Team:Calgary

From 2012.igem.org

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<h2>Project Description</h2>
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<p>Naphthenic acids (NAs) are a group of recalcitrant carboxylic acid-containing compounds that are byproducts of the bitumen extraction process. These toxic and corrosive compounds are part of the solid and liquid wastes deposited into large holding areas called tailings ponds, which pose a potential environmental and economic concern to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of NA-sensing and degrading organisms for their detection and bioremediation. Continuing from the 2011 iGEM team’s work on developing a biosensor for the detection of NAs, our team aims to better characterize a biological system for detection and quantitative measurement of these and other tailings pond compounds using an electrochemical output. New this year, our major objective is to develop procedures for the conversion of NAs into useful hydrocarbons. This requires the removal of a variety of chemical groups (carboxyl, sulfur, nitrogen, and polycyclic rings) from NAs which we will develop using known biological pathways from a variety of microorganisms. Furthermore, our group aims to develop biological (in the form of a kill switch) and structural solutions to safety problems found in the scale up process of synthetic biology industrial applications. Finally, we hope to develop aproof-of-concept bioreactor system that will be capable of converting these NAs into clean hydrocarbons suitable for industrial use. By providing both an environmental and economic benefit through the remediation of NAs, the 2012 University of Calgary iGEM team hopes to better facilitate biological methodologies for toxin remediation in Alberta, Canada, and beyond.</p>
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<h2>Detect and Destroy: Building FRED and OSCAR</h2>
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<p><b>Naphthenic acids (NAs)</b> are a group of recalcitrant carboxylic acid-containing compounds which are byproducts of the bitumen extraction process in the northern Alberta oil sands. These toxic and corrosive compounds are part of the solid and liquid wastes deposited into large holding areas called <b>tailings ponds</b>, which pose a potential environmental and economic concern to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of NA-sensing and degrading organisms for their <b>detection and bioremediation</b>.</p>
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<p><b>FRED and OSCAR</b> are the two projects we are working on this year. Take a look at the description below to learn more!</p>
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<h2>The Concept</h2>
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<p>Our project consists of three major components: FRED, OSCAR, and the overarching Human Practices considerations surrounding both of their design. Click on the boxes to your left to learn more about what iGEM Calgary has done so far!</p>
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<div class="orangebox">
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<h2>Human Practices</h2>
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<p>Great consideration was put into our Human Practices component this year, as safety was the guiding principle behind the design of FRED and OSCAR. There are many human outreach initiatives that iGEM Calgary has done this year. Roll over the boxes to see each of them!</p>
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<div class="obox1">
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<h2>Video Game</h2>
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<p>Play our iGEM Lab Escape video game! Do you have the lab skills necessary to solve the puzzle your professor gave you and escape the lab?</p>
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</div>
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<div class="obox2">
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<h2>Killswitch</h2>
 +
<p>Both FRED and OSCAR are designed to operate within enclosed environments. However, since safety is our highest priority, we decided to design and implement a killswitch in both FRED and OSCAR as an extra layer of security. The killswitch aims to to destroy the genome using two powerful non-specific nucleases in the unlikely scenario bacteria can escape into the environment. Click here to learn more!</p>
 +
</div>
 +
<div class="obox3">
 +
<h2>Interviews</h2>
 +
<p>As an undergraduate team, we looked into speaking 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>
 +
</div>
 +
<div class="obox4">
 +
<h2>Design Considerations</h2>
 +
<p>Since safety is the driving force behind our project, we need to ensure the physical design of our biosensor and bioreactor would be able to contain and manage bacterial cultures without allowing any to 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>
 +
</div>
 +
<div class="obox5">
 +
<h2>Safety</h2>
 +
<p>Click here for our safety page! Here we detail all the safety procedures, certifications, and approvals we have from our University to allow us to work this summer.</p>
 +
</div>
 +
<div class="obox6">
 +
<h2>Community Outreach</h2>
 +
<p>iGEM Calgary partnered with a number of different associations to engage the general public about science and synthetic biology. Click here to see what we've done this summer!</p>
 +
</div>
 +
<div class="greenbox">
 +
<h2>FRED</h2>
 +
<p>FRED is our <b>F</b>unctional, <b>R</b>obust <b>E</b>lectrochemical <b>D</b>etector. FRED is responsible for detecting and measuring NAs and is able to produce an electrochemical signal that can be measured. FRED can be used to measure tailings pond samples within minutes, without having to ship them to an off-site lab for testing. Click on FRED to learn more!</p>
 +
</div>
 +
<div class="gbox1">
 +
<h2>Detecting NAs</h2>
 +
<p>We conducted a transposon search for any regulatory elements that may respond to NAs. Click here to learn more!</p>
 +
</div>
 +
<div class="gbox2">
 +
<h2>Electrochemical Reporting</h2>
 +
<p>As a continuation of our 2011 iGEM project, we have designed a replacement for colourmetric assays. Electrochemical reporting can be used to measure miniscule concentrations regardless of how turbid the sample is. Click here to learn more!</p>
 +
</div>
 +
<div class="gbox3">
 +
<h2>Modelling</h2>
 +
<p>We conducted some modelling on FRED's predicted output.</p>
 +
</div>
 +
<div class="gbox4">
 +
<h2>Prototyping</h2>
 +
<p>We built a prototype biosensor in order to give FRED a home. This biosensor device is capable of performing voltage sweeps that will detect specific compounds. Click here to learn more!</p>
 +
</div>
 +
<div class="bluebox">
 +
<h2>OSCAR</h2>
 +
<p>OSCAR is our <b>O</b>ptimized <b>S</b>ystem for <b>C</b>arboxylic <b>A</b>cid <b>R</b>emediation. OSCAR is responsible for converting NAs into hydrocarbons. OSCAR is also capable of removing nitrogen and sulfur groups from NA rings to purify the hydrocarbons produced even further. Click here to learn more!</p>
 +
</div>
 +
<div class="bbox1">
 +
<h2>Decarboxylation</h2>
 +
<p>In order to convert NAs into hydrocarbons, we need to remove the carboxylic acid groups that make NAs acids. We are using the PetroBrick, from the University of Washington's 2011 iGEM team, to cleave off carboxylic acids to produce hydrocarbons. Click here to learn more!</p>
 +
</div>
 +
<div class="bbox2">
 +
<h2>Denitrogenation</h2>
 +
<p>Nitrogen heteroatoms in the ring structures reduce the efficiency of combustion in the final product. OSCAR is able to remove these nitrogen atoms. Click here to see how!</p>
 +
</div>
 +
<div class="bbox3">
 +
<h2>Desulfurization</h2>
 +
<p>OSCAR can remove sulfur atoms trapped in the rings of NAs. Click here to see how!</p>
 +
</div>
 +
<div class="bbox4">
 +
<h2>Catechol Degradation</h2>
 +
<p>Catechol is a common toxic compound found in tailings ponds. We looked into giving OSCAR the ability to degrade catechol, which would also cleave ring structures of NAs.</p>
 +
</div>
 +
<div class="bbox5">
 +
<h2>Bioreactor</h2>
 +
<p>OSCAR needed a home, so we developed an enclosed bioreactor system where NAs can be converted into hydrocarbons for output. Click here to see how we designed the bioreactor!</p>
 +
</div>
 +
<div class="bbox6">
 +
<h2>Flux-Variability Analysis</h2>
 +
<p>We wanted to optimize OSCAR's output of hydrocarbons, so we computationally modelled which genes should be regulated in order to maximize hydrocarbon output. Click here to see what we found out!</p>
 +
</div>
 +
</div>
 +
</div>
 +
 
 +
<div id="threeboxes">
 +
<a id="greybox1" href="https://2012.igem.org/Team:Calgary/Team">
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2012/b/b8/UCalgary2012_ThreeBoxTeam.png"></img>
 +
<h2>Team</h2>
 +
<p>Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!</p>
 +
</div>
 +
</a>
 +
<a id="greybox2" href="https://2012.igem.org/Team:Calgary/Project/DataPage">
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2012/9/92/UCalgary2012_ThreeBoxData.png"></img>
 +
<h2>Data Page</h2>
 +
<p>Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.</p>
 +
</div>
 +
</a>
 +
<a id="greybox3" href="https://2012.igem.org/Team:Calgary/Notebook">
 +
<div>
 +
<img src="https://static.igem.org/mediawiki/2012/1/1b/UCalgary2012_ThreeBoxNotebook.png"></img>
 +
<h2>Notebook</h2>
 +
<p>Here is a record of our summer's work. We also want to thank everybody who helped us along the way!</p>
 +
</div>
 +
</a>
 +
</div>
 +
 
 +
<div id="sponsorsbox">
 +
<h2>Thanks to Our Sponsors!</h2>
 +
<table>
 +
<tr>
 +
<td><img style="width: 284px;" src="https://static.igem.org/mediawiki/2012/d/d6/UCalgary2012_Logo_O%27Brien_Centre.png"></img></td>
 +
<td><img style="width: 166px;" src="https://static.igem.org/mediawiki/2012/4/46/UCalgary2012_Logo_U_of_C_Vertical.png"></img></td>
 +
<td><img style="width: 234px;" src="https://static.igem.org/mediawiki/2012/7/7f/UCalgary2012_Logo_AITF.png"></img></td>
 +
</tr>
 +
</table>
 +
<table>
 +
<tr>
 +
<td><img style="width: 891px;" src="https://static.igem.org/mediawiki/2012/9/98/UCalgary2012_Logo_OSLI.png"></img></td>
 +
</tr>
 +
</table>
 +
<table>
 +
<tr>
 +
<td><img style="width: 204px;" src="https://static.igem.org/mediawiki/2012/0/04/UCalgary2012_OSRIN.png"></img></td>
 +
<td><img style="width: 290px;" src="https://static.igem.org/mediawiki/2012/a/a4/UCalgary2012_Logo_Eurofins.png"></img></td>
 +
<td><img style="width: 261px;" src="https://static.igem.org/mediawiki/2012/6/6f/UCalgary2012_Logo_Telus_Spark.png"></img></td>
 +
</tr>
 +
<tr>
 +
<td><img style="width: 281px;" src="https://static.igem.org/mediawiki/2012/2/24/UCalgary2012_Logo_NEB.png"></img></td>
 +
<td><img style="width: 228px;" src="https://static.igem.org/mediawiki/2012/1/15/UCalgary2012_Logo_IDT.png"></img></td>
 +
<td><img style="width: 203px;" src="https://static.igem.org/mediawiki/2012/6/68/UCalgary2012_Logo_Genome_Alberta.png"></img></td>
 +
</tr>
 +
<tr>
 +
<td><img style="width: 274px;" src="https://static.igem.org/mediawiki/2012/f/f6/UCalgary2012_Logo_Sarstedt.png"></img></td>
 +
<td><img style="width: 160px;" src="https://static.igem.org/mediawiki/2012/b/be/UCalgary2012_Logo_TeamLab.png"></img></td>
 +
<td><img style="width: 279px;" src="https://static.igem.org/mediawiki/2012/1/11/UCalgary2012_Logo_VWR.png"></img></td>
 +
</tr>
 +
</table>
 +
</div>
 +
 
 +
</body>
</html>
</html>
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Revision as of 21:52, 29 September 2012

Detect and Destroy: Building FRED and OSCAR

Naphthenic acids (NAs) are a group of recalcitrant carboxylic acid-containing compounds which are byproducts of the bitumen extraction process in the northern Alberta oil sands. These toxic and corrosive compounds are part of the solid and liquid wastes deposited into large holding areas called tailings ponds, which pose a potential environmental and economic concern to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of NA-sensing and degrading organisms for their detection and bioremediation.

FRED and OSCAR are the two projects we are working on this year. Take a look at the description below to learn more!

The Concept

Our project consists of three major components: FRED, OSCAR, and the overarching Human Practices considerations surrounding both of their design. Click on the boxes to your left to learn more about what iGEM Calgary has done so far!

Human Practices

Great consideration was put into our Human Practices component this year, as safety was the guiding principle behind the design of FRED and OSCAR. There are many human outreach initiatives that iGEM Calgary has done this year. Roll over the boxes to see each of them!

Video Game

Play our iGEM Lab Escape video game! Do you have the lab skills necessary to solve the puzzle your professor gave you and escape the lab?

Killswitch

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 to destroy the genome using two powerful non-specific nucleases in the unlikely scenario bacteria can escape into the environment. Click here to learn more!

Interviews

As an undergraduate team, we looked into speaking 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?

Design Considerations

Since safety is the driving force behind our project, we need to ensure the physical design of our biosensor and bioreactor would be able to contain and manage bacterial cultures without allowing any to 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!

Safety

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.

Community Outreach

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!

FRED

FRED is our Functional, Robust Electrochemical Detector. FRED is responsible for detecting and measuring NAs and is able to produce an electrochemical signal that can be measured. FRED can be used to measure tailings pond samples within minutes, without having to ship them to an off-site lab for testing. Click on FRED to learn more!

Detecting NAs

We conducted a transposon search for any regulatory elements that may respond to NAs. Click here to learn more!

Electrochemical Reporting

As a continuation of our 2011 iGEM project, we have designed a replacement for colourmetric assays. Electrochemical reporting can be used to measure miniscule concentrations regardless of how turbid the sample is. Click here to learn more!

Modelling

We conducted some modelling on FRED's predicted output.

Prototyping

We built a prototype biosensor in order to give FRED a home. This biosensor device is capable of performing voltage sweeps that will detect specific compounds. Click here to learn more!

OSCAR

OSCAR is our Optimized System for Carboxylic Acid Remediation. OSCAR is responsible for converting NAs into hydrocarbons. OSCAR is also capable of removing nitrogen and sulfur groups from NA rings to purify the hydrocarbons produced even further. Click here to learn more!

Decarboxylation

In order to convert NAs into hydrocarbons, we need to remove the carboxylic acid groups that make NAs acids. 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!

Denitrogenation

Nitrogen heteroatoms in the ring structures reduce the efficiency of combustion in the final product. OSCAR is able to remove these nitrogen atoms. Click here to see how!

Desulfurization

OSCAR can remove sulfur atoms trapped in the rings of NAs. Click here to see how!

Catechol Degradation

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 NAs.

Bioreactor

OSCAR needed a home, so we developed an enclosed bioreactor system where NAs can be converted into hydrocarbons for output. Click here to see how we designed the bioreactor!

Flux-Variability Analysis

We wanted to optimize OSCAR's output of hydrocarbons, so we computationally modelled which genes should be regulated in order to maximize hydrocarbon output. Click here to see what we found out!

Thanks to Our Sponsors!

Retrieved from "http://2012.igem.org/Team:Calgary"