Difference between revisions of "Team:MIT/Description"

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{{MIT}}
 
 
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<h1>Description</h1>
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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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<h3>What should this page contain?</h3>
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<ul>
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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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<h3>Inspiration</h3>
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<p>See how other teams have described and presented their projects: </p>
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<ul>
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    .active {
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<li><a href="https://2016.igem.org/Team:Imperial_College/Description">2016 Imperial College</a></li>
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<li><a href="https://2016.igem.org/Team:Wageningen_UR/Description">2016 Wageningen UR</a></li>
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    }
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<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> 2014 UC Davis</a></li>
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<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">2014 SYSU Software</a></li>
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<h3>Advice on writing your Project Description</h3>
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<p>
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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 concise, accurate, and unambiguous in your achievements.  
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<h3>References</h3>
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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 thought about your project and what works inspired you.</p>
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    <img class="bg" src="https://i.imgur.com/1hidNYz.png" style="width:100%;">
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<div class="menu">
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        <div class="sub"><a class="active" href="#home">Home</a></div>
 +
        <div class="dropdown">
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            <div class="sub"><a href="https://2018.igem.org/Team:MIT/Team">Team</a></div>
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            <div class="dropdown-content">
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                <a href="https://2018.igem.org/Team:MIT/Team">Team Members</a>
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                <a href="#">Collaborations</a>
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            </div>
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        </div>
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        <div class="dropdown">
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            <div class="sub"><a href="#project">Project</a></div>
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            <div class="dropdown-content">
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                <a href="#">Sensing</a>
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                <a href="#">Output</a>
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                <a href="#">Biofilm Assays</a>
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            </div>
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        </div>
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        <div class="dropdown">
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            <div class="sub"><a href="#project">Parts</a></div>
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            <div class="dropdown-content">
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                <a href="#">Basic Parts</a>
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                <a href="#">Composite Parts</a>
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            </div>
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        </div>
 +
        <div class="sub"><a href="#safety">Safety</a></div>
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        <div class="dropdown">
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            <div class="sub"><a href="#project">Human Practices</a></div>
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            <div class="dropdown-content">
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                <a href="#">Integrated Human Practices</a>
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                <a href="#">Public Engagement</a>
 +
            </div>
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        </div>
 +
        <div class="sub"><a href="#awards">Awards</a></div>
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    </div>
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    <div class="h1" style="position: absolute; top: 5vw; left: 40vw;">Background</divh1>
 +
    <p1 style="position: absolute; top: 13vw; left: 5vw;">
 +
        As a chronic but non-lethal condition, dental caries are often overlooked as a target for modern therapeutics, and the quality of
 +
        dental caries treatment has lagged behind that of more life-threatening diseases such as cancer. However, it is a well established
 +
        fact that oral health affects overall health--for example, severe cavities can lead to systemic illnesses such
 +
        as heart disease. Therefore, dental caries is still a prevalent and critical issue.
 +
        <p></p>
 +
        The process of cariogenesis is highly facilitated by the growth of dense, sticky biofilm on the surface of teeth. This bioflim
 +
    cuts off the bacteria's access to oxygen, thereby forcing them to revert to anaerobic respiration. Lactic acid is released as a
 +
    byproduct of bacterial respiration, and leads to demineralization of the enamel and cavity formation. </p1>
 +
    <h1 style="position: absolute; top: 59vw; left: 38vw;">Biofilm Formation</h1>
 +
    <p1 style="position: absolute; top: 67vw; left: 5vw; ">
 +
 +
 +
        In its natural, non-pathogenic state, <i>S. mutans</i> lives planktonically (free-floating).
 +
        The transition from the planktonic to biofilm state requires expression of virulence genes, which is coordinated via
 +
        quorum sensing: a mode of communication employed by many bacteria to coordinate gene expression
 +
        and synchronous behavior across a population or species. In the case of <i>S. mutans</i>, quorum sensing results in the expression of
 +
        genes coding for extracellular glucosyltransferase (GTF) enzymes. These enzymes synthesize adhesive glucans, which are used by
 +
        the bacteria to adhere both to each other and to the enamel of the tooth.
 +
        <p></p>
 +
        Most quorum-sensing systems involve small, diffusible peptides which are sent out as a signal by one bacteria and
 +
        received by another. The peptides are detected by a receptor on the membrane or in the cytoplasm of other bacteria, which then
 +
        initiate a signal transduction pathway that upregulates the quorum-sensing peptide, as well as other genes related to the coordinated
 +
        behavior of the population. Once enough of the signal has been received by the majority of the population, bacterial behavior
 +
        shifts to perform a synchronized activity.Biofilm formation is one of the synchronized behaviors initiated by quorum sensing.
 +
        During this process, <i>S. Mutans</i> create and perpetuate the Competence Stimulating Peptide (CSP), a small molecule that is used to
 +
        initiate the formation of dental plaque. The pathway through which the cells sense and respond to CSP is referred to the ComCDE pathway. </p1>
 +
 +
    <h1 style="color: #410081; position: absolute; top: 120vw; left: 48vw;">Quorum Sensing in <i>S. mutans</i> </h1>
 +
 +
    <div class="dropdown1">
 +
    <img class="icon" src="https://i.imgur.com/lCObuBL.png" style="position: absolute; top: 127vw; left: 14.5vw;">
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        <div class="dropdown-content1">
 +
        <p2 style="position: absolute; top: 130vw; left: 42vw;">Competence Stimulating Peptide (CSP)
 +
        <p></p>
 +
        Small peptide communication signal produced by <i>S. mutans</i> in quorum sensing.
 +
            <p> </p>
 +
 +
            THIS SECTION IS STILL IN PROGRESS! WAITING ON FORMAL TEXT FROM SENSING TEAM :)
 +
 +
        </p2>
 +
        </div>
 +
    </div>
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    <div class="dropdown1">
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        <img class="icon2" src="https://i.imgur.com/QCDjdqU.png" style="position: absolute; top: 133vw; left: 13vw;">
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        <div class="dropdown-content1">
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            <p2 style="position: absolute; top: 130vw; left: 42vw;">ComD
 +
                <p></p>
 +
                ComD: Receptor of CSP
 +
            </p2>
 +
        </div>
 +
    </div>
 +
 +
    <div class="dropdown1">
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        <img class="icon3" src="https://i.imgur.com/gsdyHza.png" style="position: absolute; top: 149vw; left: 26vw;">
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        <div class="dropdown-content1">
 +
            <p2 style="position: absolute; top: 130vw; left: 42vw;">Phosphorylation
 +
                <p></p>
 +
                ComD phosphorylates the response regulator
 +
            </p2>
 +
        </div>
 +
    </div>
 +
 +
    <div class="dropdown1">
 +
        <img class="icon4" src="https://i.imgur.com/82MOpct.png" style="position: absolute; top: 152vw; left: 14.7vw;">
 +
        <div class="dropdown-content1">
 +
            <p2 style="position: absolute; top: 130vw; left: 42vw;">ComE
 +
                <p></p>
 +
                ComE: Response Regulator
 +
            </p2>
 +
        </div>
 +
    </div>
 +
 +
    <div class="dropdown1">
 +
        <img class="icon5" src="https://i.imgur.com/sWUEvMS.png" style="position: absolute; top: 166vw; left: 7vw;">
 +
        <div class="dropdown-content1">
 +
            <p2 style="position: absolute; top: 130vw; left: 42vw;">Genetic Response
 +
                <p></p>
 +
                Response regulator binds to and activates transcription of pro-biofilm genes
 +
            </p2>
 +
        </div>
 +
    </div>
 +
 +
    <p3 style="position: absolute; top: 174vw; left: 1vw;"><i>(hover over each element to learn about its role)</i></p3>
 +
 +
    <img src="https://i.imgur.com/X61EJIs.png" style="position: absolute; top: 183vw; left: 45vw; width:50vw; ">
 +
 +
    <h1 style="position: absolute; top: 180vw; left: 5vw;">Our Synthetic Circuit</h1>
 +
    <p1 style="position: absolute; top: 188vw; left: 5vw; margin-right: 58vw;">
 +
        Our goal is to port the ComCDE system into Human Embryonic Kidney (HEK) cells. This would allow our engineered cells
 +
        to sense the presence of CSP and therefore detect when biofilm formation is about to occur. ComD and ComE will be
 +
        expressed constitutively, while our three outputs (ScFv's P126 and P136, and Kappa casein) will be expressed under the ComE
 +
        promoter, which is activated by the ComE response regulator protein as described above.
 +
    </p1>
 +
 +
    <h1 style="position: absolute; top: 222vw; left: 5vw;">Outputs</h1>
 +
    <p1 style="position: absolute; top: 230vw; left: 5vw; margin-right: 5vw;">
 +
        Upon activation of our biofilm-sensing system, our cells will output proteins that have been shown to
 +
        reduce the biofilm-forming capabilities of <i>S. mutans</i>.
 +
    </p1>
 +
 +
    <p1 style="position: absolute; top: 255vw; left: 5vw; margin-right: 5vw;">
 +
        Our first protein is kappa casein, a protein derived from bovine milk. It interferes with the adhesive power of the
 +
        glucans post synthesis through a combination of hydrophilicity and negative charge (Vacca-Smith, 1994).
 +
    </p1>
 +
 +
    <p1 style="position: absolute; top: 280vw; left: 5vw; margin-right: 5vw;">
 +
        Our second option is using Single Chain Variable Fragments (ScFv's), which are comprised of the variable fragments of
 +
        monoclonal antibodies joined by a short peptide linker. Our two ScFv's, P126 and P136, bind to the N and C termini of the
 +
        glucosyltransferases, preventing the production of glucans. (Fukushima, 1992)
 +
    </p1>
 +
 +
<footer>
 +
    <p>
 +
        References:
 +
    <p></p>
 +
        Vacca-Smith, A.M., Van Wuyckhuyse, B.C., Tabak, L.A., Bowen, W.H. (1994). The effect of milk and casein proteins
 +
        on the adherence of Streptococcus mutans to saliva-coated hydroxyapatite.
 +
        <i>Archives of Oral Biology</i>, Volume 39: Issue 12. 1063-1069.
 +
    <p></p>
 +
        Fukushima, K., Okada, T., Ochiai, K. (1993). Production, characterization, and application of monoclonal antibodies
 +
        which distinguish three glucosyltransferases from Streptococcus mutans.
 +
        <i>Infect Immun.</i>, 61. 323-8.
 +
    </p>
 +
 +
</footer>
 +
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Revision as of 21:04, 13 October 2018

Home
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Integrated Human Practices Public Engagement
Awards
Background As a chronic but non-lethal condition, dental caries are often overlooked as a target for modern therapeutics, and the quality of dental caries treatment has lagged behind that of more life-threatening diseases such as cancer. However, it is a well established fact that oral health affects overall health--for example, severe cavities can lead to systemic illnesses such as heart disease. Therefore, dental caries is still a prevalent and critical issue.

The process of cariogenesis is highly facilitated by the growth of dense, sticky biofilm on the surface of teeth. This bioflim cuts off the bacteria's access to oxygen, thereby forcing them to revert to anaerobic respiration. Lactic acid is released as a byproduct of bacterial respiration, and leads to demineralization of the enamel and cavity formation.

Biofilm Formation

In its natural, non-pathogenic state, S. mutans lives planktonically (free-floating). The transition from the planktonic to biofilm state requires expression of virulence genes, which is coordinated via quorum sensing: a mode of communication employed by many bacteria to coordinate gene expression and synchronous behavior across a population or species. In the case of S. mutans, quorum sensing results in the expression of genes coding for extracellular glucosyltransferase (GTF) enzymes. These enzymes synthesize adhesive glucans, which are used by the bacteria to adhere both to each other and to the enamel of the tooth.

Most quorum-sensing systems involve small, diffusible peptides which are sent out as a signal by one bacteria and received by another. The peptides are detected by a receptor on the membrane or in the cytoplasm of other bacteria, which then initiate a signal transduction pathway that upregulates the quorum-sensing peptide, as well as other genes related to the coordinated behavior of the population. Once enough of the signal has been received by the majority of the population, bacterial behavior shifts to perform a synchronized activity.Biofilm formation is one of the synchronized behaviors initiated by quorum sensing. During this process, S. Mutans create and perpetuate the Competence Stimulating Peptide (CSP), a small molecule that is used to initiate the formation of dental plaque. The pathway through which the cells sense and respond to CSP is referred to the ComCDE pathway.

Quorum Sensing in S. mutans

Competence Stimulating Peptide (CSP)

Small peptide communication signal produced by S. mutans in quorum sensing.

THIS SECTION IS STILL IN PROGRESS! WAITING ON FORMAL TEXT FROM SENSING TEAM :)
ComD

ComD: Receptor of CSP
Phosphorylation

ComD phosphorylates the response regulator
ComE

ComE: Response Regulator
Genetic Response

Response regulator binds to and activates transcription of pro-biofilm genes
(hover over each element to learn about its role)

Our Synthetic Circuit

Our goal is to port the ComCDE system into Human Embryonic Kidney (HEK) cells. This would allow our engineered cells to sense the presence of CSP and therefore detect when biofilm formation is about to occur. ComD and ComE will be expressed constitutively, while our three outputs (ScFv's P126 and P136, and Kappa casein) will be expressed under the ComE promoter, which is activated by the ComE response regulator protein as described above.

Outputs

Upon activation of our biofilm-sensing system, our cells will output proteins that have been shown to reduce the biofilm-forming capabilities of S. mutans. Our first protein is kappa casein, a protein derived from bovine milk. It interferes with the adhesive power of the glucans post synthesis through a combination of hydrophilicity and negative charge (Vacca-Smith, 1994). Our second option is using Single Chain Variable Fragments (ScFv's), which are comprised of the variable fragments of monoclonal antibodies joined by a short peptide linker. Our two ScFv's, P126 and P136, bind to the N and C termini of the glucosyltransferases, preventing the production of glucans. (Fukushima, 1992)

References:

Vacca-Smith, A.M., Van Wuyckhuyse, B.C., Tabak, L.A., Bowen, W.H. (1994). The effect of milk and casein proteins on the adherence of Streptococcus mutans to saliva-coated hydroxyapatite. Archives of Oral Biology, Volume 39: Issue 12. 1063-1069.

Fukushima, K., Okada, T., Ochiai, K. (1993). Production, characterization, and application of monoclonal antibodies which distinguish three glucosyltransferases from Streptococcus mutans. Infect Immun., 61. 323-8.