Team:Stanford-Brown

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jQuery(document).ready(function($){
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  <div id="bottom-panel">
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    <table>
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        <td>
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<span id="abs-title" style="margin-top:-30px;"><a href="/Team:Stanford-Brown/Team/Apply">JOIN US IN 2014! CLICK HERE!</a></span>
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          <div style="width: 550px; margin-top:0px;">
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            <span id="abs-title">ABSTRACT</span>
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            <span style="float: left;">
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              <p id="abs-text">
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Communication is an integral part of life as we know it. This summer, we pursued four synthetic biology projects with the goal of improving communication across different mediums. On the atomic level, our <b>BioWires</B> project has created silver-incorporating DNA strands to use as nanowires, which could improve the cost and effectiveness of electronics. Our <b>CRISPR</B> project worked on a system for  passing DNA regulatory messages between cells, in effect creating transmissible vaccines. We also extrapolated proteins from the past to better understand early life on Earth for our <B>De-Extinction</B> project. Finally, we built a sucrose biosensor in <I>B. subtilis</I> that will be launched on the <b>EuCROPIS</B> satellite  into low-Earth orbit. <br><br>
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<big><B>We are the Stanford-Brown iGEM team, and we're connecting life on Earth to help us prepare for life beyond it.</B></big>
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            <div style="margin-top:15px; text-align:center; font-weight: 600; font-size: 18px;">ACHIEVEMENTS</div>
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              <ul>
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                <li> <a href="/Team:Stanford-Brown/Projects/BioWires">Demonstrated silver-ion incorporation in the DNA double-helix </a></li>
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function(){
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                <li> <a href="/Team:Stanford-Brown/Projects/EuCROPIS">Worked with NASA and the German Space agency to develop BioBrick constructs for the EuCROPIS Satellite Mission</a></li>
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                <li> <a href="/Team:Stanford-Brown/Projects/CRISPR">Isolated and bricked components of two CRISPR-Cas systems</a></li>
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                <li> <a href="/Team:Stanford-Brown/Projects/De-Extinction">Designed and modeled ancestral proteins to understand early conditions of earth</a></li>
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<li> <a href="/Team:Stanford-Brown/Projects/De-Extinction#Evolutionary_Modeling">Collaborated with Dr. Rich Lenski to use 25 years of evolutionary data to model and text bioinformatics software </li>
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                <li> <a href="/Team:Stanford-Brown/Projects/HumanPractices">Authored reports on the the ethics of de-extinction and the iGEM workflow </a></li>
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                <li> <a href="https://2013.igem.org/Team:UC_Davis/Database/Initial_Population">Collaborated with team UC Davis to characterize promoter strengths</a></li>
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function(){
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<li> <a href="https://2013.igem.org/Edinburgh_University">Consulted with Team Edinburgh on <i>B. subtilis</i> methods and protocols </li>
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var id = $(this).parent().parent().attr('id');
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<li> <a href="https://2013.igem.org/Team:Stanford-Brown/Team/Outreach#Teaching_a_BioEngineering_Bootcamp">Instructed high school seniors in the basics of synthetic biology and how to build an iGEM team </li>
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<li> <a href="https://2013.igem.org/Team:Stanford-Brown/Team/Outreach#Bay_Area_and_NYC_Maker_Faires">Demonstrated SynBio and iGEM to the public at Maker Faire in SF and NYC </li>
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<li> <a href="http://www.facebook.com/IgemMemes">Curated iGEM memes with additional social outreach via Instagram and Twitter </li>
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<li> <a href="https://2013.igem.org/Team:Stanford-Brown/Team/Outreach#Podcasts_and_Memes">Produced iGEM podcast to discuss SynBio topics </li>
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        </td> 
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      </tr> 
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  </div> <!-- bottom panel -->
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<div id="proj-panel">
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<div id="proj-row">
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            <div class="feature"><iframe width="210" height="160" src="//www.youtube.com/embed/RNHHZBTr7Ow?rel=0" frameborder="0" allowfullscreen></iframe>
 +
            <p class="brief">Atomic Communication
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            </p> 
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          </div>
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<!-- End stuff from Calgary -->
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          <div class="feature"><iframe width="210" height="160" src="//www.youtube.com/embed/Zza9PVbyEbY?rel=0" frameborder="0" allowfullscreen></iframe>
 +
            <p class="brief">Cellular Communication
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            </p> 
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          </div>
 +
          <div class="feature"><iframe width="210" height="160" src="//www.youtube.com/embed/qaKvX7Z__0w?rel=0" frameborder="0" allowfullscreen></iframe>
 +
            <p class="brief">Temporal Communication
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            </p> 
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          </div>
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</head>
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          <div class="feature"><iframe width="210" height="160" src="//www.youtube.com/embed/_kOq22MqGrk?rel=0" frameborder="0" allowfullscreen></iframe>
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<body>
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            <p class="brief">Spatial Communication
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<!--
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            </p>
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<div class="container">
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          </div>
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<h4>ZURB's Orbit Slider</h4>
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<a href="http://www.zurb.com/playground/orbit-jquery-image-slider">View Docs + Playground for Orbit</a> -->
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<a id="greybox4" href="http://www.youtube.com/watch?v=KHhswxo6xow" style="margin-right:4px;">
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<img src="https://static.igem.org/mediawiki/2012/0/02/UCalgary2012_ThreeBoxMusic.png"></img>
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<h2>iGEM Style!</h2>
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<p>Take a look at our music video--sung and produced by our very own members--that's taking the iGEM world by storm! </p>
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</div>
</div>
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<a id="greybox5" href="https://2012.igem.org/Team:Calgary/Project/Synergy">
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<img src="https://static.igem.org/mediawiki/2012/2/20/UCalgary2012_ThreeBoxSynergy.png"></img>
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<h2>Synergy</h2>
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<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p>
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<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p>
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<h2>The Concept</h2>
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<p>Our project consists of three major components: FRED, OSCAR, and the overarching Human Practices considerations informing their design. Click on the boxes to your left to learn more about what iGEM Calgary has done so far!</p>
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<h2>Human Practices</h2>
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<p>Great consideration was put into our Human Practices component this year, as safety was the guiding principle behind the design of FRED and OSCAR.  iGEM Calgary has undertaken many human outreach initiatives this year. Roll over the boxes to see each of them!</p>
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<p>We took the initiative with the oil sands industry and established a dialogue between industry experts, academics, and government representatives. Through these talks a roadmap for the use of synthetic biology in the oil sands was established, focusing on biosensing and bioremediation.</p>
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<p>As an undergraduate team, we spoke with experts in various fields, including the oil industry, tailings pond management, biotechnology, law, and politics to gather various opinions on our project. How useful is synthetic biology in a tailings pond environment? What design considerations should we include in our project to improve security? What legal policies must we consider before implementing our project?</p>
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<h2>Design Considerations</h2>
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<p>Since safety is the driving force behind our project, we need to ensure the physical design of our biosensor and bioreactor would contain and manage the bacteria to minimize the possibility of their escape. We needed to build devices that would ensure the safety of both the user and the outside environment during their use. Click here to learn more!</p>
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<p>Both FRED and OSCAR are designed to operate within enclosed environments. However, since safety is our highest priority, we decided to design and implement a killswitch in both FRED and OSCAR as an extra layer of security. The killswitch aims to destroy the genome using two powerful non-specific nucleases in the unlikely event that bacteria escape into the environment. Click here to learn more!</p>
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<p>Click here for our safety page! Here we detail all the safety procedures, certifications, and approvals we have from our University to allow us to work this summer.</p>
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<p>iGEM Calgary partnered with a number of different associations to engage the general public about science and synthetic biology. Click here to see what we've done this summer!</p>
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<p>FRED is our <b>F</b>unctional, <b>R</b>obust <b>E</b>lectrochemical <b>D</b>etector. FRED is responsible for detecting and measuring naphthenic acids (NAs) and is able to produce an electrochemical signal that can be measured. FRED can be used to measure toxins in tailings pond samples within minutes, without having to ship them to an off-site lab for testing. Click on FRED to learn more!</p>
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<h2>Detecting</h2>
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<p>FRED is our star detective, working around the clock to detect toxins roaming freely in tailings pond water. FRED is known for being a little unorthodox in his methods namely by using a measurable electrochemical signal rather than colored or fluorescent reporters. Using his transposon library FRED gets clues about the genetic elements that will activate in the presence of toxins. </p>
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<p>Once FRED finds the toxins he wastes no time exposing them. Building upon last year's single output electrochemical system FRED now uses the new triple output system to report the toxins. This novel approach to electrochemical reporting means that FRED is as good as he is fast. </p>
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<p>Aside from being a stellar detective FRED also dabbles in the art of mathematics and modelling. These skills are used to model the behavior of the system. The results from the modelling helped guide the wet lab experiments which in turn gave new data to refine the model.</p>
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<h2>Prototyping</h2>
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<p>FRED gets a lot of information so he stays on top of things with the help of his handy dandy physical device to test the sample and software to interpret the raw data. The device has been <b>prototyped</b> and has an accompanying software platform that works with FRED to detect the toxins. </p>
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<p>OSCAR is our <b>O</b>ptimized <b>S</b>ystem for <b>C</b>arboxylic <b>A</b>cid <b>R</b>emediation. OSCAR is responsible for converting toxins such as catechol and naphthenic acids into hydrocarbons. OSCAR is also capable of removing nitrogen and sulfur groups to further purify the hydrocarbons produced. Click on OSCAR to learn more!</p>
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<p>In order to convert tailings pond toxins fully into hydrocarbons, we need to remove carboxylic acid groups. We are using the PetroBrick, from the University of Washington's 2011 iGEM team, to cleave off carboxylic acids to produce hydrocarbons. Click here to learn more!</p>
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<h2>Catechol Degradation</h2>
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<p>Catechol is a common toxic compound found in tailings ponds. We looked into giving OSCAR the ability to degrade catechol, which would also cleave ring structures of toxins.</p>
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<h2>Flux-Variability Analysis</h2>
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<p>We wanted to optimize OSCAR's output of hydrocarbons, so we computationally modelled how we can add particular metabolites to the growth media to increase hydrocarbon output. Click here to see what we found out!</p>
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<h2>Bioreactor</h2>
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<p>OSCAR needed a home, so we developed an enclosed bioreactor system where toxins can be converted into hydrocarbons for output. Click here to see how we designed the bioreactor!</p>
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<p>Nitrogen and sulfur heteroatoms can produce nasty airborne pollutants when burned, cause acid rain and acid deposition, and can damage valuable catalysis mechanisms involved in fuel processing and emissions control. OSCAR can remove these atoms trapped in the rings. Click here to see how!</p>
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Latest revision as of 04:12, 16 November 2013

JOIN US IN 2014! CLICK HERE!
ABSTRACT

Communication is an integral part of life as we know it. This summer, we pursued four synthetic biology projects with the goal of improving communication across different mediums. On the atomic level, our BioWires project has created silver-incorporating DNA strands to use as nanowires, which could improve the cost and effectiveness of electronics. Our CRISPR project worked on a system for passing DNA regulatory messages between cells, in effect creating transmissible vaccines. We also extrapolated proteins from the past to better understand early life on Earth for our De-Extinction project. Finally, we built a sucrose biosensor in B. subtilis that will be launched on the EuCROPIS satellite into low-Earth orbit.

We are the Stanford-Brown iGEM team, and we're connecting life on Earth to help us prepare for life beyond it.

ACHIEVEMENTS

Atomic Communication

Cellular Communication

Temporal Communication

Spatial Communication

Retrieved from "http://2013.igem.org/Team:Stanford-Brown"