Team:CU-Boulder

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<li><a class="dropheader" href="https://2013.igem.org/Team:CU-Boulder/Team/AbouttheUniversity">The University</a></li>
 
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<a class="drop" href="https://2013.igem.org/Team:CU-Boulder/Project">Overview</a>
 
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<ul>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/Post-Regionals">Post-Regionals</a></li>
 
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</ul>
 
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<a class="drop" href="https://2013.igem.org/Team:CU-Boulder/Project/HumanPractices">Human Practices</a>
 
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<ul>
 
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  <li><a href="https://2013.igem.org/Team:CU-Boulder/Project/HumanPractices/Collaborations">Initiative</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/HumanPractices/Interviews">Interviews</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/HumanPractices/Design">Design</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/HumanPractices/Killswitch">Killswitch</a></li>
 
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<li><a style="margin:0 -1em 0 1em;" href="https://2013.igem.org/Team:CU-Boulder/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li>
 
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<li><a style="margin:0 -1em 0 1em;" href="https://2013.igem.org/Team:CU-Boulder/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Safety">Safety</a></li>
 
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<a class="drop" href="https://2013.igem.org/Team:CU-Boulder/Project/FRED">FRED</a>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/FRED/Detecting">Toxin Sensing</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/FRED/Reporting">Electroreporting</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/FRED/Modelling">Modelling</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/FRED/Prototype">Device Prototype</a></li>
 
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<a class="drop" href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR">OSCAR</a>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/Decarboxylation">Decarboxylation</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/CatecholDegradation">Decatecholization</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/Bioreactor">Bioreactor</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/Upgrading">Upgrading</a></li>
 
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<li><a style="margin:0 -1em 0 1em;"href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/Desulfurization">Desulfurization</a></li>
 
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<li><a style="margin:0 -1em 0 1em;"href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/Denitrogenation">Denitrogenation</a></li>
 
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</li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/Synergy">Synergy</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/References">References</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Project/Attributions">Attributions</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Parts" id="partslink">Parts</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Notebook">Journal</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Notebook/Protocols">Protocols</a></li>
 
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</ul>
 
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<li><a class="drop" href="https://2013.igem.org/Team:CU-Boulder/Outreach" id="outreachlink">Outreach</a>
 
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<ul>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Outreach/Spark">Spark Science</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Outreach/MindsInMotion">Minds in Motion</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Outreach/Blog">Blog Posts</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Outreach/TEDxCalgary">TEDxCalgary</a></li>
 
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<li><a href="http://twitter.com/iGEMCalgary" target="_blank">Follow Us!</a></li>
 
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<li><a href="https://2013.igem.org/Team:CU-Boulder/Sponsors" id="sponsorslink">Sponsors</a></li>
 
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<h2>Accessible Synthetic Biology</h2>
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<img src="https://static.igem.org/mediawiki/2013/7/7e/DIY_logo.jpg" height="500" width="477">
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<p>Basic intro about project</p>
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<p></p>
 +
<p>The main focus of the iGEM project here at CU-Boulder is to help make synthetic biology more accessible and affordable.  We spent the summer developing parts, procedures, and documentation to help make this vision a reality.  The original goal was to create the constructs and purification methods necessary to produce and isolate restriction enzymes.  Along the way we explored some novel approaches to DNA and protein purification and developed experimentally tested protocols for these and other procedures essential to Biobrick assembly.  Our purification methods exemplify the ideal of using common lab materials to make performing everyday lab techniques as accessible and inexpensive as possible.  A related aspect of our project was exploring methods of recycling consumables associated with lab work in order to reduce waste and material expenses.  We hope that our findings using this "do-it-yourself" approach of synthetic biology help make this type of research more accessible for those where funding is a limiting factor.
 +
</p>
 +
</center>
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 +
<div class="row-fluid">
 +
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 +
<a href="https://2013.igem.org/Team:CU-Boulder/Purification Methods">
 +
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 +
<img src="https://static.igem.org/mediawiki/2013/d/d5/DIY.jpg" height="230" width="275">
 +
"Do It Yourself" Synthetic Biology</a>
 +
<p>One of our main goals was making synthetic biology more accessible.  Click here to find out more!
 +
</p>
 +
</center>
 +
</div></div>
 +
<div class="span4"><div class="shadow-bottom">
 +
<a href="https://2013.igem.org/Team:CU-Boulder/MedalRequirements">
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2013/d/d7/Goldmedal.png" height="275" width="275">
 +
Medal Requirements</a>
 +
<p>Here you can find links to each of the medal requirements we have completed.
 +
</p>
 +
</center>
 +
</div></div>
 +
<div class="span4"><div class="shadow-bottom">
 +
<a href="https://2013.igem.org/Team:CU-Boulder/Notebook/Protocols">
 +
<center>
 +
<img src="https://static.igem.org/mediawiki/2013/f/f2/Validation-protocol-execution-tips.jpg" height="230" width="275">
 +
Detailed Protocols</a>
 +
<p>We have experimentally developed protocols for many of the lab techniques required for Biobrick assembly.
 +
</p>
 +
</center>
 +
</div></div>
</div>
</div>
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<img src="https://static.igem.org/mediawiki/2013/0/02/UCalgary2013_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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<a id="greybox5" href="https://2013.igem.org/Team:CU-Boulder/Project/Synergy">
 
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<img src="https://static.igem.org/mediawiki/2013/2/20/UCalgary2013_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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<h2>Intro Video</h2>
 
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<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p>
 
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<a class="gbox2 iconbox" href="https://2013.igem.org/Team:CU-Boulder/Project/FRED/Reporting">
 
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<a class="gbox3 iconbox" href="https://2013.igem.org/Team:CU-Boulder/Project/FRED/Modelling">
 
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<a class="gbox4 iconbox" href="https://2013.igem.org/Team:CU-Boulder/Project/FRED/Prototype">
 
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<img src="https://static.igem.org/mediawiki/2013/a/a7/UCalgary2013_IconFRED4.png"></img>
 
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<a class="bbox1 iconbox" href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/Decarboxylation">
 
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<img src="https://static.igem.org/mediawiki/2013/f/f1/UCalgary2013_IconOSCAR1.png"></img>
 
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<a class="bbox2 iconbox" href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/CatecholDegradation">
 
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<img src="https://static.igem.org/mediawiki/2013/0/0c/UCalgary2013_IconOSCAR4.png"></img>
 
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<a class="bbox3 iconbox" href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/FluxAnalysis">
 
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<img src="https://static.igem.org/mediawiki/2013/4/40/UCalgary2013_IconOSCAR6.png"></img>
 
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<a class="bbox4 iconbox" href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/Bioreactor">
 
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<img src="https://static.igem.org/mediawiki/2013/3/3e/UCalgary2013_IconOSCAR5.png"></img>
 
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<a class="bbox5 iconbox" href="https://2013.igem.org/Team:CU-Boulder/Project/OSCAR/Upgrading">
 
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<img src="https://static.igem.org/mediawiki/2013/4/44/UCalgary2013_IconOSCAR7.png"></img>
 
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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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</div>
 
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<div class="orangebox">
 
-
<h2>Human Practices</h2>
 
-
<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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</div>
 
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<div class="obox1">
 
-
<h2>Initiative</h2>
 
-
<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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</div>
 
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<div class="obox2">
 
-
<h2>Interviews</h2>
 
-
<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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</div>
 
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<div class="obox3">
 
-
<h2>Design Considerations</h2>
 
-
<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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</div>
 
-
<div class="obox4">
 
-
<h2>Killswitch</h2>
 
-
<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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</div>
 
-
<div class="obox5">
 
-
<h2>Safety</h2>
 
-
<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>
 
-
</div>
 
-
<div class="obox6">
 
-
<h2>Community Outreach</h2>
 
-
<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>
 
-
</div>
 
-
<div class="greenbox">
 
-
<h2>FRED</h2>
 
-
<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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</div>
 
-
<div class="gbox1">
 
-
<h2>Detecting</h2>
 
-
<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>
 
-
</div>
 
-
<div class="gbox2">
 
-
<h2>Reporting</h2>
 
-
<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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</div>
 
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<div class="gbox3">
 
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<h2>Modelling</h2>
 
-
<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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</div>
 
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<div class="gbox4">
 
-
<h2>Prototyping</h2>
 
-
<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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</div>
 
-
<div class="bluebox">
 
-
<h2>OSCAR</h2>
 
-
<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>
 
-
</div>
 
-
<div class="bbox1">
 
-
<h2>Decarboxylation</h2>
 
-
<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>
 
-
</div>
 
-
<div class="bbox2">
 
-
<h2>Catechol Degradation</h2>
 
-
<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>
 
-
</div>
 
-
<div class="bbox3">
 
-
<h2>Flux-Variability Analysis</h2>
 
-
<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>
 
-
</div>
 
-
<div class="bbox4">
 
-
<h2>Bioreactor</h2>
 
-
<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>
 
-
</div>
 
-
<div class="bbox5">
 
-
<h2>Upgrading</h2>
 
-
<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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<h2>Team</h2>
 
-
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p>
 
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<a id="greybox2" href="https://2013.igem.org/Team:CU-Boulder/Project/DataPage">
 
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<img src="https://static.igem.org/mediawiki/2013/9/92/UCalgary2013_ThreeBoxData.png"></img>
 
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<h2>Data Page</h2>
 
-
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p>
 
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<a id="greybox3" href="https://2013.igem.org/Team:CU-Boulder/Notebook">
 
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<img src="https://static.igem.org/mediawiki/2013/1/1b/UCalgary2013_ThreeBoxNotebook.png"></img>
 
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<h2>Notebook</h2>
 
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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>Thanks to Our Sponsors!</h2>
 
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<td><a href="http://www.ucalgary.ca/bhsc/node/16" target="_blank"><img style="width: 284px;" src="https://static.igem.org/mediawiki/2013/d/d6/UCalgary2013_Logo_O%27Brien_Centre.png"></img></a></td>
 
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<td><a href="http://www.ucalgary.ca" target="_blank"><img style="width: 166px;" src="https://static.igem.org/mediawiki/2013/4/46/UCalgary2013_Logo_U_of_C_Vertical.png"></img></a></td>
 
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<td><a href="http://www.albertatechfutures.ca" target="_blank"><img style="width: 234px;" src="https://static.igem.org/mediawiki/2013/7/7f/UCalgary2013_Logo_AITF.png"></img></a></td>
 
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<td><a href="http://bio.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2013/4/45/UCalgary2013_BioSci_Logo.png"></img></a></td>
 
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<td><a href="http://enel.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2013/9/9c/UCalgary2013_Schulich_Electric_Computer_Logo.png"></img></a></td>
 
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<td><a href="http://www.ucalgary.ca/bme/about/CBRE" target="_blank"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2013/5/56/UCalgary2013_CBREhz_Cropped.jpg"></img></a></td>
 
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<td><a href="http://www.osli.ca" target="_blank"><img style="width: 891px;" src="https://static.igem.org/mediawiki/2013/9/98/UCalgary2013_Logo_OSLI.png"></img></a></td>
 
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<td><a href="http://www.osrin.ualberta.ca" target="_blank"><img style="width: 204px;" src="https://static.igem.org/mediawiki/2013/0/04/UCalgary2013_OSRIN.png"></img></a></td>
 
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<td><a href="http://www.mhc.ab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2013/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a></td>
 
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<td><a href="http://www.eurofinsdna.com" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2013/a/a4/UCalgary2013_Logo_Eurofins.png"></img></a></td>
 
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<td><a href="http://www.autodesk.com" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2013/0/0b/UCalgary2013-Autodesk-Logo.png"></img></a></td>
 
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<td><a href="http://www.hyperionlab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2013/8/89/UCalgary2013_Hyperion_Research_Logo.png"></img></a></td>
 
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<td><a href="http://www.idtdna.com/site" target="_blank"><img style="width: 228px;" src="https://static.igem.org/mediawiki/2013/1/15/UCalgary2013_Logo_IDT.png"></img></a></img></a></td>
 
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<td><a href="http://www.sarstedt.com/php/main.php" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2013/f/f6/UCalgary2013_Logo_Sarstedt.png"></img></a></td>
 
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<td><a href="http://www.teamlab.com" target="_blank"><img style="width: 160px;" src="https://static.igem.org/mediawiki/2013/b/be/UCalgary2013_Logo_TeamLab.png"></img></a></td>
 
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<td><a href="http://www.vwr.com" target="_blank"><img style="width: 279px;" src="https://static.igem.org/mediawiki/2013/1/11/UCalgary2013_Logo_VWR.png"></img></a></td>
 
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<td><a href="http://genomealberta.ca" target="_blank"><img style="width: 203px;" src="https://static.igem.org/mediawiki/2013/6/68/UCalgary2013_Logo_Genome_Alberta.png"></td>
 
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<td><a href="http://www.neb.com/nebecomm/default.asp" target="_blank"><img style="width: 281px;" src="https://static.igem.org/mediawiki/2013/2/24/UCalgary2013_Logo_NEB.png"></img></a></td>
 
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<td><a href="http://www.sparkscience.ca" target="_blank"><img style="width: 261px;" src="https://static.igem.org/mediawiki/2013/6/6f/UCalgary2013_Logo_Telus_Spark.png"></img></a></td>
 
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Latest revision as of 15:34, 28 October 2013

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The main focus of the iGEM project here at CU-Boulder is to help make synthetic biology more accessible and affordable. We spent the summer developing parts, procedures, and documentation to help make this vision a reality. The original goal was to create the constructs and purification methods necessary to produce and isolate restriction enzymes. Along the way we explored some novel approaches to DNA and protein purification and developed experimentally tested protocols for these and other procedures essential to Biobrick assembly. Our purification methods exemplify the ideal of using common lab materials to make performing everyday lab techniques as accessible and inexpensive as possible. A related aspect of our project was exploring methods of recycling consumables associated with lab work in order to reduce waste and material expenses. We hope that our findings using this "do-it-yourself" approach of synthetic biology help make this type of research more accessible for those where funding is a limiting factor.

"Do It Yourself" Synthetic Biology

One of our main goals was making synthetic biology more accessible. Click here to find out more!

Medal Requirements

Here you can find links to each of the medal requirements we have completed.

Detailed Protocols

We have experimentally developed protocols for many of the lab techniques required for Biobrick assembly.

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