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| | <html> | | <html> |
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| - | <!--
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| - | * Markup for jQuery Orbit Plugin 1.2.3
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| - | * www.ZURB.com/playground
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| - | * Copyright 2010, ZURB
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| - | * Free to use under the MIT license.
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| - | * http://www.opensource.org/licenses/mit-license.php
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| - | -->
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| - |
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| - | <head>
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| - | <meta charset="utf-8" />
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| - | <title>Stanford-Brown iGEM</title>
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| - |
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| - | <!-- Attach our CSS -->
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| - | <!-- <link rel="stylesheet" href="../orbit-1.2.3.css">
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| - | <link rel="stylesheet" href="demo-style.css">
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| - | -->
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| - | <!-- Attach necessary JS --><!--
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| - | <script type="text/javascript" src="../jquery-1.5.1.min.js"></script>
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| - | <script type="text/javascript" src="../jquery.orbit-1.2.3.min.js"></script>
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| - | -->
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| - |
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| - | <!-- Attach our CSS -->
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| - | <link rel="stylesheet" href="http://www.stanford.edu/~sryoung/cgi-bin/igem/orbit-1.2.3.css">
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| - | <link rel="stylesheet" href="http://www.stanford.edu/~sryoung/cgi-bin/igem/demo/demo-style.css">
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| - |
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| - | <!-- Attach necessary JS -->
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| - | <script type="text/javascript" src="http://www.stanford.edu/~sryoung/cgi-bin/igem/jquery-1.5.1.min.js"></script>
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| - | <script type="text/javascript" src="http://www.stanford.edu/~sryoung/cgi-bin/igem/jquery.orbit-1.2.3.min.js"></script>
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| - |
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| - |
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| - | <!--[if IE]>
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| - | <style type="text/css">
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| - | .timer { display: none !important; }
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| - | div.caption { background:transparent; filter:progid:DXImageTransform.Microsoft.gradient(startColorstr=#99000000,endColorstr=#99000000);zoom: 1; }
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| - | </style>
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| - | <![endif]-->
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| - |
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| - | <!-- Run the plugin -->
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| - | <script type="text/javascript">
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| - | $(window).load(function() {
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| - | $('#featured').orbit();
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| - | });
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| - | </script>
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| - |
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| - |
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| - |
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| - | <!-- Stuff from Calgary -->
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| - |
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| - | <link rel='stylesheet' type='text/css' href="https://2013.igem.org/Team:Stanford-Brown/static/basicpageglobal.css?action=raw&ctype=text/css" />
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| - |
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| - | <style>
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| - | /*======
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| - | Desktop Styling
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| - | ======*/
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| - |
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| - | /***Body styling***/
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| - | h1{
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| - | font-size: 2.5em;
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| - | }
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| - | h2{
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| - | font-size: 1.8em;
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| - | }
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| - |
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| - | #box1{
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| - | width: 968px;
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| - | margin-top: -8px;
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| - | background: threedface;
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| - | float: left;
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| - | padding-bottom: 20px;
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| - | margin-bottom: 13px;
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| - | }
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| - | #box1 h2{
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| - | padding: 20px 20px 20px 20px;
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| - | }
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| - | #box1 p{
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| - | padding: 0px 20px 0px 20px;
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| - | font-size: 1.1em;
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| - | }
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| - |
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| - | #FredOscarFlag{
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| - | display: block;
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| - | float: left;
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| - | width: 250px;
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| - | height: 274px;
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| - | background: url('https://static.igem.org/mediawiki/2013/0/0b/UCalgary2012_FRED_and_OSCAR_Main_Page.png');
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| - | background-position: top;
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| - | margin: 15px;
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| - | }
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| - | #FredOscarFlag:hover{
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| - | background-position: bottom;
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| - | }
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| - |
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| - |
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| - | #box2{
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| - | width: 968px;
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| - | background: #C68DD8;
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| - | float: left;
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| - | margin-bottom: 13px;
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| - | }
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| - | #box2 h2{
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| - | padding: 20px 20px 20px 20px;
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| - | color: white;
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| - | }
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| - | #box2 p{
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| - | padding: 0px 20px 0px 20px;
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| - | font-size: 1.1em;
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| - | color: white;
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| - | }
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| - | #box2 img{
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| - | float: left;
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| - | margin: 15px;
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| - | height: 110px;
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| - | }
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| - | #box2:hover{
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| - | background: #D79EE9;
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| - | }
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| - |
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| - | /***positioning of elements in ZE EPIC BOX***/
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| - | #epicbox{
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| - | margin-top: 4px;
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| - | }
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| - |
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| - | #boximgcontainer{
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| - | float: left;
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| - | width: 644px;
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| - | height: 655px;
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| - | }
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| - | #boximgcontainer div{
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| - | float: left;
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| - | position: relative;
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| - | }
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| - | #orangebox{
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| - | margin-bottom: 4px;
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| - | }
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| - | #orangebox .imgbox{
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| - | width: 644px;
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| - | height: 215px;
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| - | top: 108px;
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| - | // background: #F6A82D;
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| - | //background: #33CC33;
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| - | background: #555555;
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| - | margin-bottom: 4px;
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| - | }
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| - | .oblank{
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| - | width: 644px;
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| - | height: 104px;
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| - | //background: #FFE485;
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| - | //background: #33EE33;
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| - | background: #888888;
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| - | position: relative;
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| - | top: -219px;
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| - | }
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| - | #orangebox:hover .oblank, .oblank:hover{
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| - | display: none;
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| - | }
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| - | #orangebox .iconcontainer{
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| - | position: relative;
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| - | display: none;
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| - | left: auto;
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| - | top: -219px;
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| - | }
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| - | .iconbox div, .iconbox{
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| - | width: 104px;
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| - | height: 104px;
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| - | margin-right: 4px;
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| - | }
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| - | a.obox1 div{
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| - | background: #BBBBBB;
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| - | }
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| - | a.obox2 div{
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| - | background: #AAAAAA;
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| - | }
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| - | a.obox3 div{
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| - | background: #999999;
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| - | }
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| - | a.obox4 div{
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| - | background: #888888;
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| - | }
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| - | a.obox5 div{
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| - | background: #777777;
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| - | }
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| - | a.obox6 div{
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| - | background: #666666;
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| - | margin-right: 0;
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| - | }
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| - | #orangebox div:hover, #orangebox div.iconbox:hover div{
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| - | background: #DDDDDD;
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| - | }
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| - | #orangebox:hover .iconcontainer{
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| - | display: block;
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| - | background: transparent;
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| - | }
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| - |
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| - |
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| - | #greenbox .imgbox{
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| - | width: 320px;
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| - | height: 215px;
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| - | //background: #58CD45;
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| - | //background: #888888;
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| - | //background: #33CC33;
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| - | background: #663399;
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| - | }
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| - | .gblank{
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| - | width: 320px;
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| - | height: 104px;
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| - | //background: #B6FFA3;
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| - | //background: #BBBBBB;
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| - | //background: #33EE33;
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| - | background: #9933FF;
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| - | position: relative;
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| - | top: 219px;
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| - | left: -320px;
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| - | }
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| - | #greenbox .iconcontainer{
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| - | position: relative;
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| - | margin-top: 4px;
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| - | left: -999em;
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| - | z-index: 1;
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| - | }
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| - | a.gbox1 div{
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| - | background: #9933FF;
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| - | }
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| - | a.gbox2 div{
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| - | background: #9900FF;
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| - | }
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| - | a.gbox3 div{
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| - | background: #660099;
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| - | }
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| - | a.gbox4 div{
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| - | background: #663399;
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| - | }
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| - | #greenbox div:hover, #greenbox div.iconbox:hover div{
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| - | //background: #94FF7D;
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| - | background: #9933FF;
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| - | z-index: 99; /*hovers are not overridden by OSCAR boxes*/
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| - | }
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| - | #greenbox:hover .gblank, .gblank:hover{
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| - | display: none;
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| - | }
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| - | #greenbox:hover .iconcontainer{
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| - | left: auto;
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| - | background: transparent;
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| - | }
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| - |
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| - | #bluebox{
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| - | position: relative;
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| - | top: -323px;
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| - | left: 320px;
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| - | }
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| - | #bluebox .imgbox{
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| - | width: 320px;
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| - | height: 215px;
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| - | //background: #5BB5E8;
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| - | background: #660000;
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| - | margin-left: 4px;
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| - | }
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| - | .bblank{
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| - | width: 320px;
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| - | height: 104px;
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| - | //background: #C5F0F0;
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| - | background: #996666;
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| - | position: relative;
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| - | top: 219px;
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| - | left: -320px;
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| - | z-index: 0;
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| - | }
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| - | #bluebox .iconcontainer{
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| - | position: relative;
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| - | margin-top: 4px;
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| - | left: -999em;
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| - | z-index: 0;
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| - | }
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| - | a.bbox1 div{
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| - | background: #993333;
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| - | }
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| - | a.bbox2 div{
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| - | background: #993300;
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| - | }
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| - | a.bbox3 div{
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| - | background: #990033;
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| - | }
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| - | a.bbox4 div{
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| - | background: #990000;
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| - | }
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| - | a.bbox5 div{
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| - | background: #990066;
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| - | }
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| - | a.bbox6 div{
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| - | background: #993366;
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| - | margin: 0;
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| - | }
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| - | #bluebox div:hover, #bluebox .iconbox:hover div{
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| - | //background: #7DD7FF;
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| - | background: #993333;
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| - | z-index: 99; /*hovers are not overridden by FRED boxes*/
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| - | }
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| - | #bluebox:hover .bblank, .bblank:hover{
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| - | display: none;
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| - | }
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| - | #bluebox:hover .iconcontainer{
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| - | left: -212px;
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| - | background: transparent;
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| - | }
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| - |
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| - | #boxinfo{
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| - | float: right;
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| - | position: relative;
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| - | width: 320px;
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| - | left: 3px;
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| - | // background: #555555;
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| - | background: #33CC33;
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| - | height: 650px;
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| - | margin-bottom: 12px;
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| - | }
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| - | #boxinfo h2{
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| - | color: white;
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| - | padding: 20px 20px 0px;
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| - | }
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| - | #boxinfo p{
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| - | color: white;
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| - | padding: 10px 20px 20px;
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| - | font-size: 1.2em;
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| - | }
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| - | /*initial boxinfo appearance settings*/
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| - | #boxinfo div.orangebox, #boxinfo div.obox1, #boxinfo div.obox2, #boxinfo div.obox3, #boxinfo div.obox4, #boxinfo div.obox5, #boxinfo div.obox6{
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| - | display: none;
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| - | }
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| - | #boxinfo div.greenbox, #boxinfo div.gbox1, #boxinfo div.gbox2, #boxinfo div.gbox3, #boxinfo div.gbox4,
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| - | #boxinfo div.bluebox, #boxinfo div.bbox1, #boxinfo div.bbox2, #boxinfo div.bbox3, #boxinfo div.bbox4, #boxinfo div.bbox5{
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| - | position: relative;
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| - | padding-top: 320px;
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| - | display: none;
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| - | }
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| - | /*bold colours for FRED and OSCAR*/
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| - | #boxinfo div.greenbox b{
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| - | color: #72E85B;
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| - | }
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| - | #boxinfo div.bluebox b{
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| - | color: #5EB7F0;
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| - | }
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| - | .threeboxes{
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| - | clear: both;
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| - | position: relative;
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| - | width: 968px;
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| - | margin-bottom: 12px;
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| - | }
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| - | .threeboxes a, .threeboxes a div{
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| - | width: 320px;
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| - | height: 155px;
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| - | float: left;
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| - | margin-bottom: 12px;
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| - | }
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| - | .threeboxes div h2{
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| - | padding: 20px 20px 0px;
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| - | position: relative;
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| - | top: -155px;
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| - | }
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| - | .threeboxes div p{
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| - | padding: 0px 20px;
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| - | position: relative;
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| - | top: -155px;
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| - | }
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| - | #greybox1, #greybox6{
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| - | margin-right: 4px;
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| - | //background: #58CD45;
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| - | background: #3399FF;
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| - | }
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| - | #greybox1:hover, #greybox6:hover{
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| - | background: #94FF7D;
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| - | }
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| - | #greybox2, #greybox5{
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| - | margin-right: 4px;
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| - | background: #5BB5E8;
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| - |
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| - | }
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| - | #greybox2:hover, #greybox5:hover{
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| - | background: #7DD7FF;
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| - | }
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| - | #greybox3, #greybox4{
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| - | margin: 0;
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| - | //background: #F6A82D;
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| - | background: #00CCFF;
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| - | }
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| - | #greybox3:hover, #greybox4:hover{
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| - | background: #FFE44F;
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| - | }
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| - |
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| - | #greybox4 {
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| - | background: #CCFFFF;
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| - | }
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| - | #greybox5 {
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| - | background: #CCFFFF;
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| - | }
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| - | #greybox6 {
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| - | background: #CCFFFF;
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| - | }
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| - | #greybox1:hover, #greybox2:hover, #greybox3:hover {
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| - | background: #00CC00;
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| - | }
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| - |
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| - |
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| - |
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| - |
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| - | #greybox4:hover, #greybox5:hover, #greybox6:hover {
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| - | background: #66FFFF;
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| - | }
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| - |
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| - | #greybox1 {
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| - | background: #CCFF99;
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| - | }
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| - | #greybox2 {
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| - | background: #CCFF99;
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| - | }
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| - | #greybox3 {
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| - | background: #CCFF99;
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| - | }
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| - |
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| - | #sponsorsbox{
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| - | clear: both;
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| - | position: relative;
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| - | width: 968px;
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| - | margin: 4px 0px;
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| - | background: #EEEEEE;
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| - | }
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| - | #sponsorsbox h2{
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| - | padding: 20px 20px 0px 20px;
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| - | }
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| - | #sponsorsbox p{
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| - | padding: 0px 20px;
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| - | }
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| - | #sponsorsbox table{
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| - | width: 950px;
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| - | margin-left: auto;
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| - | margin-right: auto;
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| - | background: #EEEEEE;
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| - | }
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| - | #sponsorsbox td{
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| - | padding: 15px 0px;
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| - | width: 300px;
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| - | }
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| - | #sponsorsbox img{
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| - | display: block;
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| - | margin-right: auto;
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| - | margin-left: auto;
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| - | }
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| - |
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| - | </style>
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| - |
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| - | <script>
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| - | jQuery(document).ready(function($){
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| - |
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| - | //eliminate jsnotice
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| - | $('#jsnotice').hide();
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| - |
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| - |
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| - | /*epic box info functionality*/
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| - | //small icons
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| - | $('#boximgcontainer .iconbox').hover(
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| - | function(){
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| - | var className = $(this).attr('class').split(" ");
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| - | var box = className[0];
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| - | clearinfo();
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| - | $('#boxinfo div.' + box).show();
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| - | },
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| - | function(){
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| - | clearinfo();
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| - | $('#boxinfo_default').show();
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| - | });
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| - | //large icons
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| - | $('.imgbox').hover(
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| - | function(){
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| - | var id = $(this).parent().parent().attr('id');
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| - | clearinfo();
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| - | $('#boxinfo div.' + id).show();
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| - | },
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| - | function(){
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| - | clearinfo();
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| - | $('#boxinfo_default').show();
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| - | });
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| - |
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| - | /*epic box FRED/OSCAR blank box disappearance*/
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| - | $('#bluebox').hover(
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| - | function(){
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| - | $('.gblank').hide();
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| - | $('.bblank').hide();
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| - | },
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| - | function(){
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| - | $('.gblank').show();
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| - | $('.bblank').show();
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| - | });
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| - |
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| - | $('#greenbox').hover(
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| - | function(){
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| - | $('.gblank').hide();
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| - | $('.bblank').hide();
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| - | },
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| - | function(){
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| - | $('.gblank').show();
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| - | $('.bblank').show();
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| - | });
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| - |
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| - | });
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| - |
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| - | function clearinfo(){
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| - | $('#boxinfo div').hide();
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| - | }
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| - | </script>
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| - |
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| - | <!-- End stuff from Calgary -->
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| - |
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| - |
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| - |
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| - |
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| - |
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| - | </head>
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| - | <body>
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| | | | |
| | <h2>Project Descriptions:</h2> | | <h2>Project Descriptions:</h2> |
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| | <B>EuCROPIS -</B> In 2011, the Brown-Stanford iGEM team engineered photosynthetic and nitrogen-fixing cyanobacteria to secrete sucrose, a project that they entitled PowerCell. The project was designed to address the problem of in-situ resource utilization when attempting to terraform Mars, since the secreted sucrose can be used as an energy source for other organisms. The goal of the EuCROPIS project is to validate PowerCell by building a chromogenic biosensor in <I>Bacillus subtilis</I>. <I>B. subtilis</I> forms endospores in nutrient-depleted conditions and undergoes germination when exposed to sugars. As a result, we plan to characterize various sporulation and germination reporters with a series of chromoproteins in varying colors, so that we can validate PowerCell's activity by watching <I>B. subtilis</I> change colors in a high altitude helium balloon and, in 2016, as a part of the EuCROPIS satellite mission. | | <B>EuCROPIS -</B> In 2011, the Brown-Stanford iGEM team engineered photosynthetic and nitrogen-fixing cyanobacteria to secrete sucrose, a project that they entitled PowerCell. The project was designed to address the problem of in-situ resource utilization when attempting to terraform Mars, since the secreted sucrose can be used as an energy source for other organisms. The goal of the EuCROPIS project is to validate PowerCell by building a chromogenic biosensor in <I>Bacillus subtilis</I>. <I>B. subtilis</I> forms endospores in nutrient-depleted conditions and undergoes germination when exposed to sugars. As a result, we plan to characterize various sporulation and germination reporters with a series of chromoproteins in varying colors, so that we can validate PowerCell's activity by watching <I>B. subtilis</I> change colors in a high altitude helium balloon and, in 2016, as a part of the EuCROPIS satellite mission. |
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| - | THE ACTUAL ORBIT SLIDER CONTENT
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| - | <h1>Orbit does content now.</h1>
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| - | <h3>Highlight me...I'm text.</h3>
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| - | <a href=""><img src="http://www.stanford.edu/~sryoung/cgi-bin/igem/demo/dummy-images/overflow.jpg" /></a>
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| - | <span class="orbit-caption" id="htmlCaption"><strong>I'm A Badass Caption:</strong> I can haz <a href="#">links</a>, <em>style</em> or anything that is valid markup :)</span>
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| - | <img src="https://static.igem.org/mediawiki/2013/0/02/UCalgary2012_ThreeBoxMusic.png-"></img>
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| - | <h2>Project #1</h2>
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| - | <p>Description</p>
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| - | <a id="greybox5" href="https://2013.igem.org/Team:Stanford-Brown/Project/Synergy-">
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| - | <h2>Project #2</h2>
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| - | <p>Description</p>
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| - | <h2>Project #3</h2>
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| - | <p>Description</p>
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| - | <h2>Team</h2>
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| - | <p>Who are we?</p>
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| - | <a id="greybox2" href="https://2013.igem.org/Team:Stanford-Brown/Project/DataPage">
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| - | <h2>Data Page</h2>
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| - | <p>Click here to see a summary of all our data collected so far!</p>
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| - | <p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p>
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| - | <h2>The Concept</h2>
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| - | <p>The concept</p>
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| - | <h2>Human Practices</h2>
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| - | <p>Human Practices</p>
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| - | <h2>Initiative</h2>
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| - | <p>Initiative</p>
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| - | <h2>Interviews</h2>
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| - | <p>Interviews</p>
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| - | <h2>Design Considerations</h2>
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| - | <p>Design Considerations</p>
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| - | <h2>Killswitch</h2>
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| - | <p>Kill Switch</p>
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| - | <h2>Safety</h2>
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| - | <p>Safety</p>
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| - | <h2>Community Outreach</h2>
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| - | <p>Community Outreach</p>
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| - | <h2>Project #1</h2>
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| - | <p>Project #1</p>
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| - | <h2>Detecting</h2>
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| - | <p>Project #1 Detection</p>
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| - | <h2>Reporting</h2>
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| - | <p>Project #1 Reporting</p>
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| - | <h2>Modelling</h2>
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| - | <p>Modelling for Project #1</p>
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| - | <h2>Prototyping</h2>
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| - | <p>Prototyping for Project #1</p>
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| - | <h2>Project #2</h2>
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| - | <p>Project #2</p>
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| - | <h2>Decarboxylation</h2>
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| - | <p>Project #2</p>
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| - | </div>
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| - | <h2>Catechol Degradation</h2>
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| - | <p>Project #2</p>
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| - | <h2>Flux-Variability Analysis</h2>
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| - | <p>Project #2</p>
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| - | <h2>Bioreactor</h2>
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| - | <p>Project #2</p>
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| - | <h2>Upgrading</h2>
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| - | <p>Project #2</p>
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| - | </div>
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We seek to use recent advances in nucleic acid chemistry to replace hydrogen bonds between mismatched DNA bases with cations. A chelation event has been described for mismatched pyrimidines, and we have selected a C-Ag+-C bond for silver's uniquely powerful conductivity. We will rigorously test the structural and thermodynamic properties of this bonding system. Our hope is to show that silver chelation by cytosine mismatches is able to enhance the conductivity of DNA. By engineering cytosine mismatches into synthetic oligonucleotide duplexes, we seek to establish a reliable platform for nanowire and nanodevice assembly. We will design and test various nucleic acid secondary structures, and hope to ultimately produce a DNA-based nanowire system that is conductive enough to be used in microchip design and other bioengineering applications.
Recently, the bacterial immune system protein Cas9 was adapted to activate or repress arbitrary genes. We combine Cas9 transcriptional regulation with horizontal gene transfer for two purposes: vaccination and DNA-based communication. We adapt Cas9 as a vaccine by transferring the system into pathogenic bacteria, in which it inactivates disease-causing genes without killing the cell. Because the approach avoids strong selective pressure, we believe it will circumvent the resistance mechanisms that have rendered many antibiotics therapeutically useless. We also adapt Cas9 to read and respond to DNA messages transferred into the cell. The system functions as a switch capable of uniquely responding to millions of possible messages, exponentially more than provided by existing chemical communication systems.
Like the Rosetta Stone, reconstructing ancestral versions of proteins will help us understand modern biology. Consider the amino acid alphabet. CysE, the protein that makes cysteine, contains cysteine in its structure, producing a chicken-and-egg problem. We hypothesize that there must have existed a version of CysE that did not contain cysteine in early life. By reconstructing ancestral versions of CysE and similar amino acid forming protein HisC, we will understand more about early life and its evolution. We hope not only to improve our understanding of evolution, but also to create applicative value. For this part of our project, we are focusing on CasA. An ancestral reconstruction of the modern CasA gene may give us insight into the mechanism of the CASCADE sequence. It may also demonstrate that ancient proteins were more thermostable or more resistant to acidity. We hope this will allow us to expand the functionality of the CRISPR system as it relates to our other projects. The technical aspects of De-Extinction are centered on the use of bioinformatics software to gather data on existing sequences for our genes and construct phylogenetic trees. We constructed a likelihood tree to determine which evolutionary substitution model we should use, and then worked backwards to construct the ancestral sequence, while also using software to model our protein and hypothesize how the active sites have changed over the years. We are further demonstrating the accuracy of our methods by working with Dr. Rich Lenski from Michigan State University, and we are including a bioethics section to address the moral uncertainties that arise from the idea that, one day, we may be able to reverse the extinction of entire organisms.
In 2011, the Brown-Stanford iGEM team engineered photosynthetic and nitrogen-fixing cyanobacteria to secrete sucrose, a project that they entitled PowerCell. The project was designed to address the problem of in-situ resource utilization when attempting to terraform Mars, since the secreted sucrose can be used as an energy source for other organisms. The goal of the EuCROPIS project is to validate PowerCell by building a chromogenic biosensor in
.
forms endospores in nutrient-depleted conditions and undergoes germination when exposed to sugars. As a result, we plan to characterize various sporulation and germination reporters with a series of chromoproteins in varying colors, so that we can validate PowerCell's activity by watching
change colors in a high altitude helium balloon and, in 2016, as a part of the EuCROPIS satellite mission.
"
