Biomod/2013/OSU/protocol: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
(New page: {{OhioMOD2013}} <html> <div id="protocol" style="width:65%;margin-left:auto;margin-right:auto;"> <h2>Protocol</h2> <ul> <li>E. Coli bacteria is given “scaffold” virus which allows the...)
 
No edit summary
Line 2: Line 2:


<html>
<html>
<div id="protocol" style="width:65%;margin-left:auto;margin-right:auto;">
<div id="protocol-links" style="width:65%;margin-left:auto;margin-right:auto;">
<h2>Protocol</h2>
<ul>
<ul>
<li>E. Coli bacteria is given “scaffold” virus which allows the bacteria to multiply scaffold virus while growing itself</li>
<li><a href="#">Folding Reaction</a></li>
<li>CADnano is used to design shape and used to determine what staples must be ordered to obtain desired shape</li>
<li><a href="#">Gel Preparation</a></li>
<li>The staples are organized and collected into “pre-stocks”</li>
<li><a href="#">Negative Staining for TEM</a></li>
<li>“Pre-stocks” are combined into working stocks</li>
<li><a href="#">Preparing Custom Grids for TEM</a></li>
<li>The staples are mixed with the scaffolds in high ion solution and placed in thermal ramp</li>
<li><a href="#">PEG Purification</a></li>
<li>After thermal ramp, the now folded structures are ran through an agarose gel with EtBr for purification</li>
<li><a href="#">Atomic Force Microscopy</a></li>
<li>The purified structures are cut from the gel</li>
<li>The structures are then mixed with 2 mM daunorubicin and incubated for 40 hours</li>
<li>The solution is then centrifuged and the precipitate is re-suspended in a PBS solution with 10 mM MgCl¬2</li>
<li>The absorbance of the supernatant is then measured on a plate reader to determine the concentration of daunorubicin.</li>
<li>The suspension with the structures is then diluted with cell medium to have various concentrations</li>
<li>This is then added to the resistant cells</li>
<li>After 12 hours, the structures are then washed with PBS to remove Daunorubicin and the structures</li>
<li>Next the cells are incubated for 48 hours in after which they are added to an imaging plate and observed using the TIRF microscope</li>
<li>Brightfield microscope images are taken in addition to 640 nm wavelength images to visualize dead cells (7-AAD dye)</li>
<li>The number of live/dead cells can be determined from these images</li>
<li>Additionally cell viability is investigated by placing structures with cells in a 96 well plate</li>
<li>The same procedure is followed, except after the 48 hour incubation, a MTT assay is run</li>
<li>This involves adding MTT solution (5 mg/mL) and then reading absorbance on a plate reader to quantify cell viability</li>
</ul>
</ul>
</div>
</div>
</html>
</html>

Revision as of 20:04, 6 October 2013


<html> </div> </div> </div> <head> <style type='text/css'>

.firstHeading, #column-one, #p-bookmarks, #p-history , .portlet{ display:none; }

  1. bodyContent, #content{

display:none; background-color:#FFFFFF;

}

  1. column-content, .container, #globalWrapper, body{

background-color:#FFFFFF; }

p{ color:dimgrey; text-align:center; margin-left:auto; margin-right:auto; font-gamily:Calibri; font-size: 15px; }

.selflink{ display: table-cell; 

  text-decoration: none;
  font-family: Gill Sans MT;
  outline: none;
  font-size: 20px;
  color: dimgrey;
  border-right: 2px solid dimgray;
  padding: 15px 25px; /* sets button size */
  font-weight:normal;

}

ul.navigation-bar { 

  list-style-type: none;
  border: 2px solid dimgray;
  padding: 0px;
  margin-left: 20px;

width:615px; 

  *line-height: 3.2em; /* IE6,IE7 */
  }

ul.navigation-bar li { 

  display: table-cell;

  background-image: -webkit-linear-gradient(bottom, silver, azure);
  background-image:    -moz-linear-gradient(bottom, silver, azure);
  background-image:     -ms-linear-gradient(bottom, silver, azure);
  background-image:         linear-gradient(bottom, silver, azure);
  background-color: midnightblue; /* IE6...IE9 */
  *display: inline; /* IE6,IE7 */

  }


ul.navigation-bar li:hover { 

  background-image: -webkit-linear-gradient(top, silver, azure);
  background-image:    -moz-linear-gradient(top, silver, azure);
  background-image:     -ms-linear-gradient(top, silver, azure);
  background-image:         linear-gradient(top, silver, azure);

}

ul.navigation-bar li a, ul.navigation-bar li ul li a { 

  display: table-cell;
  text-decoration: none;
  font-family: Gill Sans MT;
  outline: none;
  font-size: 20px;
  color: dimgrey;
  border-right: 0px;
  padding: 15px 25px; /* sets button size */
  }

ul.navigation-bar li ul{ list-style: none; display: none; position: absolute; padding: 0px; margin: 1px 0px 0px -1px; background-color:#FFFFFF; border: 1px solid dimgrey; z-index:5; } ul.navigation-bar li ul li{ background-image: none; background-color:#FFFFFF; border-right: none; border: 0px solid dimgray; display: block; float: none; position: relative; }

ul.navigation-bar li ul li:hover{ background-image:none; background-color: lightgrey; }

ul.navigation-bar li:hover ul{ list-style: none; display: block; position: absolute; }

ul.navigation-bar li a{ display: block; }

.profile-right{ clear:both; }

.profile-right p{ text-align:left; float: left; } .profile-right img{ float: right; padding: 20px; }

.profile-left{ clear:both; }

.profile-left p{ text-align:left; float:left; }

.profile-left img{ float: left; padding:20px; }

  1. OSUfooter{

clear:both; }


  1. protocol-content table td{

border: 1px solid black; text-align:center; }

  1. protocol-content p{

text-align:left; }

.overlay-bg{ display:none; position:fixed; top:0; left:0; height:100%; width:100%; cursor: pointer; background: #000; background: rgba(0,0,0,0.75); }

.overlay-content{ background:#fff; padding:1%; width: 60%; position: relative; top:15%; left:50%; margin: 0 0 0 -30%; cursor: default; -webkit-border-radius: 5px; -moz-border-radius: 5px; border-radius: 5px; box-shadow: 0 0 5px rgba(0,0,0,0.9);

}

.close-btn{ float:right; font-size:x-large; margin-top:-10px; }

</style>


<script src="//ajax.googleapis.com/ajax/libs/jquery/1.10.1/jquery.min.js"></script>

<script type="text/javascript"> $(document).ready(function() { 

 $('.show-popup').click(function(event){
 event.preventDefault();
 $('.overlay-bg').show();

});

$('.close-btn').click(function(){ $('.overlay-bg').hide(); });

$('.overlay-bg').click(function(){ 

 $('.overlay-bg').hide();

});

$('.overlay-content').click(function(){ return false; });

}); </script>

</head>

<!-- navbar -->

<a href="http://openwetware.org/wiki/Biomod/2013"> << Back to Team Pages</a>

<center>

<img src="http://openwetware.org/images/1/15/Ohiomod2013.jpg" height="60%" width="60%" style="margin-left:-40px;"> <div id="navbar" style="margin-left:auto; margin-right:auto;text-align:center;width:650px;height:auto;" > <ul id="homebutton" class="navigation-bar"> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU">Home</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/about">About</a> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/abstract">Abstract</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/goals">Goals</a></li>

<li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/about">Description</a> </ul> </li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/experiments">Project</a> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/experiments">Life of Project</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/protocol">Protocols</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/labnotes">Lab Notes</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/meetingnotes">Meeting Notes</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/resources">Resources</a></li> </ul> </li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/results">Results</a> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/results">Experimental Results</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/data">Data</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/futurework">Future Work</a></li> </li> </ul> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/media">Media</a> <ul> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/projectvideo">Project Video</a><li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/animations">Animations</a><li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/videoblogs">Video Blog</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/photos">Photos</a></li> </ul> </li> <li><a href="http://openwetware.org/wiki/Biomod/2013/OSU/team">Team</a></li> </ul>

</div>

</center> </html>

<html> <div id="protocol-links" style="width:65%;margin-left:auto;margin-right:auto;"> <ul> <li><a href="#">Folding Reaction</a></li> <li><a href="#">Gel Preparation</a></li> <li><a href="#">Negative Staining for TEM</a></li> <li><a href="#">Preparing Custom Grids for TEM</a></li> <li><a href="#">PEG Purification</a></li> <li><a href="#">Atomic Force Microscopy</a></li> </ul> </div> </html>


<html>

<head> <style>

  1. Footer table {
  width: 96.8%;
  max-width:2350px;
  bottom:0px;
  height:50px;   /* Height of the footer */
  font-weight:300;
  background-color: #2E2E2E;
   text-align:center;
   color: white;
   font-size:13px;
   border: 3px white solid;

}

  1. Footer {
   clear: both; /*may be omitted*/
   position: absolute;
   bottom: 12px; 
   background-color:#fffff;
   width: 100%;
   height: 40px; /* or anything you like */
}


</style> </head> <div id="Footer" > 

       <table>
           <tr>

<td id="osuicon" align="left"><a href="http://www.osu.edu" target="_blank"><img src="http://openwetware.org/images/c/cd/TheOhioStateUniversity-REV-Horiz-RGBHEX.png"height="30" width="190" /></td>

<td id="email">Contact us at <a href="mailto:theohiomod@gmail.com"><font color="white">theohiomod@gmail.com</a></td>

<td id="nblicon"><a href="http://mae.osu.edu/labs/nbl/"target="_blank"><img src="http://openwetware.org/images/e/e9/NBL_logo-RGBHEX.png"height="40" width="40"/></td>

<td id="fbicon"><a href="http://www.facebook.com/OhioMod?fref=photo"target="_blank"><img src="http://openwetware.org/images/3/3f/Facebook_icon.png"height="40" width="40"/></td> 

           </tr>
       </table>
   </div>

</html> Edit

Retrieved from "https://openwetware.org/mediawiki/index.php?title=Biomod/2013/OSU/protocol&oldid=735589"