Difference between revisions of "Team:Yale"

 
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<h1>Overview<h1>
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<p>Our iGEM research project involves porting Multiplex Automated Genome Engineering (MAGE) technology into two prokaryotic organisms—Sinorhizobium meliloti 1021 and Synechococcus sp. PCC 7002—for the production of industrially-relevant small molecules. MAGE was developed as a rapid, high efficiency tool for increasing the genetic diversity of a cell population at targeted loci within the genome. The technique has so far been ported into the model organism Escherichia coli and a few other members of the family Enterbacteriaceae. Sinorhizobium meliloti 1021 is a nitrogen-fixing bacterium capable of forming root nodules with legume plants. Synechococcus sp. PCC 7002 is a fast-growing marine cyanobacterium capable of photosynthesis. We envision numerous potential applications for MAGE in these organisms; for example, the nitrogen fixation mechanisms in Sinorhizobium meliloti 1021 could be modified to enable plant growth in otherwise hostile environments, and the lipid biosynthesis pathway of Synechococcus sp. PCC 7002 could be optimized for the production of molecules that serve as precursors to lipid biofuels.<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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<ul>
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<li>  <a href="https://2015.igem.org/Requirements">Requirements page </a> </li>
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<li> <a href="https://2015.igem.org/Wiki_How-To">Wiki Requirements page</a></li>
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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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<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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<h4> Editing your wiki </h4>
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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> <a href="https://2015.igem.org/wiki/index.php?title=Team:Yale&action=edit"> Click here to edit this page! </a></p>
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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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<h4>Templates </h4>
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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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<a href="https://2015.igem.org/TemplatesforTeams_Code_Documentation">Template Documentation </a> page.</p>
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<h4>Tips</h4>
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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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<ul>
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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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<li>You have a global audience! Consider the different backgrounds that your users come from.</li>
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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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<li>Avoid using very small fonts and low contrast colors; information should be easy to read.  </li>
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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://2015.igem.org/Calendar_of_Events">iGEM 2015 calendar</a> </li>
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<li>Have lots of fun! </li>
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<h4>Inspiration</h4>
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<p> You can also view other team wikis for inspiration! Here are some examples:</p>
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<ul>
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<li> <a href="https://2014.igem.org/Team:SDU-Denmark/"> 2014 SDU Denmark </a> </li>
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<li> <a href="https://2014.igem.org/Team:Aalto-Helsinki">2014 Aalto-Helsinki</a> </li>
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<li> <a href="https://2014.igem.org/Team:LMU-Munich">2014 LMU-Munich</a> </li>
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<li> <a href="https://2014.igem.org/Team:Michigan"> 2014 Michigan</a></li>
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<li> <a href="https://2014.igem.org/Team:ITESM-Guadalajara">2014 ITESM-Guadalajara </a></li>
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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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<h4> Uploading pictures and files </h4>
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<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 />
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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>
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<a href="https://2015.igem.org/Special:Upload">CLICK HERE TO UPLOAD FILES</a>
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    <nav class="nav-contain">
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        <li> <a href="https://2015.igem.org/Team:Yale" class="logoMark"> <span>Non</span><span>Model</span></a>
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        </li>
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        <li class="submenu"><a href="https://2015.igem.org/Team:Yale/project">Project</a>
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          <ul>
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            <li><a href="https://2015.igem.org/Team:Yale/project#overview" alt="Overview">Overview</a></li>
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            <li><a href="https://2015.igem.org/Team:Yale/methods" alt="Methods">Methods</a></li>
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            <li><a href="https://2015.igem.org/Team:Yale/results" alt="Results">Results</a></li>
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            <li><a href="https://2015.igem.org/Team:Yale/modeling" alt="Modeling">Modeling</a></li>
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            <li><a href="https://2015.igem.org/Team:Yale/parts" alt="Parts">Parts</a></li>
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          </ul>
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        </li>
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        <li class="submenu"><a href="https://2015.igem.org/Team:Yale/notebook">Notebook</a>
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          <ul>
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            <li><a href="https://2015.igem.org/Team:Yale/notebook" alt="Weekly">Weekly</a></li>
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            <li><a href="https://static.igem.org/mediawiki/2015/f/fb/Yale_iGEM_Project_Summary_2015.pdf" alt="PDF Summary">PDF Summary</a></li>
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          </ul>
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        </li>
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        <li class="submenu"><a href="https://2015.igem.org/Team:Yale/collaborations">Collaborations</a></li>
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        <li class="submenu"><a href="https://2015.igem.org/Team:Yale/practices">Human Practices</a>
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          <ul>
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            <li><a href="https://2015.igem.org/Team:Yale/practices#ssri" alt="SSRI">SSRI</a></li>
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            <li><a href="https://2015.igem.org/Team:Yale/practices#lgbtq" alt="LGBTQ Survey">LGBTQ Survey</a></li>
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          </ul>
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        </li>
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        <li class="submenu"><a href="https://2015.igem.org/Team:Yale/team">Team</a>
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          <ul>
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            <li><a href="https://2015.igem.org/Team:Yale/team" alt="People">People</a></li>
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            <li><a href="https://2015.igem.org/Team:Yale/Attributions" alt="Acknowledgements">Attributions</a></li>
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          </ul>
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        </li>
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        <li class="submenu"><a href="https://2015.igem.org/Team:Yale/standards">Standard Pages</a>
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          <ul>
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            <li><a href="https://2015.igem.org/Team:Yale/standards" alt="Gold">Standard Pages</a></li>
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            <li><a href="https://2015.igem.org/Team:Yale/standards#gold" alt="Gold">Gold Standards</a></li>
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            <li><a href="https://2015.igem.org/Team:Yale/standards#silver" alt="Silver">Silver Standards</a></li>
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            <li><a href="https://2015.igem.org/Team:Yale/standards#bronze" alt="Bronze">Bronze Standards</a></li>
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          </ul>
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        </li>
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      </ul>
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    </nav>
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    <div class="row">
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      <div class="small-12 columns home__callout">
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        <p>Not your typical role model. <a href="https://2015.igem.org/Team:Yale/project#overview">Learn more.</a></p>
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      </div>
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    </div>
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    <div class="row hero">
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      <div class="small-7 columns"><img src="https://static.igem.org/mediawiki/2015/6/62/IGEM_Tree_Round.png"></div>
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      <div class="small-5 columns hero__text">
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        <p class="hero__desc">Developing a Framework for the Genetic Manipulation of Non-Model and Environmentally Significant Microbes</p>
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        <h1 class="hero__head">Yale iGEM</h1>
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        <div class="text-center">
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          <h2 class="hero__year">2015</h2><a class="custom__button pdf__button" href="https://static.igem.org/mediawiki/2015/f/fb/Yale_iGEM_Project_Summary_2015.pdf">PDF Summary</a>
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      </div>
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    </div>
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    <section class="section-lighter">
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        <div class="small-8 columns">
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          <div class="section__text">
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            <h2 class="section__head">Project Abstract</h2>
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            <p class="abstract__text">We focused on establishing a framework to implement genetic manipulation techniques—specifically, multiplex automated genome engineering (MAGE) and CRISPR-Cas9 systems—into non-model, environmentally significant microbes using standard biological parts. The framework involves two components: (1) propagation and selection of cultures and (2) manipulation of cell genomes by MAGE and/or CRISPR. We identified design considerations for both components of the framework, and experimentally validated propagation and selection considerations using cyanobacterial strain Synechococcus sp. PCC 7002 (a fast-growing cyanobacterium capable of lipid biofuel production) and Rhizobium tropici CIAT (a nitrogen-fixing rhizobium which forms root nodules in legume plants). We then developed a workflow for the design, construction, and testing of MAGE and CRISPR technologies into non-model prokaryotes. The insights we gained from validating the propagation component of our workflow will serve to improve the versatility and robustness of our framework and will inform the development of tools for genetic manipulation in other non-model organisms.</p>
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          </div>
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        </div>
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        <div class="small-4 columns"><img src="https://static.igem.org/mediawiki/2015/f/f5/Home.jpg" class="abstract__picture"></div>
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      </div>
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    </section>
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    <section class="findout__section">
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      <h2 class="light__head">Find Out More</h2>
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      <div class="row findout__blocks">
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        <div class="small-12 switch-border">
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          <h2><a href="https://2015.igem.org/Team:Yale/project" alt="Project">Project</a></h2>
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          <h2><a href="https://2015.igem.org/Team:Yale/notebook" alt="Notebook">Notebook</a></h2>
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          <h2><a href="https://2015.igem.org/Team:Yale/collaborations" alt="Collaborations">Collaborations</a></h2>
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          <h2><a href="https://2015.igem.org/Team:Yale/team" alt="Team">Team</a></h2>
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          <h2><a href="https://2015.igem.org/Team:Yale/practices" alt="Human Practices">Human Practices</a></h2>
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          <h2><a href="https://2015.igem.org/Team:Yale/standards" alt="iGEM Standards">iGEM Standards</a></h2>
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          <h2><a href="https://static.igem.org/mediawiki/2015/f/fb/Yale_iGEM_Project_Summary_2015.pdf" alt="PDF Summary">PDF Summary</a></h2>
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        </div>
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      </div>
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        <div class="contact__section">
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            <h2 class="section__head">Contact Us: </h2>
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            <h3>Undergraduate Researchers</h3>
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            <p>Colin Hemez: colin.hemez@yale.edu</p>
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            <p>Lionel Jin: chentian.jin@yale.edu</p>
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            <p>Danny Keller: daniel.keller@yale.edu</p>
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            <p>Dan Shapiro: daniel.m.shapiro@yale.edu</p>
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            <p>Jessica Tantivit: jessica.tantivit@yale.edu</p>
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            <p>Erin Wang: erin.wang@yale.edu</p>
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            <p>Holly Zhou: holly.zhou@yale.edu</p>
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            <h3>Graduate Student Mentor</h3>
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            <p>Natalie Ma (lead mentor): natalie.ma@yale.edu</p>
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            <p>Corey Perez (mentor): corey.perez@yale.edu</p>
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            <p>Jaymin Patel (mentor): jaymin.patel@yale.edu</p>
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            <p>Paul Muir (mentor): paul.muir@yale.edu</p>
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          </div>
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          <div class="small-7 columns">
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            <h2 class="section__head">igem.yale@gmail.com</h2>
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            <h3>iGEM Team Board</h3>
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            <p>Ed Kong (president): edward.kong@yale.edu</p>
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            <p>Alex Buhimschi (vice-president): alexandru.buhimschi@yale.edu</p>
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            <p>Stephanie Mao (outreach chair): stephanie.mao@yale.edu</p>
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            <p>Yamini Naidu (treasurer): yamini.naidu@yale.edu</p>
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            <p>Ariel Hernandez-Leyva (research head): ariel.hernandez-leyva@yale.edu</p>
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            <p>Joel Sher (research adviser): joel.sher@yale.edu</p>
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            <h3>Faculty Advisors</h3>
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            <p>Farren Isaacs (Yale MCDB): farren.isaacs@yale.edu</p>
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            <p>Stephen Dellaporta (Yale MCDB): stephen.dellaporta@yale.edu</p>
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          </div>
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        </div>
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      </div>
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Latest revision as of 03:01, 19 September 2015


</div></div>

Not your typical role model. Learn more.

Developing a Framework for the Genetic Manipulation of Non-Model and Environmentally Significant Microbes

Yale iGEM

2015

PDF Summary

Project Abstract

We focused on establishing a framework to implement genetic manipulation techniques—specifically, multiplex automated genome engineering (MAGE) and CRISPR-Cas9 systems—into non-model, environmentally significant microbes using standard biological parts. The framework involves two components: (1) propagation and selection of cultures and (2) manipulation of cell genomes by MAGE and/or CRISPR. We identified design considerations for both components of the framework, and experimentally validated propagation and selection considerations using cyanobacterial strain Synechococcus sp. PCC 7002 (a fast-growing cyanobacterium capable of lipid biofuel production) and Rhizobium tropici CIAT (a nitrogen-fixing rhizobium which forms root nodules in legume plants). We then developed a workflow for the design, construction, and testing of MAGE and CRISPR technologies into non-model prokaryotes. The insights we gained from validating the propagation component of our workflow will serve to improve the versatility and robustness of our framework and will inform the development of tools for genetic manipulation in other non-model organisms.

Find Out More

Project

Notebook

Collaborations

Team

Human Practices

iGEM Standards

PDF Summary

Contact Us:

Undergraduate Researchers

Colin Hemez: colin.hemez@yale.edu

Lionel Jin: chentian.jin@yale.edu

Danny Keller: daniel.keller@yale.edu

Dan Shapiro: daniel.m.shapiro@yale.edu

Jessica Tantivit: jessica.tantivit@yale.edu

Erin Wang: erin.wang@yale.edu

Holly Zhou: holly.zhou@yale.edu

Graduate Student Mentor

Natalie Ma (lead mentor): natalie.ma@yale.edu

Corey Perez (mentor): corey.perez@yale.edu

Jaymin Patel (mentor): jaymin.patel@yale.edu

Paul Muir (mentor): paul.muir@yale.edu

igem.yale@gmail.com

iGEM Team Board

Ed Kong (president): edward.kong@yale.edu

Alex Buhimschi (vice-president): alexandru.buhimschi@yale.edu

Stephanie Mao (outreach chair): stephanie.mao@yale.edu

Yamini Naidu (treasurer): yamini.naidu@yale.edu

Ariel Hernandez-Leyva (research head): ariel.hernandez-leyva@yale.edu

Joel Sher (research adviser): joel.sher@yale.edu

Faculty Advisors

Farren Isaacs (Yale MCDB): farren.isaacs@yale.edu

Stephen Dellaporta (Yale MCDB): stephen.dellaporta@yale.edu

Yale iGEM 2015

Main Campus:

Yale Department of Molecular, Cellular & Developmental Biology

Attn: Farren Isaacs/iGEM

219 Prospect St

PO Box 208103

New Haven, CT 06520

Tel. +1(203) 432-3783

E-mail: igem.yale@gmail.com

© Yale iGEM 2015