Difference between revisions of "Team:Uppsala/Description"

 
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<!--<h2> Project Description </h2>
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<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
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<h5>What should this page contain?</h5>
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<li> A clear and concise description of your project.</li>
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<li>A detailed explanation of why your team chose to work on this particular project.</li>
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<li>References and sources to document your research.</li>
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<li>Use illustrations and other visual resources to explain your project.</li>
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<h4>Advice on writing your Project Description</h4>
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We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.
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Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
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<h4>References</h4>
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<p>iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you though about your project and what works inspired you.</p>
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  <img id="project_image" src="https://static.igem.org/mediawiki/2015/5/5a/Uppsala_NewProjectConstruct.png" usemap="#skittles">  
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  <!--<figcaption>To read more about the different parts of our project in more detail, please click on the buttons below, or on the constructs in the image above</figcaption>-->
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    <map name="skittles">
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      <area shape="rect" coords="45,180,760,100" href="https://2015.igem.org/Team:Uppsala/Enzymes" alt="Enzymatic degradation" title="Enzymatic degradation">
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      <area shape="rect" coords="40,350,810,300" href="https://2015.igem.org/Team:Uppsala/Naphthalene" alt="Naphthtalene pathway" title="Naphthalene pathway">
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      <area shape="rect" coords="145,430,535,480" href="https://2015.igem.org/Team:Uppsala/Biosurfactants" alt="Biosurfactants" title="Biosurfactants">
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    <ul id="tab_list">
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      <li><a class="tab" href="https://2015.igem.org/Team:Uppsala/Enzymes"><b><span class="smaller">Enzymatic degradation</span></b></a></li>
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      <li><a class="tab" href="https://2015.igem.org/Team:Uppsala/Naphthalene"><b><span class="smaller">Naphthalene Pathway</b></a></li>
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      <li><a class="tab" href="https://2015.igem.org/Team:Uppsala/Biosurfactants"><b>Biosurfactants</b></a></li>
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      <li><a class="tab" href="https://2015.igem.org/Team:Uppsala/Design"><b>Software</b></a></li>
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      <li><a class="tab" href="https://2015.igem.org/Team:Uppsala/Software"><b>Biosensor design</b></a></li>
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  </ul>
  
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<h4>Inspiration</h4>
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    <h1 class="header">Project</h1>
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<p>See how other teams have described and presented their projects: </p>
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    <hr>
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    <h2 class="header">Overview and aim</h2>
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    <p>
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    This is a project in synthetic biology performed during a summer by 24 dedicated and curious students from Uppsala University who planned the project over the entire spring semester – and in the fall the team will present their achievements in Boston where iGEM teams from all over the world compete with their projects.
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We have decided to develop a method for degradation and detection of the carcinogenic substances polycyclic aromatic hydrocarbons (PAHs), thus contributing to solve one of the world's many environmental problems. Our priorities are to detect those substances in an automated manner and to optimize enzyme efficiency, which will result in one distinct product.
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Four previous iGEM teams were interested in this topic and succeeded to some degree in degrading low-molecular weight PAHs. We plan to benefit from this and from our own team’s knowledge and target high-molecular weight PAHs as well.
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    </p>
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    <h2 class="header">Vision</h2>
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    <p>
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    PAHs can result from industrial practices such as: burning of fuel, wood, waste, polypropylene, polystyrene and petroleum products. Industries that use coal tar, coke or asphalt are also a target for our products. Moreover, PAHs are dominant in petrol leakages and petrol industries. Since there is always a search for a better alternative or a more effective way to degrade the PAHs, our product will be a pioneer in the market.
 +
    </p>
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    <p>
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    We aim to provide a microorganism that can degrade high- and low-molecular weight PAHs. These substances are formed during incomplete combustion or pyrolysis of organic materials and can be found in water, soil, and food products. According to researches, PAHs cause skin, lung, bladder, liver, and stomach cancers in lab mice. PAHs can also affect the hematopoietic and immune systems generating reproductive, neurologic and developmental effects. As a result, degrading these substances is an urgent necessity.
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    </p>
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    <h2 class="header">The construct</h2>
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    <p>
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    In our construct we strive to degrade both the heavy molecular weight PAHs, such as benzo(a)pyrene (BaP), as well as low molecular PAHs, such as naphthalene. The low molecular weight PAHs can freely diffuse over the bacterial cell membranes, while the heavy molecular weight PAHs diffuse at a lesser degree. PAHs found as pollutants are always found in heterogeneous mixes of heavy and low molecular weight. In our system the light weight PAH, naphthalene, will be degraded by six enzymes acquired from a naphthalene-degrading plasmid from <i>Pseudomonas putida</i>. These enzymes will degrade the naphthalene into the smaller and less toxic salicylate, which in turn will bind to the inducer NahR, acquired from the same pathway. The NahR inducer has been utilized to activate the production of two enzymes, a laccase and a dioxygenase. These two enzymes will be exported out of our cell in order to degrade the heavy-weight BaP. Since BaP will not freely enter the cell, we have attached export tags to these two enzymes in order to effectivize our system. The NahR system will also induce the production of a reporter gene such as sYFP to give a visual indication of the presence of PAHs in the medium.
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    </p>
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    <p>
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    To further optimize our construct, we have also included the expression of biosurfactant-producing enzymes RhlA and RhlB. As the PAHs are highly hydrophobic they tend to aggregate in an aqueous solution, making it difficult for the active sites of the degrading enzymes to reach their substrates. The biosurfactants will dissolve these aggregates, freeing up more PAHs for the enzymes to degrade.
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    </p>
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    <h2>The goal</h2>
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    <p>
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    First, we are working on developing a bacterium that will degrade PAHs. We aim to engineer a biobrick that contains the necessary genetic information and then transferring it into <i>E. coli</i>, which is a non-pathogenic bacterium. We are working not only to degrade PAHs, but also to provide an automated biosensor that can be used to detect the presence of these substances in different samples. The PAH biosensor can be used in food factories, waste management facilities, and water treatment plants. With our detector we can encourage industries to monitor their PAH emissions.
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    </p>
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<p>You can learn more about our project by clicking through the tabs under the Overview header!
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    </div>
  
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<li><a href="https://2014.igem.org/Team:Imperial/Project"> Imperial</a></li>
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<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> UC Davis</a></li>
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<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">SYSU Software</a></li>
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<h2>Project description</h2>
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Our project has been aimed to develop a method for degradation and detection of the carcinogenic substances PAHs (polycyclic aromatic hydrocarbons),  which results from industrial practices such as: burning of fuel, wood, waste, polypropylene, polystyrene and petroleum products. PAHs are also dominant in petrol leakages and petrol industries. Hence, breaking of these PAHs could  contribute to solve one of the world's many environmental problems. Apart from environmental issues, researchers prove that PAHs caused skin, lung, bladder, liver, and stomach cancers in lab mice. So, the importance of degrading these substances is in dire need. 
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</p>
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<p>
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Our priorities are to detect these substances in an automated manner and to optimize enzyme efficiency, which will result in one distinct product. Four previous iGEM teams were interested in this topic and succeeded to some degree in degrading low-molecular weight PAHs. We plan to benefit from this and from our own team’s knowledge and target high-molecular weight PAHs as well.
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</p>
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<h2>Goal</h2>
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<p>
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First, we are working on developing a bacterium that will degrade high and low molecular weight PAHs. We aim to engineer a biobrick that contains the necessary genetic information and then transferring it into E. coli, which is a non-pathogenic bacterium. We are working not only to degrade PAHs, but also to provide an automated biosensor that can be used to detect the presence of these substances in different samples. The PAH biosensor can be used in food factories, waste management facilities, and water treatment plants. With our detector we can encourage industries to monitor their PAH emissions.
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</p>
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<h2>The construct</h2>
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<p>
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In our construct we strive to degrade both the heavy molecular weight PAHs, such as BaP (Benzo(a)pyrene), as well as low molecular PAHs, such as naphthalene. The low molecular weight PAHs can freely diffuse over the bacterial cell membranes, while the heavy molecular weight PAHs diffuse at a lesser degree. PAHs found as pollutants are always found in heterogeneous mixes of heavy and low molecular weight. In our system the light weight PAHs, naphthalene, will be degraded by six enzymes acquired from a naphthalene-degrading plasmid from Pseudomonas putida. These enzymes will degrade the naphthalene into the smaller and less toxic salicylate, which in turn will bind to the inducer NahR, acquired from the same pathway. The NahR inducer has been utilized to activate the production of two enzymes, a laccase and a dioxygenase. These two enzymes will be exported out of our cell in order to degrade the heavy-weight BaP. Since BaP will not freely enter the cell we have attached export tags so our enzymes could work extracellularly. This NahR will also induce the production of a fluorescent protein to give a visual indication of the presence of PAHs in the medium.
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</p>
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<p>
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To further optimize our construct, we have also included the expression of biosurfactant-producing enzymes RhlA and RhlB. As the PAHs are highly hydrophobic they tend to aggregate in an aqueous solution, making it difficult for the active sites of the degrading enzymes to reach their substrates. The biosurfactants will dissolve these aggregates, freeing up more PAHs for the enzymes to degrade.
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Latest revision as of 13:15, 14 November 2015

Enzymatic degradation Naphthtalene pathway Biosurfactants

Project

Overview and aim

This is a project in synthetic biology performed during a summer by 24 dedicated and curious students from Uppsala University who planned the project over the entire spring semester – and in the fall the team will present their achievements in Boston where iGEM teams from all over the world compete with their projects. We have decided to develop a method for degradation and detection of the carcinogenic substances polycyclic aromatic hydrocarbons (PAHs), thus contributing to solve one of the world's many environmental problems. Our priorities are to detect those substances in an automated manner and to optimize enzyme efficiency, which will result in one distinct product. Four previous iGEM teams were interested in this topic and succeeded to some degree in degrading low-molecular weight PAHs. We plan to benefit from this and from our own team’s knowledge and target high-molecular weight PAHs as well.

Vision

PAHs can result from industrial practices such as: burning of fuel, wood, waste, polypropylene, polystyrene and petroleum products. Industries that use coal tar, coke or asphalt are also a target for our products. Moreover, PAHs are dominant in petrol leakages and petrol industries. Since there is always a search for a better alternative or a more effective way to degrade the PAHs, our product will be a pioneer in the market.

We aim to provide a microorganism that can degrade high- and low-molecular weight PAHs. These substances are formed during incomplete combustion or pyrolysis of organic materials and can be found in water, soil, and food products. According to researches, PAHs cause skin, lung, bladder, liver, and stomach cancers in lab mice. PAHs can also affect the hematopoietic and immune systems generating reproductive, neurologic and developmental effects. As a result, degrading these substances is an urgent necessity.

The construct

In our construct we strive to degrade both the heavy molecular weight PAHs, such as benzo(a)pyrene (BaP), as well as low molecular PAHs, such as naphthalene. The low molecular weight PAHs can freely diffuse over the bacterial cell membranes, while the heavy molecular weight PAHs diffuse at a lesser degree. PAHs found as pollutants are always found in heterogeneous mixes of heavy and low molecular weight. In our system the light weight PAH, naphthalene, will be degraded by six enzymes acquired from a naphthalene-degrading plasmid from Pseudomonas putida. These enzymes will degrade the naphthalene into the smaller and less toxic salicylate, which in turn will bind to the inducer NahR, acquired from the same pathway. The NahR inducer has been utilized to activate the production of two enzymes, a laccase and a dioxygenase. These two enzymes will be exported out of our cell in order to degrade the heavy-weight BaP. Since BaP will not freely enter the cell, we have attached export tags to these two enzymes in order to effectivize our system. The NahR system will also induce the production of a reporter gene such as sYFP to give a visual indication of the presence of PAHs in the medium.

To further optimize our construct, we have also included the expression of biosurfactant-producing enzymes RhlA and RhlB. As the PAHs are highly hydrophobic they tend to aggregate in an aqueous solution, making it difficult for the active sites of the degrading enzymes to reach their substrates. The biosurfactants will dissolve these aggregates, freeing up more PAHs for the enzymes to degrade.

The goal

First, we are working on developing a bacterium that will degrade PAHs. We aim to engineer a biobrick that contains the necessary genetic information and then transferring it into E. coli, which is a non-pathogenic bacterium. We are working not only to degrade PAHs, but also to provide an automated biosensor that can be used to detect the presence of these substances in different samples. The PAH biosensor can be used in food factories, waste management facilities, and water treatment plants. With our detector we can encourage industries to monitor their PAH emissions.

You can learn more about our project by clicking through the tabs under the Overview header!