Team:Calgary

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title=A Biosensor for Naphthenic Acids|
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<p>Hello! Our wiki is currently under heavy construction, so please check regularly for updates. Thank you for your patience.</p>
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<p>The University of Calgary iGEM team aims to build a biosensor for naphthenic acids. Naphthenic acids are a family of organic acids that are toxic to terrestrial and aquatic wildlife, and are waste products of the bitumen extraction process. Naphthenic acids are stored in on-site settling ponds called tailing ponds; not only do they poison the environment, but they also contribute to the corrosion of refinery equipment, which directly increases maintenance and replacement costs. Currently, sophisticated and expensive procedures such as mass spectroscopy and gas chromatography are needed to identify and assess the concentration of naphthenic acids in solution. A bacterial sensor, if developed, could greatly improve the cost- and time-efficiency of naphthenic acid detection, and facilitate a workable approach for remediation.</p>
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<h2>Our Approach</h2>
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<p>This project is separated into four subcomponents:</p>
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<p>The first is an examination of the native tailings pond genus <i>Pseudomonas</i> using ChIP-Seq, and attempting to find a naphthenic acid-sensitive promoter which can then be assembled with a reporter system.
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The second component involves constructing and characterizing an electrochemical reporter system that can produce quantifiable output without the need for optical measurements. This way, even cloudy tailings pond water can yield useful results.
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At the same time, we are also examining another potential chassis to detect and report naphthenic acids, in the microalgae <i>Chlamydomonas</i>.
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Finally, a software tool is currently in development that we hope will be able to locate and report degrees of non-homology between two separate genomes.</p>
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<p>More details about our project can be found on our <a href="https://2011.igem.org/Team:Calgary/Project">project page</a>, and more details on the biosafety of our project can be found on our <a href="https://2011.igem.org/Team:Calgary/Safety">safety page</a>.</p>
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<a style="position: absolute; float: right; margin-left: 788px; margin-top: 11px;" href="https://2011.igem.org/Team:Calgary/Notebook/PostRegionals"><img style="width: 150px;" src="https://static.igem.org/mediawiki/2011/0/0d/UCalgary2011_Fred_Flag.png"></img></a>
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This year, the University of Calgary iGEM team aims to build a biosensor for naphthenic acids (NAs). NAs are organic acids that are toxic to terrestrial and aquatic wildlife. Because they are waste products of the bitumen extraction process that mines petroleum from the Alberta oil sands, the accumulation of NAs in the on-site settling ponds (tailings ponds) is an environmental concern requiring constant monitoring and eventual remediation. In addition to harming the environment, NAs also contribute to refinery equipment corrosion, directly increasing maintenance and replacement costs. Currently, sophisticated and expensive procedures, such as Fourier Transform Infrared Spectrometer (FTIR) or gas chromatography-mass spectrometry, are needed to identify and assess NA concentrations in the environment. A bacterial sensor, if developed, could greatly improve the cost- and time-efficiency of NA detection, and facilitate a workable approach for remediation.
 +
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 +
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 +
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<h3>Our Naphthenic Acid Biosensor</h3>
 +
<p><br><br>A detailed description of our project can be seen <a style="color:#42ffd9;" href="https://2011.igem.org/Team:Calgary/Project">here</a>! Below is a picture of what our final product will look like. We will have our biosensing bacterium in a container that the sample to be measured can be added to.</p><br><br><p style="font-size: 14px;"><b>Roll over the bacterium below!</b></p>
 +
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 +
 
 +
<div id="subpromoter">
 +
<h3>An NA-Sensitive Promoter</h3>
 +
<p>The most critical component of our biosensor is a naphthenic acid sensory element. This would likely be a promoter element. The major challenge for this was that given the lack of available information on NA degradation, there was no NA sensitive promoter available in the literature for us to use. We needed to develop methods to search for such an element. These included our novel “fishing” method as well as our bioinformatics approach. Click on the promoter to learn more about this!</p>
 +
</div>
 +
 +
<div id="subreporter">
 +
<h3>An Electrochemical Reporter</h3>
 +
<p>We need a reliable reporter for our system. Given the highly variable and often turbid nature of oil sands tailings ponds however, we needed a special kind of reporter. We chose to use the <i>lacZ</i> gene, but characterize it as an electrochemical reporter. Click the gene to learn more!</p>
 +
</div>
 +
 +
<div id="subchassis">
 +
<h3>A Suitable Chassis</h3>
 +
<p>We need a chassis in which to house our system. Given that we intended to get our sensory element from either <i>Pseudomonas</i> or microalgae, and that these organisms are both naturally present within tailings ponds, we chose to focus on them. As such, we contributed and characterized several parts for future work in microalgae, and to move plasmids efficiently from <i>E. coli</i> to <i>Pseudomonas</i>. Click the chassis to learn more!</p>
 +
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 +
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 +
 
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<div id="box2">
 +
<h2>The Vision: A Naphthenic Acid Biosensor</h2>
 +
<p>We plan to create a relatively small, cheap biosensing device that can respond to naphthenic acids and produce an electrochemical output. Roll over the individual parts for more details.</p>
 +
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<h2>Our Sponsors</h2>
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Latest revision as of 03:55, 29 October 2011

Welcome!

This year, the University of Calgary iGEM team aims to build a biosensor for naphthenic acids (NAs). NAs are organic acids that are toxic to terrestrial and aquatic wildlife. Because they are waste products of the bitumen extraction process that mines petroleum from the Alberta oil sands, the accumulation of NAs in the on-site settling ponds (tailings ponds) is an environmental concern requiring constant monitoring and eventual remediation. In addition to harming the environment, NAs also contribute to refinery equipment corrosion, directly increasing maintenance and replacement costs. Currently, sophisticated and expensive procedures, such as Fourier Transform Infrared Spectrometer (FTIR) or gas chromatography-mass spectrometry, are needed to identify and assess NA concentrations in the environment. A bacterial sensor, if developed, could greatly improve the cost- and time-efficiency of NA detection, and facilitate a workable approach for remediation.

Our Naphthenic Acid Biosensor



A detailed description of our project can be seen here! Below is a picture of what our final product will look like. We will have our biosensing bacterium in a container that the sample to be measured can be added to.



Roll over the bacterium below!

An NA-Sensitive Promoter

The most critical component of our biosensor is a naphthenic acid sensory element. This would likely be a promoter element. The major challenge for this was that given the lack of available information on NA degradation, there was no NA sensitive promoter available in the literature for us to use. We needed to develop methods to search for such an element. These included our novel “fishing” method as well as our bioinformatics approach. Click on the promoter to learn more about this!

An Electrochemical Reporter

We need a reliable reporter for our system. Given the highly variable and often turbid nature of oil sands tailings ponds however, we needed a special kind of reporter. We chose to use the lacZ gene, but characterize it as an electrochemical reporter. Click the gene to learn more!

A Suitable Chassis

We need a chassis in which to house our system. Given that we intended to get our sensory element from either Pseudomonas or microalgae, and that these organisms are both naturally present within tailings ponds, we chose to focus on them. As such, we contributed and characterized several parts for future work in microalgae, and to move plasmids efficiently from E. coli to Pseudomonas. Click the chassis to learn more!

The Vision: A Naphthenic Acid Biosensor

We plan to create a relatively small, cheap biosensing device that can respond to naphthenic acids and produce an electrochemical output. Roll over the individual parts for more details.

Promoter Reporter Chassis

Our Sponsors

Retrieved from "http://2011.igem.org/Team:Calgary"