Team:UCSF/Project/Background2

From 2013.igem.org

(Difference between revisions)
Line 1: Line 1:
-
{{Template:12SJTU_header}}
+
<!--{{Template:12SJTU_header}}-->
-
{{Template:12SJTU_nav_project}}
+
    <!--{{Template:12SJTU_scroll2top_css}}-->
 +
<html>
 +
<head>
 +
<style type="text/css">
 +
 
 +
.back-to {
 +
    position: fixed;
 +
    bottom: 35px;
 +
    *bottom: 50px;
 +
    right: 10px;
 +
    z-index: 999;
 +
    width: 50px;
 +
    zoom: 1;
 +
background-position: -50px 0
 +
    }
 +
 
 +
 
 +
.back-to .backtotop {
 +
    float: left;
 +
    display: block;
 +
    width: 50px;
 +
    height: 50px;
 +
    background: #666 url(/wiki/images/3/3b/12SJTU_btt.png) 8px -57px no-repeat;
 +
    margin-bottom: 15px;
 +
    outline: 0 none;
 +
    text-indent: -9999em;
 +
    -webkit-border-radius: 4px;
 +
    border-radius: 4px;
 +
    position: relative
 +
    }
 +
.back-to .backtotop:hover {
 +
    background-color: #333;
 +
    background-position: 8px 13px
 +
    }
 +
.back-to .backtotop .back-tip {
 +
    position: absolute;
 +
    visibility: hidden;
 +
    top: -31px;
 +
    left: -10px
 +
    }
 +
.back-to .backtotop:hover .back-tip {
 +
    visibility: visible
 +
    }
 +
.back-to .back-top:hover {
 +
    background-position: -50px 0
 +
    }
 +
 
 +
 
 +
</style>
 +
</head>
 +
</html>
 +
    <!--End {{Template:12SJTU_scroll2top_css}}-->
 +
 
 +
    <!--{{Template:12SJTU_sliderbar}}-->
 +
<html>
 +
<head>
 +
<style type="text/css">
 +
div.bottombar{ /* bar that runs across the bottom of the menu */
 +
height: 10px;
 +
background: #1a1109;
 +
}
 +
 
 +
ul.semiopaquemenu{ /* main menu UL */
 +
font: bold 18px Verdana ;
 +
width: 100%;
 +
 
 +
padding: 11px 0 8px 0; /* padding of the 4 sides of the menu */
 +
margin: 0;
 +
text-align: center; /* set value to "left", "center", or "right" to align menu accordingly */
 +
}
 +
ul.semiopaquemenu2{
 +
padding: 0px 0 8px 6px;
 +
text-align: left;
 +
}
 +
ul.semiopaquemenu2 li{
 +
margin-left: 0px;
 +
margin-top: 12px;
 +
display:block !important;
 +
}
 +
 
 +
ul.semiopaquemenu2 li a{
 +
 
 +
margin-right: 0px; /* spacing between each menu link */
 +
margin-left: 0px;
 +
margin-top: 15px;
 +
}
 +
ul.semiopaquemenu li:hover .menubar1,ul.semiopaquemenu li:hover .menubar2,ul.semiopaquemenu li:hover .menubar3,ul.semiopaquemenu li:hover .menubar4{
 +
display:block;
 +
background-color:#fadb48;
 +
}
 +
ul.semiopaquemenu li{
 +
display: inline;
 +
}
 +
 
 +
ul.semiopaquemenu li a,ul.semiopaquemenu2 li a{
 +
color:white;
 +
padding: 6px 8px 6px 8px; /* padding of the 4 sides of each menu link */
 +
margin-right: 10px; /* spacing between each menu link */
 +
text-decoration: none;
 +
}
 +
 
 +
ul.semiopaquemenu li a:hover, ul.semiopaquemenu li a.selected{
 +
color: black;
 +
background: url(data:image/svg+xml;base64,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); /* IE9+ SVG equivalent  of linear gradients */
 +
background: -moz-linear-gradient(top,  rgba(255,255,255,0.82) 0%, rgba(255,255,255,0.16) 100%); /* fade from white (0.82 opacty) to 0.16 opacity */
 +
background: -webkit-gradient(linear, left top, left bottom, color-stop(0%,rgba(255,255,255,0.82)), color-stop(100%,rgba(255,255,255,0.16)));
 +
background: -webkit-linear-gradient(top,  rgba(255,255,255,0.82) 0%,rgba(255,255,255,0.16) 100%);
 +
background: -o-linear-gradient(top,  rgba(255,255,255,0.82) 0%,rgba(255,255,255,0.16) 100%);
 +
background: -ms-linear-gradient(top,  rgba(255,255,255,0.82) 0%,rgba(255,255,255,0.16) 100%);
 +
background: linear-gradient(top,  rgba(255,255,255,0.82) 0%,rgba(255,255,255,0.16) 100%);
 +
filter: progid:DXImageTransform.Microsoft.gradient( startColorstr='#d1ffffff', endColorstr='#29ffffff',GradientType=0 );
 +
-moz-box-shadow: 0 0 5px #595959; /* CSS3 box shadows */
 +
-webkit-box-shadow: 0 0 5px #595959;
 +
box-shadow: 0 0 5px #595959;
 +
padding-top: 12px; /* large padding to get menu item to protrude upwards */
 +
padding-bottom: 9px; /* large padding to get menu item to protrude downwards */
 +
}
 +
 
 +
</style>
 +
</head>
 +
</html>
 +
    <!--End {{Template:12SJTU_sliderbar}}-->
 +
 
 +
    <!--{{Template:12SJTU_theme_css}}-->
 +
<html>
 +
<head>
 +
<style type="text/css">
 +
 
 +
body
 +
{
 +
background-image:url(/wiki/images/3/33/12SJTU_background_1366x768.png);
 +
margin: 0px 0px 0px 0px;
 +
background-repeat:no-repeat !important;
 +
background-attachment: fixed!important;
 +
color: #000000;
 +
font-family: "Microsoft Yahei", "STHeiti", "Microsoft JhengHei", "SimHei", serif;
 +
background-color: #e6e6e6;
 +
-moz-background-size:cover !important;
 +
background-size:cover !important;
 +
padding:0px 0px 0px 0px;
 +
}
 +
body.inframe
 +
{
 +
background-image: none;
 +
background-color: transparent;
 +
}
 +
#main_wrapper{
 +
position:relative;
 +
 +
margin: 0px 0px 0px 0px;
 +
 
 +
background-repeat:no-repeat !important;
 +
background-attachment: fixed!important;
 +
color: #000000;
 +
-moz-background-size:cover !important;
 +
background-size:cover !important;
 +
}
 +
#footer {
 +
position:relative;
 +
top: 30px;
 +
padding-bottom: 60px;
 +
font-size:8pt;
 +
}
 +
table
 +
{
 +
border-right: medium none;
 +
border-top: medium none;
 +
border-left: medium none;
 +
border-bottom: medium none;
 +
border-collapse: collapse;
 +
background-color: transparent
 +
}
 +
table.head
 +
{
 +
height: 200px;
 +
width: 1012px;
 +
z-index:999;
 +
display: block;
 +
background:url(/wiki/images/2/2d/12SJTU_inner_banner.png) no-repeat;
 +
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.main
 +
{
 +
border-right: medium none;
 +
border-top: medium none;
 +
border-left: medium none;
 +
border-bottom: medium none;
 +
}
 +
 
 +
table.mainouter
 +
{
 +
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.pumpkin
 +
{
 +
height: 100px;
 +
width: 1012px;
 +
background-color: black;
 +
}
 +
#floatpumpkin
 +
{
 +
position:absolute;
 +
left:74px;
 +
top:0px;
 +
height: 95px;
 +
width: 89px;
 +
background-image:url(/wiki/images/4/4d/12SJTU_pumpkin.png);
 +
}
 +
/*-- Lavalamp --*/
 +
.navipages:after { visibility: hidden; display: block;}
 +
*:first-child+html .navipages { zoom: 1; } /* IE7 */
 +
#lavalampbg {
 +
width:89px;
 +
height:95px;
 +
margin-left:0px;
 +
position:absolute;
 +
top: 0px;
 +
left:0px;
 +
background-image:url(/wiki/images/4/4d/12SJTU_pumpkin.png);
 +
z-index: 100;
 +
}
 +
table.message
 +
{
 +
border:transparent 1px solid;
 +
}
 +
table.bottom
 +
{
 +
background: none transparent scroll repeat 0% 0%
 +
}
 +
p
 +
{
 +
font-size:106%;
 +
text-align:justify;
 +
text-indent: 2em;
 +
line-height: 1.8em;
 +
}
 +
dd
 +
{
 +
font-size:10pt;
 +
line-height: 1.8em;
 +
}
 +
a.info
 +
{
 +
z-index: 24;
 +
color: #000;
 +
position: relative;
 +
background-color: #ccc;
 +
text-decoration: none
 +
}
 +
a.info:hover
 +
{
 +
z-index: 25;
 +
background-color: #ff0
 +
}
 +
a.info span
 +
{
 +
display: none
 +
}
 +
a.info:hover span
 +
{
 +
border-right: #0cf 1px solid;
 +
border-top: #0cf 1px solid;
 +
display: block;
 +
left: 2em;
 +
border-left: #0cf 1px solid;
 +
width: 15em;
 +
color: #000;
 +
border-bottom: #0cf 1px solid;
 +
position: absolute;
 +
top: 2em;
 +
background-color: #cff;
 +
text-align: center
 +
}
 +
table.bottom
 +
{
 +
background: none transparent scroll repeat 0% 0%
 +
}
 +
h1 + p {
 +
padding-bottom: 1em;
 +
}
 +
h1 + p a b {
 +
font-weight:normal!important;
 +
}
 +
 
 +
td
 +
{
 +
border:1px solid transparent;
 +
}
 +
 
 +
td.embedded
 +
{
 +
border-right: medium none;
 +
padding-right: 0px;
 +
border-top: medium none;
 +
padding-left: 0px;
 +
padding-bottom: 0px;
 +
border-left: medium none;
 +
padding-top: 0px;
 +
border-bottom: medium none;
 +
text-align: left
 +
}
 +
td.bottom
 +
{
 +
border-right: medium none;
 +
border-top: medium none;
 +
border-left: medium none;
 +
border-bottom: medium none
 +
}
 +
td.heading
 +
{
 +
font-weight: bold
 +
}
 +
td.outer {
 +
background-image:url(/wiki/images/3/3b/12SJTU_background.png);
 +
border-collapse:separate;
 +
padding-top: 20px; padding-bottom: 20px; padding-left:0px; padding-right:0px;
 +
border-left:0px;
 +
border-right:0px;
 +
}
 +
td.text
 +
{
 +
padding-right: 10pt;
 +
padding-left: 10pt;
 +
padding-bottom: 10pt;
 +
padding-top: 10pt;
 +
background: white;
 +
}
 +
td.text[align=center] {
 +
 
 +
padding-right: 0 !important;
 +
padding-left: 0 !important;
 +
padding-bottom: 0 !important;
 +
/*padding-top: 5px!important;*/
 +
padding-top:0 !important;
 +
background-color:black;
 +
}
 +
 
 +
td.colhead,h2{
 +
color: #ffffff;
 +
border-bottom: 1px solid #AAA;
 +
border-top: 1px solid #AAA;
 +
border-right: 0px solid transparent;
 +
background-color: #ECECEC;
 +
font-size:13pt;
 +
color:black;
 +
}
 +
 
 +
h3
 +
{
 +
font-size:11pt;
 +
padding-top: 0px;
 +
padding-bottom: 0px;
 +
}
 +
h4
 +
{
 +
font-size: 5pt;
 +
font-family: Arial;
 +
font-weight: bold;
 +
}
 +
td.rowhead_left
 +
{
 +
text-align: left
 +
}
 +
td.rowhead_center
 +
{
 +
text-align: center
 +
}
 +
td.rowhead
 +
{
 +
font-weight: bold;
 +
vertical-align: top;
 +
text-align: right
 +
}
 +
t
 +
 
 +
td.navigation
 +
{
 +
border-right: medium none;
 +
border-top: medium none;
 +
font-weight: bold;
 +
border-left: medium none;
 +
border-bottom: medium none
 +
}
 +
td.clear
 +
{
 +
border-right: 0px;
 +
border-top: 0px;
 +
background: none transparent scroll repeat 0% 0%;
 +
border-left: 0px;
 +
border-bottom: 0px
 +
}
 +
td.nothing
 +
{
 +
border-right: 0px;
 +
padding-right: 0px;
 +
border-top: 0px;
 +
padding-left: 0px;
 +
background: none transparent scroll repeat 0% 0%;
 +
padding-bottom: 0px;
 +
border-left: 0px;
 +
padding-top: 0px;
 +
border-bottom: 0px
 +
}
 +
 
 +
font.gray
 +
{
 +
color: #aca899;
 +
text-decoration: underline
 +
}
 +
a:link
 +
{
 +
 
 +
text-decoration: none
 +
}
 +
li a{
 +
color: #000000;
 +
}
 +
td.colhead a {
 +
color: #000000;
 +
}
 +
td.colhead a:hover {
 +
color: #FFFFFF;
 +
}
 +
a:visited
 +
{
 +
text-decoration: none
 +
}
 +
a:hover
 +
{
 +
/* TODO */
 +
color: #777;
 +
}
 +
a.index
 +
{
 +
font-weight: bold
 +
}
 +
 
 +
img.border
 +
{
 +
border-right: #000000 1px solid;
 +
border-top: #000000 1px solid;
 +
border-left: #000000 1px solid;
 +
border-bottom: #000000 1px solid
 +
}
 +
 
 +
.mainouter tbody tr:first-child td.text .shadetabs ul {
 +
text-align: left!important;
 +
}
 +
 
 +
 
 +
</style>
 +
</head>
 +
</html>
 +
    <!--End {{Template:12SJTU_theme_css}}-->
 +
 
 +
<html>
 +
<head>
 +
<style type="text/css">
 +
 
 +
 
 +
#p-logo{
 +
  display: none;
 +
}
 +
#footer-box{
 +
  display: none;
 +
}
 +
div.thumb {
 +
    margin-bottom: .5em;
 +
    border-style: solid;
 +
    border-color: transparent;
 +
    width: auto;
 +
}
 +
#menubar li{
 +
    margin-left: 0px;
 +
}
 +
#firstHeading{
 +
    display: none;
 +
}
 +
#top-section{
 +
    border: 0px;
 +
}
 +
#content{
 +
    background: none;
 +
    border: 0px;
 +
}
 +
#contentSub{
 +
    display: none;
 +
}
 +
.firstHeading{
 +
    display: none;
 +
}
 +
#catlinks{
 +
    display: none;
 +
}
 +
#globalWrapper{
 +
 
 +
margin: 0px 0px 0px 0px;
 +
height: 0px;
 +
background-repeat:no-repeat !important;
 +
background-attachment: fixed!important;
 +
color: #000000;
 +
background-color: #e6e6e6;
 +
-moz-background-size:cover !important;
 +
background-size:cover !important;
 +
padding:0px 0px 0px 0px;
 +
}
 +
#main_wrapper{
 +
position:absolute;
 +
top:-93px;
 +
left:-20px;
 +
margin: 0px 0px 0px 0px;
 +
width:1012px;
 +
background-repeat:no-repeat !important;
 +
background-attachment: fixed!important;
 +
color: #000000;
 +
-moz-background-size:cover !important;
 +
background-size:cover !important;
 +
padding-top:8px;
 +
}
 +
#search-controls
 +
{
 +
display:none;
 +
}
 +
</style>
 +
    <script src="http://igem.bio-x.cn/home/style/jquery-1.3.2.min.js" type="text/javascript"></script>
 +
    <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4/jquery.min.js?ver=1.3.2"></script>
 +
    <script type="text/javascript">
 +
        jQuery.noConflict();
 +
        ($(function () {
 +
            var $el, leftPos, newWidth,
 +
$mainNav = $("#lavalamp");
 +
            $mainNav.append("<li id='lavalampbg'></li>");
 +
            var $magicLine = $("#lavalampbg");
 +
            $magicLine
 +
.css("left", $(".current a").position().left + $(".current a").width() / 2 - 35)
 +
.data("origLeft", $(".current a").position().left + $(".current a").width() / 2 - 35)
 +
            $("#lavalamp li").find("a").hover(function () {
 +
                $el = $(this);
 +
                leftPos = $el.position().left + $el.width() / 2 - 35;
 +
                $magicLine.stop().animate({
 +
                    left: leftPos
 +
                })
 +
            }, function () {
 +
                $magicLine.stop().animate({
 +
                    left: $magicLine.data("origLeft")
 +
                });
 +
            });
 +
        })
 +
); (jQuery);
 +
</script>
 +
 
 +
</head>
 +
<body>
 +
 
 +
<div id="main_wrapper">
 +
<table class="head" cellspacing="0" width="1012" cellpadding="0" align="center"><tbody>
 +
<td><tr></tr>
 +
</td>
 +
</tbody></table>
 +
 +
 
 +
 +
<!--      =============================================================================== -->
 +
 
 +
 
 +
<div id="toolBackTo" class="back-to" style="display:block;">
 +
<a class="backtotop" href="#top" onclick="window.scrollTo(0,0);return false;">To Top
 +
 +
</a>
 +
</div>
 +
 
 +
</body>
 +
</html>
 +
<!--End {{Template:12SJTU_header}}-->
 +
 
 +
<!--{{Template:12SJTU_nav_project}}-->
 +
<html>
 +
<head>
 +
<style type="text/css">
 +
 
 +
</style>
 +
</head>
 +
<body>
 +
<!--      =============================================================================== -->
 +
 +
<table class="mainouter" width="1012" cellspacing="0" cellpadding="5" align="center">
 +
<tbody>
 +
<tr><td class="pumpkin">
 +
</td></tr>
 +
<tr><td class="text" align="center">
 +
<table class="main" width="1010" border="0" cellspacing="0" cellpadding="0"><tbody>
 +
<tr><td class="embedded">
 +
<div>
 +
<ul class="semiopaquemenu navipages" id="lavalamp">
 +
<li><a href="/Team:SJTU-BioX-Shanghai">Home</a></li>
 +
<li class="current"><a href="/Team:SJTU-BioX-Shanghai/Project" class="selected">Project</a></li>
 +
<li><a href="/Team:SJTU-BioX-Shanghai/Parts">Parts</a></li>
 +
<li><a href="/Team:SJTU-BioX-Shanghai/Team">Team</a></li>
 +
<li><a href="/Team:SJTU-BioX-Shanghai/Notebook/protocol">Notebook</a></li>
 +
<li><a href="/Team:SJTU-BioX-Shanghai/Consideration/human">Human Practice</a></li>
 +
<li><a href="/Team:SJTU-BioX-Shanghai/Consideration/safety">Consideration</a></li>
 +
</ul>
 +
</div>
 +
 +
</td></tr>
 +
</tbody></table>
 +
</td></tr>
 +
 
 +
<tr><td align="center" class="outer">
 +
<table width="1010" class="main" border="0" cellspacing="0" cellpadding="0"><tbody>
 +
</body>
 +
</html>
 +
<!--End {{Template:12SJTU_nav_project}}-->
<table><tr>
<table><tr>
<td valign="top" width="200">
<td valign="top" width="200">
-
{{Template:12SJTU_floatnav_head}}
+
<!--{{Template:12SJTU_floatnav_head}}-->
-
<html>
+
    <!--javascript--><html>
-
<script type="text/javascript">
+
<head>
-
// <![CDATA[
+
<script type="text/javascript" >
-
var myMenu;
+
    function SDMenu(id) {
-
window.onload = function() {
+
        if (!document.getElementById || !document.getElementsByTagName)
-
myMenu = new SDMenu("my_menu");
+
            return false;
-
myMenu.oneSmOnly = true;
+
        this.menu = document.getElementById(id);
-
myMenu.remember = false;
+
        this.submenus = this.menu.getElementsByTagName("div");
-
myMenu.init();  
+
        this.remember = true;
-
myMenu.expandMenu(myMenu.submenus[1]);
+
        this.speed = 3;
-
};
+
        this.markCurrent = true;
-
// ]]>
+
        this.oneSmOnly = false;
 +
    }
 +
    SDMenu.prototype.init = function () {
 +
        var mainInstance = this;
 +
        for (var i = 0; i < this.submenus.length; i++)
 +
            this.submenus[i].getElementsByTagName("span")[0].onclick = function () {
 +
                mainInstance.toggleMenu(this.parentNode);
 +
            };
 +
        if (this.markCurrent) {
 +
            var links = this.menu.getElementsByTagName("a");
 +
            for (var i = 0; i < links.length; i++)
 +
                if (links[i].href == document.location.href) {
 +
                    links[i].className = "current";
 +
                    break;
 +
                }
 +
        }
 +
        if (this.remember) {
 +
            var regex = new RegExp("sdmenu_" + encodeURIComponent(this.menu.id) + "=([01]+)");
 +
            var match = regex.exec(document.cookie);
 +
            if (match) {
 +
                var states = match[1].split("");
 +
                for (var i = 0; i < states.length; i++)
 +
                    this.submenus[i].className = (states[i] == 0 ? "collapsed" : "");
 +
            }
 +
        }
 +
    };
 +
    SDMenu.prototype.toggleMenu = function (submenu) {
 +
        if (submenu.className == "collapsed")
 +
            this.expandMenu(submenu);
 +
        else
 +
            this.collapseMenu(submenu);
 +
        this.collapseOthers(submenu);
 +
    };
 +
    SDMenu.prototype.expandMenu = function (submenu) {
 +
        var fullHeight = submenu.getElementsByTagName("span")[0].offsetHeight;
 +
        var links = submenu.getElementsByTagName("a");
 +
 
 +
        for (var i = 0; i < links.length; i++)
 +
            fullHeight += links[i].offsetHeight;
 +
        var moveBy = Math.round(this.speed * links.length);
 +
 
 +
        var mainInstance = this;
 +
        var intId = setInterval(function () {
 +
            var curHeight = submenu.offsetHeight;
 +
            var newHeight = curHeight + moveBy;
 +
            if (newHeight < fullHeight)
 +
                submenu.style.height = newHeight + "px";
 +
            else {
 +
                clearInterval(intId);
 +
                submenu.style.height = "";
 +
                submenu.className = "";
 +
                mainInstance.memorize();
 +
            }
 +
        }, 30);
 +
        this.collapseOthers(submenu);
 +
    };
 +
    SDMenu.prototype.collapseMenu = function (submenu) {
 +
        var minHeight = submenu.getElementsByTagName("span")[0].offsetHeight;
 +
        var moveBy = Math.round(this.speed * submenu.getElementsByTagName("a").length);
 +
        var mainInstance = this;
 +
        var intId = setInterval(function () {
 +
            var curHeight = submenu.offsetHeight;
 +
            var newHeight = curHeight - moveBy;
 +
            if (newHeight > minHeight)
 +
                submenu.style.height = newHeight + "px";
 +
            else {
 +
                clearInterval(intId);
 +
                submenu.style.height = "";
 +
                submenu.className = "collapsed";
 +
                mainInstance.memorize();
 +
            }
 +
        }, 30);
 +
    };
 +
    SDMenu.prototype.collapseOthers = function (submenu) {
 +
        if (this.oneSmOnly) {
 +
            for (var i = 0; i < this.submenus.length; i++)
 +
                if (this.submenus[i] != submenu) {
 +
                    if (this.submenus[i].className != "collapsed") {
 +
                        this.collapseMenu(this.submenus[i]);
 +
                    }
 +
                }
 +
        }
 +
    };
 +
    SDMenu.prototype.expandAll = function () {
 +
        var oldOneSmOnly = this.oneSmOnly;
 +
        this.oneSmOnly = false;
 +
        for (var i = 0; i < this.submenus.length; i++)
 +
            if (this.submenus[i].className == "collapsed")
 +
                this.expandMenu(this.submenus[i]);
 +
        this.oneSmOnly = oldOneSmOnly;
 +
    };
 +
    SDMenu.prototype.collapseAll = function () {
 +
        for (var i = 0; i < this.submenus.length; i++)
 +
            if (this.submenus[i].className != "collapsed")
 +
                this.collapseMenu(this.submenus[i]);
 +
    };
 +
    SDMenu.prototype.memorize = function () {
 +
        if (this.remember) {
 +
            var states = new Array();
 +
            for (var i = 0; i < this.submenus.length; i++)
 +
                states.push(this.submenus[i].className == "collapsed" ? 0 : 1);
 +
            var d = new Date();
 +
            d.setTime(d.getTime() + (30 * 24 * 60 * 60 * 1000));
 +
            document.cookie = "sdmenu_" + encodeURIComponent(this.menu.id) + "=" + states.join("") + "; expires=" + d.toGMTString() + "; path=/";
 +
        }
 +
    };
</script>
</script>
 +
</head>
</html>
</html>
-
{{Template:12SJTU_floatnav_project}}
+
    <!--sdmenu--><html>
-
{{Template:12SJTU_floatnav_foot}}
+
<head>
 +
<style type="text/css">
 +
div.sdmenu {
-
<td valign="top" width="750">
+
font-family: Arial, sans-serif;
-
__NOTOC__
+
-
<!----------------------------------------------------从这里开始写wiki--------------------------------->
+
-
=Membrane Localization=
+
-
{{Template:12SJTU_part_summary_head}}
+
-
To make membrane into a scaffold, we must first make sure that our device is directed to inner membrane of ''E.coli''. To achieve this goal, we used native inner membrane protein of ''E.coli'' and a well-studied signaling sequence as basic components to direct fusion protein onto inner membrane. To justify this construction strategy, we constructed a novel testing fusion protein and conducted two tests to determine the localization of the engineered membrane protein.
+
padding-bottom: 10px;
-
To express multiple large proteins at the same time in ''E.coli'', we reconstructed 3 compatible plasmids with araBAD promoter.
+
color: #fff;
 +
}
 +
div.sdmenu div {
 +
background-color: #CD7D1F;
 +
overflow: hidden;
 +
}
-
{{Template:12SJTU_part_summary_foot}}
+
div.sdmenu div.collapsed {
-
==Reconstructed Vectors==
+
height: 30px;
-
Vectors used in the project for membrane protein expression are modified versions of pRSFDuet-1, pETDuet-1,pACYCDuet-1(''NOVAGEN''), which are originally regulated by T7 promoter. These plasmids can '''coexist''' in one cell.  
+
}
 +
div.sdmenu div span {
 +
display: block;
 +
padding: 6px 25px;
 +
width: 130px;
 +
font-weight: bold;
 +
color: white;
 +
background: url(/wiki/images/f/f7/12SJTU_floatnav_expanded.gif) no-repeat 10px center;
 +
cursor: default;
 +
border-bottom: 1px solid #ddd;
 +
cursor: pointer;
 +
}
 +
div.sdmenu div:hover{
 +
background-color: #f79a2d;
 +
}
 +
div.sdmenu div.collapsed span {
 +
background-image: url(/wiki/images/2/20/12SJTU_floatnav_collapsed.gif);
 +
}
 +
div.sdmenu div a {
 +
padding: 5px 10px;
 +
background: #eee;
 +
display: block;
 +
border-bottom: 1px solid #ddd;
 +
color: #014d67;
 +
}
 +
div.sdmenu div a.current {
 +
background : #ccc;
 +
}
 +
div.sdmenu div a:hover {
 +
background : #014d67 url(/wiki/images/2/2d/12SJTU_floatnav_linkarrow.gif) no-repeat right center;
 +
color: #fff;
 +
text-decoration: none;
 +
}
 +
</style>
 +
</head>
 +
</html>
 +
<html>
 +
<head>
-
Considering our multiple-enzyme system, it is necessary to use those compatible plasmids. However, T7 promoter is hard to be fine-tuned in ''E. coli''. To stress the advantage of the system, we recruited a weaker promoter, araBAD promoter, which could moderately response to a wide range of inducer (L-Arabinose) concentration. So we replaced T7 promoter in original plasmids with araBAD promoter (''Fig.1'').
+
<style type="text/css">
-
All proteins in our project are inserted into those three reconstructed vectors (pRSFDuet-Ara, pETDuet-Ara,pACYCDuet-Ara) and under control of araBAD promoter.
+
.floatbox{
-
[[Image:12SJTU-pACYC.png|700px|thumb|center|''Fig.1'' : Profile of reconstructed plasmids in ''Membrane Magic'' Project]]
+
position:absolute;
 +
width:160px;
 +
height:00px;
 +
background:#FFFFFF
 +
}
-
==Membrane Protein Construction==
+
</style>
-
To construct membrane assemblies, we must make sure that our device is directed to inner membrane of ''E.coli''.
+
-
The first step is to choose an membrane anchor upon which other components could be built. To avoid toxicity caused by foreign membrane proteins, we chose ''phosphatidylglycerol:: prolipoprotein diacylglyceryl transferase'' (Lgt) as core component of fusion protein. Lgt is an inner membrane protein of ''E.coli'' with seven transmembrane segments and has been successfully overexpressed in ''E. coli'' without causing harm to cells.
+
</head>
 +
<body>
-
SsDsbA is the signal recognition particle (SRP)-dependent signaling sequence of DsbA. SsDsbA-tagged proteins are exported to the periplasm through the SRP pathway. With ssDsbA fused to the N-terminus, fusion proteins with Lgt are expected to be anchored onto inner membrane of ''E.coli'' (''Fig.2'' ).
 
-
Flexible linker FL3 is introduced between each crucial protein domain to ensure the proper function of them.
+
<div class="floatbox" id="12SJTU_floatnav" style="top:184px; left:22px;">
 +
<table border="0" width="190" cellspacing="0" cellpadding="0">
 +
  <tr>
 +
<td width="100%">
 +
</html>
 +
<!--End {{Template:12SJTU_floatnav_head}}-->
-
[[Image:12SJTU_proteinconstruction.jpg|thumb|700px|center|''Fig.2'' : Construction details of membrane assemblies]]
+
<html>
 +
<script type="text/javascript">
 +
// <![CDATA[
 +
    var myMenu;
 +
    window.onload = function () {
 +
        myMenu = new SDMenu("my_menu");
 +
        myMenu.oneSmOnly = true;
 +
        myMenu.remember = false;
 +
        myMenu.init();
 +
        myMenu.expandMenu(myMenu.submenus[0]);
 +
    };
 +
// ]]>
 +
</script>
 +
</html>
-
==Membrane Localization Test==
+
<!--{{Template:12SJTU_nav_project}}-->
-
To justify the localization ability of fusion membrane proteins mentioned above, we constructed a novel fusion protein called '''BlaLG'''([http://partsregistry.org/wiki/index.php?title=Part:BBa_K771401 BBa_K771401]). β-lactamase is fused to the N-terminus of Lgt and GFP is fused to the C-terminus of Lgt. The fusion protein in under control of araBAD promoter (''Fig.3'' ). 
+
<html>
-
[[Image:12SJTU-project1-1.png|thumb|700px|center|''Fig.3'' : Details of fusion protein BlaLG for membrane localization]]
+
<head>
 +
<style type="text/css">
 +
</style>
 +
</head>
 +
<body>
 +
<!--      =============================================================================== -->
 +
 +
<table class="mainouter" width="1012" cellspacing="0" cellpadding="5" align="center">
 +
<tbody>
 +
<tr><td class="pumpkin">
 +
</td></tr>
 +
<tr><td class="text" align="center">
 +
<table class="main" width="1010" border="0" cellspacing="0" cellpadding="0"><tbody>
 +
<tr><td class="embedded">
 +
<div>
 +
<ul class="semiopaquemenu navipages" id="Ul1">
 +
<li><a href="/Team:SJTU-BioX-Shanghai">Home</a></li>
 +
<li class="current"><a href="/Team:SJTU-BioX-Shanghai/Project" class="selected">Project</a></li>
 +
<li><a href="/Team:SJTU-BioX-Shanghai/Parts">Parts</a></li>
 +
<li><a href="/Team:SJTU-BioX-Shanghai/Team">Team</a></li>
 +
<li><a href="/Team:SJTU-BioX-Shanghai/Notebook/protocol">Notebook</a></li>
 +
<li><a href="/Team:SJTU-BioX-Shanghai/Consideration/human">Human Practice</a></li>
 +
<li><a href="/Team:SJTU-BioX-Shanghai/Consideration/safety">Consideration</a></li>
 +
</ul>
 +
</div>
 +
 +
</td></tr>
 +
</tbody></table>
 +
</td></tr>
-
===Fluorescence Test===
+
<tr><td align="center" class="outer">
 +
<table width="1010" class="main" border="0" cellspacing="0" cellpadding="0"><tbody>
 +
</body>
 +
</html>
 +
<!--End {{Template:12SJTU_nav_project}}-->
 +
<!--{{Template:12SJTU_floatnav_foot}}-->
 +
<html>
 +
  </tr>
 +
</table>
 +
</div>
 +
<script type="text/javascript">
 +
    var id = function (o) { return document.getElementById(o) }
 +
    var scroll = function (o) {
 +
        var space = id(o).offsetTop;
 +
        id(o).style.top = space + 'px';
 +
        void function () {
 +
            var goTo = 0;
 +
            var roll = setInterval(function () {
 +
                var height = document.documentElement.scrollTop + document.body.scrollTop + space;
 +
                var top = parseInt(id(o).style.top);
 +
                if (parseInt(document.documentElement.scrollTop + document.body.scrollTop) > 98) {
 +
                    height = height - 100;
 +
                    if (parseInt(document.documentElement.scrollTop + document.body.scrollTop) > 198) {
 +
                        height = height - 100;
 +
                        if (parseInt(document.documentElement.scrollTop + document.body.scrollTop) > 298) {
 +
                            height = height - 100;
 +
                        }
 +
                    }
 +
                }
 +
                if (height != top) {
 +
                    goTo = height - parseInt((height - top) * 0.9);
 +
                    id(o).style.top = goTo + 'px';
 +
                }
 +
            }, 30);
 +
        } ()
 +
    }
 +
    scroll('12SJTU_floatnav');
 +
</script>
 +
</body>
 +
</html>
 +
<!--End {{Template:12SJTU_floatnav_foot}}-->
-
To visualize the localization of fusion protein BlaLG, we adopted fluorescence test. GFP fused to the C terminus of BlaLG enables us to have a closer look at where this fusion protein is localized (''Fig.3'').
+
<td valign="top" width="750">
-
Under laser confocal microscope, we can observe the location of green fluorescence,  thus to confirm the exact subcellular localization of the fusion protein BlaLG.
+
__NOTOC__
-
[[Image:12SJTU_MLGFP.jpg|thumb|500px|center|''Fig.4'' :Bacteria carrying BlaLG induced at different concentration of L-arabinose.]]
+
<!----------------------------------------------------从这里开始写wiki--------------------------------->
 +
=Project Overview=
 +
<!--{{Template:12SJTU_part_summary_head}}-->
 +
<html>
 +
<head>
 +
<style type="text/css">
 +
.part-summary
 +
{
 +
background-image: url(/wiki/images/8/86/12SJTU_highlight_box.png);
 +
padding: 20px;
 +
margin: 20px;
 +
border-radius: 10px;
 +
}
 +
</style>
 +
</head>
 +
<body>
 +
<div class="part-summary">
 +
<html>
 +
<!--End {{Template:12SJTU_part_summary_head}}-->
-
It is observed that green fluorescence intensity of ''E.coli'' margin is higher than that of cytoplasm. ''Fig.4'' proves that BlaLG has been localized to membrane.
+
Advance in molecular cloning technology has made it possible for mankind to entitle engineered organisms to different biochemical reactions. However, the speed of those enzymatic reactions is often limited because intermediates produced from upstream enzyme cannot be passed efficiently to downstream enzyme due to spatial obstacles. Thus, synthetic scaffold built to decrease distance between enzymes for speeding biochemical reactions is a rising topic with promising application prospect.  
-
===Antibiotics Test===
+
Moreover, although some progress has been made in fields of metabolic flux control with synthetic scaffold, these strategies remain  non-dynamic. Artificially and dynamically controlling metabolic flux has remained a challenge.
 +
<!--{{Template:12SJTU_part_summary_foot}}-->
 +
<html>
 +
</div>
 +
</body>
 +
</html>
 +
<!--End {{Template:12SJTU_part_summary_foot}}-->
-
In this section, we further tested the membrane localization ability of fusion membrane protein '''BlaLG''' by observing host cells' growth phenotype under different level of Ampicillin. Besides, we found the optimal inducer (L-arabinose) concentration for expressing membrane proteins.
+
==Introduction==
-
β-Lactamase，a bacterial enzyme which can confer Ampicillin resistance to its hosts only when it is in the periplasm. Note that N-terminus of Lgt  faces the periplasm and C-terminus faces the cytoplasm (''Fig.3''). Hence, if BlaLG is correctly anchored to membrane, β-lactamase is expected to be functional and host cells should be able to grow on culture media containing ampicillin.
+
In this year, we expanded the definition of ''scaffold'' in synthetic biology and developed two universal devices called ''Membrane Accelerator'' and ''Membrane Rudder'' respectively. Together, they made ''Membrane Magic'' happen!
-
[[Image:12SJTU_AntiTest.jpg|thumb|400px|center|''Fig.5'' :Growth phenotypes of ''E. coli'' expressing BlaLG on LB agar media with concentration of inducer L-arabinose from 0 to 0.2%. We increased the concentration of ampicillin from 0 to 200 (μg/ ml). Bacteria carrying BlaLG were able to grow at ampicillin concentration of 200 μg/ ml with induction]]
+
Previous researchers have focused on building protein, RNA or DNA scaffold as constitutive assemblies carrying enzymes. They have  succeeded in increasing product yields. However, the amount of those scaffolds could be limited by its expression or copy level, leading to restriction on further acceleration. With ''Membrane Magic'', we made ''E.coli'' membrane into a huge scaffold accommodating enzymes without limitation of scaffold amount. Moreover, protein assembly on membrane could readily receive extracellular or intracellular signal, so the whole system becomes highly tunable. The superiority of Membrane Scaffold is shown in details in '''WHY MEMBRANE'' section below.
-
''Fig.5'' showed that BlaLG has been correctly localized to membrane. Besides, a very low L-arabinose concentration at 0.02% is already enough to induce sufficient amount of membrane protein.
+
One of our devices, called ''Membrane Accelerator'', functions by localizing and organizing enzymes on membrane surface. ''E.coli'' inner membrane serves as a two-dimensional plane that can accommodate various protein assemblies linked with enzymes. Otherwise diffusing enzymes can form clusters on membrane through interacting protein domains and ligands. Enzyme clusters help substrates flow between enzymes, and  thus increase yields of sequential biological reactions. We not only applied the ''Membrane Accelerator'' into biosynthetic  pathway but also biodegradation pathway, which is proposed for the first time in synthetic biology. Previous researches on synthetic scaffold controlling metabolic flux all focused on biosynthesis.
-
To further characterize features of the Membrane Scaffold System and find optimal inducer concentration, we quantitatively tested the growth condition of ''E.coli'' carrying gene of BlaLG under different concentration of L-Arabinose and Ampicillin. We expected to see more colonies grew at high Ampicillin concentration if the inducer concentration is optimal.
 
 +
[[File:12SJTU membrane accelerator sketch.jpg|thumb|400px|center|''Fig.1:'' Sketch of ''Membrane Accelerator'']]
-
[[Image:12SJTU_Antibioticstest2.jpg|thumb|600px|center|''Fig.6'' :Growth condition of ''E. coli'' cells expressing BlaLG on LB agar media with different concentration of L-arabinose and Ampicillin. Single colony is picked and cultivated at 37℃ until OD value reaches 0.7. Bacteria cultures are diluted by 1:100000 and coated onto plates containing graded concentration of L-Arabinose and Ampicillin. Growth condition is measured through counting colonies on plates.]]
+
Although some work has been done in reaction acceleration, it has always been a challenge to artificially and dynamically control those reactions. Our ''Membrane Rudder'' device, however, offers a novel method to control the direction of biochemical reactions through varieties of signals. We further combined the whole post-translational control system with genetic circuits by recruiting RNA aptamer and its corresponding binding protein. Thus RNA signal could also be recruited to dynamically control biochemical reaction.
 +
[[File:12SJTU_overview4.gif|center|400px]]
-
The result apparently showed that at L-Arabinose concentration of 0.1% and 0.2%, more bacteria could grow on high concentration of Ampicllin. Thus, L-Arabinose concentration of 0.1% and 0.2% best suits single membrane protein expression in Project ''Membrane Magic''.
+
<center>''Fig.2:'' Sketch of ''Membrane Rudder''</center>
-
<br>
+
<br\>
-
<br>
+
<br\>
-
<br>
+
<br\>
-
=== Conclusion ===
+
==Why MEMBRANE?==
-
The result proved that fusion membrane protein with construction strategy shown in ''Fig. 2'' could be effectively localized to inner membrane of ''E.coli''. Thus membrane could readily be used as scaffold carrying various enzymes. Based on membrane scaffold, we tried to build two universal devices: [https://2012.igem.org/Team:SJTU-BioX-Shanghai/Project/project1.2 Membrane Accelerator] and [https://2012.igem.org/Team:SJTU-BioX-Shanghai/Project/project1.3 Membrane Rudder].
+
-
<br>
+
Why do we choose membrane as our primary scaffold to assemble enzymes?
-
<br>
+
{|
-
 
+
|-
-
------------------------------------------------------------------------
+
|1. '''Natural Scaffold: ''' Different from previous synthesized scaffold, membrane scaffold is an innate one. Besides, there is no limitation on scaffold amount.
 +
|[[File:12SJTU Why membrane1.png|300px|right|thumb|''Fig.3:'' Natural Scaffold]]
 +
|-
 +
|2. '''Two-Dimensional Plane: ''' Membrane Scaffold changes restricted the reaction space to a two-dimensional plane compared to discrete scaffold. Thus proteins on membrane are more likely to interact with each other (Demonstrated in [https://2012.igem.org/Team:SJTU-BioX-Shanghai/Project/project2.2 Fatty Acid Synthesis:The Refinement of Interaction]). Moreover, we can organize enzymes in 2D pattern on membrane to further facilitate metabolic flux (Demonstrated in [https://2012.igem.org/Team:SJTU-BioX-Shanghai/Project/project2.3 DBT desulfurization]).
 +
|[[File:12SJTU Why membrane2.jpg|300px|right|thumb|''Fig.4:'' Two-Dimensional Plane]]
 +
|-
 +
|3. '''Priority to Exportation: ''' Concentration of final products could be effectively increased near the membrane with Membrane Scaffold, which in turn, facilitates the transmembrane transportation. Thus final products would be more readily to be exported to extracellular media. (Demonstrated in [https://2012.igem.org/Team:SJTU-BioX-Shanghai/Project/project2.2 Fatty Acid Synthesis:The Priority to Exportation])
 +
|[[File:12SJTU Why membrane3.jpg|300px|right|thumb|''Fig.5:'' Priority to Exportation]]
 +
|-
 +
|4. '''Ability to Sense Signals: ''' Membrane Scaffold provides a platform to directly receive environmental and internal signal, So biochemical reactions could be dynamically controlled through those signals(Demonstrated in [https://2012.igem.org/Team:SJTU-BioX-Shanghai/Project/project1.3 Membrane Rudder Design] and [https://2012.igem.org/Team:SJTU-BioX-Shanghai/Project/project2.1 Violacein pathway: Membrane Rudder Application]).
 +
|[[File:12SJTU Why membrane4.jpg|300px|right|thumb|''Fig.6:'' Ability to sense signals]]
 +
|-
 +
|}
==Reference==
==Reference==
 +
1.Delebecque, C. J., A. B. Lindner, et al. (2011). "Organization of intracellular reactions with rationally designed RNA assemblies." Science 333(6041): 470.
-
1.Pailler, J., W. Aucher, et al. (2012). "Phosphatidylglycerol:: prolipoprotein diacylglyceryl transferase (Lgt) of Escherichia coli has seven transmembrane segments, and its essential residues are embedded in the membrane." Journal of bacteriology 194(9): 2142-2151.
+
2.Dueber, J. E., G. C. Wu, et al. (2009). "Synthetic protein scaffolds provide modular control over metabolic flux." Nature biotechnology 27(8): 753-759.
-
+
-
2.Schierle, C. F., M. Berkmen, et al. (2003). "The DsbA signal sequence directs efficient, cotranslational export of passenger proteins to the Escherichia coli periplasm via the signal recognition particle pathway." Journal of bacteriology 185(19): 5706-5713.
+
-
+
-
3.Skretas, G. and G. Georgiou (2010). "Simple genetic selection protocol for isolation of overexpressed genes that enhance accumulation of membrane-integrated human G protein-coupled receptors in Escherichia coli." Applied and environmental microbiology 76(17): 5852-5859.
+
 +
3.Conrado, R. J., G. C. Wu, et al. (2012). "DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency." Nucleic acids research 40(4): 1879-1889.
-
<!----------------------------------------------------end--------------------------------->
+
<!----------------------------------------------------到这里结束--------------------------------------->
-
{{Template:12SJTU_footer}}
+
</td>
 +
</tr></table>
 +
 
 +
<html>
 +
<body>
 +
 
 +
</tbody></table>
 +
</td></tr>
 +
</tbody></table>
 +
<br>
 +
 
 +
<div align="center" id="footer"> (c)  <a href="" target="_self">SJTU_BioX_iGEM2012</a> Powered by huanan1991</div>
 +
 
 +
</div>
 +
</body>
 +
</html>

Revision as of 13:26, 27 October 2013

Project Overview

Advance in molecular cloning technology has made it possible for mankind to entitle engineered organisms to different biochemical reactions. However, the speed of those enzymatic reactions is often limited because intermediates produced from upstream enzyme cannot be passed efficiently to downstream enzyme due to spatial obstacles. Thus, synthetic scaffold built to decrease distance between enzymes for speeding biochemical reactions is a rising topic with promising application prospect. Moreover, although some progress has been made in fields of metabolic flux control with synthetic scaffold, these strategies remain non-dynamic. Artificially and dynamically controlling metabolic flux has remained a challenge.

Introduction

In this year, we expanded the definition of scaffold in synthetic biology and developed two universal devices called Membrane Accelerator and Membrane Rudder respectively. Together, they made Membrane Magic happen!

Previous researchers have focused on building protein, RNA or DNA scaffold as constitutive assemblies carrying enzymes. They have succeeded in increasing product yields. However, the amount of those scaffolds could be limited by its expression or copy level, leading to restriction on further acceleration. With Membrane Magic, we made E.coli membrane into a huge scaffold accommodating enzymes without limitation of scaffold amount. Moreover, protein assembly on membrane could readily receive extracellular or intracellular signal, so the whole system becomes highly tunable. The superiority of Membrane Scaffold is shown in details in 'WHY MEMBRANE section below.

One of our devices, called Membrane Accelerator, functions by localizing and organizing enzymes on membrane surface. E.coli inner membrane serves as a two-dimensional plane that can accommodate various protein assemblies linked with enzymes. Otherwise diffusing enzymes can form clusters on membrane through interacting protein domains and ligands. Enzyme clusters help substrates flow between enzymes, and thus increase yields of sequential biological reactions. We not only applied the Membrane Accelerator into biosynthetic pathway but also biodegradation pathway, which is proposed for the first time in synthetic biology. Previous researches on synthetic scaffold controlling metabolic flux all focused on biosynthesis.


File:12SJTU membrane accelerator sketch.jpg
Fig.1: Sketch of Membrane Accelerator

Although some work has been done in reaction acceleration, it has always been a challenge to artificially and dynamically control those reactions. Our Membrane Rudder device, however, offers a novel method to control the direction of biochemical reactions through varieties of signals. We further combined the whole post-translational control system with genetic circuits by recruiting RNA aptamer and its corresponding binding protein. Thus RNA signal could also be recruited to dynamically control biochemical reaction.

400px
Fig.2: Sketch of Membrane Rudder




Why MEMBRANE?

Why do we choose membrane as our primary scaffold to assemble enzymes?

1. Natural Scaffold: Different from previous synthesized scaffold, membrane scaffold is an innate one. Besides, there is no limitation on scaffold amount.
File:12SJTU Why membrane1.png
Fig.3: Natural Scaffold
2. Two-Dimensional Plane: Membrane Scaffold changes restricted the reaction space to a two-dimensional plane compared to discrete scaffold. Thus proteins on membrane are more likely to interact with each other (Demonstrated in Fatty Acid Synthesis:The Refinement of Interaction). Moreover, we can organize enzymes in 2D pattern on membrane to further facilitate metabolic flux (Demonstrated in DBT desulfurization).
File:12SJTU Why membrane2.jpg
Fig.4: Two-Dimensional Plane
3. Priority to Exportation: Concentration of final products could be effectively increased near the membrane with Membrane Scaffold, which in turn, facilitates the transmembrane transportation. Thus final products would be more readily to be exported to extracellular media. (Demonstrated in Fatty Acid Synthesis:The Priority to Exportation)
File:12SJTU Why membrane3.jpg
Fig.5: Priority to Exportation
4. Ability to Sense Signals: Membrane Scaffold provides a platform to directly receive environmental and internal signal, So biochemical reactions could be dynamically controlled through those signals(Demonstrated in Membrane Rudder Design and Violacein pathway: Membrane Rudder Application).
File:12SJTU Why membrane4.jpg
Fig.6: Ability to sense signals

Reference

1.Delebecque, C. J., A. B. Lindner, et al. (2011). "Organization of intracellular reactions with rationally designed RNA assemblies." Science 333(6041): 470.

2.Dueber, J. E., G. C. Wu, et al. (2009). "Synthetic protein scaffolds provide modular control over metabolic flux." Nature biotechnology 27(8): 753-759.

3.Conrado, R. J., G. C. Wu, et al. (2012). "DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency." Nucleic acids research 40(4): 1879-1889.


Retrieved from "http://2013.igem.org/Team:UCSF/Project/Background2"