Difference between revisions of "Team:EPF Lausanne"

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<h2> Welcome to iGEM 2015! </h2>
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<p>Your team has been approved and you are ready to start the iGEM season! </p>
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<h4>Before you start: </h4>
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<p> Please read the following pages:</p>
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<h4> Styling your wiki </h4>
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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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      <a href="/Main_Page"
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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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        <h1 class="firstHeading">Team:EPF_Lausanne</h1>
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      <h3 id="siteSub" class='noprint'>From 2015.igem.org</h3>
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                <a href="https://2015.igem.org/Team:EPF_Lausanne" id="home">Main</a>
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                <a href="https://2015.igem.org/Team:EPF_Lausanne/Team">Team</a>
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                <a href="https://2015.igem.org/Team:EPF_Lausanne/Business">Business</a>
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                <a href="https://2015.igem.org/Team:EPF_Lausanne/Research">Research</a>
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                <a href="https://2015.igem.org/Team:EPF_Lausanne/Modeling">Modeling</a>
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                <a href="https://2015.igem.org/Team:EPF_Lausanne/Cooperation">Cooperation</a>
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                <a href="https://2015.igem.org/Team:EPF_Lausanne/Outreach">Outreach</a>
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<div id=""page-content-wrapper""><script src="//code.jquery.com/jquery-1.11.0.min.js"></script>
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            <a href="https://2015.igem.org/"><img src="https://static.igem.org/mediawiki/2014/0/09/Aalto_Helsinki_Logov_iGEM.png" class="img-responsive igem-logo"></a>
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      <h1>EPF Lausanne<br>
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        <small>BioBit</small></h1>
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        <!--<img src="https://static.igem.org/mediawiki/2014/d/dc/Aalto_Helsinki_Logov_Oma.png" class="img-responsive omalogo center-block">-->
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      <p class="bigsplashtext">
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        Getting a computer in a single cell
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    <div class="col-md-3">
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    </div>
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  </div>
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  <div class= "row splashala">
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        <div class ="col-md-12 transp scroller">
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            <a href="#Abstract">
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                Scroll down to read more
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                <img src="https://static.igem.org/mediawiki/2014/3/3e/Aalto_Helsinki_Nuoli.png" class="img-responsive center-block transp nuoli">
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            </a>
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        </div>
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  <!--<div class = "splashcopyright">
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        <p class="transp">
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            <a href="http://i-see-faces.deviantart.com/">Photo © Tanja Maria</a>
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        </p>
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    </div>-->
 
</div>
 
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<script src="https://2015.igem.org/Team:EPF_Lausanne/jquery-1.11.0.min.js?action=raw&amp;ctype=text/js"></script>
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<article>
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<div class="link" id="Abstract"></div>
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  <h2>EPF-Lausanne Bioworks<br>
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    <small>An orthogonal complex system in a single cell</small></h2>
  
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<h4> Editing your wiki </h4>
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  <h3>Project Description</h3>
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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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  <p>
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<p> <a href="https://2015.igem.org/wiki/index.php?title=Team:EPF_Lausanne&action=edit"> Click here to edit this page! </a></p>
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    Logic gates are the main components of every modern digital circuit. Digital circuits work with binary values that are either 0 or 1 and we can think of this values as representing a false or true state respectively; physically 0 and 1 (false or true), are represented by 0 V or 5 V. Logic gates are ``black boxes'' that can take many binary inputs and gives generally one binary output. For example the NOT gate takes one binary input and invert it: if the input is 0 the output will be 1, while if the input is 1 the output will be 0.  The NOT gate is one of the simplest logic gates we can imagine but many other gates with different functionalities exists. For example the AND  gate takes two inputs and gives an output: the output is true (i.e. the output value is 1) if both the inputs are true, otherwise the output is false (i.e. the output value is 0). Another common example is the OR gate, which takes two inputs and gives an output: the output is false if both inputs are false, otherwise the output is true. By combining different logic gates in sequence and in parallel is is possible to create digital circuits with complex behaviours.
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<p>See tips on how to edit your wiki on the <a href="https://2015.igem.org/TemplatesforTeams_Code_Documentation">Template Documentation</a> page.</p>  
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  </p>
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  <p>
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    The aim of our project, is to create a general framework allowing simple design of digital circuits inside living cells, using dCas9 proteins with specific gRNAs as activators or inhibitors of gene transcription.  
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  </p>
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  <p>
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  Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease enzyme which can target nearly any DNA sequence complementary to its guide RNA (gRNA). The original function of the CRISPR-Cas9 system in bacteria is to cleave foreign DNA after positive match. However, a dead version of Cas9 (dCas9) unable to cut the DNA  can be used as a repressor (by preventing the binding of the RNA polymerase to promoter sequences) or as an activator (once fused with the omega subunit of the RNA polymerase).
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  </p>
  
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<p>In our project, logic gates ...
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</p>
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    <!--<div class="row">
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            <a href="https://www.youtube.com/watch?v=Fa6qf7avM1s" target="_blank"><img src="https://static.igem.org/mediawiki/2014/7/79/Aaltohelsinki_pitc_capture.png" class="img-responsive smallerimg"></img></a>
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            <p class="kuvateksti">
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                Vidéo descriptive de Logic Gates ou dCas9?
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            </p>
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  <!--<img src="https://static.igem.org/mediawiki/2014/7/7e/Aalto_Helsinki_Logot_Oma.png" class="img-responsive center-block omalogot">-->
  
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<h4>Templates </h4>
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</article>
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<p> This year we have created templates for teams to use freely. More information on how to use and edit the templates can be found on the
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<!--<article class="abg-pcb">
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<a href="https://2015.igem.org/TemplatesforTeams_Code_Documentation">Template Documentation </a> page.</p>  
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 +
  <h2>The Story of Aalto-Helsinki Bioworks</h2>
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  <div class="row">
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    <div class="col-md-6 text-col-left">
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      <p>
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        We are Aalto-Helsinki Bioworks, the first-ever Finnish iGEM Team and one of the four teams in the new Entrepreneurship Track. Our <a href="https://2014.igem.org/Team:Aalto-Helsinki/Team">team</a> consists of nine students from Aalto University and the University of Helsinki and we are combining our interdisciplinary forces to develop something new and fascinating. We want to put Finland on the map of synthetic biology and improve undergraduate research opportunities in our universities.
 +
      </p>
 +
      <p>
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        We have <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research">designed</a> a three-channel gene switch that would make it possible to control three user-defined genes with blue light intensity. We are using <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#yf1-title">YF1</a> as our light receptor protein and the signal is mediated to lambda repressor protein (CI) production via phosphorylation pathway. The concentration of the CI protein defines the gene that should be active at a time. The secret behind this function is our modified version of the <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#lambda-title">lambda repressor</a> mechanism.
 +
      </p>
 +
      <p>
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        We constructed a mathematical <a href="https://2014.igem.org/Team:Aalto-Helsinki/Modeling">model</a> that simulates the interactions of the molecules and function of the gene switch we designed. This revealed interesting phenomena in the dynamics of our system which helps us to better understand the capabilities and limitations of the gene switch. We also made an <a href="http://igem-qsf.github.io/SimCircus/WebUI/">interactive simulation</a> available to everybody to best illustrate how our idea actually works.
 +
      </p>
 +
      <p>
 +
        To control the amount of blue light on our cell cultures, we created the <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#ledrig-title">LED rig</a> device. This enabled us to perform diverse experiments in order to characterize our light response element. These <a href="https://2014.igem.org/Team:Aalto-Helsinki/Research#Results">results</a> show that our light response element is able to regulate the downstream gene expression precisely. In addition, the response time is in a ten-minute-scale, which enables constant and nearly real-time control over bacterial cultures. In addition, we hypothesize that this system is also applicable to bioreactors, which would enable higher level of control in industrial bioprocesses. However, our fully functional prototype is still under ongoing development.
 +
      </p>
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      <p>
 +
        We have developed an open approach to <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business">biotech business</a> inspired by the business models for open source software. Following the Open Source philosophy, we will distribute open Aalto-Helsinki Bioworks technologies for free to everybody - as long as they share the improvements made on the technology. Therefore, we empower our users to participate in product development. Our <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#canvas-title">business model</a> is based on hardware and wide range of services offered to our customers.
 +
      </p>
 +
      <p>
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        During the summer we participated in Aalto Entrepreneurship Society’s <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#Sos">Summer of Startups 2014</a> incubator programme to learn the essential entrepreneurial skills, such as pitching, investor relations, customer-driven development and <a href="https://2014.igem.org/Team:Aalto-Helsinki/Business#pitch-title">explaining</a> the science for general audience. See our Demo Day video for details.
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      </p>
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      <p>
 +
        iGEM is an international experience and as the first Finnish team, we went to find advice and experience around the globe. We contributed to the iGEM community by building a <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Seekers">BioBrick Seeker</a> tool which makes it easy to find parts of your interest in the 2014 BioBrick distribution. This tool has been used by iGEM teams all over the world! We also did a lot of <a href="https://2014.igem.org/Team:Aalto-Helsinki/Cooperation#Interteam">cooperation</a>, including filling out surveys and having skype conversations and live meetings with current and previous iGEM teams from France, Colombia, Switzerland, USA and the Netherlands. We even made a <a href="http://www.youtube.com/embed/icPgP3OOVOQ?rel=0">video</a> together with ETH Zürich team to Colombia team’s challenge.
 +
      </p>
 +
      <p>
 +
        We wanted to <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach">raise awareness</a> about synthetic biology in Finland and also showcase researchers’ work to young people and undergraduate students. Therefore, we have been reaching out to general public, especially young people via <a href="https://2014.igem.org/Team:Aalto-Helsinki/Outreach#SoMe">social media</a>, including <a href="http://www.facebook.com/AaltoHelsinki">Facebook</a>, <a href="http://twitter.com/AaltoHelsinki">Twitter</a>, <a href="http://www.youtube.com/channel/UCEZliqjLu86CRpQlk57FfSw">Youtube</a>, <a href="http://www.flickr.com/photos/aaltohelsinki/">Flickr</a> and our own blog. We’ve shared stories, pictures, videos and experiences to our followers. In addition, we have been featured in radio interviews and articles on magazines and webzines. We also made a silly game: <a href="https://2014.igem.org/Team:Aalto-Helsinki/Flappycoli">Flappy Coli</a>. We have a public team webpage, <a href="http://2014.aaltohelsinki.com/">aaltohelsinki.com</a>, where you can find the latest stories of Aalto Helsinki also in the future. We lifted some of the highlights of this project on a <a href="https://2014.igem.org/Team:Aalto-Helsinki/Journal#Timeline">timeline</a>: the story of Aalto-Helsinki Bioworks is there for you to see!
 +
      </p>
 +
    </div>
 +
    <div class="col-md-6 img-100">
 +
      <img src="https://static.igem.org/mediawiki/2014/a/a2/Aalto_Helsinki_Banner.png" class="img-responsive">
 +
    </div>
 +
  </div>
  
−
<h4>Tips</h4>
 
−
<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>
 
−
<ul>
 
−
<li>State your accomplishments! Tell people what you have achieved from the start. </li>
 
−
<li>Be clear about what you are doing and how you plan to do this.</li>
 
−
<li>You have a global audience! Consider the different backgrounds that your users come from.</li>
 
−
<li>Make sure information is easy to find; nothing should be more than 3 clicks away.  </li>
 
−
<li>Avoid using very small fonts and low contrast colors; information should be easy to read.  </li>
 
−
<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://2015.igem.org/Calendar_of_Events">iGEM 2015 calendar</a> </li>
 
−
<li>Have lots of fun! </li>
 
−
</ul>
 
  
 +
</article>-->
 +
<article>
  
−
<h4>Inspiration</h4>
+
  <h2 class="kakspaddingbot">Accomplishments</h2>
−
<p> You can also view other team wikis for inspiration! Here are some examples:</p>
+
  <ul>
−
<ul>
+
    <li>Incoming</li>
−
<li> <a href="https://2014.igem.org/Team:SDU-Denmark/"> 2014 SDU Denmark </a> </li>
+
  </ul>
−
<li> <a href="https://2014.igem.org/Team:Aalto-Helsinki">2014 Aalto-Helsinki</a> </li>
+
−
<li> <a href="https://2014.igem.org/Team:LMU-Munich">2014 LMU-Munich</a> </li>
+
−
<li> <a href="https://2014.igem.org/Team:Michigan"> 2014 Michigan</a></li>
+
−
<li> <a href="https://2014.igem.org/Team:ITESM-Guadalajara">2014 ITESM-Guadalajara </a></li>
+
−
<li> <a href="https://2014.igem.org/Team:SCU-China"> 2014 SCU-China </a></li>
+
−
</ul>
+
  
−
<h4> Uploading pictures and files </h4>
+
</article>
−
<p> You can upload your pictures and files to the iGEM 2015 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 />
+
<article>
−
When you upload, set the "Destination Filename" to <code>Team: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!)</p>
+
  
−
<a href="https://2015.igem.org/Special:Upload">CLICK HERE TO UPLOAD FILES</a>
+
  <h2>Categories</h2>
  
 +
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    <div class="col-md-4 bg feat feat-left bg-team">
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        <div class="feattext-container-tall">
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            <div class ="feattext-cell">
 +
            <p class="feattext-p">
 +
              <big><big><big>Team</big></big></big><br>
 +
              We are a team of twelve students with a multicultural background.
 +
            </p>
 +
          </div>
 +
        </div>
 +
      </a>
 +
    </div>
 +
    <!--<div class="col-md-4 bg feat feat-center bg-business">
 +
      <a href="https://2015.igem.org/Team:EPF_Lausanne/Business">
 +
        <div class="feattext-container-tall">
 +
            <div class ="feattext-cell">
 +
            <p class="feattext-p">
 +
              <big><big><big>Business</big></big></big><br>
 +
              We explored the possibilities of biotech and synthetic biology business.
 +
            </p>
 +
          </div>
 +
        </div>
 +
      </a>
 +
    </div>
 +
    <div class="col-md-4 bg feat feat-right bg-research">
 +
      <a href="https://2015.igem.org/Team:EPF_Lausanne/Research">
 +
        <div class="feattext-container-tall">
 +
            <div class ="feattext-cell">
 +
            <p class="feattext-p">
 +
              <big><big><big>Research</big></big></big><br>
 +
              We engineered a three-channel switch that can be controlled with the intensity of blue light.
 +
            </p>
 +
          </div>
 +
        </div>
 +
      </a>
 +
    </div>-->
 +
  </div>
  
 +
  <!--<div class="row row-eq-height">
 +
    <div class="col-md-6 bg feat feat-left bg-modeling">
 +
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        <div class="feattext-container-tall">
 +
            <div class ="feattext-cell">
 +
            <p class="feattext-p">
 +
              <big><big><big>Modeling</big></big></big><br>
 +
              We made mathematic models of the interactions behind our gene switch.
 +
            </p>
 +
          </div>
 +
        </div>
 +
      </a>
 +
    </div>
 +
    <div class="col-md-6 bg feat feat-right bg-cooperation">
 +
      <a href="https://2015.igem.org/Team:EPF_Lausanne/Cooperation">
 +
        <div class="feattext-container-tall">
 +
            <div class ="feattext-cell">
 +
            <p class="feattext-p">
 +
              <big><big><big>Cooperation</big></big></big><br>
 +
              We got to know other iGEM teams and developed tools for everyone to use.
 +
            </p>
 +
          </div>
 +
        </div>
 +
      </a>
 +
    </div>
 +
  </div>
 +
  <div class="row row-eq-height">
 +
    <div class="col-md-6 bg feat feat-left bg-outreach">
 +
      <a href="https://2015.igem.org/Team:EPF_Lausanne/Outreach">
 +
        <div class="feattext-container-tall">
 +
            <div class ="feattext-cell">
 +
            <p class="feattext-p">
 +
              <big><big><big>Outreach</big></big></big><br>
 +
              We spread the word about iGEM and synthetic biology especially in Finland.
 +
            </p>
 +
          </div>
 +
        </div>
 +
      </a>
 +
    </div>
 +
    <div class="col-md-6 bg feat feat-right bg-journal">
 +
      <a href="https://2015.igem.org/Team:EPF_Lausanne/Journal">
 +
        <div class="feattext-container-tall">
 +
            <div class ="feattext-cell">
 +
            <p class="feattext-p">
 +
              <big><big><big>Journal</big></big></big><br>
 +
              We documented the project well.
 +
            </p>
 +
          </div>
 +
        </div>
 +
      </a>
 +
    </div>
 +
  </div>-->
  
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Revision as of 12:12, 2 July 2015

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> Team:EPF_Lausanne - 2015.igem.org

 

Team:EPF_Lausanne

From 2015.igem.org

EPF Lausanne
BioBit

Getting a computer in a single cell

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EPF-Lausanne Bioworks
An orthogonal complex system in a single cell

Project Description

Logic gates are the main components of every modern digital circuit. Digital circuits work with binary values that are either 0 or 1 and we can think of this values as representing a false or true state respectively; physically 0 and 1 (false or true), are represented by 0 V or 5 V. Logic gates are ``black boxes'' that can take many binary inputs and gives generally one binary output. For example the NOT gate takes one binary input and invert it: if the input is 0 the output will be 1, while if the input is 1 the output will be 0. The NOT gate is one of the simplest logic gates we can imagine but many other gates with different functionalities exists. For example the AND gate takes two inputs and gives an output: the output is true (i.e. the output value is 1) if both the inputs are true, otherwise the output is false (i.e. the output value is 0). Another common example is the OR gate, which takes two inputs and gives an output: the output is false if both inputs are false, otherwise the output is true. By combining different logic gates in sequence and in parallel is is possible to create digital circuits with complex behaviours.

The aim of our project, is to create a general framework allowing simple design of digital circuits inside living cells, using dCas9 proteins with specific gRNAs as activators or inhibitors of gene transcription.

Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease enzyme which can target nearly any DNA sequence complementary to its guide RNA (gRNA). The original function of the CRISPR-Cas9 system in bacteria is to cleave foreign DNA after positive match. However, a dead version of Cas9 (dCas9) unable to cut the DNA can be used as a repressor (by preventing the binding of the RNA polymerase to promoter sequences) or as an activator (once fused with the omega subunit of the RNA polymerase).

In our project, logic gates ...

Accomplishments

  • Incoming

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