Team:UCSF/Project/Background1

From 2013.igem.org

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font-family: Georgia, Serif;
font-family: Georgia, Serif;
}
}
-
#sidebar{
 
-
position: absolute;
 
-
width: 200px;
 
-
z-index: 0;
 
-
}
 
-
/*
 
-
#sidebarimg{
 
-
width: 214px;
 
-
height: 144px;
 
-
background: #ffffff;
 
-
margin: 5px 0px;
 
-
border: 3px solid #ffffff;
 
-
}
 
-
*/
 
-
 
-
#sidebar #list{
 
-
background: #ffffff;
 
-
}
 
-
#sidebar h2{
 
-
color: #008000;
 
-
padding: 20px 15px 0px 15px;
 
-
font-size: 2.0em;
 
-
}
 
-
#sidebar ul{
 
-
list-style: none;
 
-
margin: 0px 15px;
 
-
}
 
-
#sidebar #list > ul{
 
-
padding-bottom: 20px;
 
-
}
 
-
#sidebar a{
 
-
color: #008000;
 
-
font-family: Calibri, Sans-Serif;
 
-
font-size: 1.2em;
 
-
display: block;
 
-
line-height: 1.2em;
 
-
}
 
-
#sidebar a:hover{
 
-
text-decoration: none;
 
-
color: #009E99;
 
-
}
 
#box1{
#box1{
width: 750px;
width: 750px;
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<!-------------------------------------------------------------------------->
<!-------------------------------------------------------------------------->
-
<!----{{Template:12SJTU_theme_css}}---->
 
-
<style type="text/css">
 
-
table.head /*Important!*/
 
-
{
 
-
height: 200px;
 
-
width: 1012px;
 
-
z-index:999;
 
-
display: block;
 
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box-shadow: 0px 0px 16px rgba(0, 0, 0, 0.4);
 
-
-webkit-box-shadow: 0px 0px 16px rgba(0, 0, 0, 0.4);
 
-
-moz-box-shadow: 0px 0px 16px rgba(0,0,0,0.4);
 
-
}
 
-
table.mainouter /*Important*/
 
-
{
 
-
width:1012px !important;
 
-
position:relative;
 
-
box-shadow: 0px 10px 16px rgba(0,0,0,0.4);
 
-
-webkit-box-shadow: 0px 10px 16px rgba(0,0,0,0.4);
 
-
-moz-box-shadow: 0px 10px 16px rgba(0,0,0,0.4);
 
-
border-collapse:separate;
 
-
}
 
-
td.bottom /*Important*/
 
-
{
 
-
border-right: medium none;
 
-
border-top: medium none;
 
-
border-left: medium none;
 
-
border-bottom: medium none
 
-
}
 
-
</style>
 
-
<!----End {{Template:12SJTU_theme_css}}---->
 
-
 
<!----{{Template:12SJTU_js}}---->
<!----{{Template:12SJTU_js}}---->
<script type="text/javascript" >
<script type="text/javascript" >
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         this.submenus = this.menu.getElementsByTagName("div");
         this.submenus = this.menu.getElementsByTagName("div");
         this.remember = true;
         this.remember = true;
-
         this.speed = 3;
+
         this.speed = 20;
         this.markCurrent = true;
         this.markCurrent = true;
         this.oneSmOnly = false;
         this.oneSmOnly = false;
Line 329: Line 257:
                 var states = match[1].split("");
                 var states = match[1].split("");
                 for (var i = 0; i < states.length; i++)
                 for (var i = 0; i < states.length; i++)
-
                     this.submenus[i].className = (states[i] == 0 ? "collapsed" : "");
+
                     this.submenus[i].className = (states[i] == 0 ? "collapsed" : "");           }
-
            }
+
         }
         }
     };
     };
     SDMenu.prototype.toggleMenu = function (submenu) {
     SDMenu.prototype.toggleMenu = function (submenu) {
         if (submenu.className == "collapsed")
         if (submenu.className == "collapsed")
 +
            this.expandMenu(submenu);
 +
        else if (submenu.className == "collapsed_ab")
             this.expandMenu(submenu);
             this.expandMenu(submenu);
         else
         else
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                 if (this.submenus[i] != submenu) {
                 if (this.submenus[i] != submenu) {
                     if (this.submenus[i].className != "collapsed") {
                     if (this.submenus[i].className != "collapsed") {
 +
                        this.collapseMenu(this.submenus[i]);
 +
                    }
 +
                    else if (this.submenus[i].className != "collapsed_ab") {
                         this.collapseMenu(this.submenus[i]);
                         this.collapseMenu(this.submenus[i]);
                     }
                     }
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         for (var i = 0; i < this.submenus.length; i++)
         for (var i = 0; i < this.submenus.length; i++)
             if (this.submenus[i].className == "collapsed")
             if (this.submenus[i].className == "collapsed")
 +
                this.expandMenu(this.submenus[i]);
 +
            else if (this.submenus[i].className == "collapsed_ab")
                 this.expandMenu(this.submenus[i]);
                 this.expandMenu(this.submenus[i]);
         this.oneSmOnly = oldOneSmOnly;
         this.oneSmOnly = oldOneSmOnly;
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         for (var i = 0; i < this.submenus.length; i++)
         for (var i = 0; i < this.submenus.length; i++)
             if (this.submenus[i].className != "collapsed")
             if (this.submenus[i].className != "collapsed")
 +
                this.collapseMenu(this.submenus[i]);
 +
            else if (this.submenus[i].className != "collapsed_ab")
                 this.collapseMenu(this.submenus[i]);
                 this.collapseMenu(this.submenus[i]);
     };
     };
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<style type="text/css">
<style type="text/css">
div.sdmenu {
div.sdmenu {
-
 
+
font-family: Myriad Pro, Gill Sans MT, Trebuchet MS, Arial, Sans-Serif;
-
font-family: Arial, sans-serif;
+
        font-size: 1.2em;
-
 
+
padding-bottom: 5px;
-
padding-bottom: 10px;
+
-
 
+
color: #fff;
color: #fff;
}
}
div.sdmenu div {
div.sdmenu div {
-
background-color: #CD7D1F;
+
background-color: #6BAFAB;
overflow: hidden;
overflow: hidden;
}
}
div.sdmenu div.collapsed {
div.sdmenu div.collapsed {
-
height: 30px;
+
height: 30px;}
-
}
+
div.sdmenu div span {
div.sdmenu div span {
display: block;
display: block;
padding: 6px 25px;
padding: 6px 25px;
-
width: 130px;
+
width: 150px;
font-weight: bold;
font-weight: bold;
color: white;
color: white;
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}
}
div.sdmenu div:hover{
div.sdmenu div:hover{
-
background-color: #f79a2d;
+
background-color: #51C9C9;
}
}
div.sdmenu div.collapsed span {
div.sdmenu div.collapsed span {
Line 453: Line 386:
div.sdmenu div a {
div.sdmenu div a {
padding: 5px 10px;
padding: 5px 10px;
-
background: #eee;
+
background: #DDE7E2;
display: block;
display: block;
border-bottom: 1px solid #ddd;
border-bottom: 1px solid #ddd;
-
color: #014d67;
+
color: #3F7572;
}
}
div.sdmenu div a.current {
div.sdmenu div a.current {
-
background : #ccc;
+
background : #B7CDC2;
}
}
div.sdmenu div a:hover {
div.sdmenu div a:hover {
-
background : #014d67 url(/wiki/images/2/2d/12SJTU_floatnav_linkarrow.gif) no-repeat right center;
+
background : #31A29F url(/wiki/images/2/2d/12SJTU_floatnav_linkarrow.gif) no-repeat right center;
color: #fff;
color: #fff;
text-decoration: none;
text-decoration: none;
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<body>
<body>
-
<div class="floatbox" id="12SJTU_floatnav" style="top:350px; left:22px;">
+
<div class="floatbox" id="12SJTU_floatnav" style="top:200px; left:2px;">
-
<table border="0" width="190" cellspacing="0" cellpadding="0">
+
<table border="0" width="150" cellspacing="0" cellpadding="0">
  <tr>
  <tr>
<td width="100%">
<td width="100%">
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     <div style="float: left" id="my_menu" class="sdmenu">
     <div style="float: left" id="my_menu" class="sdmenu">
       <div class="collapsed">
       <div class="collapsed">
-
         <span>Overview</span>
+
         <span>Background</span>
-
         <a href="/Team:SJTU-BioX-Shanghai/Project">Project Overview</a>
+
         <a href="/Team:UCSF/Project/Background1">Background</a>
-
 
+
-
      </div>
+
-
      <div class="collapsed">
+
-
        <span>System Construction</span>
+
-
        <a href="/Team:SJTU-BioX-Shanghai/Project/project1.1">Membrane Localization</a>
+
-
        <a href="/Team:SJTU-BioX-Shanghai/Project/project1.2">Membrane Accelerator</a>
+
-
        <a href="/Team:SJTU-BioX-Shanghai/Project/project1.3">Membrane Rudder</a>
+
       </div>
       </div>
       <div class="collapsed">
       <div class="collapsed">
-
         <span>Application</span>      
+
         <span>CRISPRi Circuit</span>
-
         <a href="/Team:SJTU-BioX-Shanghai/Project/project2.2">Membrane Accelerator I  (Biosynthesis)</a>
+
         <a href="/Team:UCSF/Project/Circuit/Design">Design</a>
-
         <a href="/Team:SJTU-BioX-Shanghai/Project/project2.3">Membrane Accelerator II  (Biodegradation)</a>
+
         <a href="/Team:UCSF/Project/Circuit/Data">Data</a>
-
        <a href="/Team:SJTU-BioX-Shanghai/Project/project2.1">Membrane Rudder</a>
+
       </div>
       </div>
       <div class="collapsed">
       <div class="collapsed">
-
         <span>Modeling</span>
+
         <span>CRISPRi Conjugation</span>      
-
         <a href="/Team:SJTU-BioX-Shanghai/Project/project3">Acceleration Model</a>
+
         <a href="/Team:UCSF/Project/Conjugation/Design">Design</a>
-
         <a href="/Team:SJTU-BioX-Shanghai/Project/project3.2">Switch Model</a>
+
         <a href="/Team:UCSF/Project/Conjugation/Data">Data</a>
       </div>
       </div>
-
    </div>
+
</div>
 +
     
<!--End {{Template:12SJTU_nav_project}}-->
<!--End {{Template:12SJTU_nav_project}}-->
Line 557: Line 483:
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                var top = parseInt(id(o).style.top);
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-
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+
                            height = height - 70;
                        }
                        }
                    }
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Latest revision as of 21:47, 27 October 2013

Operation CRISPR: Deploying precision guided tools to target unique species in a complex microbiome

Rarely in nature do bacterial strains exist in isolation; they form complex microbial communities that interact with various organisms. We ourselves contain a major microbial community in our digestive tract that has shown to directly affect our health and well-being. As shown on the left, to improve and maintain healthly living it would be useful to have the ability to change the microbial community. For example, if a large of amount of a certain sugar was present in your gut ("signal #1") you might want to slow the growth of a certain bacterial populations . In another scenario ("signal #2") it might be useful to increase the growth of other specific bacteria in your gut. But targeting precise bacterial community strains and controlling their growth, activity, and outputs is difficult and requires many new tools.
At the beginning of this summer, we asked ourselves a question: “What could we introduce to a microbiome which would allow targeting and eventual gene expression changes in a specific bacteria?” The difficulty faced with this situation is in
  1. Introduce a targeting system into a defined mixture of bacteria such that you can select and introduce manipulations without negatively affecting other bacteria.
  2. Creating easy to transfer pathways or circuits that can produce a multitude of outcomes (killing, repressing, upregulating)
1. Introducing CRISPRi to a bacterial community: To selectively target and eliminate harmful bacteria, we are utilizing the CRISPRi system, a tool repurposed from a natural adaptive immunity system in bacteria (see diagram below). This tool is comprised of a catalytically dead Cas9 (dCas9) protein that complexes with guide RNAs (gRNA) complementary to the target bacteria’s DNA sequence. This complex binds to DNA complementary to the gRNA and prevents transcription, therefore repressing gene expression.

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