Biomod/2014/ASU/Project: Difference between revisions
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<div id="bodyContent"> | <div id="bodyContent"> | ||
<h3 id="siteSub">From OpenWetWare</h3> | <h3 id="siteSub">From OpenWetWare</h3> | ||
<div id="contentSub"><span class="subpages">< <a href="/wiki/Biomod" title="Biomod">Biomod</a> | <a href="/wiki/Biomod/ | <div id="contentSub"><span class="subpages">< <a href="/wiki/Biomod" title="Biomod">Biomod</a> | <a href="/wiki/Biomod/2014" title="Biomod/2014">2014</a></span></div> | ||
<div id="jump-to-nav">Jump to: <a href="#column-one">navigation</a>, <a href="#searchInput">search</a></div> <!-- start content --> | <div id="jump-to-nav">Jump to: <a href="#column-one">navigation</a>, <a href="#searchInput">search</a></div> <!-- start content --> | ||
<p> | <p> | ||
| Line 100: | Line 100: | ||
padding: 0; | padding: 0; | ||
background: #fff; | background: #fff; | ||
border: | border: none; | ||
} | } | ||
| Line 117: | Line 117: | ||
border: 0; | border: 0; | ||
font: inherit; | font: inherit; | ||
} | } | ||
| Line 145: | Line 145: | ||
h1, h2, #super-list, .box, .tagline, #index-list { | h1, h2, #super-list, .box, .tagline, #index-list { | ||
font-family: | font-family: Times New Roman; | ||
font-size: 18px; | |||
color: #000000; | |||
} | } | ||
| Line 181: | Line 183: | ||
a img { border: none; } | a img { border: none; } | ||
a.anchor{display: block; position: relative | a.anchor{display: block; position: relative; visibility: hidden;} | ||
p{ | p{ | ||
| Line 197: | Line 199: | ||
} | } | ||
nav { | nav { | ||
| Line 211: | Line 206: | ||
top: 0px; | top: 0px; | ||
left: 0px; | left: 0px; | ||
bottom: 0px; | |||
right: 0px; | right: 0px; | ||
z-index: 100; | z-index: 100; | ||
| Line 217: | Line 213: | ||
nav ul { | nav ul { | ||
width: 100%; | width: 100%; | ||
margin: 0px auto; | margin: 0px auto; | ||
padding: 0px; | padding: 0px; | ||
| Line 226: | Line 223: | ||
} | } | ||
nav ul li.selected { | nav ul li.selected { | ||
border-bottom: 10px | border-bottom: solid 10px #580000; | ||
} | } | ||
nav ul li.home { | nav ul li.home { | ||
padding: | padding: 0px; | ||
} | } | ||
nav ul a { | nav ul a { | ||
float: left; | float: left; | ||
| Line 244: | Line 237: | ||
font-size: 20px; | font-size: 20px; | ||
font-weight: 300; | font-weight: 300; | ||
padding: | padding: 0px 20px 0; | ||
} | } | ||
#content { | #content { | ||
| Line 269: | Line 247: | ||
#filters > li{ | #filters > li{ | ||
margin: | margin: 0px; | ||
display: inline-block; | display: inline-block; | ||
} | } | ||
| Line 317: | Line 295: | ||
.box.b1x2{ | .box.b1x2{ | ||
width: 930px; | width: 930px; | ||
height: | height: 1450px; | ||
} | } | ||
| Line 725: | Line 703: | ||
float: left; | float: left; | ||
overflow: hidden; | overflow: hidden; | ||
position: fixed; | position:fixed; | ||
background: #fff; | background: #fff; | ||
color: # | color: #000000; | ||
display: table-cell; | display: table-cell; | ||
text-align: center; | text-align: center; | ||
| Line 745: | Line 723: | ||
.box figcaption { | .box figcaption { | ||
background: none repeat scroll 0 0 | background: none repeat scroll 0 0 #fff; | ||
color:#000000; | |||
float:center; | |||
bottom: 0; | bottom: 0; | ||
font-size: | font-size: 16px; | ||
font-weight: | font-weight: 900; | ||
padding-left: 5px; | padding-left: 5px; | ||
text-align: center; | text-align: center; | ||
| Line 997: | Line 977: | ||
li > ul { | li > ul { | ||
margin-left: | margin-left: 10px; | ||
} | } | ||
| Line 1,016: | Line 996: | ||
width: 50%; | width: 50%; | ||
} | } | ||
#subnav-sticky-wrapper { | |||
height: 5px !important; | |||
} | } | ||
table { | |||
border-collapse: collapse; | |||
margin: auto auto 40px; | |||
- | width: 635px;; | ||
} | |||
th { | |||
background-color: #5F5F5F; | |||
border: 1px solid #999999; | |||
color: #FFFFFF; | |||
- | |||
} | } | ||
tr td { | |||
border: 1px solid #999999; | |||
text-align: center; | |||
- | |||
} | } | ||
tr.odd td { | |||
background-color: #EEEEEE; | |||
color: #000000; | |||
- | |||
} | } | ||
.ref li { | |||
font-size: 14px; | |||
font-weight: 300; | |||
- | |||
} | } | ||
</style> | |||
<link href="http://openwetware.org/images/2/29/Nano_icon.png" rel="shortcut icon"> | |||
<script src="https://biomod2013.googlecode.com/svn/trunk/js/jquery.isotope.min.js"></script> | |||
<script src="https://biomod2013.googlecode.com/svn/trunk/js/jquery.refineslide.min.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/fb/jquery.fancybox.pack.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/fb/helpers/jquery.fancybox-buttons.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/fb/helpers/jquery.fancybox-media.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/fb/helpers/jquery.fancybox-thumbs.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.easing.min.js"></script> | |||
/ | <script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.scrollUp.min.js"></script> | ||
/ | <script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.stellar.min.js"></script> | ||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.sticky.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.scrollTo.min.js"></script> | |||
<script type="text/javascript" src="http://biomod2013.googlecode.com/svn/trunk/js/jquery.localscroll.min.js"></script> | |||
} | <script> | ||
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ | |||
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), | |||
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) | |||
})(window,document,'script','//www.google-analytics.com/analytics.js','ga'); | |||
ga('create', 'UA-45176973-1', 'openwetware.org'); | |||
ga('send', 'pageview'); | |||
/ | </script> | ||
/* | <style type="text/css"> | ||
. | /*! fancyBox v2.1.5 fancyapps.com | fancyapps.com/fancybox/#license */ | ||
.fancybox-wrap, | |||
.fancybox-skin, | |||
.fancybox-outer, | |||
.fancybox-inner, | |||
.fancybox-image, | |||
.fancybox-wrap iframe, | |||
.fancybox-wrap object, | |||
.fancybox-nav, | |||
.fancybox-nav span, | |||
.fancybox-tmp | |||
{ | |||
padding: 0; | |||
margin: 0; | |||
border: 0; | |||
outline: none; | |||
vertical-align: top; | |||
. | |||
. | |||
. | |||
} | } | ||
.fancybox-wrap { | |||
position: absolute; | |||
top: 0; | |||
left: 0; | |||
z-index: 8020; | |||
} | } | ||
.fancybox-skin { | |||
position: relative; | |||
background: #f9f9f9; | |||
color: #444; | |||
text-shadow: none; | |||
-webkit-border-radius: 4px; | |||
-moz-border-radius: 4px; | |||
border-radius: 4px; | |||
} | |||
} | |||
.fancybox-opened { | |||
z-index: 8030; | |||
} | } | ||
.fancybox-opened .fancybox-skin { | |||
-webkit-box-shadow: 0 10px 25px rgba(0, 0, 0, 0.5); | |||
-moz-box-shadow: 0 10px 25px rgba(0, 0, 0, 0.5); | |||
box-shadow: 0 10px 25px rgba(0, 0, 0, 0.5); | |||
} | } | ||
.fancybox-outer, .fancybox-inner { | |||
. | position: relative; | ||
} | } | ||
.fancybox-inner { | |||
overflow: hidden; | |||
} | } | ||
.fancybox-type-iframe .fancybox-inner { | |||
-webkit-overflow-scrolling: touch; | |||
} | } | ||
.fancybox-error { | |||
color: #444; | |||
font: 14px/20px "Helvetica Neue",Helvetica,Arial,sans-serif; | |||
margin: 0; | |||
padding: 15px; | |||
white-space: nowrap; | |||
} | } | ||
. | .fancybox-image, .fancybox-iframe { | ||
display: block; | |||
width: 100%; | |||
height: 100%; | |||
} | } | ||
.fancybox-image { | |||
max-width: 100%; | |||
max-height: 100%; | |||
} | } | ||
#fancybox-loading, .fancybox-close, .fancybox-prev span, .fancybox-next span { | |||
background-image: url('http://openwetware.org/images/5/55/Fancybox_sprite.png'); | |||
/ | |||
} | } | ||
#fancybox-loading { | |||
position: fixed; | |||
top: 50%; | |||
left: 50%; | |||
margin-top: -22px; | |||
margin-left: -22px; | |||
background-position: 0 -108px; | |||
opacity: 0.8; | |||
cursor: pointer; | |||
z-index: 8060; | |||
} | } | ||
#fancybox-loading div { | |||
width: 44px; | |||
height: 44px; | |||
background: url('http://openwetware.org/images/d/d0/Fancybox_loading.gif') center center no-repeat; | |||
/ | |||
/ | |||
. | |||
} | } | ||
.fancybox-close { | |||
position: absolute; | |||
top: -18px; | |||
right: -18px; | |||
width: 36px; | |||
height: 36px; | |||
cursor: pointer; | |||
z-index: 8040; | |||
} | } | ||
/ | .fancybox-nav { | ||
position: absolute; | |||
top: 0; | |||
width: 40%; | |||
height: 100%; | |||
cursor: pointer; | |||
text-decoration: none; | |||
background: transparent url('http://openwetware.org/images/c/c0/Blank.gif'); /* helps IE */ | |||
-webkit-tap-highlight-color: rgba(0,0,0,0); | |||
z-index: 8040; | |||
} | } | ||
.fancybox-prev { | |||
left: 0; | |||
} | } | ||
.fancybox-next { | |||
right: 0; | |||
} | } | ||
.fancybox-nav span { | |||
position: absolute; | |||
top: 50%; | |||
width: 36px; | |||
height: 34px; | |||
margin-top: -18px; | |||
cursor: pointer; | |||
z-index: 8040; | |||
visibility: hidden; | |||
} | } | ||
.fancybox-prev span { | |||
left: 10px; | |||
background-position: 0 -36px; | |||
} | } | ||
.fancybox-next span { | |||
right: 10px; | |||
background-position: 0 -72px; | |||
} | } | ||
. | .fancybox-nav:hover span { | ||
visibility: visible; | |||
} | } | ||
.fancybox-tmp { | |||
position: absolute; | |||
top: -99999px; | |||
left: -99999px; | |||
visibility: hidden; | |||
max-width: 99999px; | |||
max-height: 99999px; | |||
overflow: visible !important; | |||
} | } | ||
/* | |||
. | /* Overlay helper */ | ||
.fancybox-lock { | |||
overflow: hidden !important; | |||
width: auto; | |||
} | } | ||
. | .fancybox-lock body { | ||
overflow: hidden !important; | |||
} | } | ||
. | .fancybox-lock-test { | ||
overflow-y: hidden !important; | |||
} | } | ||
. | .fancybox-overlay { | ||
position: absolute; | |||
top: 0; | |||
left: 0; | |||
overflow: hidden; | |||
display: none; | |||
z-index: 8010; | |||
background: url('http://openwetware.org/images/e/e0/Fancybox_overlay.png'); | |||
} | } | ||
. | .fancybox-overlay-fixed { | ||
position: fixed; | |||
bottom: 0; | |||
right: 0; | |||
} | } | ||
.fancybox-lock .fancybox-overlay { | |||
overflow: auto; | |||
overflow-y: scroll; | |||
} | } | ||
/* | |||
. | /* Title helper */ | ||
.fancybox-title { | |||
visibility: hidden; | |||
font: normal 13px/20px "Helvetica Neue",Helvetica,Arial,sans-serif; | |||
position: relative; | |||
text-shadow: none; | |||
z-index: 8050; | |||
} | } | ||
. | .fancybox-opened .fancybox-title { | ||
visibility: visible; | |||
} | } | ||
. | .fancybox-title-float-wrap { | ||
position: absolute; | |||
bottom: 0; | |||
right: 50%; | |||
margin-bottom: -35px; | |||
z-index: 8050; | |||
text-align: center; | |||
} | } | ||
. | .fancybox-title-float-wrap .child { | ||
display: inline-block; | |||
margin-right: -100%; | |||
padding: 2px 20px; | |||
background: transparent; /* Fallback for web browsers that doesn't support RGBa */ | |||
background: rgba(0, 0, 0, 0.8); | |||
-webkit-border-radius: 15px; | |||
-moz-border-radius: 15px; | |||
border-radius: 15px; | |||
text-shadow: 0 1px 2px #222; | |||
color: #FFF; | |||
font-weight: bold; | |||
line-height: 24px; | |||
white-space: nowrap; | |||
} | } | ||
. | .fancybox-title-outside-wrap { | ||
position: relative; | |||
margin-top: 10px; | |||
color: #fff; | |||
} | } | ||
.fancybox-title-inside-wrap { | |||
padding-top: 10px; | |||
} | } | ||
.fancybox-title-over-wrap { | |||
position: absolute; | |||
bottom: 0; | |||
left: 0; | |||
color: #fff; | |||
padding: 10px; | |||
background: #000; | |||
background: rgba(0, 0, 0, .8); | |||
} | } | ||
/*Retina graphics!*/ | |||
@media only screen and (-webkit-min-device-pixel-ratio: 1.5), | |||
only screen and (min--moz-device-pixel-ratio: 1.5), | |||
} | only screen and (min-device-pixel-ratio: 1.5){ | ||
#fancybox-loading, .fancybox-close, .fancybox-prev span, .fancybox-next span { | |||
background-image: url('http://openwetware.org/images/b/b8/Fancybox_sprite%402x.png'); | |||
background-size: 44px 152px; /*The size of the normal image, half the size of the hi-res image*/ | |||
} | |||
#fancybox-loading div { | |||
background-image: url('http://openwetware.org/images/0/01/Fancybox_loading%402x.gif'); | |||
background-size: 24px 24px; /*The size of the normal image, half the size of the hi-res image*/ | |||
} | |||
} | } | ||
#fancybox-buttons { | |||
position: fixed; | |||
left: 0; | |||
width: 100%; | |||
z-index: 8050; | |||
} | } | ||
. | |||
#fancybox-buttons.top { | |||
top: 10px; | |||
} | } | ||
#fancybox-buttons.bottom { | |||
bottom: 10px; | |||
} | |||
#fancybox-buttons ul { | |||
display: block; | |||
width: 166px; | |||
height: 30px; | |||
margin: 0 auto; | |||
padding: 0; | |||
list-style: none; | |||
border: 1px solid #111; | |||
border-radius: 3px; | |||
-webkit-box-shadow: inset 0 0 0 1px rgba(255,255,255,.05); | |||
-moz-box-shadow: inset 0 0 0 1px rgba(255,255,255,.05); | |||
box-shadow: inset 0 0 0 1px rgba(255,255,255,.05); | |||
background: rgb(50,50,50); | |||
background: -moz-linear-gradient(top, rgb(68,68,68) 0%, rgb(52,52,52) 50%, rgb(41,41,41) 50%, rgb(51,51,51) 100%); | |||
background: -webkit-gradient(linear, left top, left bottom, color-stop(0%,rgb(68,68,68)), color-stop(50%,rgb(52,52,52)), color-stop(50%,rgb(41,41,41)), color-stop(100%,rgb(51,51,51))); | |||
background: -webkit-linear-gradient(top, rgb(68,68,68) 0%,rgb(52,52,52) 50%,rgb(41,41,41) 50%,rgb(51,51,51) 100%); | |||
background: -o-linear-gradient(top, rgb(68,68,68) 0%,rgb(52,52,52) 50%,rgb(41,41,41) 50%,rgb(51,51,51) 100%); | |||
background: -ms-linear-gradient(top, rgb(68,68,68) 0%,rgb(52,52,52) 50%,rgb(41,41,41) 50%,rgb(51,51,51) 100%); | |||
background: linear-gradient(top, rgb(68,68,68) 0%,rgb(52,52,52) 50%,rgb(41,41,41) 50%,rgb(51,51,51) 100%); | |||
filter: progid:DXImageTransform.Microsoft.gradient( startColorstr='#444444', endColorstr='#222222',GradientType=0 ); | |||
} | |||
#fancybox-buttons ul li { | |||
float: left; | |||
margin: 0; | |||
padding: 0; | |||
} | |||
#fancybox-buttons a { | |||
display: block; | |||
width: 30px; | |||
height: 30px; | |||
text-indent: -9999px; | |||
background-color: transparent; | |||
background-image: url('fancybox_buttons.png'); | |||
background-repeat: no-repeat; | |||
outline: none; | outline: none; | ||
opacity: 0.8; | |||
} | } | ||
#fancybox-buttons a:hover { | |||
opacity: 1; | |||
} | } | ||
#fancybox-buttons a.btnPrev { | |||
background-position: 5px 0; | |||
background | |||
} | } | ||
#fancybox-buttons a.btnNext { | |||
background-position: -33px 0; | |||
border-right: 1px solid #3e3e3e; | |||
} | } | ||
#fancybox-buttons a.btnPlay { | |||
- | background-position: 0 -30px; | ||
} | } | ||
#fancybox-buttons a.btnPlayOn { | |||
position: | background-position: -30px -30px; | ||
} | } | ||
#fancybox-buttons a.btnToggle { | |||
background-position: 3px -60px; | |||
border-left: 1px solid #111; | |||
border-right: 1px solid #3e3e3e; | |||
width: 35px | |||
} | } | ||
#fancybox-buttons a.btnToggleOn { | |||
- | background-position: -27px -60px; | ||
} | } | ||
#fancybox-buttons a.btnClose { | |||
border-left: 1px solid #111; | |||
width: 35px; | |||
background-position: -56px 0px; | |||
} | |||
#fancybox-buttons a.btnDisabled { | |||
opacity : 0.4; | |||
cursor: default; | |||
} | } | ||
#fancybox-thumbs { | |||
position: fixed; | |||
left: 0; | |||
width: 100%; | width: 100%; | ||
overflow: hidden; | |||
z-index: 8050; | |||
} | } | ||
#fancybox-thumbs.bottom { | |||
bottom: 2px; | |||
} | } | ||
#fancybox- | #fancybox-thumbs.top { | ||
top: 2px; | |||
} | } | ||
#fancybox- | #fancybox-thumbs ul { | ||
position: | position: relative; | ||
list-style: none; | |||
margin: 0; | |||
padding: 0; | |||
margin | |||
} | } | ||
#fancybox- | #fancybox-thumbs ul li { | ||
float: left; | |||
padding: 1px; | |||
opacity: 0.5; | |||
} | } | ||
#fancybox-thumbs ul li.active { | |||
opacity: 0.75; | |||
padding: 0; | |||
border: 1px solid #fff; | |||
} | } | ||
#fancybox-thumbs ul li:hover { | |||
opacity: 1; | |||
} | } | ||
#fancybox-thumbs ul li a { | |||
display: block; | |||
position: relative; | |||
overflow: hidden; | |||
border: 1px solid #222; | |||
background: #111; | |||
outline: none; | |||
} | } | ||
#fancybox-thumbs ul li img { | |||
display: block; | |||
position: relative; | |||
border: 0; | |||
padding: 0; | |||
max-width: none; | |||
} | } | ||
p.serif { | |||
. | font-family: "Times New Roman", Times, serif; | ||
} | } | ||
.box.b1x3{ | |||
width: 853px; | |||
height: 465px; | |||
} | |||
#b2x2 | |||
{ | |||
position:fixed; | |||
} | |||
#main-nav { | |||
width: 100%; | |||
height: 67px; | |||
background: #f2f2f2; | |||
} | |||
#main-nav .subnav { | |||
display: none; | |||
position: absolute; | |||
top: 67px; | |||
left: 0px; | |||
right:0px; | |||
width: 100%; | |||
list-style-type: none; | |||
background: #f2f2f2; | |||
margin: 0; | |||
border:solid 1px #eeeeee; | |||
z-index:5; | |||
padding:0; | |||
} | } | ||
#main-nav .subnav li { | |||
display: block; | |||
border-bottom: solid 1px #580000; | |||
margin:0; | |||
} | } | ||
#main-nav .subnav li a { | |||
. | color: #333; | ||
height:18px; | |||
font-size:20px; | |||
} | |||
#main-nav .subnav li a:hover { | |||
background:#f9f9f9; | |||
} | } | ||
#nav-primary { | |||
list-style-type: none; | |||
margin: 0; | |||
float: left; | |||
padding:0; | |||
} | } | ||
#nav-primary li { | |||
float: left; | |||
position: relative; | |||
} | } | ||
#nav-primary li a { | |||
float: left; | |||
color: #000; | |||
text-align: center; | |||
font-size: 20px; | |||
height: 40px; | |||
padding-top: 35px; | |||
line-height: 13px; | |||
width:120px; | |||
text-decoration:none; | |||
} | } | ||
#nav-primary li a:hover { | |||
text-decoration:none; | |||
color:#FFCC00; | |||
} | } | ||
#nav-primary li:hover .subnav { | |||
. | display: block; | ||
} | } | ||
</style> | |||
. | </p><p> | ||
<section id="content"> | |||
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<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU"><i class="menu-icon icon-team"></i><span>Main</span></a></li> | |||
<li class = "selected"><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Project"><i class="menu-icon icon-team"></i><span>Project</span></a></li> | |||
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Design"><i class="menu-icon icon-studio"></i><span>Design</span></a></li> | |||
<li><a href="#"><i class="menu-icon icon-studio"></i><span>Experiment</span></a> | |||
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<li><a href = "http://openwetware.org/wiki/Biomod/2014/ASU/Materials"><span>Materials</span></a></li> | |||
<li><a href = "http://openwetware.org/wiki/Biomod/2014/ASU/Protocols"><span>Protocols</span></a></li> | |||
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<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Results"><i class="menu-icon icon-studio"></i><span>Results</span></a></li> | |||
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Discussion"><i class="menu-icon icon-studio"></i><span>Discussion</span></a></li> | |||
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Team"><i class="menu-icon icon-studio"></i><span>Team</span></a></li> | |||
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Acknowledgement"><i class="menu-icon icon-studio"></i><span>Acknowledgements</span></a></li> | |||
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<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Introduction</span></p> | |||
<hr> | |||
<p style = "color: #000000; font-size:18px;">In our project we investigated the creation of a DNA antibody which is able to select and specifically bind to the 3-dimensional surface of a targeted protein of interest. We created this antibody using a flat DNA tile to which 4 aptamers, comprised of random DNA sequences, were attached (see Figure P1).</p><br> | |||
<img src = "http://openwetware.org/images/0/06/Screen_Shot_2014-10-25_at_6.58.06_PM.png"><br> | |||
. | <p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Inspiration</span></p> | ||
<hr> | |||
<p style = "color: #000000;font-size:18px;">Our inspiration is the antibody, the body’s natural means for binding to specific surfaces on the outside of pathogens. The high selectivity and specificity of antibodies that allows them to bind to foreign invaders in vivo also makes them very useful in the lab. Many assays rely on this same selectivity and specificity to identify or target certain proteins. </p> | |||
<p style = "color: #000000;font-size:18px;">We hope to create a new form of antibody made from DNA which is composed of a variable region from which extend strands that cooperatively bind a protein target and a base that orders the orientation of these strands in space.</p><br> | |||
# | |||
# | |||
</ | |||
< | <p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Goals</span></p> | ||
<hr> | |||
<p style = "color: #000000;font-size:18px;">Our goal is to use the power and flexibility of DNA nanotechnology to develop a multivalent binding surface that would mimic natural antibodies. We used alpha-thrombin as our target protein since positive control aptamers are already known (Rinker 2008). We will then move to incorporating random oligonucleotide sequences into the DNA antibody to test the selection process. After showing that DNA antibodies bind a target protein we plan to recover the DNA antibody to sequence the oligonucleotides. We aim to develop a method for creating a DNA structure and a selection method that can be applicable for use for a diverse range of proteins.</p> | |||
<p style = "font-size:18px;">In order to prove the concept for this project we propose a few key targets:</p> | |||
<p style = "color: #000000; font-size: 18px;"> 1. To create a DNA structure suitable for binding a target protein.</p> | |||
<p style = "color: #000000; font-size: 18px;"> 2. To demonstrate DNA antibody binding to protein using positive control DNA strands known to</p> | |||
<p style = "color: #000000; font-size: 18px;"> bind alpha-thrombin.</p> | |||
<p style = "color: #000000; font-size: 18px;"> 3. To demonstrate DNA antibody binding to protein using randomized DNA oligonucleotides.</p> | |||
<p style = "color: #000000; font-size: 18px;"> 4. To demonstrate the recovery of the DNA antibody after binding and the amplification of the randomized </p> | |||
<p style = "color: #000000; font-size: 18px;"> oligonucleotide strands for confirmation by sequencing.</p> | |||
<p style = "color: #000000; font-size: 18px;"> 5. To create a molecular dynamics simulation as a visualization tool for the project.</p><br> | |||
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">References</span></p> | |||
<hr> | |||
<p style = "color: #000000; font-size: 18px;">1) Rinker, S., Ke, Y., Liu, Y. Chhabra, R., Yan, H. Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding. Nature Nanotechnology 3, 418-422 (2008).</p> | |||
</div> | |||
</div> | |||
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<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU"><i class="menu-icon icon-team"></i><span>Main</span></a></li>
<li class = "selected"><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Project"><i class="menu-icon icon-team"></i><span>Project</span></a></li>
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<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Results"><i class="menu-icon icon-studio"></i><span>Results</span></a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Discussion"><i class="menu-icon icon-studio"></i><span>Discussion</span></a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Team"><i class="menu-icon icon-studio"></i><span>Team</span></a></li>
<li><a href="http://openwetware.org/wiki/Biomod/2014/ASU/Acknowledgement"><i class="menu-icon icon-studio"></i><span>Acknowledgements</span></a></li>
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<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Introduction</span></p>
<hr>
<p style = "color: #000000; font-size:18px;">In our project we investigated the creation of a DNA antibody which is able to select and specifically bind to the 3-dimensional surface of a targeted protein of interest. We created this antibody using a flat DNA tile to which 4 aptamers, comprised of random DNA sequences, were attached (see Figure P1).</p><br>
<img src = "http://openwetware.org/images/0/06/Screen_Shot_2014-10-25_at_6.58.06_PM.png"><br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Inspiration</span></p>
<hr>
<p style = "color: #000000;font-size:18px;">Our inspiration is the antibody, the body’s natural means for binding to specific surfaces on the outside of pathogens. The high selectivity and specificity of antibodies that allows them to bind to foreign invaders in vivo also makes them very useful in the lab. Many assays rely on this same selectivity and specificity to identify or target certain proteins. </p>
<p style = "color: #000000;font-size:18px;">We hope to create a new form of antibody made from DNA which is composed of a variable region from which extend strands that cooperatively bind a protein target and a base that orders the orientation of these strands in space.</p><br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">Goals</span></p>
<hr>
<p style = "color: #000000;font-size:18px;">Our goal is to use the power and flexibility of DNA nanotechnology to develop a multivalent binding surface that would mimic natural antibodies. We used alpha-thrombin as our target protein since positive control aptamers are already known (Rinker 2008). We will then move to incorporating random oligonucleotide sequences into the DNA antibody to test the selection process. After showing that DNA antibodies bind a target protein we plan to recover the DNA antibody to sequence the oligonucleotides. We aim to develop a method for creating a DNA structure and a selection method that can be applicable for use for a diverse range of proteins.</p>
<p style = "font-size:18px;">In order to prove the concept for this project we propose a few key targets:</p>
<p style = "color: #000000; font-size: 18px;"> 1. To create a DNA structure suitable for binding a target protein.</p>
<p style = "color: #000000; font-size: 18px;"> 2. To demonstrate DNA antibody binding to protein using positive control DNA strands known to</p>
<p style = "color: #000000; font-size: 18px;"> bind alpha-thrombin.</p>
<p style = "color: #000000; font-size: 18px;"> 3. To demonstrate DNA antibody binding to protein using randomized DNA oligonucleotides.</p>
<p style = "color: #000000; font-size: 18px;"> 4. To demonstrate the recovery of the DNA antibody after binding and the amplification of the randomized </p>
<p style = "color: #000000; font-size: 18px;"> oligonucleotide strands for confirmation by sequencing.</p>
<p style = "color: #000000; font-size: 18px;"> 5. To create a molecular dynamics simulation as a visualization tool for the project.</p><br>
<p class = "serif" style = "color: #000000; font-size: 25px;"><span class = "mw-headline">References</span></p>
<hr>
<p style = "color: #000000; font-size: 18px;">1) Rinker, S., Ke, Y., Liu, Y. Chhabra, R., Yan, H. Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding. Nature Nanotechnology 3, 418-422 (2008).</p>
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