OpenWetWare:Getting started: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
No edit summary
(188 intermediate revisions by more than 100 users not shown)
Line 1: Line 1:
Thanks for using OpenWetWare.  Here are a few tips on getting started.
{{OhioMOD2014}}


#The most important thing to know is that every change is tracked and easily reverted.  Because of this, you should feel free to edit as much as possible.  One good way to start editing is by looking at the code of any page, like [http://openwetware.org/index.php?title=OpenWetWare:Getting_started&action=edit this one] (remember to log in).  Click on the [[Help:Contents|help]] link on the navigation bar to your left to get more info on editing options.  You can also look at the history of any page, by clicking on the history tab above.  This will show every edit that every user made. Afraid to try things out on a real page? Check out the [[Sandbox]] to play around.
<html>
#The wiki is a great place to put a public lab homepage.  For example, the Endy lab webpage ([http://web.mit.edu/endy http://web.mit.edu/endy]) points directly to a page on openwetware.  Information about the lab, such as the [[Endy:Research|research page]], can be posted and edited by everybody in the lab. The navigation bar, such as the [[Template:EndyLab|one]] on the Endy research page, is useful for traversing through webpages within the site.
<head>
#Labs can also uses the wiki for a number of lab internal functions. In the [[Endy:Back Door|Endy internal site]], they post information on their [[Endy:Lab Meetings|lab meetings]], [[Endy:2005 Summer Retreat|retreats]], [[Endy:Lab Chores|lab chores]], [[Endy:Lab Supplies|ordering]], etc.
<!--css stuff begins here-->
#Sharing the same wiki between multiple labs enables community pages, such as those listed in the Shared Technical Resources section of the [[Main Page]]. Check out the [[Equipment|equipment]] and [[Protocols|protocols]].
<style>
#*In particular, the [[Endy:Victor3 plate reader|plate reader]] is a good example. It includes useful information about [[Endy:Victor3 plate variation|plate variation]], [[Endy:Victor3 lamp energy|lamp energy]], and [[Endy:Victor3 absorbance labels|absorbance levels]].  
center {padding-bottom:50px;}
#*Each lab has their own way of doing particular protocols. Typically a lab will have a list of lab-specific [[Sauer Lab#Protocols|protocols]]. However, we are also collecting protocols from multiple labs in the shared [[Protocols|protocols]] area. A good example is [[DNA Ligation]] which provides links to the [[Endy:DNA ligation using T4 DNA ligase|Endy]] and [[Knight:DNA ligation using NEB Quick Ligation Kit|Knight]] lab protocols.
/*Aligning the Logo*/
#logo {
  width: 700px ;
  margin-left: auto ;
  margin-right: auto ;
}
 
/*Aligning the Video*/
#video {
  width: 700px ;
  margin-left: auto ;
  margin-right: auto ;
}
 
/*Aligning the Abstract*/
#abstract {
  width: 700px ;
  margin-left: auto ;
  margin-right: auto ;
}
 
/*fixed icon code start*/
#fixedbutton {
    position: fixed;
    bottom: 53px;
    right: 10px; }
/*fixed icon code end*/
 
 
</style>
<!--css stuff ends here-->
</head>
<body>
<div id="logo">
<img src="http://openwetware.org/images/e/ed/OHIOMODLOGO2.png" alt="OhioMOD">
<iframe src="//www.facebook.com/plugins/like.php?href=https%3A%2F%2Fwww.facebook.com%2FOhioMod&amp;width&amp;layout=standard&amp;action=like&amp;show_faces=true&amp;share=true&amp;height=80" scrolling="no" frameborder="0" style="border:none; overflow:hidden; height:80px;" allowTransparency="true"></iframe>
</div>
<div id="abstract">
<h1>Welcome to OhioMOD</h1>
<p1>OhioMOD is Ohio State's undergraduate biomolecular design team.  The team participates in the BIOMOD international competition each year at Harvard University.  The 2014 project will use a folded DNA structure to control miRNA gene regulation in cancer.</p1>
<h1>Abstract</h1>
<p2>MicroRNAs (miRs) are short, non-coding RNAs that regulate gene expression and control essential cellular processes, such as cell cycle progression and apoptosis, through interactions with messenger RNA. Dysregulation of miR expression levels can promote tumorigenesis either by elevating oncogene or silencing tumor suppressor gene levels implicating miRs as an attractive therapeutic target. One therapeutic approach is to decrease levels of miRs that target tumor suppressor genes such as PTEN to ultimately promote apoptosis by complementary base pair antagonism via antisense DNA, but limitations exist in regard to antisense DNA cellular delivery. A previous study demonstrated that DNA nanostructures functionalized with small interfering RNA (siRNA) underwent efficient cellular entry and executed targeted gene suppression suggesting strong potential for DNA nanostructures as a nucleotide delivery vehicle. Here, we report the fabrication of a rod-like
and a block-like DNA nanostructure incorporated with DNA overhangs capable of binding and sequestering miR-21, a PTEN targeting miR that is overexpressed in a variety of malignancies including chronic lymphocytic leukemia (CLL). Proper assembly was confirmed via gel electrophoresis and transmission electron microscopy. Incorporation and functionality of DNA overhangs complementary for miR-21 was confirmed via fluorescent gel imaging. In addition, DNA nanostructures were shown to enter the endolysosomal pathway as revealed via fluorescent microscopy. Furthermore, miR-21 complementary DNA overhang functionalized structures induced marked decreases in OSU-CLL cell viability relative to scrambled control overhang nanostructures as shown via fluorescent microscopy. Future work will directly investigate expression levels of PTEN mRNA and protein using quantitative real time PCR and immunoblot analysis respectively. Our current findings suggest that the complementary miR-21 DNA overhang functionalized DNA nanostructures effectively sequester miR-21 to induce cytotoxicity in OSU-CLL cells. Our results represent a promising antisense DNA delivery therapeutic approach in a CLL leukemia model with implications to a variety of human malignancies.</p2>
<h1>Project Video</h1>
<br>
</div>
<div id="video">
<center>
<iframe width="660" height="415" src="//www.youtube.com/embed/OzRtxW4YK2c" frameborder="0" allowfullscreen></iframe>
</center>
 
<A HREF="#top"><img src="http://openwetware.org/images/4/46/Arrow_up.png" id="fixedbutton"height="40" width="40"></A>
</br><a href="http://openwetware.org/index.php?title=Biomod/2014/OhioMOD&action=edit">Edit Main Page</a>
 
<a href="http://info.flagcounter.com/4FJ3"><img src="http://s06.flagcounter.com/count/4FJ3/bg_FFFFFF/txt_000000/border_CCCCCC/columns_8/maxflags_12/viewers_3/labels_1/pageviews_1/flags_0/" alt="Flag Counter" border="0"></a>
</div>
 
</body>
</html>
 
{{OSUFooter}}
{{OpenWetWare:Getting started/Introduction}} <!-- PLEASE DO NOT MAKE EDITS TO THIS PAGE! If you would like to make test edits, please refer here: http://openwetware.org/wiki/Sandbox -->

Revision as of 14:34, 10 August 2015

<html> <head> <script src="http://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script> <!-- Latest compiled css and JavaScript --> <script src="http://maxcdn.bootstrapcdn.com/bootstrap/3.2.0/js/bootstrap.min.js"></script> <!--j--query--> <!--Nav Bar Theme--> <link href="http://maxcdn.bootstrapcdn.com/bootswatch/3.2.0/yeti/bootstrap.min.css" rel="stylesheet"> <style>

  1. content{margin-left:0;}

.navbar{ top:8.5px; position:fixed; width:96.8%; } /*clearing the side openwetware panels*/ .firstHeading, #column-one, #p-bookmarks, #p-history , .portlet{ display:none; }

  1. bodyContent/*clearing the side openwetware panels

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

  1. content#bodyContent, {

/*display:none;*/ background-color:#FFFFFF; }

  1. OSUfooter{

clear:both; }

  1. footer{display: none;}

/*Done clearing*/




</style>

</head>




<!--Nav--> <div class="navbar navbar-default"> 

 <div class="navbar-header">
   <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-responsive-collapse">
     <span class="icon-bar"></span>
     <span class="icon-bar"></span>
     <span class="icon-bar"></span>
   </button>
   <a class="navbar-brand" href="http://openwetware.org/wiki/Biomod/2014/OhioMOD">OhioMOD</a>
 </div>
 <div class="navbar-collapse collapse navbar-responsive-collapse">
   <ul class="nav navbar-nav">
     <li ><a href="http://openwetware.org/wiki/Biomod/2014/OhioMOD">Home</a></li>
     <li><a href="http://openwetware.org/wiki/Biomod/2014/OhioMOD/project">Background</a></li>

<li><a href="http://openwetware.org/wiki/Biomod/2014/OhioMOD/results">Project and Results</a></li>

<li class="dropdown"> 

       <a href="#" class="dropdown-toggle" data-toggle="dropdown">Materials and Methods <b class="caret"></b></a>
       <ul class="dropdown-menu">
         <li><a href="http://openwetware.org/wiki/Biomod/2014/OhioMOD/protocols">Protocols</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2014/OhioMOD/equipment">Equipment</a></li>
         <li class="divider"></li>
         <li class="dropdown-header">Lab Notebook</li>
         <li><a href="http://openwetware.org/wiki/Biomod/2014/OhioMOD/LabNotebook">Experiment Schedule</a></li>
         <li><a href="http://openwetware.org/wiki/Biomod/2014/OhioMOD/experimentnotes">Experiment Notes</a></li>
       </ul>
     </li>

<li><a href="http://openwetware.org/wiki/Biomod/2014/OhioMOD/team">Team</a></li> <li><a href="http://openwetware.org/wiki/Biomod/2014/OhioMOD/sponsors">Acknowledgement</a></li> <li><a href="http://www.giveto.osu.edu/igive/OnlineGiving/fund_results.aspx?fund=314139" target="_blank">Give To OhioMOD</a></li> 

   </ul>
 </div>

</div> <!--Nav Bar Done-->

</html>

<html> <head> <!--css stuff begins here--> <style> center {padding-bottom:50px;} /*Aligning the Logo*/

  1. logo {
 width: 700px ;
 margin-left: auto ;
 margin-right: auto ;

}

/*Aligning the Video*/

  1. video {
 width: 700px ;
 margin-left: auto ;
 margin-right: auto ;

}

/*Aligning the Abstract*/

  1. abstract {
 width: 700px ;
 margin-left: auto ;
 margin-right: auto ;

}

/*fixed icon code start*/

  1. fixedbutton {
   position: fixed;
   bottom: 53px;
   right: 10px; }

/*fixed icon code end*/


</style> <!--css stuff ends here--> </head> <body> <div id="logo"> <img src="http://openwetware.org/images/e/ed/OHIOMODLOGO2.png" alt="OhioMOD"> <iframe src="//www.facebook.com/plugins/like.php?href=https%3A%2F%2Fwww.facebook.com%2FOhioMod&amp;width&amp;layout=standard&amp;action=like&amp;show_faces=true&amp;share=true&amp;height=80" scrolling="no" frameborder="0" style="border:none; overflow:hidden; height:80px;" allowTransparency="true"></iframe> </div> <div id="abstract"> <h1>Welcome to OhioMOD</h1> <p1>OhioMOD is Ohio State's undergraduate biomolecular design team. The team participates in the BIOMOD international competition each year at Harvard University. The 2014 project will use a folded DNA structure to control miRNA gene regulation in cancer.</p1> <h1>Abstract</h1> <p2>MicroRNAs (miRs) are short, non-coding RNAs that regulate gene expression and control essential cellular processes, such as cell cycle progression and apoptosis, through interactions with messenger RNA. Dysregulation of miR expression levels can promote tumorigenesis either by elevating oncogene or silencing tumor suppressor gene levels implicating miRs as an attractive therapeutic target. One therapeutic approach is to decrease levels of miRs that target tumor suppressor genes such as PTEN to ultimately promote apoptosis by complementary base pair antagonism via antisense DNA, but limitations exist in regard to antisense DNA cellular delivery. A previous study demonstrated that DNA nanostructures functionalized with small interfering RNA (siRNA) underwent efficient cellular entry and executed targeted gene suppression suggesting strong potential for DNA nanostructures as a nucleotide delivery vehicle. Here, we report the fabrication of a rod-like and a block-like DNA nanostructure incorporated with DNA overhangs capable of binding and sequestering miR-21, a PTEN targeting miR that is overexpressed in a variety of malignancies including chronic lymphocytic leukemia (CLL). Proper assembly was confirmed via gel electrophoresis and transmission electron microscopy. Incorporation and functionality of DNA overhangs complementary for miR-21 was confirmed via fluorescent gel imaging. In addition, DNA nanostructures were shown to enter the endolysosomal pathway as revealed via fluorescent microscopy. Furthermore, miR-21 complementary DNA overhang functionalized structures induced marked decreases in OSU-CLL cell viability relative to scrambled control overhang nanostructures as shown via fluorescent microscopy. Future work will directly investigate expression levels of PTEN mRNA and protein using quantitative real time PCR and immunoblot analysis respectively. Our current findings suggest that the complementary miR-21 DNA overhang functionalized DNA nanostructures effectively sequester miR-21 to induce cytotoxicity in OSU-CLL cells. Our results represent a promising antisense DNA delivery therapeutic approach in a CLL leukemia model with implications to a variety of human malignancies.</p2> <h1>Project Video</h1> <br> </div> <div id="video"> <center> <iframe width="660" height="415" src="//www.youtube.com/embed/OzRtxW4YK2c" frameborder="0" allowfullscreen></iframe> </center>

<A HREF="#top"><img src="http://openwetware.org/images/4/46/Arrow_up.png" id="fixedbutton"height="40" width="40"></A> </br><a href="http://openwetware.org/index.php?title=Biomod/2014/OhioMOD&action=edit">Edit Main Page</a>

<a href="http://info.flagcounter.com/4FJ3"><img src="http://s06.flagcounter.com/count/4FJ3/bg_FFFFFF/txt_000000/border_CCCCCC/columns_8/maxflags_12/viewers_3/labels_1/pageviews_1/flags_0/" alt="Flag Counter" border="0"></a> </div>

</body> </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>

What is OpenWetWare?

OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. Lots of people are constantly improving OpenWetWare, making frequent changes, all of which are recorded on article histories and recent changes.

The first step, if you haven't done so already, is to set up a user account so you can edit pages.

How can I help?

Click edit to change an article

Don't be afraid to edit—anyone can edit almost any page, and we encourage you to be bold (but please don't vandalize)! Find something that can be improved, either in content, grammar or formatting, and fix it.

You can't break OpenWetWare. Anything can be fixed or improved later. So go ahead, edit an article and help make OpenWetWare the best information source on the Internet!

Make your first edit right now:

  1. Click above
  2. Type a message
  3. Click to save your writing

...or to test your changes



Test edits...

Retrieved from "https://openwetware.org/mediawiki/index.php?title=OpenWetWare:Getting_started&oldid=896208"