Team:UC Davis/Project/Strain

From 2012.igem.org

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<script type="text/javascript"        src ="https://2012.igem.org/forum/forum_scripts.js"></script>
<script type="text/javascript"        src ="https://2012.igem.org/forum/forum_scripts.js"></script>
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<script type="text/javascript">
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function slider() {
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var $navicurrent = $('.progress li.current');
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if($navicurrent.length ==0) $navicurrent = $('.progress li:last');
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$navicurrent.removeClass('current previous');
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$navinext.addClass('current').animate({opacity: 1.0}, 2500, function() {
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$('.progress li').click(function(){
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var $ncurrent = $(this);
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Line 89: Line 188:
min-height:100%; /* real browsers */
min-height:100%; /* real browsers */
}
}
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#content { z-index: 1; background-color: transparent; border: none; padding: 0; margin: 0; width: 100%; overflow: hidden; margin-top: -45px !important;
+
#content { z-index: 1; background-color: transparent; border: none; padding: 0; margin: 0; width: 100%; overflow: hidden; top:-3px; margin-top: -45px !important;
height:auto !important; /* real browsers */
height:auto !important; /* real browsers */
height:100%; /* IE6: treaded as min-height*/
height:100%; /* IE6: treaded as min-height*/
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#menubar.right-menu { width:300px; display:block; float:left; margin-top:-80px; border: none;}
#menubar.right-menu { width:300px; display:block; float:left; margin-top:-80px; border: none;}
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.right-menu ul { border: none; width: 300px;}
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#footer { border: none; width: 850px; margin: 0 auto; padding: 0;}
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h3#siteSub { display: none;}
h3#siteSub { display: none;}
#contentSub {display: none;}
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h1{border:none; width: 100%; clear: both;}
h1{border:none; width: 100%; clear: both;}
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     margin: 0 auto;
     padding: 5px 5px 5px 5px;;
     padding: 5px 5px 5px 5px;;
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#topmenubar {
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         list-style-type:none;  
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#newnavi .newmenu li    {
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#newnavi .newmenu .selected {
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}
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#newnavi .newmenu li:hover a {
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}
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#newnavi .newmenu li:hover      {
#newnavi .newmenu li:hover      {
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#newnavi .newmenu li:hover ul  {
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background-color: #05bcea; text-decoration:none;       
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#newnavi .newmenu li:hover ul li a:hover {
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background: #05bcea;
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#newnavi .newmenu li ul li ul li a {
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color:#ffffff;
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#newnavi .newmenu li ul li:hover ul li {
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#newnavi .newmenu li ul li:hover ul li a {
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#myleftrightbox .fourboxes
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background-color:rgba(143,143,143,0.7);
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margin-right:3.75px solid #e8eff1;
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padding: 8.5px;
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#myleftrightbox .fourboxes-1
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background-color:rgba(143,143,143,0.7);
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margin-top: 15px;
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margin-left:3.75px solid #e8eff1;
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margin-right:3.75px solid #e8eff1;
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#myleftrightbox .fourboxes-2
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background-color:rgba(143,143,143,0.7);
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margin-top: 15px;
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margin-left:3.75px solid #e8eff1;
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margin-right:3.75px solid #e8eff1;
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padding: 8.5px;
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font: sans-serif;
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#myleftrightbox .fourboxes-3
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margin-top: 15px;
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margin-left:3.75px solid #e8eff1;
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margin-right:3.75px solid #e8eff1;
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margin-bottom:0px;
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padding: 8.5px;
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font: sans-serif;
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font-size: 13px;
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color: white;
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#myleftrightbox .fourboxes-4
 +
{
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float:left;
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background-color:rgba(143,143,143,0.7);
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margin-top: 15px;
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margin-left:3.75px solid #e8eff1;
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margin-right:3.75px solid #e8eff1;
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padding: 8.5px;
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font: sans-serif;
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font-size: 13px;
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color: white;
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#myleftrightbox .fourboxes-1:hover {
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#myleftrightbox .fourboxes-4:hover {
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background-color:#4a4a4a;
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}
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#myleftrightbox .fourboxes2
 +
{
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width:191px;
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float:left;
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background-color:rgba(143,143,143,0.7);
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margin-top: 5px;
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margin-left:3.75px solid #e8eff1;
 +
margin-right:3.75px solid #e8eff1;
 +
margin-bottom:0px;
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border-radius: 4px;
 +
padding: 8.5px;
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font: sans-serif;
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font-size: 13px;
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color: white;
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#myleftrightbox .spacebox
 +
{
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float:left;
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width:5px;
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#myleftbox
 +
{
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position:relative;
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width:625px;
 +
float:left;
 +
background-color:;
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margin-top: 0px;
 +
border-radius: 4px;
 +
padding: 0px;
 +
font: sans-serif;
 +
font-size: 13px;
 +
color: white;
 +
}
 +
#myleftbox .smallbox
 +
{
 +
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float:left;
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background-color:#bfbfbf;
 +
margin-top: 15px;
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border-radius: 4px;
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padding: 15px 15px 15px 15px;
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font: sans-serif;
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font-size: 13px;
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line-height:1.5em;
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color:black;
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#myleftbox .smallbox h1
 +
{
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#myleftbox .smallbox p
 +
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#myleftbox .smallboxsite
 +
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float:left;
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margin-top: 17px;
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border-radius: 4px;
 +
padding: 15px 15px 15px 15px;
 +
font: sans-serif;
 +
font-size: 13px;
 +
line-height:1.5em;
 +
color:black;
 +
 
 +
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 +
#myleftbox .threeboxes
 +
{
 +
width:191px;
 +
float:left;
 +
background-color:rgba(143,143,143,0.7);
 +
margin-top: 15px;
 +
border-radius: 4px;
 +
border-left:2px solid #e8eff1;
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border-right:2px solid #e8eff1;
 +
padding: 7px 7px 7px 7px;
 +
font: sans-serif;
 +
font-size: 13px;
 +
color: white;
 +
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 +
 
 +
#myleftbox .threeboxes2
 +
{
 +
width:191px;
 +
float:left;
 +
background-color:rgba(143,143,143,0.7);
 +
margin-top: 5px;
 +
border-radius: 4px;
 +
border-left:2px solid #e8eff1;
 +
border-right:2px solid #e8eff1;
 +
padding: 7px 7px 7px 7px;
 +
font: sans-serif;
 +
font-size: 13px;
 +
color: white;
 +
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 +
#myleftbox .threeleft
 +
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 +
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 +
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 +
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 +
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 +
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 +
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 +
 
 +
#myleftbox .threecenter
 +
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 +
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 +
#float:left;
 +
background-color:#ba9108;
 +
margin-top: -52px;
 +
border-radius: 4px;
 +
padding: 15px 15px 15px 15px;
 +
font: sans-serif;
 +
font-size: 13px;
 +
color: white;
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 +
#myleftbox .threeright
 +
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 +
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 +
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 +
background-color:#ba9108;
 +
margin-top: -52px;
 +
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padding: 15px 15px 15px 15px;
 +
font: sans-serif;
 +
font-size: 13px;
 +
color: white;
 +
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 +
 
 +
 
 +
 
 +
#myleftbox .twoboxes
 +
{
 +
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 +
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 +
float:left;
 +
background-color:rgba(143,143,143,0.7);
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margin-top: 15px;
 +
border-radius: 4px;
 +
border-left:2px solid #e8eff1;
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border-right:2px solid #e8eff1;
 +
padding: 7px 7px 7px 7px;
 +
font: sans-serif;
 +
font-size: 13px;
 +
color: white;
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 +
 
 +
#myleftbox .twoboxes1
 +
{
 +
width:295px;
 +
height:120px;
 +
float:left;
 +
background-color:rgba(143,143,143,0.7);
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 +
border-radius: 4px;
 +
border-left:1px solid #e8eff1;
 +
border-right:2px solid #e8eff1;
 +
padding: 7px 7px 7px 7px;
 +
font: sans-serif;
 +
font-size: 13px;
 +
color: white;
 +
left:9px;
 +
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 +
 
 +
#myleftbox .twoboxes:hover {
 +
background-color:red;
 +
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 +
 
 +
#myleftbox .twoboxes1:hover {
 +
background-color:green;
 +
}
 +
 
 +
#sponsorbox
 +
{
 +
position: relative;
 +
width: 208px;
 +
margin-top:15px;
 +
float: right;
 +
height: auto;
 +
}
 +
 
 +
#sponsorbox .sponsorfloat
 +
{
 +
left:-3px;
 +
width:198px;
 +
float: right;
 +
background-color: #004b85;
 +
margin-top: 0px;
 +
margin-bottom:5px;
 +
border-radius: 4px;
 +
padding: 5px 5px 5px 5px;
 +
font: sans-serif;
 +
font-size: 13px;
 +
color: rgba(225,225,225,1);
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 +
 
 +
#sponsorbox .sponsorfloat h2
 +
{
 +
#color:#ba9108;
 +
color:white;
 +
font-size:130%;
 +
}
 +
 
 +
#sponsorbox .sponsorfloat a
 +
{
 +
color:white;
 +
font: sans-serif;
 +
}
 +
 
 +
#sponsorbox .sponsorfloat p
 +
{
 +
font: sans-serif;
 +
}
 +
 
 +
#sponsorbox .sponsorfloat1
 +
{
 +
left:-3px;
 +
width:192px;
 +
float: right;
 +
background-color: rgba(143, 143, 143, 0.7);
 +
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 +
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 +
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 +
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 +
font: sans-serif;
 +
font-size: 13px;
 +
color: rgba(225,225,225,1);
 +
}
 +
 
 +
#sponsorbox .sponsorfloat1:hover {
 +
background: #ff0000;
 +
}
 +
 
 +
#sponsorbox .sponsorfloat2
 +
{
 +
left:-3px;
 +
width:192px;
 +
float: right;
 +
background-color: rgba(143, 143, 143, 0.7);
 +
margin-top: 0px;
 +
margin-bottom:5px;
 +
border-radius: 4px;
 +
padding: 8px 8px 8px 8px;
 +
font: sans-serif;
 +
font-size: 13px;
 +
color: rgba(225,225,225,1);
 +
}
 +
 
 +
#sponsorbox .sponsorfloat2:hover {
 +
background: #008000;
 +
}
 +
 
 +
.newsAnnouncement
 +
{
 +
width:205px;
 +
height:110px;
 +
overflow-x:hidden;
 +
overflow-y:scroll;
}
}
Line 283: Line 865:
font-weight:bold;
font-weight:bold;
font-size: 40px;
font-size: 40px;
-
color: #004b85;;
+
color: #016D8B;;
-
left:10px;
+
-
}
+
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+
-
.floatbox3 hp{
+
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font-weight:bold;
+
-
font-size: 20px;
+
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color: #004b85;;
+
left:10px;
left:10px;
}
}
Line 318: Line 893:
     padding: 0 .0em;}
     padding: 0 .0em;}
-
 
+
#catlinks {
 +
background-color:transparent;
 +
border:1px solid transparent;
 +
}
 +
#footpage {
 +
background-color:transparent;
 +
}
 +
#footer-box {
 +
background-color:rgba(191,191,191,0.5);
 +
margin-top:0px;
 +
}
#footer-box-1 {
#footer-box-1 {
          
          
Line 327: Line 912:
         border: 1px solid #444444;
         border: 1px solid #444444;
}
}
 +
#tweets {
 +
    width: 203px;
 +
    margin: 0 auto;
 +
    font: sans-serif;
 +
    font-size: 12px;
 +
}
 +
 +
#tweets .twtr-widget,
 +
#tweets .twtr-doc {
 +
 +
    width: 100%;
 +
    height: auto;
 +
}
 +
 +
#tweets .twtr-hd {
 +
    display:none;
 +
    background: #d40;
 +
    color: #fff;
 +
    -moz-border-radius: 4px 4px 0 0;
 +
    border-radius: 4px 4px 0 0;
 +
    font-family: sans-serif !important;
 +
    }
 +
 +
#tweets .twtr-hd *,
 +
#tweets .twtr-hd h4 a {
 +
 +
    background: #d40 !important;
 +
    font: sans-serif !important;
 +
}
 +
 +
#tweets .twtr-hd h3,
 +
#tweets .twtr-hd h4 {
 +
 +
    font-weight: normal;
 +
    text-align: left;
 +
    margin:0;
 +
}
 +
 +
#tweets .twtr-hd h3 {
 +
       
 +
    background: #fff !important;
 +
    color: #333 !important;
 +
    font: sans-serif;
 +
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 +
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 +
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 +
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 +
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 +
 +
#tweets .twtr-tweet {
 +
 +
    background: #fff;
 +
    font: sans-serif !important;
 +
    font-size: 12px;
 +
}
 +
 +
#tweets .twtr-tweet a:link,
 +
#tweets .twtr-tweet a:visited,
 +
#tweets .twtr-tweet a:hover {
 +
 +
    color: #c40 !important;
 +
 +
}
 +
 +
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 +
 +
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 +
    padding-bottom: 4px !important;
 +
    font: sans-serif;
 +
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 +
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 +
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#tweets .twtr-tweet .twtr-tweet-text p {
 +
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 +
    font: sans-serif;
 +
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 +
 +
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 +
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 +
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 +
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 +
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 +
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 +
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 +
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 +
 +
#lightbox {
 +
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 +
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 +
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 +
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</style>
</style>
Line 342: Line 1,023:
    <ul>
    <ul>
  <li style='color:#014457; cursor:default'><a>teams</a></li>
  <li style='color:#014457; cursor:default'><a>teams</a></li>
-
                    <li class='selected'        ><a href="https://2012.igem.org/Team:UC_Davis">Page</a></li>
+
                    <li class='selected'        ><a href="https://2012.igem.org/Team:UC_Davis/Project/Strain">Page</a></li>
-
                 <li class='new'><a href="https://2012.igem.org/wiki/index.php?title=Talk:Team:UC_Davis&amp;action=edit&amp;redlink=1">Discussion</a></li>
+
                 <li class='new'><a href="https://2012.igem.org/wiki/index.php?title=Talk:Team:UC_Davis/Project/Strain&amp;action=edit&amp;redlink=1">Discussion</a></li>
               <li><a href="https://2012.igem.org/wiki/index.php?title=Team:UC_Davis/Project/Strain&action=edit">Edit</a></li>
               <li><a href="https://2012.igem.org/wiki/index.php?title=Team:UC_Davis/Project/Strain&action=edit">Edit</a></li>
-
                           <li><a href="https://2012.igem.org/wiki/index.php?title=Team:UC_Davis&amp;action=history">History</a></li>
+
                           <li><a href="https://2012.igem.org/wiki/index.php?title=Team:UC_Davis/Project/Strain&amp;action=history">History</a></li>
-
                 <li><a href="https://2012.igem.org/Special:MovePage/Team:UC_Davis">Move</a></li>
+
                 <li><a href="https://2012.igem.org/Special:MovePage/Team:UC_Davis/Project/Strain">Move</a></li>
-
                           <li><a href="https://2012.igem.org/wiki/index.php?title=Team:UC_Davis&amp;action=watch">Watch</a></li>
+
                           <li><a href="https://2012.igem.org/wiki/index.php?title=Team:UC_Davis/Project/Strain&amp;action=watch">Watch</a></li>
  <li><a href="https://igem.org/Login">Log in</a></li>
  <li><a href="https://igem.org/Login">Log in</a></li>
Line 355: Line 1,036:
   <div id="newnavi">
   <div id="newnavi">
     <ul class="newmenu">
     <ul class="newmenu">
-
        <li ><a href="https://2012.igem.org/" title="Back to iGEM">iGEM</a></li>
+
    <li ><a target="new" href="https://2012.igem.org/" title="Back to iGEM">iGEM</a>
 +
          <ul>
 +
          <li><a target="new" href="https://2012.igem.org/">Main iGEM</a></li>
 +
          <li><a href="https://2012.igem.org/Team:UC_Davis/Criteria">Criteria</a></li>
 +
          <li><a href="https://2012.igem.org/Team:UC_Davis/Human_Practices">Human Practices</a></li>
 +
          </ul>
 +
        </li>
         <li ><a href="https://2012.igem.org/Team:UC_Davis/Attributions" title="Attributions">Attributions</a></li>
         <li ><a href="https://2012.igem.org/Team:UC_Davis/Attributions" title="Attributions">Attributions</a></li>
-
         <li ><a href="https://2012.igem.org/Team:UC_Davis/Data" title="Data">Data</a>
+
         <li ><a title="https://2012.igem.org/Team:UC_Davis/Data" title="Data">Data</a>
           <ul>
           <ul>
-
             <li ><a href="./Data.htm ">Data 1</a></li>
+
             <li ><a href="https://2012.igem.org/Team:UC_Davis/Data/Cutinase_Activity" title="Data">Cutinase Activity</a></li>
-
             <li ><a href="./Data.htm ">Data 2</a></li>
+
             <li ><a href="https://2012.igem.org/Team:UC_Davis/Data/Ethylene_Glycol"
-
            <li ><a href="./Data.htm ">Data 3</a></li>
+
title="Data">Ethylene Glycol</a></li>
-
        </ul>
+
<li ><a href="https://2012.igem.org/Team:UC_Davis/Data/Modeling"
 +
title="Data">Modeling</a></li>
 +
 
 +
            <li ><a href="https://2012.igem.org/Team:UC_Davis/Parts">Parts</a></li>
 +
          </ul>
         </li>
         </li>
         <li ><a href="https://2012.igem.org/Team:UC_Davis/Notebook" title="Notebook">Notebook</a>
         <li ><a href="https://2012.igem.org/Team:UC_Davis/Notebook" title="Notebook">Notebook</a>
           <ul>
           <ul>
-
             <li ><a href="./Notebook.htm ">Week 1</a></li>
+
             <li ><a href="https://2012.igem.org/Team:UC_Davis/Notebook">Notebook</a></li>
-
             <li ><a href="./Notebook.htm ">Week 2</a></li>
+
             <li ><a href="https://2012.igem.org/Team:UC_Davis/Notebook/Protocols ">Protocols</a></li>
-
             <li ><a href="./Notebook.htm ">Week 3</a></li>
+
             <li ><a href="https://2012.igem.org/Team:UC_Davis/Notebook/Gallery">Gallery</a></li>
           </ul>
           </ul>
         </li>
         </li>
Line 378: Line 1,069:
         <li class="selected"><a href="https://2012.igem.org/Team:UC_Davis/Project" title="Project">Project</a>
         <li class="selected"><a href="https://2012.igem.org/Team:UC_Davis/Project" title="Project">Project</a>
           <ul>
           <ul>
-
             <li ><a href="https://2012.igem.org/Team:UC_Davis/Project/Strain">Strain</a></li>
+
             <li ><a href="https://2012.igem.org/Team:UC_Davis/Project">Project Overview</a></li>
-
             <li ><a href="https://2012.igem.org/Team:UC_Davis/Project/Catalyst">Catalyst</a></li>
+
             <li ><a href="https://2012.igem.org/Team:UC_Davis/Project/Catalyst">Module Engineering</a></li>
             <li ><a href="https://2012.igem.org/Team:UC_Davis/Project/Protein_Engineering">Protein Engineering</a></li>
             <li ><a href="https://2012.igem.org/Team:UC_Davis/Project/Protein_Engineering">Protein Engineering</a></li>
 +
            <li ><a title="https://2012.igem.org/Team:UC_Davis/Project/Strain">Chassis Engineering </a>
 +
  <ul>
 +
                <li><a href="https://2012.igem.org/Team:UC_Davis/Project/Strain">Background</a></li>
 +
        <li><a href="https://2012.igem.org/Team:UC_Davis/Project/Directed_Evolution">Directed Evolution</a></li>
 +
                <li><a href="https://2012.igem.org/Team:UC_Davis/Project/Our_Strain">Rational Engineering </a></li>
 +
</ul>
 +
</li>
           </ul>
           </ul>
         </li>
         </li>
Line 387: Line 1,085:
     </ul>
     </ul>
   </div>
   </div>
 +
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 +
<div id="slides">
 +
 +
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 +
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 +
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 +
</div>
 +
    <ul class="progress">
 +
<li class="current"><a href="#n_0">1</a> </li>
 +
<li><a href="#n_1">2</a> </li>
 +
        <li><a href="#n_2">3</a> </li>
 +
        <li><a href="#n_3">4</a> </li>
 +
    </ul>
 +
slide show ends here -->
 +
 +
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 +
 +
<div id="bodyContent"> 
 +
<!--  <div id="contentSub"></div> -->
 +
<!--  </div> -->
 +
<!-- float: right; first try -->
 +
<!-- 1st row four boxes starts here -->
 +
<div id="myleftrightbox">
 +
<div id="myleftrightbox"  class="fourboxes-1">
 +
<a href="https://2012.igem.org/Team:UC_Davis/Project"><img src="https://static.igem.org/mediawiki/2012/7/73/UCD_project_small_banner.jpg
 +
"></a>
 +
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 +
<div id="myleftrightbox"  class="spacebox">
 +
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<div id="myleftrightbox"  class="fourboxes-2">
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<a href="https://2012.igem.org/Team:UC_Davis/Project/Catalyst"><img src="https://static.igem.org/mediawiki/2012/5/55/UCD_modular_small_banner.jpg
 +
"></a>
 +
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 +
<div id="myleftrightbox"  class="spacebox">
 +
<p></p>
 +
</div>
 +
<div id="myleftrightbox"  class="fourboxes-3">
 +
<a href="https://2012.igem.org/Team:UC_Davis/Project/Protein_Engineering"><img src="https://static.igem.org/mediawiki/2012/f/ff/UCD_protein_small_banner.jpg"></a>
 +
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 +
<div id="myleftrightbox"  class="spacebox">
 +
<p></p>
 +
</div>
 +
<div id="myleftrightbox"  class="fourboxes-4">
 +
<a href="https://2012.igem.org/Team:UC_Davis/Criteria"><img src="https://static.igem.org/mediawiki/2012/1/18/UCD_criteria_small_banner.jpg"></a>
 +
</div>
 +
</div>
 +
<!-- 1st row four boxes ends here -->
 +
 +
 +
<!-- <div id="sponsorbox" style="width:220px; float:right;"> -->
 +
 +
<div id="sponsorbox">
 +
 +
<div id="sponsorbox" class="sponsorfloat1">
 +
 +
<a href="https://2012.igem.org/Team:UC_Davis/Project/Directed_Evolution"><img src="https://static.igem.org/mediawiki/2012/d/df/UCD_Directed_small_banner.jpg"></a>
 +
</div>
 +
 +
<div id="sponsorbox" class="sponsorfloat2">
 +
 +
<a href="https://2012.igem.org/Team:UC_Davis/Project/Our_Strain"><img src="https://static.igem.org/mediawiki/2012/4/47/UCD_Rational_small_banner.jpg"></a>
 +
</div>
 +
 +
<div id="sponsorbox" class="sponsorfloat">
 +
<!-- twitter starts here -->
 +
</script>
 +
<div id="tweets">
 +
<center>
 +
<h2>UCDavis iGEM Tweets</h2>
 +
</center>
 +
<script charset="utf-8" src="http://widgets.twimg.com/j/2/widget.js"></script>
 +
<script>
 +
new TWTR.Widget({
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  version: 2,
 +
  type: 'profile',
 +
  rpp: 10,
 +
  interval: 30000,
 +
  width: 203,
 +
  height: 100,
 +
 
 +
  theme: {
 +
    shell: {
 +
      background: '#004b85',
 +
      color: '#ffffff'
 +
    },
 +
    tweets: {
 +
      background: '#004b85',
 +
      color: '#ffffff',
 +
      links: '#4aed05'
 +
    }
   
   
-
+
  },
-
<img src="http://img.photobucket.com/albums/v26/bluemelon/project_banner1.jpg" width="850" height="228">
+
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+
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 +
<!-- twitter ends here -->
 +
</div>
-
<br>
+
<div id="sponsorbox" class="sponsorfloat">
 +
<center>
 +
<h2>Our Sponsors</h2>
 +
<a href="http://www.novozymes.com/en/Pages/default.aspx" target="_blank"><img src="https://static.igem.org/mediawiki/2011/2/21/UCD_Novozymes-logo.jpg" width="200"></a>
 +
</center>
-
  <div class="floatbox3">
+
<center>
-
<h1> Strain </h1>
+
<a href="http://engineering.ucdavis.edu/" target="_blank"><img src="https://static.igem.org/mediawiki/2011/f/f6/UCD_CoE.png" width="200" height="40"></a>
-
<article>
+
</center>
-
text
+
<center>
 +
<a href="http://biosci.ucdavis.edu/index_js.html" target="_blank"><img src="https://static.igem.org/mediawiki/2011/b/b1/UCD_biosci_sponsor.jpg" width="200" height="90"></a>
 +
</center>
-
</article>
+
<center>
-
  </div>
+
<a href="http://www.genomecenter.ucdavis.edu/" target="_blank"><img src="https://static.igem.org/mediawiki/2011/1/1b/UCD_Genome_center_sponsor.jpg" width="200" height="60"></a>
 +
</center>
-
<br>
+
<center>
-
<div class="floatbox3">
+
<a href="http://www.cs.ucdavis.edu/" target="_blank"><img src="https://static.igem.org/mediawiki/2012/6/6b/UCD_Computer_sponsor.jpg" width="200"></a>
-
<hp>Background</hp>
+
</center>
 +
 
 +
<center>
 +
<a href="http://www.bme.ucdavis.edu/" target="_blank"><img src="https://static.igem.org/mediawiki/2011/4/40/UCD_BME_logo_minimal_copy.png" width="200 height="70"></a>
 +
</center>
 +
 
 +
<center>
 +
<a href="http://www.fishersci.com" target="_blank"><img src="https://static.igem.org/mediawiki/2011/a/a4/UCD_Fisher_Logo.gif" width="200"></a>
 +
</center>
 +
 
 +
<center>
 +
<a href="http://www.arcadiabio.com/" target="_blank"><img src="https://static.igem.org/mediawiki/2012/4/46/UCD_Arcadia_sponsor.jpg
 +
" width="200"></a>
 +
</center>
 +
 
 +
<center>
 +
<a href="http://provost.ucdavis.edu/" target="_blank"><img src="https://static.igem.org/mediawiki/2012/8/82/UCD_Provost_sponsor.jpg
 +
" width="200"></a>
 +
</center>
 +
 
 +
<center>
 +
<a href="http://www.research.ucdavis.edu/" target="_blank"><img src="https://static.igem.org/mediawiki/2012/9/99/UCD_Research_sponsor.jpg" width="200"></a>
 +
</center>
 +
 
 +
<center>
 +
<a href="http://ucomm.ucdavis.edu/" target="_blank"><img src="https://static.igem.org/mediawiki/2012/b/b4/UCD_Communications_sponsor.jpg" width="200"></a>
 +
</center>
 +
 
 +
<center>
 +
<a title="" target="_blank"><img src="https://static.igem.org/mediawiki/2012/2/25/UCD_Schultz_sponsor.jpg
 +
" width="200"></a>
 +
</center>
 +
 
 +
</div>
 +
</div>
 +
<!--  <br> -->
 +
<!-- div id="myleftbox" style="width:625px; float:left;" -->
 +
<div id="myleftbox">
 +
 
 +
<div id="myleftbox"  class="smallbox">
 +
<h1>Chassis Engineering: Background</h1>
<article>
<article>
-
Text goes here
+
Chassis or strain engineering focuses on the modification of chromosomes instead of plasmids and encompasses both <a href="https://2012.igem.org/Team:UC_Davis/Project/Directed_Evolution">directed evolution</a>
 +
and <a href="https://2012.igem.org/Team:UC_Davis/Project/Our_Strain">rational engineering</a>. This part of the project focuses on the elimination of ethylene glycol, a degradation product of PET that is metabolized to oxalic acid further downstream the metabolic pathway. Oxalic acid is toxic to the kidney and fatal to the organism (2). (For a look at how we handled these compounds safely, look at our <a href="https://2012.igem.org/Team:UC_Davis/Safety">Safety Page</a>!)
 +
<br>
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2012/f/f0/UCD_figure_chassis_background.png">
 +
</center>
 +
<br>
 +
Once we discovered the potential toxicity of our project, we searched high and low to find ways to eliminate ethylene glycol (EG) as much as possible. In the scientific literature, we found that no wild-type <i>E. coli</i> can utilize EG (1). However, we did find an <I>E. coli</I> mutant, called Strain E-15 EG3, from the University of Barcelona, that is able to grow on ethylene glycol alone (1). While the University of Barcelona's paper on Strain E-15 EG3 was published nearly 30 years ago, we contacted the authors and asked for the strain to perform our own testing. The researchers were able to find the strain in one of their freezers and ship it to our lab. We have dubbed the rediscovery of the strain "Freezer Archaeology".
 +
 
 +
<br><br>By performing various experiments on MG1655 including directed evolution, which selects the cells with the most fitness in a population, and ethyl methylsulfonate (EMS), which introduces random mutations to a population, the scientists learned that the main contributors in the degradation were propanediol oxidoreductase and glycolaldehyde dehydrogenase. These two enzymes are expressed at low levels in MG1655 but not at all in DH5α. We worked to overexpress these enzymes in MG1655 through directed strain engineering, and also clone the enzymes from MG1655 for more control, by performing our own directed evolution, EMS, rational engineering, and site-directed mutagenesis experiments. 
 +
 
</article></div>
</article></div>
 +
<br>
<br>
-
<div class="floatbox3">
+
<div id="myleftbox"  class="smallbox">
-
<hp>What we're doing</hp>
+
<h1>Pathway Goals</h1>
 +
 
<article>
<article>
-
Text goes here
+
Since ethylene glycol (EG) is a potential toxin to any mammals that consume it, we worked to break EG down as efficiently as possible so that none of the ethylene glycol is released into the environment. We have engineered our <I>E. coli</I> to degrade ethylene glycol so that no human intervention is necessary. 
-
</article></div>
+
 
 +
<br>Our main goal is for the <I>E. coli</I> to be able to live off PET as the sole carbon source. In order to do this, it must be able to sequester the carbon into its metabolism. In the diagram below, the ethylene glycol binds to the glycolaldehyde reductase to form glycolaldehyde. After, the glycolaldehyde attaches to the glycolaldehyde dehydrogenase to form glycolate. The glycolate goes in to the metabolism via further reactions with glycolate dehydrogenase and malate synthase. The (S)-malate is the final product that is incorporated in to the citric acid (TCA) cycle. As the citric acid cycle propagates, more energy is made for the cell, allowing growth and self-sufficient development on PET.
 +
 
 +
<br><br><center><a href="https://static.igem.org/mediawiki/2012/f/f8/UCD_figure-2-large.jpg" class="lightbox"><img src="https://static.igem.org/mediawiki/2012/c/c0/UCD_figure-2-b.png "> </a> </center><br>
 +
<center><b>Note: starred enzymes are what we are using in our construct</b></center>
 +
 
 +
 
 +
</article>
 +
</div>
 +
 
 +
<div id="myleftbox"  class="twoboxes">
 +
<a href="https://2012.igem.org/Team:UC_Davis/Project/Directed_Evolution"><img src="https://static.igem.org/mediawiki/2012/8/80/UCD_Directed_wide_banner-3.jpg" border="0"></a>
 +
</div>
 +
 
 +
<div id="myleftbox"  class="twoboxes1">
 +
<a href="https://2012.igem.org/Team:UC_Davis/Project/Our_Strain"><img src="https://static.igem.org/mediawiki/2012/8/86/UCD_Rational_wide_banner-1.jpg" border="0"></a>
 +
</div>
<br>
<br>
-
<div class="floatbox3">
+
<div id="myleftbox"  class="smallbox">
-
<hp>References</hp>
+
<h1>Our Strain</h1>
<article>
<article>
-
Text goes here
+
We wanted to assemble reductase and dehydrogenase to allow a modular system for simplified testing and use when compared to chromosomal testing. In addition to the use of the modular system, the sequencing of Strain E-15 EG3 shows us the other mutations in the chromosome that allow it to utilize ethylene glycol. Extracting the data from sequencing and modular testing together will help us identify the region in the MG1655 chromosome that we want to overexpress or mutate for efficient degradation of ethylene glycol.
-
</article></div>
+
<br><br>
 +
<center><img src="https://static.igem.org/mediawiki/2012/6/64/NaFx5cZLC_fH2TU4OSvWnBVEAZy_uurW8P0QrAzoAu0.jpeg" align="left"><img src="https://static.igem.org/mediawiki/2012/2/2a/R7Bks9MIS5OuvP0sCI9qS8Uv7bJQEv6Lpk3Kb3hvM3w%2CRApFZ4v4lbtF3a00zS77EKcCaRPP35jBZ-OBwQoezS8.jpeg" align="right"></center>
 +
</article>
 +
</div>
 +
 +
<br>
 +
<div id="myleftbox"  class="smallbox"><h1> References </h1>
 +
<article>
 +
1. Boronat, Albert, Caballero, Estrella, and Juan Aguilar. “Experimental Evolution of a Metabolic Pathway for Ethylene Glycol Utilization by <i>Escherichia coli</i>.” Journal of Bacteriology, Vol. 153 No. 1, pp. 134-139, January 1983. 
 +
<br>
 +
2. Bsc, S. N. and Gp Savage Bsc(hons), PhD, Nz Reg NutR. (1999), Oxalate content of foods and its effect on humans. Asia Pacific Journal of Clinical Nutrition, 8: 64–74. doi: 10.1046/j.1440-6047.1999.00038.x<br></article>
 +
</div>
 +
 +
 +
 +
 +
<!-- site map starts here -->
 +
<div id="myleftbox"  class="smallboxsite">
 +
<ul style="font-size:10px;list-style-image:none;list-style-type:none;float:left;display:inline;color:#000000;"
 +
>
 +
 +
<li style="float:left;margin:0 10px;"><a
 +
href="https://2012.igem.org/Team:UC_Davis"><p>Home</p><ul
 +
style="text-indent:-15px;
 +
list-style-image:none;list-style-type:none;color:#000000;"><li><a
 +
style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis">Welcome</a> </li><li><a
 +
style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis">Tweets</a></li><li><a
 +
style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis">Sponsors</a> </li><li><a
 +
style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Criteria">Criteria</a> </li>
 +
</ul> </a> </li>
 +
 +
<li style="float:left;margin:0 10px;"><a
 +
href="https://2012.igem.org/Team:UC_Davis/Team"><p>Team</p><ul
 +
style="text-indent:-15px;
 +
list-style-image:none;list-style-type:none;color:#000000;"><li><a
 +
style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Team">Who we are</a>
 +
</li><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Team">Students</a></li><li><a
 +
style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Team">Advisors</a> </li>
 +
</ul> </a> </li>
 +
 +
<li style="float:left ;margin:0 10px;"><a
 +
href="https://2012.igem.org/Team:UC_Davis/Project "><p>Project</p></a>
 +
<ul style="text-indent:-15px;list-style-image:none;list-style-type:none;color:#000000"><li><a
 +
style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Project">Project Overview</a>
 +
</li><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Project/Catalyst ">Module
 +
Engineering</a></li><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Project/Protein_Engineering
 +
">Protein Engineering</a></li>
 +
<li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Project/Strain ">Chassis
 +
Engineering</a></li>
 +
  <li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Project/Directed_Evolution ">
 +
- Directed Evolution</a></li>
 +
  <li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Project/Our_Strain "> -
 +
Rational Engineering</a></li>
 +
<li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Criteria">Critera</a>
 +
</li></ul> </li>
 +
 +
<li style="float:left ;margin:0 10px"><a
 +
href="https://2012.igem.org/Team:UC_Davis/Safety "> <p>Safety</p></a>
 +
<a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Safety "> Safety</a> </li>
 +
 +
<li style="float:left ;margin:0 10px;"><a
 +
href="https://2012.igem.org/Team:UC_Davis/Notebook ">
 +
<p>Notebook</p></a> <ul
 +
style="text-indent:-15px;list-style-image:none;list-style-type:none;color:#000000
 +
"><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Notebook">Notebook</a>
 +
</li><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Notebook/Protocols
 +
">Protocols</a> </li><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Notebook/Gallery">Gallery</a>
 +
</li><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Criteria">Critera</a> </li>
 +
</ul> </li>
 +
 +
<li style="float:left ;margin:0 10px;"><a
 +
title="https://2012.igem.org/Team:UC_Davis/Data "> <p>Data </p></a> <ul
 +
style="text-indent:-15px;list-style-image:none;list-style-type:none;color:#000000
 +
"><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Data/Cutinase_Activity ">
 +
Cutinase Activity</a> </li><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Data/Ethylene_Glycol ">
 +
Ethylene Glycol</a> </li><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Data/Modeling ">
 +
Modeling</a> </li><li><a style="color:#000000 "
 +
 +
href="https://2012.igem.org/Team:UC_Davis/Parts ">Parts</a></li> </ul>
 +
 +
<li style="float:left ;margin:0 10px"><a
 +
href="https://2012.igem.org/Team:UC_Davis/Attributions ">
 +
<p>Attribution </p></a><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Attributions ">
 +
Attribution</a></li>
 +
 +
<li style="float:left ;margin:0 10px"><a
 +
href="https://2012.igem.org/Main_Page "> <p>iGEM </p></a><ul
 +
style="text-indent:-15px;list-style-image:none;list-style-type:none;color:#000000
 +
"><li><a style="color:#000000 " href="https://2012.igem.org/Main_Page
 +
">Main iGEM</a> </li><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Criteria "> Criteria</a>
 +
</li><li><a style="color:#000000 "
 +
href="https://2012.igem.org/Team:UC_Davis/Human_Practices ">Human
 +
Practices</a></li> </ul>
 +
</div>
 +
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Latest revision as of 18:40, 19 October 2012

Team:UC Davis - 2012.igem.org

UCDavis iGEM Tweets

Our Sponsors

Chassis Engineering: Background

Chassis or strain engineering focuses on the modification of chromosomes instead of plasmids and encompasses both directed evolution and rational engineering. This part of the project focuses on the elimination of ethylene glycol, a degradation product of PET that is metabolized to oxalic acid further downstream the metabolic pathway. Oxalic acid is toxic to the kidney and fatal to the organism (2). (For a look at how we handled these compounds safely, look at our Safety Page!)

Once we discovered the potential toxicity of our project, we searched high and low to find ways to eliminate ethylene glycol (EG) as much as possible. In the scientific literature, we found that no wild-type E. coli can utilize EG (1). However, we did find an E. coli mutant, called Strain E-15 EG3, from the University of Barcelona, that is able to grow on ethylene glycol alone (1). While the University of Barcelona's paper on Strain E-15 EG3 was published nearly 30 years ago, we contacted the authors and asked for the strain to perform our own testing. The researchers were able to find the strain in one of their freezers and ship it to our lab. We have dubbed the rediscovery of the strain "Freezer Archaeology".

By performing various experiments on MG1655 including directed evolution, which selects the cells with the most fitness in a population, and ethyl methylsulfonate (EMS), which introduces random mutations to a population, the scientists learned that the main contributors in the degradation were propanediol oxidoreductase and glycolaldehyde dehydrogenase. These two enzymes are expressed at low levels in MG1655 but not at all in DH5α. We worked to overexpress these enzymes in MG1655 through directed strain engineering, and also clone the enzymes from MG1655 for more control, by performing our own directed evolution, EMS, rational engineering, and site-directed mutagenesis experiments.

Pathway Goals

Since ethylene glycol (EG) is a potential toxin to any mammals that consume it, we worked to break EG down as efficiently as possible so that none of the ethylene glycol is released into the environment. We have engineered our E. coli to degrade ethylene glycol so that no human intervention is necessary.
Our main goal is for the E. coli to be able to live off PET as the sole carbon source. In order to do this, it must be able to sequester the carbon into its metabolism. In the diagram below, the ethylene glycol binds to the glycolaldehyde reductase to form glycolaldehyde. After, the glycolaldehyde attaches to the glycolaldehyde dehydrogenase to form glycolate. The glycolate goes in to the metabolism via further reactions with glycolate dehydrogenase and malate synthase. The (S)-malate is the final product that is incorporated in to the citric acid (TCA) cycle. As the citric acid cycle propagates, more energy is made for the cell, allowing growth and self-sufficient development on PET.


Note: starred enzymes are what we are using in our construct

Our Strain

We wanted to assemble reductase and dehydrogenase to allow a modular system for simplified testing and use when compared to chromosomal testing. In addition to the use of the modular system, the sequencing of Strain E-15 EG3 shows us the other mutations in the chromosome that allow it to utilize ethylene glycol. Extracting the data from sequencing and modular testing together will help us identify the region in the MG1655 chromosome that we want to overexpress or mutate for efficient degradation of ethylene glycol.


References

1. Boronat, Albert, Caballero, Estrella, and Juan Aguilar. “Experimental Evolution of a Metabolic Pathway for Ethylene Glycol Utilization by Escherichia coli.” Journal of Bacteriology, Vol. 153 No. 1, pp. 134-139, January 1983.
2. Bsc, S. N. and Gp Savage Bsc(hons), PhD, Nz Reg NutR. (1999), Oxalate content of foods and its effect on humans. Asia Pacific Journal of Clinical Nutrition, 8: 64–74. doi: 10.1046/j.1440-6047.1999.00038.x

Retrieved from "http://2012.igem.org/Team:UC_Davis/Project/Strain"