Difference between revisions of "Team:Utrecht/Placeholder"

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    <title>iGEM UTRECHT Placeholder Page</title>
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<link href="https://fonts.googleapis.com/css?family=Signika" rel="stylesheet">
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<link href="https://fonts.googleapis.com/css?family=Acme" rel="stylesheet">
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<link href="https://fonts.googleapis.com/css?family=Acme|Pontano+Sans" rel="stylesheet"> 
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body{background-color: #c4e3ed }
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page_title{font-family:'Signika',sans-serif; font-size: 40px}
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project_title{font-family:'Acme',sans-serif; font-size: 60px}
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div.sec0{float:left; width:100%;font-family:'Pontano Sans',sans-serif; font-size:16px ; text-align: justify; padding:10px}
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div.sec1{float:left; width:25%; box-sizing: border-box;font-family: 'Pontano Sans',sans-serif; font-size:14px ; text-align: justify; padding: 10px}
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div.sectitle{font-family:'Acme',sans-serif; font-size:16px ; text-align: center; padding: 10px}
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  <body>
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<h1> Welcome to PLACEHOLDER UTRECHT</h1>
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<p>Your team has been approved and you are ready to start the iGEM season! </p>
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  <section style="max-width:700px; margin: auto">
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</div>  
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<div style="padding:20px; text-align:center">
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<div style="float: left; width:25%">
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<div class="clear"></div>
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<img src="https://static.igem.org/mediawiki/2017/7/7f/IGEM_Utrecht_logo_svg.svg" style="vertical-align: middle; height:200"/>
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<div class="column half_size" >
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<div style="width: 75%; vertical-align: middle">
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<h5>Before you start: </h5>
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<page_title> University 2017<br></page_title>
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<p> Please read the following pages:</p>
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<project_title>OUTCASST</project_title>
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<ul>
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</div>
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<li> <a href="https://2017.igem.org/Competition">Competition Hub</a> </li>
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</div>
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<li> <a href="https://2017.igem.org/Competition/Deliverables/Wiki">Wiki Requirements page</a></li>
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<div clear="all"></div>
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<li> <a href="https://2017.igem.org/Resources/Template_Documentation">Template documentation</a></li>
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</ul>
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<div style="text-align:center; color:#0000ff; font-size: 16px">Important note: This is a placeholder page and will be replaced in due time!</div>
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</div>
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<div style="text-align:center">
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<project_subtitle><br>OUT-of-cell CRISPR Activated Sequence-specific Signal Transducer</project_subtitle>
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<div class="column half_size" >
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<div class="sec0">
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<div class="highlight">
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  The OUTCASST sensor consist of two proteins, both expressed to the membrane of a mammalian HEK 293 cell.
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<h5> Styling your wiki </h5>
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  The first protein connects dCas9, a catalytically dead Cas9 variant, to a transmembrane domain and an intracellular transcription factor.
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<p>You may style this page as you like or you can simply leave the style as it is. You can easily keep the styling and edit the content of these default wiki pages with your project information and completely fulfill the requirement to document your project.</p>
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  The second protein connects dCpf1 to an intracellular protease. When provided with appropriate guide RNA's, the two proteins can bind to a DNA sequence.
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<p>While you may not win Best Wiki with this styling, your team is still eligible for all other awards. This default wiki meets the requirements, it improves navigability and ease of use for visitors, and you should not feel it is necessary to style beyond what has been provided.</p>
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  When one sequence brings the two proteins together, the transcription factor is released into the cytoplasm, and can activate a reporter cascade.
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</div>
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  See the scheme below for details.
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</div>
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</div>
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<img class=makefit src="https://static.igem.org/mediawiki/2017/3/3b/Figure2-v3.png" align="middle" />
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<div class="column full_size" >
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    </div>
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<h5> Wiki template information </h5>
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<p>We have created these wiki template pages to help you get started and to help you think about how your team will be evaluated. You can find a list of all the pages tied to awards here at the <a href="https://2017.igem.org/Judging/Pages_for_Awards">Pages for awards</a> link. You must edit these pages to be evaluated for medals and awards, but ultimately the design, layout, style and all other elements of your team wiki is up to you!</p>
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<section style="position: relative; width: 100%; margin-top:5px; margin-bottom:20px; padding: 0;">
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</div>  
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<div class="sec1">
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  <div class="sectitle"><b>1. Guide RNA binding:</b></div>
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  The two proteins float around freely in the membrane. Two types of guide RNA (gRNA) can be added to the cells.
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  Due to the different recognition sequences for the two proteins, the gRNA can bind specifically to the appropriate protein.
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</div>
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<div class="column half_size" >
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<h5> Editing your wiki </h5>
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<div class="sec1">
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<p>On this page you can document your project, introduce your team members, document your progress and share your iGEM experience with the rest of the world! </p>  
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  <div class="sectitle"><b>2. DNA sample addition:</b></div>
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<p> <a href="https://2017.igem.org/wiki/index.php?title=Team:Example&action=edit"> </a>Use WikiTools - Edit in the black menu bar to edit this page</p>
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  Now that the guide RNA's have been bound, both proteins are primed to bind to a specific sequence of a DNA strand.
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  A DNA sample from any source can be added and will then be bound by the protein with the guide RNA that is complementary to one of the DNA strands.
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</div>
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</div>
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<div class="sec1">
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<div class="column half_size" >
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  <div class="sectitle"><b>3. Sequence recognition:</b></div>
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<h5>Tips</h5>
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  One of the proteins has bound a DNA stretch in the sample.  
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<p>This wiki will be your team’s first interaction with the rest of the world, so here are a few tips to help you get started: </p>
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  If the other protein is bound to a guide RNA that is complementary to a sequence on the same stretch, it too will bind.
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<ul>
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</div>
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<li>State your accomplishments! Tell people what you have achieved from the start. </li>
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<li>Be clear about what you are doing and how you plan to do this.</li>
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<div class="sec1">
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<li>You have a global audience! Consider the different backgrounds that your users come from.</li>
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  <div class="sectitle"><b>4. Co-localization & cleavage:</b></div>
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<li>Make sure information is easy to find; nothing should be more than 3 clicks away.  </li>
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  If the second protein also binds the DNA, close enough to the other protein, the protease at the end of one will be able to cleave the transcription factor from the other protein.
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<li>Avoid using very small fonts and low contrast colors; information should be easy to read.  </li>
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  The transcription factor is then free to induce a reporter mechanism. In our case, this will be a fluorescent marker.
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<li>Start documenting your project as early as possible; don’t leave anything to the last minute before the Wiki Freeze. For a complete list of deadlines visit the <a href="https://2017.igem.org/Calendar">iGEM 2017 calendar</a> </li>
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</div>
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<li>Have lots of fun! </li>
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<div style="clear: both;"></div>
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</ul>  
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</div>
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<div style="text-align:center">
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<project_subtitle><br>Applications of the OUTCASST system:</project_subtitle>
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<div class="sec0">
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<div class="column half_size" >
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  So far, our team has not yet decided on a specific application of the system as there are many different fields wherein
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<h5>Inspiration</h5>
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  sequence-specific detection is of use. Right now, most DNA detection is done by Polymerase Chain Reaction (PCR) and sequencing
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<p> You can also view other team wikis for inspiration! Here are some examples:</p>
+
  techniques. These techniques rely on materials and machinery that are not available to everyone. The OUTCASST system, being
−
<ul>
+
  cell-based, culturable and thus renewable, could provide a quick and easy detection tool that does not require an expensive
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<li> <a href="https://2014.igem.org/Team:SDU-Denmark/"> 2014 SDU Denmark </a> </li>
+
  lab-setup. It only requires medium to culture the cells and the gRNA that is specific to the sequence that you want to detect.
−
<li> <a href="https://2014.igem.org/Team:Aalto-Helsinki">2014 Aalto-Helsinki</a> </li>
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  Right now, we are interviewing potential end-users to figure out what type of applications they see for our concept and to
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<li> <a href="https://2014.igem.org/Team:LMU-Munich">2014 LMU-Munich</a> </li>
+
  assess what features they wish to see in our design. So far, we have identified four possible applications for our tool:
−
<li> <a href="https://2014.igem.org/Team:Michigan"> 2014 Michigan</a></li>
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</div>
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<li> <a href="https://2014.igem.org/Team:ITESM-Guadalajara">2014 ITESM-Guadalajara </a></li>
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    </div>
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<li> <a href="https://2014.igem.org/Team:SCU-China"> 2014 SCU-China </a></li>
+
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</ul>
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</div>
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<section style="position: relative; width: 100%; margin-top:5px; margin-bottom:20px; padding: 0;">
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<div class="sec2">
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<div class="column half_size" >
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  <img src="https://2017.igem.org/wiki/images/1/1d/Baby_icon.svg" width=100px style="display:block; margin: auto">
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<h5> Uploading pictures and files </h5>
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  <div class="sectitle"><b>Prenatal Genotyping:</b></div>
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<p> You can upload your pictures and files to the iGEM 2017 server. Remember to keep all your pictures and files within your team's namespace or at least include your team's name in the file name. <br />
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  Small quantities of cell-free embryo DNA is present in the maternal peripheral blood, already early in pregnancy
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When you upload, set the "Destination Filename" to <br><code>T--YourOfficialTeamName--NameOfFile.jpg</code>. (If you don't do this, someone else might upload a different file with the same "Destination Filename", and your file would be erased!)<br><br>
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  <a target="_tab" href="http://www.sciencedirect.com/science/article/pii/S0140673689919697">(Lo et al., 1989)</a>.
−
 
+
  The detection of child-mutations by taking a serum sample from its mother reduces the risk to the unborn child. Such
−
<a href="https://2017.igem.org/Special:Upload">
+
  mutation calling is currently done by sequencing, which faces technological limitations when confronted with low sample
−
UPLOAD FILES
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  concentrations, and subsequent genotyping using bioinformatics pipelines, a process that takes days, if not weeks. We aim to create
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</a>
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  the possibility to detect specific mutations in a matter of hours, cheaply.
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</p>
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</div>
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</div>
+
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<div class="sec2">
−
 
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  <img src="https://2017.igem.org/wiki/images/1/1d/Baby_icon.svg" width=100px style="display:block; margin: auto">
−
 
+
  <div class="sectitle"><b>Pathogen Detection:</b></div>
−
 
+
  Cell-free pathogen DNA can also be sampled from a patient's serum
−
 
+
  <a target="_tab" href="https://academic.oup.com/jid/article-abstract/170/2/436/893837">(Gan et al., 1994)</a>. Again,
−
 
+
  the aim of our design is to speed up the process of diagnosis. With one batch of our organism, multiple tests can be
−
 
+
  done. By adding a small sample of our organism to each well in a 96-well plate and then adding a different subset of
 +
  gRNA sequences to each well, you could test for 96 separate pathogens. Such tests could speed up the diagnostics time
 +
  in medical labs. The sensor could even be shipped to general practitioners themselves, making more precise diagnoses
 +
  in the doctor's office possible.
 +
</div>
 +
 +
<div class="sec2">
 +
  <img src="https://2017.igem.org/wiki/images/1/1d/Baby_icon.svg" width=100px style="display:block; margin: auto">
 +
  <div class="sectitle"><b>Cancer Screening</b></div>
 +
  Cancer is becoming an increasingly important disease. Luckily, it too produces cell-free DNA that can be found in the
 +
  serum of a patient (
 +
  <a target="_tab" href="http://cancerres.aacrjournals.org/content/61/4/1659.short">(Schwarzenbach et al., 2011)</a>.
 +
  By designing gRNA that is complementary to known oncogenes, the presence of these genes in a sample thus means that the
 +
  mutation is present in the patient. Depending on the reporter plasmid, the signal intensity can depend on the amount of
 +
  dimerization and thus the amount of recognised sequence. Since the concentration of cell-free DNA depends on the growth
 +
  of the tumor, this concentration can, theoretically, be used for monitoring of the disease.
 +
</div>
 +
</div>
 +
 +
<div class="sec0" style="text-align:center">
 +
  This is a placeholder-page. In coming days, it will be replaced. <br>For now, you can follow us on facebook and twitter:
 +
  <div style="position:absolute; width:155px; left:50%; margin-left:-75px; padding:20px">
 +
  <a target="_tab" href="https://www.twitter.com/iGEM_Utrecht">
 +
  <img width=75 src="https://static.igem.org/mediawiki/2017/1/1a/Twitter_logo.png" onmouseover="this.src='https://static.igem.org/mediawiki/2017/6/64/Twitter_logo_2.png'" onmouseout="this.src='https://static.igem.org/mediawiki/2017/1/1a/Twitter_logo.png'">
 +
</a>  
 +
  <a target="_tab" href="https://www.facebook.com/igem.utrecht">
 +
  <img width=75 src="https://static.igem.org/mediawiki/2017/0/07/Facebook_logo.png" onmouseout="this.src='https://static.igem.org/mediawiki/2017/0/07/Facebook_logo.png'" onmouseover="this.src='https://static.igem.org/mediawiki/2017/0/0e/Facebook_logo_2.png'">
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</a>
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  </div>
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</div>
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</section>
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</section>
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  </body>
 
</html>
 
</html>

Revision as of 14:43, 26 June 2017

iGEM UTRECHT Placeholder Page

University 2017
 OUTCASST
Important note: This is a placeholder page and will be replaced in due time!

OUT-of-cell CRISPR Activated Sequence-specific Signal Transducer
The OUTCASST sensor consist of two proteins, both expressed to the membrane of a mammalian HEK 293 cell. The first protein connects dCas9, a catalytically dead Cas9 variant, to a transmembrane domain and an intracellular transcription factor. The second protein connects dCpf1 to an intracellular protease. When provided with appropriate guide RNA's, the two proteins can bind to a DNA sequence. When one sequence brings the two proteins together, the transcription factor is released into the cytoplasm, and can activate a reporter cascade. See the scheme below for details.
1. Guide RNA binding:
The two proteins float around freely in the membrane. Two types of guide RNA (gRNA) can be added to the cells. Due to the different recognition sequences for the two proteins, the gRNA can bind specifically to the appropriate protein.
2. DNA sample addition:
Now that the guide RNA's have been bound, both proteins are primed to bind to a specific sequence of a DNA strand. A DNA sample from any source can be added and will then be bound by the protein with the guide RNA that is complementary to one of the DNA strands.
3. Sequence recognition:
One of the proteins has bound a DNA stretch in the sample. If the other protein is bound to a guide RNA that is complementary to a sequence on the same stretch, it too will bind.
4. Co-localization & cleavage:
If the second protein also binds the DNA, close enough to the other protein, the protease at the end of one will be able to cleave the transcription factor from the other protein. The transcription factor is then free to induce a reporter mechanism. In our case, this will be a fluorescent marker.

Applications of the OUTCASST system:
So far, our team has not yet decided on a specific application of the system as there are many different fields wherein sequence-specific detection is of use. Right now, most DNA detection is done by Polymerase Chain Reaction (PCR) and sequencing techniques. These techniques rely on materials and machinery that are not available to everyone. The OUTCASST system, being cell-based, culturable and thus renewable, could provide a quick and easy detection tool that does not require an expensive lab-setup. It only requires medium to culture the cells and the gRNA that is specific to the sequence that you want to detect. Right now, we are interviewing potential end-users to figure out what type of applications they see for our concept and to assess what features they wish to see in our design. So far, we have identified four possible applications for our tool:
Prenatal Genotyping:
Small quantities of cell-free embryo DNA is present in the maternal peripheral blood, already early in pregnancy (Lo et al., 1989). The detection of child-mutations by taking a serum sample from its mother reduces the risk to the unborn child. Such mutation calling is currently done by sequencing, which faces technological limitations when confronted with low sample concentrations, and subsequent genotyping using bioinformatics pipelines, a process that takes days, if not weeks. We aim to create the possibility to detect specific mutations in a matter of hours, cheaply.
Pathogen Detection:
Cell-free pathogen DNA can also be sampled from a patient's serum (Gan et al., 1994). Again, the aim of our design is to speed up the process of diagnosis. With one batch of our organism, multiple tests can be done. By adding a small sample of our organism to each well in a 96-well plate and then adding a different subset of gRNA sequences to each well, you could test for 96 separate pathogens. Such tests could speed up the diagnostics time in medical labs. The sensor could even be shipped to general practitioners themselves, making more precise diagnoses in the doctor's office possible.
Cancer Screening
Cancer is becoming an increasingly important disease. Luckily, it too produces cell-free DNA that can be found in the serum of a patient ( (Schwarzenbach et al., 2011). By designing gRNA that is complementary to known oncogenes, the presence of these genes in a sample thus means that the mutation is present in the patient. Depending on the reporter plasmid, the signal intensity can depend on the amount of dimerization and thus the amount of recognised sequence. Since the concentration of cell-free DNA depends on the growth of the tumor, this concentration can, theoretically, be used for monitoring of the disease.
This is a placeholder-page. In coming days, it will be replaced.
For now, you can follow us on facebook and twitter: