Difference between revisions of "Team:William and Mary"

 
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<h2> Project Description </h2>
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<p>In short, our project is meant to measure transcriptional noise and characterize the noise associated with different promoters in E. coli. </p>
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        <title>NOISE - W&M iGEM</title>
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Transcription is the process of converting information stored in DNA to information stored in RNA. During this process, there is an amount of random variation in the rate of the conversion. We call this random variation ‘noise’.  Transcriptional noise is largely influenced by sequences of DNA called promoters that help “tell” the cell to begin the process of transcription. Our project is to assess how much transcriptional noise is expressed by different commonly used promoters.</p>
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We are also working on a system of targeted repression of promoters using dCas9. Perhaps the most up and coming technique in synthetic biology is CRISPR/Cas9 genome editing. A CRISPR (clustered regularly interspersed short palindromic repeat) sequence is one which codes for a crisprRNA, an RNA which targets a particular DNA sequence (called the protospacer). In natural systems, the crisprRNA would bind to the protospacer and interact with another RNA sequence called a tracrRNA (which only serves to summon the Cas9 protein). The tracrRNA interacts with the Cas9 protein which recognizes a sequence in the DNA called the protospacer adjacent motif (PAM). The Cas9 protein would then cut the protospacer several base pairs upstream from the PAM. This opens the door for a synthetic biologist to insert an alternative gene or otherwise edit the genome. Additionally, in synthetic systems, the crisprRNA and tracrRNA sequences can be combined into a single guide RNA, or gRNA for short.</p>
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However, the CRISPR/ Cas9 system has many other applications. In our project, we are using a variation of the Cas9 which has been functionally deactivated (it no longer cuts the protospacer). It does, however, still clamp onto the protospacer and block the binding of other things. Therefore, if we want to inhibit the expression of a gene, we can do so by targeting the gRNA sequence to bind to the promoter region of the gene of interest. This will allow the functionally 'dead' Cas9 (dCas9) to bind to the promoter region of the gene, preventing the RNA polymerase which would have transcribed the sequence from binding to the promoter sequence because there is a giant protein in the way. </p>
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Within our project, we are referring to the idea of dCas9 repression as the Susan System, or Susan for short. We are working on a Suite of gRNA parts which will allow any iGEM team to easily repress genes expressed under any of the top ten most common iGEM promoters and then subsequently turn on expression of the gene on demand.
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The importance of proper characterization of transcriptional noise in promoters cannot be overstated. The less transcriptional noise a cell exhibits, the more reliably and predictably a cell can manufacture proteins or functional RNA. When scientists use cells to manufacture tools, it is important that these tools be both accurate and precise. Reliable cells manufacture products with precision, and reliability requires low levels of transcriptional noise. Alternatively, a researcher could require cells with a high level of transcriptional noise. Therefore it is important to be able to identify which promoters result in which levels of transcriptional noise.
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<li> A clear and concise description of your project.</li>
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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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                            Medal Criteria
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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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                                        <p class="h1WM" style="font-family:WMSlim-Joe">NOISE</p>
  
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                                        <h5>Characterization of promoter-driven transcriptional noise in E. coli</h5>
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                            <video class="bgvid" preload="auto" loop="loop" autoplay="false" muted="muted" volume="0"><source src="https://static.igem.org/mediawiki/2015/3/39/WMCYNoise.webm" type="video/webm" responsive-src="https://2015.igem.org/Team:William_and_Mary/rubik_responsive.jpg"><source src="https://static.igem.org/mediawiki/2015/a/a7/WMCYNoise.mp4" type="video/mp4">Video not supported</video></div>
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                                                <p class="h2WM">What is noise?</p>
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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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                                            <div class="description">
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                                                <p>As synthetic biologists continue to construct increasingly complex gene regulatory networks, the need for accurate quantitative characterization of their regulatory components becomes more pressing. Despite the BioBrick registry's thorough characterization of the average strength of promoters, there is insufficient description of the variability in their expression. Our project aims to characterize this variability, or noise, for the most commonly used promoters in synthetic biology and provide additional tools for the regulation of these promoters.  
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                                                <p><a href="https://2015.igem.org/Team:William_and_Mary/Description">Read more on our Project Description page.</a>
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                                    <p class = "h2WM">Parts</p2>
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<div class = "description">                                    <p>In deciding which parts to submit to the iGEM Registry we focused on three main aspects.</p>
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<p><i>First:</i> ensuring our project is as reproducible and extensible as possible. To that end we have submitted all of new composite fluorescent protein parts that we constructed during the project.<br> <i>Second:</i> Making genome integration as straightforward as possible for iGEM teams. In order to accomplish this goal we designed, tested, and validated a new integrator cassette that allows simple genome integration using 3A or Gibson Assembly. <br> <i>Third:</i> Increasing the number of tools available for promoter-mediated regulation in synthetic biology. We created and validated an E. coli codon optimized dCas9 variant and a suite of gRNAs to target the most commonly used promoters in iGEM.  </p>
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                                                <h5>All Parts</h5>
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                                                <p>A categorized list of all parts.</p>
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                                                <h5>Part Collection</h5>
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                                                <p>Guide RNAs for iGEMs top promoters. </p>
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                                                <h5>Basic Part</h5>
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                                                <p>Targeted repression with dCAS9.</p>
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                                        <img alt="..." src="https://static.igem.org/mediawiki/2015/f/f4/WMcomposite.jpeg">
 +
                                        <a class="over-area color-black " href="https://2015.igem.org/Team:William_and_Mary/Composite_Part">
 +
                                            <div class="content">
 +
                                                <h5>Composite Part</h5>
 +
                                                <p>An original integrator suite for the E. coli chromosome.</p>
 +
                                            </div>
 +
                                        </a>
 +
                                    </div>
 +
                                </div>
 +
                            </div>
 +
                        </div>
 +
                        <!-- End Section "Our Projects" example 1: 2 Columns Full Width -->
 +
                       
 +
                    <!-- Section "What We do" example 4: Big Title & 3 columns icons -->
  
 +
                    <div class="section section-we-do-2" id="workflow2">
 +
                        <div class="container">
 +
                            <div class="row">
 +
                                <div class="title add-animation animate">
 +
<!--                                    <h5 class="text-gray">Big Title &amp; 4 Columns Icons</h5>-->
 +
                                    <p class="h2WM">Measurement & Modeling</p>
 +
                                    <p>We measured noise in fluorescence data for dual-integrated sets of CFP and YFP under three promoters: BBa_R0010, BBa_R0011, and BBa_R0051. We also developed an analytic model of the impact of plasmid copy number fluctuations on transcriptional noise, which revealed that intrinsic noise cannot be accurately measured from reporters on the pSB1X3 plasmid series.</p>
 +
                                </div>
 +
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 +
                                    <div class="card animation-1 add-animation animate">
 +
                                        <div class="icon">
 +
                                            <a href = "https://2015.igem.org/Team:William_and_Mary/Measurement"><img alt="Click to go to Measurement" src="https://static.igem.org/mediawiki/2015/0/0f/WMRulerIconColor.png" height= "100" width= "150"/></a>
 +
                                        </div>
 +
                                        <h3><a href = "https://2015.igem.org/Team:William_and_Mary/Measurement">Data & Analysis</a></h3>
 +
                                     
 +
                                    </div>
 +
                                </div>
 +
                                <div class="col-md-6">
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                                    <div class="card animation-2 add-animation animate">
 +
                                        <div class="icon">
 +
                                            <a href = "https://2015.igem.org/Team:William_and_Mary/Modeling"><img alt="Click to go to the Model." src="https://static.igem.org/mediawiki/2015/7/72/WMNormalIconColor.png" height= "100" width= "150"/></a>
 +
                                        </div>
 +
                                        <h3><a href = "https://2015.igem.org/Team:William_and_Mary/Modeling">Plasmid Fluctuation Model</a></h3>
 +
                                     
 +
                                    </div>
 +
                                </div>
 +
                            </div>
 +
                        </div>
 +
                    </div>
 +
                    <!-- End Section "What We do" example 3: Small Title & 3 columns icons -->
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 +
                        <!-- Section "What We do" example 3: Small Title & 3 columns icons -->
 +
                        <div class="section section-we-do-2" id="workflow2">
 +
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 +
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 +
                                        <p class = "h2WM">Human practices</p>
 +
                                    </div>
 +
<p>Our <a href="https://2015.igem.org/Team:William_and_Mary/Practices">Human Practices effort</a> was a multi-faceted outreach approach to science literacy, focusing specifically on spreading a basic understanding of synthetic biology to the general public. We collaborated with numerous organizations to host nine educational Synthetic Biology workshops for the public (from first graders to adults!) and to implement our <a href="https://2015.igem.org/Team:William_and_Mary/Practices#curriculum">educational 24-activity Synthetic Biology booklet</a> into schools worldwide, to further sustain our efforts for years to come.</p>
 +
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 +
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 +
                                                        <a href="https://2015.igem.org/Team:William_and_Mary/Practices"><img alt="..." src="https://static.igem.org/mediawiki/2015/2/28/WMSpeechIconColor.png" height= "100" width= "100"/></a>
 +
                                                    </div>
 +
                                                    <h3><a href="https://2015.igem.org/Team:William_and_Mary/Practices">Adult Communication</a></h3>
 +
                                                </div>
 +
                                            </div>
 +
                                            <div class="col-md-4">
 +
                                                <div class="card">
 +
                                                    <div class="icon">
 +
                                                        <a href="https://2015.igem.org/Team:William_and_Mary/Practices"><img alt="..." src="https://static.igem.org/mediawiki/2015/0/07/WMBooksIconColor.png" height= "100" width= "100"/></a>
 +
                                                    </div>
 +
                                                    <h3><a href="https://2015.igem.org/Team:William_and_Mary/Practices">Youth Education</a></h3>
 +
                                                </div>
 +
                                            </div>
 +
                                            <div class="col-md-4">
 +
                                                <div class="card">
 +
                                                    <div class="icon">
 +
                                                        <a href="https://2015.igem.org/Team:William_and_Mary/Practices"><img alt="..." src="https://static.igem.org/mediawiki/2015/3/3e/WMTimeIconColor.png" height= "100" width= "100"/></a>
 +
                                                    </div>
 +
                                                    <h3><a href="https://2015.igem.org/Team:William_and_Mary/Practices">Long-Term Sustainability</a></h3>
 +
                                                </div>
 +
                                            </div>
 +
                                        </div>
 +
                                    </div>
 +
                                </div>
 +
                            </div>
 +
                        </div>
 +
                        <!-- End Section "What We do" example 3: Small Title & 3 columns icons -->
 +
                   
 +
                    <!-- Section "Our Projects" example 2: 3 Columns Full Width -->
 +
                                            <div class="section section-we-made-1 section-with-hover" id="projects1">
 +
                                                <div class="text-area">
 +
                                                    <div class="title">
 +
                                                        <p class="h2WM">Collaboration</p>
 +
                    <!--                                    <div class="separator-container">
 +
                                                            <div class="separator line-separator">✻</div>
 +
                                                        </div>-->
 +
                                                        <p>W&M iGEM met and exceeded iGEM's collaboration requirements by collaborating with other researchers in four main ways: creating a pen pal program to connect teams with similar projects, participating in the interlab measurement study, interviewing the general public to provide data to future teams about how to communicate synthetic biology, and collaborating on individual research projects with iGEM teams from University of Georgia, University of Maryland, and Cambridge. </p>
 +
                                                    </div>
 +
                                                </div>
 +
                                                <div class="row" id="projectsLine1">
 +
                                                    <div class="col-md-4">
 +
                                                        <div class="project">
 +
                                                            <img alt="..." src="https://static.igem.org/mediawiki/2015/c/c8/WmInter.jpg">
 +
                                                            <a class="over-area color-green" href="https://2015.igem.org/Team:William_and_Mary/Interlab">
 +
                                                                <div class="content">
 +
                                                                    <h4>Interlab Study</h4>
 +
                                                                    <p>Click for details.</p>
 +
                                                                </div>
 +
                                                            </a>
 +
                                                        </div>
 +
                                                    </div>
 +
                                                    <div class="col-md-4">
 +
                                                        <div class="project">
 +
                                                            <img alt="..." src="https://static.igem.org/mediawiki/2015/6/6f/Wmpenpal.jpg">
 +
                                                            <a class="over-area color-black" href="https://2015.igem.org/Team:William_and_Mary/Collaborations#penpals">
 +
                                                                <div class="content">
 +
                                                                    <h4>PenPal Program</h4>
 +
                                                                    <p>Click for details.</p>
 +
                                                                </div>
 +
                                                            </a>
 +
                                                        </div>
 +
                                                    </div>
 +
                                                    <div class="col-md-4">
 +
                                                        <div class="project">
 +
                                                            <img alt="..." src="https://static.igem.org/mediawiki/2015/a/af/WmCollCam.png">                                   
 +
                                                            <a class="over-area color-blue " href="https://2015.igem.org/Team:William_and_Mary/Collaborations#otherteams">
 +
                                                                <div class="content">
 +
                                                                    <h4>With Other Teams</h4>
 +
                                                                    <p>Click for details.</p>
 +
                                                                </div>
 +
                                                            </a>
 +
                                                        </div>
 +
                                                    </div>
 +
                                                </div>
 +
                                            </div>
 +
                                            <!-- End Section "Our Projects" example 2: 3 Columns Full Width -->
 +
                   
 +
<!-- MEDAL CRITERIA HERE -->
  
−
<h4>Inspiration</h4>
+
<div class="section section-we-are-2">
−
<p>See how other teams have described and presented their projects: </p>
+
                            <div class="text-area">
 +
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                                        <div class="col-md-4">
 +
                                            <div class="title">
 +
                                                <p class="h2WM">Medal Criteria</p>
 +
                                            </div>
 +
                                        </div>
 +
                                        <div class="col-md-7 col-md-offset-1">
 +
                                            <div class="content">
 +
                                                <p><a href="https://2015.igem.org/Team:William_and_Mary/Medal_Criteria">We're very proud of all of our accomplishments from over the summer! Click here to learn more about what we did to reach our goals.</a></p>
 +
                                            </div>
 +
                                        </div>
 +
                                    </div>
 +
                                </div>
 +
                            </div>
 +
                        </div>
  
−
<ul>
+
<!--End Medal Criteria -->                  
−
<li><a href="https://2014.igem.org/Team:Imperial/Project"> Imperial</a></li>
+
−
<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> UC Davis</a></li>
+
−
<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">SYSU Software</a></li>
+
−
</ul>
+
  
 +
<!--Software starts here! -->
 +
<div class="section section-we-are-2">
 +
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 +
                                <div class="container">
 +
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 +
                                            <div class="content">
 +
                                                <p><a href="https://2015.igem.org/Team:William_and_Mary/Software">Click here to check out the software we made to help us make sense of sequencing results of complex parts!</a> </p>
 +
                                            </div>
 +
                                        </div>
 +
<div class="col-md-4">
 +
                                            <div class="title">
 +
                                                <p class="h2WM">Software</p>
 +
                                            </div>
 +
                                        </div>
 +
                                    </div>
 +
                                </div>
 +
                            </div>
 +
                        </div>
 +
<!--End software -->
 +
 +
 +
 +
 +
                   
 +
                        <!-- Section "Team" example 1: Title & Full Image -->
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                        <div class="section section-team-1" id="team1">
 +
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 +
                                <div class="text-area">
 +
                                    <div class="title">
 +
                                        <p class="h2WM">Team</p>
 +
<!--                                        <div class="separator-container">
 +
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 +
                                        </div>-->
 +
<div class="content">
 +
                                        <a href="https://2015.igem.org/Team:William_and_Mary/Team"><p>Click here to learn more about our team.</p></a>
 
</div>
 
</div>
 +
                                    </div>
 +
                                </div>
 +
                            </div>
 +
                            <div class="full-image gradient-image">
 +
                                <img alt="..." src="https://static.igem.org/mediawiki/2015/f/f5/WmTeam15a.png">
 +
                            </div>
 +
                        </div>
 +
                        <!-- End Section "Team" example 1: Description & Full Image -->
 +
                   
 +
 +
 +
<!--Software starts here! -->
 +
<div class="section section-we-are-2">
 +
                            <div class="text-area">
 +
                                <div class="container">
 +
                                    <div class="row">
 +
<div class="title">
 +
<p class="h2WM">2015 Jamboree Results</p>
 +
</div>
 +
                                        <div class="col-md-7 col-md-offset-1">
 +
                                            <div class="content">
 +
                                                <p><img src="https://static.igem.org/mediawiki/2015/b/b7/WM_Wins.jpg" width=600px> </p>
 +
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                                                <p>Undergraduate Grand Prize Winner<br><br>Best in Track: Measurement<br><br>Best Education & Public Engagement<br><br>Best Presentation<br><br>Nominee: Best Mathematical Model</p>
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Latest revision as of 03:18, 23 November 2015

NOISE - W&M iGEM

NOISE

Characterization of promoter-driven transcriptional noise in E. coli

Parts

In deciding which parts to submit to the iGEM Registry we focused on three main aspects.

First: ensuring our project is as reproducible and extensible as possible. To that end we have submitted all of new composite fluorescent protein parts that we constructed during the project.
Second: Making genome integration as straightforward as possible for iGEM teams. In order to accomplish this goal we designed, tested, and validated a new integrator cassette that allows simple genome integration using 3A or Gibson Assembly.
Third: Increasing the number of tools available for promoter-mediated regulation in synthetic biology. We created and validated an E. coli codon optimized dCas9 variant and a suite of gRNAs to target the most commonly used promoters in iGEM.

Measurement & Modeling

We measured noise in fluorescence data for dual-integrated sets of CFP and YFP under three promoters: BBa_R0010, BBa_R0011, and BBa_R0051. We also developed an analytic model of the impact of plasmid copy number fluctuations on transcriptional noise, which revealed that intrinsic noise cannot be accurately measured from reporters on the pSB1X3 plasmid series.

Click to go to Measurement

Data & Analysis

Click to go to the Model.

Plasmid Fluctuation Model

Human practices

Our Human Practices effort was a multi-faceted outreach approach to science literacy, focusing specifically on spreading a basic understanding of synthetic biology to the general public. We collaborated with numerous organizations to host nine educational Synthetic Biology workshops for the public (from first graders to adults!) and to implement our educational 24-activity Synthetic Biology booklet into schools worldwide, to further sustain our efforts for years to come.

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Adult Communication

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Youth Education

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Long-Term Sustainability

Collaboration

W&M iGEM met and exceeded iGEM's collaboration requirements by collaborating with other researchers in four main ways: creating a pen pal program to connect teams with similar projects, participating in the interlab measurement study, interviewing the general public to provide data to future teams about how to communicate synthetic biology, and collaborating on individual research projects with iGEM teams from University of Georgia, University of Maryland, and Cambridge.

Medal Criteria

We're very proud of all of our accomplishments from over the summer! Click here to learn more about what we did to reach our goals.

Click here to check out the software we made to help us make sense of sequencing results of complex parts!

Software

2015 Jamboree Results

Undergraduate Grand Prize Winner

Best in Track: Measurement

Best Education & Public Engagement

Best Presentation

Nominee: Best Mathematical Model