Difference between revisions of "Team:CMUQ/Design"

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<h1>Design</h1>
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<p>
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Design is the first step in the design-build-test cycle in engineering and synthetic biology. Use this page to describe the process that you used in the design of your parts. You should clearly explain the engineering principles used to design your project.
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This page is different to the "Applied Design Award" page. Please see the <a href="https://2017.igem.org/Team:CMUQ/Applied_Design">Applied Design</a> page for more information on how to compete for that award.
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<!--- THIS IS WHERE THE HTML BEGINS --->
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      <!-- Brand and toggle get grouped for better mobile display -->
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        <a class="navbar-brand" href="https://2017.igem.org/Team:CMUQ" >CMUQ</a>
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      <!-- Collect the nav links, forms, and other content for toggling -->
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                <a class="dropdown-toggle" data-toggle="dropdown" href="#">PROJECT <span class="caret"> </span></a>
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                <ul class="dropdown-menu">
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                            <li><a href="https://2017.igem.org/Team:CMUQ/descritpion">Description</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/design">Design</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/safety">Safety</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/Demonstrate">Demonstrate</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/Model">Model</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/Collaborations">Collaborations</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/JudgingForm">Judging Form </a> </li>
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                </ul>
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            </li>
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            <li class="dropdown">
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                <a class="dropdown-toggle" data-toggle="dropdown" href="#"> COMMUNITY INVOLVEMENT <span class="caret"> </span></a>
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                <ul class="dropdown-menu">
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                            <li><a href="https://2017.igem.org/Team:CMUQ/humanpractices">Human Practices</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/HP/Silver"> Silver HP </a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/Engagement"> Outreach</a></li>
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                <a class="dropdown-toggle" data-toggle="dropdown" href="#"> LAB WORK <span class="caret"> </span></a>
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                <ul class="dropdown-menu">
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                            <li><a href="https://2017.igem.org/Team:CMUQ/Notebook">Notebook</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/protocols">Procedures</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/InterLab">InterLab Study</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/results">Analysis</a></li>
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                </ul>
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                <a class="dropdown-toggle" data-toggle="dropdown" href="#"> TEAM <span class="caret"> </span></a>
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                <ul class="dropdown-menu">
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                    <li><a href="https://2017.igem.org/Team:CMUQ/Team">Team</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/Attributions">Attributions</a></li>
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                </ul>
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            </li>
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            <li><a href="https://2017.igem.org/Team:CMUQ/gallery">GALLERY</a></li>
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<div class="main">
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<div class="centered"> <h1>Design </h1> </div>
 
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<body>
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<h5>What should this page contain?</h5>
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<ul>
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<li>Explanation of the engineering principles your team used in your design</li>
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<li>Discussion of the design iterations your team went through</li>
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<li>Experimental plan to test your designs</li>
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</ul>
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<div>
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<p style="font-family: 'Lora', serif; margin-right: 120px; margin-left:120px;font-size:25px;margin-top:30px;">
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Our team will focus on developing an <b>eco-friendly approach</b> to combat biocorrosion in water cooling systems, specifically in the <b>oil-production industry</b>. A wide range of bacterial species are found in the areas near oil extraction facilities. Many of these organisms cause serious problems for the oil industry by producing corrosive by-products. Sulfate-reducing bacteria (SRB), the main species involved in the <b>Microbial Induced Corrosion (MIC)</b>, can colonize on the pipelines by forming bacterial biofilms with the release of Extracellular Matrix Substances (EMS) for adhesion and colony growth. Currently, biocides are commonly used in the oil industry for targeting these bacteria. But, these chemicals ultimately end up in the sea water which poses a huge threat to marine life.
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</p>
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<br>
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<p style="font-family: 'Lora', serif; margin-right: 120px; margin-left:120px;font-size:25px;margin-top:30px;">
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Bacteria can <b>sense</b> a vast range of environmental signals, from the concentrations of nutrients and toxins to oxygen levels, pH and <b>osmolarity</b>. For our project, we plan to genetically engineer both <b>sensor and remediation bacteria</b> to sense osmolarity of the water used to cool oil pipelines and then to secrete an enzyme to degrade the extracellular matrix of the biofilm
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</p>
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<br>
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<p style="font-family: 'Lora', serif; margin-right: 120px; margin-left:120px;font-size:25px;margin-top:30px;">
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Halanaerobium which is the major SRB found in these pipelines live on high salt concentrations (optimally at NaCl concentrations 1.7–2.5 M and requiring a minimum of 0.3–1.7 M NaCl for growth). Therefore, we plan to use water samples obtained from an oil extraction company in Qatar to determine the exact concentrations required for optimal growth of the SRB’s. We plan to use this data for determining if fresh water can be used to kill these bacteria. If successful, this idea can work as a novel method for non-invasive treatment of biofilms in oil-cooling pipelines. We will construct a salt biosensor using the osmo-responsive promoter of the ProU operon to drive a Red Fluorescent Protein (RFP) expression, which can be measured using fluorescence and a plate reader. This will allow us to monitor the osmolarity of outflow to determine if the SRB are likely to grow. After osmolarity biosensor is added, samples from the water can be taken frequently and the RFP’s fluorescence can be measured using simple fluorescence measurement in a plate reader.
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</p>
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<br>
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<p style="font-family: 'Lora', serif; margin-right: 120px; margin-left:120px;font-size:25px;margin-top:30px;">
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If salt is still high after mixing with fresh water we can then use the ProU induction to increase expression of the Dispersin B (DspB) gene, which codes for a protein that digests the polysaccharides, a major component of the gram-positive bacterial cell wall and biofilms.
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</p>
 
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<h5>Inspiration</h5>
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<ul>
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<div class="footer">
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<li><a href="https://2016.igem.org/Team:MIT/Experiments/Promoters">2016 MIT</a></li>
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<li><a href="https://2016.igem.org/Team:BostonU/Proof">2016 BostonU</a></li>
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<span class="glyphicon glyphicon-chevron-up"></span>
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<li><a href="https://2016.igem.org/Team:NCTU_Formosa/Design">2016 NCTU Formosa</a></li>
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Revision as of 17:06, 1 November 2017

Design

Our team will focus on developing an eco-friendly approach to combat biocorrosion in water cooling systems, specifically in the oil-production industry. A wide range of bacterial species are found in the areas near oil extraction facilities. Many of these organisms cause serious problems for the oil industry by producing corrosive by-products. Sulfate-reducing bacteria (SRB), the main species involved in the Microbial Induced Corrosion (MIC), can colonize on the pipelines by forming bacterial biofilms with the release of Extracellular Matrix Substances (EMS) for adhesion and colony growth. Currently, biocides are commonly used in the oil industry for targeting these bacteria. But, these chemicals ultimately end up in the sea water which poses a huge threat to marine life.


Bacteria can sense a vast range of environmental signals, from the concentrations of nutrients and toxins to oxygen levels, pH and osmolarity. For our project, we plan to genetically engineer both sensor and remediation bacteria to sense osmolarity of the water used to cool oil pipelines and then to secrete an enzyme to degrade the extracellular matrix of the biofilm


Halanaerobium which is the major SRB found in these pipelines live on high salt concentrations (optimally at NaCl concentrations 1.7–2.5 M and requiring a minimum of 0.3–1.7 M NaCl for growth). Therefore, we plan to use water samples obtained from an oil extraction company in Qatar to determine the exact concentrations required for optimal growth of the SRB’s. We plan to use this data for determining if fresh water can be used to kill these bacteria. If successful, this idea can work as a novel method for non-invasive treatment of biofilms in oil-cooling pipelines. We will construct a salt biosensor using the osmo-responsive promoter of the ProU operon to drive a Red Fluorescent Protein (RFP) expression, which can be measured using fluorescence and a plate reader. This will allow us to monitor the osmolarity of outflow to determine if the SRB are likely to grow. After osmolarity biosensor is added, samples from the water can be taken frequently and the RFP’s fluorescence can be measured using simple fluorescence measurement in a plate reader.


If salt is still high after mixing with fresh water we can then use the ProU induction to increase expression of the Dispersin B (DspB) gene, which codes for a protein that digests the polysaccharides, a major component of the gram-positive bacterial cell wall and biofilms.