http://2012.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=250&target=Pjwu&year=&month=2012.igem.org - User contributions [en]2024-03-28T10:05:15ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:CalgaryTeam:Calgary2013-08-13T04:53:42Z<p>Pjwu: Undo revision 301256 by Wyjilily (talk)</p>
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<a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals" id="FredOscarFlag"><br />
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<h2>Detect and Destroy: Building FRED and OSCAR</h2><br />
<p><b>Tailings ponds</b> are large bodies of water containing <b>toxic compounds</b> that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential <b>environmental and economic concern</b> to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms <b>to detect and destroy (bioremediate) the toxins</b>, turning them into useable <b>hydrocarbons</b>.</p><br />
<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the descriptions below to learn more!</p><br />
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<img src="https://static.igem.org/mediawiki/2012/0/02/UCalgary2012_ThreeBoxMusic.png"></img><br />
<h2>iGEM Style!</h2><br />
<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><br />
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<a id="greybox5" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><br />
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<h2>Synergy</h2><br />
<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p><br />
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<h2>Intro Video</h2><br />
<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p><br />
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<h2>The Concept</h2><br />
<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><br />
</div><br />
<div class="orangebox"><br />
<h2>Human Practices</h2><br />
<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><br />
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<div class="obox1"><br />
<h2>Initiative</h2><br />
<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><br />
</div><br />
<div class="obox2"><br />
<h2>Interviews</h2><br />
<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><br />
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<div class="obox3"><br />
<h2>Design Considerations</h2><br />
<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><br />
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<div class="obox4"><br />
<h2>Killswitch</h2><br />
<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><br />
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<div class="obox5"><br />
<h2>Safety</h2><br />
<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><br />
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<div class="obox6"><br />
<h2>Community Outreach</h2><br />
<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><br />
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<h2>FRED</h2><br />
<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><br />
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<div class="gbox1"><br />
<h2>Detecting</h2><br />
<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><br />
</div><br />
<div class="gbox2"><br />
<h2>Reporting</h2><br />
<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><br />
</div><br />
<div class="gbox3"><br />
<h2>Modelling</h2><br />
<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><br />
</div><br />
<div class="gbox4"><br />
<h2>Prototyping</h2><br />
<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><br />
</div><br />
<div class="bluebox"><br />
<h2>OSCAR</h2><br />
<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><br />
</div><br />
<div class="bbox1"><br />
<h2>Decarboxylation</h2><br />
<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><br />
</div><br />
<div class="bbox2"><br />
<h2>Catechol Degradation</h2><br />
<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><br />
</div><br />
<div class="bbox3"><br />
<h2>Flux-Variability Analysis</h2><br />
<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><br />
</div><br />
<div class="bbox4"><br />
<h2>Bioreactor</h2><br />
<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><br />
</div><br />
<div class="bbox5"><br />
<h2>Upgrading</h2><br />
<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><br />
</div><br />
</div><br />
</div><br />
<br />
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<div><br />
<img src="https://static.igem.org/mediawiki/2012/b/b8/UCalgary2012_ThreeBoxTeam.png"></img><br />
<h2>Team</h2><br />
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p><br />
</div><br />
</a><br />
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<div><br />
<img src="https://static.igem.org/mediawiki/2012/9/92/UCalgary2012_ThreeBoxData.png"></img><br />
<h2>Data Page</h2><br />
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p><br />
</div><br />
</a><br />
<a id="greybox3" href="https://2012.igem.org/Team:Calgary/Notebook"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/1/1b/UCalgary2012_ThreeBoxNotebook.png"></img><br />
<h2>Notebook</h2><br />
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p><br />
</div><br />
</a><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">Killswitch</a></li><br />
<li><a style="margin:0 -1em 0 1em;" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li><br />
<li><a style="margin:0 -1em 0 1em;" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li> <br />
<li><a href="https://2012.igem.org/Team:Calgary/Safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><br />
<li><a style="margin:0 -1em 0 1em;"href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a style="margin:0 -1em 0 1em;"href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
<br />
</ul><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Parts" id="partslink">Parts</a></li><br />
<li><a class="drop" href="https://2012.igem.org/Team:Calgary/Notebook" id="notebooklink">Notebook</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook">Journal</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols">Protocols</a></li><br />
</ul><br />
</li><br />
<li><a class="drop" href="https://2012.igem.org/Team:Calgary/Outreach" id="outreachlink">Outreach</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/VideoGame">LAB ESCAPE!</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/Spark">Spark Science</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/MindsInMotion">Minds in Motion</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/Blog">Blog Posts</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/TEDxCalgary">TEDxCalgary</a></li><br />
<li><a href="http://twitter.com/iGEMCalgary" target="_blank">Follow Us!</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Sponsors" id="sponsorslink">Sponsors</a></li><br />
<li><a href="https://2012.igem.org" target="_blank">iGEM</a></li><br />
</ul><br />
<br />
</div><br />
</header><br />
<br />
<br />
</body><br />
</html></div>Pjwuhttp://2012.igem.org/Template:Team:Calgary/MainHeaderTemplate:Team:Calgary/MainHeader2013-06-23T21:40:20Z<p>Pjwu: </p>
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<div id="headerimage"><img src="https://static.igem.org/mediawiki/2012/f/fc/UCalgary2012_MainHeaderImage.png"></img></div><br />
<a id="logo" href="https://2012.igem.org/Team:Calgary"></html>{{{1|<html><img src="https://static.igem.org/mediawiki/2012/4/48/UCalgary2012_White_Low-Res_Official_Logo.png"></img></html>}}}<html></a><br />
<div id="nav-wrap"><br />
<ul id="nav"><br />
<li><a href="https://2012.igem.org/Team:Calgary" id="homelink">Home</a></li><br />
<li><a class="drop" href="https://2012.igem.org/Team:Calgary/Team" id="teamlink">Team</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Team">Members</a></li><br />
<li><a class="dropheader" href="http://ung.igem.org/Team.cgi?id=902">Official Profile</a></li><br />
<li><a class="dropheader" href="https://2012.igem.org/Team:Calgary/Team/AbouttheUniversity">The University</a></li><br />
<li><a class="dropheader" href="https://2012.igem.org/Team:Calgary/Team/Outtakes">Outtakes</a></li><br />
<li><a class="dropheader" href="https://2012.igem.org/Team:Calgary/ContactUs">Contact Us</a></li><br />
</ul><br />
</li><br />
<li><a class="drop" href="https://2012.igem.org/Team:Calgary/Project" id="projectlink">Project</a><br />
<ul><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Regionals</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">Initiative</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Interviews</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design">Design</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">Killswitch</a></li><br />
<li><a style="margin:0 -1em 0 1em;" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li><br />
<li><a style="margin:0 -1em 0 1em;" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li> <br />
<li><a href="https://2012.igem.org/Team:Calgary/Safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><br />
<li><a style="margin:0 -1em 0 1em;"href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a style="margin:0 -1em 0 1em;"href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
<br />
</ul><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Parts" id="partslink">Parts</a></li><br />
<li><a class="drop" href="https://2012.igem.org/Team:Calgary/Notebook" id="notebooklink">Notebook</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook">Journal</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols">Protocols</a></li><br />
</ul><br />
</li><br />
<li><a class="drop" href="https://2012.igem.org/Team:Calgary/Outreach" id="outreachlink">Outreach</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/VideoGame">LAB ESCAPE!</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/Spark">Spark Science</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/MindsInMotion">Minds in Motion</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/Blog">Blog Posts</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/TEDxCalgary">TEDxCalgary</a></li><br />
<li><a href="http://twitter.com/iGEMCalgary" target="_blank">Follow Us!</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Sponsors" id="sponsorslink">Sponsors</a></li><br />
<li><a href="https://2012.igem.org" target="_blank">iGEM</a></li><br />
</ul><br />
<br />
</div><br />
</header><br />
<br />
<br />
</body><br />
</html></div>Pjwuhttp://2012.igem.org/Team:Calgary/geekStarterDemoTeam:Calgary/geekStarterDemo2013-03-24T06:18:57Z<p>Pjwu: </p>
<hr />
<div><html><br />
<head><br />
<style type="text/css"><br />
p{<br />
background-color: #DDDDDD;<br />
padding: 15px;<br />
margin-top: 40px;<br />
border: 4px solid red;<br />
}<br />
</style><br />
</head><br />
<br />
<body><br />
<h1>Sample Page</h1><br />
<br />
<a href="https://2013hs.igem.org"><br />
<img src="https://static.igem.org/mediawiki/2012/5/59/Calgary2012_iGEM_Logo.png"></img><br />
</a><br />
<br />
<p>Within academia, <a href="http://en.wikipedia.org/wiki/Plagiarism">plagiarism</a> by students, professors, or researchers is considered academic dishonesty or academic fraud, and offenders are subject to academic censure, up to and including expulsion. In journalism, plagiarism is considered a breach of journalistic ethics, and reporters caught plagiarizing typically face disciplinary measures ranging from suspension to termination of employment. Some individuals caught plagiarizing in academic or journalistic contexts claim that they plagiarized unintentionally, by failing to include quotations or give the appropriate citation. While plagiarism in scholarship and journalism has a centuries-old history, the development of the Internet, where articles appear as electronic text, has made the physical act of copying the work of others much easier.</p><br />
<br />
<p>Plagiarism is defined in multiple ways in higher education institutions and universities. To name a few: Stanford sees plagiarism as “use, without giving reasonable and appropriate credit to or acknowledging the author or source, of another person's original work, whether such work is made up of code, formulas, ideas, language, research, strategies, writing or other form”; [16] Yale views plagiarism as “the use of another’s work, words, or ideas without attribution” which included “using a source’s language without quoting, using information from a source without attribution, and paraphrasing a source in a form that stays too close to the original”; [17] Princeton perceives plagiarism as the deliberate use of “someone else’s language, ideas, or other original (not common-knowledge) material without acknowledging its source”; [18] Oxford characterizes plagiarism as the use of “a writer's ideas or phraseology without giving due credit”; [19] and Brown explains plagiarism to be “appropriating another person's ideas or words (spoken or written) without attributing those word or ideas to their true source”. [20] As well-known institutions, they reflect a common academic definition of plagiarism. Lack of citation, giving credit, or attribution is considered to be plagiarism. In academics, committing plagiarism comes down to failing to cite sources.</p><br />
</body><br />
</html></div>Pjwuhttp://2012.igem.org/Team:Calgary/geekStarterDemoTeam:Calgary/geekStarterDemo2013-03-24T06:04:26Z<p>Pjwu: </p>
<hr />
<div><html><br />
<head><br />
</head><br />
<br />
<body><br />
<h1>Sample Page</h1><br />
<br />
<a href="https://2013hs.igem.org"><br />
<img src="https://static.igem.org/mediawiki/2012/5/59/Calgary2012_iGEM_Logo.png"></img><br />
</a><br />
<br />
<p>Within academia, <a href="http://en.wikipedia.org/wiki/Plagiarism">plagiarism</a> by students, professors, or researchers is considered academic dishonesty or academic fraud, and offenders are subject to academic censure, up to and including expulsion. In journalism, plagiarism is considered a breach of journalistic ethics, and reporters caught plagiarizing typically face disciplinary measures ranging from suspension to termination of employment. Some individuals caught plagiarizing in academic or journalistic contexts claim that they plagiarized unintentionally, by failing to include quotations or give the appropriate citation.<br />
<br />
<br />
<br />
While plagiarism in scholarship and journalism has a centuries-old history, the development of the Internet, where articles appear as electronic text, has made the physical act of copying the work of others much easier.</p><br />
<br />
<p>Plagiarism is defined in multiple ways in higher education institutions and universities. To name a few: Stanford sees plagiarism as “use, without giving reasonable and appropriate credit to or acknowledging the author or source, of another person's original work, whether such work is made up of code, formulas, ideas, language, research, strategies, writing or other form”; [16] Yale views plagiarism as “the use of another’s work, words, or ideas without attribution” which included “using a source’s language without quoting, using information from a source without attribution, and paraphrasing a source in a form that stays too close to the original”; [17] Princeton perceives plagiarism as the deliberate use of “someone else’s language, ideas, or other original (not common-knowledge) material without acknowledging its source”; [18] Oxford characterizes plagiarism as the use of “a writer's ideas or phraseology without giving due credit”; [19] and Brown explains plagiarism to be “appropriating another person's ideas or words (spoken or written) without attributing those word or ideas to their true source”. [20] As well-known institutions, they reflect a common academic definition of plagiarism. Lack of citation, giving credit, or attribution is considered to be plagiarism. In academics, committing plagiarism comes down to failing to cite sources.</p><br />
</body><br />
</html></div>Pjwuhttp://2012.igem.org/Team:Calgary/geekStarterDemoTeam:Calgary/geekStarterDemo2013-03-24T06:03:24Z<p>Pjwu: </p>
<hr />
<div><html><br />
<head><br />
</head><br />
<br />
<body><br />
<h1>Sample Page</h1><br />
<br />
<a href="https://2013hs.igem.org"><br />
<img src="https://static.igem.org/mediawiki/2012/5/59/Calgary2012_iGEM_Logo.png"></img><br />
</a><br />
<br />
<p>Within academia, plagiarism by students, professors, or researchers is considered academic dishonesty or academic fraud, and offenders are subject to academic censure, up to and including expulsion. In journalism, plagiarism is considered a breach of journalistic ethics, and reporters caught plagiarizing typically face disciplinary measures ranging from suspension to termination of employment. Some individuals caught plagiarizing in academic or journalistic contexts claim that they plagiarized unintentionally, by failing to include quotations or give the appropriate citation.<br />
<br />
<br />
<br />
While plagiarism in scholarship and journalism has a centuries-old history, the development of the Internet, where articles appear as electronic text, has made the physical act of copying the work of others much easier.</p><br />
<br />
<p>Plagiarism is defined in multiple ways in higher education institutions and universities. To name a few: Stanford sees plagiarism as “use, without giving reasonable and appropriate credit to or acknowledging the author or source, of another person's original work, whether such work is made up of code, formulas, ideas, language, research, strategies, writing or other form”; [16] Yale views plagiarism as “the use of another’s work, words, or ideas without attribution” which included “using a source’s language without quoting, using information from a source without attribution, and paraphrasing a source in a form that stays too close to the original”; [17] Princeton perceives plagiarism as the deliberate use of “someone else’s language, ideas, or other original (not common-knowledge) material without acknowledging its source”; [18] Oxford characterizes plagiarism as the use of “a writer's ideas or phraseology without giving due credit”; [19] and Brown explains plagiarism to be “appropriating another person's ideas or words (spoken or written) without attributing those word or ideas to their true source”. [20] As well-known institutions, they reflect a common academic definition of plagiarism. Lack of citation, giving credit, or attribution is considered to be plagiarism. In academics, committing plagiarism comes down to failing to cite sources.</p><br />
</body><br />
</html></div>Pjwuhttp://2012.igem.org/Team:Calgary/geekStarterDemoTeam:Calgary/geekStarterDemo2013-03-24T06:01:52Z<p>Pjwu: </p>
<hr />
<div><html><br />
<head><br />
</head><br />
<br />
<body><br />
<h1>Sample Page</h1><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/5/59/Calgary2012_iGEM_Logo.png"></img><br />
<br />
<p>Within academia, plagiarism by students, professors, or researchers is considered academic dishonesty or academic fraud, and offenders are subject to academic censure, up to and including expulsion. In journalism, plagiarism is considered a breach of journalistic ethics, and reporters caught plagiarizing typically face disciplinary measures ranging from suspension to termination of employment. Some individuals caught plagiarizing in academic or journalistic contexts claim that they plagiarized unintentionally, by failing to include quotations or give the appropriate citation.<br />
<br />
<br />
<br />
While plagiarism in scholarship and journalism has a centuries-old history, the development of the Internet, where articles appear as electronic text, has made the physical act of copying the work of others much easier.</p><br />
<br />
<p>Plagiarism is defined in multiple ways in higher education institutions and universities. To name a few: Stanford sees plagiarism as “use, without giving reasonable and appropriate credit to or acknowledging the author or source, of another person's original work, whether such work is made up of code, formulas, ideas, language, research, strategies, writing or other form”; [16] Yale views plagiarism as “the use of another’s work, words, or ideas without attribution” which included “using a source’s language without quoting, using information from a source without attribution, and paraphrasing a source in a form that stays too close to the original”; [17] Princeton perceives plagiarism as the deliberate use of “someone else’s language, ideas, or other original (not common-knowledge) material without acknowledging its source”; [18] Oxford characterizes plagiarism as the use of “a writer's ideas or phraseology without giving due credit”; [19] and Brown explains plagiarism to be “appropriating another person's ideas or words (spoken or written) without attributing those word or ideas to their true source”. [20] As well-known institutions, they reflect a common academic definition of plagiarism. Lack of citation, giving credit, or attribution is considered to be plagiarism. In academics, committing plagiarism comes down to failing to cite sources.</p><br />
</body><br />
</html></div>Pjwuhttp://2012.igem.org/File:Calgary2012_iGEM_Logo.pngFile:Calgary2012 iGEM Logo.png2013-03-24T06:00:13Z<p>Pjwu: </p>
<hr />
<div></div>Pjwuhttp://2012.igem.org/Team:Calgary/geekStarterDemoTeam:Calgary/geekStarterDemo2013-03-24T05:54:21Z<p>Pjwu: </p>
<hr />
<div><html><br />
<head><br />
</head><br />
<br />
<body><br />
<h1>Sample Page</h1><br />
<p>Within academia, plagiarism by students, professors, or researchers is considered academic dishonesty or academic fraud, and offenders are subject to academic censure, up to and including expulsion. In journalism, plagiarism is considered a breach of journalistic ethics, and reporters caught plagiarizing typically face disciplinary measures ranging from suspension to termination of employment. Some individuals caught plagiarizing in academic or journalistic contexts claim that they plagiarized unintentionally, by failing to include quotations or give the appropriate citation. While plagiarism in scholarship and journalism has a centuries-old history, the development of the Internet, where articles appear as electronic text, has made the physical act of copying the work of others much easier.</p><br />
<br />
<p>Plagiarism is defined in multiple ways in higher education institutions and universities. To name a few: Stanford sees plagiarism as “use, without giving reasonable and appropriate credit to or acknowledging the author or source, of another person's original work, whether such work is made up of code, formulas, ideas, language, research, strategies, writing or other form”; [16] Yale views plagiarism as “the use of another’s work, words, or ideas without attribution” which included “using a source’s language without quoting, using information from a source without attribution, and paraphrasing a source in a form that stays too close to the original”; [17] Princeton perceives plagiarism as the deliberate use of “someone else’s language, ideas, or other original (not common-knowledge) material without acknowledging its source”; [18] Oxford characterizes plagiarism as the use of “a writer's ideas or phraseology without giving due credit”; [19] and Brown explains plagiarism to be “appropriating another person's ideas or words (spoken or written) without attributing those word or ideas to their true source”. [20] As well-known institutions, they reflect a common academic definition of plagiarism. Lack of citation, giving credit, or attribution is considered to be plagiarism. In academics, committing plagiarism comes down to failing to cite sources.</p><br />
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<h2> Tight Regulation </h2><br />
<p>Inducible kill systems are not new to iGEM. Looking through the registry, there are several constructs such as the inducible BamHI system contributed by Berkley in 2007 (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_I716462">BBa_I716462</a>) and <a href="http://partsregistry.org/Image:UoflBamHIdatasheet.png">tested by Lethbridge in 2011</a>. This uses a <i>BamHI</i> gene downsteam of an arabinose-inducible promoter. Another example is an IPTG inducible Colicin construct (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K117009">BBa_K117009</a>) submitted by NTU-Singapore in 2008. One major problem with these systems however is a lack of tight control. As was demonstrated by the Lethbridge 2011 team, this part has leaky expression when inducer compound is not present. The frequently used lacI promoter has similar problems when not used in conjunction with strong plasmid-mediated expression of lacI. This can be seen in our electrochemical characterization of the UidA hydrolase enzyme (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902002">BBa_K902002</a>) shown here. Tight control is not only a problem for kill switch application, but for any application requiring strict regulation. As such, we decided that expanding the registry repertoire of control elements would be useful for our system as well as a variety of other applications. Therefore we added a new level of regulation in addition to the promoter, a riboswitch.</p><br />
<h2> Introducing the Riboswitch </h2><br />
<p>Riboswitches are small pieces of mRNA which bind ligands to modify translation of downstream genes. These sites are engineered into circuits by replacing traditional ribosome binding sites with riboswitches. The riboswitch is able to bind its respective ligand to inhibit or promote binding of translational machinery (Vitreschak <i>et al</i>, 2004). Riboswitches can be used in tandem with an appropriate promoter to enable tighter control of gene expression. Given this opportunity for control, and that ligands for riboswitches are often inexpensive small ions, these methods might be a feasible solution for controlling the kill switch in our industrial bioreactor.</p><br />
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</html> [[File:UofC_RIBOSWITCH.png|thumb|350px|centre|Figure 1: A simple diagram illustrating the riboswitch and the three metabolite, magnesium, manganese and molybdenum, we have tested.]] <html><br />
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<p>We explored 3 different riboswitches, each responsive to a different metabolite (magnesium, manganese or molybdate co-factor) that would be inexpensive to implement into a bioreactor environment. Additionally, we also investigated a repressible and inducible promoter, responsive to glucose and rhamnose respectively.</p><br />
<p>The general approach taken to build the system was constructing the promoter with the respective riboswitch followed by the kill genes. </p><br />
<h2>Magnesium riboswitch</h2><br />
<p>The magnesium riboswitch that we looked at is repressed in the presence of magnesium ions. This system has two control components – a promoter and a riboswitch. Normally the magnesium (mgtA) promoter (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902009">BBa_K902009</a>) and the magnesium (mgtA) riboswitch (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902008">BBa_K902009</a>) are activated if there is a deficiency of magnesium in the cell (Groisman, 2001). The sequence of the <i>mgtA</i> promoter and riboswitch was obtained from Winnie and Groisman. A lack of magnesium activates other genes in <i>E. coli </i>to allow influx of magnesium into the cell. The two proteins in the cascade that activate the system are <i>PhoP</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902010">BBa_K902010</a>) and <i>PhoQ</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902011">BBa_K902011</a>). <i>PhoQ</i> is the trans-membrane protein which gets activated in the absence of magnesium and phosphorylates <i>PhoP</i>. <i>PhoP</i> in turn binds to the mgtA promoter and transcribes genes downstream (Groisman, 2001).</p><br />
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<h2>Manganese riboswitch</h2><br />
<p> Manganese is an essential micronutrient. It is an important co-factor for enzymes and it also reduces oxidative stress in the cell (Waters <i>et al</i>. 2011). Despite being an important micronutrient, it is toxic to cells at high levels. MntR protein detects the level of manganese in the cell and acts as a transcription factor to control the expression of manganese transporter such as MntH, MntP and MntABCDE. In order to regulate these genes <i>mntR</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902030">BBa_K902030</a>) binds to the mntP promoter (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902073">BBa_K902073</a>). The manganese homeostasis is also controlled by the manganese riboswitch <i>mntPrb</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902074">BBa_K90274</a>). The sequences of the <i>mntP</i> promoter and the <i>mntP</i> riboswitch was obtained from the Waters et al, 2011.</p><br />
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[[File:Ucalgary2012 KillswitchstuffsystemsAandB.png|thumb|800px|left|Figure 2: '''A)''' MgtA pathway in <i>E. coli</i>. <i>PhoQ</i> is the transmembrane receptor which, upon detecting low magnesium concentrations, phosphorylates <i>PhoP</i> which acts as a transcription factor, transcribing genes downstream of the MgtA promoter necessary for bringing magnesium into the cell. There is a second level of control with the magnesium riboswitch. In the presence of high magnesium the riboswitch forms a secondary structure which does not allow the ribosome to bind to the transcript, thus inhibiting translation. '''B)''' In the presence of manganese, the <i>MntR</i> protein represses the <i>mntH</i> transporter, preventing the movement of manganese and also upregulating the putative efflux pump. Genes downstream of the mntP promoter are thus transcribed in the presence of manganese. The addition of the <i>MntR</i> protein in this system allows for tighter regulation of the system.]]<html><br />
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<h2> The Moco Riboswitch </h2><br />
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<p>The molybdenum cofactor riboswitch (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902023">BBa_K902023</a>) is an RNA element which responds to the presence of the metabolite molybdenum cofactor (MOCO) (Regulski et al, 2008). This RNA element is located in the <i>E.coli</i> genome just upstream of the <i>moaABCDE</i> operon (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902024">BBa_K902024</a>), containing the MOCO synthesis genes. MOCO is an important co-factor in many different enzymes. The MOCO riboswitch has 2 regions: an aptamer domain and the expression platform. When MOCO is present in the cell it will bind to the aptamer region in the riboswitch causing an allosteric change. This allosteric change affects the expression platform by physically hiding the ribosome binding site which prevents translation.</p><br />
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[[File:Moco_riboswitchCalgary2012.jpg|thumb|750px|center|Figure 3: This picture depicts the MOCO RNA motif which is upstream of the <i>moaABCDE</i> operon. ]]<html> <br />
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<h2> Building the Systems </h2><br />
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<p> Using these riboswitches, we wanted to design a system where we would place our kill genes downstream, and then supplement our bioreactor with the appropriate ions to keep the systems turned off. We biobricked and submitted DNA for the the <i>mgtaP</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902009">BBa_K902009</a>) and mntP promoter (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902073">BBa_K902073</a>) as well as their respective riboswitches (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902008">BBa_K902008</a>) (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902074">BBa_K902074</a>) and the MOCO riboswitch (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902023">BBa_K902023</a>). In addition, we also biobricked some of the regulatory proteins: <i>PhoP</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902010">BBa_K902010</a>), <i>PhoQ</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902011">BBa_K902011</a>), <i>mntR</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902030">BBa_K902030</a>) and the Moa Operon (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902024">BBa_K902024</a>). Our final system would inovolve constitutive expression of these necessary regulatory elements upstream of our riboswitches and kill genes. An example of the manganese system is shown in Figure 4. </p><br />
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</html>[[File:U.Calgary.2012_10.02.2012_Final_Construct_1.png|thumb|600px|center|Figure 4: Final construct for the manganese system. The circuit includes a TetR promoter, RBS, mntR, double terminator, mntP promoter, mntP riboswitch, <i>S7</i>, mntP riboswitch and <i>CViAII</i>.]]<html><br />
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<a name="killswitch"></a><h2> Characterizing the riboswitches </h2><br />
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<h3> GFP testing</h3><br />
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</html>[[File:MgtA circuits Ucalgary1.png|thumb|150px|right|Figure 5: In these sets of circuits, <i>TetR</i>-RBS-K082003 serves as a positive control and the <i>mgtAp-mgtArb</i> serves as a negative control.]]<html><br />
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<p> In order to test the control of these promoters and riboswitches, we constructed them independently and together upstream of GFP (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K082003">BBa_K082003</a>) with an LVA tag. Figure 5 shows these circuits for the mgtA system. Identical circuits were designed for all three systems, however only the top two were needed for the MOCO riboswitch system.</p><br />
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<p>We then tested the aforementioned circuits by growing cells containing our circuits with varying concentrations of their respective ions. Our detailed protocols can be found <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mgcircuit">here</a>. We then measured fluorescent output, normalizing to a negative control not expressing GFP.</p><br />
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<h3> Results </h3><br />
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<p>So far, we have been able to obtain results for our magnesium system, as can be seen in Figure 6. </html><br />
[[File:Magmesium graph ucalgary2.png|thumb|500px|left|Figure 6: This graph represents the relative fluorescence units from the mgtA promoter riboswitch construct as well as the riboswitch construct under the TetR promoter (BBa_R0040). We can see a decrease in the level of GFP output with increasing concentrations of magnesium. There is much steeper decrease in the GFP output in the construct with the magnesium promoter and riboswitch compared to the construct with just the riboswitch alone.]]<html></p><br />
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<p>As the graph shows, there is a much larger decrease in the GFP output when the mgtA promoter and riboswitch are working together as compared to the <i>mgtA</i> riboswitch alone under the control of TetR promoter (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_J13002">BBa_J13002</a>). This suggests that having both the promoter and the riboswitch together provides a tighter control over the genes expressed downstream. This also suggests that the magnesium riboswitch alone is sufficient in reducing gene expression downstream of a constitutive promoter.</p><br />
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<p> It is important to consider however that the control elements of the system, <a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902010"><i>PhoP</i> </a> and <a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902011"> <i>PhoQ</i></a>, that were described above were not present in the circuits tested and therefore there is GFP expression in at the inhibitory concentration (10 mM MgCl<sub>2</sub>). We believe that having the regulatory elements would give us better control and limit the leakiness.</p><br />
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<p>Although the magnesium system is highly regulated, it is not a suitable system for the purposes of our bioreactor. The tailings are composed of very high concentration of magnesium, as high as 120 mM (Kim <i>et al</i>. 2011). As can be seen, this would inhibit the system. Therefore, if our bacteria were to escape into the tailings, the kill genes would not be activated and the bacteria would be able to survive. However, we feel that this could still be an incredibly useful system for other teams for both killswitch and non-killswitch-related applications, making it still a valuable contribution to the registry. </p><br />
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<h3> Kill Gene Testing </h3><br />
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<p> While building our systems with GFP in order to test their control, we also constructed them with our kill genes. This was delayed substantially however due to problems in their synthesis. Specifically, the micrococcal nuclease that arrived from IDT had a 1bp point mutation which changed an isoleucine residue into a lysine. Initially, our systems resulted in no killing of cells. Therefore we had to mutate this residue using <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mutagenesis"> site-directed mutagenesis</a>. Once completed, we were able to begin testing. With our GFP data collected, we moved on to characterizing the mgtA control system upstream of our <i>S7</i> kill gene (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902019">BBa_K902019</a>). To test the circuits, we incubated cells expressing our construct with varying concentrations of magnesium. We then measured both Colony Forming Units (CFU) and OD 600. For a detailed protocol, see <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mgtacircuit">here</a>.</p><br />
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<h3> Results </h3><br />
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</html>[[File: 24 hour assay with mgtap-rb-S7-1.png|thumb|750px|center| Figure 7: This shows the OD600 values of mgtA circuits with S7 both mutated and unmutated. The negative control consists of <i>mgtAp-mgtArb</i>.]]<html><br />
<p> Figure 7 shows that the mgtAp-mgtArb-S7 (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902018">BBa_K902018</a>) starts acting approximately 4 hours after induction. However, it also shows that 10mM MgCl<sub>2</sub> is not enough salt to inhibit the entire system because there is no difference in OD600 measurement at 4hr time point between 10mM and the 0mM concentrations. This test needs to be repeated with higher concentrations of Mg<sup>2+</sup> however this data suggests that the mutagenesis was successful and <i>S7</i> is active and killing the cells at approximately 4hr which does not necessarily reflect solely upon the activity of <i>S7</i> but also on the response time of the mgtA system.</p><br />
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<h2>An alternative: a glucose repressible system</h2><br />
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<p>Based on the problem with the magnesium system in relation to tailings pond conditions, we wanted to find an alternative. We found a promoter that was induced by rhamnose and repressed by glucose. This seemed to be a very suitable candidate for controlling the kill switch in the bioreactor since the promoter was shown to be tightly repressed by glucose. We could supplement the bioreactor with glucose to inhibit expression of the kill genes in the bioreactor. Escape of bacteria into the tailings ponds would cause expression of the kill genes due to lack of glucose in the surrounding environment.<br />
</p> <br />
<p>This promoter, known as <i>pRha</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902065">BBa_K902065</a>), is responsible for regulating genes related to rhamnose metabolism and contains a separate promoter on its leading and reverse strands (see Figure 8). <i>RhaR</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902069">BBa_K902069</a>) and <i>RhaS</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902068">BBa_K902068</a>) serve to regulate expression of the rhamnose metabolism operon <i>rhaBAD</i>. The <i>RhaR</i> transcription factor is activated by L-rhamnose to up-regulate expression <i>rhaSR</i> operon. In turn, the resulting <i>RhaS</i> activates the <i>rhaBAD</i> operon to generate the rhamnose metabolism genes (Egan & Schleif, 1993).</p><br />
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</html>[[File:NativeRhamnosePromoter_Calgary2012.jpg|thumb|600px|center|Figure 8: The rhamnose metabolism genes as they exist in Top Ten <i>E. coli</i>]]<br />
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</html>[[File:PrhaFinal.png|thumb|600px|center|Figure 9: The rhamnose metabolism genes native to <i>E. coli</i>]]<br />
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<p>Our kill system is different from the native rhamnose system with the <i>rhaR</i> and <i>rhaS</i> control genes. We have constitutively expressed <i>RhaS</i> to overcome dependency on rhamnose to cause activation of the kill switch. While <i>RhaS</i> is continuously present, the system is shut off in the presence of glucose. However, in the outside environment glucose levels are lower such that <i>RhaS</i> is able to activate the kill genes.</p><br />
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<a name="Prha_results"></a><br />
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<h3>Building the system</h3><br />
<p>Our team had <i>pRha</i> promoter (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902065">BBa_K902065</a>) commercially synthesized as per the sequence given by Jeske and Altenbuchner (2010). The <i>rhaS</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902068">BBa_K902068</a>) and <i>rhaR</i> (<a href="http://partsregistry.org/wiki/index.php/Part:BBa_K902069">BBa_K902069</a>) genes were amplified via PCR from Top 10 <i>E. coli</i> using Kapa HiFi polymerase. </p><br />
<p>We tested the unoptimized rhamnose system using a fluorescent output. </html> [[File:Calgary_RhaGFPFinal.png|thumb|600px|centre|Figure 10: This has Prha-RBS-GFP that was incubated under different conditions. We can see a large increase with 0.2% rhamnose, 0.5% rhamnose whereas there is no GFP expression in the cells incubated with glucose.]] <html> </p><br />
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<p> Figure 10 shows that the rhamnose system works as expected. The system is turned off with 0.2% glucose whereas GFP is significantly upregulated with 0.2% rhamnose and even more with 0.5% rhamnose. In this system we do not have the RhaS constitutively expressed and therefore GFP may not be expressed in the the control without either glucose or rhamnose. But, we are currently working on building this circuit and will be characterizing the RhaS with Prha and Prha by itself using GFP as a reporter.<br />
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</p><br />
<p>Additionally, we also tested the rhamnose system with micrococcal nuclease in the presence of glucose and rhamnose in both Top10 cells as well as glyA knockout from the Keio knockout collection on the <a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy Page</a> to compare the GlyA knockout alone, GlyA knockout with killswitch, Top10 with killswitch. </p><br />
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<p><br />
<h2> The Glycine Auxotroph </h2><br />
<p> The idea of using an auxotropic system was initially considered, however due to the pricing of this system we felt it to be inappropriate for a large scale bioreactor. Auxotrophic systems that we had looked into included the 5-fluoro-orotic acid and histidine, which were both found to be expensive. This idea was reconsidered when our <a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Variability Analysis</a> showed that the Petrobrick system can be optimized with glycine added to the media. The production of hydrocarbons increased by a factor of 3 with our glycine media when compared to Washington’s production media. This finding justified our introduction of a glycine auxotrophic system as the increased efficiency of the Petrobrick in addition to another safety feature far outweighed the cost of implementing the system. This is feasible because glycine is not readily found in the environment and is relatively inexpensive to supplement on a large scale. </p> <p> We used a knockout strain JW2535-1 from the Keio collection in which the gene responsible for the synthesis of glycine was knocked out. The bacteria become dependent on glycine in the environment. The JW2535-1 knockout strain used works directly on glyA which is a component of the glycine hydroxymethyltransferase by mutating the glyA into Kan which overall prevents the bacteria’s growth. A glycine assay was set up to determine concentrations of glycine needed for the survival of the bacteria. The bacteria were grown on minimal media plate with glycine concentrations ranging from 1 nM to 100 mM. When zero glycine was added to the media there was some bacterial growth over time. This system will therefore need to work in conjunction with the kill switch system as another layer of security to reduce possibility of escapers. Please see our <a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy Page</a> for more information. </p><br />
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}}</div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/HumanPractices/InterviewsTeam:Calgary/Project/HumanPractices/Interviews2012-12-15T20:28:44Z<p>Pjwu: </p>
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<h2>Purpose</h2><br />
<p> This year the Calgary iGEM team undertook our project with human practices in mind. While we had established a research objective to produce a biosensor and bioreactor system, we wanted to ensure that our system was relevant to the industry where it would be employed. As well, we wanted to ensure that academic, government, and industry professionals' concerns were taken into consideration during the design process of our system. In order to best accomplish this, we conducted interviews with two leaders in oilsands reclamation. We approached a major oilsands company, Suncor, and talked to Christine Daly, an Ecologist who works in Environmental Cleanup. We then approached Ryan Radke, the president of BioAlberta. BioAlberta focuses on bringing biotechnology to our province and develop these in an industrial setting. His experience allowed us to better predict if our project would raise concerns among legislators and industrial leaders. <br />
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<h2>Initial Interviews</h2><br />
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<h3>Talking with Suncor's Christine Daly on Biology in the Oil Sands</h3><br />
<p>We spoke with Christine Daly, an Aquatic Reclamation Research Coordinator at Suncor Energy Inc. Christine expressed an interest in our <a href="https://2011.igem.org/Team:Calgary">project in 2011</a> and was willing to discuss this year’s project design with us. One major point that was brought up early on was that engineered organisms might outcompete existing tailings ponds bacteria, and Christine had similar reservations. To address these concerns, we created our <a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">bioreactor</a> system, which would physically contain our bacteria, and also a <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">genetic killswitch mechanism</a>. Another interesting point brought up in this discussion was how the oil industry is currently looking into biology as one of many potential alternative methods to remediate the toxic components of tailings ponds and the oil sands in general. There is research using other systems such as algal bioremediation, but practical implementations of biology in the oil sands are rare. Oil industries do, however, appear to show an increased interest in biology (and in turn, synthetic biology) as a possible solution to various problems, a sentiment reflected in <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">our dialogue with the Oil Sands Leadership Initiative</a>.</p><br />
<p>The full interview can be viewed below.</p><br />
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<h3>BioAlberta's Ryan Radke on Biology in the Oil Sands</h3><br />
<p>We were also able to consult with BioAlberta president Ryan Radke on the viability of using biologically based systems in the petroleum industry. He believed that bioremediation technologies will be critical to the future of the oil sands in the next 10-15 years, however he raised the concern of how we could sell biotechnology to an industry that is already very successful from a profit point of view. He emphasized the social welfare benefits that the industry, under heavy environmental criticism, could gain from this technology as a major selling point and stressed the need to educate the oil industry about the benefits of synthetic biology. This would involve putting aspects of our system into large-scale, comprehensive terms to sell to those without a biology background. For example, quantifying the amount of toxins that the system can process per unit time and the value of hydrocarbons produced is something that could potentially appeal to investors. We feel as though the synthetic biology <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">dialogue with the Oil Sands Leadership Initiative</a> was a great start to bridging the gap between the petroleum industry and synthetic biology. From a public perspective point of view we discussed the need to stress the fact our system is simply a modification of "natural" processes - that is we are only modifying bacteria native to the tailings ponds, not introducing new organisms to the environment. To further address safety concerns, we also need to emphasize the multiple layers of <a href="https://2012.igem.org/Team:Calgary/Safety">biological and physical control</a> that we plan to design.</p> <br />
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<h2>Follow-Up Interviews</h2><br />
<p>Our second iteration of interviews were conducted once we had a more concrete product built. The purpose of these interviews was to see whether we had successfully addressed the concerns of the first iteration interviews. We also wanted to see whether any new issues with the design existed, which would provide us with potential future directions to take FRED and OSCAR. Kelly Roberge, an independent oil consultant, suggested we investigate ways of dealing with the clay and silt particles in tailings pond water that would enter our bioreactor system. This can be a major problem since these mature fine tailings have a thick consistency that could clog the system.</p><br />
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<h3>Kelly Roberge, of K. Roberge Consulting Ltd. Discussing Bioreactor Improvements</h3><br />
<p>We spoke to Kelly Roberge of K. Roberge Consulting Ltd. who is an independent consultant for the oil sands focusing on mature fine tailings (MFT). He mentioned that in the past 4 years, there has been an increase in looking at biological techniques in the oil sands for remediation, both in understanding natively present microbial life as well as introducing engineered systems.</p><br />
<p> The major concerns that he had with our present design were issues with scale-up. These were things such as the amount of toxins that would have to be processed to provide constant generation of product, residence time in the bioreactor, as well as the ability for our system to be scaled up to an industrial size. Though we still have much research to do toward this goal of reaching industrial capacity, we did a model scale-up experiment of OSCAR by growing the PetroBrick containing <i>E. coli</i> in our model bioreactor system. The results of this experiment can be found on our <a class="purple" href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a> page.</p><br />
<p>In addition, there was a concern raised with the composition of the tailings themselves, due to the mature fine tailings sludge (MFT). In the future we should look at addressing the capacity of OSCAR to deal with these MFT components. Some suggestions that were made would be to utilize OSCAR in parallel with MFT settling techniques or with runoff water from the tailings drying processes. The sensitivity of our system to these fine tailings and to bitumen would also have to be evaluated and made compatible with the substrates we will be adding in to the system.</p><br />
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<h3>William Sawchuk, of ARC Resources</h3><br />
<p>William Sawchuk, a reservoir engineer at Arc resources, agreed to talk with us about the main parts of our project. This interview confirmed that biological methods, and specifically our project, are definite possibilities of remediation in the oil sands if they can prove to be faster and less harmful than current methods. One concern that Mr. Sawchuk brought up was that there needs to be extra safety features put in place to avoid posing danger to the environment. This again, serves to further validate the approach that we took to safety, designing both <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design"> structural and genetic killswitch devices</a>. In the later part of our project, we have also been trying to work on establishing a <a class="purple" href="https://2012.igem.org/Team:Calgary/Project/Synergy">glycine auxotrophic killswitch</a> to add yet another layer of safety which we feel is necessary. </p><br />
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<p>Similar to Mr. Roberge, another thing Mr. Sawchuk brought up was scale-up. Specifically, he talked about feasibility and how much a scale-up of the project would cost and if this is less expensive than the current remediation methods. To this end, we have been experimenting with getting our bioreactor to work and have performed an initial validation assay to demonstrate that we can use it in conjunction with our belt skimmer to produce and harvest hydrocarbons, which can be found on our <a class="purple" href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a> page. The next step is to scale-up further! Calculating exact costs is a tricky. Since the conversion of toxins in the tailings ponds into useful hydrocarbons is a relatively novel idea, it is somewhat difficult to analyze what the cost of a scale-up would be at this point. This is an extremely important future direction for us however.</p><br />
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<h3>Gordon Lambert, VP Sustainable Development at Suncor Inc.</h3><br />
<p>Gordon Lambert is the VP Sustainable Development at Suncor Energy Inc. We asked him whether or not the oil sands industry would find technology such as this useful. There was a very positive response. The Oil Sands Leadership Initiative is very keen on searching for any solutions to tackle the tailings ponds, which are considered to be one of the biggest issues in the oil sands currently. <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">OSLI</a> is collaborating with organizations that run competitions globally for oil sands solutions and other bodies such the Canada's Oil Sands Innovation Alliance (COSIA). Similar to Kelly Roberge's comment, mature fine tailings can be dried and solidified, but in turn it liberates water from the clay and sand. This water cannot be used for any industrial purposes until it is detoxified. Ideally, this water can be detoxified sufficiently to be returned as tailings pond surface water and become reusable in the bitumen extraction process.</p><br />
<p>In order to deploy our biosensor and bioreactor system, it was suggested that we look into various regulatory boards within Alberta such as Alberta Environment and the Energy Resources Conservation Board (ERCB) to attempt to obtain permits to begin attempting pilot programs. <a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Scale up</a> of the bioreactor is also a major consideration in order for us to push it off the bench and into the field.</p><br />
<p>The full interview can be found below.</p><br />
<br />
<div align="center"><br />
<iframe width="600" height="450" src="http://www.youtube.com/embed/7KbEjQVUsFA" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<h3>Zvonko Burkus from Alberta Environment Discusses the Project in Detail</h3><br />
<p>Zvonko is a process water and policy specialist for Alberta Environment. Zvonko was happy to discuss with us at length about this project. Notably, there were concerns about the use of both <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED </a> and <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a> in active tailings ponds, since naphthenic acids are known surfactants which help with bitumen detachment from the sand particles. FRED was seen as something which could be more useful in a live-monitoring system, since currently there are no such systems for organic compounds, which is a possible direction for us.</p><br />
<p>We were warned that the oil industry is rather traditional, but as we have seen from our <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">OSLI dialogue</a>, it appears that more companies are beginning to see the potential benefit of biology in solving various issues with the oil sands.</p><br />
<p>Some interesting points for us to explore further included examining whether or not the intermediates of our metabolic pathways were more or less toxic than the starting compounds, and expanding our scope to target other compounds such as polyaromatic hydrocarbons, chlorides, composite tailings, polyphenols, and hydrogen sulfide.</p><br />
<p>The interview, in full, has been divided into six parts. Please click the links below to download them.</p><br />
<p><a href="https://static.igem.org/mediawiki/2012/a/aa/UCalgary2012_Zvonko_Burkus_Interview-01.mp3">Part 1</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/b/ba/UCalgary2012_Zvonko_Burkus_Interview-02.mp3">Part 2</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/0/0e/UCalgary2012_Zvonko_Burkus_Interview-03.mp3">Part 3</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/b/b8/UCalgary2012_Zvonko_Burkus_Interview-04.mp3">Part 4</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/c/c1/UCalgary2012_Zvonko_Burkus_Interview-05.mp3">Part 5</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/7/70/UCalgary2012_Zvonko_Burkus_Interview-06.mp3">Part 6</a><br/></p><br />
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<a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals" id="FredOscarFlag"><br />
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<h2>Detect and Destroy: Building FRED and OSCAR</h2><br />
<p><b>Tailings ponds</b> are large bodies of water containing <b>toxic compounds</b> that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential <b>environmental and economic concern</b> to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms <b>to detect and destroy (bioremediate) the toxins</b>, turning them into useable <b>hydrocarbons</b>.</p><br />
<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the descriptions below to learn more!</p><br />
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<h2>iGEM Style!</h2><br />
<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><br />
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<h2>Synergy</h2><br />
<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p><br />
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<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p><br />
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<a class="bbox2 iconbox" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation"><br />
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<img src="https://static.igem.org/mediawiki/2012/0/0c/UCalgary2012_IconOSCAR4.png"></img><br />
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</a><br />
<a class="bbox3 iconbox" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/4/40/UCalgary2012_IconOSCAR6.png"></img><br />
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</a><br />
<a class="bbox4 iconbox" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor"><br />
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<img src="https://static.igem.org/mediawiki/2012/3/3e/UCalgary2012_IconOSCAR5.png"></img><br />
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</a><br />
<a class="bbox5 iconbox" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/4/44/UCalgary2012_IconOSCAR7.png"></img><br />
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</a><br />
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</a><br />
</div><br />
</div><br />
<div id="boxinfo"><br />
<div id="boxinfo_default"><br />
<h2>The Concept</h2><br />
<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><br />
</div><br />
<div class="orangebox"><br />
<h2>Human Practices</h2><br />
<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><br />
</div><br />
<div class="obox1"><br />
<h2>Initiative</h2><br />
<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><br />
</div><br />
<div class="obox2"><br />
<h2>Interviews</h2><br />
<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><br />
</div><br />
<div class="obox3"><br />
<h2>Design Considerations</h2><br />
<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><br />
</div><br />
<div class="obox4"><br />
<h2>Killswitch</h2><br />
<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><br />
</div><br />
<div class="obox5"><br />
<h2>Safety</h2><br />
<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><br />
</div><br />
<div class="obox6"><br />
<h2>Community Outreach</h2><br />
<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><br />
</div><br />
<div class="greenbox"><br />
<h2>FRED</h2><br />
<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><br />
</div><br />
<div class="gbox1"><br />
<h2>Detecting</h2><br />
<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><br />
</div><br />
<div class="gbox2"><br />
<h2>Reporting</h2><br />
<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><br />
</div><br />
<div class="gbox3"><br />
<h2>Modelling</h2><br />
<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><br />
</div><br />
<div class="gbox4"><br />
<h2>Prototyping</h2><br />
<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><br />
</div><br />
<div class="bluebox"><br />
<h2>OSCAR</h2><br />
<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><br />
</div><br />
<div class="bbox1"><br />
<h2>Decarboxylation</h2><br />
<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><br />
</div><br />
<div class="bbox2"><br />
<h2>Catechol Degradation</h2><br />
<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><br />
</div><br />
<div class="bbox3"><br />
<h2>Flux-Variability Analysis</h2><br />
<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><br />
</div><br />
<div class="bbox4"><br />
<h2>Bioreactor</h2><br />
<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><br />
</div><br />
<div class="bbox5"><br />
<h2>Upgrading</h2><br />
<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><br />
</div><br />
</div><br />
</div><br />
<br />
<div class="threeboxes"><br />
<a id="greybox1" href="https://2012.igem.org/Team:Calgary/Team"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/b/b8/UCalgary2012_ThreeBoxTeam.png"></img><br />
<h2>Team</h2><br />
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p><br />
</div><br />
</a><br />
<a id="greybox2" href="https://2012.igem.org/Team:Calgary/Project/DataPage"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/9/92/UCalgary2012_ThreeBoxData.png"></img><br />
<h2>Data Page</h2><br />
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p><br />
</div><br />
</a><br />
<a id="greybox3" href="https://2012.igem.org/Team:Calgary/Notebook"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/1/1b/UCalgary2012_ThreeBoxNotebook.png"></img><br />
<h2>Notebook</h2><br />
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p><br />
</div><br />
</a><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<div id="sponsorsbox"><br />
<h2>Thanks to Our Sponsors!</h2><br />
<table><br />
<tr><br />
<td><a href="http://www.ucalgary.ca/bhsc/node/16" target="_blank"><img style="width: 284px;" src="https://static.igem.org/mediawiki/2012/d/d6/UCalgary2012_Logo_O%27Brien_Centre.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca" target="_blank"><img style="width: 166px;" src="https://static.igem.org/mediawiki/2012/4/46/UCalgary2012_Logo_U_of_C_Vertical.png"></img></a></td><br />
<td><a href="http://www.albertatechfutures.ca" target="_blank"><img style="width: 234px;" src="https://static.igem.org/mediawiki/2012/7/7f/UCalgary2012_Logo_AITF.png"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://bio.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/4/45/UCalgary2012_BioSci_Logo.png"></img></a></td><br />
<td><a href="http://enel.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/9/9c/UCalgary2012_Schulich_Electric_Computer_Logo.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca/bme/about/CBRE" target="_blank"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2012/5/56/UCalgary2012_CBREhz_Cropped.jpg"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://www.osli.ca" target="_blank"><img style="width: 891px;" src="https://static.igem.org/mediawiki/2012/9/98/UCalgary2012_Logo_OSLI.png"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://www.osrin.ualberta.ca" target="_blank"><img style="width: 204px;" src="https://static.igem.org/mediawiki/2012/0/04/UCalgary2012_OSRIN.png"></img></a></td><br />
<td><a href="http://www.mhc.ab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a></td><br />
<br />
<td><a href="http://www.eurofinsdna.com" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a></td><br />
<br />
</tr><br />
<tr><br />
<td><a href="http://www.autodesk.com" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/0/0b/UCalgary2012-Autodesk-Logo.png"></img></a></td><br />
<td><a href="http://www.hyperionlab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/8/89/UCalgary2012_Hyperion_Research_Logo.png"></img></a></td><br />
<td><a href="http://www.idtdna.com/site" target="_blank"><img style="width: 228px;" src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a></img></a></td><br />
</tr><br />
<tr><br />
<td><a href="http://www.sarstedt.com/php/main.php" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/f/f6/UCalgary2012_Logo_Sarstedt.png"></img></a></td><br />
<td><a href="http://www.teamlab.com" target="_blank"><img style="width: 160px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a></td><br />
<td><a href="http://www.vwr.com" target="_blank"><img style="width: 279px;" src="https://static.igem.org/mediawiki/2012/1/11/UCalgary2012_Logo_VWR.png"></img></a></td><br />
</tr><br />
<tr><br />
<table><tr><br />
<td><a href="http://genomealberta.ca" target="_blank"><img style="width: 203px;" src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></td><br />
<td><a href="http://www.neb.com/nebecomm/default.asp" target="_blank"><img style="width: 281px;" src="https://static.igem.org/mediawiki/2012/2/24/UCalgary2012_Logo_NEB.png"></img></a></td><br />
<td><a href="http://www.sparkscience.ca" target="_blank"><img style="width: 261px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a></td><br />
<br />
</tr></table><br />
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</table><br />
</div><br />
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</body><br />
</html></div>Pjwuhttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-11-28T20:13:00Z<p>Pjwu: </p>
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<a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals" id="FredOscarFlag"><br />
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<h2>Detect and Destroy: Building FRED and OSCAR</h2><br />
<p><b>Tailings ponds</b> are large bodies of water containing <b>toxic compounds</b> that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential <b>environmental and economic concern</b> to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms <b>to detect and destroy (bioremediate) the toxins</b>, turning them into useable <b>hydrocarbons</b>.</p><br />
<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the descriptions below to learn more!</p><br />
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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><br />
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<h2>Synergy</h2><br />
<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p><br />
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<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p><br />
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<h2>The Concept</h2><br />
<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><br />
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<h2>Human Practices</h2><br />
<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><br />
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<div class="obox1"><br />
<h2>Initiative</h2><br />
<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><br />
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<h2>Interviews</h2><br />
<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><br />
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<h2>Design Considerations</h2><br />
<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><br />
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<h2>Killswitch</h2><br />
<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><br />
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<h2>Safety</h2><br />
<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><br />
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<h2>Community Outreach</h2><br />
<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><br />
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<h2>FRED</h2><br />
<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><br />
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<h2>Detecting</h2><br />
<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><br />
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<h2>Reporting</h2><br />
<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><br />
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<h2>Modelling</h2><br />
<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><br />
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<h2>Prototyping</h2><br />
<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><br />
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<h2>OSCAR</h2><br />
<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><br />
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<h2>Decarboxylation</h2><br />
<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><br />
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<h2>Catechol Degradation</h2><br />
<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><br />
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<h2>Flux-Variability Analysis</h2><br />
<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><br />
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<h2>Bioreactor</h2><br />
<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><br />
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<h2>Upgrading</h2><br />
<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><br />
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<h2>Team</h2><br />
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p><br />
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<h2>Data Page</h2><br />
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p><br />
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<h2>Notebook</h2><br />
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p><br />
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<h2>Thanks to Our Sponsors!</h2><br />
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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/2012/d/d6/UCalgary2012_Logo_O%27Brien_Centre.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca" target="_blank"><img style="width: 166px;" src="https://static.igem.org/mediawiki/2012/4/46/UCalgary2012_Logo_U_of_C_Vertical.png"></img></a></td><br />
<td><a href="http://www.albertatechfutures.ca" target="_blank"><img style="width: 234px;" src="https://static.igem.org/mediawiki/2012/7/7f/UCalgary2012_Logo_AITF.png"></img></a></td><br />
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<td><a href="http://bio.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/4/45/UCalgary2012_BioSci_Logo.png"></img></a></td><br />
<td><a href="http://enel.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/9/9c/UCalgary2012_Schulich_Electric_Computer_Logo.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca/bme/about/CBRE" target="_blank"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2012/5/56/UCalgary2012_CBREhz_Cropped.jpg"></img></a></td><br />
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<td><a href="http://www.osli.ca" target="_blank"><img style="width: 891px;" src="https://static.igem.org/mediawiki/2012/9/98/UCalgary2012_Logo_OSLI.png"></img></a></td><br />
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<td><a href="http://www.osrin.ualberta.ca" target="_blank"><img style="width: 204px;" src="https://static.igem.org/mediawiki/2012/0/04/UCalgary2012_OSRIN.png"></img></a></td><br />
<td><a href="http://www.mhc.ab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a></td><br />
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<td><a href="http://www.eurofinsdna.com" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a></td><br />
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<td><a href="http://www.autodesk.com" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/0/0b/UCalgary2012-Autodesk-Logo.png"></img></a></td><br />
<td><a href="http://www.hyperionlab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/8/89/UCalgary2012_Hyperion_Research_Logo.png"></img></a></td><br />
<td><a href="http://www.idtdna.com/site" target="_blank"><img style="width: 228px;" src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a></img></a></td><br />
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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/2012/f/f6/UCalgary2012_Logo_Sarstedt.png"></img></a></td><br />
<td><a href="http://www.teamlab.com" target="_blank"><img style="width: 160px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a></td><br />
<td><a href="http://www.vwr.com" target="_blank"><img style="width: 279px;" src="https://static.igem.org/mediawiki/2012/1/11/UCalgary2012_Logo_VWR.png"></img></a></td><br />
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<td><a href="http://genomealberta.ca" target="_blank"><img style="width: 203px;" src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></td><br />
<td><a href="http://www.neb.com/nebecomm/default.asp" target="_blank"><img style="width: 281px;" src="https://static.igem.org/mediawiki/2012/2/24/UCalgary2012_Logo_NEB.png"></img></a></td><br />
<td><a href="http://www.sparkscience.ca" target="_blank"><img style="width: 261px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a></td><br />
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</html></div>Pjwuhttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-11-26T06:33:04Z<p>Pjwu: </p>
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<body><br />
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<div id="box1" align="justify"><br />
<a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals" id="FredOscarFlag"><br />
<br />
</a><br />
<h2>Detect and Destroy: Building FRED and OSCAR</h2><br />
<p><b>Tailings ponds</b> are large bodies of water containing <b>toxic compounds</b> that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential <b>environmental and economic concern</b> to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms <b>to detect and destroy (bioremediate) the toxins</b>, turning them into useable <b>hydrocarbons</b>.</p><br />
<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the descriptions below to learn more!</p><br />
<br />
</div><br />
<br />
<div class="threeboxes"><br />
<a id="greybox4" href="http://www.youtube.com/watch?v=KHhswxo6xow" style="margin-right:4px;"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/0/02/UCalgary2012_ThreeBoxMusic.png"></img><br />
<h2>iGEM Style!</h2><br />
<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><br />
</div><br />
</a><br />
<a id="greybox5" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/2/20/UCalgary2012_ThreeBoxSynergy.png"></img><br />
<h2>Synergy</h2><br />
<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p><br />
</div><br />
</a><br />
<a id="greybox6" href="http://www.youtube.com/watch?v=vluDpf4ao6c" style="margin:0;"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/b/b1/UCalgary2012_ThreeBoxFilm.png"></img><br />
<h2>Intro Video</h2><br />
<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p><br />
</div><br />
</a><br />
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<a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices"><br />
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<a class="obox1 iconbox" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations"><br />
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<a class="obox4 iconbox" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch"><br />
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<a href="https://2012.igem.org/Team:Calgary/Project/FRED"><br />
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<a class="bbox4 iconbox" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor"><br />
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<div id="boxinfo"><br />
<div id="boxinfo_default"><br />
<h2>The Concept</h2><br />
<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><br />
</div><br />
<div class="orangebox"><br />
<h2>Human Practices</h2><br />
<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><br />
</div><br />
<div class="obox1"><br />
<h2>Initiative</h2><br />
<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><br />
</div><br />
<div class="obox2"><br />
<h2>Interviews</h2><br />
<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><br />
</div><br />
<div class="obox3"><br />
<h2>Design Considerations</h2><br />
<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><br />
</div><br />
<div class="obox4"><br />
<h2>Killswitch</h2><br />
<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><br />
</div><br />
<div class="obox5"><br />
<h2>Safety</h2><br />
<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><br />
</div><br />
<div class="obox6"><br />
<h2>Community Outreach</h2><br />
<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><br />
</div><br />
<div class="greenbox"><br />
<h2>FRED</h2><br />
<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><br />
</div><br />
<div class="gbox1"><br />
<h2>Detecting</h2><br />
<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><br />
</div><br />
<div class="gbox2"><br />
<h2>Reporting</h2><br />
<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><br />
</div><br />
<div class="gbox3"><br />
<h2>Modelling</h2><br />
<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><br />
</div><br />
<div class="gbox4"><br />
<h2>Prototyping</h2><br />
<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><br />
</div><br />
<div class="bluebox"><br />
<h2>OSCAR</h2><br />
<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><br />
</div><br />
<div class="bbox1"><br />
<h2>Decarboxylation</h2><br />
<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><br />
</div><br />
<div class="bbox2"><br />
<h2>Catechol Degradation</h2><br />
<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><br />
</div><br />
<div class="bbox3"><br />
<h2>Flux-Variability Analysis</h2><br />
<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><br />
</div><br />
<div class="bbox4"><br />
<h2>Bioreactor</h2><br />
<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><br />
</div><br />
<div class="bbox5"><br />
<h2>Upgrading</h2><br />
<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><br />
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<a id="greybox1" href="https://2012.igem.org/Team:Calgary/Team" style="margin-top:4px;"><br />
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<img src="https://static.igem.org/mediawiki/2012/b/b8/UCalgary2012_ThreeBoxTeam.png"></img><br />
<h2>Team</h2><br />
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p><br />
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</a><br />
<a id="greybox2" href="https://2012.igem.org/Team:Calgary/Project/DataPage"><br />
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<img src="https://static.igem.org/mediawiki/2012/9/92/UCalgary2012_ThreeBoxData.png"></img><br />
<h2>Data Page</h2><br />
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p><br />
</div><br />
</a><br />
<a id="greybox3" href="https://2012.igem.org/Team:Calgary/Notebook"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/1/1b/UCalgary2012_ThreeBoxNotebook.png"></img><br />
<h2>Notebook</h2><br />
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p><br />
</div><br />
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<h2>Thanks to Our Sponsors!</h2><br />
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</html></div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/SynergyTeam:Calgary/Project/Synergy2012-11-18T17:32:23Z<p>Pjwu: </p>
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<div>{{Team:Calgary/MainHeader | <html><img src="https://static.igem.org/mediawiki/2012/8/82/UCalgary2012_Offical_Logo_Purple.png"></img></html>}}<br />
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<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Jamboree</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">Initiative</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Interviews</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design">Design</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">Killswitch</a></li><ul><li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li></ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Safety">Safety</a></li><br />
</ul><br />
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<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
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<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li></ul> <br />
</ul><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
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TITLE=Synergy: Putting it all Together|CONTENT=<br />
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<img src="https://static.igem.org/mediawiki/2012/0/03/UCalgary2012_FRED_and_OSCAR_Synergy.png" style="padding: 10px; float: right;"></img><br />
<h2>Incorporating Human Practices in the Design of our System </h2><br />
<p>In the earlier stages of our project, we realized that in order to give our project the best chance of being implemented, we needed to do it in a way that was in line with both industry’s wants and needs. To ensure that we did this, we established a dialogue with several experts in order to get their opinions on how we should approach our project. This led to an <b>informed design</b> of our system, in which we emphasized the need for both physical and genetic containment devices. </p><br />
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<h2>Have we accomplished our goal?</h2><br />
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<p>Nearing the end of our project however, we wanted to see if we had accomplished what we set out to do. So we decided to go back to the experts, this time taking the progress we had made on our project with us. We got a variety of different perspectives from suggestions on the scale up of our project, to the cost and environmental impact of our numerous components. The results of all of these can be found on our <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews"><b>Interviews</b></a> page. One major concern was <b>scale-up</b>. One expert wanted to know how feasible this system would actually be. We have some FRED components, OSCAR components, and killswitch components, but how functional are these parts, and how do they work together? Our next major goal was therefore to <u><b>establish synergy:</b> to put these pieces together in order to assess how far we have actually gotten</u>.</p><br />
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<p>Here we demonstrate that we can develop a <b>comprehensive kill switch</b> consisting of both an auxotroph and an inducible kill switch which work together to contain FRED and OSCAR. With FRED, we show that we can detect <b>toxins selectively in tailing ponds</b> using our identified transposon. Finally, with OSCAR we show that <b>our killswitch auxotroph dramatically increases the production of hydrocarbons in the system</b> and that we are capable of <b>scaling up</b> OSCAR's bioreactor and selectively collect hydrocarbons with our belt skimmer device.</p><br />
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<h2><u>Putting our Killswitch Together</u></h2><br />
<h2>Testing the Requirement of Glycine With our Auxotroph</h2><br />
<p>Our <a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis"><b>flux-based analysis</b></a> allowed us to realize the potential for glycine to be used not only as a way to increase the yield of OSCAR, but also as an auxotrophic killswitch. This allowed our model to be used not only to inform our wetlab, but also our human practices. We wanted to see how this auxotrophic marker system could work with one of our inducible killswitch constructs. We procured a Keio Knockout Collection Strain which deleted <i>glyA</i> an important enzyme in glycine metabolism making it auxotrophic for this compound. We wanted to identify the concentration of glycine required for its growth as shown below.<br />
<br />
</html>[[File:Calgary GlycineKODeathAssay.png|thumb|500px|center|Figure 1: Glycine requirements for growth of <i>glyA</i> knockout strain JW2535-1. The bacteria was grown in LB overnight, washed, and subcultured into M9 minimal media, glucose, with various different concentration of glycine (from 1nM logarithmically to 100 mM). Interestingly, the glycine knockout grew best at concentrations of 1 - 10 mM. However, the auxotroph was not strong enough even at low concentrations to completely abolish growth.]]<html><br />
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<p>As identified by the growth assay, the glycine knockout is not capable of completely preventing growth of the strain even at very low concentrations of glycine. This identifies that it is important to continue to use our kill switch mechanism in combination with the auxotroph to control the cells. Now, with the concentrations ideal for glycine growth determined, we transformed our rhamnose inducible killswitch construct containing S7 <b>(<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902084">BBa_K902084</a>)</b> into our glycine knockout strain and attempted to characterize cell death over a variety of conditions.</p><br />
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<h2>Testing the Auxotrophic Marker as a Kill Switch</h2><br />
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<p>To test if using the <i>glyA</i> knockout strain in conjunction with our kill switch was effective, we transformed our Prha-S7 construct into the knockout strain as shown in Figure 2.</p><br />
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</html>[[File:Calgary Rha S7 Data.png|thumb|500px|center|Figure 2: pRHA-S7 construct demonstrating our kill switch in TOP10 wild type cells and <i>glyA</i> knockout cells. This demonstrates that our system is capable of being induced by the sugar rhamnose and repressed in the presence of glucose. There is no growth in rhamnose with our system as the <i>RhaBAD</i> operon has been deleted in the knockout strain we are using.]]<html><br />
<p>This data suggests that our killswitch system can act synergistically with the glycine auxotroph. In the prescence of glucose you see growth of both TOP10 and <i>glyA</i> knockout cells showing that our system is repressed. There is less growth in our glycine knockout as there was not a significant amount of glycine used in the media. The TOP10 control cell line did not show growth over 24 hours which was likely due to error in the read. In the presence of rhamnose, the kill switch is capable of being induced in both TOP10 and glycine knockout strains as shown by the decrease in CFU counts. This demonstrates a functional kill switch mechanism with the Prha promoter and auxotroph.</p><br />
<br />
<h2> <u>Putting FRED together</u> </h2><br />
<h2>Can we sense toxins?</h2><br />
<br />
<p>Now that we’ve been able to show that we can indeed sense three compounds electrochemically and simultaneously using our hydrolase system, and characterized genetic circuits for two of these outputs, our next goal was to actually try to sense toxins. Despite the fact that we have encountered significant difficulty in trying to sequence our transposon clones, given that we designed our transposon library to use <i>lacZ</i>, we could actually use our transposon directly in our electrochemical reporter system without actually knowing the identity of the sensory element. Although we do plan to BioBrick this in the future, for now, we grew up cultures of our transposon and tested the ability of our FRED system to sense toxins. We didn't just want to sense toxins however, we wanted to be able to sense toxins in tailings ponds. To do this, we grew up our transposon clone in media, aspirated the media and then placed it in tailings pond water samples. Upon addition of our sugar-reporter conjugate, CPRG, we monitored the formation of CPR electrochemically, which would be indicative of LacZ production, indicating activity of our toxin sensory element. The results of this assay can be shown below.</p><br />
<br />
</html>[[File:UOFCTailingsPondWinData!.png|thumb|550px|centre|Figure 3. Current change over time illustrating <i>lacZ</i> induction by our identified transposon sensory element in a tailings pond water sample. The blue curve represents the tailings water test while the red curves shows the basal expression of the sensory element without tailings pond water present. This shows that our transposon clone has the ability to sense something within tailings pond water samples. ]]<html><br />
<br />
<p>This result was extremely exciting for us, as we see clear induction of the system in the presence of tailings, as compared to the control. Although we don't know exactly what we are sensing, (remember that our transposon is sensitive to 3 different toxins: DBT, Carbazole and NAs),we are definitely sensing something! <b>This shows that FRED is functional and more than that, FRED is functional in the application for which he was designed!</b> The next step will be to quantify toxins present in tailings pond water samples in order to calibrate our reporter. </p><br />
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<a name="field"></a><br />
<h2> Taking FRED out to the field! </h2><br />
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<p> Once we knew that we had a promoter/reporter system that could actually detect toxins found in tailings ponds within the laboratory, the next challenge was to detect tailings pond toxins with our FRED prototype on site. Unfortunately, there are very strict regulations surrounding tailings ponds, and the publication of information pertaining to their contents. As such, obtaining permissions for a tailing pond field test was not possible within the time frame of our project. Because we did want to perform a kind of field test with FRED to show that the prototype that we built is feasible and easy to use, we investigated whether it would be permissable or advisable to try FRED outside of the lab. We performed a literature search to look for any regulations that might exist. Nothing pertaining to our province could be found, so we looked to Ontario and the United States. The concise guide to U.S. federal guidelines, rules and regulations for synthetic biology outlined the rules pertaining to field tests and indicated that in cases where organisms are going to be released into the environment, the EPA (environmental protection agency) requires a TSCA (Toxic Substances Control Act) Experimental Release Application (TERA) to be completed 60 days before the trial begins and the APHIS (Animal and Plant Health Inspection Service) requires a permit or notification. Although we specifically designed FRED to not release the microbes but rather to contain them, the prototype is too much in its infancy to remove it from the lab and be <b>absolutely</b> assured that it won’t be released. What we did instead, was took our prototype without bacteria in it to collect a water sample in a nearby river in Calgary. The video of this experience can be found below. </p><br />
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<h2> Putting our Killswitch into OSCAR - Can we use our Auxotroph with the Petrobrick?</h2><br />
<p><b>In fact it's better!</b> The glycine auxotroph will be used as a second layer of regulation with our kill switch in the event that our bacterium is capable of escaping the bioreactor. However in order to ensure that the glycine knockout we are using does not compromise the production of hydrocarbons and we can continue to see the high yield of hydrocarbons as predicted with our flux balance modelling, we performed an experiment to look at the relative amount of hydrocarbon production as in the flux balance analysis model. As seen in the figure below, using the <i>glyA</i> knockout greatly increased the output of hydrocarbons much higher than in the wild type <i>E. coli</i> strain. This was extremely exciting showing that our system could not only be safe, with a second layer of control for safety, and an increase in output.</p><br />
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<br />
</html>[[File:Calgary glyAKOPetrobrick.png|thumb|500px|center|Figure 4: Relative production of hydrocarbons per cell as discussed in the flux balance analysis section of our wiki. Wild type <i>E. coli</i> TOP10 cells were incubated with minimal media 1% glucose (Negative) or 50:50 LB:Washington Production Media (Positive). Additionally, the <i>glyA</i> knockout was incubated in minimal media in the presence of glycine. Production of C15 hydrocarbon was standardized to OD<sub>600</sub> measurements and normalized to the positive control. Surprisingly, the <i>glyA</i> knockout greatly increased the amount of hydrocarbons (almost 3x the amount of hydrocarbons per cell) produced compared to both controls.]]<html><br />
<br />
<H2> Putting OSCAR into Action! </h2><br />
<p>Once we had tested FRED and shown that we could use him to detect toxins in tailings samples we wanted to put OSCAR into action in his home the bioreactor. By the end of the summer, we had designed and built a lab scale prototype of our bioreactor system. However, to better understand the needs of the oil sands industry we approached <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Kelly Roberge</a>, an oil sands consultant specializing in tailings ponds. Through speaking with Mr. Roberge, we were able to better understand the concerns that the oil sands industry has with the use and building synthetic biology systems to solve the challenges they face. In particular, Mr. Roberge had questions that surrounded the feasibility of scaling up our bioreactor to an industrial scale. As it turns out there are a number of considerations that should be made when moving from the lab scale to industrial scale. Particularly, because these transitions can be an imperfect when moving from the lab scale to industrial scale (>1000L tanks). Therefore we thought it would be important to test the feasibility of <b>using our bioreactor, belt skimmer, and Petrobrick, to demonstrate we can produce and isolate hydrocarbons</b>. These results are illustrated in the video below!</p><br />
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<iframe width="640" height="360" src="http://www.youtube.com/embed/4NcOKCwHCBI" frameborder="0" allowfullscreen></iframe><br />
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<p>In short, the bioreactor was filled with 50:50 LB:Washington Production Media and we allowed the Petrobrick to grow over a 72 hour period. Afterwards, we demonstrated how our belt skimmer could be used for removal of the hydrocarbons. Because the hydrocarbons need to be extracted, we added ethyl acetate to allow for extraction, and demonstrated that our belt skimmer could selectively pick up the organic layer. Finally we ensured that this organic phase contained hydrocarbons by running this segment on the GC/MS as illustrated below.</p><br />
<br />
</html>[[File:Calgary BioreactorValidation.png|thumb|500px|center|Figure 5: The GC chromatograph from the solvent layer which was selectively used with the belt skimmer. A large peak was observed much greater than any of the others, suggesting that hydrocarbons were being selectively removed with the belt skimmer.]]<html><br />
</html>[[File:Calgary BioreactorValidationMS.png|thumb|300px|center|Figure 6: MS data for the peak with a retention time of 12.7 min. The spectra suggests that the compound is a C16 hyrocarbon, validating that the upscaled bioreactor/belt skimmer combination can be used to isolate hydrocarbons.]]<html><br />
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<p>With these experiments we have been able to demonstrate that both FRED and OSCAR are functional and can work on their respective applications even in the context of a large scale! By listening to professionals and bringing an <b>informed design</b> to our project we have been able to provide systems with real world applications. FRED can <b>detect compounds in tailings ponds</b> and we have been able to <b>scale up and optimize</b> OSCAR through our bioreactor and flux balance analysis work. Additionally, we have connected our projects together by providing a <b>double kill switch system </b> with both an auxotroph and inducible exonuclease system that increases the production of hydrocarbons in OSCAR! With these systems in place and a clear concept of the value of what our project has to offer, we look forward to seeing what the future holds for FRED and OSCAR!</p><br />
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}}</div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/Post-RegionalsTeam:Calgary/Project/Post-Regionals2012-11-18T17:31:22Z<p>Pjwu: </p>
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<div>{{Team:Calgary/MainHeader | <html><img src="https://static.igem.org/mediawiki/2012/8/82/UCalgary2012_Offical_Logo_Purple.png"></img></html>}}<br />
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<br />
<ul><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Jamboree</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">Initiative</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Interviews</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design">Design</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">Killswitch</a></li><ul><li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li></ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li></ul> <br />
</ul><br />
<br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
</ul><br />
</html>|<br />
<br />
TITLE=Post-Jamboree Accomplishments|CONTENT=<br />
<html><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/3/3d/UCalgary2012_FRED_and_OSCAR_Achievements.png" style="width: 280px; float: right; padding: 10px;"></img><br />
<h2>Our team has accomplished so much this year!</h2><br />
<br />
<ul><br />
<li><p>Gold Medallist</p></li><br />
<li><p>Best Human Practices, Americas West</p></li><br />
<li><p>Best Wiki, Americas West</p></li><br />
<li><p>Best Poster, Americas West</p></li><br />
<li><p>Best Model, Americas West</p></li><br />
<li><p>Safety Commendation, Americas West</p></li><br />
<li><p>Best Human Practices, World Championship</p></li><br />
<li><p>"Sweet Sixteen", World Championship</p></li><br />
</ul><br />
<br />
<p>See all of the iGEM 2012 results <a href="https://2012.igem.org/Jamborees" target="_blank">here</a> and <a href="https://igem.org/Results?year=2012&region=Championship&division=igem" target="_blank">here</a>!</p><br />
<br />
<h2>See what we accomplished since the Americas West Regionals!</h2><br />
<br />
<p><b>In our <FONT COLOR="FF7A00">Human Practices</FONT> project, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews"><b>Returned to industry experts</b></a> to see if we accomplished our goals and what the <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>next steps</b></a> should be.</li></p><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation#Prha_results"><b>Characterized</b></a> the functionality of our previously submitted <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902066"><b><i>Prha</i> (BBa_K902066)</b></a> promoter using GFP fluorescence.</li></p><br />
<br />
<br />
<li><p>Tested an additional <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation"><b>complete kill switch device</b></a> using the <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902084"><b><i>Prha</i> (BBa_K902084)</b></a> promoter with our S7 kill gene.</li></p><br />
<br />
<br />
<br />
<li><p>Tested a <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>glycine auxotroph killswitch</b></a>.</li></p></ul><br />
<br />
<br><br />
<p><b>In terms of <FONT COLOR=#159900>FRED</FONT>, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting"><b>Electrochemically characterized</b></a> an inducible <a class="green" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902090"><b><i>lacz</i> (BBa_K902090)</b></a> circuit, replacing a faulty existing circuit in the registry containing a frameshift.</p></li><br />
<br />
<br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Tested one of our transposon library hits</b></a> with our electrochemical reporter, showing that we can use our system to <b>detect toxins electrochemically</b>.</p></li><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated our system with tailings</b></a> using our transposon system and electrochemical reporter to be able to selectively detect toxins on <b>real oil sands samples</b>.</p></li><br />
</ul><br />
<br />
<br><br />
<br />
<p><b>In terms of <FONT COLOR=#1088CC>OSCAR</FONT>, we...</b></p><br />
<ul><br />
<li><p>Obtained <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis"><b>additional characterization data</b></a> in validation of our flux-variability analysis model.</p></li><br />
<br />
<li><p>Characterized the ability of our <b>novel</b> <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902041"><b><i>amdA</i> (BBa_K902041)</b></a> <b>BioBrick</b> to selectively remove primary amides from ring structures with remarkable efficiency, turning them into a substrate that the <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025"><b>Petrobrick (BBa_K590025)</b></a> can likely convert into hydrocarbons.</p></li><br />
<br />
<br />
<li><p><a class="blue" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated a scale up model</b></a> for using our bioreactor/belt skimmer system in producing and extracting hydrocarbons.</p></li><br />
</ul><br />
<br />
<h2> <br />
<ul><br />
<br />
</p><br />
</html><br />
}}</div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/Post-RegionalsTeam:Calgary/Project/Post-Regionals2012-11-18T17:30:55Z<p>Pjwu: </p>
<hr />
<div>{{Team:Calgary/MainHeader | <html><img src="https://static.igem.org/mediawiki/2012/8/82/UCalgary2012_Offical_Logo_Purple.png"></img></html>}}<br />
{{Team:Calgary/BasicPage|proj_hp|<br />
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SIDELIST =<br />
<html><br />
<head><br />
<style><br />
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color: #159900 !important;<br />
}<br />
a.blue{<br />
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a.orange{<br />
color: #FF7A00 !important;<br />
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}<br />
<br />
</style><br />
</head><br />
<br />
<ul><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Jamboree</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">Initiative</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Interviews</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design">Design</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">Killswitch</a></li><ul><li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li></ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li></ul> <br />
</ul><br />
<br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
</ul><br />
</html>|<br />
<br />
TITLE=Post-Jamboree Accomplishments|CONTENT=<br />
<html><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/3/3d/UCalgary2012_FRED_and_OSCAR_Achievements.png" style="width: 280px; float: right; padding: 10px;"></img><br />
<br />
<br />
<h2>See what we accomplished since the Americas West Regionals!</h2><br />
<br />
<p><b>In our <FONT COLOR="FF7A00">Human Practices</FONT> project, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews"><b>Returned to industry experts</b></a> to see if we accomplished our goals and what the <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>next steps</b></a> should be.</li></p><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation#Prha_results"><b>Characterized</b></a> the functionality of our previously submitted <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902066"><b><i>Prha</i> (BBa_K902066)</b></a> promoter using GFP fluorescence.</li></p><br />
<br />
<br />
<li><p>Tested an additional <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation"><b>complete kill switch device</b></a> using the <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902084"><b><i>Prha</i> (BBa_K902084)</b></a> promoter with our S7 kill gene.</li></p><br />
<br />
<br />
<br />
<li><p>Tested a <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>glycine auxotroph killswitch</b></a>.</li></p></ul><br />
<br />
<br><br />
<p><b>In terms of <FONT COLOR=#159900>FRED</FONT>, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting"><b>Electrochemically characterized</b></a> an inducible <a class="green" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902090"><b><i>lacz</i> (BBa_K902090)</b></a> circuit, replacing a faulty existing circuit in the registry containing a frameshift.</p></li><br />
<br />
<br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Tested one of our transposon library hits</b></a> with our electrochemical reporter, showing that we can use our system to <b>detect toxins electrochemically</b>.</p></li><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated our system with tailings</b></a> using our transposon system and electrochemical reporter to be able to selectively detect toxins on <b>real oil sands samples</b>.</p></li><br />
</ul><br />
<br />
<br><br />
<br />
<p><b>In terms of <FONT COLOR=#1088CC>OSCAR</FONT>, we...</b></p><br />
<ul><br />
<li><p>Obtained <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis"><b>additional characterization data</b></a> in validation of our flux-variability analysis model.</p></li><br />
<br />
<li><p>Characterized the ability of our <b>novel</b> <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902041"><b><i>amdA</i> (BBa_K902041)</b></a> <b>BioBrick</b> to selectively remove primary amides from ring structures with remarkable efficiency, turning them into a substrate that the <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025"><b>Petrobrick (BBa_K590025)</b></a> can likely convert into hydrocarbons.</p></li><br />
<br />
<br />
<li><p><a class="blue" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated a scale up model</b></a> for using our bioreactor/belt skimmer system in producing and extracting hydrocarbons.</p></li><br />
</ul><br />
<br />
<h2> <br />
<ul><br />
<br />
</p><br />
</html><br />
}}</div>Pjwuhttp://2012.igem.org/Template:Team:Calgary/TemplateProjectGreenTemplate:Team:Calgary/TemplateProjectGreen2012-11-18T17:30:19Z<p>Pjwu: </p>
<hr />
<div>{{Team:Calgary/MainHeader | <html><img src="https://static.igem.org/mediawiki/2012/7/76/UCalgary2012_HeaderLogoGreen.png"></img></html>}}<br />
{{Team:Calgary/BasicPage|proj_f|<br />
SECTION = Project|<br />
SIDELIST =<br />
<html><br />
<ul><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Jamboree</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">Initiative</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Interviews</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design">Design</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">Killswitch</a></li><ul><li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li></ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li></ul> <br />
</ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
</ul><br />
</html>|<br />
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TITLE={{{TITLE|Project (FRED) Template}}}|<br />
CONTENT={{{CONTENT|<br />
<br />
<html><br />
<p>Hello! We are sorry to say that this page has yet to be created. Please check back shortly to see any new updates that we may have.</p><br />
<br />
<h2>Under Construction!</h2><br />
<p>Currently this wiki is under construction. We hope to bring the entire site running up to full speed as soon as we can. For the time being, there will be broken links and navigation issues until we iron out the kinks. We apologize for any inconvenience.</p><br />
</html>}}}<br />
<br />
<br />
}}</div>Pjwuhttp://2012.igem.org/Template:Team:Calgary/TemplateProjectBlueTemplate:Team:Calgary/TemplateProjectBlue2012-11-18T17:30:07Z<p>Pjwu: </p>
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<div>{{Team:Calgary/MainHeader | <html><img src="https://static.igem.org/mediawiki/2012/4/48/UCalgary2012_White_Low-Res_Official_Logo.png"></img></html>}}<br />
{{Team:Calgary/BasicPage|proj_o|<br />
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<ul><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Jamboree</a></li><br />
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<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
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<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><ul><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
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}}</div>Pjwuhttp://2012.igem.org/Template:Team:Calgary/TemplateProjectOrangeTemplate:Team:Calgary/TemplateProjectOrange2012-11-18T17:29:52Z<p>Pjwu: </p>
<hr />
<div>{{Team:Calgary/MainHeader | <html><img src="https://static.igem.org/mediawiki/2012/c/c5/UCalgary2012_HeaderLogoOrange.png"></img></html>}}<br />
{{Team:Calgary/BasicPage|proj_hp|<br />
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<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Jamboree</a></li><br />
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<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li></ul><br />
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<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
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<br />
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</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
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<p>Currently this wiki is under construction. We hope to bring the entire site running up to full speed as soon as we can. For the time being, there will be broken links and navigation issues until we iron out the kinks. We apologize for any inconvenience.</p><br />
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}}</div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/Post-RegionalsTeam:Calgary/Project/Post-Regionals2012-11-18T17:29:35Z<p>Pjwu: </p>
<hr />
<div>{{Team:Calgary/MainHeader | <html><img src="https://static.igem.org/mediawiki/2012/8/82/UCalgary2012_Offical_Logo_Purple.png"></img></html>}}<br />
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<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Jamboree</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">Initiative</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Interviews</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design">Design</a></li><br />
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<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
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<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li></ul> <br />
</ul><br />
<br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
</ul><br />
</html>|<br />
<br />
TITLE=Post-Jamboree Accomplishments|CONTENT=<br />
<html><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/3/3d/UCalgary2012_FRED_and_OSCAR_Achievements.png" style="width: 280px; float: right; padding: 10px;"></img><br />
<h2>Our team has accomplished so much this year!</h2><br />
<br />
<ul><br />
<li><p>Gold Medallist</p></li><br />
<li><p>Best Human Practices, Americas West</p></li><br />
<li><p>Best Wiki, Americas West</p></li><br />
<li><p>Best Poster, Americas West</p></li><br />
<li><p>Best Model, Americas West</p></li><br />
<li><p>Safety Commendation, Americas West</p></li><br />
<li><p>Best Human Practices, World Championship</p></li><br />
<li><p>"Sweet Sixteen", World Championship</p></li><br />
</ul><br />
<br />
<p>See all of the iGEM 2012 results <a href="https://2012.igem.org/Jamborees" target="_blank">here</a> and <a href="https://igem.org/Results?year=2012&region=Championship&division=igem" target="_blank">here</a>!</p><br />
<br />
<h2>See what we accomplished since the Americas West Regionals!</h2><br />
<br />
<p><b>In our <FONT COLOR="FF7A00">Human Practices</FONT> project, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews"><b>Returned to industry experts</b></a> to see if we accomplished our goals and what the <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>next steps</b></a> should be.</li></p><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation#Prha_results"><b>Characterized</b></a> the functionality of our previously submitted <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902066"><b><i>Prha</i> (BBa_K902066)</b></a> promoter using GFP fluorescence.</li></p><br />
<br />
<br />
<li><p>Tested an additional <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation"><b>complete kill switch device</b></a> using the <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902084"><b><i>Prha</i> (BBa_K902084)</b></a> promoter with our S7 kill gene.</li></p><br />
<br />
<br />
<br />
<li><p>Tested a <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>glycine auxotroph killswitch</b></a>.</li></p></ul><br />
<br />
<br><br />
<p><b>In terms of <FONT COLOR=#159900>FRED</FONT>, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting"><b>Electrochemically characterized</b></a> an inducible <a class="green" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902090"><b><i>lacz</i> (BBa_K902090)</b></a> circuit, replacing a faulty existing circuit in the registry containing a frameshift.</p></li><br />
<br />
<br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Tested one of our transposon library hits</b></a> with our electrochemical reporter, showing that we can use our system to <b>detect toxins electrochemically</b>.</p></li><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated our system with tailings</b></a> using our transposon system and electrochemical reporter to be able to selectively detect toxins on <b>real oil sands samples</b>.</p></li><br />
</ul><br />
<br />
<br><br />
<br />
<p><b>In terms of <FONT COLOR=#1088CC>OSCAR</FONT>, we...</b></p><br />
<ul><br />
<li><p>Obtained <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis"><b>additional characterization data</b></a> in validation of our flux-variability analysis model.</p></li><br />
<br />
<li><p>Characterized the ability of our <b>novel</b> <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902041"><b><i>amdA</i> (BBa_K902041)</b></a> <b>BioBrick</b> to selectively remove primary amides from ring structures with remarkable efficiency, turning them into a substrate that the <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025"><b>Petrobrick (BBa_K590025)</b></a> can likely convert into hydrocarbons.</p></li><br />
<br />
<br />
<li><p><a class="blue" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated a scale up model</b></a> for using our bioreactor/belt skimmer system in producing and extracting hydrocarbons.</p></li><br />
</ul><br />
<br />
<h2> <br />
<ul><br />
<br />
</p><br />
</html><br />
}}</div>Pjwuhttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-11-14T17:02:29Z<p>Pjwu: </p>
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<a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals" id="FredOscarFlag"><br />
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<h2>Detect and Destroy: Building FRED and OSCAR</h2><br />
<p><b>Tailings ponds</b> are large bodies of water containing <b>toxic compounds</b> that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential <b>environmental and economic concern</b> to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms <b>to detect and destroy (bioremediate) the toxins</b>, turning them into useable <b>hydrocarbons</b>.</p><br />
<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the descriptions below to learn more!</p><br />
<p><b>Click on the links to the left to learn more about our work after the Americas West Regionals!</b></p><br />
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<h2>iGEM Style!</h2><br />
<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><br />
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<a id="greybox5" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><br />
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<h2>Synergy</h2><br />
<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p><br />
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<h2>Intro Video</h2><br />
<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p><br />
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<h2>The Concept</h2><br />
<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><br />
</div><br />
<div class="orangebox"><br />
<h2>Human Practices</h2><br />
<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><br />
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<div class="obox1"><br />
<h2>Initiative</h2><br />
<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><br />
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<div class="obox2"><br />
<h2>Interviews</h2><br />
<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><br />
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<h2>Design Considerations</h2><br />
<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><br />
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<h2>Killswitch</h2><br />
<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><br />
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<h2>Safety</h2><br />
<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><br />
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<div class="obox6"><br />
<h2>Community Outreach</h2><br />
<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><br />
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<h2>FRED</h2><br />
<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><br />
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<h2>Detecting</h2><br />
<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><br />
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<h2>Reporting</h2><br />
<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><br />
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<h2>Modelling</h2><br />
<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><br />
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<h2>Prototyping</h2><br />
<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><br />
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<div class="bluebox"><br />
<h2>OSCAR</h2><br />
<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><br />
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<h2>Decarboxylation</h2><br />
<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><br />
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<h2>Catechol Degradation</h2><br />
<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><br />
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<h2>Flux-Variability Analysis</h2><br />
<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><br />
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<h2>Bioreactor</h2><br />
<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><br />
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<h2>Upgrading</h2><br />
<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><br />
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<h2>Team</h2><br />
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p><br />
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<h2>Data Page</h2><br />
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p><br />
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<h2>Notebook</h2><br />
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p><br />
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<h2>Thanks to Our Sponsors!</h2><br />
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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/2012/d/d6/UCalgary2012_Logo_O%27Brien_Centre.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca" target="_blank"><img style="width: 166px;" src="https://static.igem.org/mediawiki/2012/4/46/UCalgary2012_Logo_U_of_C_Vertical.png"></img></a></td><br />
<td><a href="http://www.albertatechfutures.ca" target="_blank"><img style="width: 234px;" src="https://static.igem.org/mediawiki/2012/7/7f/UCalgary2012_Logo_AITF.png"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://bio.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/4/45/UCalgary2012_BioSci_Logo.png"></img></a></td><br />
<td><a href="http://enel.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/9/9c/UCalgary2012_Schulich_Electric_Computer_Logo.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca/bme/about/CBRE" target="_blank"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2012/5/56/UCalgary2012_CBREhz_Cropped.jpg"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://www.osli.ca" target="_blank"><img style="width: 891px;" src="https://static.igem.org/mediawiki/2012/9/98/UCalgary2012_Logo_OSLI.png"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://www.osrin.ualberta.ca" target="_blank"><img style="width: 204px;" src="https://static.igem.org/mediawiki/2012/0/04/UCalgary2012_OSRIN.png"></img></a></td><br />
<td><a href="http://www.mhc.ab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a></td><br />
<br />
<td><a href="http://www.eurofinsdna.com" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a></td><br />
<br />
</tr><br />
<tr><br />
<td><a href="http://www.autodesk.com" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/0/0b/UCalgary2012-Autodesk-Logo.png"></img></a></td><br />
<td><a href="http://www.hyperionlab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/8/89/UCalgary2012_Hyperion_Research_Logo.png"></img></a></td><br />
<td><a href="http://www.idtdna.com/site" target="_blank"><img style="width: 228px;" src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a></img></a></td><br />
</tr><br />
<tr><br />
<td><a href="http://www.sarstedt.com/php/main.php" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/f/f6/UCalgary2012_Logo_Sarstedt.png"></img></a></td><br />
<td><a href="http://www.teamlab.com" target="_blank"><img style="width: 160px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a></td><br />
<td><a href="http://www.vwr.com" target="_blank"><img style="width: 279px;" src="https://static.igem.org/mediawiki/2012/1/11/UCalgary2012_Logo_VWR.png"></img></a></td><br />
</tr><br />
<tr><br />
<table><tr><br />
<td><a href="http://genomealberta.ca" target="_blank"><img style="width: 203px;" src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></td><br />
<td><a href="http://www.neb.com/nebecomm/default.asp" target="_blank"><img style="width: 281px;" src="https://static.igem.org/mediawiki/2012/2/24/UCalgary2012_Logo_NEB.png"></img></a></td><br />
<td><a href="http://www.sparkscience.ca" target="_blank"><img style="width: 261px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a></td><br />
<br />
</tr></table><br />
</tr><br />
</table><br />
</div><br />
<br />
</body><br />
</html></div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/Post-RegionalsTeam:Calgary/Project/Post-Regionals2012-11-11T17:15:32Z<p>Pjwu: </p>
<hr />
<div>{{Team:Calgary/MainHeader | <html><img src="https://static.igem.org/mediawiki/2012/8/82/UCalgary2012_Offical_Logo_Purple.png"></img></html>}}<br />
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<br />
<ul><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Regionals</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">Initiative</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Interviews</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design">Design</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">Killswitch</a></li><ul><li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li></ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li></ul> <br />
</ul><br />
<br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
</ul><br />
</html>|<br />
<br />
TITLE=Post-Regional Accomplishments|CONTENT=<br />
<html><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/3/3d/UCalgary2012_FRED_and_OSCAR_Achievements.png" style="width: 280px; float: right; padding: 10px;"></img><br />
<h2>Our team has accomplished so much this year!</h2><br />
<br />
<ul><br />
<li><p>Gold Medallist</p></li><br />
<li><p>Best Human Practices, Americas West</p></li><br />
<li><p>Best Wiki, Americas West</p></li><br />
<li><p>Best Poster, Americas West</p></li><br />
<li><p>Best Model, Americas West</p></li><br />
<li><p>Safety Commendation, Americas West</p></li><br />
<li><p>Best Human Practices, World Championship</p></li><br />
<li><p>"Sweet Sixteen", World Championship</p></li><br />
</ul><br />
<br />
<p>See all of the iGEM 2012 results <a href="https://2012.igem.org/Jamborees" target="_blank">here</a> and <a href="https://igem.org/Results?year=2012&region=Championship&division=igem" target="_blank">here</a>!</p><br />
<br />
<h2>See what we accomplished since the Americas West Regionals!</h2><br />
<br />
<p><b>In our <FONT COLOR="FF7A00">Human Practices</FONT> project, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews"><b>Returned to industry experts</b></a> to see if we accomplished our goals and what the <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>next steps</b></a> should be.</li></p><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation#Prha_results"><b>Characterized</b></a> the functionality of our previously submitted <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902066"><b><i>Prha</i> (BBa_K902066)</b></a> promoter using GFP fluorescence.</li></p><br />
<br />
<br />
<li><p>Tested an additional <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation"><b>complete kill switch device</b></a> using the <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902084"><b><i>Prha</i> (BBa_K902084)</b></a> promoter with our S7 kill gene.</li></p><br />
<br />
<br />
<br />
<li><p>Tested a <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>glycine auxotroph killswitch</b></a>.</li></p></ul><br />
<br />
<br><br />
<p><b>In terms of <FONT COLOR=#159900>FRED</FONT>, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting"><b>Electrochemically characterized</b></a> an inducible <a class="green" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902090"><b><i>lacz</i> (BBa_K902090)</b></a> circuit, replacing a faulty existing circuit in the registry containing a frameshift.</p></li><br />
<br />
<br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Tested one of our transposon library hits</b></a> with our electrochemical reporter, showing that we can use our system to <b>detect toxins electrochemically</b>.</p></li><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated our system with tailings</b></a> using our transposon system and electrochemical reporter to be able to selectively detect toxins on <b>real oil sands samples</b>.</p></li><br />
</ul><br />
<br />
<br><br />
<br />
<p><b>In terms of <FONT COLOR=#1088CC>OSCAR</FONT>, we...</b></p><br />
<ul><br />
<li><p>Obtained <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis"><b>additional characterization data</b></a> in validation of our flux-variability analysis model.</p></li><br />
<br />
<li><p>Characterized the ability of our <b>novel</b> <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902041"><b><i>amdA</i> (BBa_K902041)</b></a> <b>BioBrick</b> to selectively remove primary amides from ring structures with remarkable efficiency, turning them into a substrate that the <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025"><b>Petrobrick (BBa_K590025)</b></a> can likely convert into hydrocarbons.</p></li><br />
<br />
<br />
<li><p><a class="blue" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated a scale up model</b></a> for using our bioreactor/belt skimmer system in producing and extracting hydrocarbons.</p></li><br />
</ul><br />
<br />
<h2> <br />
<ul><br />
<br />
</p><br />
</html><br />
}}</div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/Post-RegionalsTeam:Calgary/Project/Post-Regionals2012-11-11T17:14:49Z<p>Pjwu: </p>
<hr />
<div>{{Team:Calgary/MainHeader | <html><img src="https://static.igem.org/mediawiki/2012/8/82/UCalgary2012_Offical_Logo_Purple.png"></img></html>}}<br />
{{Team:Calgary/BasicPage|proj_hp|<br />
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<ul><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Regionals</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">Initiative</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Interviews</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design">Design</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">Killswitch</a></li><ul><li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li></ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li></ul> <br />
</ul><br />
<br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
</ul><br />
</html>|<br />
<br />
TITLE=Post-Regional Accomplishments|CONTENT=<br />
<html><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/3/3d/UCalgary2012_FRED_and_OSCAR_Achievements.png" style="width: 280px; float: right; padding: 10px;"></img><br />
<h2>Our team has accomplished so much this year!</h2><br />
<br />
<ul><br />
<li><p>Gold Medallist</p></li><br />
<li><p>Best Human Practices, Americas West</p></li><br />
<li><p>Best Wiki, Americas West</p></li><br />
<li><p>Best Poster, Americas West</p></li><br />
<li><p>Best Model, Americas West</p></li><br />
<li><p>Safety Commendation, Americas West</p></li><br />
<li><p>Best Human Practices, World Championship</p></li><br />
<li><p>"Sweet Sixteen", World Championship</p></li><br />
</ul><br />
<br />
<p>See all of the iGEM 2012 results <a href="https://2012.igem.org/Jamborees" target="_blank">here</a>!</p><br />
<br />
<h2>See what we accomplished since the Americas West Regionals!</h2><br />
<br />
<p><b>In our <FONT COLOR="FF7A00">Human Practices</FONT> project, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews"><b>Returned to industry experts</b></a> to see if we accomplished our goals and what the <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>next steps</b></a> should be.</li></p><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation#Prha_results"><b>Characterized</b></a> the functionality of our previously submitted <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902066"><b><i>Prha</i> (BBa_K902066)</b></a> promoter using GFP fluorescence.</li></p><br />
<br />
<br />
<li><p>Tested an additional <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation"><b>complete kill switch device</b></a> using the <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902084"><b><i>Prha</i> (BBa_K902084)</b></a> promoter with our S7 kill gene.</li></p><br />
<br />
<br />
<br />
<li><p>Tested a <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>glycine auxotroph killswitch</b></a>.</li></p></ul><br />
<br />
<br><br />
<p><b>In terms of <FONT COLOR=#159900>FRED</FONT>, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting"><b>Electrochemically characterized</b></a> an inducible <a class="green" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902090"><b><i>lacz</i> (BBa_K902090)</b></a> circuit, replacing a faulty existing circuit in the registry containing a frameshift.</p></li><br />
<br />
<br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Tested one of our transposon library hits</b></a> with our electrochemical reporter, showing that we can use our system to <b>detect toxins electrochemically</b>.</p></li><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated our system with tailings</b></a> using our transposon system and electrochemical reporter to be able to selectively detect toxins on <b>real oil sands samples</b>.</p></li><br />
</ul><br />
<br />
<br><br />
<br />
<p><b>In terms of <FONT COLOR=#1088CC>OSCAR</FONT>, we...</b></p><br />
<ul><br />
<li><p>Obtained <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis"><b>additional characterization data</b></a> in validation of our flux-variability analysis model.</p></li><br />
<br />
<li><p>Characterized the ability of our <b>novel</b> <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902041"><b><i>amdA</i> (BBa_K902041)</b></a> <b>BioBrick</b> to selectively remove primary amides from ring structures with remarkable efficiency, turning them into a substrate that the <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025"><b>Petrobrick (BBa_K590025)</b></a> can likely convert into hydrocarbons.</p></li><br />
<br />
<br />
<li><p><a class="blue" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated a scale up model</b></a> for using our bioreactor/belt skimmer system in producing and extracting hydrocarbons.</p></li><br />
</ul><br />
<br />
<h2> <br />
<ul><br />
<br />
</p><br />
</html><br />
}}</div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/Post-RegionalsTeam:Calgary/Project/Post-Regionals2012-11-11T17:13:52Z<p>Pjwu: </p>
<hr />
<div>{{Team:Calgary/MainHeader | <html><img src="https://static.igem.org/mediawiki/2012/8/82/UCalgary2012_Offical_Logo_Purple.png"></img></html>}}<br />
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<ul><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Regionals</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">Initiative</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Interviews</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design">Design</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">Killswitch</a></li><ul><li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li></ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li></ul> <br />
</ul><br />
<br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
</ul><br />
</html>|<br />
<br />
TITLE=Post-Regional Accomplishments|CONTENT=<br />
<html><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/3/3d/UCalgary2012_FRED_and_OSCAR_Achievements.png" style="width: 280px; float: right; padding: 10px;"></img><br />
<h2>Our team has accomplished so much this year!</h2><br />
<br />
<ul><br />
<li><p>Gold Medallist</p></li><br />
<li><p>Best Human Practices, Americas West</p></li><br />
<li><p>Best Wiki, Americas West</p></li><br />
<li><p>Best Poster, Americas West</p></li><br />
<li><p>Best Model, Americas West</p></li><br />
<li><p>Safety Commendation, Americas West</p></li><br />
<li><p>Best Human Practices, World Championship</p></li><br />
<li><p>"Sweet Sixteen", World Championship</p></li><br />
</ul><br />
<br />
<p>See all of the iGEM 2012 results <a href="https://igem.org/Results" target="_blank">here</a>!</p><br />
<br />
<h2>See what we accomplished since the Americas West Regionals!</h2><br />
<br />
<p><b>In our <FONT COLOR="FF7A00">Human Practices</FONT> project, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews"><b>Returned to industry experts</b></a> to see if we accomplished our goals and what the <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>next steps</b></a> should be.</li></p><br />
<br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation#Prha_results"><b>Characterized</b></a> the functionality of our previously submitted <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902066"><b><i>Prha</i> (BBa_K902066)</b></a> promoter using GFP fluorescence.</li></p><br />
<br />
<br />
<li><p>Tested an additional <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation"><b>complete kill switch device</b></a> using the <a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902084"><b><i>Prha</i> (BBa_K902084)</b></a> promoter with our S7 kill gene.</li></p><br />
<br />
<br />
<br />
<li><p>Tested a <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>glycine auxotroph killswitch</b></a>.</li></p></ul><br />
<br />
<br><br />
<p><b>In terms of <FONT COLOR=#159900>FRED</FONT>, we...</b></p><br />
<ul><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting"><b>Electrochemically characterized</b></a> an inducible <a class="green" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902090"><b><i>lacz</i> (BBa_K902090)</b></a> circuit, replacing a faulty existing circuit in the registry containing a frameshift.</p></li><br />
<br />
<br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Tested one of our transposon library hits</b></a> with our electrochemical reporter, showing that we can use our system to <b>detect toxins electrochemically</b>.</p></li><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated our system with tailings</b></a> using our transposon system and electrochemical reporter to be able to selectively detect toxins on <b>real oil sands samples</b>.</p></li><br />
</ul><br />
<br />
<br><br />
<br />
<p><b>In terms of <FONT COLOR=#1088CC>OSCAR</FONT>, we...</b></p><br />
<ul><br />
<li><p>Obtained <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis"><b>additional characterization data</b></a> in validation of our flux-variability analysis model.</p></li><br />
<br />
<li><p>Characterized the ability of our <b>novel</b> <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902041"><b><i>amdA</i> (BBa_K902041)</b></a> <b>BioBrick</b> to selectively remove primary amides from ring structures with remarkable efficiency, turning them into a substrate that the <a class="blue" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025"><b>Petrobrick (BBa_K590025)</b></a> can likely convert into hydrocarbons.</p></li><br />
<br />
<br />
<li><p><a class="blue" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><b>Validated a scale up model</b></a> for using our bioreactor/belt skimmer system in producing and extracting hydrocarbons.</p></li><br />
</ul><br />
<br />
<h2> <br />
<ul><br />
<br />
</p><br />
</html><br />
}}</div>Pjwuhttp://2012.igem.org/Template:Team:Calgary/MainHeaderTemplate:Team:Calgary/MainHeader2012-11-11T16:49:56Z<p>Pjwu: </p>
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<li><a class="dropheader" href="http://ung.igem.org/Team.cgi?id=902">Official Profile</a></li><br />
<li><a class="dropheader" href="https://2012.igem.org/Team:Calgary/Team/AbouttheUniversity">The University</a></li><br />
<li><a class="dropheader" href="https://2012.igem.org/Team:Calgary/Team/Outtakes">Outtakes</a></li><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Regionals</a></li><br />
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<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">Initiative</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Interviews</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design">Design</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">Killswitch</a></li><br />
<li><a style="margin:0 -1em 0 1em;" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li><br />
<li><a style="margin:0 -1em 0 1em;" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li> <br />
<li><a href="https://2012.igem.org/Team:Calgary/Safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><br />
<li><a style="margin:0 -1em 0 1em;"href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a style="margin:0 -1em 0 1em;"href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li><br />
</ul><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
<br />
</ul><br />
</li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Parts" id="partslink">Parts</a></li><br />
<li><a class="drop" href="https://2012.igem.org/Team:Calgary/Notebook" id="notebooklink">Notebook</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook">Journal</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols">Protocols</a></li><br />
</ul><br />
</li><br />
<li><a class="drop" href="https://2012.igem.org/Team:Calgary/Outreach" id="outreachlink">Outreach</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/VideoGame">LAB ESCAPE!</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/Spark">Spark Science</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/MindsInMotion">Minds in Motion</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/Blog">Blog Posts</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Outreach/TEDxCalgary">TEDxCalgary</a></li><br />
<li><a href="http://twitter.com/iGEMCalgary" target="_blank">Follow Us!</a></li><br />
</ul><br />
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<li><a href="https://2012.igem.org" target="_blank">iGEM</a></li><br />
</ul><br />
<br />
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</html></div>Pjwuhttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-11-10T05:04:24Z<p>Pjwu: </p>
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<a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals" id="FredOscarFlag"><br />
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<h2>Detect and Destroy: Building FRED and OSCAR</h2><br />
<p><b>Tailings ponds</b> are large bodies of water containing <b>toxic compounds</b> that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential <b>environmental and economic concern</b> to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms <b>to detect and destroy (bioremediate) the toxins</b>, turning them into useable <b>hydrocarbons</b>.</p><br />
<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the descriptions below to learn more!</p><br />
<p><b>Click on the links to the left to learn more about our work after the Americas West Regionals!</b></p><br />
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<a id="greybox4" href="http://www.youtube.com/watch?v=KHhswxo6xow" style="margin-right:4px;"><br />
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<img src="https://static.igem.org/mediawiki/2012/0/02/UCalgary2012_ThreeBoxMusic.png"></img><br />
<h2>iGEM Style!</h2><br />
<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><br />
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</a><br />
<a id="greybox5" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><br />
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<img src="https://static.igem.org/mediawiki/2012/2/20/UCalgary2012_ThreeBoxSynergy.png"></img><br />
<h2>Synergy</h2><br />
<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p><br />
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<a id="greybox6" href="http://www.youtube.com/watch?v=vluDpf4ao6c" style="margin:0;"><br />
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<img src="https://static.igem.org/mediawiki/2012/b/b1/UCalgary2012_ThreeBoxFilm.png"></img><br />
<h2>Intro Video</h2><br />
<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p><br />
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<h2>The Concept</h2><br />
<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><br />
</div><br />
<div class="orangebox"><br />
<h2>Human Practices</h2><br />
<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><br />
</div><br />
<div class="obox1"><br />
<h2>Initiative</h2><br />
<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><br />
</div><br />
<div class="obox2"><br />
<h2>Interviews</h2><br />
<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><br />
</div><br />
<div class="obox3"><br />
<h2>Design Considerations</h2><br />
<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><br />
</div><br />
<div class="obox4"><br />
<h2>Killswitch</h2><br />
<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><br />
</div><br />
<div class="obox5"><br />
<h2>Safety</h2><br />
<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><br />
</div><br />
<div class="obox6"><br />
<h2>Community Outreach</h2><br />
<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><br />
</div><br />
<div class="greenbox"><br />
<h2>FRED</h2><br />
<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><br />
</div><br />
<div class="gbox1"><br />
<h2>Detecting</h2><br />
<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><br />
</div><br />
<div class="gbox2"><br />
<h2>Reporting</h2><br />
<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><br />
</div><br />
<div class="gbox3"><br />
<h2>Modelling</h2><br />
<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><br />
</div><br />
<div class="gbox4"><br />
<h2>Prototyping</h2><br />
<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><br />
</div><br />
<div class="bluebox"><br />
<h2>OSCAR</h2><br />
<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><br />
</div><br />
<div class="bbox1"><br />
<h2>Decarboxylation</h2><br />
<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><br />
</div><br />
<div class="bbox2"><br />
<h2>Catechol Degradation</h2><br />
<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><br />
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<div class="bbox3"><br />
<h2>Flux-Variability Analysis</h2><br />
<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><br />
</div><br />
<div class="bbox4"><br />
<h2>Bioreactor</h2><br />
<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><br />
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<div class="bbox5"><br />
<h2>Upgrading</h2><br />
<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><br />
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<h2>Team</h2><br />
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p><br />
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<h2>Data Page</h2><br />
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p><br />
</div><br />
</a><br />
<a id="greybox3" href="https://2012.igem.org/Team:Calgary/Notebook"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/1/1b/UCalgary2012_ThreeBoxNotebook.png"></img><br />
<h2>Notebook</h2><br />
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p><br />
</div><br />
</a><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<div id="sponsorsbox"><br />
<h2>Thanks to Our Sponsors!</h2><br />
<table><br />
<tr><br />
<td><a href="http://www.ucalgary.ca/bhsc/node/16" target="_blank"><img style="width: 284px;" src="https://static.igem.org/mediawiki/2012/d/d6/UCalgary2012_Logo_O%27Brien_Centre.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca" target="_blank"><img style="width: 166px;" src="https://static.igem.org/mediawiki/2012/4/46/UCalgary2012_Logo_U_of_C_Vertical.png"></img></a></td><br />
<td><a href="http://www.albertatechfutures.ca" target="_blank"><img style="width: 234px;" src="https://static.igem.org/mediawiki/2012/7/7f/UCalgary2012_Logo_AITF.png"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://bio.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/4/45/UCalgary2012_BioSci_Logo.png"></img></a></td><br />
<td><a href="http://enel.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/9/9c/UCalgary2012_Schulich_Electric_Computer_Logo.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca/bme/about/CBRE" target="_blank"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2012/5/56/UCalgary2012_CBREhz_Cropped.jpg"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://www.osli.ca" target="_blank"><img style="width: 891px;" src="https://static.igem.org/mediawiki/2012/9/98/UCalgary2012_Logo_OSLI.png"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://www.osrin.ualberta.ca" target="_blank"><img style="width: 204px;" src="https://static.igem.org/mediawiki/2012/0/04/UCalgary2012_OSRIN.png"></img></a></td><br />
<td><a href="http://www.mhc.ab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a></td><br />
<br />
<td><a href="http://www.eurofinsdna.com" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a></td><br />
<br />
</tr><br />
<tr><br />
<td><a href="http://www.autodesk.com" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/0/0b/UCalgary2012-Autodesk-Logo.png"></img></a></td><br />
<td><a href="http://www.hyperionlab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/8/89/UCalgary2012_Hyperion_Research_Logo.png"></img></a></td><br />
<td><a href="http://www.idtdna.com/site" target="_blank"><img style="width: 228px;" src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a></img></a></td><br />
</tr><br />
<tr><br />
<td><a href="http://www.sarstedt.com/php/main.php" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/f/f6/UCalgary2012_Logo_Sarstedt.png"></img></a></td><br />
<td><a href="http://www.teamlab.com" target="_blank"><img style="width: 160px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a></td><br />
<td><a href="http://www.vwr.com" target="_blank"><img style="width: 279px;" src="https://static.igem.org/mediawiki/2012/1/11/UCalgary2012_Logo_VWR.png"></img></a></td><br />
</tr><br />
<tr><br />
<table><tr><br />
<td><a href="http://genomealberta.ca" target="_blank"><img style="width: 203px;" src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></td><br />
<td><a href="http://www.neb.com/nebecomm/default.asp" target="_blank"><img style="width: 281px;" src="https://static.igem.org/mediawiki/2012/2/24/UCalgary2012_Logo_NEB.png"></img></a></td><br />
<td><a href="http://www.sparkscience.ca" target="_blank"><img style="width: 261px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a></td><br />
<br />
</tr></table><br />
</tr><br />
</table><br />
</div><br />
<br />
</body><br />
</html></div>Pjwuhttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-11-10T04:38:18Z<p>Pjwu: </p>
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<div id="box1" align="justify"><br />
<a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals" id="FredOscarFlag"><br />
<br />
</a><br />
<h2>Detect and Destroy: Building FRED and OSCAR</h2><br />
<p><b>Tailings ponds</b> are large bodies of water containing <b>toxic compounds</b> that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential <b>environmental and economic concern</b> to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms <b>to detect and destroy (bioremediate) the toxins</b>, turning them into useable <b>hydrocarbons</b>.</p><br />
<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the descriptions below to learn more!</p><br />
<p><b>Click on the links to the left to learn more about our work after the Americas West Regionals!</b></p><br />
<br />
</div><br />
<br />
<div class="threeboxes"><br />
<a id="greybox4" href="https://2012.igem.org/Team:Calgary/Team" style="margin-right:4px;"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/0/02/UCalgary2012_ThreeBoxMusic.png"></img><br />
<h2>iGEM Style!</h2><br />
<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><br />
</div><br />
</a><br />
<a id="greybox5" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/2/20/UCalgary2012_ThreeBoxSynergy.png"></img><br />
<h2>Synergy</h2><br />
<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p><br />
</div><br />
</a><br />
<a id="greybox6" href="http://www.youtube.com/watch?v=vluDpf4ao6c" style="margin:0;"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/b/b1/UCalgary2012_ThreeBoxFilm.png"></img><br />
<h2>Intro Video</h2><br />
<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p><br />
</div><br />
</a><br />
<br />
</div><br />
<br />
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</a><br />
<a class="gbox4 iconbox" href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype"><br />
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<a href="https://2012.igem.org/Team:Calgary/Project/OSCAR"><br />
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<a class="bbox1 iconbox" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation"><br />
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<img src="https://static.igem.org/mediawiki/2012/f/f1/UCalgary2012_IconOSCAR1.png"></img><br />
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</a><br />
<a class="bbox2 iconbox" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation"><br />
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<img src="https://static.igem.org/mediawiki/2012/0/0c/UCalgary2012_IconOSCAR4.png"></img><br />
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<div id="boxinfo"><br />
<div id="boxinfo_default"><br />
<h2>The Concept</h2><br />
<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><br />
</div><br />
<div class="orangebox"><br />
<h2>Human Practices</h2><br />
<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><br />
</div><br />
<div class="obox1"><br />
<h2>Initiative</h2><br />
<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><br />
</div><br />
<div class="obox2"><br />
<h2>Interviews</h2><br />
<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><br />
</div><br />
<div class="obox3"><br />
<h2>Design Considerations</h2><br />
<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><br />
</div><br />
<div class="obox4"><br />
<h2>Killswitch</h2><br />
<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><br />
</div><br />
<div class="obox5"><br />
<h2>Safety</h2><br />
<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><br />
</div><br />
<div class="obox6"><br />
<h2>Community Outreach</h2><br />
<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><br />
</div><br />
<div class="greenbox"><br />
<h2>FRED</h2><br />
<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><br />
</div><br />
<div class="gbox1"><br />
<h2>Detecting</h2><br />
<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><br />
</div><br />
<div class="gbox2"><br />
<h2>Reporting</h2><br />
<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><br />
</div><br />
<div class="gbox3"><br />
<h2>Modelling</h2><br />
<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><br />
</div><br />
<div class="gbox4"><br />
<h2>Prototyping</h2><br />
<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><br />
</div><br />
<div class="bluebox"><br />
<h2>OSCAR</h2><br />
<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><br />
</div><br />
<div class="bbox1"><br />
<h2>Decarboxylation</h2><br />
<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><br />
</div><br />
<div class="bbox2"><br />
<h2>Catechol Degradation</h2><br />
<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><br />
</div><br />
<div class="bbox3"><br />
<h2>Flux-Variability Analysis</h2><br />
<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><br />
</div><br />
<div class="bbox4"><br />
<h2>Bioreactor</h2><br />
<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><br />
</div><br />
<div class="bbox5"><br />
<h2>Upgrading</h2><br />
<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><br />
</div><br />
</div><br />
</div><br />
<br />
<div class="threeboxes"><br />
<a id="greybox1" href="https://2012.igem.org/Team:Calgary/Team"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/b/b8/UCalgary2012_ThreeBoxTeam.png"></img><br />
<h2>Team</h2><br />
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p><br />
</div><br />
</a><br />
<a id="greybox2" href="https://2012.igem.org/Team:Calgary/Project/DataPage"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/9/92/UCalgary2012_ThreeBoxData.png"></img><br />
<h2>Data Page</h2><br />
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p><br />
</div><br />
</a><br />
<a id="greybox3" href="https://2012.igem.org/Team:Calgary/Notebook"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/1/1b/UCalgary2012_ThreeBoxNotebook.png"></img><br />
<h2>Notebook</h2><br />
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p><br />
</div><br />
</a><br />
</div><br />
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<h2>Thanks to Our Sponsors!</h2><br />
<table><br />
<tr><br />
<td><a href="http://www.ucalgary.ca/bhsc/node/16" target="_blank"><img style="width: 284px;" src="https://static.igem.org/mediawiki/2012/d/d6/UCalgary2012_Logo_O%27Brien_Centre.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca" target="_blank"><img style="width: 166px;" src="https://static.igem.org/mediawiki/2012/4/46/UCalgary2012_Logo_U_of_C_Vertical.png"></img></a></td><br />
<td><a href="http://www.albertatechfutures.ca" target="_blank"><img style="width: 234px;" src="https://static.igem.org/mediawiki/2012/7/7f/UCalgary2012_Logo_AITF.png"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://bio.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/4/45/UCalgary2012_BioSci_Logo.png"></img></a></td><br />
<td><a href="http://enel.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/9/9c/UCalgary2012_Schulich_Electric_Computer_Logo.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca/bme/about/CBRE" target="_blank"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2012/5/56/UCalgary2012_CBREhz_Cropped.jpg"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://www.osli.ca" target="_blank"><img style="width: 891px;" src="https://static.igem.org/mediawiki/2012/9/98/UCalgary2012_Logo_OSLI.png"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://www.osrin.ualberta.ca" target="_blank"><img style="width: 204px;" src="https://static.igem.org/mediawiki/2012/0/04/UCalgary2012_OSRIN.png"></img></a></td><br />
<td><a href="http://www.mhc.ab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a></td><br />
<br />
<td><a href="http://www.eurofinsdna.com" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a></td><br />
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<tr><br />
<td><a href="http://www.autodesk.com" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/0/0b/UCalgary2012-Autodesk-Logo.png"></img></a></td><br />
<td><a href="http://www.hyperionlab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/8/89/UCalgary2012_Hyperion_Research_Logo.png"></img></a></td><br />
<td><a href="http://www.idtdna.com/site" target="_blank"><img style="width: 228px;" src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a></img></a></td><br />
</tr><br />
<tr><br />
<td><a href="http://www.sarstedt.com/php/main.php" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/f/f6/UCalgary2012_Logo_Sarstedt.png"></img></a></td><br />
<td><a href="http://www.teamlab.com" target="_blank"><img style="width: 160px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a></td><br />
<td><a href="http://www.vwr.com" target="_blank"><img style="width: 279px;" src="https://static.igem.org/mediawiki/2012/1/11/UCalgary2012_Logo_VWR.png"></img></a></td><br />
</tr><br />
<tr><br />
<table><tr><br />
<td><a href="http://genomealberta.ca" target="_blank"><img style="width: 203px;" src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></td><br />
<td><a href="http://www.neb.com/nebecomm/default.asp" target="_blank"><img style="width: 281px;" src="https://static.igem.org/mediawiki/2012/2/24/UCalgary2012_Logo_NEB.png"></img></a></td><br />
<td><a href="http://www.sparkscience.ca" target="_blank"><img style="width: 261px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a></td><br />
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</html></div>Pjwuhttp://2012.igem.org/File:UCalgary2012_FRED_and_OSCAR_Main_Page.pngFile:UCalgary2012 FRED and OSCAR Main Page.png2012-11-10T04:37:30Z<p>Pjwu: uploaded a new version of &quot;File:UCalgary2012 FRED and OSCAR Main Page.png&quot;</p>
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<div></div>Pjwuhttp://2012.igem.org/File:UCalgary2012_FRED_and_OSCAR_Main_Page.pngFile:UCalgary2012 FRED and OSCAR Main Page.png2012-11-10T04:32:40Z<p>Pjwu: </p>
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<div></div>Pjwuhttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-11-10T04:13:37Z<p>Pjwu: </p>
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<h2>Detect and Destroy: Building FRED and OSCAR</h2><br />
<p><b>Tailings ponds</b> are large bodies of water containing <b>toxic compounds</b> that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential <b>environmental and economic concern</b> to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms <b>to detect and destroy (bioremediate) the toxins</b>, turning them into useable <b>hydrocarbons</b>.</p><br />
<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the descriptions below to learn more!</p><br />
<p><b>Click on the links to the left to learn more about our work after the Americas West Regionals!</b></p><br />
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<h2>iGEM Style!</h2><br />
<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><br />
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<h2>Synergy</h2><br />
<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p><br />
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<h2>Intro Video</h2><br />
<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p><br />
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<h2>The Concept</h2><br />
<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><br />
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<h2>Human Practices</h2><br />
<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><br />
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<h2>Initiative</h2><br />
<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><br />
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<h2>Interviews</h2><br />
<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><br />
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<h2>Design Considerations</h2><br />
<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><br />
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<h2>Killswitch</h2><br />
<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><br />
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<h2>Safety</h2><br />
<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><br />
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<h2>Community Outreach</h2><br />
<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><br />
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<h2>FRED</h2><br />
<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><br />
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<h2>Detecting</h2><br />
<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><br />
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<h2>Reporting</h2><br />
<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><br />
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<h2>Modelling</h2><br />
<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><br />
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<h2>Prototyping</h2><br />
<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><br />
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<h2>OSCAR</h2><br />
<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><br />
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<h2>Decarboxylation</h2><br />
<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><br />
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<h2>Catechol Degradation</h2><br />
<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><br />
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<h2>Flux-Variability Analysis</h2><br />
<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><br />
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<h2>Bioreactor</h2><br />
<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><br />
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<h2>Upgrading</h2><br />
<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><br />
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<h2>Team</h2><br />
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p><br />
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<h2>Data Page</h2><br />
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p><br />
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<h2>Notebook</h2><br />
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p><br />
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<h2>Thanks to Our Sponsors!</h2><br />
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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/2012/d/d6/UCalgary2012_Logo_O%27Brien_Centre.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca" target="_blank"><img style="width: 166px;" src="https://static.igem.org/mediawiki/2012/4/46/UCalgary2012_Logo_U_of_C_Vertical.png"></img></a></td><br />
<td><a href="http://www.albertatechfutures.ca" target="_blank"><img style="width: 234px;" src="https://static.igem.org/mediawiki/2012/7/7f/UCalgary2012_Logo_AITF.png"></img></a></td><br />
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<td><a href="http://bio.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/4/45/UCalgary2012_BioSci_Logo.png"></img></a></td><br />
<td><a href="http://enel.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/9/9c/UCalgary2012_Schulich_Electric_Computer_Logo.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca/bme/about/CBRE" target="_blank"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2012/5/56/UCalgary2012_CBREhz_Cropped.jpg"></img></a></td><br />
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<td><a href="http://www.osli.ca" target="_blank"><img style="width: 891px;" src="https://static.igem.org/mediawiki/2012/9/98/UCalgary2012_Logo_OSLI.png"></img></a></td><br />
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<td><a href="http://www.osrin.ualberta.ca" target="_blank"><img style="width: 204px;" src="https://static.igem.org/mediawiki/2012/0/04/UCalgary2012_OSRIN.png"></img></a></td><br />
<td><a href="http://www.mhc.ab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a></td><br />
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<td><a href="http://www.eurofinsdna.com" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a></td><br />
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<td><a href="http://www.autodesk.com" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/0/0b/UCalgary2012-Autodesk-Logo.png"></img></a></td><br />
<td><a href="http://www.hyperionlab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/8/89/UCalgary2012_Hyperion_Research_Logo.png"></img></a></td><br />
<td><a href="http://www.idtdna.com/site" target="_blank"><img style="width: 228px;" src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a></img></a></td><br />
</tr><br />
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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/2012/f/f6/UCalgary2012_Logo_Sarstedt.png"></img></a></td><br />
<td><a href="http://www.teamlab.com" target="_blank"><img style="width: 160px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a></td><br />
<td><a href="http://www.vwr.com" target="_blank"><img style="width: 279px;" src="https://static.igem.org/mediawiki/2012/1/11/UCalgary2012_Logo_VWR.png"></img></a></td><br />
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<table><tr><br />
<td><a href="http://genomealberta.ca" target="_blank"><img style="width: 203px;" src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></td><br />
<td><a href="http://www.neb.com/nebecomm/default.asp" target="_blank"><img style="width: 281px;" src="https://static.igem.org/mediawiki/2012/2/24/UCalgary2012_Logo_NEB.png"></img></a></td><br />
<td><a href="http://www.sparkscience.ca" target="_blank"><img style="width: 261px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a></td><br />
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</html></div>Pjwuhttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-11-10T04:13:02Z<p>Pjwu: </p>
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<a id="boattop" href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals"></a><br />
<a id="boatbottom" href="https://2012.igem.org/Team:Calgary/Project/Synergy"></a><br />
</div><br />
<h2>Detect and Destroy: Building FRED and OSCAR</h2><br />
<p><b>Tailings ponds</b> are large bodies of water containing <b>toxic compounds</b> that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential <b>environmental and economic concern</b> to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms <b>to detect and destroy (bioremediate) the toxins</b>, turning them into useable <b>hydrocarbons</b>.</p><br />
<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the descriptions below to learn more!</p><br />
<p><b>Click on the links to the left to learn more about our work after the Americas West Regionals!</b></p><br />
<br />
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<img src="https://static.igem.org/mediawiki/2012/0/02/UCalgary2012_ThreeBoxMusic.png"></img><br />
<h2>iGEM Style!</h2><br />
<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><br />
</div><br />
</a><br />
<a id="greybox5" href="https://2012.igem.org/Team:Calgary/Project/Synergy"><br />
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<h2>Synergy</h2><br />
<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p><br />
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</a><br />
<a id="greybox6" href="http://www.youtube.com/watch?v=vluDpf4ao6c" style="margin:0;"><br />
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<h2>Intro Video</h2><br />
<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p><br />
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<div id="boxinfo"><br />
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<h2>The Concept</h2><br />
<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><br />
</div><br />
<div class="orangebox"><br />
<h2>Human Practices</h2><br />
<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><br />
</div><br />
<div class="obox1"><br />
<h2>Initiative</h2><br />
<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><br />
</div><br />
<div class="obox2"><br />
<h2>Interviews</h2><br />
<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><br />
</div><br />
<div class="obox3"><br />
<h2>Design Considerations</h2><br />
<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><br />
</div><br />
<div class="obox4"><br />
<h2>Killswitch</h2><br />
<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><br />
</div><br />
<div class="obox5"><br />
<h2>Safety</h2><br />
<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><br />
</div><br />
<div class="obox6"><br />
<h2>Community Outreach</h2><br />
<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><br />
</div><br />
<div class="greenbox"><br />
<h2>FRED</h2><br />
<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><br />
</div><br />
<div class="gbox1"><br />
<h2>Detecting</h2><br />
<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><br />
</div><br />
<div class="gbox2"><br />
<h2>Reporting</h2><br />
<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><br />
</div><br />
<div class="gbox3"><br />
<h2>Modelling</h2><br />
<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><br />
</div><br />
<div class="gbox4"><br />
<h2>Prototyping</h2><br />
<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><br />
</div><br />
<div class="bluebox"><br />
<h2>OSCAR</h2><br />
<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><br />
</div><br />
<div class="bbox1"><br />
<h2>Decarboxylation</h2><br />
<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><br />
</div><br />
<div class="bbox2"><br />
<h2>Catechol Degradation</h2><br />
<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><br />
</div><br />
<div class="bbox3"><br />
<h2>Flux-Variability Analysis</h2><br />
<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><br />
</div><br />
<div class="bbox4"><br />
<h2>Bioreactor</h2><br />
<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><br />
</div><br />
<div class="bbox5"><br />
<h2>Upgrading</h2><br />
<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><br />
</div><br />
</div><br />
</div><br />
<br />
<div class="threeboxes"><br />
<a id="greybox1" href="https://2012.igem.org/Team:Calgary/Team"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/b/b8/UCalgary2012_ThreeBoxTeam.png"></img><br />
<h2>Team</h2><br />
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p><br />
</div><br />
</a><br />
<a id="greybox2" href="https://2012.igem.org/Team:Calgary/Project/DataPage"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/9/92/UCalgary2012_ThreeBoxData.png"></img><br />
<h2>Data Page</h2><br />
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p><br />
</div><br />
</a><br />
<a id="greybox3" href="https://2012.igem.org/Team:Calgary/Notebook"><br />
<div><br />
<img src="https://static.igem.org/mediawiki/2012/1/1b/UCalgary2012_ThreeBoxNotebook.png"></img><br />
<h2>Notebook</h2><br />
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p><br />
</div><br />
</a><br />
</div><br />
<br />
<br />
<br />
<br />
<br />
<div id="sponsorsbox"><br />
<h2>Thanks to Our Sponsors!</h2><br />
<table><br />
<tr><br />
<td><a href="http://www.ucalgary.ca/bhsc/node/16" target="_blank"><img style="width: 284px;" src="https://static.igem.org/mediawiki/2012/d/d6/UCalgary2012_Logo_O%27Brien_Centre.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca" target="_blank"><img style="width: 166px;" src="https://static.igem.org/mediawiki/2012/4/46/UCalgary2012_Logo_U_of_C_Vertical.png"></img></a></td><br />
<td><a href="http://www.albertatechfutures.ca" target="_blank"><img style="width: 234px;" src="https://static.igem.org/mediawiki/2012/7/7f/UCalgary2012_Logo_AITF.png"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://bio.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/4/45/UCalgary2012_BioSci_Logo.png"></img></a></td><br />
<td><a href="http://enel.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/9/9c/UCalgary2012_Schulich_Electric_Computer_Logo.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca/bme/about/CBRE" target="_blank"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2012/5/56/UCalgary2012_CBREhz_Cropped.jpg"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://www.osli.ca" target="_blank"><img style="width: 891px;" src="https://static.igem.org/mediawiki/2012/9/98/UCalgary2012_Logo_OSLI.png"></img></a></td><br />
</tr><br />
</table><br />
<table><br />
<tr><br />
<td><a href="http://www.osrin.ualberta.ca" target="_blank"><img style="width: 204px;" src="https://static.igem.org/mediawiki/2012/0/04/UCalgary2012_OSRIN.png"></img></a></td><br />
<td><a href="http://www.mhc.ab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a></td><br />
<br />
<td><a href="http://www.eurofinsdna.com" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a></td><br />
<br />
</tr><br />
<tr><br />
<td><a href="http://www.autodesk.com" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/0/0b/UCalgary2012-Autodesk-Logo.png"></img></a></td><br />
<td><a href="http://www.hyperionlab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/8/89/UCalgary2012_Hyperion_Research_Logo.png"></img></a></td><br />
<td><a href="http://www.idtdna.com/site" target="_blank"><img style="width: 228px;" src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a></img></a></td><br />
</tr><br />
<tr><br />
<td><a href="http://www.sarstedt.com/php/main.php" target="_blank"><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/f/f6/UCalgary2012_Logo_Sarstedt.png"></img></a></td><br />
<td><a href="http://www.teamlab.com" target="_blank"><img style="width: 160px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a></td><br />
<td><a href="http://www.vwr.com" target="_blank"><img style="width: 279px;" src="https://static.igem.org/mediawiki/2012/1/11/UCalgary2012_Logo_VWR.png"></img></a></td><br />
</tr><br />
<tr><br />
<table><tr><br />
<td><a href="http://genomealberta.ca" target="_blank"><img style="width: 203px;" src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></td><br />
<td><a href="http://www.neb.com/nebecomm/default.asp" target="_blank"><img style="width: 281px;" src="https://static.igem.org/mediawiki/2012/2/24/UCalgary2012_Logo_NEB.png"></img></a></td><br />
<td><a href="http://www.sparkscience.ca" target="_blank"><img style="width: 261px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a></td><br />
<br />
</tr></table><br />
</tr><br />
</table><br />
</div><br />
<br />
</body><br />
</html></div>Pjwuhttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-11-10T04:01:26Z<p>Pjwu: </p>
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<div id="box1" align="justify"><br />
<div id="FredOscarBoat"><br />
<a id="boattop" href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals"></a><br />
<a id="boatbottom" href="https://2012.igem.org/Team:Calgary/Project/Synergy"></a><br />
</div><br />
<h2>Detect and Destroy: Building FRED and OSCAR</h2><br />
<p><b>Tailings ponds</b> are large bodies of water containing <b>toxic compounds</b> that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential <b>environmental and economic concern</b> to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms <b>to detect and destroy (bioremediate) the toxins</b>, turning them into useable <b>hydrocarbons</b>.</p><br />
<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the descriptions below to learn more!</p><br />
<p><b>Click on the links to the left to learn more about our work after the Americas West Regionals!</b></p><br />
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<h2>iGEM Style</h2><br />
<p>Take a look at our music video, taking the SynBio world by storm! (We hope so, at least!)</p><br />
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<h2>Synergy</h2><br />
<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p><br />
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<h2>Intro Video</h2><br />
<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p><br />
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<h2>The Concept</h2><br />
<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><br />
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<h2>Human Practices</h2><br />
<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><br />
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<h2>Initiative</h2><br />
<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><br />
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<h2>Interviews</h2><br />
<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><br />
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<h2>Design Considerations</h2><br />
<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><br />
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<h2>Killswitch</h2><br />
<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><br />
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<h2>Safety</h2><br />
<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><br />
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<h2>Community Outreach</h2><br />
<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><br />
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<h2>FRED</h2><br />
<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><br />
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<h2>Detecting</h2><br />
<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><br />
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<h2>Reporting</h2><br />
<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><br />
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<h2>Modelling</h2><br />
<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><br />
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<h2>Prototyping</h2><br />
<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><br />
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<h2>OSCAR</h2><br />
<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><br />
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<h2>Decarboxylation</h2><br />
<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><br />
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<h2>Catechol Degradation</h2><br />
<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><br />
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<h2>Flux-Variability Analysis</h2><br />
<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><br />
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<h2>Bioreactor</h2><br />
<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><br />
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<h2>Upgrading</h2><br />
<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><br />
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<h2>Team</h2><br />
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p><br />
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<h2>Data Page</h2><br />
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p><br />
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<h2>Notebook</h2><br />
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p><br />
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<h2>Thanks to Our Sponsors!</h2><br />
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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/2012/d/d6/UCalgary2012_Logo_O%27Brien_Centre.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca" target="_blank"><img style="width: 166px;" src="https://static.igem.org/mediawiki/2012/4/46/UCalgary2012_Logo_U_of_C_Vertical.png"></img></a></td><br />
<td><a href="http://www.albertatechfutures.ca" target="_blank"><img style="width: 234px;" src="https://static.igem.org/mediawiki/2012/7/7f/UCalgary2012_Logo_AITF.png"></img></a></td><br />
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<td><a href="http://bio.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/4/45/UCalgary2012_BioSci_Logo.png"></img></a></td><br />
<td><a href="http://enel.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/9/9c/UCalgary2012_Schulich_Electric_Computer_Logo.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca/bme/about/CBRE" target="_blank"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2012/5/56/UCalgary2012_CBREhz_Cropped.jpg"></img></a></td><br />
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<td><a href="http://www.osli.ca" target="_blank"><img style="width: 891px;" src="https://static.igem.org/mediawiki/2012/9/98/UCalgary2012_Logo_OSLI.png"></img></a></td><br />
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<td><a href="http://www.mhc.ab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a></td><br />
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<td><a href="http://www.eurofinsdna.com" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a></td><br />
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<td><a href="http://www.hyperionlab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/8/89/UCalgary2012_Hyperion_Research_Logo.png"></img></a></td><br />
<td><a href="http://www.idtdna.com/site" target="_blank"><img style="width: 228px;" src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a></img></a></td><br />
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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/2012/f/f6/UCalgary2012_Logo_Sarstedt.png"></img></a></td><br />
<td><a href="http://www.teamlab.com" target="_blank"><img style="width: 160px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a></td><br />
<td><a href="http://www.vwr.com" target="_blank"><img style="width: 279px;" src="https://static.igem.org/mediawiki/2012/1/11/UCalgary2012_Logo_VWR.png"></img></a></td><br />
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<td><a href="http://genomealberta.ca" target="_blank"><img style="width: 203px;" src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></td><br />
<td><a href="http://www.neb.com/nebecomm/default.asp" target="_blank"><img style="width: 281px;" src="https://static.igem.org/mediawiki/2012/2/24/UCalgary2012_Logo_NEB.png"></img></a></td><br />
<td><a href="http://www.sparkscience.ca" target="_blank"><img style="width: 261px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a></td><br />
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</html></div>Pjwuhttp://2012.igem.org/File:UCalgary2012_ThreeBoxFilm.pngFile:UCalgary2012 ThreeBoxFilm.png2012-11-10T03:57:01Z<p>Pjwu: </p>
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<div></div>Pjwuhttp://2012.igem.org/File:UCalgary2012_ThreeBoxSynergy.pngFile:UCalgary2012 ThreeBoxSynergy.png2012-11-10T03:54:14Z<p>Pjwu: </p>
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<div></div>Pjwuhttp://2012.igem.org/File:UCalgary2012_ThreeBoxMusic.pngFile:UCalgary2012 ThreeBoxMusic.png2012-11-10T03:47:37Z<p>Pjwu: </p>
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<div></div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/AccomplishTeam:Calgary/Project/Accomplish2012-10-27T04:04:27Z<p>Pjwu: </p>
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<h2> Our team had many accomplishments throughout the summer of 2012!</h2><br />
<p>Please see the <b>Post Regional</b> page for our results between Regionals and the Finals!<br />
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<p><b>In our <FONT COLOR="FF7A00">Human Practices</FONT> project, we...</b></p><br />
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<ul><li><p> Established a <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">dialogue between industry experts</a> in order to inform the design of our project.</p></li><br />
<li><p>Led a discussion through the oil sands leadership initiative (OSLI) on the need and potential usefulness of <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations#initiative"><br />
synthetic biology in the oil sands</a>.</p></li><br />
<li><p>Submitted <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">novel riboswitch, promoter and regulatory parts</a> for use in the tight control of killswitch applications and beyond.</p></li><br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation#killswitch">Submitted and characterized</a> both a magnesium riboswitch/promoter GFP construct and a magnesium riboswitch/promoter kill gene construct.</p></li><br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization#UBC">Partnered with the UBC iGEM team</a> in order to build and better optimize the <i>dsz</i> desulfurization operon.</p></li><br />
<li><p>Showcased our project to our city and the world through various outreach initiatives including a <a class="orange" href="https://2012.igem.org/Team:Calgary/Outreach/TEDxCalgary">TEDxCalgary City 2.0 talk</a>.</p></li><br />
<li><p>Premiered and beta-tested our <a class="orange" href="https://2012.igem.org/Team:Calgary/Outreach/VideoGame">video game LAB ESCAPE!</a> at the <a class="orange" href="http://www.sparkscience.ca">Calgary Telus Spark World of Science</a>.</p></li><br />
<li><p> Characterize the rhamnose and mgtA system with the S7 nuclease. <a class="orange"</a></li><br />
<li><p> Characterize a glycine auxotroph system to work in conjunction the rhamnose system.<a class="orange"></a></li> <br />
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<br />
<p><b>In terms of <FONT COLOR=#159900>FRED</FONT>, we...</b></p><br />
<img src="https://static.igem.org/mediawiki/2012/3/31/UCalgary2012_FRED_Index_Box.png" style="float: right; padding: 10px;"></img><br />
<ul><br />
<li><p> Constructed a <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting#library">transposon library</a> in <i>Pseudomonas</i>, identifying two positive hits sensitive to a variety of tailings pond toxins.</p></li><br />
<li><p>Submitted and electrochemically characterized the function of <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting#hydrolase">two novel hydrolase enzymes</a> from <i>E. coli</i>, demonstrating the validity and potential of a <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting#output">triple-output system</a> with high sensitivity and little background noise.</p></li><br />
<li><p>Designed and wet-lab verified a <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">kinetic model</a> of electrochemical gene expression.</p></li><br />
<li><P>Designed both <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype#hardware">hardware</a> and <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype#software">software</a> for a biosensor prototype.</p></li></ul><br />
<br />
<br />
<br><br />
<br />
<p><b>In terms of <FONT COLOR=#1088CC>OSCAR</FONT>, we...</b></p><br />
<img src="https://static.igem.org/mediawiki/2012/c/c3/UCalgary2012_OSCAR_Index_Box.png" style="float: right; padding: 10px;"></img><br />
<ul><br />
<br />
<li><p>Demonstrated the successful conversion of <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation#Petrobrick"><br />
naphthenic acids into hydrocarbons</a> using Washington 2011's PetroBrick.</p></li><br />
<br />
<li><P>Documented the functionality of the enzyme <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation#OleT">OleT</a>, an alternative enzyme to the PetroBrick for producing <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation#TestingOleT"><br />
alkenes from fatty acids</a>.</p></li><br />
<li><P>Modified an <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">existing <i>xylE</i></a> part to show the degradation of <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation#Catechol">catechol into a product, which is then degraded into hydrocarbons</a> using the PetroBrick or OleT.</p></li><br />
<li><P>Designed, built, and tested a <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">functioning bioreactor</a> system in which to house our toxin degrading strain.</p></li><br />
<li><P>Used flux variability analysis to <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis#Flux"><br />
optimize the production of our hydrocarbons</a>, surpassing Washington’s previous results through modification of growth media.</p></li><br />
<li><P>Demonstrated the successful <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization#Degradation">degradation of carbazole and DBT</a> by our model strains.</p></li><br />
<li><P>Submitted sequenced BioBricks for the removal of <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation#nitrogen">nitrogen</a> and <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization#sulfur"><br />
sulfur</a> from various compounds and mutagenized eight separate genes to remove illegal cut sites.</p></li><br />
<li><P>Submitted and characterized a new <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization#catalase">catalase generator</a> as well as a <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization#catalase">novel oxido-reductase enzyme</a> for use in our desulfurization project.</p></li><br />
<li><P><b><FONT COLOR=#1088CC>Had an amazing summer and learned a ton!</FONT></b></p></li></ul><br />
<br />
</html><br />
}}</div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/AccomplishTeam:Calgary/Project/Accomplish2012-10-27T04:04:04Z<p>Pjwu: </p>
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<br />
<h2> Our team had many accomplishments throughout the summer of 2012!</h2><br />
<p>Please see the <b>Post Regional</b> page for our results between Regionals and the Finals!<br />
<br />
<p><b>In our <FONT COLOR="FF7A00">Human Practices</FONT> project, we...</b></p><br />
<img src="https://static.igem.org/mediawiki/2012/1/17/UCalgary2012_FRED_and_OSCAR_HP.png" style="float: right; width: 250px; padding: 10px;"></img><br />
<ul><li><p> Established a <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">dialogue between industry experts</a> in order to inform the design of our project.</p></li><br />
<li><p>Led a discussion through the oil sands leadership initiative (OSLI) on the need and potential usefulness of <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations#initiative"><br />
synthetic biology in the oil sands</a>.</p></li><br />
<li><p>Submitted <a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">novel riboswitch, promoter and regulatory parts</a> for use in the tight control of killswitch applications and beyond.</p></li><br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation#killswitch">Submitted and characterized</a> both a magnesium riboswitch/promoter GFP construct and a magnesium riboswitch/promoter kill gene construct.</p></li><br />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization#UBC">Partnered with the UBC iGEM team</a> in order to build and better optimize the <i>dsz</i> desulfurization operon.</p></li><br />
<li><p>Showcased our project to our city and the world through various outreach initiatives including a <a class="orange" href="https://2012.igem.org/Team:Calgary/Outreach/TEDxCalgary">TEDxCalgary City 2.0 talk</a>.</p></li><br />
<li><p>Premiered and beta-tested our <a class="orange" href="https://2012.igem.org/Team:Calgary/Outreach/VideoGame">video game LAB ESCAPE!</a> at the <a class="orange" href="http://www.sparkscience.ca">Calgary Telus Spark World of Science</a>.</p></li><br />
<li><p> Characterize the rhamnose and mgtA system with the S7 nuclease. <a class="orange"</a></li><br />
<li><p> Characterize a glycine auxotroph system to work in conjunction the rhamnose system.<a class="orange"></a></li> <br />
</ul><br />
<br />
<br><br />
<br />
<p><b>In terms of <FONT COLOR=#159900>FRED</FONT>, we...</b></p><br />
<img src="https://static.igem.org/mediawiki/2012/3/31/UCalgary2012_FRED_Index_Box.png" style="float: right; padding: 10px;"></img><br />
<ul><br />
<li><p> Constructed a <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting#library">transposon library</a> in <i>Pseudomonas</i>, identifying two positive hits sensitive to a variety of tailings pond toxins.</p></li><br />
<li><p>Submitted and electrochemically characterized the function of <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting#hydrolase">two novel hydrolase enzymes</a> from <i>E. coli</i>, demonstrating the validity and potential of a <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting#output">triple-output system</a> with high sensitivity and little background noise.</p></li><br />
<li><p>Designed and wet-lab verified a <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">kinetic model</a> of electrochemical gene expression.</p></li><br />
<li><P>Designed both <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype#hardware">hardware</a> and <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype#software">software</a> for a biosensor prototype.</p></li></ul><br />
<br />
<br />
<br><br />
<br />
<p><b>In terms of <FONT COLOR=#1088CC>OCSAR</FONT>, we...</b></p><br />
<img src="https://static.igem.org/mediawiki/2012/c/c3/UCalgary2012_OSCAR_Index_Box.png" style="float: right; padding: 10px;"></img><br />
<ul><br />
<br />
<li><p>Demonstrated the successful conversion of <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation#Petrobrick"><br />
naphthenic acids into hydrocarbons</a> using Washington 2011's PetroBrick.</p></li><br />
<br />
<li><P>Documented the functionality of the enzyme <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation#OleT">OleT</a>, an alternative enzyme to the PetroBrick for producing <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation#TestingOleT"><br />
alkenes from fatty acids</a>.</p></li><br />
<li><P>Modified an <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">existing <i>xylE</i></a> part to show the degradation of <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation#Catechol">catechol into a product, which is then degraded into hydrocarbons</a> using the PetroBrick or OleT.</p></li><br />
<li><P>Designed, built, and tested a <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">functioning bioreactor</a> system in which to house our toxin degrading strain.</p></li><br />
<li><P>Used flux variability analysis to <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis#Flux"><br />
optimize the production of our hydrocarbons</a>, surpassing Washington’s previous results through modification of growth media.</p></li><br />
<li><P>Demonstrated the successful <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization#Degradation">degradation of carbazole and DBT</a> by our model strains.</p></li><br />
<li><P>Submitted sequenced BioBricks for the removal of <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation#nitrogen">nitrogen</a> and <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization#sulfur"><br />
sulfur</a> from various compounds and mutagenized eight separate genes to remove illegal cut sites.</p></li><br />
<li><P>Submitted and characterized a new <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization#catalase">catalase generator</a> as well as a <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization#catalase">novel oxido-reductase enzyme</a> for use in our desulfurization project.</p></li><br />
<li><P><b><FONT COLOR=#1088CC>Had an amazing summer and learned a ton!</FONT></b></p></li></ul><br />
<br />
</html><br />
}}</div>Pjwuhttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-10-27T04:00:00Z<p>Pjwu: </p>
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<h2>Detect and Destroy: Building FRED and OSCAR</h2><br />
<p><b>Tailings ponds</b> are large bodies of water containing <b>toxic compounds</b> that accumulate as a byproduct of the oil extraction process in the oil sands of northern Alberta. These toxic and corrosive compounds are a potential <b>environmental and economic concern</b> to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms <b>to detect and destroy (bioremediate) the toxins</b>, turning them into useable <b>hydrocarbons</b>.</p><br />
<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the descriptions below to learn more!</p><br />
<p><b>Click on the links to the left to learn more about our work after the Americas West Regionals!</b></p><br />
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<h2>Americas West Regionals Intro Video</h2><br />
<p>Click here to see our introductory video that we played at the beginning of our presentation at the iGEM Americas West Regionals!</p><br />
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<h2>The Concept</h2><br />
<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><br />
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<h2>Human Practices</h2><br />
<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><br />
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<h2>Initiative</h2><br />
<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><br />
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<h2>Interviews</h2><br />
<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><br />
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<h2>Design Considerations</h2><br />
<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><br />
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<h2>Killswitch</h2><br />
<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><br />
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<h2>Safety</h2><br />
<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><br />
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<h2>Community Outreach</h2><br />
<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><br />
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<h2>FRED</h2><br />
<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><br />
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<h2>Detecting</h2><br />
<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><br />
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<h2>Reporting</h2><br />
<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><br />
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<h2>Modelling</h2><br />
<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><br />
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<h2>Prototyping</h2><br />
<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><br />
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<h2>OSCAR</h2><br />
<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><br />
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<h2>Decarboxylation</h2><br />
<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><br />
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<h2>Catechol Degradation</h2><br />
<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><br />
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<h2>Flux-Variability Analysis</h2><br />
<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><br />
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<h2>Bioreactor</h2><br />
<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><br />
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<h2>Upgrading</h2><br />
<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><br />
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<h2>Team</h2><br />
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p><br />
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<h2>Data Page</h2><br />
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p><br />
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<h2>Notebook</h2><br />
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p><br />
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<h2>Thanks to Our Sponsors!</h2><br />
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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/2012/d/d6/UCalgary2012_Logo_O%27Brien_Centre.png"></img></a></td><br />
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<td><a href="http://enel.ucalgary.ca/" target="_blank"><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/9/9c/UCalgary2012_Schulich_Electric_Computer_Logo.png"></img></a></td><br />
<td><a href="http://www.ucalgary.ca/bme/about/CBRE" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/5/56/UCalgary2012_CBREhz_Cropped.jpg"></img></a></td><br />
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<td><a href="http://www.osli.ca" target="_blank"><img style="width: 891px;" src="https://static.igem.org/mediawiki/2012/9/98/UCalgary2012_Logo_OSLI.png"></img></a></td><br />
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<td><a href="http://www.mhc.ab.ca/" target="_blank"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a></td><br />
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<td style="width: 300px"><a href="http://genomealberta.ca" target="_blank"><img style="width: 203px;" src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></td><br />
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<td><a href="http://www.sparkscience.ca" target="_blank"><img style="width: 261px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a></td><br />
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</html></div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/FRED/ReportingTeam:Calgary/Project/FRED/Reporting2012-10-27T03:58:49Z<p>Pjwu: </p>
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<p>For FRED to be able to tell us about the toxins he's sensing we needed a good reporter system that could function in a wide array of environments. Unfortunately the traditional fluorescent or luminescent reporters have significant drawbacks that prevent them from being useful in a tailings environment that is murky and potentially anaerobic. Due to these limitations we decided to improve upon <a href="https://2011.igem.org/Team:Calgary">last year's single output electrochemical sensor</a> using the <i>lacZ</i> gene to cleave a substrate into an easily detectable analyte. Our team has developed a novel system that utilizes <b>three separate reporter genes</b> to provide a triple-output electrochemical biosensor and can be used in a wide variety of applications. This system overcomes traditional reporters in that it is <b>fast</b>,<b> accurate</b>, and can <b>function in turbid environments</b> and even in the <b>absence of oxygen!</b></p><br />
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<br><h2>Why Choose Hydrolases?</h2><br />
<p>To get our bacterial biosensors to report toxic compounds present in the tailings ponds, we needed a quick and reliable system that would function in a variety of aqueous environments. We turned to electrochemistry for this, as the turbidity of the solution doesn't affect the results and nanomolar levels of chemicals can consistently be detected. The idea behind electrochemistry is that the bacteria would either cleave a substrate to produce an oxidizable product (analyte), or transfer electrons directly into an electrode. The three most common methods through which bacteria produce an electrical response are the activities of phosphatases, hydrolases, and metal respiration. </p><br />
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<p>The first system, that of the respiration of metals, involves using an organism that uses metal ions, such as Fe<sup>3+</sup>, as the terminal electron acceptors in the cellular respiration pathways. While this kind of a system has the potential to be useful in creating bioelectricity, its use as a biosensor is limited. This is because it requires putting one of the essential electron transport genes under an inducible promoter, such that when the promoter is activated, respiration is enabled causing a change in current. Although these bacteria can usually respire more than one type of metal, they bottleneck to a single pathway and output.</p><br />
<p>The second system relies on phosphatases: enzymes that remove a phosphate group from an electrochemical analyte. When the phosphate group is removed the resultant product could be oxidized or reduced at an electrode to produce a response that would be measured as a change in current. While this method solves the problem of reduced cell viability created in the first system, it also is limited to a single output, as the non-specific phosphatases would act on all substrates in a solution. The effectiveness of the system could be further reduced by background expression of phosphatases in the bacterium, as these enzymes are essential for processes such as signalling and metabolism. </p><br />
<p>With this in mind we favoured a hydrolase based system, which offers the versatility and sensitivity of electrochemistry, without the pitfalls of disrupting metabolism or the limitations of a single channel output.</p><br />
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<br><h2>How Does it Work?</h2><br />
<a name="hydrolase"></a><p>The enzymes encoded by our reporter genes are specific sugar hydrolases. This means that they target one kind of sugar and remove it from whatever compound they are attached to. We have chosen to use the sugars glucose, glucuronide, and galactose for our system. The genes responsible for their respective hydrolases are <i>bglX</i> (<a href="http://partsregistry.org/Part:BBa_K902004">BBa_K902004</a>), <i>uidA</i> (<a href="http://partsregistry.org/Part:BBa_K902000">BBa_K902000</a>), and <i>lacZ</i> (<a href="http://partsregistry.org/Part:BBa_I732005">BBa_I732005</a>). By having our electrochemical analyte conjugated to this sugar, when the hydrolase is expressed the sugar is cleaved from the analyte, allowing for its electrochemical detection. A diagrammatic representation of this system is shown below in Figure 1.</p><br />
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[[File:Calgary2012 EchemWikiFig1.jpg|thumb|600px|center|Figure 1: Representation of cleavage of the sugar-analyte substrate by a hydrolase enzyme.]]<br />
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<p>After the analyte is released we need to detect it. Electrochemistry is an excellent approach for this because of its fast and quantitative nature. A voltage is applied between two electrodes compared to a reference electrode and the resulting current is measured. By changing the applied voltage to that of the oxidation voltage of one of our analytes, the increase in current due to its oxidation when compared to an analyte free baseline is proportional to the amount of analyte present in the solution. This process happens so quickly that you can have an output value in a matter of seconds.</p><br />
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<br><br />
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<p>We used two different electrochemical techniques in our testing depending on what question the experiment was trying to answer. When we were characterizing the voltages at which our products oxidized we used <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/cvs">cyclic voltammetry</a>, which is where you apply a voltage and then slowly increase and decrease it over a designated sweep range. Any bumps in the graph are due to a reaction and can be standardized against baseline measurements. After the oxidation potential has been localized we can speed up our experiments by using <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/potstd">potentiostatic runs</a>. In this case, instead of sweeping the voltage we apply to the solution we hold it steady at the voltage that will oxidize our compound the moment it is released into the solution. Both of these techniques require the three electrodes in an electrolyte solution such as phosphate buffered saline and can routinely detect nanomolar concentrations of electrochemical analytes.</p><br />
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<h2>Genes, Chemicals, and Circuits</h2><br />
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<p>For our system to have a triple output we need three separate genetic circuits with three analytes possessing unique oxidation potentials. If one chemical overlaps with another we could get false-positives of one chemical due to oxidation of another. To this end we have chosen to use chlorophenol red (CPR), para-diphenol (PDP), and para-nitrophenol (PNP). These compounds are conjugated with their sugars to form CPR-&beta;-D-galactopyranoside (CPRG), PDP-&beta;-D-glucopyranoside (PDPG), and PNP-&beta;-D-glucuronide (PNPG). An easy way to tell the analytes from their sugar conjugates is the addition of the letter G to the acronym. These chemicals are summarized below in Figure 2 along with the reporter genes used with each one.</p><br />
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[[File:Calgary2012 ECHEMWikiFig2.png|thumb|700px|center|Figure 2: Analyte/sugar combinations as well as the reporter genes responsible for the detection of each compound.]]<br />
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<a name="output"></a><p>Out of the three sugar conjugates the only one that exhibits any electrochemical activity is PDPG, with it's oxidation potential at 0.6V vs. the reduction of hydrogen reference electrode (RHE). The three analytes have potentials at 0.825V for PDP, 1.325V for CPR, and 1.6V for PNP vs RHE. As none of these peaks overlap and no sugar conjugates interfere with their signals the three chemicals can be detected in the same solution. Figure 3 shows sensitive simultaneous detection of our three analytes with no background interference.</p><br />
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[[File:Calgary2012 FRED triple.png|thumb|500px|center|Figure 3: Cyclic voltammogram of the three electrochemical analytes vs RHE. PDP has a peak at 0.825V, while CPR is at 1.325V and PNP is at 1.6V. The concentration of all analytes was 40&micro;M]]<br />
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<p>With the chemicals finalized we now needed to construct our circuits. <br />
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There is a <i>lacZ</i> gene under the control of the <i>lacI</i> promoter in the registry already registry (<a class="green" href="http://partsregistry.org/Part:BBa_I732901">BBa_I732901</a>). Upon testing this circuit however, it was determined to not be functional. In a simple assay where we added CPRG to cells expressing this part and induced with 200 mM IPTG, we saw no color change, as we would have expected if the LacZ enzyme was being produced and cleaving the CPRG (yellow) into CPR (red). This can be seen below</p> <p></html>[[File:UofC LacZ assay data.jpg|250px]][[File:UofC_LacZ2!.jpg|400px]]<html></p>.<br />
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<p> Sequencing of this part showed that it had a frameshift mutation. Original validation of our system was thus done using one of the constitutive <i>lacZ</i> hits from the <a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">transposon screen</a>. After Regionals, a new circuit was constructed and submitted as <a href="http://partsregistry.org/Part:BBa_K902090">BBa_K902090</a>. A similar assay was performed and the results can be seen above as well. On the right is the new circuit, while on the left, the old circuit. The red color indicates that the new pat is indeed functional. This circuit was used in later testing using the LacZ enzyme. The <i>bglX</i> and <i>uidA</i> genes were amplified from the <i>E. coli</i> genome using PCR and biobricked as <a href="http://partsregistry.org/Part:BBa_K902004">BBa_K902004</a> and <a href="http://partsregistry.org/Part:BBa_K902000">BBa_K902000</a> respectively. These genes were then constructed under the <a href="http://partsregistry.org/Part:BBa_R0010"><i>lacI</i> promoter</a> to allow for comparison testing.</p><br />
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<h2>Does it Work?</h2><br />
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<p>Yes! We have been able to show that we can detect the action of our hydrolase enzymes acting on the sugar-conjugated compounds to give us an electrochemical signal (<b>Figure 4</b>).</p><br><br />
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</html><br />
[[File:UCalgary2012-Electrochem-Robert.jpg|thumb|700px|center|Figure 4: A) Detection of <i>lacZ</i> activity on CPRG at 1.325V vs RHE through the production of CPR. B) Cleavage of PDPG into PDP by <i>bglX</i> being detected at 0.825V vs RHE. C) The action of <i>uidA</i> on PNPG at 1.6V vs RHE when under the control of the <html><a href="http://partsregistry.org/Part:BBa_R0010">R0010</a></html> promoter induced with IPTG or uninduced.]]<br />
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<br />
<p>These graphs show two main points. The first being that we can successfully use hydrolase enzymes as reporters for gene expression with a sensitive output. This gives us the power to accurately watch bacteria respond to a stimuli in real time with the ability to differentiate between minute differences in expression strength. As these reporters do not rely on having a colour or fluorescence output they can be used in turbid solutions and even solutions free from oxygen. This removes two of the major limitations of current biosensors, allowing this branch of biotechnology to access a broad new market.</p><br />
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<p>The second interesting conclusion that can be drawn for part C of Figure 4 is the leakiness of the <a href="http://partsregistry.org/Part:BBa_R0010">BBa_R0010</a> promoter. The bacteria were induced at time zero and a clear increase is seen almost immediately for the induced trial, but the current does still increase over time for the uninduced test. The leaky expression of the genes downstream of this promoter could be detrimental in situations such as toxic gene expression or time dependent events.</p><br />
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[[File:CALGARYROBERTOMGTHISPICROCKS.png|thumb|600px|center|Figure 5: Current production from the <i>lacZ</i> and <i>uidA</i> systems under the IPTG inducible promoter. Both samples were run with the same conditions and held at the oxidation potentials of their respective analytes.]]<br />
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<p>We have also been able to directly compare the <i>lacZ</i> and <i>uidA</i> circuits under the same promoter, as shown in Figure 5. In doing this we see twice the current in the <i>uidA</i> system as opposed to the <i>lacZ</i> system with the same conditions. This is because the analyte produced through the action of <i>uidA</i> produces a product that oxidizes to release two electrons while the <i>lacZ</i> product only releases one electron when oxidized. As the current we measure is this release of electrons, a similar amount of the two enzymes would results in the doubling of current for <i>uidA</i> that we saw, showing that our systems are working as expected.</p><br />
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<h2>What Next?</h2><br />
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<p>With our electrochemical system functioning properly we can now hook up our reporter genes to promoters found in the <a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">transposon library</a> for a final detection system. We have also created a <a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">hardware and software platform</a> for a field-ready biosensor. Our system has also been <a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">mathematically modeled</a> in MATLAB to aid us in planning time courses for the experiments and the final prototype. When combined with the mechanical and biological containment mechanisms used in our system these genes create a novel and safe approach to biosensing in the oil sands and in many other potential applications.</p><br />
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}}</div>Pjwuhttp://2012.igem.org/File:UCalgary2012_CBREhz_Cropped.jpgFile:UCalgary2012 CBREhz Cropped.jpg2012-10-27T03:55:28Z<p>Pjwu: </p>
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<div></div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/SynergyTeam:Calgary/Project/Synergy2012-10-27T03:52:57Z<p>Pjwu: </p>
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<a class="drop" href="https://2012.igem.org/Team:Calgary/Project">Overview</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/DataPage">Data Page</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Accomplish">Accomplishments</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals">Post-Regionals</a></li><br />
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<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices">Human Practices</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">Initiative</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Interviews</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design">Design</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">Killswitch</a></li><ul><li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation">Regulation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/KillGenes">Kill Genes</a></li></ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Safety">Safety</a></li><br />
</ul><br />
</li><br />
<li><br />
<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Detecting">Toxin Sensing</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting">Electroreporting</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling">Modelling</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/FRED/Prototype">Device Prototype</a></li><br />
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<a class="drop" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Decarboxylation">Decarboxylation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/CatecholDegradation">Decatecholization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis">Flux Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">Bioreactor</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Upgrading">Upgrading</a></li><ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Desulfurization">Desulfurization</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Denitrogenation">Denitrogenation</a></li></ul> <br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a></li><br />
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<li><a href="https://2012.igem.org/Team:Calgary/Project/References">References</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Project/Attributions">Attributions</a></li><br />
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TITLE=Synergy: Putting it all Together|CONTENT=<br />
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<h2>Incorporating Human Practices in the Design of our System </h2><br />
<p>In the earlier stages of our project, we realized that in order to give our project the best chance of being implemented, we needed to do it in a way that was in line with both industry’s wants and needs. To ensure that we did this, we established a dialogue with several experts in order to get their opinions on how we should approach our project. This led to an <b>informed design</b> of our system, in which we emphasized the need for both physical and genetic containment devices. </p><br />
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<h2>Have we accomplished our goal?</h2><br />
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<p>Nearing the end of our project however, we wanted to see if we had accomplished what we set out to do. So we decided to go back to the experts, this time taking the progress we had made on our project with us. We got a variety of different perspectives from suggestions on the scale up of our project, to the cost and environmental impact of our numerous components. The results of all of these can be found on our <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews"><b>Interviews</b></a> page. One major concern was <b>scale-up</b>. One expert wanted to know how feasible this system would actually be. We have some FRED components, OSCAR components, and killswitch components, but how functional are these parts, and how do they work together? Our next major goal was therefore to <u><b>establish synergy:</b> to put these pieces together in order to assess how far we have actually gotten</u>.</p><br />
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<p>Here we demonstrate that we can develop a <b>comprehensive kill switch</b> consisting of both an auxotroph and an inducible kill switch which work together to contain FRED and OSCAR. With FRED, we show that we can detect <b>toxins selectively in tailing ponds</b> using our identified transposon. Finally, with OSCAR we show that <b>our killswitch auxotroph dramatically increases the production of hydrocarbons in the system</b> and that we are capable of <b>scaling up</b> OSCAR's bioreactor and selectively collect hydrocarbons with our belt skimmer device.</p><br />
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<h2><u>Putting our Killswitch Together</u></h2><br />
<h2>Testing the Requirement of Glycine With our Auxotroph</h2><br />
<p>Our <a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis"><b>flux-based analysis</b></a> allowed us to realize the potential for glycine to be used not only as a way to increase the yield of OSCAR, but also as an auxotrophic killswitch. This allowed our model to be used not only to inform our wetlab, but also our human practices. We wanted to see how this auxotrophic marker system could work with one of our inducible killswitch constructs. We procured a Keio Knockout Collection Strain which deleted <i>glyA</i> an important enzyme in glycine metabolism making it auxotrophic for this compound. We wanted to identify the concentration of glycine required for its growth as shown below.<br />
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</html>[[File:Calgary GlycineKODeathAssay.png|thumb|500px|center|Figure 1: Glycine requirements for growth of <i>glyA</i> knockout strain JW2535-1. The bacteria was grown in LB overnight, washed, and subcultured into M9 minimal media, glucose, with various different concentration of glycine (from 1nM logarithmically to 100 mM). Interestingly, the glycine knockout grew best at concentrations of 1 - 10 mM. However, the auxotroph was not strong enough even at low concentrations to completely abolish growth.]]<html><br />
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<p>As identified by the growth assay, the glycine knockout is not capable of completely preventing growth of the strain even at very low concentrations of glycine. This identifies that it is important to continue to use our kill switch mechanism in combination with the auxotroph to control the cells. Now, with the concentrations ideal for glycine growth determined, we transformed our rhamnose inducible killswitch construct containing S7 <b>(<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902084">BBa_K902084</a>)</b> into our glycine knockout strain and attempted to characterize cell death over a variety of conditions.</p><br />
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<h2>Testing the Auxotrophic Marker as a Kill Switch</h2><br />
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<p>To test if using the <i>glyA</i> knockout strain in conjunction with our kill switch was effective, we transformed our Prha-S7 construct into the knockout strain as shown in Figure 2.</p><br />
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</html>[[File:Calgary Rha S7 Data.png|thumb|500px|center|Figure 2: pRHA-S7 construct demonstrating our kill switch in TOP10 wild type cells and <i>glyA</i> knockout cells. This demonstrates that our system is capable of being induced by the sugar rhamnose and repressed in the presence of glucose. There is no growth in rhamnose with our system as the <i>RhaBAD</i> operon has been deleted in the knockout strain we are using.]]<html><br />
<p>This data suggests that our killswitch system can act synergistically with the glycine auxotroph. In the prescence of glucose you see growth of both TOP10 and <i>glyA</i> knockout cells showing that our system is repressed. There is less growth in our glycine knockout as there was not a significant amount of glycine used in the media. The TOP10 control cell line did not show growth over 24 hours which was likely due to error in the read. In the presence of rhamnose, the kill switch is capable of being induced in both TOP10 and glycine knockout strains as shown by the decrease in CFU counts. This demonstrates a functional kill switch mechanism with the Prha promoter and auxotroph.</p><br />
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<h2> <u>Putting FRED together</u> </h2><br />
<h2>Can we sense toxins?</h2><br />
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<p>Now that we’ve been able to show that we can indeed sense three compounds electrochemically and simultaneously using our hydrolase system, and characterized genetic circuits for two of these outputs, our next goal was to actually try to sense toxins. Despite the fact that we have encountered significant difficulty in trying to sequence our transposon clones, given that we designed our transposon library to use <i>lacZ</i>, we could actually use our transposon directly in our electrochemical reporter system without actually knowing the identity of the sensory element. Although we do plan to BioBrick this in the future, for now, we grew up cultures of our transposon and tested the ability of our FRED system to sense toxins. We didn't just want to sense toxins however, we wanted to be able to sense toxins in tailings ponds. To do this, we grew up our transposon clone in media, aspirated the media and then placed it in tailings pond water samples. Upon addition of our sugar-reporter conjugate, CPRG, we monitored the formation of CPR electrochemically, which would be indicative of LacZ production, indicating activity of our toxin sensory element. The results of this assay can be shown below.</p><br />
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</html>[[File:UOFCTailingsPondWinData!.png|thumb|550px|centre|Figure 3. Current change over time illustrating <i>lacZ</i> induction by our identified transposon sensory element in a tailings pond water sample. The blue curve represents the tailings water test while the red curves shows the basal expression of the sensory element without tailings pond water present. This shows that our transposon clone has the ability to sense something within tailings pond water samples. ]]<html><br />
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<p>This result was extremely exciting for us, as we see clear induction of the system in the presence of tailings, as compared to the control. Although we don't know exactly what we are sensing, (remember that our transposon is sensitive to 3 different toxins: DBT, Carbazole and NAs),we are definitely sensing something! <b>This shows that FRED is functional and more than that, FRED is functional in the application for which he was designed!</b> The next step will be to quantify toxins present in tailings pond water samples in order to calibrate our reporter. </p><br />
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<h2> Taking FRED out to the field! </h2><br />
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<p> Once we knew that we had a promoter/reporter system that could actually detect toxins found in tailings ponds within the laboratory, the next challenge was to detect tailings pond toxins with our FRED prototype on site. Unfortunately, there are very strict regulations surrounding tailings ponds, and the publication of information pertaining to their contents. As such, obtaining permissions for a tailing pond field test was not possible within the time frame of our project. Because we did want to perform a kind of field test with FRED to show that the prototype that we built is feasible and easy to use, we investigated whether it would be permissable or advisable to try FRED outside of the lab. We performed a literature search to look for any regulations that might exist. Nothing pertaining to our province could be found, so we looked to Ontario and the United States. The concise guide to U.S. federal guidelines, rules and regulations for synthetic biology outlined the rules pertaining to field tests and indicated that in cases where organisms are going to be released into the environment, the EPA (environmental protection agency) requires a TSCA (Toxic Substances Control Act) Experimental Release Application (TERA) to be completed 60 days before the trial begins and the APHIS (Animal and Plant Health Inspection Service) requires a permit or notification. Although we specifically designed FRED to not release the microbes but rather to contain them, the prototype is too much in its infancy to remove it from the lab and be <b>absolutely</b> assured that it won’t be released. What we did instead, was took our prototype without bacteria in it to collect a water sample in a nearby river in Calgary. The video of this experience can be found below. </p><br />
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<h2> Putting our Killswitch into OSCAR - Can we use our Auxotroph with the Petrobrick?</h2><br />
<p><b>In fact it's better!</b> The glycine auxotroph will be used as a second layer of regulation with our kill switch in the event that our bacterium is capable of escaping the bioreactor. However in order to ensure that the glycine knockout we are using does not compromise the production of hydrocarbons and we can continue to see the high yield of hydrocarbons as predicted with our flux balance modelling, we performed an experiment to look at the relative amount of hydrocarbon production as in the flux balance analysis model. As seen in the figure below, using the <i>glyA</i> knockout greatly increased the output of hydrocarbons much higher than in the wild type <i>E. coli</i> strain. This was extremely exciting showing that our system could not only be safe, with a second layer of control for safety, and an increase in output.</p><br />
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</html>[[File:Calgary glyAKOPetrobrick.png|thumb|500px|center|Figure 4: Relative production of hydrocarbons per cell as discussed in the flux balance analysis section of our wiki. Wild type <i>E. coli</i> TOP10 cells were incubated with minimal media 1% glucose (Negative) or 50:50 LB:Washington Production Media (Positive). Additionally, the <i>glyA</i> knockout was incubated in minimal media in the presence of glycine. Production of C15 hydrocarbon was standardized to OD<sub>600</sub> measurements and normalized to the positive control. Surprisingly, the <i>glyA</i> knockout greatly increased the amount of hydrocarbons (almost 3x the amount of hydrocarbons per cell) produced compared to both controls.]]<html><br />
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<H2> Putting OSCAR into Action! </h2><br />
<p>Once we had tested FRED and shown that we could use him to detect toxins in tailings samples we wanted to put OSCAR into action in his home the bioreactor. By the end of the summer, we had designed and built a lab scale prototype of our bioreactor system. However, to better understand the needs of the oil sands industry we approached <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Interviews">Kelly Roberge</a>, an oil sands consultant specializing in tailings ponds. Through speaking with Mr. Roberge, we were able to better understand the concerns that the oil sands industry has with the use and building synthetic biology systems to solve the challenges they face. In particular, Mr. Roberge had questions that surrounded the feasibility of scaling up our bioreactor to an industrial scale. As it turns out there are a number of considerations that should be made when moving from the lab scale to industrial scale. Particularly, because these transitions can be an imperfect when moving from the lab scale to industrial scale (>1000L tanks). Therefore we thought it would be important to test the feasibility of <b>using our bioreactor, belt skimmer, and Petrobrick, to demonstrate we can produce and isolate hydrocarbons</b>. These results are illustrated in the video below!</p><br />
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<p>In short, the bioreactor was fillwed with 50:50 LB:Washington Production Media and we allowed the Petrobrick to grow over a 72 hour period. Afterwards, we demonstrated how our belt skimmer could be used for removal of the hydrocarbons. Because the hydrocarbons need to be extracted, we added ethyl acetate to allow for extraction, and demonstrated that our belt skimmer could selectively pick up the organic layer. Finally we ensured that this organic phase contained hydrocarbons by running this segment on the GC/MS as illustrated below.</p><br />
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</html>[[File:Calgary BioreactorValidation.png|thumb|500px|center|Figure 5: The GC chromatograph from the solvent layer which was selectively used with the belt skimmer. A large peak was observed much greater than any of the others, suggesting that hydrocarbons were being selectively removed with the belt skimmer.]]<html><br />
</html>[[File:Calgary BioreactorValidationMS.png|thumb|300px|center|Figure 6: MS data for the peak with a retention time of 12.7 min. The spectra suggests that the compound is a C16 hyrocarbon, validating that the upscaled bioreactor/belt skimmer combination can be used to isolate hydrocarbons.]]<html><br />
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<p>With these experiments we have been able to demonstrate that both FRED and OSCAR are functional and can work on their respective applications even in the context of a large scale! By listening to professionals and bringing an <b>informed design</b> to our project we have been able to provide systems with real world applications. FRED can <b>detect compounds in tailings ponds</b> and we have been able to <b>scale up and optimize</b> OSCAR through our bioreactor and flux balance analysis work. Additionally, we have connected our projects together by providing a <b>double kill switch system </b> with both an auxotroph and inducible exonuclease system that increases the production of hydrocarbons in OSCAR! With these systems in place and a clear concept of the value of what our project has to offer, we look forward to seeing what the future holds for FRED and OSCAR!</p><br />
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}}</div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/HumanPractices/InterviewsTeam:Calgary/Project/HumanPractices/Interviews2012-10-27T03:44:11Z<p>Pjwu: </p>
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<div>{{Team:Calgary/TemplateProjectOrange|<br />
TITLE=Interviews|<br />
CONTENT=<br />
<html><br />
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<img src="https://static.igem.org/mediawiki/2012/e/e8/UCalgary2012_FRED_and_OSCAR_Interviews_Low-Res.png" style="float: right; padding: 10px; width: 280px;"></img><br />
<h2>Purpose</h2><br />
<p> This year the Calgary iGEM team undertook our project with human practices in mind. While we had established a research objective to produce a biosensor and bioreactor system, we wanted to ensure that our system was relevant to the industry where it would be employed. As well, we wanted to ensure that academic, government, and industry professionals' concerns were taken into consideration during the design process of our system. In order to best accomplish this, we conducted interviews with two leaders in oilsands reclamation. We approached a major oilsands company, Suncor, and talked to Christine Daly, an Ecologist who works in Environmental Cleanup. We then approached Ryan Radke, the president of BioAlberta. BioAlberta focuses on bringing biotechnology to our province and develop these in an industrial setting. His experience allowed us to better predict if our project would raise concerns among legislators and industrial leaders. <br />
</p><br />
<br />
<h2> <u>Initial Interviews</u> </h2><br />
<br />
<h3>Talking with Suncor's Christine Daly on Biology in the Oil Sands</h3><br />
<p>We spoke with Christine Daly, an Aquatic Reclamation Research Coordinator at Suncor Energy Inc. Christine expressed an interest in our <a href="https://2011.igem.org/Team:Calgary">project in 2011</a> and was willing to discuss this year’s project design with us. One major point that was brought up early on was that engineered organisms might outcompete existing tailings ponds bacteria, and Christine had similar reservations. To address these concerns, we created our <a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">bioreactor</a> system, which would physically contain our bacteria, and also a <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">genetic killswitch mechanism</a>. Another interesting point brought up in this discussion was how the oil industry is currently looking into biology as one of many potential alternative methods to remediate the toxic components of tailings ponds and the oil sands in general. There is research using other systems such as algal bioremediation, but practical implementations of biology in the oil sands are rare. Oil industries do, however, appear to show an increased interest in biology (and in turn, synthetic biology) as a possible solution to various problems, a sentiment reflected in <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">our dialogue with the Oil Sands Leadership Initiative</a>.</p><br />
<p>The full interview can be viewed below.</p><br />
<div align="center"><br />
<iframe width="600" height="450" align="center" src="http://www.youtube.com/embed/GiM6EIC9XBo" frameborder="0" allowfullscreen></iframe><br />
<br />
</div><br />
<br />
<h3>BioAlberta's Ryan Radke on Biology in the Oil Sands</h3><br />
<p>We were also able to consult with BioAlberta president Ryan Radke on the viability of using biologically based systems in the petroleum industry. He believed that bioremediation technologies will be critical to the future of the oil sands in the next 10-15 years, however he raised the concern of how we could sell biotechnology to an industry that is already very successful from a profit point of view. He emphasized the social welfare benefits that the industry, under heavy environmental criticism, could gain from this technology as a major selling point and stressed the need to educate the oil industry about the benefits of synthetic biology. This would involve putting aspects of our system into large-scale, comprehensive terms to sell to those without a biology background. For example, quantifying the amount of toxins that the system can process per unit time and the value of hydrocarbons produced is something that could potentially appeal to investors. We feel as though the synthetic biology <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">dialogue with the Oil Sands Leadership Initiative</a> was a great start to bridging the gap between the petroleum industry and synthetic biology. From a public perspective point of view we discussed the need to stress the fact our system is simply a modification of "natural" processes - that is we are only modifying bacteria native to the tailings ponds, not introducing new organisms to the environment. To further address safety concerns, we also need to emphasize the multiple layers of <a href="https://2012.igem.org/Team:Calgary/Safety">biological and physical control</a> that we plan to design.</p> <br />
<div align="center"><br />
<iframe width="600" height="450" align="center" src="http://www.youtube.com/embed/86XQ-Kg5fJ4" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<a name="postregionals"></a><br />
<h2><u>Follow-Up Interviews</u></h2><br />
<p>Our second iteration of interviews were conducted once we had a more concrete product built. The purpose of these interviews was to see whether we had successfully addressed the concerns of the first iteration interviews. We also wanted to see whether any new issues with the design existed, which would provide us with potential future directions to take FRED and OSCAR. Kelly Roberge, an independent oil consultant, suggested we investigate ways of dealing with the clay and silt particles in tailings pond water that would enter our bioreactor system. This can be a major problem since these mature fine tailings have a thick consistency that could clog the system.</p><br />
<br />
<h3>Kelly Roberge, of K. Roberge Consulting Ltd. Discussing Bioreactor Improvements</h3><br />
<p>We spoke to Kelly Roberge of K. Roberge Consulting Ltd. who is an independent consultant for the oil sands focusing on mature fine tailings (MFT). He mentioned that in the past 4 years, there has been an increase in looking at biological techniques in the oil sands for remediation, both in understanding natively present microbial life as well as introducing engineered systems.</p><br />
<p> The major concerns that he had with our present design were issues with scale-up. These were things such as the amount of toxins that would have to be processed to provide constant generation of product, residence time in the bioreactor, as well as the ability for our system to be scaled up to an industrial size. Though we still have much research to do toward this goal of reaching industrial capacity, we did a model scale-up experiment of OSCAR by growing the PetroBrick containing <i>E. coli</i> in our model bioreactor system. The results of this experiment can be found on our <a class="purple" href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a> page.</p><br />
<p>In addition, there was a concern raised with the composition of the tailings themselves, due to the mature fine tailings sludge (MFT). In the future we should look at addressing the capacity of OSCAR to deal with these MFT components. Some suggestions that were made would be to utilize OSCAR in parallel with MFT settling techniques or with runoff water from the tailings drying processes. The sensitivity of our system to these fine tailings and to bitumen would also have to be evaluated and made compatible with the substrates we will be adding in to the system.</p><br />
<br />
<div align="center"><br />
<iframe width="600" height="450" src="http://www.youtube.com/embed/e5ePaqw5zk4" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<h3>William Sawchuk, of ARC Resources</h3><br />
<p>William Sawchuk, a reservoir engineer at Arc resources, agreed to talk with us about the main parts of our project. This interview confirmed that biological methods, and specifically our project, are definite possibilities of remediation in the oil sands if they can prove to be faster and less harmful than current methods. One concern that Mr. Sawchuk brought up was that there needs to be extra safety features put in place to avoid posing danger to the environment. This again, serves to further validate the approach that we took to safety, designing both <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design"> structural and genetic killswitch devices</a>. In the later part of our project, we have also been trying to work on establishing a <a class="purple" href="https://2012.igem.org/Team:Calgary/Project/Synergy">glycine auxotrophic killswitch</a> to add yet another layer of safety which we feel is necessary. </p><br />
<br />
<p>Similar to Mr. Roberge, another thing Mr. Sawchuk brought up was scale-up. Specifically, he talked about feasibility and how much a scale-up of the project would cost and if this is less expensive than the current remediation methods. To this end, we have been experimenting with getting our bioreactor to work and have performed an initial validation assay to demonstrate that we can use it in conjunction with our belt skimmer to produce and harvest hydrocarbons, which can be found on our <a class="purple" href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a> page. The next step is to scale-up further! Calculating exact costs is a tricky. Since the conversion of toxins in the tailings ponds into useful hydrocarbons is a relatively novel idea, it is somewhat difficult to analyze what the cost of a scale-up would be at this point. This is an extremely important future direction for us however.</p><br />
<br />
<div align="center"><br />
<iframe width="600" height="450" src="http://www.youtube.com/embed/nLeupM1Ype8" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<h3>Gordon Lambert, VP Sustainable Development at Suncor Inc.</h3><br />
<p>Gordon Lambert is the VP Sustainable Development at Suncor Energy Inc. We asked him whether or not the oil sands industry would find technology such as this useful. There was a very positive response. The Oil Sands Leadership Initiative is very keen on searching for any solutions to tackle the tailings ponds, which are considered to be one of the biggest issues in the oil sands currently. <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">OSLI</a> is collaborating with organizations that run competitions globally for oil sands solutions and other bodies such the Canada's Oil Sands Innovation Alliance (COSIA). Similar to Kelly Roberge's comment, mature fine tailings can be dried and solidified, but in turn it liberates water from the clay and sand. This water cannot be used for any industrial purposes until it is detoxified. Ideally, this water can be detoxified sufficiently to be returned as tailings pond surface water and become reusable in the bitumen extraction process.</p><br />
<p>In order to deploy our biosensor and bioreactor system, it was suggested that we look into various regulatory boards within Alberta such as Alberta Environment and the Energy Resources Conservation Board (ERCB) to attempt to obtain permits to begin attempting pilot programs. <a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Scale up</a> of the bioreactor is also a major consideration in order for us to push it off the bench and into the field.</p><br />
<p>The full interview can be found below.</p><br />
<br />
<div align="center"><br />
<iframe width="600" height="450" src="http://www.youtube.com/embed/7KbEjQVUsFA" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<h3>Zvonko Burkus from Alberta Environment Discusses the Project in Detail</h3><br />
<p>Zvonko is a process water and policy specialist for Alberta Environment. Zvonko was happy to discuss with us at length about this project. Notably, there were concerns about the use of both <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED </a> and <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a> in active tailings ponds, since naphthenic acids are known surfactants which help with bitumen detachment from the sand particles. FRED was seen as something which could be more useful in a live-monitoring system, since currently there are no such systems for organic compounds, which is a possible direction for us.</p><br />
<p>We were warned that the oil industry is rather traditional, but as we have seen from our <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">OSLI dialogue</a>, it appears that more companies are beginning to see the potential benefit of biology in solving various issues with the oil sands.</p><br />
<p>Some interesting points for us to explore further included examining whether or not the intermediates of our metabolic pathways were more or less toxic than the starting compounds, and expanding our scope to target other compounds such as polyaromatic hydrocarbons, chlorides, composite tailings, polyphenols, and hydrogen sulfide.</p><br />
<p>The interview, in full, has been divided into six parts. Please click the links below to download them.</p><br />
<p><a href="https://static.igem.org/mediawiki/2012/a/aa/UCalgary2012_Zvonko_Burkus_Interview-01.mp3">Part 1</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/b/ba/UCalgary2012_Zvonko_Burkus_Interview-02.mp3">Part 2</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/0/0e/UCalgary2012_Zvonko_Burkus_Interview-03.mp3">Part 3</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/b/b8/UCalgary2012_Zvonko_Burkus_Interview-04.mp3">Part 4</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/c/c1/UCalgary2012_Zvonko_Burkus_Interview-05.mp3">Part 5</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/7/70/UCalgary2012_Zvonko_Burkus_Interview-06.mp3">Part 6</a><br/></p><br />
<br />
<br />
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</html><br />
}}</div>Pjwuhttp://2012.igem.org/Team:Calgary/Project/HumanPractices/InterviewsTeam:Calgary/Project/HumanPractices/Interviews2012-10-27T03:43:22Z<p>Pjwu: </p>
<hr />
<div>{{Team:Calgary/TemplateProjectOrange|<br />
TITLE=Interviews|<br />
CONTENT=<br />
<html><br />
<br />
<img src="https://static.igem.org/mediawiki/2012/e/e8/UCalgary2012_FRED_and_OSCAR_Interviews_Low-Res.png" style="float: right; padding: 10px; width: 280px;"></img><br />
<h2>Purpose</h2><br />
<p> This year the Calgary iGEM team undertook our project with human practices in mind. While we had established a research objective to produce a biosensor and bioreactor system, we wanted to ensure that our system was relevant to the industry where it would be employed. As well, we wanted to ensure that academic, government, and industry professionals' concerns were taken into consideration during the design process of our system. In order to best accomplish this, we conducted interviews with two leaders in oilsands reclamation. We approached a major oilsands company, Suncor, and talked to Christine Daly, an Ecologist who works in Environmental Cleanup. We then approached Ryan Radke, the president of BioAlberta. BioAlberta focuses on bringing biotechnology to our province and develop these in an industrial setting. His experience allowed us to better predict if our project would raise concerns among legislators and industrial leaders. <br />
</p><br />
<br />
<h2> <u>Initial Interviews</u> </h2><br />
<br />
<h3>Talking with Suncor's Christine Daly on Biology in the Oil Sands</h3><br />
<p>We spoke with Christine Daly, an Aquatic Reclamation Research Coordinator at Suncor Energy Inc. Christine expressed an interest in our <a href="https://2011.igem.org/Team:Calgary">project in 2011</a> and was willing to discuss this year’s project design with us. One major point that was brought up early on was that engineered organisms might outcompete existing tailings ponds bacteria, and Christine had similar reservations. To address these concerns, we created our <a href="https://2012.igem.org/Team:Calgary/Project/OSCAR/Bioreactor">bioreactor</a> system, which would physically contain our bacteria, and also a <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">genetic killswitch mechanism</a>. Another interesting point brought up in this discussion was how the oil industry is currently looking into biology as one of many potential alternative methods to remediate the toxic components of tailings ponds and the oil sands in general. There is research using other systems such as algal bioremediation, but practical implementations of biology in the oil sands are rare. Oil industries do, however, appear to show an increased interest in biology (and in turn, synthetic biology) as a possible solution to various problems, a sentiment reflected in <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">our dialogue with the Oil Sands Leadership Initiative</a>.</p><br />
<p>The full interview can be viewed below.</p><br />
<div align="center"><br />
<iframe width="600" height="450" align="center" src="http://www.youtube.com/embed/GiM6EIC9XBo" frameborder="0" allowfullscreen></iframe><br />
<br />
</div><br />
<br />
<h3>BioAlberta's Ryan Radke on Biology in the Oil Sands</h3><br />
<p>We were also able to consult with BioAlberta president Ryan Radke on the viability of using biologically based systems in the petroleum industry. He believed that bioremediation technologies will be critical to the future of the oil sands in the next 10-15 years, however he raised the concern of how we could sell biotechnology to an industry that is already very successful from a profit point of view. He emphasized the social welfare benefits that the industry, under heavy environmental criticism, could gain from this technology as a major selling point and stressed the need to educate the oil industry about the benefits of synthetic biology. This would involve putting aspects of our system into large-scale, comprehensive terms to sell to those without a biology background. For example, quantifying the amount of toxins that the system can process per unit time and the value of hydrocarbons produced is something that could potentially appeal to investors. We feel as though the synthetic biology <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">dialogue with the Oil Sands Leadership Initiative</a> was a great start to bridging the gap between the petroleum industry and synthetic biology. From a public perspective point of view we discussed the need to stress the fact our system is simply a modification of "natural" processes - that is we are only modifying bacteria native to the tailings ponds, not introducing new organisms to the environment. To further address safety concerns, we also need to emphasize the multiple layers of <a href="https://2012.igem.org/Team:Calgary/Safety">biological and physical control</a> that we plan to design.</p> <br />
<div align="center"><br />
<iframe width="600" height="450" align="center" src="http://www.youtube.com/embed/86XQ-Kg5fJ4" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<a name="postregionals"></a><br />
<h2><u>Follow-Up Interviews</u></h2><br />
<p>Our second iteration of interviews were conducted once we had a more concrete product built. The purpose of these interviews was to see whether we had successfully addressed the concerns of the first iteration interviews. We also wanted to see whether any new issues with the design existed, which would provide us with potential future directions to take FRED and OSCAR. Kelly Roberge, an independent oil consultant, suggested we investigate ways of dealing with the clay and silt particles in tailings pond water that would enter our bioreactor system. This can be a major problem since these mature fine tailings have a thick consistency that could clog the system.</p><br />
<br />
<h3>Kelly Roberge, of K. Roberge Consulting Ltd. Discussing Bioreactor Improvements</h3><br />
<p>We spoke to Kelly Roberge of K. Roberge Consulting Ltd. who is an independent consultant for the oil sands focusing on mature fine tailings (MFT). He mentioned that in the past 4 years, there has been an increase in looking at biological techniques in the oil sands for remediation, both in understanding natively present microbial life as well as introducing engineered systems.</p><br />
<p> The major concerns that he had with our present design were issues with scale-up. These were things such as the amount of toxins that would have to be processed to provide constant generation of product, residence time in the bioreactor, as well as the ability for our system to be scaled up to an industrial size. Though we still have much research to do toward this goal of reaching industrial capacity, we did a model scale-up experiment of OSCAR by growing the PetroBrick containing <i>E. coli</i> in our model bioreactor system. The results of this experiment can be found on our <a class="purple" href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a> page.</p><br />
<p>In addition, there was a concern raised with the composition of the tailings themselves, due to the mature fine tailings sludge (MFT). In the future we should look at addressing the capacity of OSCAR to deal with these MFT components. Some suggestions that were made would be to utilize OSCAR in parallel with MFT settling techniques or with runoff water from the tailings drying processes. The sensitivity of our system to these fine tailings and to bitumen would also have to be evaluated and made compatible with the substrates we will be adding in to the system.</p><br />
<br />
<div align="center"><br />
<iframe width="600" height="450" src="http://www.youtube.com/embed/e5ePaqw5zk4" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<h3>William Sawchuk, of ARC Resources</h3><br />
<p>William Sawchuk, a reservoir engineer at Arc resources, agreed to talk with us about the main parts of our project. This interview confirmed that biological methods, and specifically our project, are definite possibilities of remediation in the oil sands if they can prove to be faster and less harmful than current methods. One concern that Mr. Sawchuk brought up was that there needs to be extra safety features put in place to avoid posing danger to the environment. This again, serves to further validate the approach that we took to safety, designing both <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Design"> structural and genetic killswitch devices</a>. In the later part of our project, we have also been trying to work on establishing a <a class="purple" href="https://2012.igem.org/Team:Calgary/Project/Synergy">glycine auxotrophic killswitch</a> to add yet another layer of safety which we feel is necessary. </p><br />
<br />
<p>Similar to Mr. Roberge, another thing Mr. Sawchuk brought up was scale-up. Specifically, he talked about feasibility and how much a scale-up of the project would cost and if this is less expensive than the current remediation methods. To this end, we have been experimenting with getting our bioreactor to work and have performed an initial validation assay to demonstrate that we can use it in conjunction with our belt skimmer to produce and harvest hydrocarbons, which can be found on our <a class="purple" href="https://2012.igem.org/Team:Calgary/Project/Synergy">Synergy</a> page. The next step is to scale-up further! Calculating exact costs is a tricky. Since the conversion of toxins in the tailings ponds into useful hydrocarbons is a relatively novel idea, it is somewhat difficult to analyze what the cost of a scale-up would be at this point. This is an extremely important future direction for us however.</p><br />
<br />
<div align="center"><br />
<iframe width="600" height="450" src="http://www.youtube.com/embed/nLeupM1Ype8" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<h3>Gordon Lambert, VP Sustainable Development at Suncor Inc.</h3><br />
<p>Gordon Lambert is the VP Sustainable Development at Suncor Energy Inc. We asked him whether or not the oil sands industry would find technology such as this useful. There was a very positive response. The Oil Sands Leadership Initiative is very keen on searching for any solutions to tackle the tailings ponds, which are considered to be one of the biggest issues in the oil sands currently. <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">OSLI</a> is collaborating with organizations that run competitions globally for oil sands solutions and other bodies such the Canada's Oil Sands Innovation Alliance (COSIA). Similar to Kelly Roberge's comment, mature fine tailings can be dried and solidified, but in turn it liberates water from the clay and sand. This water cannot be used for any industrial purposes until it is detoxified. Ideally, this water can be detoxified sufficiently to be returned as tailings pond surface water and become reusable in the bitumen extraction process.</p><br />
<p>In order to deploy our biosensor and bioreactor system, it was suggested that we look into various regulatory boards within Alberta such as Alberta Environment and the Energy Resources Conservation Board (ERCB) to attempt to obtain permits to begin attempting pilot programs. <a href="https://2012.igem.org/Team:Calgary/Project/Synergy">Scale up</a> of the bioreactor is also a major consideration in order for us to push it off the bench and into the field.</p><br />
<p>The full interview can be found below.</p><br />
<br />
<div align="center"><br />
<iframe width="600" height="450" src="http://www.youtube.com/embed/7KbEjQVUsFA" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<h3>Zvonko Burkus from Alberta Environment Discusses the Project in Detail</h3><br />
<p>Zvonko is a process water and policy specialist for Alberta Environment. Zvonko was happy to discuss with us at length about this project. Notably, there were concerns about the use of both <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED </a> and <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a> in active tailings ponds, since naphthenic acids are known surfactants which help with bitumen detachment from the sand particles. FRED was seen as something which could be more useful in a live-monitoring system, since currently there are no such systems for organic compounds, which is a possible direction for us.</p><br />
<p>We were warned that the oil industry is rather traditional, but as we have seen from our <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Collaborations">OSLI dialogue</a>, it appears that more companies are beginning to see the potential benefit of biology in solving various issues with the oil sands.</p><br />
<p>Some interesting points for us to explore further included examining whether or not the intermediates of our metabolic pathways were more or less toxic than the starting compounds, and expanding our scope to target other compounds such as polyaromatic hydrocarbons, chlorides, composite tailings, polyphenols, and hydrogen sulfide.</p><br />
<p>The interview, in full, has been divided into four parts. Please click the links below to download them.</p><br />
<p><a href="https://static.igem.org/mediawiki/2012/a/aa/UCalgary2012_Zvonko_Burkus_Interview-01.mp3">Part 1</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/b/ba/UCalgary2012_Zvonko_Burkus_Interview-02.mp3">Part 2</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/0/0e/UCalgary2012_Zvonko_Burkus_Interview-03.mp3">Part 3</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/b/b8/UCalgary2012_Zvonko_Burkus_Interview-04.mp3">Part 4</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/c/c1/UCalgary2012_Zvonko_Burkus_Interview-05.mp3">Part 5</a><br/></p><br />
<p><a href="https://static.igem.org/mediawiki/2012/7/70/UCalgary2012_Zvonko_Burkus_Interview-06.mp3">Part 6</a><br/></p><br />
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}}</div>Pjwuhttp://2012.igem.org/File:UCalgary2012_Zvonko_Burkus_Interview-06.mp3File:UCalgary2012 Zvonko Burkus Interview-06.mp32012-10-27T03:41:34Z<p>Pjwu: </p>
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<div></div>Pjwuhttp://2012.igem.org/File:UCalgary2012_Zvonko_Burkus_Interview-05.mp3File:UCalgary2012 Zvonko Burkus Interview-05.mp32012-10-27T03:40:54Z<p>Pjwu: </p>
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