (QS2 producer) from pCpcG2/TetR and pCpcG2, respectively. cI can activate rather pRM or pRM434, depending on its concentration. pRM transcribes RFP and cI434, the latter repressing pRM434. The community then enters <b>state 3</b>. As [cI] increases, pRM gets repressed and pRM434 is allowed to be activated by cI; BFP is then transcribed from pRM434. That would be <b>state 4</b>.</p><p>In the dotted box, red light-activated HHL auntoinducer synthetase from cell one which produces PAI molecules (QS1). LasR is constitutively produced in cell two. When QS1 molecules reach cell two, they bind to LasR and the complex activates transcription of TetR and cI434 from pLasR/PAI. TetR represses pCpcG2/tetR inhibiting cI's further transcription; cI434 represses pRM434 enforcing cell's two off state. Note that aisHHL does not get repressed by red light. The λ operators OL and OR, spaced ∼2.4 kb apart, allow DNA looping required for the <span class="content-link"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Mechanism#Molecularly" title="Why DNA looping?">biphasic switch</a> </span>.  
  </p>
  </p>
Line 1,115: Line 180:
<div class = "img-holder" style="width:686px; font-size: 18px;">  
<div class = "img-holder" style="width:686px; font-size: 18px;">  
-
<img src="http://www.genobiotec2011.org/iGEMwiki/images/circuit2.jpg"width="686px" height="320px" alt="Circuit Cell Two" align="center">
+
<a href="https://static.igem.org/mediawiki/2011/8/87/Circuit2.jpg" rel="lightbox" title="<b>Green light induced, red light repressed.</b> Remember cells one and two share a very similar mechanism. Green light induces cI's expression as well as HHL auntoinducer synthetase (QS2 producer) from pCpcG2/TetR and pCpcG2, respectively. cI can activate rather pRM or pRM434, depending on its concentration. pRM transcribes RFP and cI434, the latter repressing pRM434. The community then enters <b>state 3</b>. As [cI] increases, pRM gets repressed and pRM434 is allowed to be activated by cI; BFP is then transcribed from pRM434. That would be <b>state 4</b>.</p><p>In the dotted box, red light-activated HHL auntoinducer synthetase from cell one which produces PAI molecules (QS1). LasR is constitutively produced in cell two. When QS1 molecules reach cell two, they bind to LasR and the complex activates transcription of TetR and cI434 from pLasR/PAI. TetR represses pCpcG2/tetR inhibiting cI's further transcription; cI434 represses pRM434 enforcing cell's two off state. Note that aisHHL does not get repressed by red light. The λ operators OL and OR, spaced ∼2.4 kb apart, allow DNA looping required for the biphasic switch.">
-
 
+
<img src="https://static.igem.org/mediawiki/2011/8/87/Circuit2.jpg"width="686px" height="320px" alt="Circuit Cell Two" align="center"></a>
 +
</div>
</center>
</center>
Line 1,128: Line 194:
      
      
     <div id="header-project-column">
     <div id="header-project-column">
-
<div class="br2"></div><div class="br2"></div><div class="br2"></div><div class="br2"></div> <div class="br2"></div>             
+
<div class="br2"></div>
 +
<div class="br2"></div>
 +
<div class="br2"></div>             
         <a name="three"></a>Cell Three
         <a name="three"></a>Cell Three
-
        <div class = "goBackToTop">
+
<div class="br2"></div>
-
        <a href="#top">Go back to top</a>
+
<div class="br2"></div>
-
 
+
<div class="br2"></div>  
-
    </div>
+
<div class="br2"></div>         
<div class="br2"></div>         
       </div>
       </div>
-
<p><b>Green AND Red Light induced.</b> When both lights are on, cells one and two repress each other but keep producing QS molecules (through aisPAI and aisHSL, in the dotted boxes); cell three then gets active. LasR and RhIR are constitutively expressed in cell three. Mnt represses pMnt, inhibiting CFP's transcription. There are two Mnt genes placed under a different promoter each. PAI molecules (QS1) coming from cell one bind to LasR and the complex activates cI's transcription from pLasR/PAI. cI then represses pR, inhibiting Mnt's transcription. HSL molecules (QS2) coming from cell two bind to RhIR and the complex activates TetR's transcription from pRhIR/HSL. TetR then represses the second Mnt's transcription from pTet. Only when both Mnt genes are repressed (Mnt NOR Mnt), CFP  is allowed to be expressed from pMnt; then the community enters state 5. Even if a NOR gate is directly implied in CFP's expression, we consider this globally as an <span class="content-link"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Mechanism#Gate" title="AND gate description">AND gate</a> </span> as both lights need to be present to induce CFP expression.</p>
+
<p><b>Green AND Red Light induced.</b> When both lights are on, cells one and two repress each other but keep producing QS molecules (through aisPAI and aisHHL, in the dotted boxes); cell three then gets active. LasR and RhIR are constitutively expressed in cell three. Mnt represses pMnt, inhibiting CFP's transcription. There are two Mnt genes placed under a different promoter each. PAI molecules (QS1) coming from cell one bind to LasR and the complex activates cI's transcription from pLasR/PAI. cI then represses pR, inhibiting Mnt's transcription. HHL molecules (QS2) coming from cell two bind to RhIR and the complex activates TetR's transcription from pRhIR/HHL. TetR then represses the second Mnt's transcription from pTet. Only when both Mnt genes are repressed (Mnt NOR Mnt), CFP  is allowed to be expressed from pMnt; then the community enters <b>state 5</b>. Even if a NOR gate is directly implied in CFP's expression, we consider this globally as an <span class="content-link"><a href="https://2011.igem.org/Team:UANL_Mty-Mexico/Project/Mechanism#Gate" title="AND gate description">AND gate</a> </span> as both lights need to be present to induce CFP expression.</p>
<div class="br"></div>
<div class="br"></div>
<div class="br"></div>
<div class="br"></div>
Line 1,142: Line 209:
<center>
<center>
<div class = "img-holder" style="width:686px">  
<div class = "img-holder" style="width:686px">  
-
 
+
<a href="https://static.igem.org/mediawiki/2011/0/0e/Circuit3-new.png" rel="lightbox" title="<b>Green AND Red Light induced.</b> When both lights are on, cells one and two repress each other but keep producing QS molecules (through aisPAI and aisHHL, in the dotted boxes); cell three then gets active. LasR and RhIR are constitutively expressed in cell three. Mnt represses pMnt, inhibiting CFP's transcription. There are two Mnt genes placed under a different promoter each. PAI molecules (QS1) coming from cell one bind to LasR and the complex activates cI's transcription from pLasR/PAI. cI then represses pR, inhibiting Mnt's transcription. HHL molecules (QS2) coming from cell two bind to RhIR and the complex activates TetR's transcription from pRhIR/HHL. TetR then represses the second Mnt's transcription from pTet. Only when both Mnt genes are repressed (Mnt NOR Mnt), CFP  is allowed to be expressed from pMnt; then the community enters <b>state 5</b>. Even if a NOR gate is directly implied in CFP's expression, we consider this globally as an AND gate as both lights need to be present to induce CFP expression.">
-
<img src="http://www.genobiotec2011.org/iGEMwiki/images/circuit3-new.png"width="671" height="330" alt="Circuit Cell Three" align="center">
+
<img src="https://static.igem.org/mediawiki/2011/0/0e/Circuit3-new.png"width="671" height="330" alt="Circuit Cell Three" align="center">
 +
</a>
</div>
</div>
</center>
</center>
Line 1,153: Line 221:
     <div id="header-project-column">
     <div id="header-project-column">
-
<div class="br2"></div><div class="br2"></div><div class="br2"></div><div class="br2"></div> <div class="br2"></div>          
+
<div class="br2"></div>
-
        <a name="bio"></a>BioBricks
+
<div class="br2"></div>
-
        <div class = "goBackToTop">
+
<div class="br2"></div>          
-
        <a href="#top">Go back to top</a>
+
        <a name="BioBricks"></a>BioBricks
-
    </div>
+
<div class="br2"></div>
-
 
+
<div class="br2"></div>
-
<div class="br2"></div>            
+
<div class="br2"></div>          
       </div>
       </div>
Line 1,166: Line 234:
-
<table width="700" border="1">
+
<table width="700px">
-
   <tr>
+
   <tr class="yellow">  
-
     <th width="150" height="43" scope="col"><center>BioBrick</center></th>
+
     <td class="width">BioBrick</td>
-
     <th width="108" scope="col"><center>Part Name</center></th>
+
     <td class="adjacent">Part name</td>
-
     <th width="420" scope="col"><center>
+
     <td class="adjacent">Description</td>
-
 
+
-
      Description
+
-
    </center></th>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th align="center" scope="row">pConst+RBS</th>
+
     <td class="bold">pConst+RBS</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_K081005" title="Mechanism Description">BBa_K081005</a> </span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K081005">BBa_K081005</a></td>
-
     <td>Constitutive promoter plus Strong Ribosome Binding Site</td>
+
     <td class="final">Constitutive promoter plus Strong Ribosome Binding Site</td>
   </tr>
   </tr>
-
 
   <tr>
   <tr>
-
     <th align="center" scope="row">RBS (strong)</th>
+
     <td class="bold">RBS (strong)</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_B0030" title="Mechanism Description">BBa_B0030</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_B0030">BBa_B0030</a></td>
-
     <td>Strong Ribosome Binding Site </td>
+
     <td class="final">Strong Ribosome Binding Site </td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th align="center" scope="row">RBS (elowitz)</th>
+
     <td class="bold">mRFP</td>
-
 
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_J06505">BBa_J06505</a></td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_B0034" title="Mechanism Description">BBa_B0034</a></span></td>
+
     <td class="final">Red Fluorescent Protein with LVA tag</td>
-
     <td>Standard Ribosome Binding Site</td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th align="center" scope="row">mRFP</th>
+
     <td class="bold">GFP</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_J06505" title="Mechanism Description">BBa_J06505</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K145015">BBa_K145015</a></td>
-
     <td>Red Fluorescent Protein with LVA tag</td>
+
     <td class="final">Green Fluorescent Protein with LVA tag</td>
-
 
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th align="center" scope="row">GFP</th>
+
     <td class="bold">CFP</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_K145015" title="Mechanism Description">BBa_K145015</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_E0022">BBa_E0022</a></td>
-
     <td>Green Fluorescent Protein with LVA tag</td>
+
     <td class="final">Cyan Fluorescent Protein with LVA tag</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
 
+
     <td class="bold">YFP</td>
-
     <th align="center" scope="row">CFP</th>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_E0032">BBa_E0032</a></td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_E0022" title="Mechanism Description">BBa_E0022</a></span></td>
+
     <td class="final">Yellow Fluorescent Protein with LVA tag</td>
-
     <td>Cyan Fluorescent Protein with LVA tag</td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th align="center" scope="row">YFP</th>
+
     <td class="bold">BFP</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_E0032" title="Mechanism Description">BBa_E0032</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K156010">BBa_K156010</a></td>
-
 
+
     <td class="final">Blue Fluorescent Protein with LVA tag</td>
-
     <td>Yellow Fluorescent Protein with LVA tag</td>
+
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th align="center" scope="row">BFP</th>
+
     <td class="bold">Double Ter</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_K156010" title="Mechanism Description">BBa_K156010</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_B0015">BBa_B0015</a></td>
-
     <td>Blue Fluorescent Protein with LVA tag</td>
+
     <td class="final">Double transcriptional terminator</td>
   </tr>
   </tr>
-
 
   <tr>
   <tr>
-
     <th align="center" scope="row">Double Ter</th>
+
     <td class="bold">Double Ter</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_B0015" title="Mechanism Description">BBa_B0015</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_B0014">BBa_B0014</a></td>
-
     <td>Double Transcriptional Terminator</td>
+
     <td class="final">Double transcriptional terminator</td>
   </tr>
   </tr>
   <tr>
   <tr>
-
     <th align="center" scope="row">Double Ter</th>
+
     <td class="bold">Mnt</td>
-
 
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_B0030">BBa_B0030</a></td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_B0014" title="Mechanism Description">BBa_B0014</a></span></td>
+
     <td class="final">Mnt Repressor</td>
-
     <td>Double Transcriptional Terminator</td>
+
   </tr>
   </tr>
 +
 
   <tr>
   <tr>
-
     <th align="center" scope="row">Mnt</th>
+
     <td class="bold">pRM434</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_C0072" title="Mechanism Description">BBa_C0072</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_I12006">BBa_I12006</a></td>
-
     <td>Mnt Repressor</td>
+
     <td class="final">Hybrid Promoter, induced by cI and repressed by cI434</td>
-
 
+
   </tr>  
-
   </tr>
+
 
   <tr>
   <tr>
-
     <th align="center" scope="row">pRM434</th>
+
     <td class="bold">pLasR/PAl</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_I12006" title="Mechanism Description">BBa_I12006</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_R0079">BBa_R0079</a></td>
-
     <td>Hybrid Promoter, induced by cI and repressed by cI434</td>
+
     <td class="final">LasR &amp; PAl regulated Promoter (Quorum sensing)</td>
-
   </tr>
+
   </tr>  
 +
 
   <tr>
   <tr>
 +
    <td class="bold">pRhlR/HHL</td>
 +
    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_R0071" title="Mechanism Description">BBa_R0071</a></td>
 +
    <td class="final">RhlR &amp; HHL regulated Promoter (Quorum sensing)</td>
 +
  </tr> 
-
    <th align="center" scope="row">pLasR/PAl</th>
 
-
    <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_R0079" title="Mechanism Description">BBa_R0079</a></span></td>
 
-
    <td>LasR &amp; PAl regulated Promoter (Quorum sensing)</td>
 
-
  </tr>
 
   <tr>
   <tr>
-
     <th align="center" scope="row">pRhlR/HSL</th>
+
     <td class="bold">aisHHL</td>
-
 
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_C0070">BBa_C0070</a></td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_R0071" title="Mechanism Description">BBa_R0071</a></span></td>
+
     <td class="final">Autoinducer synthesis protein that produces N-butyryl-HHL which binds to RhlR</td>
-
     <td>RhlR &amp; HSL regulated Promoter (Quorum sensing)</td>
+
   </tr>
-
   </tr>
+
 
   <tr>
   <tr>
-
     <th align="center" scope="row">aisHSL</th>
+
     <td class="bold">RhlR</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_C0070" title="Mechanism Description">BBa_C0070</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_C0071" title="Mechanism Description">BBa_C0071</a></td>
-
 
+
     <td class="final">Transcriptional regulator, in complex with RhlR binds to the RhlR promoter</td>
-
     <td>Autoinducer synthesis protein that produces N-butyryl-HSL wich binds to RhlR</td>
+
   </tr>
-
   </tr>
+
 
   <tr>
   <tr>
-
     <th align="center" scope="row">RhlR</th>
+
     <td class="bold">aisPAl</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_C0071" title="Mechanism Description">BBa_C0071</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_C0078">BBa_C0078</a></td>
-
     <td>Transcriptional regulator, in complex with RhlR binds to the RhlR promoter</td>
+
     <td class="final">Autoinducer synthesis protein that produces PAI-1 [N-(3-oxododecanoyl)-L-homoserine lactone] which binds to LasR</td>
-
   </tr>
+
   </tr>
-
 
+
 
   <tr>
   <tr>
-
     <th align="center" scope="row">aisPAl</th>
+
     <td class="bold">LasR</td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_C0078" title="Mechanism Description">BBa_C0078</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_C0079" >BBa_C0079</a></td>
-
     <td>Autoinducer synthesis protein that produces PAI-1 [N-(3-oxododecanoyl)-L-homoserine lactone] which binds to LasR</td>
+
     <td class="final">Transcriptional regulator, in complex with PAI binds to LasR promoter</td>
-
   </tr>
+
   </tr>  
 +
 
   <tr>
   <tr>
-
     <th align="center" scope="row">LasR</th>
+
     <td class="bold">pMnt</td>
 +
    <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_R0073" >BBa_R0073</a></td>
 +
    <td class="final">Mnt Reprressible Promoter</td>
 +
  </tr>  
-
    <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_C0079" title="Mechanism Description">BBa_C0079</a></span></td>
 
-
    <td>Transcriptional regulator, in complex with PAI binds to LasR promoter</td>
 
-
  </tr>
 
   <tr>
   <tr>
-
    <th align="center" scope="row">pMnt</th>
+
     <td class="bold">RBS.2 (weak)</th>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_R0073" title="Mechanism Description">BBa_R0073</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_B0030" >BBa_B0030</a></td>
-
    <td>Mnt Repressible Promoter</td>
+
     <td class="final">Weak Ribosome Binding Site</td>
-
 
+
-
  </tr>
+
-
  <tr>
+
-
    <th align="center" scope="row">RBS.2 (weak)</th>
+
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_B0030" title="Mechanism Description">BBa_B0030</a></span></td>
+
-
     <td>Weak Ribosome Binding Site</td>
+
   </tr>
   </tr>
 +
 
   <tr>
   <tr>
-
     <th align="center" scope="row">RBS.3 (medium)</th>
+
     <td class="bold">RBS.3 (medium)</th>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_B0032" title="Mechanism Description">BBa_B0032</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_B0032">BBa_B0032</a></td>
-
     <td>Medium Ribosome Binding Site</td>
+
     <td class="final">Medium Ribosome Binding Site</td>
   </tr>
   </tr>
 +
 
   <tr>
   <tr>
-
     <th align="center" scope="row">RBS.4 (weaker)</th>
+
     <td class="bold">RBS.4 (weaker)</th>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_B0033" title="Mechanism Description">BBa_B0033</a></span></td>
+
     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_B0033">BBa_B0033</a></td>
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     <td class="final">Weaker Ribosome Binding Site</td>
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     <td>Weaker Ribosome Binding Site</td>
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   </tr>
   </tr>
 +
 
   <tr>
   <tr>
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     <th align="center" scope="row">TetR</th>
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     <td class="bold">TetR</th>
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     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_C0040" title="Mechanism Description">BBa_C0040</a></span></td>
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     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_C0040">BBa_C0040</a></td>
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     <td>Tetracycline Repressor with LVA tag</td>
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     <td class="final">Tetracycline Repressor with LVA tag</td>
   </tr>
   </tr>
   <tr>
   <tr>
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     <th align="center" scope="row">cI</th>
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     <td class="bold">cI</th>
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     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_C0051" title="Mechanism Description">BBa_C0051</a></span></td>
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     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_C0051" >BBa_C0051</a></td>
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     <td>cI protein from phage lambda</td>
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     <td class="final">cI protein from phage lambda</td>
   </tr>
   </tr>
 +
 
   <tr>
   <tr>
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     <th align="center" scope="row">cI434</th>
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     <td class="bold">cI434</th>
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     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_C0052" >BBa_C0052</a></td>
-
     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_C0052" title="Mechanism Description">BBa_C0052</a></span></td>
+
     <td class="final">cI protein from phage 434</td>
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     <td>cI protein from phage 434</td>
+
   </tr>
   </tr>
 +
 
   <tr>
   <tr>
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     <th align="center" scope="row">pTetR</th>
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     <td class="bold">pTetR</th>
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     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_R0040" title="Mechanism Description">BBa_R0040</a></span></td>
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     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_R0040" >BBa_R0040</a></td>
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     <td>TetR repressible Promoter</td>
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     <td class="final">TetR repressible Promoter</td>
   </tr>
   </tr>
 +
 
   <tr>
   <tr>
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     <th align="center" scope="row">pR</th>
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     <td class="bold">pR</th>
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     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_R0051" title="Mechanism Description">BBa_R0051</a></span></td>
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     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_R0051" >BBa_R0051</a></td>
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     <td>Right Promoter from Phage lambda</td>
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     <td class="final">Right Promoter from Phage lambda</td>
   </tr>
   </tr>
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     <th align="center" scope="row">pTetMnt</th>
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     <td class="bold">pTetMnt</th>
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     <td><span class="content-link"><a href="http://partsregistry.org/Part:BBa_K091105" title="Mechanism Description">BBa_K091105</a></span></td>
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     <td class="adjacent"><a href="http://partsregistry.org/Part:BBa_K091105" >BBa_K091105</a></td>
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     <td>Mnt and TetR repressible Promoter</td>
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     <td class="final">Mnt and TetR repressible Promoter</td>
   </tr>
   </tr>
</table>
</table>
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Latest revision as of 16:56, 13 February 2012

banner-main iGEM-logo
Team: UANL_Mty-Mexico
Team: UANL_Mty-Mexico
Project: Circuit
The Whole Genetic Circuit

Once explained the mechanism through which the community processes the information, it is time to have a look at the whole genetic circuit. A brief description of each figure is provided in sake of clarity.

Most of the circuit is made up of biobricks, listed at the bottom of the page. However, some of the parts are yet to be submitted to the registry of biological parts. The genetic light induction system is described in the Photochassis section.

Cell One

Red light induced, green light repressed. Red light induces cI's expression as well as PAI auntoinducer synthetase (QS1 producer) from pTetMnt and pMnt, respectively. cI can activate rather pRM or pRM434, depending on its concentration. pRM transcribes GFP and cI434, the latter repressing pRM434. The community then enters state 1. As [cI] increases, pRM gets repressed and pRM434 is allowed to be activated by cI; YFP is then transcribed from pRM434. That would mean state 2.

In the dotted box, green light-activated HHL auntoinducer synthetase from cell two which produces HHL molecules (QS2). RhIR is constitutively produced in cell one. When QS2 molecules reach cell one, they bind to RhIR and the complex activates transcription of TetR and cI434 from pRhIR/HHL. TetR represses pTetMnt inhibiting cI's further transcription; cI434 represses pRM434 enforcing cell's one off state. Note that aisPAI does not get repressed by green light. The λ operators OL and OR, spaced ∼2.4 kb apart, allow DNA looping required for the biphasic switch .

Circuit Cell One
Cell Two

Green light induced, red light repressed. Remember cells one and two share a very similar mechanism. Green light induces cI's expression as well as HHL auntoinducer synthetase (QS2 producer) from pCpcG2/TetR and pCpcG2, respectively. cI can activate rather pRM or pRM434, depending on its concentration. pRM transcribes RFP and cI434, the latter repressing pRM434. The community then enters state 3. As [cI] increases, pRM gets repressed and pRM434 is allowed to be activated by cI; BFP is then transcribed from pRM434. That would be state 4.

In the dotted box, red light-activated HHL auntoinducer synthetase from cell one which produces PAI molecules (QS1). LasR is constitutively produced in cell two. When QS1 molecules reach cell two, they bind to LasR and the complex activates transcription of TetR and cI434 from pLasR/PAI. TetR represses pCpcG2/tetR inhibiting cI's further transcription; cI434 represses pRM434 enforcing cell's two off state. Note that aisHHL does not get repressed by red light. The λ operators OL and OR, spaced ∼2.4 kb apart, allow DNA looping required for the biphasic switch .

Circuit Cell Two
Cell Three

Green AND Red Light induced. When both lights are on, cells one and two repress each other but keep producing QS molecules (through aisPAI and aisHHL, in the dotted boxes); cell three then gets active. LasR and RhIR are constitutively expressed in cell three. Mnt represses pMnt, inhibiting CFP's transcription. There are two Mnt genes placed under a different promoter each. PAI molecules (QS1) coming from cell one bind to LasR and the complex activates cI's transcription from pLasR/PAI. cI then represses pR, inhibiting Mnt's transcription. HHL molecules (QS2) coming from cell two bind to RhIR and the complex activates TetR's transcription from pRhIR/HHL. TetR then represses the second Mnt's transcription from pTet. Only when both Mnt genes are repressed (Mnt NOR Mnt), CFP is allowed to be expressed from pMnt; then the community enters state 5. Even if a NOR gate is directly implied in CFP's expression, we consider this globally as an AND gate as both lights need to be present to induce CFP expression.

Circuit Cell Three
BioBricks
BioBrick Part name Description
pConst+RBS BBa_K081005 Constitutive promoter plus Strong Ribosome Binding Site
RBS (strong) BBa_B0030 Strong Ribosome Binding Site
mRFP BBa_J06505 Red Fluorescent Protein with LVA tag
GFP BBa_K145015 Green Fluorescent Protein with LVA tag
CFP BBa_E0022 Cyan Fluorescent Protein with LVA tag
YFP BBa_E0032 Yellow Fluorescent Protein with LVA tag
BFP BBa_K156010 Blue Fluorescent Protein with LVA tag
Double Ter BBa_B0015 Double transcriptional terminator
Double Ter BBa_B0014 Double transcriptional terminator
Mnt BBa_B0030 Mnt Repressor
pRM434 BBa_I12006 Hybrid Promoter, induced by cI and repressed by cI434
pLasR/PAl BBa_R0079 LasR & PAl regulated Promoter (Quorum sensing)
pRhlR/HHL BBa_R0071 RhlR & HHL regulated Promoter (Quorum sensing)
aisHHL BBa_C0070 Autoinducer synthesis protein that produces N-butyryl-HHL which binds to RhlR
RhlR BBa_C0071 Transcriptional regulator, in complex with RhlR binds to the RhlR promoter
aisPAl BBa_C0078 Autoinducer synthesis protein that produces PAI-1 [N-(3-oxododecanoyl)-L-homoserine lactone] which binds to LasR
LasR BBa_C0079 Transcriptional regulator, in complex with PAI binds to LasR promoter
pMnt BBa_R0073 Mnt Reprressible Promoter
RBS.2 (weak) BBa_B0030 Weak Ribosome Binding Site
RBS.3 (medium) BBa_B0032 Medium Ribosome Binding Site
RBS.4 (weaker) BBa_B0033 Weaker Ribosome Binding Site
TetR BBa_C0040 Tetracycline Repressor with LVA tag
cI BBa_C0051 cI protein from phage lambda
cI434 BBa_C0052 cI protein from phage 434
pTetR BBa_R0040 TetR repressible Promoter
pR BBa_R0051 Right Promoter from Phage lambda
pTetMnt BBa_K091105 Mnt and TetR repressible Promoter

OurSymbol

Team: UANL_Mty-Mexico

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