http://2012.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=20&target=Vzepeda&year=&month=2012.igem.org - User contributions [en]2024-03-28T22:43:01ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Template:UCSF/MainHeaderTemplate:UCSF/MainHeader2013-09-16T17:31:19Z<p>Vzepeda: </p>
<hr />
<div><!--Main Head from Calgary 2012--><br />
<html><br />
<br />
<head><br />
<!--CSS styles: global--><br />
<style type="text/css"><br />
/***<br />
Minimal header: removes the search bar and header image and readjusts font colours in the menus.<br />
Thanks a lot to the 2011 Brown-Stanford, 2012 Lethbridge iGEM and 2012 Calgary teams for snippets of their code!<br />
Check out their wikis at:<br />
https://2011.igem.org/Team:Brown-Stanford<br />
https://2012.igem.org/Team:Lethbridge<br />
https://2012.igem.org/Team:Calgary<br />
***/<br />
<br />
#content h1.firstHeading {<br />
visibility:hidden;<br />
}<br />
#p-logo {<br />
display: none;<br />
}<br />
#searchform {<br />
display: none;<br />
}<br />
<br />
.left-menu {<br />
background-color: #555;<br />
<br />
}<br />
.left-menu a {<br />
color: #000;<br />
}<br />
<br />
div#top-section{ /*the div containing the entire top bar*/<br />
height: 20px;<br />
margin-bottom: 0px !important;<br />
border: none;<br />
}<br />
<br />
<br />
#content{<br />
margin-top: 0px;<br />
}<br />
<br />
#search-controls {<br />
overflow:hidden;<br />
display:none;<br />
background: none;<br />
position: absolute;<br />
top: 170px;<br />
right: 40px;<br />
} <br />
<br />
<br />
div#header {<br />
width: 975px;<br />
text-align: left;<br />
margin-left: auto;<br />
margin-right: auto;<br />
margin-bottom: 0px !important;<br />
} <br />
<br />
#menubar {<br />
position: absolute;<br />
background: none;<br />
color: black;<br />
}<br />
<br />
.left-menu, .right-menu{<br />
position: absolute;<br />
background: none;<br />
color: black;<br />
}<br />
<br />
.left-menu li a, .right-menu li a {<br />
color: #000 !important;<br />
}<br />
<br />
<br />
.left-menu ul li, .right-menu ul li a{<br />
background: none;<br />
color: #000 !important;<br />
}<br />
<br />
.left-menu li a:hover, .right-menu li a:hover, .right-menu li a:visited, .right-menu li a:active {<br />
color: #000 !important;<br />
}<br />
<br />
#catlinks{<br />
display:none;<br />
}<br />
<br />
/*important for background colours*/<br />
.mediawiki{<br />
background: #ffffff;<br />
}<br />
<br />
/***End minimal header***/<br />
<br />
/*Base styles*/<br />
#content{<br />
border: none;<br />
}<br />
h1, h2, h3, h4, #css-full, #css-mobi{<br />
font-family: Myriad Pro, Gill Sans MT, Trebuchet MS, Arial, Sans-Serif;<br />
border: 0;<br />
font-weight: 400;<br />
}<br />
p, div.thumb div div.thumbcaption{<br />
font-family: Georgia, Serif;<br />
font-size: 1.1em;<br />
font-weight: normal;<br />
color: black;<br />
margin-bottom: 10px;<br />
padding-left: 5px;<br />
}<br />
<br />
#css-full, #css-mobi{<br />
position: absolute;<br />
float: right;<br />
color: black;<br />
font-size: 1.3em;<br />
top: 0px;<br />
right: 15px;<br />
display: block;<br />
padding: 10px;<br />
}<br />
<br />
#jsnotice{<br />
background-color: #4ED92F;<br />
}<br />
<br />
#table{<br />
margin: 10px;<br />
}<br />
</style><br />
<br />
<!--desktop--><br />
<style type="text/css"><br />
/*======<br />
Desktop Styling<br />
Thanks a lot to the 2012 Calgary team for snippets of their code!<br />
Check out their wiki at:<br />
https://2012.igem.org/Team:Calgary<br />
======*/<br />
<br />
/***Nav styling***/<br />
header{<br />
position: relative;<br />
top: -45px;<br />
z-index: 999;<br />
}<br />
<br />
#nav-wrap{<br />
height: 0px;<br />
margin-top: -45px;<br />
}<br />
<br />
#nav, #nav ul{<br />
list-style: none;<br />
margin: 0;<br />
padding: 0;<br />
width: 965px;<br />
height: 100%;<br />
display: table;<br />
<br />
<br />
}<br />
<br />
/*To be moved to JQ block*/<br />
#menu-icon{<br />
display: none;<br />
}<br />
<br />
/*menu*/<br />
#nav li{<br />
height: auto;<br />
padding: 0;<br />
list-style: none;<br />
float: left;<br />
width: auto;<br />
margin: 0;<br />
background: #333333;<br />
position: relative;<br />
}<br />
#nav > li a{<br />
padding: 0 15px;<br />
}<br />
#nav > li{<br />
background: transparent;<br />
}<br />
<br />
/*submenu*/<br />
#nav li ul {<br />
position: absolute;<br />
width: 200px;<br />
display: none;<br />
}<br />
#nav li:hover ul {<br />
display: block;<br />
}<br />
/*sub-submenu*/<br />
#nav li ul ul{<br />
margin-left: 230px;<br />
margin-top: -15px;<br />
}<br />
#nav li:hover ul ul{<br />
display: none;<br />
}<br />
#nav li:hover ul, #nav li li:hover ul{<br />
display: block;<br />
}<br />
#nav a{<br />
display: block;<br />
font-family: Myriad Pro, Gill Sans MT, Trebuchet MS, Arial, Sans-Serif;<br />
color: white;<br />
}<br />
#nav li a{<br />
line-height: 1.4em; /*centers the text vertically*/<br />
font-size: 2em;<br />
}<br />
#nav ul li > a{<br />
width: 200px;<br />
}<br />
/*color change after rollover*/<br />
#nav li a:hover, #nav li li a.drop:hover::after{<br />
display: block;<br />
text-decoration: none;<br />
color: #4e9600;<br />
}<br />
#nav li ul li ul{<br />
margin-top: -32px;<br />
position: absolute;<br />
}<br />
/*submenu and sub-submenu*/<br />
#nav li ul li ul li a, #nav li ul li a{<br />
font-size: 1.8em;<br />
}<br />
#nav li li a.drop:after{<br />
content: '>';<br />
padding-left: 20px;<br />
color: #BBB;<br />
display: inline;<br />
float: right;<br />
}<br />
<br />
/***End nav styling***/<br />
<br />
/***Headerimage***/<br />
#headerimage{<br />
width: 968px;<br />
position: relative;<br />
margin-left: 0px;<br />
margin-bottom: 10px;<br />
top: 0px;<br />
}<br />
#css-full{<br />
display: none;<br />
}<br />
#css-mobi{<br />
display: block;<br />
top: 0px;<br />
}<br />
<br />
/***Logo styling***/<br />
#logo{<br />
position: absolute;<br />
top: 10px;<br />
right: 20px;<br />
float: right;<br />
}<br />
<br />
#logo img{<br />
width: 260px;<br />
}<br />
<br />
/***Body styling***/<br />
h1{<br />
font-size: 2.3em;<br />
line-height: 1em;<br />
}<br />
h2{<br />
font-size: 1.8em;<br />
line-height: 1.2em;<br />
}<br />
h3{<br />
font-size: 1.6em;<br />
margin: 0px 15px;<br />
font-weight: bold;<br />
}<br />
h4{<br />
font-size: 1.4em;<br />
color: #333333;<br />
margin: 0px 20px;<br />
font-weight: bold;<br />
}<br />
#bodycontainer p{<br />
font-size: 1.2em;<br />
}<br />
#pagetitle{<br />
border-bottom: 2px solid black;<br />
padding-bottom: 10px;<br />
padding-left: 10px;<br />
}<br />
#bodycontainer h2{<br />
margin-left: 10px;<br />
margin-right: 10px;<br />
}<br />
#bodycontainer p{<br />
margin-left: 20px;<br />
margin-right: 10px;<br />
}<br />
#bodycontainer{<br />
margin-left: 220px;<br />
}<br />
#bodycontainer ul{<br />
margin-left: 5.0em;<br />
}<br />
#bodycontainer li{<br />
font-family: Georgia, Serif;<br />
}<br />
#sidebar{<br />
position: absolute;<br />
width: 210px;<br />
z-index: 0;<br />
}<br />
/*<br />
#sidebarimg{<br />
width: 214px;<br />
height: 144px;<br />
background: #43bbff;<br />
margin: 5px 0px;<br />
border: 3px solid #333333;<br />
}<br />
*/<br />
<br />
#sidebar #list{<br />
background: #333333;<br />
}<br />
#sidebar h2{<br />
color: white;<br />
padding: 20px 15px 0px 15px;<br />
font-size: 2.0em;<br />
}<br />
#sidebar ul{<br />
list-style: none;<br />
margin: 0px 15px;<br />
}<br />
#sidebar #list > ul{<br />
padding-bottom: 20px;<br />
}<br />
#sidebar a{<br />
color: white;<br />
font-family: Georgia, Serif;<br />
font-size: 1.4em;<br />
display: block;<br />
line-height: 1.4em;<br />
}<br />
#sidebar a:hover{<br />
text-decoration: none;<br />
color: #43BBFF;<br />
}<br />
<br />
<br />
/* thumbnails */<br />
div.thumb {<br />
margin-bottom: .5em;<br />
border-style: solid;<br />
border-color: transparent;<br />
width: auto;<br />
}<br />
div.thumb div {<br />
border: 0px;<br />
padding: 3px !important;<br />
font-size: 94%;<br />
text-align: center;<br />
overflow: hidden;<br />
background: transparent;<br />
}<br />
div.thumb div a img {<br />
border: none;<br />
}<br />
div.thumb div div.thumbcaption {<br />
border: none;<br />
text-align: left;<br />
line-height: 1.4em;<br />
padding: .3em 0 .1em 0;<br />
<br />
}<br />
div.magnify {<br />
float: right;<br />
border: none !important;<br />
background: none !important;<br />
}<br />
div.magnify a, div.magnify img {<br />
display: block;<br />
border: none !important;<br />
background: none !important;<br />
}<br />
div.tright {<br />
clear: right;<br />
float: right;<br />
border-width: .5em 0 .8em 1.4em;<br />
}<br />
div.tleft {<br />
float: left;<br />
margin-right: .5em;<br />
border-width: .5em 1.4em .8em 0;<br />
}<br />
<br />
/*colouring*/<br />
/*oranges: current page and all sidebar rollovers*/<br />
#home header #homelink, #home #sidebar #list a:hover, #home #nav li a:hover, #home #nav li a.drop:hover::after,<br />
#team header #teamlink, #team #sidebar #list a:hover, #team #nav li a:hover, #team #nav li a.drop:hover::after,<br />
#proj_hp header #projectlink, #proj_hp #sidebar #list a:hover, #proj_hp #nav li a:hover, #proj_hp #nav li a.drop:hover::after,<br />
#parts header #partslink, #parts #sidebar #list a:hover, #parts #nav li a:hover, #parts #nav li a.drop:hover::after,<br />
#notebook header #notebooklink, #notebook #sidebar #list a:hover, #notebook #nav li a:hover, #notebook #nav li a.drop:hover::after,<br />
#outreach header #outreachlink, #outreach #sidebar #list a:hover, #outreach #nav li a:hover, #outreach #nav li a.drop:hover::after,<br />
#sponsors header #sponsorslink, #sponsors #sidebar #list a:hover, #sponsors #nav li a:hover, #sponsors #nav li a.drop:hover::after{<br />
color: #F6A82D;<br />
}<br />
/*oranges: sidebar border*/<br />
#home #sidebar #list,<br />
#team #sidebar #list,<br />
#proj_hp #sidebar #list,<br />
#parts #sidebar #list,<br />
#notebook #sidebar #list,<br />
#outreach #sidebar #list,<br />
#sponsors #sidebar #list{<br />
border-left: 10px solid #F6A82D;<br />
}<br />
/*oranges: links*/<br />
#team #bodycontainer a,<br />
#proj_hp #bodycontainer a,<br />
#parts #bodycontainer a,<br />
#notebook #bodycontainer a,<br />
#outreach #bodycontainer a,<br />
#sponsors #bodycontainer a{<br />
color: #FF7A00;<br />
}<br />
#team #bodycontainer a:visited,<br />
#proj_hp #bodycontainer a:visited,<br />
#parts #bodycontainer a:visited,<br />
#notebook #bodycontainer a:visited,<br />
#outreach #bodycontainer a:visited,<br />
#sponsors #bodycontainer a:visited{<br />
color: #C40;<br />
}<br />
<br />
/*blues: current page, all rollover links in nav, all sidebar hovers and dropdown menus*/<br />
#proj_o header #projectlink, #proj_o #sidebar #list a:hover, #proj_o #nav li a:hover, #proj_o #nav li a.drop:hover::after, <br />
#note_o header #notebooklink, #note_o #sidebar #list a:hover, #note_o #nav li a:hover, #note_o #nav li a.drop:hover::after{<br />
color: #43BBFF;<br />
}<br />
/*blues: sidebar border*/<br />
#proj_o #sidebar #list,<br />
#note_o #sidebar #list{<br />
border-left: 10px solid #43BBFF;<br />
}<br />
/*blues: links*/<br />
#proj_o #bodycontainer a,<br />
#note_o #bodycontainer a{<br />
color: #1088CC;<br />
}<br />
#proj_o #bodycontainer a:visited,<br />
#note_o #bodycontainer a:visited{<br />
color: #05B;<br />
}<br />
<br />
/*greens: current page, all rollover links in nav, all sidebar hovers, and dropdown menus*/<br />
#proj_f header #projectlink, #proj_f #sidebar #list a:hover, #proj_f #nav li a:hover, #proj_f #nav li a.drop:hover::after, <br />
#note_f header #notebooklink, #note_f #sidebar #list a:hover, #note_f #nav li a:hover, #note_f #nav li a.drop:hover::after{<br />
color: #58CD45;<br />
}<br />
/*greens: sidebar border*/<br />
#proj_f #sidebar #list,<br />
#note_f #sidebar #list{<br />
border-left: 10px solid #58CD45;<br />
}<br />
/*greens: links*/<br />
#proj_f #bodycontainer a,<br />
#proj_f #bodycontainer a{<br />
color: #159900;<br />
}<br />
/*greens: links*/<br />
#proj_f #bodycontainer a:visited,<br />
#proj_f #bodycontainer a:visited{<br />
color: #06660B;<br />
}<br />
<br />
/*hub page CSS*/<br />
a.hublink{<br />
text-decoration: none;<br />
margin-left: 15px;<br />
margin-right: 15px;<br />
}<br />
div.hubbox{<br />
margin-left: 15px;<br />
}<br />
div.hubbox img{<br />
float: left;<br />
padding: 15px;<br />
}<br />
div.hubbox h2{<br />
color: white;<br />
padding: 15px 15px 0px 15px;<br />
font-size: 2.0em;<br />
margin-left: 120px !important;<br />
}<br />
div.hubbox p{<br />
color: white;<br />
padding: 0px 15px 15px 15px;<br />
margin-left: 120px !important;<br />
}<br />
div.hubbox b{<br />
font-size: 1.1em;<br />
}<br />
</style><br />
<br />
<script type="text/javascript"><br />
<br />
jQuery(document).ready(function ($) {<br />
<br />
//eliminate jsnotice<br />
$('#jsnotice').hide();<br />
<br />
//prepend menu icon<br />
$('#nav-wrap').prepend('<div id="menu-icon">Menu</div>');<br />
<br />
//toggle nav<br />
$("#menu-icon").click(function () {<br />
$("#nav").slideToggle('fast');<br />
$(this).toggleClass("active");<br />
<br />
});<br />
<br />
//hide url bar<br />
window.scrollTo(0, 1);<br />
<br />
<br />
<br />
});<br />
<br />
</script><br />
<br />
<!--switching function: thanks to http://www.digital-web.com/articles/strategies_for_css_switching/--><br />
<br />
<script type="text/javascript"><br />
<br />
var _gaq = _gaq || [];<br />
_gaq.push(['_setAccount', 'UA-32774032-1']);<br />
_gaq.push(['_trackPageview']);<br />
<br />
(function () {<br />
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;<br />
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';<br />
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);<br />
})();<br />
<br />
</script><br />
<br />
</head><br />
<br />
<body><br />
<br />
<header><br />
<!--<br />
<a id="css-full" href="#default">Full View</a><br />
<a id="css-mobi" href="#mobile">Mobile View</a><br />
--><br />
<div id="headerimage"><img src="https://static.igem.org/mediawiki/2013/b/b8/Leaf1.png"></img></div><br />
<a id="logo" href="https://2013.igem.org/Team:UCSF"></html>{{{1|<html><img src="https://static.igem.org/mediawiki/2013/b/be/Ucsf_sig_rgb_1.png"></img></html>}}}<html></a><br />
<div id="nav-wrap"><br />
<ul id="nav"><br />
<li><a href="https://2013.igem.org/Team:UCSF/lily2" id="homelink">Home</a></li><br />
<li><a class="drop" id="team">Team</a><br />
<ul><br />
<li><a href="https://2013.igem.org/Team:UCSF/Background">Team Background</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Team">Members</a></li><br />
<br />
<li><a href="https://2013.igem.org/Team:UCSF/Advisors">Advisors</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Mentors&Instructors">Mentors</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=UCSF">Profile</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/ContactUs">Contact Us</a></li><br />
</ul><br />
</li><br />
<li><a class="drop" href="https://2013.igem.org/Team:UCSF/Project" id="projectlink">Project</a><br />
<ul><br />
<li><br />
<a class="drop" href="https://2013.igem.org/Team:UCSF/Project">Medal Req's</a><br />
<ul><br />
<li><a href="https://2013.igem.org/Team:UCSF/Project/Attribute">Attributions</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Parts">Parts</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Safety">Safety</a></li><br />
<!--<li><a href="https://2013.igem.org/Team:UCSF/Project/Post-Regionals">Post-Regionals</a></li>--><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2013.igem.org/Team:UCSF/Project/Conjugation">Conjugation</a><br />
<!--<br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
--><br />
</li><br />
<li><br />
<a class="drop" href="https://2013.igem.org/Team:UCSF/Project/Circuit">Synthetic Circuit</a><br />
<br />
</li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Project/References">References</a></li><br />
</ul><br />
</li><br />
<li><a class="drop" href="https://2013.igem.org/Team:UCSF/Modeling" id="Modeling">Modeling</a></li><br />
<br />
<br />
<br />
<li><a class="drop" id="outreachlink">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:UCSF/Exploratorium">Exploratorium</a></li><br />
<li><a href="https://2012.igem.org/Team:UCSF/ALHS Project">Lincoln High</a></li><br />
<li><a href="https://2012.igem.org/Team:UCSF/Collaborations">Collaborations</a></li><br />
</ul><br />
</li><br />
<br />
<br />
<br />
<li><a class="drop" href="https://2013.igem.org/Team:UCSF/Protocols" id="notebooklink">Protocols</a><br />
<ul><br />
<li><a href="https://2013.igem.org/Team:UCSF/Bootcamp">Bootcamp</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Protocols">General Protocols</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Protocols2">Project Protocols</a></li><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:UCSF/Protocols">General Protocols</a></li><br />
<li><a href="https://2012.igem.org/Team:UCSF/Protocols2">Project Protocols</a></li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><a class="drop" id="outreachlink">Gallery</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:UCSF/Video">Videos</a></li><br />
<li><a href="https://2012.igem.org/Team:UCSF/Photos">Photos</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2013.igem.org" target="_blank">iGEM</a></li><br />
</ul><br />
<br />
</div><br />
</header><br />
<br />
<br />
</body><br />
</html></div>Vzepedahttp://2012.igem.org/Team:UCSF/CollaborationsTeam:UCSF/Collaborations2013-09-16T17:30:02Z<p>Vzepeda: Created page with "{{Template:UCSF/MainHeader}} <html> <head> <!--CSS styles: global--> <link rel='stylesheet' type='text/css' href="https://2012.igem.org/Team:Calgary/static/basicpageglobal.css?ac..."</p>
<hr />
<div>{{Template:UCSF/MainHeader}}<br />
<br />
<html><br />
<head><br />
<!--CSS styles: global--><br />
<link rel='stylesheet' type='text/css' href="https://2012.igem.org/Team:Calgary/static/basicpageglobal.css?action=raw&ctype=text/css" /><br />
<style><br />
/*======<br />
Desktop Styling<br />
======*/<br />
<br />
/***Body styling***/<br />
h1{<br />
font-size: 2.5em;<br />
}<br />
h2{<br />
font-size: 1.8em;<br />
}<br />
<br />
</style><br />
</head><br />
<body></div>Vzepedahttp://2012.igem.org/Team:UCSF/ExploratoriumTeam:UCSF/Exploratorium2013-09-13T00:13:50Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF/MainHeader}}<br />
<br />
<html><br />
<br />
<br />
<link rel="stylesheet" type="text/css" href="https://2013.igem.org/Team:UCSF/stylesheet"/><br />
<head><br />
<br />
<br />
<style><br />
<br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:755px; float:right; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1800px; float: left; margin-top:0px;} <br />
#rightcontenttext {width:900px; float:right; background-color: #FFFFFF; margin-left:8px; padding: 10px; margin-top:8px;} <br />
<br />
<br />
</style><br />
<br />
<br />
<div id="description" style = "width:950px; height:150px"><br />
<font face="arial" size = "5"><center>Human Practices: Exploratorium</font> </center> <br><br />
<br />
<p> <font face="arial" size = "4"><br />
<b>Teaching Synthetic Biology to the General Public:</b> Usually the general public relates Synthetic Biology (or commonly known as Biotechnology) with the current ethical issue of Genetically Modified Organism within the food that we consume every day. The 2013 UCSF iGEM team wanted to change the perspective many have toward synthetic biology by introducing the basic ideas of Synthetic Biology in an after dark event at the San Francisco Exploratorium. <p><br />
</div><br />
<br />
<div id="photos"><br />
<img align="center" style="margin-bottom:8px; style="margin-left:50px; padding:0;" <br />
src="https://static.igem.org/mediawiki/2013/5/52/Exploratorium_Logo.png"> <br><br />
<br />
<br />
<div id="description" style = "width:950px; height:200px"><br />
<font face="arial" size = "4"><br />
The Exploratorium http://www.exploratorium.edu/ is a museum dedicated to various science related exhibits aimed to teach and inspire learning to its guests. The night event is an 18 and older event that approximately 4-5,000 people attend every first Thursday of the month. Each event revolves around a unique theme, and the theme when we presented was “Transformations”. Transformations ranged from origami folding, to metamorphosis, to ice cutting, and our focus was on “Transformations in cells”. In accordance with the theme, our team presented information involving the central dogma of DNA and basic in-vitro transformation in order to show the benefits of synthetic biology and the many applications it can have in the future. <br />
</font> <br />
</div></div>Vzepedahttp://2012.igem.org/Template:UCSF/MainHeaderTemplate:UCSF/MainHeader2013-09-12T23:38:02Z<p>Vzepeda: Created page with "<!--Main Head from Calgary 2012--> <html> <head> <!--CSS styles: global--> <style type="text/css"> /*** Minimal header: removes the search bar and header image and readjusts..."</p>
<hr />
<div><!--Main Head from Calgary 2012--><br />
<html><br />
<br />
<head><br />
<!--CSS styles: global--><br />
<style type="text/css"><br />
/***<br />
Minimal header: removes the search bar and header image and readjusts font colours in the menus.<br />
Thanks a lot to the 2011 Brown-Stanford, 2012 Lethbridge iGEM and 2012 Calgary teams for snippets of their code!<br />
Check out their wikis at:<br />
https://2011.igem.org/Team:Brown-Stanford<br />
https://2012.igem.org/Team:Lethbridge<br />
https://2012.igem.org/Team:Calgary<br />
***/<br />
<br />
#content h1.firstHeading {<br />
visibility:hidden;<br />
}<br />
#p-logo {<br />
display: none;<br />
}<br />
#searchform {<br />
display: none;<br />
}<br />
<br />
.left-menu {<br />
background-color: #555;<br />
<br />
}<br />
.left-menu a {<br />
color: #000;<br />
}<br />
<br />
div#top-section{ /*the div containing the entire top bar*/<br />
height: 20px;<br />
margin-bottom: 0px !important;<br />
border: none;<br />
}<br />
<br />
<br />
#content{<br />
margin-top: 0px;<br />
}<br />
<br />
#search-controls {<br />
overflow:hidden;<br />
display:none;<br />
background: none;<br />
position: absolute;<br />
top: 170px;<br />
right: 40px;<br />
} <br />
<br />
<br />
div#header {<br />
width: 975px;<br />
text-align: left;<br />
margin-left: auto;<br />
margin-right: auto;<br />
margin-bottom: 0px !important;<br />
} <br />
<br />
#menubar {<br />
position: absolute;<br />
background: none;<br />
color: black;<br />
}<br />
<br />
.left-menu, .right-menu{<br />
position: absolute;<br />
background: none;<br />
color: black;<br />
}<br />
<br />
.left-menu li a, .right-menu li a {<br />
color: #000 !important;<br />
}<br />
<br />
<br />
.left-menu ul li, .right-menu ul li a{<br />
background: none;<br />
color: #000 !important;<br />
}<br />
<br />
.left-menu li a:hover, .right-menu li a:hover, .right-menu li a:visited, .right-menu li a:active {<br />
color: #000 !important;<br />
}<br />
<br />
#catlinks{<br />
display:none;<br />
}<br />
<br />
/*important for background colours*/<br />
.mediawiki{<br />
background: #ffffff;<br />
}<br />
<br />
/***End minimal header***/<br />
<br />
/*Base styles*/<br />
#content{<br />
border: none;<br />
}<br />
h1, h2, h3, h4, #css-full, #css-mobi{<br />
font-family: Myriad Pro, Gill Sans MT, Trebuchet MS, Arial, Sans-Serif;<br />
border: 0;<br />
font-weight: 400;<br />
}<br />
p, div.thumb div div.thumbcaption{<br />
font-family: Georgia, Serif;<br />
font-size: 1.1em;<br />
font-weight: normal;<br />
color: black;<br />
margin-bottom: 10px;<br />
padding-left: 5px;<br />
}<br />
<br />
#css-full, #css-mobi{<br />
position: absolute;<br />
float: right;<br />
color: black;<br />
font-size: 1.3em;<br />
top: 0px;<br />
right: 15px;<br />
display: block;<br />
padding: 10px;<br />
}<br />
<br />
#jsnotice{<br />
background-color: #4ED92F;<br />
}<br />
<br />
#table{<br />
margin: 10px;<br />
}<br />
</style><br />
<br />
<!--desktop--><br />
<style type="text/css"><br />
/*======<br />
Desktop Styling<br />
Thanks a lot to the 2012 Calgary team for snippets of their code!<br />
Check out their wiki at:<br />
https://2012.igem.org/Team:Calgary<br />
======*/<br />
<br />
/***Nav styling***/<br />
header{<br />
position: relative;<br />
top: -45px;<br />
z-index: 999;<br />
}<br />
<br />
#nav-wrap{<br />
height: 0px;<br />
margin-top: -45px;<br />
}<br />
<br />
#nav, #nav ul{<br />
list-style: none;<br />
margin: 0;<br />
padding: 0;<br />
width: 965px;<br />
height: 100%;<br />
display: table;<br />
<br />
<br />
}<br />
<br />
/*To be moved to JQ block*/<br />
#menu-icon{<br />
display: none;<br />
}<br />
<br />
/*menu*/<br />
#nav li{<br />
height: auto;<br />
padding: 0;<br />
list-style: none;<br />
float: left;<br />
width: auto;<br />
margin: 0;<br />
background: #333333;<br />
position: relative;<br />
}<br />
#nav > li a{<br />
padding: 0 15px;<br />
}<br />
#nav > li{<br />
background: transparent;<br />
}<br />
<br />
/*submenu*/<br />
#nav li ul {<br />
position: absolute;<br />
width: 200px;<br />
display: none;<br />
}<br />
#nav li:hover ul {<br />
display: block;<br />
}<br />
/*sub-submenu*/<br />
#nav li ul ul{<br />
margin-left: 230px;<br />
margin-top: -15px;<br />
}<br />
#nav li:hover ul ul{<br />
display: none;<br />
}<br />
#nav li:hover ul, #nav li li:hover ul{<br />
display: block;<br />
}<br />
#nav a{<br />
display: block;<br />
font-family: Myriad Pro, Gill Sans MT, Trebuchet MS, Arial, Sans-Serif;<br />
color: white;<br />
}<br />
#nav li a{<br />
line-height: 1.4em; /*centers the text vertically*/<br />
font-size: 2em;<br />
}<br />
#nav ul li > a{<br />
width: 200px;<br />
}<br />
/*color change after rollover*/<br />
#nav li a:hover, #nav li li a.drop:hover::after{<br />
display: block;<br />
text-decoration: none;<br />
color: #4e9600;<br />
}<br />
#nav li ul li ul{<br />
margin-top: -32px;<br />
position: absolute;<br />
}<br />
/*submenu and sub-submenu*/<br />
#nav li ul li ul li a, #nav li ul li a{<br />
font-size: 1.8em;<br />
}<br />
#nav li li a.drop:after{<br />
content: '>';<br />
padding-left: 20px;<br />
color: #BBB;<br />
display: inline;<br />
float: right;<br />
}<br />
<br />
/***End nav styling***/<br />
<br />
/***Headerimage***/<br />
#headerimage{<br />
width: 968px;<br />
position: relative;<br />
margin-left: 0px;<br />
margin-bottom: 10px;<br />
top: 0px;<br />
}<br />
#css-full{<br />
display: none;<br />
}<br />
#css-mobi{<br />
display: block;<br />
top: 0px;<br />
}<br />
<br />
/***Logo styling***/<br />
#logo{<br />
position: absolute;<br />
top: 10px;<br />
right: 20px;<br />
float: right;<br />
}<br />
<br />
#logo img{<br />
width: 260px;<br />
}<br />
<br />
/***Body styling***/<br />
h1{<br />
font-size: 2.3em;<br />
line-height: 1em;<br />
}<br />
h2{<br />
font-size: 1.8em;<br />
line-height: 1.2em;<br />
}<br />
h3{<br />
font-size: 1.6em;<br />
margin: 0px 15px;<br />
font-weight: bold;<br />
}<br />
h4{<br />
font-size: 1.4em;<br />
color: #333333;<br />
margin: 0px 20px;<br />
font-weight: bold;<br />
}<br />
#bodycontainer p{<br />
font-size: 1.2em;<br />
}<br />
#pagetitle{<br />
border-bottom: 2px solid black;<br />
padding-bottom: 10px;<br />
padding-left: 10px;<br />
}<br />
#bodycontainer h2{<br />
margin-left: 10px;<br />
margin-right: 10px;<br />
}<br />
#bodycontainer p{<br />
margin-left: 20px;<br />
margin-right: 10px;<br />
}<br />
#bodycontainer{<br />
margin-left: 220px;<br />
}<br />
#bodycontainer ul{<br />
margin-left: 5.0em;<br />
}<br />
#bodycontainer li{<br />
font-family: Georgia, Serif;<br />
}<br />
#sidebar{<br />
position: absolute;<br />
width: 210px;<br />
z-index: 0;<br />
}<br />
/*<br />
#sidebarimg{<br />
width: 214px;<br />
height: 144px;<br />
background: #43bbff;<br />
margin: 5px 0px;<br />
border: 3px solid #333333;<br />
}<br />
*/<br />
<br />
#sidebar #list{<br />
background: #333333;<br />
}<br />
#sidebar h2{<br />
color: white;<br />
padding: 20px 15px 0px 15px;<br />
font-size: 2.0em;<br />
}<br />
#sidebar ul{<br />
list-style: none;<br />
margin: 0px 15px;<br />
}<br />
#sidebar #list > ul{<br />
padding-bottom: 20px;<br />
}<br />
#sidebar a{<br />
color: white;<br />
font-family: Georgia, Serif;<br />
font-size: 1.4em;<br />
display: block;<br />
line-height: 1.4em;<br />
}<br />
#sidebar a:hover{<br />
text-decoration: none;<br />
color: #43BBFF;<br />
}<br />
<br />
<br />
/* thumbnails */<br />
div.thumb {<br />
margin-bottom: .5em;<br />
border-style: solid;<br />
border-color: transparent;<br />
width: auto;<br />
}<br />
div.thumb div {<br />
border: 0px;<br />
padding: 3px !important;<br />
font-size: 94%;<br />
text-align: center;<br />
overflow: hidden;<br />
background: transparent;<br />
}<br />
div.thumb div a img {<br />
border: none;<br />
}<br />
div.thumb div div.thumbcaption {<br />
border: none;<br />
text-align: left;<br />
line-height: 1.4em;<br />
padding: .3em 0 .1em 0;<br />
<br />
}<br />
div.magnify {<br />
float: right;<br />
border: none !important;<br />
background: none !important;<br />
}<br />
div.magnify a, div.magnify img {<br />
display: block;<br />
border: none !important;<br />
background: none !important;<br />
}<br />
div.tright {<br />
clear: right;<br />
float: right;<br />
border-width: .5em 0 .8em 1.4em;<br />
}<br />
div.tleft {<br />
float: left;<br />
margin-right: .5em;<br />
border-width: .5em 1.4em .8em 0;<br />
}<br />
<br />
/*colouring*/<br />
/*oranges: current page and all sidebar rollovers*/<br />
#home header #homelink, #home #sidebar #list a:hover, #home #nav li a:hover, #home #nav li a.drop:hover::after,<br />
#team header #teamlink, #team #sidebar #list a:hover, #team #nav li a:hover, #team #nav li a.drop:hover::after,<br />
#proj_hp header #projectlink, #proj_hp #sidebar #list a:hover, #proj_hp #nav li a:hover, #proj_hp #nav li a.drop:hover::after,<br />
#parts header #partslink, #parts #sidebar #list a:hover, #parts #nav li a:hover, #parts #nav li a.drop:hover::after,<br />
#notebook header #notebooklink, #notebook #sidebar #list a:hover, #notebook #nav li a:hover, #notebook #nav li a.drop:hover::after,<br />
#outreach header #outreachlink, #outreach #sidebar #list a:hover, #outreach #nav li a:hover, #outreach #nav li a.drop:hover::after,<br />
#sponsors header #sponsorslink, #sponsors #sidebar #list a:hover, #sponsors #nav li a:hover, #sponsors #nav li a.drop:hover::after{<br />
color: #F6A82D;<br />
}<br />
/*oranges: sidebar border*/<br />
#home #sidebar #list,<br />
#team #sidebar #list,<br />
#proj_hp #sidebar #list,<br />
#parts #sidebar #list,<br />
#notebook #sidebar #list,<br />
#outreach #sidebar #list,<br />
#sponsors #sidebar #list{<br />
border-left: 10px solid #F6A82D;<br />
}<br />
/*oranges: links*/<br />
#team #bodycontainer a,<br />
#proj_hp #bodycontainer a,<br />
#parts #bodycontainer a,<br />
#notebook #bodycontainer a,<br />
#outreach #bodycontainer a,<br />
#sponsors #bodycontainer a{<br />
color: #FF7A00;<br />
}<br />
#team #bodycontainer a:visited,<br />
#proj_hp #bodycontainer a:visited,<br />
#parts #bodycontainer a:visited,<br />
#notebook #bodycontainer a:visited,<br />
#outreach #bodycontainer a:visited,<br />
#sponsors #bodycontainer a:visited{<br />
color: #C40;<br />
}<br />
<br />
/*blues: current page, all rollover links in nav, all sidebar hovers and dropdown menus*/<br />
#proj_o header #projectlink, #proj_o #sidebar #list a:hover, #proj_o #nav li a:hover, #proj_o #nav li a.drop:hover::after, <br />
#note_o header #notebooklink, #note_o #sidebar #list a:hover, #note_o #nav li a:hover, #note_o #nav li a.drop:hover::after{<br />
color: #43BBFF;<br />
}<br />
/*blues: sidebar border*/<br />
#proj_o #sidebar #list,<br />
#note_o #sidebar #list{<br />
border-left: 10px solid #43BBFF;<br />
}<br />
/*blues: links*/<br />
#proj_o #bodycontainer a,<br />
#note_o #bodycontainer a{<br />
color: #1088CC;<br />
}<br />
#proj_o #bodycontainer a:visited,<br />
#note_o #bodycontainer a:visited{<br />
color: #05B;<br />
}<br />
<br />
/*greens: current page, all rollover links in nav, all sidebar hovers, and dropdown menus*/<br />
#proj_f header #projectlink, #proj_f #sidebar #list a:hover, #proj_f #nav li a:hover, #proj_f #nav li a.drop:hover::after, <br />
#note_f header #notebooklink, #note_f #sidebar #list a:hover, #note_f #nav li a:hover, #note_f #nav li a.drop:hover::after{<br />
color: #58CD45;<br />
}<br />
/*greens: sidebar border*/<br />
#proj_f #sidebar #list,<br />
#note_f #sidebar #list{<br />
border-left: 10px solid #58CD45;<br />
}<br />
/*greens: links*/<br />
#proj_f #bodycontainer a,<br />
#proj_f #bodycontainer a{<br />
color: #159900;<br />
}<br />
/*greens: links*/<br />
#proj_f #bodycontainer a:visited,<br />
#proj_f #bodycontainer a:visited{<br />
color: #06660B;<br />
}<br />
<br />
/*hub page CSS*/<br />
a.hublink{<br />
text-decoration: none;<br />
margin-left: 15px;<br />
margin-right: 15px;<br />
}<br />
div.hubbox{<br />
margin-left: 15px;<br />
}<br />
div.hubbox img{<br />
float: left;<br />
padding: 15px;<br />
}<br />
div.hubbox h2{<br />
color: white;<br />
padding: 15px 15px 0px 15px;<br />
font-size: 2.0em;<br />
margin-left: 120px !important;<br />
}<br />
div.hubbox p{<br />
color: white;<br />
padding: 0px 15px 15px 15px;<br />
margin-left: 120px !important;<br />
}<br />
div.hubbox b{<br />
font-size: 1.1em;<br />
}<br />
</style><br />
<br />
<script type="text/javascript"><br />
<br />
jQuery(document).ready(function ($) {<br />
<br />
//eliminate jsnotice<br />
$('#jsnotice').hide();<br />
<br />
//prepend menu icon<br />
$('#nav-wrap').prepend('<div id="menu-icon">Menu</div>');<br />
<br />
//toggle nav<br />
$("#menu-icon").click(function () {<br />
$("#nav").slideToggle('fast');<br />
$(this).toggleClass("active");<br />
<br />
});<br />
<br />
//hide url bar<br />
window.scrollTo(0, 1);<br />
<br />
<br />
<br />
});<br />
<br />
</script><br />
<br />
<!--switching function: thanks to http://www.digital-web.com/articles/strategies_for_css_switching/--><br />
<br />
<script type="text/javascript"><br />
<br />
var _gaq = _gaq || [];<br />
_gaq.push(['_setAccount', 'UA-32774032-1']);<br />
_gaq.push(['_trackPageview']);<br />
<br />
(function () {<br />
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;<br />
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';<br />
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);<br />
})();<br />
<br />
</script><br />
<br />
</head><br />
<br />
<body><br />
<br />
<header><br />
<!--<br />
<a id="css-full" href="#default">Full View</a><br />
<a id="css-mobi" href="#mobile">Mobile View</a><br />
--><br />
<div id="headerimage"><img src="https://static.igem.org/mediawiki/2013/b/b8/Leaf1.png"></img></div><br />
<a id="logo" href="https://2013.igem.org/Team:UCSF"></html>{{{1|<html><img src="https://static.igem.org/mediawiki/2013/b/be/Ucsf_sig_rgb_1.png"></img></html>}}}<html></a><br />
<div id="nav-wrap"><br />
<ul id="nav"><br />
<li><a href="https://2013.igem.org/Team:UCSF/lily2" id="homelink">Home</a></li><br />
<li><a class="drop" id="team">Team</a><br />
<ul><br />
<li><a href="https://2013.igem.org/Team:UCSF/Background">Team Background</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Team">Members</a></li><br />
<br />
<li><a href="https://2013.igem.org/Team:UCSF/Advisors">Advisors</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Mentors&Instructors">Mentors</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2013&team_name=UCSF">Profile</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/ContactUs">Contact Us</a></li><br />
</ul><br />
</li><br />
<li><a class="drop" href="https://2013.igem.org/Team:UCSF/Project" id="projectlink">Project</a><br />
<ul><br />
<li><br />
<a class="drop" href="https://2013.igem.org/Team:UCSF/Project">Medal Req's</a><br />
<ul><br />
<li><a href="https://2013.igem.org/Team:UCSF/Project/Attribute">Attributions</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Parts">Parts</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Safety">Safety</a></li><br />
<!--<li><a href="https://2013.igem.org/Team:UCSF/Project/Post-Regionals">Post-Regionals</a></li>--><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2013.igem.org/Team:UCSF/Project/Conjugation">Conjugation</a><br />
<!--<br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
--><br />
</li><br />
<li><br />
<a class="drop" href="https://2013.igem.org/Team:UCSF/Project/Circuit">Synthetic Circuit</a><br />
<br />
</li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Project/References">References</a></li><br />
</ul><br />
</li><br />
<li><a class="drop" href="https://2013.igem.org/Team:UCSF/Modeling" id="Modeling">Modeling</a></li><br />
<br />
<br />
<br />
<li><a class="drop" id="outreachlink">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:UCSF/Exploratorium">Exploratorium</a></li><br />
<li><a href="https://2012.igem.org/Team:UCSF/ALHS Project">Lincoln High</a></li><br />
</ul><br />
</li><br />
<br />
<br />
<br />
<li><a class="drop" href="https://2013.igem.org/Team:UCSF/Protocols" id="notebooklink">Protocols</a><br />
<ul><br />
<li><a href="https://2013.igem.org/Team:UCSF/Bootcamp">Bootcamp</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Protocols">General Protocols</a></li><br />
<li><a href="https://2013.igem.org/Team:UCSF/Protocols2">Project Protocols</a></li><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:UCSF/Protocols">General Protocols</a></li><br />
<li><a href="https://2012.igem.org/Team:UCSF/Protocols2">Project Protocols</a></li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
<li><a class="drop" id="outreachlink">Gallery</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:UCSF/Video">Videos</a></li><br />
<li><a href="https://2012.igem.org/Team:UCSF/Photos">Photos</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2013.igem.org" target="_blank">iGEM</a></li><br />
</ul><br />
<br />
</div><br />
</header><br />
<br />
<br />
</body><br />
</html></div>Vzepedahttp://2012.igem.org/Team:UCSF/ExploratoriumTeam:UCSF/Exploratorium2013-09-12T23:31:14Z<p>Vzepeda: Created page with "{{Template:UCSF/MainHeader}} <html> <link rel="stylesheet" type="text/css" href="https://2013.igem.org/Team:UCSF/stylesheet"/> <head> <style> #mission {width: 500px; float:l..."</p>
<hr />
<div>{{Template:UCSF/MainHeader}}<br />
<br />
<html><br />
<br />
<br />
<link rel="stylesheet" type="text/css" href="https://2013.igem.org/Team:UCSF/stylesheet"/><br />
<head><br />
<br />
<br />
<style><br />
<br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:755px; float:right; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1800px; float: left; margin-top:0px;} <br />
#rightcontenttext {width:900px; float:right; background-color: #FFFFFF; margin-left:8px; padding: 10px; margin-top:8px;} <br />
<br />
<br />
</style><br />
<br />
<br />
<div id="description" style = "width:610px; height:180px"><br />
<font face="arial" size = "5">Human Practices: Exploratorium</font> <br />
<br />
<p> <font face="arial" size = "4"><br />
<b>Teaching Synthetic Biology to the General Public:</b> Usually the general public relates Synthetic Biology (or commonly known as Biotechnology) with the current ethical issue of Genetically Modified Organism within the food that we consume every day. The 2013 UCSF iGEM team wanted to change the perspective many have toward synthetic biology by introducing the basic ideas of Synthetic Biology in an after dark event at the San Francisco Exploratorium. The Exploratorium http://www.exploratorium.edu/ is a museum dedicated to various science related exhibits aimed to teach and inspire learning to its guests. The night event is an 18 and older event that approximately 4-5 thousand people attend every first Thursday of the month. Each event revolves around a unique theme, and the theme when we presented was “Transformations”. Transformations ranged from origami folding, to metamorphosis, to ice cutting, and our focus was on “Transformations in cells”. In accordance with the theme, our team presented information involving the central dogma of DNA and basic in-vitro transformation in order to show the benefits of synthetic biology and the many applications it can have in the future. <br />
</font> <br />
</div></div>Vzepedahttp://2012.igem.org/Team:UCSF/AdvisorsTeam:UCSF/Advisors2013-09-09T20:10:24Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<html><br />
<br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<head><br />
<br />
<br />
<br />
<br />
<style><br />
#mission {width: 400px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:755px; float:right; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:120px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
<br />
</style><br />
<br />
<div id="rightcontent"><br />
<br />
<div id="rightcontent"><br />
<br />
</div><br />
<br />
</head><br />
<br />
<div id="rightcontenttext"><br />
<br />
<p><p><br />
<h3orange>Coordinator </h3orange> <p><br />
<br />
<div id="photos"><br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://dl.dropbox.com/u/24404809/Veronica%20Lab1.jpg" ><br />
<br />
<br />
</div><br />
<br />
<div id="description"><br />
<h3orange1>Veronica Zepeda</h3orange1> <p> <regulartext1>This is Veronica's second year working with the UCSF iGEM team! She previously was a graduate student in the Cate Lab at UC Berkeley and graduated in May 2011. She is having a lot of fun learning about the field of Synthetic Biology. </regulartext1><br />
</div><br />
<br />
</div><br />
<br />
<div id="rightcontenttext"><br />
<p><p><br />
<h3orange> Advisors </h3orange> <p><br />
<br />
<div id="photos"><br />
<br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://i51.tinypic.com/2r4r4oj.jpg" ><br />
<br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://dl.dropbox.com/u/24404809/Connie.jpg"> <br />
<br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/Stephen%20Wakulchik"><br />
<br />
</div><br />
<br />
<div id="description"><br />
<br />
<h3orange1>Wendell Lim</h3orange1> <br> <br />
<regulartext1> Wendell has had a lab at UCSF for over 15 years and has been an adviser to the UCSF team since it started in 2007. He enjoys working with bright, open-minded young scientists and seeing their ideas develop into scientific projects. </regulartext1><br />
</div><br />
<BR><BR><BR><BR><BR><BR><BR><BR><br />
<div id="description"><br />
<br />
<h3orange1>Connie Lee</h3orange1> <br> <br />
<regulartext1>Connie is the Associate Director for the Center for Systems and Synthetic Biology. She is a cell biologist by training and has spent the last 11 years working as a scientific editor, most recently as Deputy Editor at Cell. She enjoys being back in an academic environment and interacting with the iGEM team throughout the summer.</regulartext<br />
<BR><BR><BR><br />
<h3orange1>Stephen Wakulchik</h3orange1> <br><br />
<regulartext1>Stephen is a Teach for America corps Member teaching biology and physics at Dewey Academy in Oakland, CA. He is joining the UCSF iGEM team through an IISME teaching fellowship. Stephen, or “Waka” as he’s fondly referred to by his students, loves genetic engineering and is excited to help the team manifest their own biological mastery.</regulartext><br />
<br />
</div><br />
<br />
<br />
<br />
</div><br />
<br />
</div><br />
<br />
</div></div>Vzepedahttp://2012.igem.org/Team:UCSF/AdvisorsTeam:UCSF/Advisors2013-09-09T20:09:42Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF/MainHeader}}<br />
<html><br />
<br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<head><br />
<br />
<br />
<br />
<br />
<style><br />
#mission {width: 400px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:755px; float:right; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:120px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
<br />
</style><br />
<br />
<div id="rightcontent"><br />
<br />
<div id="rightcontent"><br />
<br />
</div><br />
<br />
</head><br />
<br />
<div id="rightcontenttext"><br />
<br />
<p><p><br />
<h3orange>Coordinator </h3orange> <p><br />
<br />
<div id="photos"><br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://dl.dropbox.com/u/24404809/Veronica%20Lab1.jpg" ><br />
<br />
<br />
</div><br />
<br />
<div id="description"><br />
<h3orange1>Veronica Zepeda</h3orange1> <p> <regulartext1>This is Veronica's second year working with the UCSF iGEM team! She previously was a graduate student in the Cate Lab at UC Berkeley and graduated in May 2011. She is having a lot of fun learning about the field of Synthetic Biology. </regulartext1><br />
</div><br />
<br />
</div><br />
<br />
<div id="rightcontenttext"><br />
<p><p><br />
<h3orange> Advisors </h3orange> <p><br />
<br />
<div id="photos"><br />
<br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://i51.tinypic.com/2r4r4oj.jpg" ><br />
<br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://dl.dropbox.com/u/24404809/Connie.jpg"> <br />
<br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/Stephen%20Wakulchik"><br />
<br />
</div><br />
<br />
<div id="description"><br />
<br />
<h3orange1>Wendell Lim</h3orange1> <br> <br />
<regulartext1> Wendell has had a lab at UCSF for over 15 years and has been an adviser to the UCSF team since it started in 2007. He enjoys working with bright, open-minded young scientists and seeing their ideas develop into scientific projects. </regulartext1><br />
</div><br />
<BR><BR><BR><BR><BR><BR><BR><BR><br />
<div id="description"><br />
<br />
<h3orange1>Connie Lee</h3orange1> <br> <br />
<regulartext1>Connie is the Associate Director for the Center for Systems and Synthetic Biology. She is a cell biologist by training and has spent the last 11 years working as a scientific editor, most recently as Deputy Editor at Cell. She enjoys being back in an academic environment and interacting with the iGEM team throughout the summer.</regulartext<br />
<BR><BR><BR><br />
<h3orange1>Stephen Wakulchik</h3orange1> <br><br />
<regulartext1>Stephen is a Teach for America corps Member teaching biology and physics at Dewey Academy in Oakland, CA. He is joining the UCSF iGEM team through an IISME teaching fellowship. Stephen, or “Waka” as he’s fondly referred to by his students, loves genetic engineering and is excited to help the team manifest their own biological mastery.</regulartext><br />
<br />
</div><br />
<br />
<br />
<br />
</div><br />
<br />
</div><br />
<br />
</div></div>Vzepedahttp://2012.igem.org/Team:UCSF/AdvisorsTeam:UCSF/Advisors2013-09-09T20:07:54Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<html><br />
<br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<head><br />
<br />
<br />
<br />
<br />
<style><br />
#mission {width: 400px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:755px; float:right; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:120px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
<br />
</style><br />
<br />
<div id="rightcontent"><br />
<br />
<div id="rightcontent"><br />
<br />
</div><br />
<br />
</head><br />
<br />
<div id="rightcontenttext"><br />
<br />
<p><p><br />
<h3orange>Coordinator </h3orange> <p><br />
<br />
<div id="photos"><br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://dl.dropbox.com/u/24404809/Veronica%20Lab1.jpg" ><br />
<br />
<br />
</div><br />
<br />
<div id="description"><br />
<h3orange1>Veronica Zepeda</h3orange1> <p> <regulartext1>This is Veronica's second year working with the UCSF iGEM team! She previously was a graduate student in the Cate Lab at UC Berkeley and graduated in May 2011. She is having a lot of fun learning about the field of Synthetic Biology. </regulartext1><br />
</div><br />
<br />
</div><br />
<br />
<div id="rightcontenttext"><br />
<p><p><br />
<h3orange> Advisors </h3orange> <p><br />
<br />
<div id="photos"><br />
<br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://i51.tinypic.com/2r4r4oj.jpg" ><br />
<br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://dl.dropbox.com/u/24404809/Connie.jpg"> <br />
<br />
<img align="left" style="margin-bottom:8px; width:150px; padding:0;" src="http://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/Stephen%20Wakulchik"><br />
<br />
</div><br />
<br />
<div id="description"><br />
<br />
<h3orange1>Wendell Lim</h3orange1> <br> <br />
<regulartext1> Wendell has had a lab at UCSF for over 15 years and has been an adviser to the UCSF team since it started in 2007. He enjoys working with bright, open-minded young scientists and seeing their ideas develop into scientific projects. </regulartext1><br />
</div><br />
<BR><BR><BR><BR><BR><BR><BR><BR><br />
<div id="description"><br />
<br />
<h3orange1>Connie Lee</h3orange1> <br> <br />
<regulartext1>Connie is the Associate Director for the Center for Systems and Synthetic Biology. She is a cell biologist by training and has spent the last 11 years working as a scientific editor, most recently as Deputy Editor at Cell. She enjoys being back in an academic environment and interacting with the iGEM team throughout the summer.</regulartext<br />
<BR><BR><BR><br />
<h3orange1>Stephen Wakulchik</h3orange1> <br><br />
<regulartext1>Stephen is a Teach for America corps Member teaching biology and physics at Dewey Academy in Oakland, CA. He is joining the UCSF iGEM team through an IISME teaching fellowship. Stephen, or “Waka” as he’s fondly referred to by his students, loves genetic engineering and is excited to help the team manifest their own biological mastery.</regulartext><br />
<br />
</div><br />
<br />
<br />
<br />
</div><br />
<br />
</div><br />
<br />
</div></div>Vzepedahttp://2012.igem.org/Team:UCSF/Violacein_ResultsTeam:UCSF/Violacein Results2012-10-04T04:06:18Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<style><br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:785px; float:right; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1200px; float: left; margin-bottom:20px;} <br />
#rightcolumntotal{width:200px; height:2100px; float: right; margin-top:0px;} <br />
</style><br />
<br />
<h3red>Production of Violacein by an <i>E. coli</i> Co-Culture<br />
<p><br />
<br><regulartext><br />
<br />
Before we started our experiments, we obtained a violacein standard from Sigma-Aldrich,<a href="http://www.sigmaaldrich.com/catalog/product/sigma/v9389?lang=en&region=US">Item:V9389-1MG </a><span>. We used this standard to measure the absorbance of violacein at varying concentrations, obtaining the standard curve shown below. Full wavelength scans were obtained, but as shown by previous iGEM teams (<a href="https://2009.igem.org/Team:Cambridge/Project/Violacein">Cambridge 2009 </a>) the maximum absorbance of violacein is seen at 575nm and is reported here. <br><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100212vio_std_cf.jpg"><br />
<br />
<br />
<regulartext> During our experiments we worked with several different strains of <i>E. coli</i>, each containing plasmids with different violacein constructs:<br />
<ul><br />
<regulartext><br />
<li>Strain 1: pcdfDuet+VioABE</li><br />
<li>Strain 2:pcdfDuet+VioDC</li><br />
<li>Strain 3: pcdfDuet:VioABE+VioDC (full operon)</li><br />
<br />
<img align="left" style="margin-right:78px;margin-bottom:28px; width:655px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/VioPlates.jpg" <br><br />
<P><br />
<regulartext><br />
While other teams and papers have reported that extracting pigment from cultures is the best way to perform analysis and quantification, several different solvents have been reported. The 2009 Cambridge iGEM team used acetone to extract, so we tested extraction of violacen from Strain 3 (full violacein operon) using acetone as well as methanol and ethanol. <p><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112op_solvents.jpg"><br />
<br />
<regulartext><br />
Our results show that ethanol was the best solvent to use for extraction and so the rest of our extractions were performed in ethanol. The details of growth and sample analysis can be found on our protocols page. <p><p><p><br />
<br />
<br />
<regulartext> <br />
<h3red>Violacein Mono- and Co-Culture Wavelength Scans:</h3red><br />
<br><br />
Strain 1, which only has the first half of the enzymes necessary to produce violacein is still able to produce a green pigment. When the pigment is extracted from cells, the wavelength scan shown in dark blue is obtained. <br />
<br><br />
Strain 2, which has the second half of the violacein pathway, produces no pigment. This is expected because without the first half of the pathway, no pigment can be produced. <br />
<br><br />
Strain 3, which contains the entire violacein operon produces a wavelength scan similar to our standard obtained from Sigma-Aldrich, with violacein having a maximum absorbance near 575nm. <br />
<br><b><br />
Co-Culture: Strain 1 and Strain 2 grown together (red line) produce a wavelength scan that indicates production of violacein. </b><br />
<br />
<img align="left" style="margin-top:18px; margin-left:48px;margin-right:78px;width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112vio_wavelengths.jpg"><br />
<br><br />
<br />
<h3red>Violacein Mono- and Co-Culture Extractions:</h3red><br />
<br><br />
<regulartext> When monocultures of strain 1 was grown, a dark green pigment was clearly observed. As seen in the plate above, strain 2 did not have any pigment on its own. However, when co-cultures of strain 1 and strain 2 were grown and the pigment extracted a purple pigment was seen and based on wavelength scans (above) appears to be violacein. <br />
<br />
<img align="left" style="margin-top:18px;margin-bottom:18px; margin-left:318px;margin-right:288px;width:255px;height:150px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/Extracts.png"><p><br />
<br><br />
<br />
<br />
<h3red>Addressing Efficiency and Metabolic Burden</h3red><br><br />
<br />
Using linear interpolation (from the maximum absorbance at 575nm, wavelength scans above) we found that the co-culture produces 3.6199 mg/ml violacein and the total operon produces 3.5945mg/ml. While this amount is nearly equal, we believe that the production of violacein could be optimized such that it would produce much more violacein than the monoculture. <br />
<br><p><br />
<br />
The growth rates of strains decrease when inducer is added, as shown in the left graph. By comparing the rate of induced and uninduced growth, we can see how the cells are affected by production of their respective enzymes, and therefore how high the metabolic burden is. In the bar graph, Strain1+Strain2 (coculture) clearly is least affected by metabolic burden, showing that splitting a metabolic pathway does seem to lessen metabolic burden. <br> <p><br />
<img align="left" style="margin-top:18px; margin-left:118px;margin-right:78px;width:700px;height:350px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/vio_growth_diff_vert.jpg"></div>Vzepedahttp://2012.igem.org/Team:UCSF/Violacein_ResultsTeam:UCSF/Violacein Results2012-10-04T04:02:59Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<style><br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:785px; float:right; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1200px; float: left; margin-bottom:20px;} <br />
#rightcolumntotal{width:200px; height:2100px; float: right; margin-top:0px;} <br />
</style><br />
<br />
<h3red>Production of Violacein by an <i>E. coli</i> Co-Culture<br />
<p><br />
<br><regulartext><br />
<br />
Before we started our experiments, we obtained a violacein standard from Sigma-Aldrich,<a href="http://www.sigmaaldrich.com/catalog/product/sigma/v9389?lang=en&region=US">Item:V9389-1MG </a><span>. We used this standard to measure the absorbance of violacein at varying concentrations, obtaining the standard curve shown below. Full wavelength scans were obtained, but as shown by previous iGEM teams (<a href="https://2009.igem.org/Team:Cambridge/Project/Violacein">Cambridge 2009 </a>) the maximum absorbance of violacein is seen at 575nm and is reported here. <br><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100212vio_std_cf.jpg"><br />
<br />
<br />
<regulartext> During our experiments we worked with several different strains of <i>E. coli</i>, each containing plasmids with different violacein constructs:<br />
<ul><br />
<regulartext><br />
<li>Strain 1: pcdfDuet+VioABE</li><br />
<li>Strain 2:pcdfDuet+VioDC</li><br />
<li>Strain 3: pcdfDuet:VioABE+VioDC (full operon)</li><br />
<br />
<img align="left" style="margin-right:78px;margin-bottom:28px; width:655px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/VioPlates.jpg" <br><br />
<P><br />
<regulartext><br />
While other teams and papers have reported that extracting pigment from cultures is the best way to perform analysis and quantification, several different solvents have been reported. The 2009 Cambridge iGEM team used acetone to extract, so we tested extraction of violacen from Strain 3 (full violacein operon) using acetone as well as methanol and ethanol. <p><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112op_solvents.jpg"><br />
<br />
<regulartext><br />
Our results show that ethanol was the best solvent to use for extraction and so the rest of our extractions were performed in ethanol. The details of growth and sample analysis can be found on our protocols page. <p><p><p><br />
<br />
<br />
<regulartext> <br />
<h3red>Violacein Mono- and Co-Culture Wavelength Scans:</h3red><br />
<br><br />
Strain 1, which only has the first half of the enzymes necessary to produce violacein is still able to produce a green pigment. When the pigment is extracted from cells, the wavelength scan shown in dark blue is obtained. <br />
<br><br />
Strain 2, which has the second half of the violacein pathway, produces no pigment. This is expected because without the first half of the pathway, no pigment can be produced. <br />
<br><br />
Strain 3, which contains the entire violacein operon produces a wavelength scan similar to our standard obtained from Sigma-Aldrich, with violacein having a maximum absorbance near 575nm. <br />
<br><b><br />
Co-Culture: Strain 1 and Strain 2 grown together (red line) produce a wavelength scan that indicates production of violacein. </b><br />
<br />
<img align="left" style="margin-top:18px; margin-left:48px;margin-right:78px;width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112vio_wavelengths.jpg"><br />
<br><br />
<br />
<h3red>Violacein Mono- and Co-Culture Extractions:</h3red><br />
<br><br />
<regulartext> When monocultures of strain 1 was grown, a dark green pigment was clearly observed. As seen in the plate above, strain 2 did not have any pigment on its own. However, when co-cultures of strain 1 and strain 2 were grown and the pigment extracted a purple pigment was seen and based on wavelength scans (above) appears to be violacein. <br />
<br />
<img align="left" style="margin-top:18px;margin-bottom:18px; margin-left:318px;margin-right:288px;width:255px;height:150px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/Extracts.png"><p><br />
<br><br />
<br />
<br />
<h3red>Addressing Efficiency and Metabolic Burden</h3red><br><br />
<br />
Using linear interpolation (from the maximum absorbance at 575nm, wavelength scans above) we found that the co-culture produces 3.6199 mg/ml violacein and the total operon produces 3.5945mg/ml. While this amount is nearly equal, we believe that the production of violacein could be optimized such that it would produce much more violacein than the monoculture. <br />
<br><p><br />
<br />
The growth rates of strains decrease when inducer is added, as shown in the left graph. By comparing the rate of induced and uninduced growth, we can see how the cells are affected by production of their respective enzymes, and therefore how high the metabolic burden is. In the bar graph, Strain1+Strain2 (coculture) clearly is least affected by metabolic burden, showing that splitting a metabolic pathway does seem to lessen metabolic burden. <br> <p><br />
<img align="left" style="margin-top:18px; margin-left:118px;margin-right:78px;width:700px;height:350px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/vio_growth_diff_vert.jpg"><br />
<br />
<img align="left" style="margin-top:18px; margin-left:118px;margin-right:78px;width:700px;height:350px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/vio_growth_diff_horizontal.jpg"></div>Vzepedahttp://2012.igem.org/Team:UCSF/Violacein_ResultsTeam:UCSF/Violacein Results2012-10-04T04:02:07Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<style><br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:785px; float:right; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1200px; float: left; margin-bottom:20px;} <br />
#rightcolumntotal{width:200px; height:2100px; float: right; margin-top:0px;} <br />
</style><br />
<br />
<h3red>Production of Violacein by an <i>E. coli</i> Co-Culture<br />
<p><br />
<br><regulartext><br />
<br />
Before we started our experiments, we obtained a violacein standard from Sigma-Aldrich,<a href="http://www.sigmaaldrich.com/catalog/product/sigma/v9389?lang=en&region=US">Item:V9389-1MG </a><span>. We used this standard to measure the absorbance of violacein at varying concentrations, obtaining the standard curve shown below. Full wavelength scans were obtained, but as shown by previous iGEM teams (<a href="https://2009.igem.org/Team:Cambridge/Project/Violacein">Cambridge 2009 </a>) the maximum absorbance of violacein is seen at 575nm and is reported here. <br><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100212vio_std_cf.jpg"><br />
<br />
<br />
<regulartext> During our experiments we worked with several different strains of <i>E. coli</i>, each containing plasmids with different violacein constructs:<br />
<ul><br />
<regulartext><br />
<li>Strain 1: pcdfDuet+VioABE</li><br />
<li>Strain 2:pcdfDuet+VioDC</li><br />
<li>Strain 3: pcdfDuet:VioABE+VioDC (full operon)</li><br />
<br />
<img align="left" style="margin-right:78px;margin-bottom:28px; width:655px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/VioPlates.jpg" <br><br />
<P><br />
<regulartext><br />
While other teams and papers have reported that extracting pigment from cultures is the best way to perform analysis and quantification, several different solvents have been reported. The 2009 Cambridge iGEM team used acetone to extract, so we tested extraction of violacen from Strain 3 (full violacein operon) using acetone as well as methanol and ethanol. <p><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112op_solvents.jpg"><br />
<br />
<regulartext><br />
Our results show that ethanol was the best solvent to use for extraction and so the rest of our extractions were performed in ethanol. The details of growth and sample analysis can be found on our protocols page. <p><p><p><br />
<br />
<br />
<regulartext> <br />
<h3red>Violacein Mono- and Co-Culture Wavelength Scans:</h3red><br />
<br><br />
Strain 1, which only has the first half of the enzymes necessary to produce violacein is still able to produce a green pigment. When the pigment is extracted from cells, the wavelength scan shown in dark blue is obtained. <br />
<br><br />
Strain 2, which has the second half of the violacein pathway, produces no pigment. This is expected because without the first half of the pathway, no pigment can be produced. <br />
<br><br />
Strain 3, which contains the entire violacein operon produces a wavelength scan similar to our standard obtained from Sigma-Aldrich, with violacein having a maximum absorbance near 575nm. <br />
<br><b><br />
Co-Culture: Strain 1 and Strain 2 grown together (red line) produce a wavelength scan that indicates production of violacein. </b><br />
<br />
<img align="left" style="margin-top:18px; margin-left:48px;margin-right:78px;width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112vio_wavelengths.jpg"><br />
<br><br />
<br />
<h3red>Violacein Mono- and Co-Culture Extractions:</h3red><br />
<br><br />
<regulartext> When monocultures of strain 1 was grown, a dark green pigment was clearly observed. As seen in the plate above, strain 2 did not have any pigment on its own. However, when co-cultures of strain 1 and strain 2 were grown and the pigment extracted a purple pigment was seen and based on wavelength scans (above) appears to be violacein. <br />
<br />
<img align="left" style="margin-top:18px;margin-bottom:18px; margin-left:318px;margin-right:288px;width:255px;height:150px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/Extracts.png"><p><br />
<br><br />
<br />
<br />
<h3red>Addressing Efficiency and Metabolic Burden</h3red><br><br />
<br />
Using linear interpolation (from the maximum absorbance at 575nm, wavelength scans above) we found that the co-culture produces 3.6199 mg/ml violacein and the total operon produces 3.5945mg/ml. While this amount is nearly equal, we believe that the production of violacein could be optimized such that it would produce much more violacein than the monoculture. <br />
<br><p><br />
<img align="left" style="margin-top:18px; margin-left:118px;margin-right:78px;width:700px;height:350px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/vio_growth_diff_vert.jpg"><br />
<br />
<img align="left" style="margin-top:18px; margin-left:118px;margin-right:78px;width:700px;height:350px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/vio_growth_diff_horizontal.jpg"></div>Vzepedahttp://2012.igem.org/Team:UCSF/Toxin_SystemTeam:UCSF/Toxin System2012-10-04T03:58:35Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br><br />
<h3orange> Toxin/Antitoxin Systems in <i> E. coli</i> </h3orange><br />
<p><br />
<br />
<br />
<regulartext> <br />
<br><br />
Within the <i>E. coli</i> genome, there is the naturally occurring toxin-antitoxin system whose production is altered in response to various types of stress. In layman’s terms, a toxin-antitoxin system consists of two genes: one coding for the toxin, or “poison”, and one coding for the antitoxin, or “antidote”.<br />
There are three different types of toxin/antitoxin systems, all with different products effectively committing apoptosis. A general overview of all types are listed below.<br />
<br />
<ul><br />
<li> Type 1: Inhibition takes place when the antitoxin RNA binds to the complementary toxin mRNA. If there is not enough antitoxin RNA being transcribed, toxin proteins will be produced, inducing toxicity through cell membrane damage. Toxin RNA has a half life of ~20 minutes, while antitoxin RNA has a half life of ~30 seconds.</li><br />
<br />
<li> Type 2: both genes code for separate proteins, which bind to each other in a normal, unstressed state. While undergoing stressful conditions, the production of antitoxins will drastically decrease, allowing the toxin protein to act as a pseudo-RNAase, cleaving mRNA.</li><br />
<br />
<li> Type 3: The most recently discovered, inhibition of this toxin requires the interplay between a toxin protein and an antitoxin RNA gene. There is only one example of this system so far - the ToxIN system from the bacterial plant pathogen <i>Erwinia carotovora</i>. </li><br />
<br><br />
<regulartext><br />
For our purposes (tuning population ratios of symbiotic strains), Type 2 systems were determined to be ideal, since they have the greatest chance of longevity/sustainability as proteins, rather than RNA strands. There are also at least thirty-three toxin-antitoxin pairs in <i>E. coli</i> alone, giving us a greater selection to work with in our project.<br />
<br />
<br />
<img align="center" style="margin-bottom:10px; width: 250px;height:100; margin-top:20px; padding:2; margin-left:200px;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/toxins/Toxin1.jpg"><br />
<regulartext> <br> In a Type 2 system (diagrammed above), the antitoxin gene is usually upstream of the toxin gene, and the antitoxin is usually the more unstable of the two, degrading much more rapidly than the toxin. As this is the case, antitoxin proteins are produced in a much larger quantity in order to counteract the toxin. Antitoxin and toxin pairs are coded into proteins and bind to each other to prevent an accumulation of toxin. In stressful situations – when there is DNA damage, drastic change in temperature, or lack of nutrients – stress-induced proteases cleave antitoxins and leave the toxins to cleave the mRNA strands. <br><br />
<p><br />
<regulartext>In order for us to work on our project, we had to pick a few toxin-antitoxin pairs to work with. We chose MazE/MazF, RelB/RelE, and YefM/YoeB based on the size of the antitoxin (~95-115 aa). Each pair is classified under the Type 2 category.<br />
<p> <regulartext><br />
<br />
<center><h3orange> How could Toxin/Antitoxin pairs be used to tune or regulate strain ratios in <i> E. coli</i>? </h3orange></center><br />
<p><regulartext><br />
<br />
Although toxin-antitoxin pairs usually function within one cell, we propose to use the system as a way of controlling ratios of two different cells (almost like a kill switch, but perhaps the antitoxin could be a "life switch"). So, instead of using amino acids to feed cells and allow them to survive, we could feed cells varying amounts of a toxin or antitoxin to determine their presence in a co-culture. <p><br />
<regulartext><br />
We designed primers and PCR'd each individual gene off of the <i>E. coli</i> genome and used Seamless Cloning (Life Technologies) to insert the gene into the plasmid we were using: pCDFDuet (Novagen). We then transformed each plasmid into <i>E. coli</i>, grew them up, and performed experiments to see if:<br />
<ol><br />
<li> the expression of the individual toxin or antitoxin had an effect on growth<br />
<li> the toxin or antitoxin could be leaked into the media<br />
<li> a strain producing antitoxin could affect the growth of a strain producing toxin (or vice versa)</div>Vzepedahttp://2012.igem.org/Team:UCSF/Violacein_ResultsTeam:UCSF/Violacein Results2012-10-04T03:54:08Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<style><br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:785px; float:right; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1200px; float: left; margin-bottom:20px;} <br />
#rightcolumntotal{width:200px; height:2100px; float: right; margin-top:0px;} <br />
</style><br />
<br />
<h3red>Production of Violacein by an <i>E. coli</i> Co-Culture<br />
<p><br />
<br><regulartext><br />
<br />
Before we started our experiments, we obtained a violacein standard from Sigma-Aldrich,<a href="http://www.sigmaaldrich.com/catalog/product/sigma/v9389?lang=en&region=US">Item:V9389-1MG </a><span>. We used this standard to measure the absorbance of violacein at varying concentrations, obtaining the standard curve shown below. Full wavelength scans were obtained, but as shown by previous iGEM teams (<a href="https://2009.igem.org/Team:Cambridge/Project/Violacein">Cambridge 2009 </a>) the maximum absorbance of violacein is seen at 575nm and is reported here. <br><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100212vio_std_cf.jpg"><br />
<br />
<br />
<regulartext> During our experiments we worked with several different strains of <i>E. coli</i>, each containing plasmids with different violacein constructs:<br />
<ul><br />
<regulartext><br />
<li>Strain 1: pcdfDuet+VioABE</li><br />
<li>Strain 2:pcdfDuet+VioDC</li><br />
<li>Strain 3: pcdfDuet:VioABE+VioDC (full operon)</li><br />
<br />
<img align="left" style="margin-right:78px;margin-bottom:28px; width:655px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/VioPlates.jpg" <br><br />
<P><br />
<regulartext><br />
While other teams and papers have reported that extracting pigment from cultures is the best way to perform analysis and quantification, several different solvents have been reported. The 2009 Cambridge iGEM team used acetone to extract, so we tested extraction of violacen from Strain 3 (full violacein operon) using acetone as well as methanol and ethanol. <p><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112op_solvents.jpg"><br />
<br />
<regulartext><br />
Our results show that ethanol was the best solvent to use for extraction and so the rest of our extractions were performed in ethanol. The details of growth and sample analysis can be found on our protocols page. <p><p><p><br />
<br />
<br />
<regulartext> <br />
<h3red>Violacein Mono- and Co-Culture Wavelength Scans:</h3red><br />
<br><br />
Strain 1, which only has the first half of the enzymes necessary to produce violacein is still able to produce a green pigment. When the pigment is extracted from cells, the wavelength scan shown in dark blue is obtained. <br />
<br><br />
Strain 2, which has the second half of the violacein pathway, produces no pigment. This is expected because without the first half of the pathway, no pigment can be produced. <br />
<br><br />
Strain 3, which contains the entire violacein operon produces a wavelength scan similar to our standard obtained from Sigma-Aldrich, with violacein having a maximum absorbance near 575nm. <br />
<br><b><br />
Co-Culture: Strain 1 and Strain 2 grown together (red line) produce a wavelength scan that indicates production of violacein. </b><br />
<br />
<img align="left" style="margin-top:18px; margin-left:48px;margin-right:78px;width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112vio_wavelengths.jpg"><br />
<br><br />
<br />
<h3red>Violacein Mono- and Co-Culture Extractions:</h3red><br />
<br><br />
<regulartext> When monocultures of strain 1 was grown, a dark green pigment was clearly observed. As seen in the plate above, strain 2 did not have any pigment on its own. However, when co-cultures of strain 1 and strain 2 were grown and the pigment extracted a purple pigment was seen and based on wavelength scans (above) appears to be violacein. <br />
<br />
<img align="left" style="margin-top:18px;margin-bottom:18px; margin-left:318px;margin-right:288px;width:255px;height:150px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/Extracts.png"><p><br />
<br><br />
<br />
<br />
<h3red>Addressing Efficiency and Metabolic Burden</h3red><br />
<img align="left" style="margin-top:18px; margin-left:118px;margin-right:78px;width:700px;height:350px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/vio_growth_diff_vert.jpg"><br />
<br />
<img align="left" style="margin-top:18px; margin-left:118px;margin-right:78px;width:700px;height:350px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/vio_growth_diff_horizontal.jpg"></div>Vzepedahttp://2012.igem.org/Team:UCSF/Violacein_ResultsTeam:UCSF/Violacein Results2012-10-04T03:52:41Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<style><br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:785px; float:right; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1200px; float: left; margin-bottom:20px;} <br />
#rightcolumntotal{width:200px; height:2100px; float: right; margin-top:0px;} <br />
</style><br />
<br />
<h3red>Production of Violacein by an <i>E. coli</i> Co-Culture<br />
<p><br />
<br><regulartext><br />
<br />
Before we started our experiments, we obtained a violacein standard from Sigma-Aldrich,<a href="http://www.sigmaaldrich.com/catalog/product/sigma/v9389?lang=en&region=US">Item:V9389-1MG </a><span>. We used this standard to measure the absorbance of violacein at varying concentrations, obtaining the standard curve shown below. Full wavelength scans were obtained, but as shown by previous iGEM teams (<a href="https://2009.igem.org/Team:Cambridge/Project/Violacein">Cambridge 2009 </a>) the maximum absorbance of violacein is seen at 575nm and is reported here. <br><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100212vio_std_cf.jpg"><br />
<br />
<br />
<regulartext> During our experiments we worked with several different strains of <i>E. coli</i>, each containing plasmids with different violacein constructs:<br />
<ul><br />
<regulartext><br />
<li>Strain 1: pcdfDuet+VioABE</li><br />
<li>Strain 2:pcdfDuet+VioDC</li><br />
<li>Strain 3: pcdfDuet:VioABE+VioDC (full operon)</li><br />
<br />
<img align="left" style="margin-right:78px;margin-bottom:28px; width:655px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/VioPlates.jpg" <br><br />
<P><br />
<regulartext><br />
While other teams and papers have reported that extracting pigment from cultures is the best way to perform analysis and quantification, several different solvents have been reported. The 2009 Cambridge iGEM team used acetone to extract, so we tested extraction of violacen from Strain 3 (full violacein operon) using acetone as well as methanol and ethanol. <p><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112op_solvents.jpg"><br />
<br />
<regulartext><br />
Our results show that ethanol was the best solvent to use for extraction and so the rest of our extractions were performed in ethanol. The details of growth and sample analysis can be found on our protocols page. <p><p><p><br />
<br />
<br />
<regulartext> <br />
<h3red>Violacein Mono- and Co-Culture Wavelength Scans:</h3red><br />
<br><br />
Strain 1, which only has the first half of the enzymes necessary to produce violacein is still able to produce a green pigment. When the pigment is extracted from cells, the wavelength scan shown in dark blue is obtained. <br />
<br><br />
Strain 2, which has the second half of the violacein pathway, produces no pigment. This is expected because without the first half of the pathway, no pigment can be produced. <br />
<br><br />
Strain 3, which contains the entire violacein operon produces a wavelength scan similar to our standard obtained from Sigma-Aldrich, with violacein having a maximum absorbance near 575nm. <br />
<br><b><br />
Co-Culture: Strain 1 and Strain 2 grown together (red line) produce a wavelength scan that indicates production of violacein. </b><br />
<br />
<img align="left" style="margin-top:18px; margin-left:48px;margin-right:78px;width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112vio_wavelengths.jpg"><br />
<br><br />
<br />
<h3red>Violacein Mono- and Co-Culture Extractions:</h3red><br />
<br><br />
<regulartext> When monocultures of strain 1 was grown, a dark green pigment was clearly observed. As seen in the plate above, strain 2 did not have any pigment on its own. However, when co-cultures of strain 1 and strain 2 were grown and the pigment extracted a purple pigment was seen and based on wavelength scans (above) appears to be violacein. <br />
<br />
<img align="left" style="margin-top:18px;margin-bottom:18px; margin-left:318px;margin-right:288px;width:255px;height:150px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/Extracts.png"><p><br />
<br><br />
<br />
<br />
<h3red>Addressing Efficiency and Metabolic Burden</h3red><br />
<img align="left" style="margin-top:18px; margin-left:218px;margin-right:78px;width:700px;height:350px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/vio_growth_diff_vert.jpg"></div>Vzepedahttp://2012.igem.org/Team:UCSF/Violacein_ResultsTeam:UCSF/Violacein Results2012-10-04T03:52:04Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<style><br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:785px; float:right; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1200px; float: left; margin-bottom:20px;} <br />
#rightcolumntotal{width:200px; height:2100px; float: right; margin-top:0px;} <br />
</style><br />
<br />
<h3red>Production of Violacein by an <i>E. coli</i> Co-Culture<br />
<p><br />
<br><regulartext><br />
<br />
Before we started our experiments, we obtained a violacein standard from Sigma-Aldrich,<a href="http://www.sigmaaldrich.com/catalog/product/sigma/v9389?lang=en&region=US">Item:V9389-1MG </a><span>. We used this standard to measure the absorbance of violacein at varying concentrations, obtaining the standard curve shown below. Full wavelength scans were obtained, but as shown by previous iGEM teams (<a href="https://2009.igem.org/Team:Cambridge/Project/Violacein">Cambridge 2009 </a>) the maximum absorbance of violacein is seen at 575nm and is reported here. <br><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100212vio_std_cf.jpg"><br />
<br />
<br />
<regulartext> During our experiments we worked with several different strains of <i>E. coli</i>, each containing plasmids with different violacein constructs:<br />
<ul><br />
<regulartext><br />
<li>Strain 1: pcdfDuet+VioABE</li><br />
<li>Strain 2:pcdfDuet+VioDC</li><br />
<li>Strain 3: pcdfDuet:VioABE+VioDC (full operon)</li><br />
<br />
<img align="left" style="margin-right:78px;margin-bottom:28px; width:655px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/VioPlates.jpg" <br><br />
<P><br />
<regulartext><br />
While other teams and papers have reported that extracting pigment from cultures is the best way to perform analysis and quantification, several different solvents have been reported. The 2009 Cambridge iGEM team used acetone to extract, so we tested extraction of violacen from Strain 3 (full violacein operon) using acetone as well as methanol and ethanol. <p><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112op_solvents.jpg"><br />
<br />
<regulartext><br />
Our results show that ethanol was the best solvent to use for extraction and so the rest of our extractions were performed in ethanol. The details of growth and sample analysis can be found on our protocols page. <p><p><p><br />
<br />
<br />
<regulartext> <br />
<h3red>Violacein Mono- and Co-Culture Wavelength Scans:</h3red><br />
<br><br />
Strain 1, which only has the first half of the enzymes necessary to produce violacein is still able to produce a green pigment. When the pigment is extracted from cells, the wavelength scan shown in dark blue is obtained. <br />
<br><br />
Strain 2, which has the second half of the violacein pathway, produces no pigment. This is expected because without the first half of the pathway, no pigment can be produced. <br />
<br><br />
Strain 3, which contains the entire violacein operon produces a wavelength scan similar to our standard obtained from Sigma-Aldrich, with violacein having a maximum absorbance near 575nm. <br />
<br><b><br />
Co-Culture: Strain 1 and Strain 2 grown together (red line) produce a wavelength scan that indicates production of violacein. </b><br />
<br />
<img align="left" style="margin-top:18px; margin-left:48px;margin-right:78px;width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112vio_wavelengths.jpg"><br />
<br><br />
<br />
<h3red>Violacein Mono- and Co-Culture Extractions:</h3red><br />
<br><br />
<regulartext> When monocultures of strain 1 was grown, a dark green pigment was clearly observed. As seen in the plate above, strain 2 did not have any pigment on its own. However, when co-cultures of strain 1 and strain 2 were grown and the pigment extracted a purple pigment was seen and based on wavelength scans (above) appears to be violacein. <br />
<br />
<img align="left" style="margin-top:18px;margin-bottom:18px; margin-left:318px;margin-right:288px;width:255px;height:150px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/Extracts.png"><p><br />
<br><br />
<br />
<br />
<h3red>Addressing Efficiency and Metabolic Burden</h3red><br />
<img align="left" style="margin-top:18px; margin-left:318px;margin-right:78px;width:600px;height:300px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/vio_growth_diff_vert.jpg"></div>Vzepedahttp://2012.igem.org/Team:UCSF/Auxotroph_DataTeam:UCSF/Auxotroph Data2012-10-04T03:47:31Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<style><br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:785px; float:right; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1200px; float: left; margin-bottom:20px;} <br />
#rightcolumntotal{width:200px; height:2100px; float: right; margin-top:0px;} <br />
</style><br />
<br />
<h3red>Growth and Analysis of Auxotroph System in <i>E. coli</i> <br />
<p><br />
<br><regulartext><br />
<br />
The W3 and Y3 strains (tryptophan ad tyrosine auxotrophs) that we obtained from the Lin Lab at the University of Michigan had already been studied in a paper published earlier this year. <br />
<br />
<a href="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/Kerner%202012%20PLoS%20ONE.pdf"><b>A Programmable <i>Escherichia coli</i> Consortium via Tunable Symbiosis </b> </a>. They showed some experimental analysis which were the first steps at showing that these strains could be induced at varying levels to get a range of ratios between the two strains. <br><br />
<p><br><br />
<regulartext>Based on comments made in the discussion section of the Kerner paper, we believed that it was necessary to determine whether the population of the two strains could be determined based on an equation relating the total OD of the two strains and the YFP reading from one of the strains (Y3). For this reason we created a standard curve of YFP fluorescence versus cell density. <br> <p><br />
<br />
<img align="left" style="margin-right:128px;margin-left:68px; width:555px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/yfp_std.jpg"> <br> <p><br />
<br />
<regulartext> We were able to create our own version of the model presented in the Kerner 2012 paper, using parameters we found in the literature and obtained through our own data collection. <br />
<br />
<br />
<img align="left" style="margin-right:178px;margin-left:68px; margin-bottom:8px; width:500px;height:250px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/Surface-model.jpg"><br><p><br />
<br />
<br />
<p> <regulartext>Based on this model, it seems that a wide variety of ratios of the two strains could be obtained. <br />
<p><br><br />
<br />
<p> <regulartext>So, we performed experiments to determine the ratios of the two strains that could be collected in a variety of inducer conditions. However, based on our results from the YFP standard curve (above) we realized that the data would only be accurate in a small range of cell concentrations. The details of our experimental setup can be found on our Project Protocols page: <a href="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/Protocols/Coculturing%20of%20Auxotrophs.pdf"><b> Co-culturing of Auxotroph Strains </b> </a>. <br />
<p><br />
<br />
<regulartext> A 3D surface of that graph was obtained and a slice of the graph are shown below: <br> <p><br />
<h3> While in some amounts of inducer concentrations, the system seems tunable, it is not nearly as robust as the model predicts. Thus, we turned to our toxin/antitoxin system as a new approach to tuning communities of cells. <br><p><br />
<br />
<img align="left" style="margin-bottom:18px; width:555px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/surf-data.png"><br />
<br />
<img align="left" style="margin-left:168px;margin-bottom:8px; width:555px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/slice.png"></div>Vzepedahttp://2012.igem.org/Team:UCSF/Violacein_ResultsTeam:UCSF/Violacein Results2012-10-04T03:42:15Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<style><br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:785px; float:right; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1200px; float: left; margin-bottom:20px;} <br />
#rightcolumntotal{width:200px; height:2100px; float: right; margin-top:0px;} <br />
</style><br />
<br />
<h3red>Production of Violacein by an <i>E. coli</i> Co-Culture<br />
<p><br />
<br><regulartext><br />
<br />
Before we started our experiments, we obtained a violacein standard from Sigma-Aldrich,<a href="http://www.sigmaaldrich.com/catalog/product/sigma/v9389?lang=en&region=US">Item:V9389-1MG </a><span>. We used this standard to measure the absorbance of violacein at varying concentrations, obtaining the standard curve shown below. Full wavelength scans were obtained, but as shown by previous iGEM teams (<a href="https://2009.igem.org/Team:Cambridge/Project/Violacein">Cambridge 2009 </a>) the maximum absorbance of violacein is seen at 575nm and is reported here. <br><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100212vio_std_cf.jpg"><br />
<br />
<br />
<regulartext> During our experiments we worked with several different strains of <i>E. coli</i>, each containing plasmids with different violacein constructs:<br />
<ul><br />
<regulartext><br />
<li>Strain 1: pcdfDuet+VioABE</li><br />
<li>Strain 2:pcdfDuet+VioDC</li><br />
<li>Strain 3: pcdfDuet:VioABE+VioDC (full operon)</li><br />
<br />
<img align="left" style="margin-right:78px;margin-bottom:28px; width:655px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/VioPlates.jpg" <br><br />
<P><br />
<regulartext><br />
While other teams and papers have reported that extracting pigment from cultures is the best way to perform analysis and quantification, several different solvents have been reported. The 2009 Cambridge iGEM team used acetone to extract, so we tested extraction of violacen from Strain 3 (full violacein operon) using acetone as well as methanol and ethanol. <p><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112op_solvents.jpg"><br />
<br />
<regulartext><br />
Our results show that ethanol was the best solvent to use for extraction and so the rest of our extractions were performed in ethanol. The details of growth and sample analysis can be found on our protocols page. <p><p><p><br />
<br />
<br />
<regulartext> <br />
<h3red>Violacein Mono- and Co-Culture Wavelength Scans:</h3red><br />
<br><br />
Strain 1, which only has the first half of the enzymes necessary to produce violacein is still able to produce a green pigment. When the pigment is extracted from cells, the wavelength scan shown in dark blue is obtained. <br />
<br><br />
Strain 2, which has the second half of the violacein pathway, produces no pigment. This is expected because without the first half of the pathway, no pigment can be produced. <br />
<br><br />
Strain 3, which contains the entire violacein operon produces a wavelength scan similar to our standard obtained from Sigma-Aldrich, with violacein having a maximum absorbance near 575nm. <br />
<br><b><br />
Co-Culture: Strain 1 and Strain 2 grown together (red line) produce a wavelength scan that indicates production of violacein. </b><br />
<br />
<img align="left" style="margin-top:18px; margin-left:48px;margin-right:78px;width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112vio_wavelengths.jpg"><br />
<br><br />
<br />
<h3red>Violacein Mono- and Co-Culture Extractions:</h3red><br />
<br><br />
<regulartext> When monocultures of strain 1 was grown, a dark green pigment was clearly observed. As seen in the plate above, strain 2 did not have any pigment on its own. However, when co-cultures of strain 1 and strain 2 were grown and the pigment extracted a purple pigment was seen and based on wavelength scans (above) appears to be violacein. <br />
<br />
<img align="left" style="margin-top:18px; margin-left:318px;margin-right:78px;width:255px;height:150px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/Extracts.png"><br />
<br></div>Vzepedahttp://2012.igem.org/Team:UCSF/Violacein_ResultsTeam:UCSF/Violacein Results2012-10-04T03:34:39Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<style><br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:785px; float:right; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1200px; float: left; margin-bottom:20px;} <br />
#rightcolumntotal{width:200px; height:2100px; float: right; margin-top:0px;} <br />
</style><br />
<br />
<h3red>Production of Violacein by an <i>E. coli</i> Co-Culture<br />
<p><br />
<br><regulartext><br />
<br />
Before we started our experiments, we obtained a violacein standard from Sigma-Aldrich,<a href="http://www.sigmaaldrich.com/catalog/product/sigma/v9389?lang=en&region=US">Item:V9389-1MG </a><span>. We used this standard to measure the absorbance of violacein at varying concentrations, obtaining the standard curve shown below. Full wavelength scans were obtained, but as shown by previous iGEM teams (<a href="https://2009.igem.org/Team:Cambridge/Project/Violacein">Cambridge 2009 </a>) the maximum absorbance of violacein is seen at 575nm and is reported here. <br><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100212vio_std_cf.jpg"><br />
<br />
<br />
<regulartext> During our experiments we worked with several different strains of <i>E. coli</i>, each containing plasmids with different violacein constructs:<br />
<ul><br />
<regulartext><br />
<li>Strain 1: pcdfDuet+VioABE</li><br />
<li>Strain 2:pcdfDuet+VioDC</li><br />
<li>Strain 3: pcdfDuet:VioABE+VioDC (full operon)</li><br />
<br />
<img align="left" style="margin-right:78px;margin-bottom:28px; width:655px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/VioPlates.jpg" <br><br />
<P><br />
<regulartext><br />
While other teams and papers have reported that extracting pigment from cultures is the best way to perform analysis and quantification, several different solvents have been reported. The 2009 Cambridge iGEM team used acetone to extract, so we tested extraction of violacen from Strain 3 (full violacein operon) using acetone as well as methanol and ethanol. <p><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112op_solvents.jpg"><br />
<br />
<regulartext><br />
Our results show that ethanol was the best solvent to use for extraction and so the rest of our extractions were performed in ethanol. The details of growth and sample analysis can be found on our protocols page. <p><p><p><br />
<br />
<br />
<regulartext> <br />
<h3red>Violacein Mono- and Co-Culture Wavelength Scans:</h3red><br />
<br><br />
Strain 1, which only has the first half of the enzymes necessary to produce violacein is still able to produce a green pigment. When the pigment is extracted from cells, the wavelength scan shown in dark blue is obtained. <br />
<br><br />
Strain 2, which has the second half of the violacein pathway, produces no pigment. This is expected because without the first half of the pathway, no pigment can be produced. <br />
<br><br />
Strain 3, which contains the entire violacein operon produces a wavelength scan similar to our standard obtained from Sigma-Aldrich, with violacein having a maximum absorbance near 575nm. <br />
<br><b><br />
Co-Culture: Strain 1 and Strain 2 grown together (red line) produce a wavelength scan that indicates production of violacein. </b><br />
<br />
<img align="left" style="margin-top:18px; margin-left:48px;margin-right:78px;width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112vio_wavelengths.jpg"><br />
<br><br />
<br />
<h3red>Violacein Mono- and Co-Culture Extractions:</h3red><br />
<br></div>Vzepedahttp://2012.igem.org/Team:UCSF/Violacein_ResultsTeam:UCSF/Violacein Results2012-10-04T03:31:45Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<style><br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:785px; float:right; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1200px; float: left; margin-bottom:20px;} <br />
#rightcolumntotal{width:200px; height:2100px; float: right; margin-top:0px;} <br />
</style><br />
<br />
<h3red>Production of Violacein by an <i>E. coli</i> Co-Culture<br />
<p><br />
<br><regulartext><br />
<br />
Before we started our experiments, we obtained a violacein standard from Sigma-Aldrich,<a href="http://www.sigmaaldrich.com/catalog/product/sigma/v9389?lang=en&region=US">Item:V9389-1MG </a><span>. We used this standard to measure the absorbance of violacein at varying concentrations, obtaining the standard curve shown below. Full wavelength scans were obtained, but as shown by previous iGEM teams (<a href="https://2009.igem.org/Team:Cambridge/Project/Violacein">Cambridge 2009 </a>) the maximum absorbance of violacein is seen at 575nm and is reported here. <br><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100212vio_std_cf.jpg"><br />
<br />
<br />
<regulartext> During our experiments we worked with several different strains of <i>E. coli</i>, each containing plasmids with different violacein constructs:<br />
<ul><br />
<regulartext><br />
<li>Strain 1: pcdfDuet+VioABE</li><br />
<li>Strain 2:pcdfDuet+VioDC</li><br />
<li>Strain 3: pcdfDuet:VioABE+VioDC (full operon)</li><br />
<br />
<img align="left" style="margin-right:78px; width:655px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/VioPlates.jpg" <br><br />
<P><br />
<p><br />
<regulartext><br />
While other teams and papers have reported that extracting pigment from cultures is the best way to perform analysis and quantification, several different solvents have been reported. The 2009 Cambridge iGEM team used acetone to extract, so we tested extraction of violacen from Strain 3 (full violacein operon) using acetone as well as methanol and ethanol. <p><br />
<br />
<img align="left" style="margin-bottom:8px; width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112op_solvents.jpg"><br />
<br />
<regulartext><br />
Our results show that ethanol was the best solvent to use for extraction and so the rest of our extractions were performed in ethanol. The details of growth and sample analysis can be found on our protocols page. <p><p><p><br />
<br />
<br />
<regulartext> <br />
<h3red>Violacein Mono- and Co-Culture Wavelength Scans:</h3red><br />
<br><br />
Strain 1, which only has the first half of the enzymes necessary to produce violacein is still able to produce a green pigment. When the pigment is extracted from cells, the wavelength scan shown in dark blue is obtained. <br />
<br><br />
Strain 2, which has the second half of the violacein pathway, produces no pigment. This is expected because without the first half of the pathway, no pigment can be produced. <br />
<br><br />
Strain 3, which contains the entire violacein operon produces a wavelength scan similar to our standard obtained from Sigma-Aldrich, with violacein having a maximum absorbance near 575nm. <br />
<br><b><br />
Co-Culture: Strain 1 and Strain 2 grown together (red line) produce a wavelength scan that indicates production of violacein. </b><br />
<br />
<img align="left" style="margin-top:18px; margin-left:28px;width:755px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/violacein/100112vio_wavelengths.jpg"></div>Vzepedahttp://2012.igem.org/Team:UCSF/Protocols2Team:UCSF/Protocols22012-10-04T03:25:22Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<br />
<br />
<style><br />
#rightcontent {width:655px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
<br />
</style><br />
<br />
</head><br />
<br />
<br />
<br />
<br />
<h3red>Violacein Production Protocols</h3red> <p><br />
<regulartext><br />
<ul><br />
<regulartext><br />
<br />
<br />
<li>Extracting Pigments</li><br />
<regulartext> To extract pigments, samples were taken from each culture and centrifuged to pellet the cells. For most experiments a 2ml culture was sufficient and this cell pellet was resuspended in the desired solvent. As seen in our data page, several solvents were tested but our final analysis was done with an ethanol extraction. After addition of the solvent (~300ul) the sample was vortexed and then centrifuged again to remove cell precipitate. The resulting organic phase was used for analysis. <br />
<br />
</ul><br />
<p><p><br><br />
<br />
<br />
<h3red>Auxotroph System Protocols</h3red> <p><br />
<ul><br />
<regulartext><br />
<br />
<li><a href="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/Protocols/monoprotocol.pdf"> Monoculture of Auxotroph Strains</a> to determine growth rate in presence of amino acids<br></li><br />
<li><a href="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/Protocols/Coculturing%20of%20Auxotrophs.pdf"> Co-culturing of Auxotroph Strains</a> <br></li></ul><br />
<br><br />
<br />
<h3red>Toxin/Antitoxin System Protocols</h3red><br><br />
<ul> <regulartext><br />
<li><a href="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/Protocols/Toxin-Antitoxin%20Expression%20Protocol-3.pdf"> Inducing for Protein Production</a></li><br />
<li><a href="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/Protocols/Toxin-Antitox%20Exchange%20Protocol.pdf"> Toxin-Antitoxin Exchange Protocol</a></li><br />
</ul><br />
<br></div>Vzepedahttp://2012.igem.org/Team:UCSF/Auxotroph_DataTeam:UCSF/Auxotroph Data2012-10-04T03:12:13Z<p>Vzepeda: </p>
<hr />
<div>{{Template:UCSF}}<br />
<br />
<html><br />
<br />
<link rel="stylesheet" type="text/css" href="http://tinyurl.com/twilightsparkles"/><br />
<br />
<style><br />
#mission {width: 500px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#opensource {width:306px; float:left; background-color: #F5F5F5; margin-left:8px; padding: 10px; margin-top:8px;}<br />
#rightcontent {width:785px; float:right; background-color: #FFFFFF; margin-left: 8px; margin-top:10px;}<br />
#photos {width:155px; float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#description{width:450px; height:110px;float:left; background-color: #F5F5F5; margin-left: 8px; margin-top:10px;}<br />
#flickr{width:755px; float:right;} <br />
#leftcolumntotal{width:200px; height:1200px; float: left; margin-bottom:20px;} <br />
#rightcolumntotal{width:200px; height:2100px; float: right; margin-top:0px;} <br />
</style><br />
<br />
<h3red>Growth and Analysis of Auxotroph System in <i>E. coli</i> <br />
<p><br />
<br><regulartext><br />
<br />
The W3 and Y3 strains (tryptophan ad tyrosine auxotrophs) that we obtained from the Lin Lab at the University of Michigan had already been studied in a paper published earlier this year. <br />
<br />
<a href="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/Kerner%202012%20PLoS%20ONE.pdf"><b>A Programmable <i>Escherichia coli</i> Consortium via Tunable Symbiosis </b> </a>. They showed some experimental analysis which were the first steps at showing that these strains could be induced at varying levels to get a range of ratios between the two strains. <br><br />
<p><br><br />
<regulartext>Based on comments made in the discussion section of the Kerner paper, we believed that it was necessary to determine whether the population of the two strains could be determined based on an equation relating the total OD of the two strains and the YFP reading from one of the strains (Y3). For this reason we created a standard curve of YFP fluorescence versus cell density. <br> <p><br />
<br />
<img align="left" style="margin-right:128px;margin-left:68px; width:555px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/yfp_std.jpg"> <br> <p><br />
<br />
<regulartext> We were able to create our own version of the model presented in the Kerner 2012 paper, using parameters we found in the literature and obtained through our own data collection. <br />
<br />
<br />
<img align="left" style="margin-right:178px;margin-left:68px; margin-bottom:8px; width:500px;height:250px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/Surface-model.jpg"><br><p><br />
<br />
<br />
<p> <regulartext>Based on this model, it seems that a wide variety of ratios of the two strains could be obtained. <br />
<p><br><br />
<br />
<p> <regulartext>So, we performed experiments to determine the ratios of the two strains that could be collected in a variety of inducer conditions. However, based on our results from the YFP standard curve (above) we realized that the data would only be accurate in a small range of cell concentrations. The details of our experimental setup can be found on our Project Protocols page: <a href="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/Protocols/Coculturing%20of%20Auxotrophs.pdf"><b> Co-culturing of Auxotroph Strains </b> </a>. <br />
<p><br />
<br />
<regulartext> A 3D surface of that graph was obtained and a slice of the graph is shown here: <br />
<br />
<img align="left" style="margin-bottom:18px; width:555px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/surf-data.png"><br />
<br />
<img align="left" style="margin-left:168px;margin-bottom:8px; width:555px;height:410px; padding:0;" src="https://dl.dropbox.com/u/24404809/iGEM%202012/igem%202012%20website%20photos/auxotrophs/slice.png"></div>Vzepeda