Team:Calgary

From 2011.igem.org

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<img id="titlebar" src="https://static.igem.org/mediawiki/2011/4/42/UCalgary_TitleBar.png"></img>
<h1 id="pagetitle">Welcome!</h1>
<h1 id="pagetitle">Welcome!</h1>
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<img class="boxtop1" src="https://static.igem.org/mediawiki/2011/c/cf/UCalgary_MainPageBox1.png"></img>
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The University of Calgary’s iGEM team is working on developing an electrochemical biosensor for Naphthenic Acids (NAs). NAs are toxic surfactants released into tailings ponds as a by-product of the bitumen extraction process of oil sands.  Microorganisms indigenous to tailings ponds that are uniquely capable of degrading NAs suggest that bioremediation may be a viable solution. To be successful, however, levels of NAs need to be monitored and existing methods for detection are costly and offsite. Using two NA-degrading organisms relatively new to iGEM: microalgae and pseudomonads, we used bioinformatics and a novel NA affinity-based screen in an attempt to identify a sensory element. In the process, we have characterized an electrochemical reporter system and built a working measurement device.  We have also submitted new parts for future work in microalgae, as well as novel parts to move constructs between Pseudomonas and E. coli.  
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<p>
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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.
</p>
</p>
 +
</div>
<img class="boxbottom1" src="https://static.igem.org/mediawiki/2011/1/11/UCalgary_MainPageBox1Bottom.png"></img>
<img class="boxbottom1" src="https://static.igem.org/mediawiki/2011/1/11/UCalgary_MainPageBox1Bottom.png"></img>
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</div>
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<div id="subdefault">
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<h3>Our Naphthenic Acid Biosensor</h3>
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<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>
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<div id="subpromoter">
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<h3>An NA-Sensitive Promoter</h3>
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<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>
 +
</div>
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</div>
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<div id="box2">
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<h2>The Vision: A Naphthenic Acid Biosensor</h2>
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<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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<img id="sensorimage" src="https://static.igem.org/mediawiki/2011/f/f8/UCalgary2011_MainPageDevice.png"></img>
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<a id="promoter" href="https://2011.igem.org/Team:Calgary/Project/Promoter">Promoter</a>
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<a id="reporter" href="https://2011.igem.org/Team:Calgary/Project/Reporter">Reporter</a>
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<a id="chassis" href="https://2011.igem.org/Team:Calgary/Project/Chassis">Chassis</a>
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<h2>Our Sponsors</h2>
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<td><a href="http://www.mhc.ab.ca/"><img src="https://static.igem.org/mediawiki/2011/7/78/UCalgary2011_Medicine_Hat_College_Logo.png"></img></a></td>
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<script src="http://widgets.twimg.com/j/2/widget.js"></script>
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</div>
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<div id="box2">
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<a id="likebutton" href="http://www.facebook.com/pages/Calgary-iGEM/215971681759173">
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<h2>Building a Naphthenic Acid Biosensor</h2>
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<img src="https://static.igem.org/mediawiki/2011/5/57/UCalgary_FacebookLikeButton_Small.png"></img>
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<p>This project is separated into four subcomponents:</p>
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</a>
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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 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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<img class="boxtop3" src="https://static.igem.org/mediawiki/2011/2/22/UCalgary_MainPageBox3.png"></img>
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<h2>Our Sponsors</h2>
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<td><img src="https://static.igem.org/mediawiki/2011/9/9a/UCalgary_OSRIN_Logo.png"></img></td>
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<td><img src="https://static.igem.org/mediawiki/2011/8/8a/UCalgary_Sigma_Aldrich_Logo.png"></img></td>
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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

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