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Team:Calgary
From 2012.igem.org
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| - | <h2>Detecting | + | <h2>Detecting</h2> |
| - | <p>We | + | <p>The first part of any biosensor is to be able to detect that a compound is present. This traditionally relies on promoters that are responsive to a certain compound. We have created a <b>transposon library</b> that will determine genetic elements that will activate in the presence of toxins. We used naphthenic acids as the initial screening compound due to the difficulty in detecting them and their role as one of the most hazardous toxins in the tailings ponds.</p> |
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| - | <h2> | + | <h2>Reporting</h2> |
| - | <p> | + | <p>After being able to detect the compounds we need FRED to be able to tell us about them. With the challenges provided by the tailings ponds we decided to improve upon last year's single output electrochemical system to create a <b>triple output system</b>. This novel approach to electrochemical reporting has provided us with a fast and accurate measurement approach that can function in environments where fluorescence or luminescence would fail.</p> |
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<h2>Modelling</h2> | <h2>Modelling</h2> | ||
| - | <p> | + | <p>Due to the novel nature of our electrochemical system there were a lot of questions that were raised in the design phase of this system. One big concern was if the response would be fast enough. Rather than wasting reagents testing a multitude of timecourses a <b>mathematical model</b> was made to see how the system would behave. The results from the modelling helped guide the wetlab experiments which in turn gave new data for the model to run on.</p> |
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<h2>Prototyping</h2> | <h2>Prototyping</h2> | ||
| - | <p> | + | <p>Having the biological systems working was only one part of the system though, as there still needs to be a physical device to use and software to interpret the raw data. With this in mind we also designed and built a <b>prototype and accompanying software platform</b> that works with FRED to detect toxins. This is building upon the rudimentary prototype of last year by adding in electrical filters, variable detection settings, diagnostic LEDs and miniaturizing it all at the same time.</p> |
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Revision as of 09:28, 3 October 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
The first part of any biosensor is to be able to detect that a compound is present. This traditionally relies on promoters that are responsive to a certain compound. We have created a transposon library that will determine genetic elements that will activate in the presence of toxins. We used naphthenic acids as the initial screening compound due to the difficulty in detecting them and their role as one of the most hazardous toxins in the tailings ponds.
Reporting
After being able to detect the compounds we need FRED to be able to tell us about them. With the challenges provided by the tailings ponds we decided to improve upon last year's single output electrochemical system to create a triple output system. This novel approach to electrochemical reporting has provided us with a fast and accurate measurement approach that can function in environments where fluorescence or luminescence would fail.
Modelling
Due to the novel nature of our electrochemical system there were a lot of questions that were raised in the design phase of this system. One big concern was if the response would be fast enough. Rather than wasting reagents testing a multitude of timecourses a mathematical model was made to see how the system would behave. The results from the modelling helped guide the wetlab experiments which in turn gave new data for the model to run on.
Prototyping
Having the biological systems working was only one part of the system though, as there still needs to be a physical device to use and software to interpret the raw data. With this in mind we also designed and built a prototype and accompanying software platform that works with FRED to detect toxins. This is building upon the rudimentary prototype of last year by adding in electrical filters, variable detection settings, diagnostic LEDs and miniaturizing it all at the same time.
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!
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.
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!
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!
Upgrading
Nitrogen and 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 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!
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