Team:Calgary

From 2012.igem.org

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<body>
<body>
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<h2>Detect and Destroy: Building FRED and OSCAR</h2>
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<a href="https://2012.igem.org/Team:Calgary/Project/Post-Regionals" id="FredOscarFlag">
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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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</a>
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<h2>Detect and Destroy: Building FRED and OSCAR</h2>
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<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>
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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 descriptions below to learn more!</p>
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<div class="threeboxes">
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<a id="greybox4" href="http://www.youtube.com/watch?v=KHhswxo6xow" style="margin-right:4px;">
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<div>
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<img src="https://static.igem.org/mediawiki/2012/0/02/UCalgary2012_ThreeBoxMusic.png"></img>
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<h2>iGEM Style!</h2>
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<p>Take a look at our music video--sung and produced by our very own members--that's taking the iGEM world by storm! </p>
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</a>
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<a id="greybox5" href="https://2012.igem.org/Team:Calgary/Project/Synergy">
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<img src="https://static.igem.org/mediawiki/2012/2/20/UCalgary2012_ThreeBoxSynergy.png"></img>
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<h2>Synergy</h2>
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<p>We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!</p>
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<img src="https://static.igem.org/mediawiki/2012/b/b1/UCalgary2012_ThreeBoxFilm.png"></img>
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<h2>Intro Video</h2>
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<p>Click here to see the introductory video we played at the beginning of our Jamboree presentations!</p>
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</a>
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<a class="obox2 iconbox" href="https://2012.igem.org/Team:Calgary/Project/HumanPractices/Killswitch">
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<div id="boxinfo_default">
<h2>The Concept</h2>
<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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<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>
</div>
</div>
<div class="orangebox">
<div class="orangebox">
<h2>Human Practices</h2>
<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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<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>
</div>
</div>
<div class="obox1">
<div class="obox1">
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<h2>Video Game</h2>
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<h2>Initiative</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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<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>
</div>
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<div class="obox2">
<div class="obox2">
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<h2>Killswitch</h2>
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<h2>Interviews</h2>
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<p>Both FRED and OSCAR are designed to operate within enclosed environments. However, since safety is our highest priority, we decided to design and implement a killswitch in both FRED and OSCAR as an extra layer of security. The killswitch aims to 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>
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<p>As an undergraduate team, we spoke with experts in various fields, including the oil industry, tailings pond management, biotechnology, law, and politics to gather various opinions on our project. How useful is synthetic biology in a tailings pond environment? What design considerations should we include in our project to improve security? What legal policies must we consider before implementing our project?</p>
</div>
</div>
<div class="obox3">
<div class="obox3">
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<h2>Interviews</h2>
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<h2>Design Considerations</h2>
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<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>
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<p>Since safety is the driving force behind our project, we need to ensure the physical design of our biosensor and bioreactor would contain and manage the bacteria to minimize the possibility of their escape. We needed to build devices that would ensure the safety of both the user and the outside environment during their use. Click here to learn more!</p>
</div>
</div>
<div class="obox4">
<div class="obox4">
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<h2>Design Considerations</h2>
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<h2>Killswitch</h2>
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<p>Since safety is the driving force behind our project, we need to ensure the physical design of our biosensor and bioreactor would 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>
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<p>Both FRED and OSCAR are designed to operate within enclosed environments. However, since safety is our highest priority, we decided to design and implement a killswitch in both FRED and OSCAR as an extra layer of security. The killswitch aims to destroy the genome using two powerful non-specific nucleases in the unlikely event that bacteria escape into the environment. Click here to learn more!</p>
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<h2>FRED</h2>
<h2>FRED</h2>
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<p>FRED is our <b>F</b>unctional, <b>R</b>obust <b>E</b>lectrochemical <b>D</b>etector. FRED is responsible for detecting and measuring 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>
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<p>FRED is our <b>F</b>unctional, <b>R</b>obust <b>E</b>lectrochemical <b>D</b>etector. FRED is responsible for detecting and measuring naphthenic acids (NAs) and is able to produce an electrochemical signal that can be measured. FRED can be used to measure toxins in tailings pond samples within minutes, without having to ship them to an off-site lab for testing. Click on FRED to learn more!</p>
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<h2>Detecting</h2>
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<h2>Detecting NAs</h2>
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<p>FRED is our star detective, working around the clock to detect toxins roaming freely in tailings pond water. FRED is known for being a little unorthodox in his methods namely by using a measurable electrochemical signal rather than colored or fluorescent reporters. Using his transposon library FRED gets clues about the genetic elements that will activate in the presence of toxins. </p>
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<p>We conducted a transposon search for any regulatory elements that may respond to NAs. Click here to learn more!</p>
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<h2>Reporting</h2>
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<h2>Electrochemical Reporting</h2>
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<p>Once FRED finds the toxins he wastes no time exposing them. Building upon last year's single output electrochemical system FRED now uses the new triple output system to report the toxins. This novel approach to electrochemical reporting means that FRED is as good as he is fast. </p>
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<p>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>
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<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
 
<h2>Modelling</h2>
<h2>Modelling</h2>
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<p>We conducted some modelling on FRED's predicted output and then tested it in the lab. Click here to learn more!</p>
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<p>Aside from being a stellar detective FRED also dabbles in the art of mathematics and modelling. These skills are used to model the behavior of the system. The results from the modelling helped guide the wet lab experiments which in turn gave new data to refine the model.</p>
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<h2>Prototyping</h2>
<h2>Prototyping</h2>
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<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>
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<p>FRED gets a lot of information so he stays on top of things with the help of his handy dandy physical device to test the sample and software to interpret the raw data. The device has been <b>prototyped</b> and has an accompanying software platform that works with FRED to detect the toxins. </p>
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<div class="bluebox">
<div class="bluebox">
<h2>OSCAR</h2>
<h2>OSCAR</h2>
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<p>OSCAR is our <b>O</b>ptimized <b>S</b>ystem for <b>C</b>arboxylic <b>A</b>cid <b>R</b>emediation. OSCAR is responsible for converting 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>
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<p>OSCAR is our <b>O</b>ptimized <b>S</b>ystem for <b>C</b>arboxylic <b>A</b>cid <b>R</b>emediation. OSCAR is responsible for converting toxins such as catechol and naphthenic acids into hydrocarbons. OSCAR is also capable of removing nitrogen and sulfur groups to further purify the hydrocarbons produced. Click on OSCAR to learn more!</p>
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<h2>Decarboxylation</h2>
<h2>Decarboxylation</h2>
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<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>
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<p>In order to convert tailings pond toxins fully into hydrocarbons, we need to remove carboxylic acid groups. We are using the PetroBrick, from the University of Washington's 2011 iGEM team, to cleave off carboxylic acids to produce hydrocarbons. Click here to learn more!</p>
</div>
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<h2>Denitrogenation</h2>
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<h2>Catechol Degradation</h2>
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<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>
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<p>Catechol is a common toxic compound found in tailings ponds. We looked into giving OSCAR the ability to degrade catechol, which would also cleave ring structures of toxins.</p>
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<p>Sulfur heteroatoms can produce nasty 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 sulfur atoms trapped in the rings. Click here to see how!</p>
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<p>We wanted to optimize OSCAR's output of hydrocarbons, so we computationally modelled how we can add particular metabolites to the growth media to increase hydrocarbon output. Click here to see what we found out!</p>
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<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>
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<p>OSCAR needed a home, so we developed an enclosed bioreactor system where toxins can be converted into hydrocarbons for output. Click here to see how we designed the bioreactor!</p>
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<p>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>
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<p>Nitrogen and sulfur heteroatoms can produce nasty airborne pollutants when burned, cause acid rain and acid deposition, and can damage valuable catalysis mechanisms involved in fuel processing and emissions control. OSCAR can remove these atoms trapped in the rings. Click here to see how!</p>
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<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>
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Latest revision as of 04:53, 13 August 2013

Detect and Destroy: Building FRED and OSCAR

Tailings ponds are large bodies of water containing toxic compounds 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 environmental and economic concern to Alberta and to other areas. The University of Calgary 2012 iGEM team aims to develop a collection of toxin-sensing and degrading organisms to detect and destroy (bioremediate) the toxins, turning them into useable hydrocarbons.

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

iGEM Style!

Take a look at our music video--sung and produced by our very own members--that's taking the iGEM world by storm!

Synergy

We have lots of new data since Regionals! Click here to see how we brought the three aspects of our project together!

Intro Video

Click here to see the introductory video we played at the beginning of our Jamboree presentations!

The Concept

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!

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. iGEM Calgary has undertaken many human outreach initiatives this year. Roll over the boxes to see each of them!

Initiative

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.

Interviews

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?

Design Considerations

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!

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 destroy the genome using two powerful non-specific nucleases in the unlikely event that bacteria escape into the environment. 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 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!

Detecting

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.

Reporting

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.

Modelling

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.

Prototyping

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 prototyped and has an accompanying software platform that works with FRED to detect the toxins.

OSCAR

OSCAR is our Optimized System for Carboxylic Acid Remediation. 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!

Decarboxylation

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!

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 toxins.

Flux-Variability Analysis

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!

Bioreactor

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!

Upgrading

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!

Team

Who are we? What did we do? Where is this Calgary place, anyway? Click here to read our team profiles!

Data Page

Click here to see a summary of all our data collected so far! Details on FRED and OSCAR can be found above.

Notebook

Here is a record of our summer's work. We also want to thank everybody who helped us along the way!

Thanks to Our Sponsors!

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