http://2012.igem.org/wiki/index.php?title=Special:Contributions&feed=atom&limit=50&target=Iaingeorge&year=&month=2012.igem.org - User contributions [en]2024-03-28T15:37:59ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:CalgaryTeam:Calgary2013-01-13T23:59:45Z<p>Iaingeorge: Undo revision 299477 by Iaingeorge (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 />
<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>Iaingeorgehttp://2012.igem.org/Team:CalgaryTeam:Calgary2013-01-13T23:53:49Z<p>Iaingeorge: </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 />
<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 />
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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 />
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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 />
</tr><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>Iaingeorgehttp://2012.igem.org/Team:Calgary/Outreach/BlogTeam:Calgary/Outreach/Blog2012-11-09T22:56:58Z<p>Iaingeorge: another blog post</p>
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<div>{{Team:Calgary/TemplateOutreach|<br />
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<p>Genome Alberta sponsored us this year to share with their website's audience some of the interesting things we were doing with genetics and synthetic biology this year. We have authored a number of the blog posts and been featured in one of their writer's blog posts. This was a great way to interface with industry and show a more 'humanistic' side of iGEM. It also provided a great opportunity to connect with Alberta and Canada's scientific community and industries. More blog posts will find their way up over the next few weeks!</p><br />
<br />
<h2>The Blog Posts</h2><br />
<br />
<h2></html>[http://genomealberta.ca/blogs/tackling-tailings-ponds-the-igem-way.aspx Tackling Tailings Ponds - the iGEM Way]<html></h2><br />
<br />
<p><br />
<br />
<h2></html>[http://genomealberta.ca/blogs/jumpin-at-the-agem-jamboree.aspx Jumpin' at the aGEM Jamboree]<html></h2><br />
<br />
<p><br />
<br />
<h2></html>[http://genomealberta.ca/blogs/sleepless-nights-in-the-lab.aspx Sleepless Nights in the Lab]<html></h2><br />
<br />
<p><br />
<br />
<h2></html>[http://genomealberta.ca/blogs/igem-calgary-headed-to-boston.aspx iGEM Calgary Headed to Boston]<html></h2><br />
<br />
<p><br />
<br />
</html><br />
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<br />
}}</div>Iaingeorgehttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-11-09T22:55:15Z<p>Iaingeorge: cleanup sponsors page</p>
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<a id="boatbottom" href="https://2012.igem.org/Team:Calgary/Project/Synergy"></a><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 href="http://www.youtube.com/watch?v=vluDpf4ao6c"><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 />
</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 />
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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 />
</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 />
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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 />
</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 />
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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 />
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</body><br />
</html></div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_CBREhz_Cropped.jpgFile:UCalgary2012 CBREhz Cropped.jpg2012-11-09T22:53:39Z<p>Iaingeorge: uploaded a new version of &quot;File:UCalgary2012 CBREhz Cropped.jpg&quot;</p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Team/OuttakesTeam:Calgary/Team/Outtakes2012-10-27T04:04:56Z<p>Iaingeorge: </p>
<hr />
<div>{{Team:Calgary/TemplateTeam|<br />
TITLE=Outtakes, Bloopers, Shenanigans|<br />
CONTENT=<br />
<html><br />
<head><br />
<style><br />
#box-table-a<br />
{<br />
font-family: "Lucida Sans Unicode", "Lucida Grande", Sans-Serif;<br />
font-size: 12px;<br />
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</head><br />
<br />
<h2>Supplies Usage</h2><br />
<p>Below is a rough enumeration of the total number of supplies our team used in our experiments over the summer and into the fall. We couldn't quite believe some of these numbers when we started calculating them.<br />
<p><table id="box-table-a" summary="Employee Pay Sheet"><br />
<thead><br />
<tr><br />
<th scope="col">Lab Supply</th><br />
<th scope="col">Quantity Used</th><br />
</tr><br />
</thead><br />
<tbody><br />
<tr><br />
<td>Antibiotic Agar Plates</td><br />
<td>4,400</td><br />
</tr><br />
<tr><br />
<td>DNA Minipreps</td><br />
<td>6,160</td><br />
</tr><br />
<tr><br />
<td>Falcon Tubes</td><br />
<td>7,700</td><br />
</tr> <br />
<tr><br />
<td>Microcentrifuge Tubes</td><br />
<td>66,000</td><br />
</tr><br />
<tr><br />
<td>PCR Tubes</td><br />
<td>33,000</td><br />
</tr><br />
<tr><br />
<td>Pipette Tips</td><br />
<td>158,000</td><br />
</tr><br />
</tbody><br />
</table><br />
<br />
<h2>Wiki Freeze Panic</h2><br />
<div align="center"><br />
<iframe width="600" height="450" align="center" src="http://www.youtube.com/embed/9bOgnLj9bEI" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<h2>Coffee Usage - Wiki Freeze Night - 8:00 PM</h2><br />
<p>Yay! Coffee is what keeps us going!</p><br />
</html>[[File:UCalgary-Pyramid-of-Coffee.jpg|745px]]<html><br />
<br />
<h2>Sleeping Jeff</h2><br />
<p>What keeps him going? Maybe all the Tim's from above?</p><br />
</html>[[File:UCalgary_Jeff_Sleep.jpg|745px]]<html><br />
<br />
<h2>Pipette Tip Cards</h2><br />
<p>This could be tricky! Don't fall, don't fall!</p><br />
</html>[[File:UCalgary Pipette Tip Brackets.jpg|745px]]<html><br />
<br />
</html><br />
}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Team/OuttakesTeam:Calgary/Team/Outtakes2012-10-27T04:03:52Z<p>Iaingeorge: </p>
<hr />
<div>{{Team:Calgary/TemplateTeam|<br />
TITLE=Outtakes, Bloopers, Shenanigans|<br />
CONTENT=<br />
<html><br />
<head><br />
<style><br />
#box-table-a<br />
{<br />
font-family: "Lucida Sans Unicode", "Lucida Grande", Sans-Serif;<br />
font-size: 12px;<br />
margin: 0 0 0 125px;<br />
width: 480px;<br />
text-align: center;<br />
border-collapse: collapse;<br />
}<br />
#box-table-a th<br />
{<br />
font-size: 13px;<br />
font-weight: normal;<br />
padding: 8px;<br />
background: #90d7ff;<br />
//border-top: 4px solid #aabcfe;<br />
border-bottom: 1px solid #fff;<br />
color: #039;<br />
}<br />
#box-table-a td<br />
{<br />
padding: 8px;<br />
background: #dcf2ff; <br />
border-bottom: 1px solid #fff;<br />
color: #669;<br />
border-top: 1px solid transparent;<br />
}<br />
#box-table-a tr:hover td<br />
{<br />
background: #c9ebff;<br />
color: #004167;<br />
}<br />
</style><br />
</head><br />
<br />
<h2>Supplies Usage</h2><br />
<p>Below is a rough enumeration of the total number of supplies our team used in our experiments over the summer and into the fall. We couldn't quite believe some of these numbers when we started calculating them.<br />
<p><table id="box-table-a" summary="Employee Pay Sheet"><br />
<thead><br />
<tr><br />
<th scope="col">Lab Supply</th><br />
<th scope="col">Quantity Used</th><br />
</tr><br />
</thead><br />
<tbody><br />
<tr><br />
<td>Antibiotic Agar Plates</td><br />
<td>4,400</td><br />
</tr><br />
<tr><br />
<td>DNA Minipreps</td><br />
<td>6,160</td><br />
</tr><br />
<tr><br />
<td>Falcon Tubes</td><br />
<td>7,700</td><br />
</tr> <br />
<tr><br />
<td>Microcentrifuge Tubes</td><br />
<td>66,000</td><br />
</tr><br />
<tr><br />
<td>PCR Tubes</td><br />
<td>33,000</td><br />
</tr><br />
<tr><br />
<td>Pipette Tips</td><br />
<td>158,000</td><br />
</tr><br />
</tbody><br />
</table><br />
<br />
<h2>Wiki Freeze Panic</h2><br />
<div align="center"><br />
<iframe width="600" height="450" align="center" src="http://www.youtube.com/embed/9bOgnLj9bEI" frameborder="0" allowfullscreen></iframe><br />
</div><br />
<br />
<h2>Coffee Usage - Wiki Freeze Night - 8:00 PM</h2><br />
<p>Yay! Coffee is what keeps us going!</p><br />
</html>[[File:UCalgary-Pyramid-of-Coffee.jpg|745px]]<html><br />
<br />
<h2>Jeff Sleeping</h2><br />
<p>What keeps him going?</p><br />
</html>[[File:UCalgary_Jeff_Sleep.jpg|745px]]<html><br />
<br />
<h2>Pipette Tip Cards</h2><br />
<p>This could be tricky! Don't fall, don't fall!</p><br />
</html>[[File:UCalgary Pipette Tip Brackets.jpg|745px]]<html><br />
<br />
</html><br />
}}</div>Iaingeorgehttp://2012.igem.org/File:UCalgary_Jeff_Sleep.jpgFile:UCalgary Jeff Sleep.jpg2012-10-27T04:03:10Z<p>Iaingeorge: </p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Project/SynergyTeam:Calgary/Project/Synergy2012-10-27T00:25:02Z<p>Iaingeorge: </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 />
SECTION = Project|<br />
SIDELIST =<br />
<html><br />
<head><br />
<style><br />
/*colouring: current page and all sidebar rollovers*/<br />
#projectlink, #sidebar #list a:hover, #nav li a:hover, #nav li a.drop:hover::after{<br />
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</style><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 />
</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=Synergy: Putting it all Together|CONTENT=<br />
<html><br />
<img src="https://static.igem.org/mediawiki/2012/0/03/UCalgary2012_FRED_and_OSCAR_Synergy.png" style="padding: 10px; width: 280px; 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 />
<br />
<h2>Have we accomplished our goal?</h2><br />
<br />
<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’ve made on our project with us. We got a variety of different perspectives from suggestions on the...... 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, we have OSCAR components, and we have some killswitch components, but how functional are some of these parts, and how do they work together. So our next major goal was to <b>establish synergy:</b> try to put some of these pieces together in order to assess how far we’d actually gotten.</p><br />
<br />
<h2> Putting FRED together </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, 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 hat</p><br />
<br />
<h2> Can we sense toxins in tailings ponds? </h2><br />
<br />
<h2> Putting together our killswitches </h2><br />
<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. So 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 />
<br />
<h2> Putting our Killswitch into OSCAR</h2><br />
<br />
<p>The next thing we wanted to validate was that our glycine knockout strain would in fact work as we wanted it to in OSCAR. Namely, we wanted to know if putting the PetroBrick into our glycine knockout strain and growing it in the presence of glycine would still give us the same increased hydrocarbon production that we saw when validating our model. We transformed the PetroBrick into the knockout strain and repeated the PetroBrick validation assay protocol. Our results are shown below:</p><br />
<br />
<h2> Taking FRED out to the field! </h2><br />
<br />
<p> Once we knew that FRED could actually detect toxins found in tailings ponds within a laboratory setting, the next challenge would be to take FRED out to a tailings pond to out him to the test. 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. We still felt that testing FRED out in the real world, demonstrating that our prototype was easy to use and functional outside of a lab environment was extremely important. As such, we decided to do a field test of a body of water in our own city. The first thing we worried about though, was if there was any regulation surrounding water sampling, or performing a field test with a genetically modified organism (GMO). So we did a literature search to look for any regulations that might exist. We couldn’t find anything that pertained to our province, so we looked to Ontario and the United States. We looked at the concise guide to U.S. federal guidelines, rules and regulations for synthetic biology. In this guide, rules pertaining to field tests are covered. 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.</p><br />
<br />
<H2> Putting OSCAR in 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 Kelly Roberge, 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). To start with, we would need to consider the amount of naphthenic acids needed to provide steady throughput in our system and just how much hydrocarbon can be produced in a full cycle of our system. He recommended that we use computer modelling to explore these challenges. This could allow us to determine the possible hydrocarbon output of our lab scale experiments once they are up and running. Additionally, we would need to take into consideration the composition of tailings pond solution, especially the sludge and bitumen content. The sludge could be physically harmful to our bioreactor and reduce its overall efficiency as well. A possible way to tackle this challenge would be to use current mature fine tailings drying techniques used to help speed the reuse of water in the tailings ponds. As tailings fines settle the resulting tailings water component would be left behind. This would be an ideal input into our system for potential remediation and production of hydrocarbons as it would contain a large proportion of the compounds thought to be most toxic in the tailings. By using this matured tailings as the input to our system it could help increase the efficiency of our bioreactor and provide for a smoother scale up from the lab bench to an industrial bioreactor.</p><br />
<br />
</html>[[File:Calgary BioreactorValidation.png|thumb|500px|center|Figure X: 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 X: 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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}}</div>Iaingeorgehttp://2012.igem.org/File:UofC_OleT_Assay_1.pngFile:UofC OleT Assay 1.png2012-10-26T23:18:33Z<p>Iaingeorge: uploaded a new version of &quot;File:UofC OleT Assay 1.png&quot;</p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Project/OSCAR/DecarboxylationTeam:Calgary/Project/OSCAR/Decarboxylation2012-10-26T23:06:21Z<p>Iaingeorge: </p>
<hr />
<div>{{Team:Calgary/TemplateProjectBlue|<br />
TITLE=Decarboxylation|<br />
<br />
CONTENT=<html><br />
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<br />
<img src="https://static.igem.org/mediawiki/2012/c/c3/UCalgary2012_OSCAR_Decarboxylation_Low-Res.png" style="float: right; padding: 10px; width: 300px;"></img><br />
<h2>Why Decarboxylation?</h2><br />
<br />
<p>Among the toxins found in the tailing ponds, naphthenic acids (NAs) are among the most harmful and the most common. Though there is great diversity within the NAs class of compounds, all share the common chemical feature of a carboxylic acid group. The carboxyl group is the primary cause for their toxicity, allowing these chemicals to traverse cell membranes and react with cellular materials (Frank <i>et al</i>. 2009). NAs are recalcitrant (not easily degraded), potentially harmful to the surrounding ecosystem (Clemente & Fedorak, 2005) and corrosive to extraction and transport equipment of petroleum materials (Slavcheva <i>et al</i>. 1999). Corrosion of pipelines leads to higher maintenance costs as well as the grim possibility of these and other toxins leaking into the environment. <br />
There is a need for methods to degrade NAs that are not prohibitively expensive or that would result in production of other hazardous chemicals.</p> <br />
<br />
<p>The main goal of OSCAR is to turn toxins like these into useable hydrocarbons by removing the carboxylic acid group(s) (Behar & Albrecht, 1984). <br />
<br />
Since NAs from petroleum deposits are a variable mixture, an enzymatic process with broad specificity is necessary. With the removal of the carboxylic acid moiety, we aim to produce alkanes suitable for use as fuel. The goal of this subproject was to find one or more suitable pathways to accomplish the decarboxylation of compounds such as NAs with the broadest specificity.</p><br />
<br />
<br />
<h2>The PetroBrick</h2><br />
<br />
<p>The 2011 Washington iGEM team developed the PetroBrick (<a <br />
<br />
href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025">BBa_K590025.</a>), a BioBrick consisting of two primary genes. These include acyl-ACP reductase (<i><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590032">AAR</a></i>), which reduces fatty acids bound to ACP to fatty aldehydes, and a second gene called aldehyde decarbonylase (<i><a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590031">ADC</a></i>), which subsequently cleaves the entire aldehyde group and results in a hydrocarbon chain (Sukovich, 2010). Essentially this allows for hydrocarbons to be produced from glucose. What we realized though, is that the fatty acids that the PetroBrick targets, have a very similar structure to NAs.</p><br />
<br />
</html>[[File:UCalgary-Fatty-Acids-vs-NAs.jpg|550px|centre|thumb|Figure 1: A comparison of the structure of fatty acids and naphthenic acids]]<html><br />
<br />
<p>We predicted that the PetroBrick may have the potential to turn NAs in to hydrocarbons and be a perfect solution to remediating NAs! First though, we needed to show that the PetroBrick did in fact work as expected. We had some difficulty with the DNA from the registry and had to request the constructs directly from the Washington team. Once we had the PetroBrick, we needed to verify that the PetroBrick would work in our hands as it did for the <a href="https://2011.igem.org/Team:Washington">2011 Washington team</a>.<br />
<br />
Figures 2 and 3 demonstrate the function of the PetroBrick.</p><br />
<br />
</html>[[File:Calgary2012_PetrobrickVerificationGC.jpg|center|thumb|Figure 2: Gas chromatograph of the differences in peak composition between an <i>E. coli</i> control and the PetroBrick. There was a large increase in a peak with a retention time of 12.25 min, suggesting that the PetroBrick was producing a new hydrocarbon compound.|650px]]<html><br />
<br />
</html>[[File:Calgary2012_PetrobrickVerificationMS.jpg|center|thumb|Figure 3: Mass spectra of the gas chromatograph peak at 12.25 min. This spectra suggests that the PetroBrick is selectively producing a C15 alkane, which resemble the results from the Washington 2011 iGEM team.|750px]]<html><br />
<br />
<p>With the PetroBrick able to successfully produce alkanes, we next wanted to test the PetroBrick on NAs to see if they could be selectively converted into alkanes! This experiment used commercial NAs fractions, which included a large number of different complex NAs compounds. </p><br />
<br />
<a name="Petrobrick"></a><h2>Successful conversion of NAs into hydrocarbons!</h2><br />
<br />
</html>[[File:Ucalgary_Decarboxylation_NaphthenicAcids_Results.png|center|thumb|Figure 4: The relative intensity of alkane production from NAs as measured with GC-MS over a retention time in <i>E. coli</i> with and without the PetroBrick . Concentrated NA standard was included for comparison of peaks.|700px]]<html><br />
<br />
</html>[[File:Ucalgary_Decarboxylation_Alkanes_Alkenes_Results.png|center|700px|thumb|Figure 5: Mass spectrums of alkanes and alkenes produced from NAs with <i>E. coli</i> containing the PetroBrick as in Figure 2. Relative intensity of mass-to -charge ratio (m/z) was compared.]]<html><br />
<br />
<p> Results from Figure 4 and 5 indicate that hydrocarbons were successfully produced from <i>E. coli</i> that contained the PetroBrick construct, as analysed with GC-MS. In Figure 2, <i>E. coli</i> containing the PetroBrick had higher hydrocarbon peaks than the <i>E. coli</i> without the PetroBrick. Not only was the PetroBrick able to degrade NAs into alkanes, the PetroBrick could produce alkenes (Figure 3), indicating that the PetroBrick worked as expected! </p><br />
<br />
<br />
<h2><i>Nocardia</i> Carboxylic Acid Reductase (CAR)- Can we do better?</h2><br />
<br />
<p>Although we successfully used the PetroBrick to remove carboxyl groups from NAs, we wanted to improve on our results to get a higher yield and/or possibly target other compounds. One of our original concerns in using the PetroBrick to decarboyxlate NAs was that the first enzyme AAR only targeted fatty acids bound to ACP, and non-compatibility with NAs. Therefore, we searched for another enzyme carboxylic acid reductase (CAR) from <i>N. iowensis</i> known to perform a similar task as AAR - converting fatty acids to aldehydes, but with much lower specificity (He <i>et al</i>. 2004). Unlike AAR, CAR does not require covalent attachment to ACP, and likely to have broader substrate specificity. The use of CAR did require a second gene from <i>N. iowensis</i> called <i>Nocardia</i> phosphopantetheinyl transferase (<i>npt</i>) to append a 4’- phosphopantetheine prosthetic group to CAR required for its full function (Venkitasubramanian <i>et al.</i>, 2006).</p><br />
<br />
</html>[[File:Ucalgary Decarboxylation Team CAR Mechanism.jpg|center|700px|thumb|Figure 6: Mechanism of CAR catalysis. Taken from He <i>et al.</i>, 2004.]]<html><br />
<br />
<a name="OleT"></a><p>Another enzyme with the potential to remove carboxyl groups from NAs is olefin-forming fatty acid decarboxylase (<i><a href="http://partsregistry.org/Part:BBa_K902048:Experience">OleT</a></i>) from <i>Jeotgalicoccus</i> sp. ATCC 8456. <i>OleT</i> of the cytochrome P450 family acts on fatty acids, but does have low substrate specificity (Rude <i>et al</i>. 2011). Using <i>oleT</i> was beneficial because this single enzyme could do the job of the entire PetroBrick! Given our decarboxylation approach was valid, we started testing and comparing <i>oleT</i> to the PetroBrick.</p><br />
<br />
<h2> Progress so far </h2><br />
<br />
<p>Genes <i>car</i> and <i>npt</i> were cloned from the host organism <i>N. iowensis</i> (NRRL 5646). <i>car</i> was ligated into the pET vector and verified by a restriction digest while <i>npt</i> was cloned into pSB1C3 (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902061">BBa_K902061</a>) and similarly verified.</p><br />
<br />
<p><i>car</i> was cloned into pET47b+ plasmid to remove six illegal cut-sites (one XbaI site, two EcoRI sites, and three NotI sites), as it was unsuitable for the BioBrick construction vectors. We first attempted to use a multi-site mutagenesis derived from the QuikChange<sup>®</sup> Multi-Site Directed Mutagenesis Kit, but had little success. Instead, a more time-consuming but effective series of conventional single-site <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mutagenesis">mutagenesis procedure</a> was used with the KAPA Hi-Fi polymerase. The XbaI and EcoRI sites were eliminated first so that <i>car</i> can be moved from the pET Vector and ligated into the PSB1C3 vector (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902062">BBa_K902062</a>). <br />
<br />
<p>The <i>oleT</i> was successfully amplified from the <i>Jeotgalicoccus</i> sp. ATCC 8456.<br />
<p> </p><br />
<p>Like <i>car</i>, <i>oleT</i> was inserted in a pET47b+ (Novagen) vector before placing it into a BioBrick vector, as two illegal cut sites adjacent to one another needed to be mutagenized. This part is now being ligated into pSB1C3. We are currently in the process of constructing all three parts under control of a <i>tetR</i> promoter and ribosomal binding site (<a href="http://partsregistry.org/Part:BBa_J13002">BBa_J13002</a>), and then constructing these composite parts together as outlined below.</p><br />
<br />
<h2>Final testing constructs</h2><br />
<br />
<p>Final testing constructs are nearly complete. These are illustrated in Figure 7 and will allow us to compare the three different approaches. Unfortunately, Washington only sent us the PetroBrick and not the two individual components, we will have to compare a combination of the PetroBrick and <i>car/npt</i> to the PetroBrick alone and to <i>oleT</i>. </p><br />
<br />
<p></html>[[File:Ucalgary_Decarboxylation_Team_J13002+car+J13002+npt+PetroBrick.png|centre|600px]]<html><br />
</html>[[File:Ucalgary Decarboxylation Team J13002+oleT.png|centre|280px|thumb|Figure 7: Final constructs required for validating and comparing different decarboxylation approaches]]<html></p><br />
<br />
<a name="TestingOleT"></a><h2> Testing OleT </h2><br />
<br />
<p>One major stumbling block in testing out <i>oleT</i> has been significant difficulty in trying to ligate it into a vector, which has prevented us from submitting it as a BioBrick. As such, we chose to try some assays on the host organism: <i>Jeotgalicoccus</i> sp. ATCC 8456. This way we could at least validate that this gene was functional before we had our BioBricks. We started by trying to verify the results by Rude <i>et al</i>., 2011, namely that OleT could convert fatty acids into alkenes. We grew up cultures based on this <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/oleT_in_Validation_Assay">protocol</a> and used GC-MS to analyze any alkene production (Figure 8 and 9).</p><br />
<br />
<h2> Formation of alkanes by <i>Jeotgalicoccus</i> sp. ATCC 8456</h2><br />
<br />
</html>[[File:UofC_OleT_Assay_1.png|centre|700px|thumb|Figure 8. Gas chromatograph demonstrating the production of olefins (alkenes) from fatty acids as shown from the increase in the peak with a retention time of 14.7 min. The dramatic change in peak intensity at this point suggests that we are producing hydrocarbons.]]<br />
[[File:UofC_OleT_2nd_Assay.png|centre|700px|thumb|Figure 9. Mass spectra of the peak in Figure 8 at retention time 14.7 min. Demonstrating that this peak is an olefin, which is known to be produced in <i>Micrococcus</i>. This verifies our proof-of-concept that the <i>Micrococcus</i> species can degrade fatty acids into olefins. ]]<html><br />
<br />
<p>Based on the additional peak we saw in the gas chromatograph, we could show that our <i>E. coli</i> can produce alkenes with the <i>oleT</i>. This is may be an improvement over the PetroBrick since OleT is only one enzyme instead of two; however, future testing is still needed. Now that we have validated the function of OleT in producing alkenes, the next step is to test it out on complex naphthenic acids in order to compare it to the PetroBrick. This testing is still underway.</p><br />
<br />
</html><br />
<br />
}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Notebook/ProtocolsTeam:Calgary/Notebook/Protocols2012-10-26T23:01:39Z<p>Iaingeorge: </p>
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<p>Here is a list of all the procedures we used this summer. Each contains a description and list of materials required.</p><br />
<ul><br />
<br />
<h2>General Protocols</h2><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/agarosegel">Agarose Gel Electrophresis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/gemomicprep">Bacterial Genomic DNA Purification</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/transformation">Bacterial Transformation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/construction">Construction Techniques</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/Carbazole GC-MS Analysis">GC-MS Analysis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/gelextraction">Gel Extraction</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/Gibson Assembly">Gibson Assembly</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/lbagar">LB Agar Plates</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/m9media">M9 Minimal Media Preparation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/oextraction">Organic Extraction</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/onculture">Overnight Cultures</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/pcrpurification">PCR Purification</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/picogreen">PicoGreen Assay</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/plasmidminiprep">Plasmid Purification (from <i>E. coli</i>)</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/compcells">Preparing Chemically Competent Cells (<i>E. coli</i>)</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/glycerolstock">Preparing Glycerol Stocks (<i>E. coli</i>)<br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/dnarehydration">Rehydration of Registry DNA</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/dmszfreezedry">Reviving Freeze-dried Bacterial Cultures from DSMZ</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mutagenesis">Site-Directed Mutagenesis</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/soe">Splice Overlap Extension PCR (SOE PCR)</a></li><br />
<br />
<br />
<br />
<h2>Electrochemistry Protocols</h2><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/cvs">Cyclic Voltammetry</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/potstd">Potentiostatic Standard Curve Generation</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/potentiostatic">Reporter Expression Detection</a></li><br />
<br />
<br />
<h2>Desulfurization Protocols</h2><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/catalase">Catalase assay</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/desulfur">Desulfurization Assay</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/hpac">HpaC assay</a></li><br />
<br />
<h2>Decarboxylation Protocols</h2><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/PetroBrick Validation Assay">PetroBrick Validation Assay </a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/oleT in Validation Assay">oleT Validation Assay </a></li><br />
<br />
<h2>Denitrogenation Protocols</h2><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/carbazole">Carbazole Degradation Assay</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/AmidaseAssay"><i>AmdA</i> Characterization Assay</a></li><br />
<br />
<h2>Decatecholization Protocols</h2><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/decatecholization">Decatecholization Assay</a></li><br />
<h2>Transposon Mutant Library for Toxin Detection</h2><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/tnscreen">Transposon-Mediated Mutant Library Generation</a></li><br />
<br />
<h2>Kill Switch Protocols</h2><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mgcircuit">Characterization of mgtA regulation with GFP </a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mgtacircuit">Characterization of mgtA regulation with S7 killgene </a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/nucleaseassay">Nuclease assay</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/Prha Characterization">Characterization of <i>P<sub>rha</sub></i> with GFP</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/GlycineAssays">Glycine Auxotrophic Assays (Glycine Media Test, Petrobrick Test, and Killswitch Testing)</a></li><br />
<br />
<h2>Bioreactor Assays Protocols</h2><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/bacgrowth">Bacterial Growth Experiments</a></li><br />
<p>Belt Selection Tests:</p><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/bactest">Bacteria Test</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/hcseptest">Hydrocarbon Separation Test</a></li><li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/hctest">Hydrocarbon Test</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/hdbeltskim">NA and Hexadecane Belt Skim Test</a></li><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/tailingtest">Tailings Test</a></li><br />
</ul><br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<h2>Modeling Protocols</h2><br />
<li><a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/Modelvalidation">Modelling validation experiments</a></li><br />
<br />
<br />
<br />
</ul><br />
<br />
</html><br />
}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Notebook/Protocols/gemomicprepTeam:Calgary/Notebook/Protocols/gemomicprep2012-10-26T21:23:03Z<p>Iaingeorge: </p>
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TITLE=Bacterial Genomic DNA Extraction|<br />
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<br />
<p>DNA extraction from unknown bacterial colonies extracted from biofilms and planktonic cultures grown on a variety of media types. This protocol is based of protocols from Monika Schwering and MP Bio's DNA Spin Kit extraction protocol.</p><br />
<br />
<p>Materials:</p><br />
<ul><br />
<li>MP Bio FastPrep bead beater</li><br />
<li>Micro-centrifuge</li><br />
<li>Heating Block</li><br />
</ul><br />
<p>MP Bio FastDNA SPIN Kit (cat # 6540-600)</p><br />
<ul><br />
<li>Lysing Matrix A Tubes</li><br />
<li>DNA catch tubes</li><br />
<li> 2.0 mL eppendorf tubes</li><br />
<li> 1.5 mL eppendorf tubes</li><br />
<li> CLS-TC buffer</li><br />
<li> DNA binding matrix</li><br />
<li>SEWS-M diluted with ethanol</li><br />
<li>DES water</li><br />
<br />
<li>Lysozyme (EC 3.2.1.17)</li><br />
<br />
<li>Lysis buffer (20 mM Tris, 2 mM EDTA, 1% Triton X-100, adjusted to pH 8.0)</li><br />
<li>Proteinase K</li><br />
</ul><br />
<p>Procedure:</p><br />
<ol><br />
<li>Prepare 5mL overnight cultures of each organism to be extracted in a 15mL Falcon tube. Incubate overnight in a shaker at the required growth temperature and rotation speed for the organism of interest.</li><br />
<br />
<li>Centrifuge the overnight cultures at 3000rpm for 10 minutes. Dump the supernatant and use a 200 µL pipette tip to remove any excess supernatant remaining in the tube.</li><br />
<br />
<li>Prepare the lysis buffer () with 20 mg/mL concentration of lysozyme.</li> <br />
<font size="1.5"><p>a. First, calculate the total volume of lysis buffer needed for the experiment:</p><br />
<p>i. (# of samples + 0.5 for pipetting error) * 0.200 mL of lysis buffer per sample</p><br />
<p>ii. ie: (12 samples + 0.5) * 0.200 mL = 2.5 mL of lysis buffer</p><br />
<p>b. Next, calculate the quantity of lysozyme required to achieve a concentration of 20 mg/mL of lysozyme in the lysis buffer:</p><br />
<p>i. Total volume of lysis buffer * 20 mg/mL of lysozyme</p><br />
<p>ii. ie: 2.5 mL * 20 mg/mL = 50 mg of lysozyme</p><br />
</font><br />
<li>Add 200 µL of lysis buffer to each samples tube and vortex each sample to re-suspend the mixture. Place the tubes on a shaker in a 37ºC incubator for 30 minutes.</li><br />
<br />
<li>Assemble one lysing matrix A tube for each sample and place 880 µL of CLS-TC and 20 µL of proteinase K in each tube.</li><br />
<br />
<li>Set a heating block to 55ºC.</li><br />
<br />
<li>Remove the samples from the shaker in the 37ºC incubator. Vortex each samples to re-suspend any precipitate and pipette all of the sample (using a pipette set at 300 µL) into a separate lysing matrix A tube.</li><br />
<br />
<li>Bead beat the samples for 40 seconds at speed 6.0.</li><br />
<br />
<li>Place the samples on the 56ºC heating block for 30 minutes.</li><br />
<br />
<li>Spin the samples for 10 minutes at 14,000xg.</li><br />
<br />
<li>Prepare one 2.0 mL eppendorf tube for each sample and pipette 800 µL of DNA binding matrix into each tube. Then pipette, 800 µL of the supernatant from each lysing matrix A tube into the corresponding tube. Ensure that the precipitate is not disturbed during this process.</li><br />
<br />
<li>Invert the tubes for 5 minutes by hand.</li><br />
<br />
<li>Gently invert each sample tube to ensure that there is no precipitate and pipette 800 µL (1/2 of the sample) into a catch tube.</li><br />
<br />
<li>Spin the catch tubes for 1 minute at 14,000xg</li><br />
<br />
<li>Empty each catch tube and transfer the remaining ~800 µL of sample into the corresponding catch tubes.</li><br />
<br />
<li>Spin the catch tubes for 1 minute at 14,000xg. Empty the catch tubes.</li><br />
<br />
<li>Add 500 µL of SEWS-M/ethanol to each catch tube and pipetting up and down to re-suspend the pellet</li><br />
<br />
<li>Spin the catch tubes for 1 minute at 14,000xg. Empty the catch tubes.</li><br />
<br />
<li>Spin the catch tubes again for 2 minutes at 14,000xg to dry out the pellets.</li><br />
<br />
<li>Replace the recovery tubes with fresh 2.0 mL eppendorf tubes with final storage labeling.</li><br />
<br />
<li>Add 100 µL of DES water and re-suspend the pellets by pipetting up and down. Incubate the tubes at 55ºC for 30 minutes in a heating block.</li><br />
<br />
<li>Spin down the tubes for 2 minutes at 14,000xg. Keep the liquid and tube. Dispose of the filter column.</li><br />
<br />
<li>Storage: place the tubes into a -20ºC freezer.</li><br />
<br />
</ol><br />
<br />
</html>}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Project/AttributionsTeam:Calgary/Project/Attributions2012-10-26T21:21:54Z<p>Iaingeorge: </p>
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<h2>University of Calgary Support</h2><br />
<p>The University of Calgary iGEM team would like to thank and acknowledge all of the support from the University in terms of student stipends, facilities, and materials which made this project possible. This included the Department of Biological Sciences as well as the O'Brien Centre for their contribution of lab space this summer. Additionally, a special thanks to all departments and faculties which financially contributed to our project.</p><br />
<br />
<h2>Advisor and Instructor Support</h2><br />
<p>All research work was performed by the undergraduate students part of the Calgary Team. Our professors and advisors contributed support and ideas to the students and facilitated a safe and efficient laboratory environment for the students. Special thanks to <b>Dr. Lisa Gieg</b>, whose experience in petroleum microbiology provided the facilitates and protocols required to make our work possible (including GC/MS and culturing of various organisms). And thanks to <b>Dr. Anders Nygren</b> for his help with engineering the electrical circuits used in the our biosensor prototypes. Finally, thanks to <b>Dr. Mayi Arcellana-Panlilio</b> for her troubleshooting advice.</p><br />
<br />
<h2>Support From Additional Professors and University Staff</h2><br />
<p>Special thanks to <b>Dr. Doug Meunch</b>, one of our advisors whose support made it possible for us to obtain our laboratory space in Biological Sciences. In addition, we would like to acknowledge other professors in the department of Biological Sciences including <b>Dr. Greg Moorhead</b>, <b>Dr. C. C. Chinnappa</b> (both for supplying equipment), <b>Dr. Michael Hynes</b>, <b>Dr. Ray Turner</b>, <b>Dr. Gerrit Voordouw</b>, <b>Dr. Howard Ceri</b>, <b>Dr. Denice Bay</b>, and <b>Monika Schwering</b> for their support with supplies and protocols. Additionally we would like to recognize <b>Dr. Viola Birss</b>, <b>Bri Campbell</b>, and <b>Anusha Abhayawardhana</b> in the Department of Chemistry for their assistance with the electrochemical studies conducted by our team. Finally we would like to thank <b>Dr. Arin Sen</b> in the Department of Chemical and Petroleum Engineering for his advice with the design of our bioreactor and <b>Dr. Jennifer Cobb</b>, <b>Deirdre Lobb</b>, <b>Dr. Steve Robbins</b>, and the <b>SACRI Research Group</b> for their donation of chemicals. </p> <br />
<br />
<h2><i>Outside of University</i> Research and Technical Support</h2><br />
<p>We would like to thank and acknowledge the support of various individuals from other Universities. This includes<br />
<b>Dr. Michael Ellison</b> for his lab's contribution of Keio Collection Knockout strains used in this project, the <b>2011 University of Washington iGEM team</b> for sending us plasmid DNA of the Petrobrick as the DNA construct available in the registry was incorrect. Thanks to <b>Dr. Josie L. Garcia</b> from the Consejo Superior de Investigaciones, Madrid Spain for contribution of a plasmid containg the <i>hpaC</i> gene. <b>Dr. John Kilbane</b> for the contribution of the <i>Rhodococcus baikonurensis</i> containing the <i>Rhodococcus</i> IGTS8 <i>dszABC</i> plasmid. Special thanks to our professor <b>Dr. Lisa Gieg</b> for her contribution of a <i>Pseudomonas sp.</i> LD2 species previously reported to degrade carbazole. Finally, special thanks to <b>Abanacai Corporation</b>, Ohio for their samples of a oil skimming sample kit used in our bioreactor design. </p><br />
<br />
<h2><i>Outside of University</i> Additional Support</h2><br />
<p>We would like to thank the individuals who we had requested to do interviews with <b>Christine Daly</b> (Suncor Inc.) and <b>Ryan Radke</b> (BioAlberta). We would like to thank our representative <b>Claudia Bustos</b> for all of her hard work and support of our team from the Telus Spark Science Centre. Thank you to <b>Robert Kotch</b> from the Bonniebrook Waste Treatment Plant for allowing us access to their facility to learn more about how their reactors were designed. We would also like to thank <b>Lorne and Laurie Swalm</b> for their generous support of our project.</p> <br />
<br />
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}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Project/AttributionsTeam:Calgary/Project/Attributions2012-10-26T21:21:38Z<p>Iaingeorge: </p>
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<h2>University of Calgary Support</h2><br />
<p>The University of Calgary iGEM team would like to thank and acknowledge all of the support from the University in terms of student stipends, facilities, and materials which made this project possible. This included the Department of Biological Sciences as well as the O'Brien Centre for their contribution of lab space this summer. Additionally, a special thanks to all departments and faculties which financially contributed to our project.</p><br />
<br />
<h2>Advisor and Instructor Support</h2><br />
<p>All research work was performed by the undergraduate students part of the Calgary Team. Our professors and advisors contributed support and ideas to the students and facilitated a safe and efficient laboratory environment for the students. Special thanks to <b>Dr. Lisa Gieg</b>, whose experience in petroleum microbiology provided the facilitates and protocols required to make our work possible (including GC/MS and culturing of various organisms). And thanks to <b>Dr. Anders Nygren</b> for his help with engineering the electrical circuits used in the our biosensor prototypes. Finally, thanks to <b>Dr. Mayi Arcellana-Panlilio</b> for her troubleshooting advice.</p><br />
<br />
<h2>Support From Additional Professors and University Staff</h2><br />
<p>Special thanks to <b>Dr. Doug Meunch</b>, one of our advisors whose support made it possible for us to obtain our laboratory space in Biological Sciences. In addition, we would like to acknowledge other professors in the department of Biological Sciences including <b>Dr. Greg Moorhead</b>, <b>Dr. C. C. Chinnappa</b> (both for supplying equipment), <b>Dr. Michael Hynes</b>, <b>Dr. Ray Turner</b>, <b>Dr. Gerrit Voordouw</b>, <b>Dr. Howard Ceri</b>, <b>Dr. Denice Bay</b>, and <b>Monika Schwering</b> for their support with supplies and protocols. Additionally we would like to recognize <b>Dr. Viola Birss</b>, <b>Bri Campbell</b>, and <b>Anusha Abhayawardhana</b> in the Department of Chemistry for their assistance with the electrochemical studies conducted by our team. Finally we would like to thank <b>Dr. Arin Sen</b> in the Department of Chemical and Petroleum Engineering for his advice with the design of our bioreactor and <b>Dr. Jennifer Cobb</b>, <b>Deirdre Lobb</b>, <b>Dr. Steve Robbins</b>, and the <b>SACRI Research Group</b> for their donation of chemicals. </p> <br />
<br />
<h2><i>Outside of University</i> Research and Technical Support</h2><br />
<p>We would like to thank and acknowledge the support of various individuals from other Universities. This includes<br />
<b>Dr. Michael Ellison</b> for his lab's contribution of Keio Collection Knockout strains used in this project, the <b>2011 University of Washington iGEM team</b> for sending us plasmid DNA of the Petrobrick as the DNA construct available in the registry was incorrect. Thanks to <b>Dr. Josie L. Garcia</b> from the Consejo Superior de Investigaciones, Madrid Spain for contribution of a plasmid containg the <i>hpaC</i> gene. <b>Dr. John Kilbane</b> for the contribution of the <i>Rhodococcus baikonurensis</i> containing the <i>Rhodococcus</i> IGTS8 <i>dszABC</i> plasmid. Special thanks to our professor <b>Dr. Lisa Gieg</b> for her contribution of a <i>Pseudomonas sp.</i> LD2 species previously reported to degrade carbazole. Finally, special thanks to <b>Abanacai Corporation</b>, Ohio for their samples of a oil skimming sample kit used in our bioreactor design. </p><br />
<br />
<h2><i>Outside of University</i> Additional Support</h2><br />
<p>We would like to thank the individuals who we had requested to do interviews with <b>Christine Daly</b> (Suncor Inc.) and <b>Ryan Radke</b> (BioAlberta). We would like to thank our representative <b>Claudia Bustos</b> for all of her hard work and support of our team from the Telus Spark Science Centre. Thank you to <b>Robert Kotch</b> from the Bonniebrook Waste Treatment Plant for allowing us access to their facility to learn more about how their reactors were designed. We would also like to thank <b>Lorne and Laurie Swalm</b> for their generous support for our project.</p> <br />
<br />
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}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Project/AttributionsTeam:Calgary/Project/Attributions2012-10-26T21:21:20Z<p>Iaingeorge: </p>
<hr />
<div>{{Team:Calgary/TemplateProjectOrange|<br />
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<h2>University of Calgary Support</h2><br />
<p>The University of Calgary iGEM team would like to thank and acknowledge all of the support from the University in terms of student stipends, facilities, and materials which made this project possible. This included the Department of Biological Sciences as well as the O'Brien Centre for their contribution of lab space this summer. Additionally, a special thanks to all departments and faculties which financially contributed to our project.</p><br />
<br />
<h2>Advisor and Instructor Support</h2><br />
<p>All research work was performed by the undergraduate students part of the Calgary Team. Our professors and advisors contributed support and ideas to the students and facilitated a safe and efficient laboratory environment for the students. Special thanks to <b>Dr. Lisa Gieg</b>, whose experience in petroleum microbiology provided the facilitates and protocols required to make our work possible (including GC/MS and culturing of various organisms). And thanks to <b>Dr. Anders Nygren</b> for his help with engineering the electrical circuits used in the our biosensor prototypes. Finally, thanks to <b>Dr. Mayi Arcellana-Panlilio</b> for her troubleshooting advice.</p><br />
<br />
<h2>Support From Additional Professors and University Staff</h2><br />
<p>Special thanks to <b>Dr. Doug Meunch</b>, one of our advisors whose support made it possible for us to obtain our laboratory space in Biological Sciences. In addition, we would like to acknowledge other professors in the department of Biological Sciences including <b>Dr. Greg Moorhead</b>, <b>Dr. C. C. Chinnappa</b> (both for supplying equipment), <b>Dr. Michael Hynes</b>, <b>Dr. Ray Turner</b>, <b>Dr. Gerrit Voordouw</b>, <b>Dr. Howard Ceri</b>, <b>Dr. Denice Bay</b>, and <b>Monika Schwering</b> for their support with supplies and protocols. Additionally we would like to recognize <b>Dr. Viola Birss</b>, <b>Bri Campbell</b>, and <b>Anusha Abhayawardhana</b> in the Department of Chemistry for their assistance with the electrochemical studies conducted by our team. Finally we would like to thank <b>Dr. Arin Sen</b> in the Department of Chemical and Petroleum Engineering for his advice with the design of our bioreactor and <b>Dr. Jennifer Cobb</b>, <b>Deirdre Lobb</b>, <b>Dr. Steve Robbins</b>, and the <b>SACRI Research Group</b> for their donation of chemicals. </p> <br />
<br />
<h2><i>Outside of University</i> Research and Technical Support</h2><br />
<p>We would like to thank and acknowledge the support of various individuals from other Universities. This includes<br />
<b>Dr. Michael Ellison</b> for his lab's contribution of Keio Collection Knockout strains used in this project, the <b>2011 University of Washington iGEM team</b> for sending us plasmid DNA of the Petrobrick as the DNA construct available in the registry was incorrect. Thanks to <b>Dr. Josie L. Garcia</b> from the Consejo Superior de Investigaciones, Madrid Spain for contribution of a plasmid containg the <i>hpaC</i> gene. <b>Dr. John Kilbane</b> for the contribution of the <i>Rhodococcus baikonurensis</i> containing the <i>Rhodococcus</i> IGTS8 <i>dszABC</i> plasmid. Special thanks to our professor <b>Dr. Lisa Gieg</b> for her contribution of a <i>Pseudomonas sp.</i> LD2 species previously reported to degrade carbazole. Finally, special thanks to <b>Abanacai Corporation</b>, Ohio for their samples of a oil skimming sample kit used in our bioreactor design. </p><br />
<br />
<h2><i>Outside of University</i> Additional Support</h2><br />
<p>We would like to thank the individuals who we had requested to do interviews with <b>Christine Daly</b> (Suncor Inc.) and <b>Ryan Radke</b> (BioAlberta). We would like to thank our representative <b>Claudia Bustos</b> for all of her hard work and support of our team from the Telus Spark Science Centre. Thank you to <b>Robert Kotch</b> from the Bonniebrook Waste Treatment Plant for allowing us access to their facility to learn more about how their reactors were designed. We would also like to thank Lorne and Laurie Swalm for their generous support for our project.</p> <br />
<br />
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}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Project/FRED/PrototypeTeam:Calgary/Project/FRED/Prototype2012-10-26T21:18:10Z<p>Iaingeorge: </p>
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<p><br />
In order to put our toxin-detecting bacteria to use, we developed the hardware and software needed to work with FRED. After assembling many prototypes and designs, we have developed a portable and affordable open source hardware-software package that uses FRED's reporter genes for electrochemical detection. This field-ready system can be used for quick and quantitative analysis of samples and can measure the concentrations of multiple compounds simultaneously. </p><br />
<br />
<p>Last year, the Calgary iGEM team developed a potentiostat circuit whose function was quite limited. In essence, the device could run only half of the desired voltage sweep, and was inconsistent and lacking in sensitivity. Rather than give a quantitative measurement of a given compound, the primitive prototype could only produce a voltammogram with peaks that had to be interpreted by the user. </p><br />
<p>This year, we significantly improved the design and function of the potentiostat. We also designed and developed hardware for housing the circuitry and samples, as well as a software package for controlling the hardware and analyzing the data. We have also created a standard protocol for how to build and use a system such as this. <a href="https://static.igem.org/mediawiki/2012/c/c8/BuildingABiosenor.pdf">Download our walkthrough here.</a> You can also download the needed code <a href="https://static.igem.org/mediawiki/2012/3/34/Test.m">here</a> and <a href="https://static.igem.org/mediawiki/2012/d/df/Output.m">here.</a></p><br />
<h2>The Potentiostat</h2><br />
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[[File:UCalgary-Prototype-Electronics.jpg|thumb|745px|left|Figure 1: From validating the breadboarded circuit, to making the final circuit, to assembling the prototype.]]<br />
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<p>A potentiostat is an electrical circuit used to conduct eletroanalytical experimentation to study redox reactions. It controls a three electrode system by changing the voltage difference between two of the electrodes, the working electrode and counter electrode. The third electrode is the reference electrode, that acts as a virtual zero voltage against which all voltage values are measured. The potentiostat will then record the current produced at the working electrode. Common experiments that use potentiostats are <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/cvs">cyclic voltammetry</a> and <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/potstd">potentiostatic runs</a>.</p><br />
<br />
<p>FRED needs a potentiostat to be able to talk to us, however traditional laboratory potentiostats have a few significant drawbacks:</p><br />
<ul><br />
<li><p>Expense: Commercial potentiostats often cost thousands of dollars, with some costing over fifty thousand dollars</p></li><br />
<li><p>Size: Although newer models are smaller (and more costly), most commercial potentiostats are large and heavy pieces of hardware</p></li><br />
<li><p>Immobility: In addition to being very bulky, most commercial potentiostats require a 120 V power outlet and are not designed for portability</p></li><br />
</ul><br />
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<p>In order for our biosensor to be viable for use in the field (e.g., samples in/around Alberta's oil sands tailings ponds) we needed it to be inexpensive, small, and portable. This led us to investigate the possibility of assembling our own customized potentiostat. We came across a paper (Gopinath and Russel, 2006) that described a simple, inexpensive design for a three-electrode potentiostat. This informed the design of last year’s potentiostat circuit which achieved portability through the use of 9 V batteries, but was limited in its function. This year, we made many upgrades: we tweaked the circuit to run in our desired -2 V -> +2 V sweeping range, added hardware filters to eliminate noise in our readings, implemented a variable dip switch for changing resistors values to alter measurement sensitivity, and had it milled onto a compact and durable circuit board with a diameter of only 6 cm. A software platform with a graphical user interface was developed to interface with the circuit and analyze the raw data.</p><br />
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<a name="hardware"></a><h2>The Hardware</h2><br />
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[[File:Prototype_board.png|thumb|350px|left|Figure 2: Early design, featuring portable power, a variable dip switch, and LEDs]]<br />
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<p>Our preliminary designs were relatively small, battery powered and had exposed electrodes that were inserted into a beaker of solution. One of our more seriously developed prototypes was a black box that housed the circuitry and the DAQ, featured power switches and LEDs to report on what stage of the experiment was currently underway. As we <br />
continued to compact the potentiostat circuit, the designs continued to get smaller and more lightweight until the same circuit was concentrated onto a 6cm printer circuit board. </p><br />
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[[File:Calgary2012 James Photo tube.jpg|thumb|200px|right|Figure 3: Cartridge containing a sealed electrode and one-way valve.]]<br />
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<br><br />
<p>Another consideration we made pertained to containment of the bacteria. We developed a disposable cartridge system that allows for safe and easy sampling, while remaining inexpensive. One of the main features of our final prototype is the material we used. Rather than having our design manufactured, we used supplies and materials that were readily available around a molecular biology lab. The main shell of the biosensor is a cylindrical plastic Nalgene container, and the disposable cartridges have been built out of 15 mL falcon tubes. The Nalgene shell houses the potentiostat circuit, two 9 V batteries, and a port for the insertion of cartridges. Each cartridge is a sealed vessel containing our bacteria. One end houses an electrode strip on the interior, and the connectors protrude from the exterior for connection to the circuit. There is also a one-way valve for injection of samples, so the field tests can be conducted without the bacteria escaping. </p><br />
<br />
<a name="software"></a><h2>The Software</h2><br />
<br />
<p>To run our hardware, we developed a personalized software package with the MATLAB platform. Software was required to run the DAQ’s inputs and outputs, as well as to interpolate the data acquired and format it for the user to view.</p><br />
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[[File:UCalgary-Prototype-ElectroSoftware.jpg|thumb|745px|left|Figure 4: Snippet of source code from the biosensor software package and a view of the GUI detecting PDP]]<br />
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<br />
<p>There were several outputs that needed to be operated through the software, mainly the initial voltage sweep that was the basis of our potentiostat, as well as the three indicator LEDs. All of this was possible through our simple, yet sophisticated software package. Within this package it is easy for the user to enter a wide range of voltage sweeps they would like to test in, as well as the rate of each sweep. This package also outputs a holding voltage, so when the program is finished executing, the electrodes don’t get damaged by swinging between voltages randomly.</p><br />
<br />
<p>Along with the outputs there were two input channels. One input channel measured the voltage applied to the solution, while the other one measured the current produced by the solution. Although this was the easiest part of the software to write, the more challenging issue was the interpolation of this acquired data. With our software, it is possible to produce a standard curve as well as determine the concentration of whatever chemical agent we are testing for with the user having to only click a button.</p><br />
<br />
<p>All of this software is completely stand-alone, built with MATLABs own compiler, and includes a functional Graphical User Interface (GUI) for easy modification of parameters, allowing others to make use of this technology for other applications.<br />
</p><br />
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}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Project/HumanPractices/InterviewsTeam:Calgary/Project/HumanPractices/Interviews2012-10-26T21:13:13Z<p>Iaingeorge: </p>
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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 began 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 have any concerns amongst legislators and industrial leaders. <br />
</p><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 in our design was that there is an opportunity for engineered organisms to outcompete existing tailings ponds bacteria, and we were pleased to hear that Christine had a similar concern. 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. Research exists with other systems such as algal bioremediation, but practical implementations of biology in the oil sands appear to be rather few and far between. 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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<iframe width="600" height="450" align="center" src="http://www.youtube.com/embed/GiM6EIC9XBo" frameborder="0" allowfullscreen></iframe><br />
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</div><br />
<br />
<h3>BioAlberta's Ryan Radke on Biology in the Oil Sands</h3><br />
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<iframe width="600" height="450" align="center" src="http://www.youtube.com/embed/86XQ-Kg5fJ4" frameborder="0" allowfullscreen></iframe><br />
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<br />
<a name="postregionals"></a><br />
<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 look into various ways to deal with the clay and silt particles that can enter our bioreactor system, which can be a major problem since 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 />
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<h3>William Sawcuk, of ARC Resources</h3><br />
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}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/SponsorsTeam:Calgary/Sponsors2012-10-26T21:09:46Z<p>Iaingeorge: </p>
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<p>The University of Calgary's 2012 iGEM Team would like to thank all of our generous sponsors! </p><br />
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<a name="uofc"></a><br />
<a href="http://www.ucalgary.ca"><img style="width: 190px; padding: 25px 50px 0px 50px;" src="https://static.igem.org/mediawiki/2011/b/b7/UCalgary_Logo_Small.png"></img></a><br />
<br />
<h2>University of Calgary</h2><br />
<p>We graciously thank the Department of Cell Biology and Anatomy, the Department of Electrical and Computer Engineering, the Centre for Bioengineering Research and Education and the Department of Biological Sciences for all their support. We also wish to thank the Faculty of Medicine for their additional support as well. Additionally, we wish to thank the office of the Vice President of Research for their generous support.</p> <br />
<br />
<a href="http://www.ucalgary.ca/bhsc"><img style="clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2011/c/c7/UCalgary_BHSc_Logo.png"></img></a><br />
<h2>O'Brien Centre for the BHSc</h2><br />
<p>The O'Brien Centre for the Bachelor of Health Sciences is a part of the University of Calgary, located in the Foothills campus. It is responsible for providing iGEM team with lab space as well as funding. The O’Brien Centre was founded in part by a generous $5-million donation by David and Gail O’ Brien, after whom the Centre was named. David O'Brien has been a member of the University's Board of Governors, while Gail O'Brien has chaired the Faculty of Medicine's Dean's Advisory Council. The O’Brien Centre is the hub of top-notch research, interdisciplinary research, and education. It is responsible for providing approximately $9-million/year for researchers. The 2012 iGEM team thanks O’Brien Centre for its generous contribution of the O’Brien Centre Summer Studentship as well as lab space this year.</p><br />
<br />
<a href="http://bio.ucalgary.ca/"><img style="width: 215px; clear:both; margin-top: -20px; margin-left: -10px;" src="https://static.igem.org/mediawiki/2012/4/47/UCalgary2012_BioSci_Logo.JPG"></img></a><br />
<h2>Department of Biological Sciences</h2><br />
<p>The Department of Biological Sciences at the University of Calgary is a community of scholars who share a commitment to insightful, innovative and integrative research in diverse areas of life sciences, from biomolecules to the biosphere, and to the development of future leaders in the basic and applied biological sciences through excellence in our undergraduate and graduate programs.</p><br />
<br />
<a href="http://enel.ucalgary.ca"><img style="width: 250px; clear:both; margin-top: -20px; margin-left: -20px; margin-bottom: -10px;" src="https://static.igem.org/mediawiki/2012/e/e6/UCalgary2012_Schulich_Electric_Computer_Logo.jpg"></img></a><br />
<h2>Schulich School of Engineering Department of Electrical and Computer Engineering</h2><br />
<p>The Department of Electrical and Computer Engineering in the Schulich School of Engineering offers both undergraduate and graduate degree programs. The Department is highly regarded internationally for its leadership in biomedical engineering, radio systems, software engineering, micro- and nano-scale systems, and power and energy research.</p><br />
<a href="http://www.albertatechfutures.ca/"><img src="https://static.igem.org/mediawiki/2011/3/3f/UCalgary2011_AITF_Logo_Small.png"></img></a><br />
<br />
<h2>Alberta Innovates Technology Futures</h2><br />
<p>Alberta Innovates Technology Futures facilitates the growth of technical industries by supporting quality research in Alberta's particular fields of expertise. These include nanotechnology, information communication technology, and genomics. AITF works in joint effort with entrepreneurs and researchers to ensure that Alberta’s technologies can be sustained at a business level through commercialization and growth. This is accomplished by ensuring that useful products, protocols and services are delivered to meet global demands.</p><br />
<br />
<a href="http://www.autodesk.com/"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/0/0b/UCalgary2012-Autodesk-Logo.png"></img></a><br />
<br />
<h2>Autodesk</h2><br />
<p>Autodesk, Inc., is a leader in 3D design, engineering and entertainment software. Customers across the manufacturing, architecture, building, construction, and media and entertainment industries—including the last 17 Academy Award winners for Best Visual Effects—use Autodesk software to design, visualize, and simulate their ideas before they're ever built or created. From blockbuster visual effects and buildings that create their own energy to electric cars and the batteries that power them, the work of Autodesk's 3D software customers is everywhere you look.</p><br />
<br />
<a href="http://www.eurofins.com/en.aspx"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a><br />
<h2>Eurofins MWG Operon</h2><br />
<p>Eurofins MWG Operon, founded in 1990 and member of the Eurofins Group, is an international provider of genomic services established around the core business lines next generation sequencing, custom DNA sequencing, oligonucleotides, siRNA and gene synthesis. The company's main mission is focussed on customer convenience and high quality services in industrial scale for the life science industries and academic research institutions around the world.</p><br />
<br />
<a href="http://genomealberta.ca/"><img src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></img></a><br />
<br />
<h2>Genome Alberta</h2><br />
<p>In partnership with Genome Canada Industry Canada and the Province of Alberta, Genome Alberta was established in 2005. They are a publicly funded non-profit corporation that initiates, funds, and manages genomics research and partnerships. <br />
Genome Alberta strives to be the leading source of information and administration related to genomics, proteomics, bioinformatics and bioethics research in Alberta. Genome Alberta is dedicated to informing students, researchers, research organizations, our partners, and the public regarding opportunities and challenges in genomics and proteomics, and in encouraging the development of a Life Sciences research industry in Alberta. <br />
</p><br />
<br />
<a href="http://www.hyperionlab.ca/"><img style="width: 190px;" src="https://static.igem.org/mediawiki/2012/8/89/UCalgary2012_Hyperion_Research_Logo.png"></img></a><br />
<br />
<h2>Hyperion Research Ltd.</h2><br />
<p>Hyperion Research Ltd., specializes in the analysis of water and sewage samples for the protozoan parasites <i>Giardia</i> and <i>Cryptosporidium</i>. They also provide sampling equipment and analysis for the Microscopic Particulate Analysis to determine Groundwater Under the Direct Influence (GUDI) of surface water. Hyperion's laboratory is located in Medicine Hat, Alberta, and where they serve the water treatment industry across Canada. Hyperion is also active in research into waterborne disease problems and has numerous international contacts.<br />
</p> <br />
<br />
<a href="http://www.idtdna.com/site"><img src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a><br />
<br />
<h2>IDT (Integrated DNA Technologies)</h2><br />
<p>Integrated DNA Technologies (IDT) is a leader in manufacturing and developing products for the research and diagnostic life science market. IDT serves the areas of academic research, biotechnology, and pharmaceutical development. Founded by Dr. Joseph Walder in 1987, IDT’s development has been guided by an uncompromising approach to quality, a belief in the value of good service, and a determination to minimize consumer costs. IDT now has over 500 employees and ships over 20,000 oligos per day. <br />
<br />
Serving over 70,000 life sciences researchers, IDT is widely recognized as the industry leader in custom oligonucleotides. </p><br />
<br />
<a href="http://www.mhc.ab.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a><br />
<br />
<h2>Medicine Hat College</h2><br />
<p>Medicine Hat College is a public, board governed, comprehensive community college serving a large region of southeastern Alberta and southwestern Saskatchewan, Canada. The MHC is located in the city of Medicine Hat, Alberta, Canada. MHC has been serving students in southeastern Alberta and beyond since 1965. MHC’s main campus services almost 2,500 students each year with another 200 attending Brooks Campus, located 100 km west of Medicine Hat. Currently, more than 30 diplomas and certificates are offered along with 25 university transfer programs. There are also several opportunities for degree completion at MHC including nursing, applied arts, and social work. A partnership with the University of Calgary makes it possible for nursing students to complete a full bachelor’s degree at Medicine Hat College while graduates from diploma programs such as Police and Security may also complete degrees. Medicine Hat College offers other unique diploma programs such as Addictions Counselor, Technical Illustrator, Paramedic, and Deaf and Blind Support Specialist. New applied degrees are also offered in Ecotourism and Outdoor Leadership and Visual Communications.<br />
</p><br />
<br />
<a href="http://www.neb.com/nebecomm/default.asp"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2011/d/d6/UCalgary_NEB_Logo.png"></img></a><br />
<br />
<h2>New England Biolabs</h2><br />
<p>For over 30 years, New England Biolabs has led the industry in the discovery and production of enzymes for molecular biology applications. At NEB, enzyme production is linked to basic research in the cloning and overexpression of restriction/modification systems. Their focus on providing the largest selection of recombinant enzymes has resulted in lower dollar-per-unit costs and improved purity and consistency of product. Presently, NEB supplies more than 240 restriction enzymes, over 160 of which are available in recombinant form, as well as numerous recombinant DNA and protein modifying enzymes.</p><br />
<br />
<a href="http://www.osli.ca/"><img style="width:200px;" src="https://static.igem.org/mediawiki/2012/2/27/Ucalgary2012_Full_OSLI_Swirl.png"></a><br />
<a href="http://www.osrin.ualberta.ca/"><img style="clear: both; width: 200px;" src="https://static.igem.org/mediawiki/2011/9/9a/UCalgary_OSRIN_Logo.png"></img></a><br />
<h2>OSLI/OSRIN</h2><br />
<p>The Oil Sands Leadership Initiative (OSLI) and the Oil Sands Research and Information Network (OSRIN) are graciously supporting iGEM this year. OSLI is a collaborative network between Nexen Inc., ConocoPhillips Canada, Statoil Canada, Suncor Energy Inc., and Total E&P Canada. OSLI strives to improve the reputation of the oil sands and lead the industry to responsible development of Alberta's bitument resources.</p><br />
<p>OSRIN is an independent organization within the School of Energy and Environment at the University of Alberta. OSRIN compiles, interprets, analyzes, and communicates data to and from oil sands mining and the area surrounding them. The organization strives for a future where Alberta can economically benefit from oil sands development without harming the environment.</p><br />
<br/><br/><br/><br />
<br />
<a href="http://www.sarstedt.com/php/main.php"><img style="height:50px;" src="https://static.igem.org/mediawiki/2011/e/ee/UCalgary_Sarstedt_Logo.png"></img></a><br />
<br />
<h2>Sarstedt</h2><br />
<p>The Sarstedt Group develops, manufactures and sells equipment and consumables in the field of medicine and research. Ever since it was set up in 1961 the company has continued to grow to the point where it now employs a workforce of 2,500. They produce consumables and analytical equipment for medical diagnostics and consumables for use in medical patient care as well as for research laboratories and also for environmental analytical work. The Sarstedt group manufactures their own products at their own production sites as well as develops concepts and finished products in their own R&D centre.</p><br />
<br />
<a href="http://www.sparkscience.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a> <br />
<br />
<h2>Telus Spark</h2><br />
<p>The culmination of over a decade of planning, design and construction to bring Calgary’s new Science Centre to life will light a spark of wonder and excitement in Southern Alberta. Facilitators will fuel curiosity. Exhibits and programs will ignite a sense of wonder and excitement. Conferences and events will act as a catalyst for innovation and new ideas. TELUS Spark is a place for people of all ages and abilities to let go and embrace the desire to explore and discover science, technology and art in a way that their normal day-to-day life doesn’t allow for.</p><br />
<br />
<a href="http://www.teamlab.com/"><img style="width: 130px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a><br />
<br />
<h2>Team Lab</h2><br />
<p>TeamLab is a multifunctional online service for business collaboration, document and project management. It has been developed by Ascensio System SIA, a fast-growing company that offers IT-solutions for personal and corporate use.<br />
TeamLab was founded on the idea of making social networking and project management efficient. It combines a wide range of features that assist a company team to work as one organism at solving common tasks and achieving results.<br />
</p><br />
<br />
<a href="http://www.vwr.com/"><img style="margin-bottom: 5px; height: 90px;" src="https://static.igem.org/mediawiki/2011/6/65/UCalgary_VWR_Logo.png"></img></a><br />
<br />
<h2>VWR</h2><br />
<p>VWR International is one of the world leaders in the distribution of laboratory materials. There are currently over 250 000 customers in North America and Europe, which is quite large for a biotechnology distributor. They are based in West Chester, Pennsylvania and specialize in the supply of chemicals, equipment, instruments, lab apparel, and lab furniture. They have many offices based worldwide from Northern Ireland to Switzerland and even one based in Singapore. The unique guarantee that they offer is the shipping of ordered material within 24 hours, due to large quantities of stock and many distribution offices in various countries. They have been a significant sponsor of our iGEM team in the past and we appreciate their contribution to our team this year.</p><br />
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}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/SafetyTeam:Calgary/Safety2012-10-26T21:08:23Z<p>Iaingeorge: </p>
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<h2>The Risks of FRED and OSCAR</h2><br />
<br />
<p>Our project utilizes two types of engineered bacteria to detoxify tailings water. To quantify the amount of the toxic compounds present in the tailings water we are relying on <a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED">FRED</a>, a biosensor bacterium, that will work inside a closed environment to detect the toxins. Within our bioreactor system, we intend to introduce <a class="blue" href="https://2012.igem.org/Team:Calgary/Project/OSCAR">OSCAR</a>, a bacterium capable of detoxifying toxic compounds, to process large volumes of tailings water. </p><br />
<p>Whenever engineered bacteria are used, there is an inherent risk that the bacteria might escape from their containment vessels into the surrounding environment. There is no direct evidence to suggest the genetic systems we have implemented would have a negative impact on the environment. However, the implications of horizontal gene transfer to native microorganisms in tailings ponds and the surrounding environment must be addressed. This issue has been raised by numerous leaders in the oil industry as well as individuals living near tailing ponds. Our approach to biosafety was inspired by a comment published in Nature (Dana <i>et al</i>., 2012) which suggested multiple ways to prevent “Synthetic Biology Disaster”. We strongly believe that we must tackle four major safety concerns with our project. First, the synthetically engineered bacteria may be harmful to natural flora in the environment. Second, the bacteria may not only survive in the tailing pond environment but thrive in it, allowing it to outcompete naturally occurring bacteria. Third, genes may be transferred from our synthetic bacteria to native organisms. Fourth, if any of our genetically modified bacteria were to be able to grow in the tailings pond, evolution may allow for mutations which prevent our safety measures from working.</p><br />
<p> To address these four major safety concerns, we have engineered mechanical and biological safety measures that function to contain genetic elements of our synthetic bacteria. The first two concerns have been addressed through mechanical engineered controls by physically separating our organisms from the native environment. The third concern has been addressed through the development of a novel <a href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">kill switch system</a> to prevent our engineered organisms' DNA from spreading to other organisms. The fourth concern will be addressed by producing redundancy in our kill switch system which can be applied in the scale-up process of our project. By integrating these controls, we have taken a proactive approach to the biosafety of FRED and OSCAR.</p><br />
<br />
<br />
<a name="mechanical"></a><br />
<h2>Mechanical Engineered Controls</h2><br />
<h3><font color="159900">FRED</font></h3><br />
<p>Our team has established a series of controls which we hope to implement in our biosensor during field testing and optimization of the final product. The final product will contain FRED within one-time use closed containers, with one-way valves. The operator will insert water samples through the one way valve, isolating FRED from the operator and the environment. Once testing is completed, the operator will be instructed to simply twist the cap of the tube to release a pre-measured aliquot of bleach to destroy FRED prior to proper disposal of the container. </p><br />
<h3><font color="1088CC">OSCAR</font></h3><br />
<p>The goal of OSCAR is to be able to detoxify tailings ponds compounds through the removal of nitrogen, sulfur, and carboxylic acid functional groups. OSCAR has been designed to function in a closed system to which tailings pond water is added, as opposed to adding OSCAR directly into the environment. Hydrocarbon products generated in the bioreactor after microbial remediation are collected from the culture with a continuous belt skimming device. There is potential for OSCAR in the bioreactor vessel to escape by adhering to the belt. To counter this risk, the belt is treated with UV irradiation as it exits the bioreactor solution. This process will destroy OSCAR on the belt while simultaneously maintaining integrity of the generated hydrocarbons. The extracted solution is then sent through fractional distillation, a process which heats the hydrocarbon solution to over 400&deg;C, killing any OSCARs that may have survived UV exposure.</p><br />
<br />
<br />
<h2>Biological Engineered Controls</h2><br />
<p>Kill switches that have previously been entered into the registry often rely on methods that induce cell lysis. In these systems, genetic material is left intact, allowing for the remaining DNA to be taken up by bacteria and introducing the possibility that synthetic genes escape into the environment. We feel that lysis based kill switches are insufficient for use in FRED and OSCAR, necessitating design of novel kill switches. </p><br />
<p>To ensure that synthetic genetic elements cannot escape the closed systems in which FRED and OSCAR will be used, we engineered novel biological kill switches which we named "Ribo-Kill-Switches." These Ribo-Kill-Switches initiate cell death through degradation of genomic and plasmid DNA. Through a unique cell culture condition within the closed bioreactor and biosensor systems the kill switch genes can be suppressed. Should bacteria escape, the lack of the unique suppression conditions enables the kill switch system to become active. </p><br />
<p>Activation of the kill switch system causes the engineered cell to produce micrococcal nuclease and CviAII restriction enzyme. Our kill switch mechanisms are superior to previous nuclease-based kill switches because we have improved the completeness of DNA degradation. CviAII and micrococcal nuclease work in tandem: the endonuclease CviAII creates DNA double strand breaks at multiple sites while the micrococcal exonuclease activity degrades remaining strands into single nucleotides. The degradative enzymes chosen for our system were specifically selected for their ability to function at low temperatures, in variable pH conditions, and to work quickly to degrade as much of the genetic material as possible. These engineered biological controls ensure that synthetic genetic elements are completely destroyed in the event that FRED or OSCAR escape from the closed bioreactor or biosensor systems.</p><br />
<br />
<h2>Laboratory Personal Safety</h2><br />
<p>All of the students working with the iGEM 2012 Calgary Team received appropriate safety training as described by the University of Calgary’s safety policies. This included a Biosafety course which introduced the students to proper handling of biological materials. In addition, all iGEM students were required to attend proper Workplace Hazardous Materials Information System (WHMIS) training sessions. All safety procedures and guidelines of “Level 2 Biohazard Labs” were followed. Students were also supervised at all times by at least one authorized senior member, lab coordinator, teaching assistant, or professor. </p><br />
<p>The bacterial strains (<i>Nocardia</i>, <i>Rhodoccocus</i>, <i>Pseudomonas</i>, and <i>Escherichia</i>) used in the research are lab strains rated as Biosafety Level 1 and do not pose a health risk to laboratory workers, the general public, or the environment. The team also practiced appropriate procedures for working with and the disposal of tailings water samples. Appropriate handling measures were also applied for genetically modified bacteria and materials contaminated with bacteria. All measures outlined in the Material Safety Data Sheets (MSDS) and the biosafety regulations present at the University of Calgary were followed. </p> <br />
<p>Through these procedures, none of the genetically modified bacteria could have a chance of being introduced into the environment. The constructs that we have built to test our systems in the laboratory all used a safe, non-pathogenic bacterial strain of <i>E. coli</i> commonly used in labs worldwide. Other bacteria which were used for characterization of their genes, as listed above, are also non-pathogenic.</p><br />
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}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Project/Post-RegionalsTeam:Calgary/Project/Post-Regionals2012-10-26T20:37:18Z<p>Iaingeorge: </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 />
</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 />
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TITLE=Post-Regional Accomplishments|CONTENT=<br />
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<h2> Our team has had many accomplishments since the regional jamboree!</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="purple" 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"><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 />
<li><p><a class="orange" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch/Regulation"><b>Further characterized</b></a> our previously validated <b>magnesium riboswitch kill gene construct</b><a class="orange" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902018"> <b>(BBa_K902018)</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 />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting"><b>Electrochemically characterized</b></a> a constitutive <a class="green" href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902005"><b><i>bglX</i> (BBa_K902005)</b></a> <b>generator</b> in terms of its electrochemical activity.</p></li><br />
<br />
<li><p><a class="green" href="https://2012.igem.org/Team:Calgary/Project/FRED/Reporting"><b>Characterized</b></a> and demonstrated how <b>3 different hydrolase-producing circuits</b> can be used simultaneously in order to create a <b>multiplex biosensor.</b> </p></li><br />
<br />
<li><p><a class="purple" 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="purple" 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 oilsands 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 amines 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="purple" 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>Iaingeorgehttp://2012.igem.org/Team:Calgary/Outreach/TEDxCalgaryTeam:Calgary/Outreach/TEDxCalgary2012-10-26T06:26:39Z<p>Iaingeorge: </p>
<hr />
<div>{{Team:Calgary/TemplateOutreach|<br />
TITLE=TEDxCalgary|<br />
CONTENT=<br />
<html><br />
<br />
<h2> Check Out Our Talk! </h2><br />
<br />
<p> This year our team had the opportunity to partner with <a href="http://tedxcalgary.ca/events/city-2-0" target="_blank">TEDxCalgary</a> in developing a TEDx talk which we presented on October 13th in Calgary. This was a great opportunity to present to not only our city, but also a part of a larger, international event. We had a lot of fun thinking about synthetic biology and our project and the best way to share that in an inspirational and meaningful way.</p><br />
<br />
<p>Find our talk after the Regional Jamboree on the <a href="http://www.youtube.com/user/TEDxCalgary" target="_blank">TEDxCalgary Youtube Channel</a>.</p><br />
<br />
</html>[[File:UofC_CiTYPicture.png|700px|centre]]<html><br />
<br />
<h2> City 2.0 </h2><br />
<p>Our talk was part of <a href="http://www.thecity2.org/" target="_blank"> City 2.0</a>. This international event was awarded the <a href="http://www.tedprize.org/the-city-2-0/" target="_blank">TED prize</a> of the year, which occurred concurrentlly in over 50 cities around the world on October 13th. This event was inspired by many ideas around building vibrant and sustainable cities, but is trying to move on to the next step: taking action. The themes involve Art, Food, Education, Public Space, Health and more! The ultimate goal is to create the city of the future that are “inclusive, innovative, healthy, soulful, and thriving!”</p><br />
<br />
</html>[[File:UofC_City_2.0_Picture.png|700px|centre]]<br />
<br />
<html><br />
<br />
<h2> "Ideas Worth Spreading" </h2><br />
<br />
<p>In accordance with TED’s mandate, we needed an idea worth spreading. We had a lot of ideas about our project, the iGEM competition and synthetic biology in general. The hard part was coming up with the right theme for our presentation; one that would resonate with the general public both within and outside Alberta. <br />
One of the reasons we chose the project that we did is that it is something important to Alberta but that can also have implications around the globe – environment and energy. There are obvious implications of our project for the oil sands in Alberta, but also to a broader audience in terms of environmental remediation. This was clearly an important theme to us. We felt that the fact that the bacteria we are designing can not only remediate wastes, but can convert them into reusable fuels was particularly important. Every day, the landfills around the world have been growing incessantly. Communicating the potential for applying synthetic biology to clean or recycle the wastes and reclaim these lands would be an interesting focus. What is more exciting is the potential that synthetical biology gives to maintain a self-sustainable environment. Instead of relying on the city for energy and waste processing, we could use synthetic biology to clean our cities and generate energy from waste products for our cities.<br></p><br />
<br />
</html>[[File:TEDxCalgary for the city.jpg|700px|centre]]<html><br />
<br />
<p><br>Outside of the environmental implications of our project, open source was also an interesting theme as it is a major underlying premise of both synthetic biology and iGEM in general. The open access nature coupled with the drive for abstraction in synthetic biology make it something with huge potential for participation, something missing from other scientific fields. The amount of knowledge required to master biology is immense, but building systems with standard parts is not so hard. Just take a look at the things coming out of iGEM each year and you’ll understand. Undergraduates on small budgets can accomplish quite a lot in a summer! This idea of democratizing science was thus another angle worth exploring.</p><br />
<br />
<p>The theme we chose to go with was merging these two. We wanted to emphasize the potential synthetic biology could have in remediation, while showing that this technology can be used by many, allowing people to actively participate in science and synthetic biology, and in turn help improve the environment.<br />
Through our TED talk, we want to emphasize the democratization of science and generate new discussions and ideas for improving our health and our cities’ health through better environment, raising more questions on how to build a self-sustainable city!<br />
</p><br />
<br />
<h2> Building Healthy and Self-Sustaining Cities: Big Problems and Small Solutions </h2><br />
<br />
<div style="float:left;"><br />
<div style="width: 70%; float:left;"><p> In our talk, we hoped to give people a peek into the fascinating world of synthetic biology. In addition, we hoped to inspire people to take actions in working together to building better cities and healthier environments, by following their passions and using science. The story was developed around how we use the smallest living organism to take on some of the toughest challenges we face as a society, overcoming adversity and being creative with our limited resources. The talk raised people’s interests in joining the revolution of democratizing science. It also raised questions on how looking beyond the ordinary and realizing the potentials of insignificant things can potentially change the world.</p></div><div style="width: 30%; font-size:16px; float:right;"><p>“What bacteria hold in billions of years of evolution is the key to the revolution of healthy and self-sustaining cities!”<br><p style="font-size:15px; text-align: right;"> &mdash; Jay Wang</p></p></div><br />
<br />
</div><br />
<br />
<div style="float:left;"><br />
<img style="width: 35%; margin-left: 20px; float:left;" src="https://static.igem.org/mediawiki/2012/9/91/UCalgary2012_TED_Talk_Jay.png"></img><br />
<br />
<div style="width: 62%; float:left;"><p>The talk was very successful and received overwhelming feedback from the audience! Our topic sparked numerous discussions in both online and offline communities. There were people walking up to our speaker and saying that they were very inspired and entrigued by the talk; audiences surrounded our speaker with questions and comments right after the talk expressing interests in the ideas. There were high school students who want to be where we are when they are in university and who expressed interests in joining the team. Also, there were national media approaching us for potential interviews. We had supporters from the university at the talk as well - one of our university staff went to the TEDx event primarily to listen to our talk. </p></div><br />
</div><br />
<br />
</html><br />
}}</div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_TED_Talk_Jay.pngFile:UCalgary2012 TED Talk Jay.png2012-10-26T06:26:02Z<p>Iaingeorge: uploaded a new version of &quot;File:UCalgary2012 TED Talk Jay.png&quot;</p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Outreach/TEDxCalgaryTeam:Calgary/Outreach/TEDxCalgary2012-10-26T06:24:01Z<p>Iaingeorge: </p>
<hr />
<div>{{Team:Calgary/TemplateOutreach|<br />
TITLE=TEDxCalgary|<br />
CONTENT=<br />
<html><br />
<br />
<h2> Check Out the Talk! </h2><br />
<br />
<p> This year our team had the opportunity to partner with <a href="http://tedxcalgary.ca/events/city-2-0" target="_blank">TEDxCalgary</a> in developing a TEDx talk which we presented on October 13th in Calgary. This was a great opportunity to present to not only our city, but also a part of a larger, international event. We had a lot of fun thinking about synthetic biology and our project and the best way to share that in an inspirational and meaningful way.</p><br />
<br />
<p>Find our talk after the Regional Jamboree on the <a href="http://www.youtube.com/user/TEDxCalgary" target="_blank">TEDxCalgary Youtube Channel</a>.</p><br />
<br />
</html>[[File:UofC_CiTYPicture.png|700px|centre]]<html><br />
<br />
<h2> City 2.0 </h2><br />
<p>Our talk was part of <a href="http://www.thecity2.org/" target="_blank"> City 2.0</a>. This international event was awarded the <a href="http://www.tedprize.org/the-city-2-0/" target="_blank">TED prize</a> of the year, which occurred concurrentlly in over 50 cities around the world on October 13th. This event was inspired by many ideas around building vibrant and sustainable cities, but is trying to move on to the next step: taking action. The themes involve Art, Food, Education, Public Space, Health and more! The ultimate goal is to create the city of the future that are “inclusive, innovative, healthy, soulful, and thriving!”</p><br />
<br />
</html>[[File:UofC_City_2.0_Picture.png|700px|centre]]<br />
<br />
<html><br />
<br />
<h2> "Ideas Worth Spreading" </h2><br />
<br />
<p>In accordance with TED’s mandate, we needed an idea worth spreading. We had a lot of ideas about our project, the iGEM competition and synthetic biology in general. The hard part was coming up with the right theme for our presentation; one that would resonate with the general public both within and outside Alberta. <br />
One of the reasons we chose the project that we did is that it is something important to Alberta but that can also have implications around the globe – environment and energy. There are obvious implications of our project for the oil sands in Alberta, but also to a broader audience in terms of environmental remediation. This was clearly an important theme to us. We felt that the fact that the bacteria we are designing can not only remediate wastes, but can convert them into reusable fuels was particularly important. Every day, the landfills around the world have been growing incessantly. Communicating the potential for applying synthetic biology to clean or recycle the wastes and reclaim these lands would be an interesting focus. What is more exciting is the potential that synthetical biology gives to maintain a self-sustainable environment. Instead of relying on the city for energy and waste processing, we could use synthetic biology to clean our cities and generate energy from waste products for our cities.<br></p><br />
<br />
</html>[[File:TEDxCalgary for the city.jpg|700px|centre]]<html><br />
<br />
<p><br>Outside of the environmental implications of our project, open source was also an interesting theme as it is a major underlying premise of both synthetic biology and iGEM in general. The open access nature coupled with the drive for abstraction in synthetic biology make it something with huge potential for participation, something missing from other scientific fields. The amount of knowledge required to master biology is immense, but building systems with standard parts is not so hard. Just take a look at the things coming out of iGEM each year and you’ll understand. Undergraduates on small budgets can accomplish quite a lot in a summer! This idea of democratizing science was thus another angle worth exploring.</p><br />
<br />
<p>The theme we chose to go with was merging these two. We wanted to emphasize the potential synthetic biology could have in remediation, while showing that this technology can be used by many, allowing people to actively participate in science and synthetic biology, and in turn help improve the environment.<br />
Through our TED talk, we want to emphasize the democratization of science and generate new discussions and ideas for improving our health and our cities’ health through better environment, raising more questions on how to build a self-sustainable city!<br />
</p><br />
<br />
<h2> Building Healthy and Self-Sustaining Cities: Big Problems and Small Solutions </h2><br />
<br />
<div style="float:left;"><br />
<div style="width: 70%; float:left;"><p> In our talk, we hoped to give people a peek into the fascinating world of synthetic biology. In addition, we hoped to inspire people to take actions in working together to building better cities and healthier environments, by following their passions and using science. The story was developed around how we use the smallest living organism to take on some of the toughest challenges we face as a society, overcoming adversity and being creative with our limited resources. The talk raised people’s interests in joining the revolution of democratizing science. It also raised questions on how looking beyond the ordinary and realizing the potentials of insignificant things can potentially change the world.</p></div><div style="width: 30%; font-size:16px; float:right;"><p>“What bacteria hold in billions of years of evolution is the key to the revolution of healthy and self-sustaining cities!”<br><p style="font-size:15px; text-align: right;"> &mdash; Jay Wang</p></p></div><br />
<br />
</div><br />
<br />
<div style="float:left;"><br />
<img style="width: 35%; margin-left: 20px; float:left;" src="https://static.igem.org/mediawiki/2012/9/91/UCalgary2012_TED_Talk_Jay.png"></img><br />
<br />
<div style="width: 62%; float:left;"><p>The talk was very successful and received overwhelming feedback from the audience! Our topic sparked numerous discussions in both online and offline communities. There were people walking up to our speaker and saying that they were very inspired and entrigued by the talk; audiences surrounded our speaker with questions and comments right after the talk expressing interests in the ideas. There were high school students who want to be where we are when they are in university and who expressed interests in joining the team. Also, there were national media approaching us for potential interviews. We had supporters from the university at the talk as well - one of our university staff went to the TEDx event primarily to listen to our talk. </p></div><br />
</div><br />
<br />
</html><br />
}}</div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_TED_Talk_Jay.pngFile:UCalgary2012 TED Talk Jay.png2012-10-26T06:19:01Z<p>Iaingeorge: uploaded a new version of &quot;File:UCalgary2012 TED Talk Jay.png&quot;</p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_TED_Talk_Jay.pngFile:UCalgary2012 TED Talk Jay.png2012-10-26T06:12:42Z<p>Iaingeorge: uploaded a new version of &quot;File:UCalgary2012 TED Talk Jay.png&quot;</p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_TED_Talk_Jay.pngFile:UCalgary2012 TED Talk Jay.png2012-10-26T06:10:55Z<p>Iaingeorge: uploaded a new version of &quot;File:UCalgary2012 TED Talk Jay.png&quot;</p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_TED_Talk_Jay.pngFile:UCalgary2012 TED Talk Jay.png2012-10-26T06:09:32Z<p>Iaingeorge: </p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/File:TEDxCalgary_for_the_city.jpgFile:TEDxCalgary for the city.jpg2012-10-26T06:07:53Z<p>Iaingeorge: uploaded a new version of &quot;File:TEDxCalgary for the city.jpg&quot;</p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Outreach/TEDxCalgaryTeam:Calgary/Outreach/TEDxCalgary2012-10-26T06:05:02Z<p>Iaingeorge: </p>
<hr />
<div>{{Team:Calgary/TemplateOutreach|<br />
TITLE=TEDxCalgary|<br />
CONTENT=<br />
<html><br />
<br />
<h2> Check Out the Talk! </h2><br />
<br />
<p> This year our team had the opportunity to partner with <a href="http://tedxcalgary.ca/events/city-2-0" target="_blank">TEDxCalgary</a> in developing a TEDx talk which we presented on October 13th in Calgary. This was a great opportunity to present to not only our city, but also a part of a larger, international event. We had a lot of fun thinking about synthetic biology and our project and the best way to share that in an inspirational and meaningful way.</p><br />
<br />
<p>Find our talk after the Regional Jamboree on the <a href="http://www.youtube.com/user/TEDxCalgary" target="_blank">TEDxCalgary Youtube Channel</a>.</p><br />
<br />
</html>[[File:UofC_CiTYPicture.png|700px|centre]]<html><br />
<br />
<h2> City 2.0 </h2><br />
<p>Our talk was part of <a href="http://www.thecity2.org/" target="_blank"> City 2.0</a>. This international event was awarded the <a href="http://www.tedprize.org/the-city-2-0/" target="_blank">TED prize</a> of the year, which occurred concurrentlly in over 50 cities around the world on October 13th. This event was inspired by many ideas around building vibrant and sustainable cities, but is trying to move on to the next step: taking action. The themes involve Art, Food, Education, Public Space, Health and more! The ultimate goal is to create the city of the future that are “inclusive, innovative, healthy, soulful, and thriving!”</p><br />
<br />
</html>[[File:UofC_City_2.0_Picture.png|700px|centre]]<br />
<br />
<html><br />
<br />
<h2> "Ideas Worth Spreading" </h2><br />
<br />
<p>In accordance with TED’s mandate, we needed an idea worth spreading. We had a lot of ideas about our project, the iGEM competition and synthetic biology in general. The hard part was coming up with the right theme for our presentation; one that would resonate with the general public both within and outside Alberta. <br />
One of the reasons we chose the project that we did is that it is something important to Alberta but that can also have implications around the globe – environment and energy. There are obvious implications of our project for the oil sands in Alberta, but also to a broader audience in terms of environmental remediation. This was clearly an important theme to us. We felt that the fact that the bacteria we are designing can not only remediate wastes, but can convert them into reusable fuels was particularly important. Every day, the landfills around the world have been growing incessantly. Communicating the potential for applying synthetic biology to clean or recycle the wastes and reclaim these lands would be an interesting focus. What is more exciting is the potential that synthetical biology gives to maintain a self-sustainable environment. Instead of relying on the city for energy and waste processing, we could use synthetic biology to clean our cities and generate energy from waste products for our cities.<br></p><br />
<br />
</html>[[File:TEDxCalgary for the city.jpg|700px|centre]]<html><br />
<br />
<p><br>Outside of the environmental implications of our project, open source was also an interesting theme as it is a major underlying premise of both synthetic biology and iGEM in general. The open access nature coupled with the drive for abstraction in synthetic biology make it something with huge potential for participation, something missing from other scientific fields. The amount of knowledge required to master biology is immense, but building systems with standard parts is not so hard. Just take a look at the things coming out of iGEM each year and you’ll understand. Undergraduates on small budgets can accomplish quite a lot in a summer! This idea of democratizing science was thus another angle worth exploring.</p><br />
<br />
<p>The theme we chose to go with was merging these two. We wanted to emphasize the potential synthetic biology could have in remediation, while showing that this technology can be used by many, allowing people to actively participate in science and synthetic biology, and in turn help improve the environment.<br />
Through our TED talk, we want to emphasize the democratization of science and generate new discussions and ideas for improving our health and our cities’ health through better environment, raising more questions on how to build a self-sustainable city!<br />
</p><br />
<br />
<h2> Building Healthy and Self-Sustaining Cities: Big Problems and Small Solutions </h2><br />
<br />
<div style="float:left;"><br />
<div style="width: 70%; float:left;"><p> In our talk, we hoped to give people a peek into the fascinating world of synthetic biology. In addition, we hoped to inspire people to take actions in working together to building better cities and healthier environments, by following their passions and using science. The story was developed around how we use the smallest living organism to take on some of the toughest challenges we face as a society, overcoming adversity and being creative with our limited resources. The talk raised people’s interests in joining the revolution of democratizing science. It also raised questions on how looking beyond the ordinary and realizing the potentials of insignificant things can potentially change the world.</p></div><div style="width: 30%; font-size:16px; float:right;"><p>“What bacteria hold in billions of years of evolution is the key to the revolution of healthy and self-sustaining cities!”<br><p style="font-size:15px; text-align: right;"> &mdash; Jay Wang</p></p></div><br />
<br />
</div><br />
<br />
<p>The talk was very successful and received overwhelming feedback from the audience! Our topic sparked numerous discussions in both online and offline communities. There were people walking up to our speaker and saying that they were very inspired and entrigued by the talk; audiences surrounded our speaker with questions and comments right after the talk expressing interests in the ideas. There were high school students who want to be where we are when they are in university and who expressed interests in joining the team. Also, there were national media approaching us for potential interviews. We had supporters from the university at the talk as well - one of our university staff went to the TEDx event primarily to listen to our talk. </p><br />
<br />
</html> [[File:Ucalgary TEDxCalgary.jpg|700px|centre]]<html><br />
<br />
</html><br />
}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/SponsorsTeam:Calgary/Sponsors2012-10-26T05:38:49Z<p>Iaingeorge: </p>
<hr />
<div>{{Team:Calgary/MainHeader|<html><img src="https://static.igem.org/mediawiki/2012/c/c5/UCalgary2012_HeaderLogoOrange.png"></img></html>}}<br />
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<p>The University of Calgary's 2012 iGEM Team would like to thank all of our generous sponsors! </p><br />
<head><br />
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float: right;<br />
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<a name="uofc"></a><br />
<a href="http://www.ucalgary.ca"><img style="width: 190px; padding: 25px 50px 0px 50px;" src="https://static.igem.org/mediawiki/2011/b/b7/UCalgary_Logo_Small.png"></img></a><br />
<br />
<h2>University of Calgary</h2><br />
<p>We graciously thank the Department of Cell Biology and Anatomy, the Department of Electrical and Computer Engineering, the Centre for Bioengineering Research and Education and the Department of Biological Sciences for all their support. We also wish to thank the Faculty of Medicine for their additional support as well. Additionally, we wish to thank the office of the Vice President of Research for their generous support.</p> <br />
<br />
<a href="http://www.ucalgary.ca/bhsc"><img style="clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2011/c/c7/UCalgary_BHSc_Logo.png"></img></a><br />
<h2>O'Brien Centre for the BHSc</h2><br />
<p>The O'Brien Centre for the Bachelor of Health Sciences is a part of the University of Calgary, located in the Foothills campus. It is responsible for providing iGEM team with lab space as well as funding. The O’Brien Centre was founded in part by a generous $5-million donation by David and Gail O’ Brien, after whom the Centre was named. David O'Brien has been a member of the University's Board of Governors, while Gail O'Brien has chaired the Faculty of Medicine's Dean's Advisory Council. The O’Brien Centre is the hub of top-notch research, interdisciplinary research, and education. It is responsible for providing approximately $9-million/year for researchers. The 2012 iGEM team thanks O’Brien Centre for its generous contribution of the O’Brien Centre Summer Studentship as well as lab space this year.</p><br />
<br />
<a href="http://bio.ucalgary.ca/"><img style="width: 215px; clear:both; margin-top: -20px; margin-left: -10px;" src="https://static.igem.org/mediawiki/2012/4/47/UCalgary2012_BioSci_Logo.JPG"></img></a><br />
<h2>Department of Biological Sciences</h2><br />
<p>The Department of Biological Sciences at the University of Calgary is a community of scholars who share a commitment to insightful, innovative and integrative research in diverse areas of life sciences, from biomolecules to the biosphere, and to the development of future leaders in the basic and applied biological sciences through excellence in our undergraduate and graduate programs.</p><br />
<br />
<a href="http://enel.ucalgary.ca"><img style="width: 250px; clear:both; margin-top: -20px; margin-left: -20px; margin-bottom: -10px;" src="https://static.igem.org/mediawiki/2012/e/e6/UCalgary2012_Schulich_Electric_Computer_Logo.jpg"></img></a><br />
<h2>Schulich School of Engineering Department of Electrical and Computer Engineering</h2><br />
<p>The Department of Electrical and Computer Engineering in the Schulich School of Engineering offers both undergraduate and graduate degree programs. The Department is highly regarded internationally for its leadership in biomedical engineering, radio systems, software engineering, micro- and nano-scale systems, and power and energy research.</p><br />
<a href="http://www.albertatechfutures.ca/"><img src="https://static.igem.org/mediawiki/2011/3/3f/UCalgary2011_AITF_Logo_Small.png"></img></a><br />
<br />
<h2>Alberta Innovates Technology Futures</h2><br />
<p>Alberta Innovates Technology Futures facilitates the growth of technical industries by supporting quality research in Alberta's particular fields of expertise. These include nanotechnology, information communication technology, and genomics. AITF works in joint effort with entrepreneurs and researchers to ensure that Alberta’s technologies can be sustained at a business level through commercialization and growth. This is accomplished by ensuring that useful products, protocols and services are delivered to meet global demands.</p><br />
<br />
<a href="http://www.autodesk.com/"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/0/0b/UCalgary2012-Autodesk-Logo.png"></img></a><br />
<br />
<h2>Autodesk</h2><br />
<p>Autodesk, Inc., is a leader in 3D design, engineering and entertainment software. Customers across the manufacturing, architecture, building, construction, and media and entertainment industries—including the last 17 Academy Award winners for Best Visual Effects—use Autodesk software to design, visualize, and simulate their ideas before they're ever built or created. From blockbuster visual effects and buildings that create their own energy to electric cars and the batteries that power them, the work of our 3D software customers is everywhere you look.</p><br />
<br />
<a href="http://www.eurofins.com/en.aspx"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a><br />
<h2>Eurofins MWG Operon</h2><br />
<p>Eurofins MWG Operon, founded in 1990 and member of the Eurofins Group, is an international provider of genomic services established around the core business lines next generation sequencing, custom DNA sequencing, oligonucleotides, siRNA and gene synthesis. The company's main mission is focussed on customer convenience and high quality services in industrial scale for the life science industries and academic research institutions around the world.</p><br />
<br />
<a href="http://genomealberta.ca/"><img src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></img></a><br />
<br />
<h2>Genome Alberta</h2><br />
<p>In partnership with Genome Canada Industry Canada and the Province of Alberta, Genome Alberta was established in 2005. They are a publicly funded non-profit corporation that initiates, funds, and manages genomics research and partnerships. <br />
Genome Alberta strives to be the leading source of information and administration related to genomics, proteomics, bioinformatics and bioethics research in Alberta. Genome Alberta is dedicated to informing students, researchers, research organizations, our partners, and the public regarding opportunities and challenges in genomics and proteomics, and in encouraging the development of a Life Sciences research industry in Alberta. <br />
</p><br />
<br />
<a href="http://www.hyperionlab.ca/"><img style="width: 190px;" src="https://static.igem.org/mediawiki/2012/8/89/UCalgary2012_Hyperion_Research_Logo.png"></img></a><br />
<br />
<h2>Hyperion Research Ltd.</h2><br />
<p>Hyperion Research Ltd., specializes in the analysis of water and sewage samples for the protozoan parasites <i>Giardia</i> and <i>Cryptosporidium</i>. They also provide sampling equipment and analysis for the Microscopic Particulate Analysis to determine Groundwater Under the Direct Influence (GUDI) of surface water. Hyperion's laboratory is located in Medicine Hat, Alberta, and where they serve the water treatment industry across Canada. Hyperion is also active in research into waterborne disease problems and has numerous international contacts.<br />
</p> <br />
<br />
<a href="http://www.idtdna.com/site"><img src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a><br />
<br />
<h2>IDT (Integrated DNA Technologies)</h2><br />
<p>Integrated DNA Technologies (IDT) is a leader in manufacturing and developing products for the research and diagnostic life science market. IDT serves the areas of academic research, biotechnology, and pharmaceutical development. Founded by Dr. Joseph Walder in 1987, IDT’s development has been guided by an uncompromising approach to quality, a belief in the value of good service, and a determination to minimize consumer costs. IDT now has over 500 employees and ships over 20,000 oligos per day. <br />
<br />
Serving over 70,000 life sciences researchers, IDT is widely recognized as the industry leader in custom oligonucleotides. </p><br />
<br />
<a href="http://www.mhc.ab.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a><br />
<br />
<h2>Medicine Hat College</h2><br />
<p>Medicine Hat College is a public, board governed, comprehensive community college serving a large region of southeastern Alberta and southwestern Saskatchewan, Canada. The MHC is located in the city of Medicine Hat, Alberta, Canada. MHC has been serving students in southeastern Alberta and beyond since 1965. MHC’s main campus services almost 2,500 students each year with another 200 attending Brooks Campus, located 100 km west of Medicine Hat. Currently, more than 30 diplomas and certificates are offered along with 25 university transfer programs. There are also several opportunities for degree completion at MHC including nursing, applied arts, and social work. A partnership with the University of Calgary makes it possible for nursing students to complete a full bachelor’s degree at Medicine Hat College while graduates from diploma programs such as Police and Security may also complete degrees. Medicine Hat College offers other unique diploma programs such as Addictions Counselor, Technical Illustrator, Paramedic, and Deaf and Blind Support Specialist. New applied degrees are also offered in Ecotourism and Outdoor Leadership and Visual Communications.<br />
</p><br />
<br />
<a href="http://www.neb.com/nebecomm/default.asp"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2011/d/d6/UCalgary_NEB_Logo.png"></img></a><br />
<br />
<h2>New England Biolabs</h2><br />
<p>For over 30 years, New England Biolabs has led the industry in the discovery and production of enzymes for molecular biology applications. At NEB, enzyme production is linked to basic research in the cloning and overexpression of restriction/modification systems. Their focus on providing the largest selection of recombinant enzymes has resulted in lower dollar-per-unit costs and improved purity and consistency of product. Presently, NEB supplies more than 240 restriction enzymes, over 160 of which are available in recombinant form, as well as numerous recombinant DNA and protein modifying enzymes.</p><br />
<br />
<a href="http://www.osli.ca/"><img style="width:200px;" src="https://static.igem.org/mediawiki/2012/2/27/Ucalgary2012_Full_OSLI_Swirl.png"></a><br />
<a href="http://www.osrin.ualberta.ca/"><img style="clear: both; width: 200px;" src="https://static.igem.org/mediawiki/2011/9/9a/UCalgary_OSRIN_Logo.png"></img></a><br />
<h2>OSLI/OSRIN</h2><br />
<p>The Oil Sands Leadership Initiative (OSLI) and the Oil Sands Research and Information Network (OSRIN) are graciously supporting iGEM this year. OSLI is a collaborative network between Nexen Inc., ConocoPhillips Canada, Statoil Canada, Suncor Energy Inc., and Total E&P Canada. OSLI strives to improve the reputation of the oil sands and lead the industry to responsible development of Alberta's bitument resources.</p><br />
<p>OSRIN is an independent organization within the School of Energy and Environment at the University of Alberta. OSRIN compiles, interprets, analyzes, and communicates data to and from oil sands mining and the area surrounding them. The organization strives for a future where Alberta can economically benefit from oil sands development without harming the environment.</p><br />
<br/><br/><br/><br />
<br />
<a href="http://www.sarstedt.com/php/main.php"><img style="height:50px;" src="https://static.igem.org/mediawiki/2011/e/ee/UCalgary_Sarstedt_Logo.png"></img></a><br />
<br />
<h2>Sarstedt</h2><br />
<p>The Sarstedt Group develops, manufactures and sells equipment and consumables in the field of medicine and research. Ever since it was set up in 1961 the company has continued to grow to the point where it now employs a workforce of 2,500. They produce consumables and analytical equipment for medical diagnostics and consumables for use in medical patient care as well as for research laboratories and also for environmental analytical work. The Sarstedt group manufactures their own products at their own production sites as well as develops concepts and finished products in their own R&D centre.</p><br />
<br />
<a href="http://www.sparkscience.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a> <br />
<br />
<h2>Telus Spark</h2><br />
<p>The culmination of over a decade of planning, design and construction to bring Calgary’s new Science Centre to life will light a spark of wonder and excitement in Southern Alberta. Facilitators will fuel curiosity. Exhibits and programs will ignite a sense of wonder and excitement. Conferences and events will act as a catalyst for innovation and new ideas. TELUS Spark is a place for people of all ages and abilities to let go and embrace the desire to explore and discover science, technology and art in a way that their normal day-to-day life doesn’t allow for.</p><br />
<br />
<a href="http://www.teamlab.com/"><img style="width: 130px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a><br />
<br />
<h2>Team Lab</h2><br />
<p>TeamLab is a multifunctional online service for business collaboration, document and project management. It has been developed by Ascensio System SIA, a fast-growing company that offers IT-solutions for personal and corporate use.<br />
TeamLab was founded on the idea of making social networking and project management efficient. It combines a wide range of features that assist a company team to work as one organism at solving common tasks and achieving results.<br />
</p><br />
<br />
<a href="http://www.vwr.com/"><img style="margin-bottom: 5px; height: 90px;" src="https://static.igem.org/mediawiki/2011/6/65/UCalgary_VWR_Logo.png"></img></a><br />
<br />
<h2>VWR</h2><br />
<p>VWR International is one of the world leaders in the distribution of laboratory materials. There are currently over 250 000 customers in North America and Europe, which is quite large for a biotechnology distributor. They are based in West Chester, Pennsylvania and specialize in the supply of chemicals, equipment, instruments, lab apparel, and lab furniture. They have many offices based worldwide from Northern Ireland to Switzerland and even one based in Singapore. The unique guarantee that they offer is the shipping of ordered material within 24 hours, due to large quantities of stock and many distribution offices in various countries. They have been a significant sponsor of our iGEM team in the past and we appreciate their contribution to our team this year.</p><br />
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}}</div>Iaingeorgehttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-10-26T05:11:53Z<p>Iaingeorge: </p>
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<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 />
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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 class="gbox3 iconbox" href="https://2012.igem.org/Team:Calgary/Project/FRED/Modelling"><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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<a class="bbox3 iconbox" href="https://2012.igem.org/Team:Calgary/Project/OSCAR/FluxAnalysis"><br />
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<img src="https://static.igem.org/mediawiki/2012/4/40/UCalgary2012_IconOSCAR6.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 id="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 />
<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.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 />
</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.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 />
<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 />
</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 style="width: 150px"></td><br />
<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 />
<td style="width: 300px"><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 style="width: 150px"></td><br />
</tr></table><br />
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</table><br />
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<br />
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</html></div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012-Autodesk-Logo.pngFile:UCalgary2012-Autodesk-Logo.png2012-10-26T04:55:11Z<p>Iaingeorge: </p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/Team:CalgaryTeam:Calgary2012-10-26T04:51:05Z<p>Iaingeorge: </p>
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<a id="boatbottom" href="https://2012.igem.org/Team:Calgary/Project/Synergy"></a><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>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 />
</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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<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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<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 />
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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: 225px;" 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: 225px;" src="https://static.igem.org/mediawiki/2012/9/9c/UCalgary2012_Schulich_Electric_Computer_Logo.png"></img></a></td><br />
<td><a href="http://www.mhc.ab.ca/" target="_blank"><img style="width: 234px;" 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.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 />
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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.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 />
<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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<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.idtdna.com/site" target="_blank"><img style="width: 228px;" src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a></td><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"></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><br />
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</html></div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_Schulich_Electric_Computer_Logo.pngFile:UCalgary2012 Schulich Electric Computer Logo.png2012-10-26T04:50:08Z<p>Iaingeorge: </p>
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<div></div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_BioSci_Logo.pngFile:UCalgary2012 BioSci Logo.png2012-10-26T04:49:45Z<p>Iaingeorge: </p>
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<div></div>Iaingeorgehttp://2012.igem.org/Team:Calgary/SponsorsTeam:Calgary/Sponsors2012-10-26T04:46:26Z<p>Iaingeorge: </p>
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<p>The University of Calgary's 2012 iGEM Team would like to thank all of our generous sponsors! </p><br />
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<a href="http://www.ucalgary.ca"><img style="width: 190px; padding: 25px 50px 0px 50px;" src="https://static.igem.org/mediawiki/2011/b/b7/UCalgary_Logo_Small.png"></img></a><br />
<a href="http://www.ucalgary.ca/bhsc"><img style="clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2011/c/c7/UCalgary_BHSc_Logo.png"></img></a><br />
<a href="http://bio.ucalgary.ca/"><img style="width: 215px; clear:both; margin-top: -20px; margin-left: -10px;" src="https://static.igem.org/mediawiki/2012/4/47/UCalgary2012_BioSci_Logo.JPG"></img></a><br />
<a href="http://enel.ucalgary.ca"><img style="width: 250px; clear:both; margin-top: -20px; margin-left: -20px; margin-bottom: -10px;" src="https://static.igem.org/mediawiki/2012/e/e6/UCalgary2012_Schulich_Electric_Computer_Logo.jpg"></img></a><br />
<br />
<h2>University of Calgary and the O'Brien Centre for the BHSc</h2><br />
<p>We graciously thank the Department of Cell Biology and Anatomy, the Department of Electrical and Computer Engineering, the Centre for Bioengineering Research and Education and the Department of Biological Sciences for all their support. We also wish to thank the Faculty of Medicine for their additional support as well. Additionally, we wish to thank the office of the Vice President of Research for their generous support.</p> <br />
<p>The O'Brien Centre for the Bachelor of Health Sciences is a part of the University of Calgary, located in the Foothills campus. It is responsible for providing iGEM team with lab space as well as funding. The O’Brien Centre was founded in part by a generous $5-million donation by David and Gail O’ Brien, after whom the Centre was named. David O'Brien has been a member of the University's Board of Governors, while Gail O'Brien has chaired the Faculty of Medicine's Dean's Advisory Council. The O’Brien Centre is the hub of top-notch research, interdisciplinary research, and education. It is responsible for providing approximately $9-million/year for researchers. The 2012 iGEM team thanks O’Brien Centre for its generous contribution of the O’Brien Centre Summer Studentship as well as lab space this year.</p><br />
<p>The Department of Biological Sciences at the University of Calgary is a community of scholars who share a commitment to insightful, innovative and integrative research in diverse areas of life sciences, from biomolecules to the biosphere, and to the development of future leaders in the basic and applied biological sciences through excellence in our undergraduate and graduate programs.</p><br />
<p>The Department of Electrical and Computer Engineering in the Schulich School of Engineering offers both undergraduate and graduate degree programs. The Department is highly regarded internationally for its leadership in biomedical engineering, radio systems, software engineering, micro- and nano-scale systems, and power and energy research.</p><br />
<a href="http://www.albertatechfutures.ca/"><img src="https://static.igem.org/mediawiki/2011/3/3f/UCalgary2011_AITF_Logo_Small.png"></img></a><br />
<br />
<h2>Alberta Innovates Technology Futures</h2><br />
<p>Alberta Innovates Technology Futures facilitates the growth of technical industries by supporting quality research in Alberta's particular fields of expertise. These include nanotechnology, information communication technology, and genomics. AITF works in joint effort with entrepreneurs and researchers to ensure that Alberta’s technologies can be sustained at a business level through commercialization and growth. This is accomplished by ensuring that useful products, protocols and services are delivered to meet global demands.</p><br />
<br />
<a href="http://www.osli.ca/"><img style="width:200px;" src="https://static.igem.org/mediawiki/2012/2/27/Ucalgary2012_Full_OSLI_Swirl.png"></a><br />
<a href="http://www.osrin.ualberta.ca/"><img style="clear: both; width: 200px;" src="https://static.igem.org/mediawiki/2011/9/9a/UCalgary_OSRIN_Logo.png"></img></a><br />
<h2>OSLI/OSRIN</h2><br />
<p>The Oil Sands Leadership Initiative (OSLI) and the Oil Sands Research and Information Network (OSRIN) are graciously supporting iGEM this year. OSLI is a collaborative network between Nexen Inc., ConocoPhillips Canada, Statoil Canada, Suncor Energy Inc., and Total E&P Canada. OSLI strives to improve the reputation of the oil sands and lead the industry to responsible development of Alberta's bitument resources.</p><br />
<p>OSRIN is an independent organization within the School of Energy and Environment at the University of Alberta. OSRIN compiles, interprets, analyzes, and communicates data to and from oil sands mining and the area surrounding them. The organization strives for a future where Alberta can economically benefit from oil sands development without harming the environment.</p><br />
<br/><br/><br/><br />
<a href="http://www.vwr.com/"><img style="margin-bottom: 5px; height: 90px;" src="https://static.igem.org/mediawiki/2011/6/65/UCalgary_VWR_Logo.png"></img></a><br />
<br />
<h2>VWR</h2><br />
<p>VWR International is one of the world leaders in the distribution of laboratory materials. There are currently over 250 000 customers in North America and Europe, which is quite large for a biotechnology distributor. They are based in West Chester, Pennsylvania and specialize in the supply of chemicals, equipment, instruments, lab apparel, and lab furniture. They have many offices based worldwide from Northern Ireland to Switzerland and even one based in Singapore. The unique guarantee that they offer is the shipping of ordered material within 24 hours, due to large quantities of stock and many distribution offices in various countries. They have been a significant sponsor of our iGEM team in the past and we appreciate their contribution to our team this year.</p><br />
<br />
<br />
<a href="http://www.neb.com/nebecomm/default.asp"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2011/d/d6/UCalgary_NEB_Logo.png"></img></a><br />
<br />
<h2>New England Biolabs</h2><br />
<p>For over 30 years, New England Biolabs has led the industry in the discovery and production of enzymes for molecular biology applications. At NEB, enzyme production is linked to basic research in the cloning and overexpression of restriction/modification systems. Their focus on providing the largest selection of recombinant enzymes has resulted in lower dollar-per-unit costs and improved purity and consistency of product. Presently, NEB supplies more than 240 restriction enzymes, over 160 of which are available in recombinant form, as well as numerous recombinant DNA and protein modifying enzymes.</p><br />
<a href="http://www.sarstedt.com/php/main.php"><img style="height:50px;" src="https://static.igem.org/mediawiki/2011/e/ee/UCalgary_Sarstedt_Logo.png"></img></a><br />
<br />
<h2>Sarstedt</h2><br />
<p>The Sarstedt Group develops, manufactures and sells equipment and consumables in the field of medicine and research. Ever since it was set up in 1961 the company has continued to grow to the point where it now employs a workforce of 2,500. They produce consumables and analytical equipment for medical diagnostics and consumables for use in medical patient care as well as for research laboratories and also for environmental analytical work. The Sarstedt group manufactures their own products at their own production sites as well as develops concepts and finished products in their own R&D centre.</p><br />
<a href="http://www.eurofins.com/en.aspx"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a><br />
<h2>Eurofins MWG Operon</h2><br />
<p>Eurofins MWG Operon, founded in 1990 and member of the Eurofins Group, is an international provider of genomic services established around the core business lines next generation sequencing, custom DNA sequencing, oligonucleotides, siRNA and gene synthesis. The company's main mission is focussed on customer convenience and high quality services in industrial scale for the life science industries and academic research institutions around the world.</p><br />
<a href="http://www.sparkscience.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a><br />
<br />
<h2>Telus Spark</h2><br />
<p>The culmination of over a decade of planning, design and construction to bring Calgary’s new Science Centre to life will light a spark of wonder and excitement in Southern Alberta. Facilitators will fuel curiosity. Exhibits and programs will ignite a sense of wonder and excitement. Conferences and events will act as a catalyst for innovation and new ideas. TELUS Spark is a place for people of all ages and abilities to let go and embrace the desire to explore and discover science, technology and art in a way that their normal day-to-day life doesn’t allow for.</p><br />
<a href="http://www.idtdna.com/site"><img src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a><br />
<br />
<h2>IDT (Integrated DNA Technologies)</h2><br />
<p>Integrated DNA Technologies (IDT) is a leader in manufacturing and developing products for the research and diagnostic life science market. IDT serves the areas of academic research, biotechnology, and pharmaceutical development. Founded by Dr. Joseph Walder in 1987, IDT’s development has been guided by an uncompromising approach to quality, a belief in the value of good service, and a determination to minimize consumer costs. IDT now has over 500 employees and ships over 20,000 oligos per day. <br />
<br />
Serving over 70,000 life sciences researchers, IDT is widely recognized as the industry leader in custom oligonucleotides. </p><br />
<a href="http://genomealberta.ca/"><img src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></img></a><br />
<br />
<h2>Genome Alberta</h2><br />
<p>In partnership with Genome Canada Industry Canada and the Province of Alberta, Genome Alberta was established in 2005. They are a publicly funded non-profit corporation that initiates, funds, and manages genomics research and partnerships. <br />
Genome Alberta strives to be the leading source of information and administration related to genomics, proteomics, bioinformatics and bioethics research in Alberta. Genome Alberta is dedicated to informing students, researchers, research organizations, our partners, and the public regarding opportunities and challenges in genomics and proteomics, and in encouraging the development of a Life Sciences research industry in Alberta. <br />
</p><br />
<br />
<br />
<a href="http://www.teamlab.com/"><img style="width: 130px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a><br />
<br />
<h2>Team Lab</h2><br />
<p>TeamLab is a multifunctional online service for business collaboration, document and project management. It has been developed by Ascensio System SIA, a fast-growing company that offers IT-solutions for personal and corporate use.<br />
TeamLab was founded on the idea of making social networking and project management efficient. It combines a wide range of features that assist a company team to work as one organism at solving common tasks and achieving results.<br />
</p><br />
<br />
<a href="http://www.mhc.ab.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a><br />
<br />
<h2>Medicine Hat College</h2><br />
<p>Medicine Hat College is a public, board governed, comprehensive community college serving a large region of southeastern Alberta and southwestern Saskatchewan, Canada. The MHC is located in the city of Medicine Hat, Alberta, Canada. MHC has been serving students in southeastern Alberta and beyond since 1965. MHC’s main campus services almost 2,500 students each year with another 200 attending Brooks Campus, located 100 km west of Medicine Hat. Currently, more than 30 diplomas and certificates are offered along with 25 university transfer programs. There are also several opportunities for degree completion at MHC including nursing, applied arts, and social work. A partnership with the University of Calgary makes it possible for nursing students to complete a full bachelor’s degree at Medicine Hat College while graduates from diploma programs such as Police and Security may also complete degrees. Medicine Hat College offers other unique diploma programs such as Addictions Counselor, Technical Illustrator, Paramedic, and Deaf and Blind Support Specialist. New applied degrees are also offered in Ecotourism and Outdoor Leadership and Visual Communications.<br />
</p><br />
<br />
<a href="http://www.hyperionlab.ca/"><img style="width: 190px;" src="https://static.igem.org/mediawiki/2012/8/89/UCalgary2012_Hyperion_Research_Logo.png"></img></a><br />
<br />
<h2>Hyperion Research Ltd.</h2><br />
<p>Hyperion Research Ltd., specializes in the analysis of water and sewage samples for the protozoan parasites <i>Giardia</i> and <i>Cryptosporidium</i>. They also provide sampling equipment and analysis for the Microscopic Particulate Analysis to determine Groundwater Under the Direct Influence (GUDI) of surface water. Hyperion's laboratory is located in Medicine Hat, Alberta, and where they serve the water treatment industry across Canada. Hyperion is also active in research into waterborne disease problems and has numerous international contacts.<br />
</p><br />
<br />
</body><br />
<br />
</html><br />
<br />
}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/SponsorsTeam:Calgary/Sponsors2012-10-26T04:45:39Z<p>Iaingeorge: </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|sponsors|<br />
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</ul><br />
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<br />
TITLE=Sponsors|<br />
CONTENT=<br />
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<p>The University of Calgary's 2012 iGEM Team would like to thank all of our generous sponsors! </p><br />
<head><br />
<style><br />
#bodycontainer img{<br />
float: right;<br />
margin: 15px 15px 5px 15px;<br />
padding-top: 15px;<br />
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<img style="display: block; margin: auto; padding: 0;float: none;" src="https://static.igem.org/mediawiki/2012/6/65/UCalgary2012_FRED_and_OSCAR_Sponsors.png"></img><br />
<a name="uofc"></a><br />
<a href="http://www.ucalgary.ca"><img style="width: 190px; padding: 25px 50px 0px 50px;" src="https://static.igem.org/mediawiki/2011/b/b7/UCalgary_Logo_Small.png"></img></a><br />
<a href="http://www.ucalgary.ca/bhsc"><img style="clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2011/c/c7/UCalgary_BHSc_Logo.png"></img></a><br />
<a href="http://bio.ucalgary.ca/"><img style="width: 215px; clear:both; margin-top: -20px; margin-left: -10px;" src="https://static.igem.org/mediawiki/2012/4/47/UCalgary2012_BioSci_Logo.JPG"></img></a><br />
<a href="http://enel.ucalgary.ca"><img style="width: 250px; clear:both; margin-top: -20px; margin-left: -20px; margin-bottom: -10px;" src="https://static.igem.org/mediawiki/2012/e/e6/UCalgary2012_Schulich_Electric_Computer_Logo.jpg"></img></a><br />
<br />
<h2>University of Calgary and the O'Brien Centre for the BHSc</h2><br />
<p>We graciously thank the Department of Cell Biology and Anatomy, the Department of Electrical and Computer Engineering, the Centre for Bioengineering Research and Education and the Department of Biological Sciences for all their support. We also wish to thank the Faculty of Medicine for their additional support as well. Additionally, we wish to thank the office of the Vice President of Research for their generous support.</p> <br />
<p>The O'Brien Centre for the Bachelor of Health Sciences is a part of the University of Calgary, located in the Foothills campus. It is responsible for providing iGEM team with lab space as well as funding. The O’Brien Centre was founded in part by a generous $5-million donation by David and Gail O’ Brien, after whom the Centre was named. David O'Brien has been a member of the University's Board of Governors, while Gail O'Brien has chaired the Faculty of Medicine's Dean's Advisory Council. The O’Brien Centre is the hub of top-notch research, interdisciplinary research, and education. It is responsible for providing approximately $9-million/year for researchers. The 2012 iGEM team thanks O’Brien Centre for its generous contribution of the O’Brien Centre Summer Studentship as well as lab space this year.</p><br />
<p>The Department of Biological Sciences at the University of Calgary is a community of scholars who share a commitment to insightful, innovative and integrative research in diverse areas of life sciences, from biomolecules to the biosphere, and to the development of future leaders in the basic and applied biological sciences through excellence in our undergraduate and graduate programs.</p><br />
<p>The Department of Electrical and Computer Engineering in the Schulich School of Engineering offers both undergraduate and graduate degree programs. The Department is highly regarded internationally for its leadership in biomedical engineering, radio systems, software engineering, micro- and nano-scale systems, and power and energy research.</p><br />
<a href="http://www.albertatechfutures.ca/"><img src="https://static.igem.org/mediawiki/2011/3/3f/UCalgary2011_AITF_Logo_Small.png"></img></a><br />
<br />
<h2>Alberta Innovates Technology Futures</h2><br />
<p>Alberta Innovates Technology Futures facilitates the growth of technical industries by supporting quality research in Alberta's particular fields of expertise. These include nanotechnology, information communication technology, and genomics. AITF works in joint effort with entrepreneurs and researchers to ensure that Alberta’s technologies can be sustained at a business level through commercialization and growth. This is accomplished by ensuring that useful products, protocols and services are delivered to meet global demands.</p><br />
<br />
<a href="http://www.osli.ca/"><img style="width:200px;" src="https://static.igem.org/mediawiki/2012/2/27/Ucalgary2012_Full_OSLI_Swirl.png"></a><br />
<a href="http://www.osrin.ualberta.ca/"><img style="clear: both; width: 200px;" src="https://static.igem.org/mediawiki/2011/9/9a/UCalgary_OSRIN_Logo.png"></img></a><br />
<h2>OSLI/OSRIN</h2><br />
<p>The Oil Sands Leadership Initiative (OSLI) and the Oil Sands Research and Information Network (OSRIN) are graciously supporting iGEM this year. OSLI is a collaborative network between Nexen Inc., ConocoPhillips Canada, Statoil Canada, Suncor Energy Inc., and Total E&P Canada. OSLI strives to improve the reputation of the oil sands and lead the industry to responsible development of Alberta's bitument resources.</p><br />
<p>OSRIN is an independent organization within the School of Energy and Environment at the University of Alberta. OSRIN compiles, interprets, analyzes, and communicates data to and from oil sands mining and the area surrounding them. The organization strives for a future where Alberta can economically benefit from oil sands development without harming the environment.</p><br />
<br/><br/><br/><br />
<a href="http://www.vwr.com/"><img style="margin-bottom: 5px; height: 90px;" src="https://static.igem.org/mediawiki/2011/6/65/UCalgary_VWR_Logo.png"></img></a><br />
<br />
<h2>VWR</h2><br />
<p>VWR International is one of the world leaders in the distribution of laboratory materials. There are currently over 250 000 customers in North America and Europe, which is quite large for a biotechnology distributor. They are based in West Chester, Pennsylvania and specialize in the supply of chemicals, equipment, instruments, lab apparel, and lab furniture. They have many offices based worldwide from Northern Ireland to Switzerland and even one based in Singapore. The unique guarantee that they offer is the shipping of ordered material within 24 hours, due to large quantities of stock and many distribution offices in various countries. They have been a significant sponsor of our iGEM team in the past and we appreciate their contribution to our team this year.</p><br />
<br />
<br />
<a href="http://www.neb.com/nebecomm/default.asp"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2011/d/d6/UCalgary_NEB_Logo.png"></img></a><br />
<br />
<h2>New England Biolabs</h2><br />
<p>For over 30 years, New England Biolabs has led the industry in the discovery and production of enzymes for molecular biology applications. At NEB, enzyme production is linked to basic research in the cloning and overexpression of restriction/modification systems. Their focus on providing the largest selection of recombinant enzymes has resulted in lower dollar-per-unit costs and improved purity and consistency of product. Presently, NEB supplies more than 240 restriction enzymes, over 160 of which are available in recombinant form, as well as numerous recombinant DNA and protein modifying enzymes.</p><br />
<a href="http://www.sarstedt.com/php/main.php"><img style="height:50px;" src="https://static.igem.org/mediawiki/2011/e/ee/UCalgary_Sarstedt_Logo.png"></img></a><br />
<br />
<h2>Sarstedt</h2><br />
<p>The Sarstedt Group develops, manufactures and sells equipment and consumables in the field of medicine and research. Ever since it was set up in 1961 the company has continued to grow to the point where it now employs a workforce of 2,500. They produce consumables and analytical equipment for medical diagnostics and consumables for use in medical patient care as well as for research laboratories and also for environmental analytical work. The Sarstedt group manufactures their own products at their own production sites as well as develops concepts and finished products in their own R&D centre.</p><br />
<a href="http://www.eurofins.com/en.aspx"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a><br />
<h2>Eurofins MWG Operon</h2><br />
<p>Eurofins MWG Operon, founded in 1990 and member of the Eurofins Group, is an international provider of genomic services established around the core business lines next generation sequencing, custom DNA sequencing, oligonucleotides, siRNA and gene synthesis. The company's main mission is focussed on customer convenience and high quality services in industrial scale for the life science industries and academic research institutions around the world.</p><br />
<a href="http://www.sparkscience.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a><br />
<br />
<h2>Telus Spark</h2><br />
<p>The culmination of over a decade of planning, design and construction to bring Calgary’s new Science Centre to life will light a spark of wonder and excitement in Southern Alberta. Facilitators will fuel curiosity. Exhibits and programs will ignite a sense of wonder and excitement. Conferences and events will act as a catalyst for innovation and new ideas. TELUS Spark is a place for people of all ages and abilities to let go and embrace the desire to explore and discover science, technology and art in a way that their normal day-to-day life doesn’t allow for.</p><br />
<a href="http://www.idtdna.com/site"><img src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a><br />
<br />
<h2>IDT (Integrated DNA Technologies)</h2><br />
<p>Integrated DNA Technologies (IDT) is a leader in manufacturing and developing products for the research and diagnostic life science market. IDT serves the areas of academic research, biotechnology, and pharmaceutical development. Founded by Dr. Joseph Walder in 1987, IDT’s development has been guided by an uncompromising approach to quality, a belief in the value of good service, and a determination to minimize consumer costs. IDT now has over 500 employees and ships over 20,000 oligos per day. <br />
<br />
Serving over 70,000 life sciences researchers, IDT is widely recognized as the industry leader in custom oligonucleotides. </p><br />
<a href="http://genomealberta.ca/"><img src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></img></a><br />
<br />
<h2>Genome Alberta</h2><br />
<p>In partnership with Genome Canada Industry Canada and the Province of Alberta, Genome Alberta was established in 2005. They are a publicly funded non-profit corporation that initiates, funds, and manages genomics research and partnerships. <br />
Genome Alberta strives to be the leading source of information and administration related to genomics, proteomics, bioinformatics and bioethics research in Alberta. Genome Alberta is dedicated to informing students, researchers, research organizations, our partners, and the public regarding opportunities and challenges in genomics and proteomics, and in encouraging the development of a Life Sciences research industry in Alberta. <br />
</p><br />
<br />
<br />
<a href="http://www.teamlab.com/"><img style="width: 130px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a><br />
<br />
<h2>Team Lab</h2><br />
<p>TeamLab is a multifunctional online service for business collaboration, document and project management. It has been developed by Ascensio System SIA, a fast-growing company that offers IT-solutions for personal and corporate use.<br />
TeamLab was founded on the idea of making social networking and project management efficient. It combines a wide range of features that assist a company team to work as one organism at solving common tasks and achieving results.<br />
</p><br />
<br />
<a href="http://www.mhc.ab.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a><br />
<br />
<h2>Medicine Hat College</h2><br />
<p>Medicine Hat College is a public, board governed, comprehensive community college serving a large region of southeastern Alberta and southwestern Saskatchewan, Canada. The MHC is located in the city of Medicine Hat, Alberta, Canada. MHC has been serving students in southeastern Alberta and beyond since 1965. MHC’s main campus services almost 2,500 students each year with another 200 attending Brooks Campus, located 100 km west of Medicine Hat. Currently, more than 30 diplomas and certificates are offered along with 25 university transfer programs. There are also several opportunities for degree completion at MHC including nursing, applied arts, and social work. A partnership with the University of Calgary makes it possible for nursing students to complete a full bachelor’s degree at Medicine Hat College while graduates from diploma programs such as Police and Security may also complete degrees. Medicine Hat College offers other unique diploma programs such as Addictions Counselor, Technical Illustrator, Paramedic, and Deaf and Blind Support Specialist. New applied degrees are also offered in Ecotourism and Outdoor Leadership and Visual Communications.<br />
</p><br />
<br />
<a href="http://www.hyperionlab.ca/"><img style="width: 190px;" src="https://static.igem.org/mediawiki/2012/d/df/UCalgary2012_Hyperion_Research_Logo.png"></img></a><br />
<br />
<h2>Hyperion Research Ltd.</h2><br />
<p>Hyperion Research Ltd., specializes in the analysis of water and sewage samples for the protozoan parasites <i>Giardia</i> and <i>Cryptosporidium</i>. They also provide sampling equipment and analysis for the Microscopic Particulate Analysis to determine Groundwater Under the Direct Influence (GUDI) of surface water. Hyperion's laboratory is located in Medicine Hat, Alberta, and where they serve the water treatment industry across Canada. Hyperion is also active in research into waterborne disease problems and has numerous international contacts.<br />
</p><br />
<br />
</body><br />
<br />
</html><br />
<br />
}}</div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_Hyperion_Research_Logo.pngFile:UCalgary2012 Hyperion Research Logo.png2012-10-26T04:45:09Z<p>Iaingeorge: </p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/File:UCalgary2011_Medicine_Hat_College_Logo.pngFile:UCalgary2011 Medicine Hat College Logo.png2012-10-26T04:43:33Z<p>Iaingeorge: uploaded a new version of &quot;File:UCalgary2011 Medicine Hat College Logo.png&quot;</p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/Team:Calgary/SponsorsTeam:Calgary/Sponsors2012-10-26T04:30:02Z<p>Iaingeorge: </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|sponsors|<br />
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TITLE=Sponsors|<br />
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<p>The University of Calgary's 2012 iGEM Team would like to thank all of our generous sponsors! </p><br />
<head><br />
<style><br />
#bodycontainer img{<br />
float: right;<br />
margin: 15px 15px 5px 15px;<br />
padding-top: 15px;<br />
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<body><br />
<img style="display: block; margin: auto; padding: 0;float: none;" src="https://static.igem.org/mediawiki/2012/6/65/UCalgary2012_FRED_and_OSCAR_Sponsors.png"></img><br />
<a name="uofc"></a><br />
<a href="http://www.ucalgary.ca"><img style="width: 190px; padding: 25px 50px 0px 50px;" src="https://static.igem.org/mediawiki/2011/b/b7/UCalgary_Logo_Small.png"></img></a><br />
<a href="http://www.ucalgary.ca/bhsc"><img style="clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2011/c/c7/UCalgary_BHSc_Logo.png"></img></a><br />
<a href="http://bio.ucalgary.ca/"><img style="width: 215px; clear:both; margin-top: -20px; margin-left: -10px;" src="https://static.igem.org/mediawiki/2012/4/47/UCalgary2012_BioSci_Logo.JPG"></img></a><br />
<a href="http://enel.ucalgary.ca"><img style="width: 250px; clear:both; margin-top: -20px; margin-left: -20px; margin-bottom: -10px;" src="https://static.igem.org/mediawiki/2012/e/e6/UCalgary2012_Schulich_Electric_Computer_Logo.jpg"></img></a><br />
<br />
<h2>University of Calgary and the O'Brien Centre for the BHSc</h2><br />
<p>We graciously thank the Department of Cell Biology and Anatomy, the Department of Electrical and Computer Engineering, the Centre for Bioengineering Research and Education and the Department of Biological Sciences for all their support. We also wish to thank the Faculty of Medicine for their additional support as well. Additionally, we wish to thank the office of the Vice President of Research for their generous support.</p> <br />
<p>The O'Brien Centre for the Bachelor of Health Sciences is a part of the University of Calgary, located in the Foothills campus. It is responsible for providing iGEM team with lab space as well as funding. The O’Brien Centre was founded in part by a generous $5-million donation by David and Gail O’ Brien, after whom the Centre was named. David O'Brien has been a member of the University's Board of Governors, while Gail O'Brien has chaired the Faculty of Medicine's Dean's Advisory Council. The O’Brien Centre is the hub of top-notch research, interdisciplinary research, and education. It is responsible for providing approximately $9-million/year for researchers. The 2012 iGEM team thanks O’Brien Centre for its generous contribution of the O’Brien Centre Summer Studentship as well as lab space this year.</p><br />
<p>The Department of Biological Sciences at the University of Calgary is a community of scholars who share a commitment to insightful, innovative and integrative research in diverse areas of life sciences, from biomolecules to the biosphere, and to the development of future leaders in the basic and applied biological sciences through excellence in our undergraduate and graduate programs.</p><br />
<p>The Department of Electrical and Computer Engineering in the Schulich School of Engineering offers both undergraduate and graduate degree programs. The Department is highly regarded internationally for its leadership in biomedical engineering, radio systems, software engineering, micro- and nano-scale systems, and power and energy research.</p><br />
<a href="http://www.albertatechfutures.ca/"><img src="https://static.igem.org/mediawiki/2011/3/3f/UCalgary2011_AITF_Logo_Small.png"></img></a><br />
<br />
<h2>Alberta Innovates Technology Futures</h2><br />
<p>Alberta Innovates Technology Futures facilitates the growth of technical industries by supporting quality research in Alberta's particular fields of expertise. These include nanotechnology, information communication technology, and genomics. AITF works in joint effort with entrepreneurs and researchers to ensure that Alberta’s technologies can be sustained at a business level through commercialization and growth. This is accomplished by ensuring that useful products, protocols and services are delivered to meet global demands.</p><br />
<br />
<a href="http://www.osli.ca/"><img style="width:200px;" src="https://static.igem.org/mediawiki/2012/2/27/Ucalgary2012_Full_OSLI_Swirl.png"></a><br />
<a href="http://www.osrin.ualberta.ca/"><img style="clear: both; width: 200px;" src="https://static.igem.org/mediawiki/2011/9/9a/UCalgary_OSRIN_Logo.png"></img></a><br />
<h2>OSLI/OSRIN</h2><br />
<p>The Oil Sands Leadership Initiative (OSLI) and the Oil Sands Research and Information Network (OSRIN) are graciously supporting iGEM this year. OSLI is a collaborative network between Nexen Inc., ConocoPhillips Canada, Statoil Canada, Suncor Energy Inc., and Total E&P Canada. OSLI strives to improve the reputation of the oil sands and lead the industry to responsible development of Alberta's bitument resources.</p><br />
<p>OSRIN is an independent organization within the School of Energy and Environment at the University of Alberta. OSRIN compiles, interprets, analyzes, and communicates data to and from oil sands mining and the area surrounding them. The organization strives for a future where Alberta can economically benefit from oil sands development without harming the environment.</p><br />
<br/><br/><br/><br />
<a href="http://www.vwr.com/"><img style="margin-bottom: 5px; height: 90px;" src="https://static.igem.org/mediawiki/2011/6/65/UCalgary_VWR_Logo.png"></img></a><br />
<br />
<h2>VWR</h2><br />
<p>VWR International is one of the world leaders in the distribution of laboratory materials. There are currently over 250 000 customers in North America and Europe, which is quite large for a biotechnology distributor. They are based in West Chester, Pennsylvania and specialize in the supply of chemicals, equipment, instruments, lab apparel, and lab furniture. They have many offices based worldwide from Northern Ireland to Switzerland and even one based in Singapore. The unique guarantee that they offer is the shipping of ordered material within 24 hours, due to large quantities of stock and many distribution offices in various countries. They have been a significant sponsor of our iGEM team in the past and we appreciate their contribution to our team this year.</p><br />
<br />
<br />
<a href="http://www.neb.com/nebecomm/default.asp"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2011/d/d6/UCalgary_NEB_Logo.png"></img></a><br />
<br />
<h2>New England Biolabs</h2><br />
<p>For over 30 years, New England Biolabs has led the industry in the discovery and production of enzymes for molecular biology applications. At NEB, enzyme production is linked to basic research in the cloning and overexpression of restriction/modification systems. Their focus on providing the largest selection of recombinant enzymes has resulted in lower dollar-per-unit costs and improved purity and consistency of product. Presently, NEB supplies more than 240 restriction enzymes, over 160 of which are available in recombinant form, as well as numerous recombinant DNA and protein modifying enzymes.</p><br />
<a href="http://www.sarstedt.com/php/main.php"><img style="height:50px;" src="https://static.igem.org/mediawiki/2011/e/ee/UCalgary_Sarstedt_Logo.png"></img></a><br />
<br />
<h2>Sarstedt</h2><br />
<p>The Sarstedt Group develops, manufactures and sells equipment and consumables in the field of medicine and research. Ever since it was set up in 1961 the company has continued to grow to the point where it now employs a workforce of 2,500. They produce consumables and analytical equipment for medical diagnostics and consumables for use in medical patient care as well as for research laboratories and also for environmental analytical work. The Sarstedt group manufactures their own products at their own production sites as well as develops concepts and finished products in their own R&D centre.</p><br />
<a href="http://www.eurofins.com/en.aspx"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a><br />
<h2>Eurofins MWG Operon</h2><br />
<p>Eurofins MWG Operon, founded in 1990 and member of the Eurofins Group, is an international provider of genomic services established around the core business lines next generation sequencing, custom DNA sequencing, oligonucleotides, siRNA and gene synthesis. The company's main mission is focussed on customer convenience and high quality services in industrial scale for the life science industries and academic research institutions around the world.</p><br />
<a href="http://www.sparkscience.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a><br />
<br />
<h2>Telus Spark</h2><br />
<p>The culmination of over a decade of planning, design and construction to bring Calgary’s new Science Centre to life will light a spark of wonder and excitement in Southern Alberta. Facilitators will fuel curiosity. Exhibits and programs will ignite a sense of wonder and excitement. Conferences and events will act as a catalyst for innovation and new ideas. TELUS Spark is a place for people of all ages and abilities to let go and embrace the desire to explore and discover science, technology and art in a way that their normal day-to-day life doesn’t allow for.</p><br />
<a href="http://www.idtdna.com/site"><img src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a><br />
<br />
<h2>IDT (Integrated DNA Technologies)</h2><br />
<p>Integrated DNA Technologies (IDT) is a leader in manufacturing and developing products for the research and diagnostic life science market. IDT serves the areas of academic research, biotechnology, and pharmaceutical development. Founded by Dr. Joseph Walder in 1987, IDT’s development has been guided by an uncompromising approach to quality, a belief in the value of good service, and a determination to minimize consumer costs. IDT now has over 500 employees and ships over 20,000 oligos per day. <br />
<br />
Serving over 70,000 life sciences researchers, IDT is widely recognized as the industry leader in custom oligonucleotides. </p><br />
<a href="http://genomealberta.ca/"><img src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></img></a><br />
<br />
<h2>Genome Alberta</h2><br />
<p>In partnership with Genome Canada Industry Canada and the Province of Alberta, Genome Alberta was established in 2005. They are a publicly funded non-profit corporation that initiates, funds, and manages genomics research and partnerships. <br />
Genome Alberta strives to be the leading source of information and administration related to genomics, proteomics, bioinformatics and bioethics research in Alberta. Genome Alberta is dedicated to informing students, researchers, research organizations, our partners, and the public regarding opportunities and challenges in genomics and proteomics, and in encouraging the development of a Life Sciences research industry in Alberta. <br />
</p><br />
<br />
<br />
<a href="http://www.teamlab.com/"><img style="width: 130px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a><br />
<br />
<h2>Team Lab</h2><br />
<p>TeamLab is a multifunctional online service for business collaboration, document and project management. It has been developed by Ascensio System SIA, a fast-growing company that offers IT-solutions for personal and corporate use.<br />
TeamLab was founded on the idea of making social networking and project management efficient. It combines a wide range of features that assist a company team to work as one organism at solving common tasks and achieving results.<br />
</p><br />
<br />
<a href="http://www.mhc.ab.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a><br />
<br />
<h2>Medicine Hat College</h2><br />
<p>Medicine Hat College is a public, board governed, comprehensive community college serving a large region of southeastern Alberta and southwestern Saskatchewan, Canada. The MHC is located in the city of Medicine Hat, Alberta, Canada. MHC has been serving students in southeastern Alberta and beyond since 1965. MHC’s main campus services almost 2,500 students each year with another 200 attending Brooks Campus, located 100 km west of Medicine Hat. Currently, more than 30 diplomas and certificates are offered along with 25 university transfer programs. There are also several opportunities for degree completion at MHC including nursing, applied arts, and social work. A partnership with the University of Calgary makes it possible for nursing students to complete a full bachelor’s degree at Medicine Hat College while graduates from diploma programs such as Police and Security may also complete degrees. Medicine Hat College offers other unique diploma programs such as Addictions Counselor, Technical Illustrator, Paramedic, and Deaf and Blind Support Specialist. New applied degrees are also offered in Ecotourism and Outdoor Leadership and Visual Communications.<br />
</p><br />
<br />
<a href="http://www.hyperionlab.ca/"><img style="width: 190px;" src="https://static.igem.org/mediawiki/2012/d/df/UCalgary2012_Hyperion_Research_Logo.jpg"></img></a><br />
<br />
<h2>Hyperion Research Ltd.</h2><br />
<p>Hyperion Research Ltd., specializes in the analysis of water and sewage samples for the protozoan parasites <i>Giardia</i> and <i>Cryptosporidium</i>. They also provide sampling equipment and analysis for the Microscopic Particulate Analysis to determine Groundwater Under the Direct Influence (GUDI) of surface water. Hyperion's laboratory is located in Medicine Hat, Alberta, and where they serve the water treatment industry across Canada. Hyperion is also active in research into waterborne disease problems and has numerous international contacts.<br />
</p><br />
<br />
</body><br />
<br />
</html><br />
<br />
}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/SponsorsTeam:Calgary/Sponsors2012-10-25T06:23:31Z<p>Iaingeorge: </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|sponsors|<br />
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SIDELIST=<br />
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CONTENT=<br />
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<p>The University of Calgary's 2012 iGEM Team would like to thank all of our generous sponsors! </p><br />
<head><br />
<style><br />
#bodycontainer img{<br />
float: right;<br />
margin: 15px 15px 5px 15px;<br />
padding-top: 15px;<br />
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<body><br />
<img style="display: block; margin: auto; padding: 0;float: none;" src="https://static.igem.org/mediawiki/2012/6/65/UCalgary2012_FRED_and_OSCAR_Sponsors.png"></img><br />
<a name="uofc"></a><br />
<a href="http://www.ucalgary.ca"><img style="width: 190px; padding: 25px 50px 0px 50px;" src="https://static.igem.org/mediawiki/2011/b/b7/UCalgary_Logo_Small.png"></img></a><br />
<a href="http://www.ucalgary.ca/bhsc"><img style="clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2011/c/c7/UCalgary_BHSc_Logo.png"></img></a><br />
<a href="http://bio.ucalgary.ca/"><img style="width: 250px; clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2012/4/47/UCalgary2012_BioSci_Logo.JPG"></img></a><br />
<a href="http://enel.ucalgary.ca"><img style="width: 250px; clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2012/e/e6/UCalgary2012_Schulich_Electric_Computer_Logo.jpg"></img></a><br />
<br />
<h2>University of Calgary and the O'Brien Centre for the BHSc</h2><br />
<p>We graciously thank the Department of Cell Biology and Anatomy, the Department of Electrical and Computer Engineering, the Centre for Bioengineering Research and Education and the Department of Biological Sciences for all their support. We also wish to thank the Faculty of Medicine for their additional support as well. Additionally, we wish to thank the office of the Vice President of Research for their generous support.</p> <br />
<p>The O'Brien Centre for the Bachelor of Health Sciences is a part of the University of Calgary, located in the Foothills campus. It is responsible for providing iGEM team with lab space as well as funding. The O’Brien Centre was founded in part by a generous $5-million donation by David and Gail O’ Brien, after whom the Centre was named. David O'Brien has been a member of the University's Board of Governors, while Gail O'Brien has chaired the Faculty of Medicine's Dean's Advisory Council. The O’Brien Centre is the hub of top-notch research, interdisciplinary research, and education. It is responsible for providing approximately $9-million/year for researchers. The 2012 iGEM team thanks O’Brien Centre for its generous contribution of the O’Brien Centre Summer Studentship as well as lab space this year.</p><br />
<br />
<a href="http://www.albertatechfutures.ca/"><img src="https://static.igem.org/mediawiki/2011/3/3f/UCalgary2011_AITF_Logo_Small.png"></img></a><br />
<br />
<h2>Alberta Innovates Technology Futures</h2><br />
<p>Alberta Innovates Technology Futures facilitates the growth of technical industries by supporting quality research in Alberta's particular fields of expertise. These include nanotechnology, information communication technology, and genomics. AITF works in joint effort with entrepreneurs and researchers to ensure that Alberta’s technologies can be sustained at a business level through commercialization and growth. This is accomplished by ensuring that useful products, protocols and services are delivered to meet global demands.</p><br />
<br />
<a href="http://www.osli.ca/"><img style="width:200px;" src="https://static.igem.org/mediawiki/2012/2/27/Ucalgary2012_Full_OSLI_Swirl.png"></a><br />
<a href="http://www.osrin.ualberta.ca/"><img style="clear: both; width: 200px;" src="https://static.igem.org/mediawiki/2011/9/9a/UCalgary_OSRIN_Logo.png"></img></a><br />
<h2>OSLI/OSRIN</h2><br />
<p>The Oil Sands Leadership Initiative (OSLI) and the Oil Sands Research and Information Network (OSRIN) are graciously supporting iGEM this year. OSLI is a collaborative network between Nexen Inc., ConocoPhillips Canada, Statoil Canada, Suncor Energy Inc., and Total E&P Canada. OSLI strives to improve the reputation of the oil sands and lead the industry to responsible development of Alberta's bitument resources.</p><br />
<p>OSRIN is an independent organization within the School of Energy and Environment at the University of Alberta. OSRIN compiles, interprets, analyzes, and communicates data to and from oil sands mining and the area surrounding them. The organization strives for a future where Alberta can economically benefit from oil sands development without harming the environment.</p><br />
<br/><br/><br/><br />
<a href="http://www.vwr.com/"><img style="margin-bottom: 5px; height: 90px;" src="https://static.igem.org/mediawiki/2011/6/65/UCalgary_VWR_Logo.png"></img></a><br />
<br />
<h2>VWR</h2><br />
<p>VWR International is one of the world leaders in the distribution of laboratory materials. There are currently over 250 000 customers in North America and Europe, which is quite large for a biotechnology distributor. They are based in West Chester, Pennsylvania and specialize in the supply of chemicals, equipment, instruments, lab apparel, and lab furniture. They have many offices based worldwide from Northern Ireland to Switzerland and even one based in Singapore. The unique guarantee that they offer is the shipping of ordered material within 24 hours, due to large quantities of stock and many distribution offices in various countries. They have been a significant sponsor of our iGEM team in the past and we appreciate their contribution to our team this year.</p><br />
<br />
<br />
<a href="http://www.neb.com/nebecomm/default.asp"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2011/d/d6/UCalgary_NEB_Logo.png"></img></a><br />
<br />
<h2>New England Biolabs</h2><br />
<p>For over 30 years, New England Biolabs has led the industry in the discovery and production of enzymes for molecular biology applications. At NEB, enzyme production is linked to basic research in the cloning and overexpression of restriction/modification systems. Their focus on providing the largest selection of recombinant enzymes has resulted in lower dollar-per-unit costs and improved purity and consistency of product. Presently, NEB supplies more than 240 restriction enzymes, over 160 of which are available in recombinant form, as well as numerous recombinant DNA and protein modifying enzymes.</p><br />
<a href="http://www.sarstedt.com/php/main.php"><img style="height:50px;" src="https://static.igem.org/mediawiki/2011/e/ee/UCalgary_Sarstedt_Logo.png"></img></a><br />
<br />
<h2>Sarstedt</h2><br />
<p>The Sarstedt Group develops, manufactures and sells equipment and consumables in the field of medicine and research. Ever since it was set up in 1961 the company has continued to grow to the point where it now employs a workforce of 2,500. They produce consumables and analytical equipment for medical diagnostics and consumables for use in medical patient care as well as for research laboratories and also for environmental analytical work. The Sarstedt group manufactures their own products at their own production sites as well as develops concepts and finished products in their own R&D centre.</p><br />
<a href="http://www.eurofins.com/en.aspx"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a><br />
<h2>Eurofins MWG Operon</h2><br />
<p>Eurofins MWG Operon, founded in 1990 and member of the Eurofins Group, is an international provider of genomic services established around the core business lines next generation sequencing, custom DNA sequencing, oligonucleotides, siRNA and gene synthesis. The company's main mission is focussed on customer convenience and high quality services in industrial scale for the life science industries and academic research institutions around the world.</p><br />
<a href="http://www.sparkscience.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a><br />
<br />
<h2>Telus Spark</h2><br />
<p>The culmination of over a decade of planning, design and construction to bring Calgary’s new Science Centre to life will light a spark of wonder and excitement in Southern Alberta. Facilitators will fuel curiosity. Exhibits and programs will ignite a sense of wonder and excitement. Conferences and events will act as a catalyst for innovation and new ideas. TELUS Spark is a place for people of all ages and abilities to let go and embrace the desire to explore and discover science, technology and art in a way that their normal day-to-day life doesn’t allow for.</p><br />
<a href="http://www.idtdna.com/site"><img src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a><br />
<br />
<h2>IDT (Integrated DNA Technologies)</h2><br />
<p>Integrated DNA Technologies (IDT) is a leader in manufacturing and developing products for the research and diagnostic life science market. IDT serves the areas of academic research, biotechnology, and pharmaceutical development. Founded by Dr. Joseph Walder in 1987, IDT’s development has been guided by an uncompromising approach to quality, a belief in the value of good service, and a determination to minimize consumer costs. IDT now has over 500 employees and ships over 20,000 oligos per day. <br />
<br />
Serving over 70,000 life sciences researchers, IDT is widely recognized as the industry leader in custom oligonucleotides. </p><br />
<a href="http://genomealberta.ca/"><img src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></img></a><br />
<br />
<h2>Genome Alberta</h2><br />
<p>In partnership with Genome Canada Industry Canada and the Province of Alberta, Genome Alberta was established in 2005. They are a publicly funded non-profit corporation that initiates, funds, and manages genomics research and partnerships. <br />
Genome Alberta strives to be the leading source of information and administration related to genomics, proteomics, bioinformatics and bioethics research in Alberta. Genome Alberta is dedicated to informing students, researchers, research organizations, our partners, and the public regarding opportunities and challenges in genomics and proteomics, and in encouraging the development of a Life Sciences research industry in Alberta. <br />
</p><br />
<br />
<br />
<a href="http://www.teamlab.com/"><img style="width: 130px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a><br />
<br />
<h2>Team Lab</h2><br />
<p>TeamLab is a multifunctional online service for business collaboration, document and project management. It has been developed by Ascensio System SIA, a fast-growing company that offers IT-solutions for personal and corporate use.<br />
TeamLab was founded on the idea of making social networking and project management efficient. It combines a wide range of features that assist a company team to work as one organism at solving common tasks and achieving results.<br />
</p><br />
<br />
<a href="http://www.mhc.ab.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a><br />
<br />
<h2>Medicine Hat College</h2><br />
<p>Medicine Hat College is a public, board governed, comprehensive community college serving a large region of southeastern Alberta and southwestern Saskatchewan, Canada. The MHC is located in the city of Medicine Hat, Alberta, Canada. MHC has been serving students in southeastern Alberta and beyond since 1965. MHC’s main campus services almost 2,500 students each year with another 200 attending Brooks Campus, located 100 km west of Medicine Hat. Currently, more than 30 diplomas and certificates are offered along with 25 university transfer programs. There are also several opportunities for degree completion at MHC including nursing, applied arts, and social work. A partnership with the University of Calgary makes it possible for nursing students to complete a full bachelor’s degree at Medicine Hat College while graduates from diploma programs such as Police and Security may also complete degrees. Medicine Hat College offers other unique diploma programs such as Addictions Counselor, Technical Illustrator, Paramedic, and Deaf and Blind Support Specialist. New applied degrees are also offered in Ecotourism and Outdoor Leadership and Visual Communications.<br />
</p><br />
<br />
<a href="http://www.hyperionlab.ca/"><img style="width: 190px;" src="https://static.igem.org/mediawiki/2012/d/df/UCalgary2012_Hyperion_Research_Logo.jpg"></img></a><br />
<br />
<h2>Hyperion Research Ltd.</h2><br />
<p>Hyperion Research Ltd., specializes in the analysis of water and sewage samples for the protozoan parasites <i>Giardia</i> and <i>Cryptosporidium</i>. They also provide sampling equipment and analysis for the Microscopic Particulate Analysis to determine Groundwater Under the Direct Influence (GUDI) of surface water. Hyperion's laboratory is located in Medicine Hat, Alberta, and where they serve the water treatment industry across Canada. Hyperion is also active in research into waterborne disease problems and has numerous international contacts.<br />
</p><br />
<br />
</body><br />
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</html><br />
<br />
}}</div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_Schulich_Electric_Computer_Logo.jpgFile:UCalgary2012 Schulich Electric Computer Logo.jpg2012-10-25T06:21:43Z<p>Iaingeorge: </p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/Team:Calgary/SponsorsTeam:Calgary/Sponsors2012-10-25T06:11:13Z<p>Iaingeorge: </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|sponsors|<br />
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TITLE=Sponsors|<br />
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<p>The University of Calgary's 2012 iGEM Team would like to thank all of our generous sponsors! </p><br />
<head><br />
<style><br />
#bodycontainer img{<br />
float: right;<br />
margin: 15px 15px 5px 15px;<br />
padding-top: 15px;<br />
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<img style="display: block; margin: auto; padding: 0;float: none;" src="https://static.igem.org/mediawiki/2012/6/65/UCalgary2012_FRED_and_OSCAR_Sponsors.png"></img><br />
<a name="uofc"></a><br />
<a href="http://www.ucalgary.ca"><img style="width: 190px; padding: 25px 50px 0px 50px;" src="https://static.igem.org/mediawiki/2011/b/b7/UCalgary_Logo_Small.png"></img></a><br />
<a href="http://www.ucalgary.ca/bhsc"><img style="clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2011/c/c7/UCalgary_BHSc_Logo.png"></img></a><br />
<a href="http://bio.ucalgary.ca/"><img style="width: 250px; clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2012/4/47/UCalgary2012_BioSci_Logo.JPG"></img></a><br />
<h2>University of Calgary and the O'Brien Centre for the BHSc</h2><br />
<p>We graciously thank the Department of Cell Biology and Anatomy, the Department of Electrical and Computer Engineering, the Centre for Bioengineering Research and Education and the Department of Biological Sciences for all their support. We also wish to thank the Faculty of Medicine for their additional support as well. Additionally, we wish to thank the office of the Vice President of Research for their generous support.</p> <br />
<p>The O'Brien Centre for the Bachelor of Health Sciences is a part of the University of Calgary, located in the Foothills campus. It is responsible for providing iGEM team with lab space as well as funding. The O’Brien Centre was founded in part by a generous $5-million donation by David and Gail O’ Brien, after whom the Centre was named. David O'Brien has been a member of the University's Board of Governors, while Gail O'Brien has chaired the Faculty of Medicine's Dean's Advisory Council. The O’Brien Centre is the hub of top-notch research, interdisciplinary research, and education. It is responsible for providing approximately $9-million/year for researchers. The 2012 iGEM team thanks O’Brien Centre for its generous contribution of the O’Brien Centre Summer Studentship as well as lab space this year.</p><br />
<br />
<a href="http://www.albertatechfutures.ca/"><img src="https://static.igem.org/mediawiki/2011/3/3f/UCalgary2011_AITF_Logo_Small.png"></img></a><br />
<br />
<h2>Alberta Innovates Technology Futures</h2><br />
<p>Alberta Innovates Technology Futures facilitates the growth of technical industries by supporting quality research in Alberta's particular fields of expertise. These include nanotechnology, information communication technology, and genomics. AITF works in joint effort with entrepreneurs and researchers to ensure that Alberta’s technologies can be sustained at a business level through commercialization and growth. This is accomplished by ensuring that useful products, protocols and services are delivered to meet global demands.</p><br />
<br />
<a href="http://www.osli.ca/"><img style="width:200px;" src="https://static.igem.org/mediawiki/2012/2/27/Ucalgary2012_Full_OSLI_Swirl.png"></a><br />
<a href="http://www.osrin.ualberta.ca/"><img style="clear: both; width: 200px;" src="https://static.igem.org/mediawiki/2011/9/9a/UCalgary_OSRIN_Logo.png"></img></a><br />
<h2>OSLI/OSRIN</h2><br />
<p>The Oil Sands Leadership Initiative (OSLI) and the Oil Sands Research and Information Network (OSRIN) are graciously supporting iGEM this year. OSLI is a collaborative network between Nexen Inc., ConocoPhillips Canada, Statoil Canada, Suncor Energy Inc., and Total E&P Canada. OSLI strives to improve the reputation of the oil sands and lead the industry to responsible development of Alberta's bitument resources.</p><br />
<p>OSRIN is an independent organization within the School of Energy and Environment at the University of Alberta. OSRIN compiles, interprets, analyzes, and communicates data to and from oil sands mining and the area surrounding them. The organization strives for a future where Alberta can economically benefit from oil sands development without harming the environment.</p><br />
<br/><br/><br/><br />
<a href="http://www.vwr.com/"><img style="margin-bottom: 5px; height: 90px;" src="https://static.igem.org/mediawiki/2011/6/65/UCalgary_VWR_Logo.png"></img></a><br />
<br />
<h2>VWR</h2><br />
<p>VWR International is one of the world leaders in the distribution of laboratory materials. There are currently over 250 000 customers in North America and Europe, which is quite large for a biotechnology distributor. They are based in West Chester, Pennsylvania and specialize in the supply of chemicals, equipment, instruments, lab apparel, and lab furniture. They have many offices based worldwide from Northern Ireland to Switzerland and even one based in Singapore. The unique guarantee that they offer is the shipping of ordered material within 24 hours, due to large quantities of stock and many distribution offices in various countries. They have been a significant sponsor of our iGEM team in the past and we appreciate their contribution to our team this year.</p><br />
<br />
<br />
<a href="http://www.neb.com/nebecomm/default.asp"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2011/d/d6/UCalgary_NEB_Logo.png"></img></a><br />
<br />
<h2>New England Biolabs</h2><br />
<p>For over 30 years, New England Biolabs has led the industry in the discovery and production of enzymes for molecular biology applications. At NEB, enzyme production is linked to basic research in the cloning and overexpression of restriction/modification systems. Their focus on providing the largest selection of recombinant enzymes has resulted in lower dollar-per-unit costs and improved purity and consistency of product. Presently, NEB supplies more than 240 restriction enzymes, over 160 of which are available in recombinant form, as well as numerous recombinant DNA and protein modifying enzymes.</p><br />
<a href="http://www.sarstedt.com/php/main.php"><img style="height:50px;" src="https://static.igem.org/mediawiki/2011/e/ee/UCalgary_Sarstedt_Logo.png"></img></a><br />
<br />
<h2>Sarstedt</h2><br />
<p>The Sarstedt Group develops, manufactures and sells equipment and consumables in the field of medicine and research. Ever since it was set up in 1961 the company has continued to grow to the point where it now employs a workforce of 2,500. They produce consumables and analytical equipment for medical diagnostics and consumables for use in medical patient care as well as for research laboratories and also for environmental analytical work. The Sarstedt group manufactures their own products at their own production sites as well as develops concepts and finished products in their own R&D centre.</p><br />
<a href="http://www.eurofins.com/en.aspx"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a><br />
<h2>Eurofins MWG Operon</h2><br />
<p>Eurofins MWG Operon, founded in 1990 and member of the Eurofins Group, is an international provider of genomic services established around the core business lines next generation sequencing, custom DNA sequencing, oligonucleotides, siRNA and gene synthesis. The company's main mission is focussed on customer convenience and high quality services in industrial scale for the life science industries and academic research institutions around the world.</p><br />
<a href="http://www.sparkscience.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a><br />
<br />
<h2>Telus Spark</h2><br />
<p>The culmination of over a decade of planning, design and construction to bring Calgary’s new Science Centre to life will light a spark of wonder and excitement in Southern Alberta. Facilitators will fuel curiosity. Exhibits and programs will ignite a sense of wonder and excitement. Conferences and events will act as a catalyst for innovation and new ideas. TELUS Spark is a place for people of all ages and abilities to let go and embrace the desire to explore and discover science, technology and art in a way that their normal day-to-day life doesn’t allow for.</p><br />
<a href="http://www.idtdna.com/site"><img src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a><br />
<br />
<h2>IDT (Integrated DNA Technologies)</h2><br />
<p>Integrated DNA Technologies (IDT) is a leader in manufacturing and developing products for the research and diagnostic life science market. IDT serves the areas of academic research, biotechnology, and pharmaceutical development. Founded by Dr. Joseph Walder in 1987, IDT’s development has been guided by an uncompromising approach to quality, a belief in the value of good service, and a determination to minimize consumer costs. IDT now has over 500 employees and ships over 20,000 oligos per day. <br />
<br />
Serving over 70,000 life sciences researchers, IDT is widely recognized as the industry leader in custom oligonucleotides. </p><br />
<a href="http://genomealberta.ca/"><img src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></img></a><br />
<br />
<h2>Genome Alberta</h2><br />
<p>In partnership with Genome Canada Industry Canada and the Province of Alberta, Genome Alberta was established in 2005. They are a publicly funded non-profit corporation that initiates, funds, and manages genomics research and partnerships. <br />
Genome Alberta strives to be the leading source of information and administration related to genomics, proteomics, bioinformatics and bioethics research in Alberta. Genome Alberta is dedicated to informing students, researchers, research organizations, our partners, and the public regarding opportunities and challenges in genomics and proteomics, and in encouraging the development of a Life Sciences research industry in Alberta. <br />
</p><br />
<br />
<br />
<a href="http://www.teamlab.com/"><img style="width: 130px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a><br />
<br />
<h2>Team Lab</h2><br />
<p>TeamLab is a multifunctional online service for business collaboration, document and project management. It has been developed by Ascensio System SIA, a fast-growing company that offers IT-solutions for personal and corporate use.<br />
TeamLab was founded on the idea of making social networking and project management efficient. It combines a wide range of features that assist a company team to work as one organism at solving common tasks and achieving results.<br />
</p><br />
<br />
<a href="http://www.mhc.ab.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a><br />
<br />
<h2>Medicine Hat College</h2><br />
<p>Medicine Hat College is a public, board governed, comprehensive community college serving a large region of southeastern Alberta and southwestern Saskatchewan, Canada. The MHC is located in the city of Medicine Hat, Alberta, Canada. MHC has been serving students in southeastern Alberta and beyond since 1965. MHC’s main campus services almost 2,500 students each year with another 200 attending Brooks Campus, located 100 km west of Medicine Hat. Currently, more than 30 diplomas and certificates are offered along with 25 university transfer programs. There are also several opportunities for degree completion at MHC including nursing, applied arts, and social work. A partnership with the University of Calgary makes it possible for nursing students to complete a full bachelor’s degree at Medicine Hat College while graduates from diploma programs such as Police and Security may also complete degrees. Medicine Hat College offers other unique diploma programs such as Addictions Counselor, Technical Illustrator, Paramedic, and Deaf and Blind Support Specialist. New applied degrees are also offered in Ecotourism and Outdoor Leadership and Visual Communications.<br />
</p><br />
<br />
<a href="http://www.hyperionlab.ca/"><img style="width: 190px;" src="https://static.igem.org/mediawiki/2012/d/df/UCalgary2012_Hyperion_Research_Logo.jpg"></img></a><br />
<br />
<h2>Hyperion Research Ltd.</h2><br />
<p>Hyperion Research Ltd., specializes in the analysis of water and sewage samples for the protozoan parasites <i>Giardia</i> and <i>Cryptosporidium</i>. They also provide sampling equipment and analysis for the Microscopic Particulate Analysis to determine Groundwater Under the Direct Influence (GUDI) of surface water. Hyperion's laboratory is located in Medicine Hat, Alberta, and where they serve the water treatment industry across Canada. Hyperion is also active in research into waterborne disease problems and has numerous international contacts.<br />
</p><br />
<br />
</body><br />
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}}</div>Iaingeorgehttp://2012.igem.org/Team:Calgary/SponsorsTeam:Calgary/Sponsors2012-10-25T03:54:46Z<p>Iaingeorge: </p>
<hr />
<div>{{Team:Calgary/MainHeader|<html><img src="https://static.igem.org/mediawiki/2012/c/c5/UCalgary2012_HeaderLogoOrange.png"></img></html>}}<br />
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<p>The University of Calgary's 2012 iGEM Team would like to thank all of our generous sponsors! </p><br />
<head><br />
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<body><br />
<img style="display: block; margin: auto; padding: 0;float: none;" src="https://static.igem.org/mediawiki/2012/6/65/UCalgary2012_FRED_and_OSCAR_Sponsors.png"></img><br />
<a name="uofc"></a><br />
<a href="http://www.ucalgary.ca"><img style="width: 190px; padding: 25px 50px 0px 50px;" src="https://static.igem.org/mediawiki/2011/b/b7/UCalgary_Logo_Small.png"></img></a><br />
<a href="http://www.ucalgary.ca/bhsc"><img style="clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2011/c/c7/UCalgary_BHSc_Logo.png"></img></a><br />
<a href="http://bio.ucalgary.ca/"><img style="width: 250px; clear:both; margin-top: 0px;" src="https://static.igem.org/mediawiki/2012/4/47/UCalgary2012_BioSci_Logo.JPG"></img></a><br />
<h2>University of Calgary and the O'Brien Centre for the BHSc</h2><br />
<p>We graciously thank the Department of Cell Biology and Anatomy, the Department of Electrical and Computer Engineering, the Centre for Bioengineering Research and Education and the Department of Biological Sciences for all their support. We also wish to thank the Faculty of Medicine for their additional support as well. Additionally, we wish to thank the office of the Vice President of Research for their generous support.</p> <br />
<p>The O'Brien Centre for the Bachelor of Health Sciences is a part of the University of Calgary, located in the Foothills campus. It is responsible for providing iGEM team with lab space as well as funding. The O’Brien Centre was founded in part by a generous $5-million donation by David and Gail O’ Brien, after whom the Centre was named. David O'Brien has been a member of the University's Board of Governors, while Gail O'Brien has chaired the Faculty of Medicine's Dean's Advisory Council. The O’Brien Centre is the hub of top-notch research, interdisciplinary research, and education. It is responsible for providing approximately $9-million/year for researchers. The 2012 iGEM team thanks O’Brien Centre for its generous contribution of the O’Brien Centre Summer Studentship as well as lab space this year.</p><br />
<br />
<a href="http://www.albertatechfutures.ca/"><img src="https://static.igem.org/mediawiki/2011/3/3f/UCalgary2011_AITF_Logo_Small.png"></img></a><br />
<br />
<h2>Alberta Innovates Technology Futures</h2><br />
<p>Alberta Innovates Technology Futures facilitates the growth of technical industries by supporting quality research in Alberta's particular fields of expertise. These include nanotechnology, information communication technology, and genomics. AITF works in joint effort with entrepreneurs and researchers to ensure that Alberta’s technologies can be sustained at a business level through commercialization and growth. This is accomplished by ensuring that useful products, protocols and services are delivered to meet global demands.</p><br />
<br />
<a href="http://www.osli.ca/"><img style="width:200px;" src="https://static.igem.org/mediawiki/2012/2/27/Ucalgary2012_Full_OSLI_Swirl.png"></a><br />
<a href="http://www.osrin.ualberta.ca/"><img style="clear: both; width: 200px;" src="https://static.igem.org/mediawiki/2011/9/9a/UCalgary_OSRIN_Logo.png"></img></a><br />
<h2>OSLI/OSRIN</h2><br />
<p>The Oil Sands Leadership Initiative (OSLI) and the Oil Sands Research and Information Network (OSRIN) are graciously supporting iGEM this year. OSLI is a collaborative network between Nexen Inc., ConocoPhillips Canada, Statoil Canada, Suncor Energy Inc., and Total E&P Canada. OSLI strives to improve the reputation of the oil sands and lead the industry to responsible development of Alberta's bitument resources.</p><br />
<p>OSRIN is an independent organization within the School of Energy and Environment at the University of Alberta. OSRIN compiles, interprets, analyzes, and communicates data to and from oil sands mining and the area surrounding them. The organization strives for a future where Alberta can economically benefit from oil sands development without harming the environment.</p><br />
<br/><br/><br/><br />
<a href="http://www.vwr.com/"><img style="margin-bottom: 5px; height: 90px;" src="https://static.igem.org/mediawiki/2011/6/65/UCalgary_VWR_Logo.png"></img></a><br />
<br />
<h2>VWR</h2><br />
<p>VWR International is one of the world leaders in the distribution of laboratory materials. There are currently over 250 000 customers in North America and Europe, which is quite large for a biotechnology distributor. They are based in West Chester, Pennsylvania and specialize in the supply of chemicals, equipment, instruments, lab apparel, and lab furniture. They have many offices based worldwide from Northern Ireland to Switzerland and even one based in Singapore. The unique guarantee that they offer is the shipping of ordered material within 24 hours, due to large quantities of stock and many distribution offices in various countries. They have been a significant sponsor of our iGEM team in the past and we appreciate their contribution to our team this year.</p><br />
<br />
<br />
<a href="http://www.neb.com/nebecomm/default.asp"><img style="width: 220px;" src="https://static.igem.org/mediawiki/2011/d/d6/UCalgary_NEB_Logo.png"></img></a><br />
<br />
<h2>New England Biolabs</h2><br />
<p>For over 30 years, New England Biolabs has led the industry in the discovery and production of enzymes for molecular biology applications. At NEB, enzyme production is linked to basic research in the cloning and overexpression of restriction/modification systems. Their focus on providing the largest selection of recombinant enzymes has resulted in lower dollar-per-unit costs and improved purity and consistency of product. Presently, NEB supplies more than 240 restriction enzymes, over 160 of which are available in recombinant form, as well as numerous recombinant DNA and protein modifying enzymes.</p><br />
<a href="http://www.sarstedt.com/php/main.php"><img style="height:50px;" src="https://static.igem.org/mediawiki/2011/e/ee/UCalgary_Sarstedt_Logo.png"></img></a><br />
<br />
<h2>Sarstedt</h2><br />
<p>The Sarstedt Group develops, manufactures and sells equipment and consumables in the field of medicine and research. Ever since it was set up in 1961 the company has continued to grow to the point where it now employs a workforce of 2,500. They produce consumables and analytical equipment for medical diagnostics and consumables for use in medical patient care as well as for research laboratories and also for environmental analytical work. The Sarstedt group manufactures their own products at their own production sites as well as develops concepts and finished products in their own R&D centre.</p><br />
<a href="http://www.eurofins.com/en.aspx"><img style="width: 250px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></a><br />
<h2>Eurofins MWG Operon</h2><br />
<p>Eurofins MWG Operon, founded in 1990 and member of the Eurofins Group, is an international provider of genomic services established around the core business lines next generation sequencing, custom DNA sequencing, oligonucleotides, siRNA and gene synthesis. The company's main mission is focussed on customer convenience and high quality services in industrial scale for the life science industries and academic research institutions around the world.</p><br />
<a href="http://www.sparkscience.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></a><br />
<br />
<h2>Telus Spark</h2><br />
<p>The culmination of over a decade of planning, design and construction to bring Calgary’s new Science Centre to life will light a spark of wonder and excitement in Southern Alberta. Facilitators will fuel curiosity. Exhibits and programs will ignite a sense of wonder and excitement. Conferences and events will act as a catalyst for innovation and new ideas. TELUS Spark is a place for people of all ages and abilities to let go and embrace the desire to explore and discover science, technology and art in a way that their normal day-to-day life doesn’t allow for.</p><br />
<a href="http://www.idtdna.com/site"><img src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></a><br />
<br />
<h2>IDT (Integrated DNA Technologies)</h2><br />
<p>Integrated DNA Technologies (IDT) is a leader in manufacturing and developing products for the research and diagnostic life science market. IDT serves the areas of academic research, biotechnology, and pharmaceutical development. Founded by Dr. Joseph Walder in 1987, IDT’s development has been guided by an uncompromising approach to quality, a belief in the value of good service, and a determination to minimize consumer costs. IDT now has over 500 employees and ships over 20,000 oligos per day. <br />
<br />
Serving over 70,000 life sciences researchers, IDT is widely recognized as the industry leader in custom oligonucleotides. </p><br />
<a href="http://genomealberta.ca/"><img src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></img></a><br />
<br />
<h2>Genome Alberta</h2><br />
<p>In partnership with Genome Canada Industry Canada and the Province of Alberta, Genome Alberta was established in 2005. They are a publicly funded non-profit corporation that initiates, funds, and manages genomics research and partnerships. <br />
Genome Alberta strives to be the leading source of information and administration related to genomics, proteomics, bioinformatics and bioethics research in Alberta. Genome Alberta is dedicated to informing students, researchers, research organizations, our partners, and the public regarding opportunities and challenges in genomics and proteomics, and in encouraging the development of a Life Sciences research industry in Alberta. <br />
</p><br />
<br />
<br />
<a href="http://www.teamlab.com/"><img style="width: 130px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></a><br />
<br />
<h2>Team Lab</h2><br />
<p>TeamLab is a multifunctional online service for business collaboration, document and project management. It has been developed by Ascensio System SIA, a fast-growing company that offers IT-solutions for personal and corporate use.<br />
TeamLab was founded on the idea of making social networking and project management efficient. It combines a wide range of features that assist a company team to work as one organism at solving common tasks and achieving results.<br />
</p><br />
<br />
<a href="http://www.mhc.ab.ca/"><img style="width: 230px;" src="https://static.igem.org/mediawiki/2012/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a><br />
<br />
<h2>Medicine Hat College</h2><br />
<p>Medicine Hat College is a public, board governed, comprehensive community college serving a large region of southeastern Alberta and southwestern Saskatchewan, Canada. The MHC is located in the city of Medicine Hat, Alberta, Canada. MHC has been serving students in southeastern Alberta and beyond since 1965. MHC’s main campus services almost 2,500 students each year with another 200 attending Brooks Campus, located 100 km west of Medicine Hat. Currently, more than 30 diplomas and certificates are offered along with 25 university transfer programs. There are also several opportunities for degree completion at MHC including nursing, applied arts, and social work. A partnership with the University of Calgary makes it possible for nursing students to complete a full bachelor’s degree at Medicine Hat College while graduates from diploma programs such as Police and Security may also complete degrees. Medicine Hat College offers other unique diploma programs such as Addictions Counselor, Technical Illustrator, Paramedic, and Deaf and Blind Support Specialist. New applied degrees are also offered in Ecotourism and Outdoor Leadership and Visual Communications.<br />
</p><br />
</body><br />
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</html><br />
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}}</div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_Hyperion_Research_Logo.jpgFile:UCalgary2012 Hyperion Research Logo.jpg2012-10-25T03:51:08Z<p>Iaingeorge: </p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/File:UCalgary2012_BioSci_Logo.JPGFile:UCalgary2012 BioSci Logo.JPG2012-10-25T03:43:44Z<p>Iaingeorge: </p>
<hr />
<div></div>Iaingeorgehttp://2012.igem.org/Team:Calgary/Project/OSCAR/DecarboxylationTeam:Calgary/Project/OSCAR/Decarboxylation2012-10-25T03:33:22Z<p>Iaingeorge: </p>
<hr />
<div>{{Team:Calgary/TemplateProjectBlue|<br />
TITLE=Decarboxylation|<br />
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CONTENT=<html><br />
<br />
<br />
<img src="https://static.igem.org/mediawiki/2012/c/c3/UCalgary2012_OSCAR_Decarboxylation_Low-Res.png" style="float: right; padding: 10px; width: 300px;"></img><br />
<h2>Why Decarboxylation?</h2><br />
<br />
<p>Among the toxins found in the tailing ponds, naphthenic acids (NAs) are among the most harmful and the most common. Though there is great diversity within the NAs class of compounds, all share the common chemical feature of a carboxylic acid group. The carboxyl group is the primary cause for their toxicity, allowing these chemicals to traverse cell membranes and react with cellular materials (Frank <i>et al</i>. 2009). NAs are recalcitrant (not easily degraded), potentially harmful to the surrounding ecosystem (Clemente & Fedorak, 2005) and corrosive to extraction and transport equipment of petroleum materials (Slavcheva <i>et al</i>. 1999). Corrosion of pipelines leads to higher maintenance costs as well as the grim possibility of these and other toxins leaking into the environment. <br />
There is a need for methods to degrade NAs that are not prohibitively expensive or that would result in production of other hazardous chemicals.</p> <br />
<br />
<p>The main goal of OSCAR is to turn toxins like these into useable hydrocarbons by removing the carboxylic acid group(s) (Behar & Albrecht, 1984). <br />
<br />
Since NAs from petroleum deposits are a variable mixture, an enzymatic process with broad specificity is necessary. With the removal of the carboxylic acid moiety, we aim to produce alkanes suitable for use as fuel. The goal of this subproject was to find one or more suitable pathways to accomplish the decarboxylation of compounds such as NAs with the broadest specificity.</p><br />
<br />
<br />
<h2>The PetroBrick</h2><br />
<br />
<p>The 2011 Washington iGEM team developed the PetroBrick (<a <br />
<br />
href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K590025">BBa_K590025.</a>), a BioBrick consisting of two primary genes. These include acyl-ACP reductase (<i>aar</i>), which reduces fatty acids bound to ACP to fatty aldehydes, and a second gene called aldehyde decarbonylase (<i>adc</i>), which subsequently cleaves the entire aldehyde group and results in a hydrocarbon chain (Sukovich, 2010). Essentially this allows for hydrocarbons to be produced from glucose. What we realized though, is that the fatty acids that the PetroBrick targets, have a very similar structure to NAs.</p><br />
<br />
</html>[[File:UCalgary-Fatty-Acids-vs-NAs.jpg|550px|centre|thumb|Figure 1: A comparison of the structure of fatty acids and naphthenic acids]]<html><br />
<br />
<p>We predicted that the PetroBrick may have the potential to turn NAs in to hydrocarbons and be a perfect solution to remediating NAs! First though, we needed to show that the PetroBrick did in fact work as expected. We had some difficulty with the DNA from the registry and had to request the constructs directly from the Washington team. Once we had the PetroBrick, we needed to verify that the PetroBrick would work in our hands as it did for the <a href="https://2011.igem.org/Team:Washington">2011 Washington team</a>.<br />
<br />
Figures 2 and 3 demonstrate the function of the PetroBrick.</p><br />
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</html>[[File:Calgary2012_PetrobrickVerificationGC.jpg|center|thumb|Figure 2: Gas chromatograph of the differences in peak composition between an <i>E. coli</i> control and the PetroBrick. There was a large increase in a peak with a retention time of 12.25 min, suggesting that the PetroBrick was producing a new hydrocarbon compound.|650px]]<html><br />
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</html>[[File:Calgary2012_PetrobrickVerificationMS.jpg|center|thumb|Figure 3: Mass spectra of the gas chromatograph peak at 12.25 min. This spectra suggests that the PetroBrick is selectively producing a C15 alkane, which resemble the results from the Washington 2011 iGEM team.|750px]]<html><br />
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<p>With the PetroBrick able to successfully produce alkanes, we next wanted to test the PetroBrick on NAs to see if they could be selectively converted into alkanes! This experiment used commercial NAs fractions, which included a large number of different complex NAs compounds. </p><br />
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<a name="Petrobrick"></a><h2>Successful conversion of NAs into hydrocarbons!</h2><br />
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</html>[[File:Ucalgary_Decarboxylation_NaphthenicAcids_Results.png|center|thumb|Figure 4: The relative intensity of alkane production from NAs as measured with GC-MS over a retention time in <i>E. coli</i> with and without the PetroBrick . Concentrated NA standard was included for comparison of peaks.|700px]]<html><br />
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</html>[[File:Ucalgary_Decarboxylation_Alkanes_Alkenes_Results.png|center|700px|thumb|Figure 5: Mass spectrums of alkanes and alkenes produced from NAs with <i>E. coli</i> containing the PetroBrick as in Figure 2. Relative intensity of mass-to -charge ratio (m/z) was compared.]]<html><br />
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<p> Results from Figure 4 and 5 indicate that hydrocarbons were successfully produced from <i>E. coli</i> that contained the PetroBrick construct, as analysed with GC-MS. In Figure 2, <i>E. coli</i> containing the PetroBrick had higher hydrocarbon peaks than the <i>E. coli</i> without the PetroBrick. Not only was the PetroBrick able to degrade NAs into alkanes, the PetroBrick could produce alkenes (Figure 3), indicating that the PetroBrick worked as expected! </p><br />
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<h2><i>Nocardia</i> Carboxylic Acid Reductase (CAR)- Can we do better?</h2><br />
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<p>Although we successfully used the PetroBrick to remove carboxyl groups from NAs, we wanted to improve on our results to get a higher yield and/or possibly target other compounds. One of our original concerns in using the PetroBrick to decarboyxlate NAs was that the first enzyme AAR only targeted fatty acids bound to ACP, and non-compatibility with NAs. Therefore, we searched for another enzyme carboxylic acid reductase (CAR) from <i>N. iowensis</i> known to perform a similar task as AAR - converting fatty acids to aldehydes, but with much lower specificity (He <i>et al</i>. 2004). Unlike AAR, CAR does not require covalent attachment to ACP, and likely to have broader substrate specificity. The use of CAR did require a second gene from <i>N. iowensis</i> called <i>Nocardia</i> phosphopantetheinyl transferase (<i>npt</i>) to append a 4’- phosphopantetheine prosthetic group to CAR required for its full function (Venkitasubramanian <i>et al.</i>, 2006).</p><br />
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</html>[[File:Ucalgary Decarboxylation Team CAR Mechanism.jpg|center|700px|thumb|Figure 6: Mechanism of CAR catalysis. Taken from He <i>et al.</i>, 2004.]]<html><br />
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<a name="OleT"></a><p>Another enzyme with the potential to remove carboxyl groups from NAs is olefin-forming fatty acid decarboxylase (OleT) from <i>Jeotgalicoccus</i> sp. ATCC 8456. OleT of the cytochrome P450 family acts on fatty acids, but does have low substrate specificity (Rude <i>et al</i>. 2011). Using OleT was beneficial because this single enzyme could do the job of the entire PetroBrick! Given our decarboxylation approach was valid, we started testing and comparing <i>oleT</i> to the PetroBrick.</p><br />
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<h2> Progress so far </h2><br />
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<p>Genes <i>car</i> and <i>npt</i> were cloned from the host organism <i>N. iowensis</i> (NRRL 5646). <i>car</i> was ligated into the pET vector and verified by a restriction digest while <i>npt</i> was cloned into pSB1C3(<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902061">BBa_K902061</a>) and similarly verified.</p><br />
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<p><i>car</i> was cloned into pET47b+ plasmid to remove six illegal cut-sites (one XbaI site, two EcoRI sites, and three NotI sites), as it was unsuitable for the BioBrick construction vectors. We first attempted to use a multi-site mutagenesis derived from the QuikChange<sup>®</sup> Multi-Site Directed Mutagenesis Kit, but had little success. Instead, a more time-consuming but effective series of conventional single-site <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/mutagenesis">mutagenesis procedure</a> was used with the KAPA Hi-Fi polymerase. The XbaI and EcoRI sites were eliminated first so that <i>car</i> can be moved from the pET Vector and ligated into the PSB1C3 vector (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K902062">BBa_K902062</a>). <br />
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<p>The <i>oleT</i> was successfully amplified from the <i>Jeotgalicoccus</i> sp. ATCC 8456.<br />
<p> </p><br />
<p>Like <i>car</i>, <i>oleT</i> was inserted in a pET47b+ (Novagen) vector before placing it into a BioBrick vector, as two illegal cut sites adjacent to one another needed to be mutagenized. This part is now being ligated into pSB1C3. We are currently in the process of constructing all three parts under control of a <i>tetR</i> promoter and ribosomal binding site (<a href="http://partsregistry.org/Part:BBa_J13002">BBa_J13002</a>), and then constructing these composite parts together as outlined below.</p><br />
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<h2>Final testing constructs</h2><br />
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<p>Final testing constructs are nearly complete. These are illustrated in Figure 7 and will allow us to compare the three different approaches. Unfortunately, Washington only sent us the PetroBrick and not the two individual components, we will have to compare a combination of the PetroBrick and <i>car/npt</i> to the PetroBrick alone and to <i>oleT</i>. </p><br />
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<p></html>[[File:Ucalgary_Decarboxylation_Team_J13002+car+J13002+npt+PetroBrick.png|centre|600px]]<html><br />
</html>[[File:Ucalgary Decarboxylation Team J13002+oleT.png|centre|280px|thumb|Figure 7: Final constructs required for validating and comparing different decarboxylation approaches]]<html></p><br />
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<a name="TestingOleT"></a><h2> Testing OleT </h2><br />
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<p>One major stumbling block in testing out <i>oleT</i> has been significant difficulty in trying to ligate it into a vector, which has prevented us from submitting it as a BioBrick. As such, we chose to try some assays on the host organism: <i>Jeotgalicoccus</i> sp. ATCC 8456. This way we could at least validate that this gene was functional before we had our BioBricks. We started by trying to verify the results by Rude <i>et al</i>., 2011, namely that OleT could convert fatty acids into alkenes. We grew up cultures according to this <a href="https://2012.igem.org/Team:Calgary/Notebook/Protocols/oleT_in_Validation_Assay">protocol</a> and used GC-MS to analyze any alkene production (Figure 8 and 9).</p><br />
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<h2> Formation of alkanes by <i>Jeotgalicoccus</i> sp. ATCC 8456</h2><br />
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</html>[[File:UofC_OleT_Assay_1.png|centre|650px|thumb|Figure 8. Gas chromatograph demonstrating the production of olefins (alkenes) from fatty acids as shown from the increase in the peak with a retention time of 14.7 min. The dramatic change in peak intensity at this point suggests that we are producing hydrocarbons.]]<br />
[[File:UofC_OleT_2nd_Assay.png|centre|700px|thumb|Figure 9. Mass spectra of the peak in Figure 8 at retention time 14.7 min. Demonstrating that this peak is an olefin, which is known to be produced in <i>Micrococcus</i>. This verifies our proof-of-concept that the <i>Micrococcus</i> species can degrade fatty acids into olefins. ]]<html><br />
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<p>Based on the additional peak we saw in the gas chromatograph, we could show that our <i>E. coli</i> can produce alkenes with the <i>oleT</i>. This is may be an improvement over the PetroBrick since OleT is only one enzyme instead of two; however, future testing is still needed. Now that we have validated the function of OleT in producing alkenes, the next step is to test it out on complex naphthenic acids in order to compare it to the PetroBrick. This testing is still underway.</p><br />
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}}</div>Iaingeorgehttp://2012.igem.org/File:Ucalgary_Decarboxylation_Team_CAR_Mechanism.jpgFile:Ucalgary Decarboxylation Team CAR Mechanism.jpg2012-10-25T03:30:09Z<p>Iaingeorge: uploaded a new version of &quot;File:Ucalgary Decarboxylation Team CAR Mechanism.jpg&quot;</p>
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<div>CAR mechanism for wiki.</div>Iaingeorgehttp://2012.igem.org/File:Ucalgary_Decarboxylation_Team_CAR_Mechanism.jpgFile:Ucalgary Decarboxylation Team CAR Mechanism.jpg2012-10-25T03:29:24Z<p>Iaingeorge: uploaded a new version of &quot;File:Ucalgary Decarboxylation Team CAR Mechanism.jpg&quot;</p>
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<div>CAR mechanism for wiki.</div>Iaingeorgehttp://2012.igem.org/File:Ucalgary_Decarboxylation_Team_CAR_Mechanism.jpgFile:Ucalgary Decarboxylation Team CAR Mechanism.jpg2012-10-25T03:27:44Z<p>Iaingeorge: uploaded a new version of &quot;File:Ucalgary Decarboxylation Team CAR Mechanism.jpg&quot;</p>
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<div>CAR mechanism for wiki.</div>Iaingeorge