Difference between revisions of "Team:William and Mary/Basic Part"

(Prototype team page)
 
Line 1: Line 1:
−
{{William_and_Mary}}
 
−
<html>
 
  
−
<h2> Basic Parts</h2>
+
<html lang="en">
 +
<cfheader name="X-XSS-Protection" value="1">
 +
    <head>
 +
        <meta charset="utf-8" />
 +
<link rel="icon" type="image/png" href="https://static.igem.org/mediawiki/2015/e/ea/WMFavicon.png">
  
 +
        <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1" />
 +
        <title>NOISE - W&M iGEM</title>
 +
        <meta content='width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=0' name='viewport' />
 +
        <link href="https://2015.igem.org/Team:William_and_Mary/bootstrap?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
<link href="https://2015.igem.org/Team:Stockholm/fixbootstrap?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
        <link href="https://2015.igem.org/Team:William_and_Mary/rubick?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
        <link href="https://2015.igem.org/Team:William_and_Mary/demo?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
        <link rel="stylesheet" type="text/css" href="https://2015.igem.org/Template:William_and_Mary/jquerybxsliderCSS?action=raw&ctype=text/css" />
  
−
<div class="highlightBox">
+
        <!--    Fonts and icons    -->
−
<h4>Note</h4>
+
        <link href="http://maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet" type="text/css"/>
−
<p>In order to be considered for the <a href="https://2015.igem.org/Judging/Awards#SpecialPrizes">Best New Basic Part award</a>, you must fill out this page. Please give links to the Registry entries for the Basic parts you have made. Please see the Registry's <a href="http://parts.igem.org/Help:Parts#Basic_and_Composite_Parts"> Help:Parts page</a> for more information on part types.</p>
+
        <link href='http://fonts.googleapis.com/css?family=Droid+Serif:400,700' rel='stylesheet' type='text/css'>
−
</div>
+
        <link href="https://2015.igem.org/Team:William_and_Mary/pe-icon-7-stroke?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
        <link href="https://2015.igem.org/Team:William_and_Mary/Rubik-Fonts?action=raw&amp;ctype=text/css" rel="stylesheet" type="text/css"/>
 +
       
 +
<!-- the wiki settings in the section immediately below are from UC San Diego 2015 -->
 +
        <style type="text/css">
 +
/* WIKI SETTINGS*/
 +
 +
/* Hide first heading */
 +
.firstHeading {
 +
display: none;
 +
}
 +
 +
/*-- Remove borders, float content left and remove padding/margin */
 +
#globalWrapper, #content{
 +
background-color: transparent;
 +
border: none;
 +
float: center;
 +
                                width: 101%;
 +
margin-left: -3px;
 +
margin-top: -8px;
 +
padding: auto;
 +
}
  
 +
/*left align Black Menu Bar */
 +
#top_menu_inside {
 +
margin-left: 0px;
 +
}
 +
</style>
 +
 +
    </head>
 +
    <body class="landing-page">
 +
        <nav class="navbar navbar-default navbar-fixed-top navbar-burger" role="navigation">
 +
            <!-- if you want to keep the navbar hidden you can add this class to the navbar "navbar-burger"-->
 +
            <div class="container">
 +
                <div class="navbar-header">
 +
                    <button id="menu-toggle" type="button" class="navbar-toggle" data-toggle="collapse" data-target="#example">
 +
                    <span class="sr-only">Toggle navigation</span>
 +
                    <span class="icon-bar bar1"></span>
 +
                    <span class="icon-bar bar2"></span>
 +
                    <span class="icon-bar bar3"></span>
 +
                    </button>
 +
<a href="https://2015.igem.org/Team:William_and_Mary" class="navbar-brand">W&M iGEM 2015</a>
 +
                </div>
 +
                <div class="collapse navbar-collapse">
 +
                    <ul class="nav navbar-nav navbar-right navbar-uppercase">
 +
<p>    </p>
 +
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary">
 +
                            Home
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Description">
 +
                            Project Description
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary#parts">
 +
                            Parts
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Measurement">
 +
                            Measurement
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Interlab_Study">
 +
                            Interlab Study
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Collaborations">
 +
                            Collaboration
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Software">
 +
                          Software
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Practices">
 +
                            Human Practices
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="http://issuu.com/wmigem/docs/wmigemsynbiodraft150806">
 +
                            Curriculum on ISSUU.com
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary#ref">
 +
                            Notebook, Safety, & Attributions
 +
                            </a>
 +
                        </li>
 +
                        <li>
 +
                            <a href="https://2015.igem.org/Team:William_and_Mary/Medal_Criteria">
 +
                            Medal Criteria
 +
                            </a>
 +
                        </li>
 +
                    </ul>
 +
                </div>
 +
            </div>
 +
        </nav>
 +
       
 +
       
 +
       
 +
       
 +
       
 +
       
 +
       
 +
        <div class="wrapper">
 +
       
 +
       
 +
       
 +
            <!--    replace this line with the code generated with the rubik-builder.html              -->
 +
 +
<div class="section section-we-are-2" id="projectdesc">
 +
                        <A NAME="whatis">
 +
                            <div class="text-area">
 +
                                <div class="container">
 +
                                    <div class="row">
 +
                                        <div class="col-md-4">
 +
                                            <div class="title">
 +
 +
                                                <p class="h2WM">Basic Part</p>
 +
                                            </div>
 +
                                        </div>
 +
                                        <div class="col-md-7 col-md-offset-1">
 +
                                            <div class="description">
 +
                                                <p>Despite the extensive characterization of the average strength of the promoters available on the Biobrick registry, very few have information pertaining to the variability in their expression. This variability, also commonly referred to as stochasticity or noise, in gene expression can be split into two components: extrinsic and intrinsic noise.
 +
                                                </p>
 +
</div>
 +
</div>
 +
<div class = "description">
 
<p>
 
<p>
−
A <b>basic part</b> is a functional unit of DNA that cannot be subdivided into smaller component parts. <a href="http://parts.igem.org/wiki/index.php/Part:BBa_R0051">BBa_R0051</a> is an example of a basic part, a promoter regulated by lambda cl.
+
CRISPR/Cas9 has seen an explosion in use over the last five years, both within and outside of iGEM. Recent developments have extended the functionality of the Cas9 protein by modifying the nuclease domain to remove its catalytic function. This Cas9 variant, dCas9, can be used to simply target and bind to DNA. If dCas9 is targeted to a promoter, this binding causes steric hindrance, preventing RNAP from binding to and activating transcription. (Bikard, David, et al. "Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system." Nucleic acids research41.15 (2013): 7429-7437.Gilbert, Luke A., et al. "Genome-scale CRISPR-mediated control of gene repression and activation." Cell 159.3 (2014): 647-661. Qi, Lei S., et al. "Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression." Cell 152.5 (2013): 1173-1183.)
−
</p>
+
</p><p>
 +
However, despite several iGEM teams using both Cas9 and dCas9 variants in previous years, there have been no codon-optimized versions of the Cas9 protein made for E. coli. Part BBa_K1795000 is a dCas9 protein-coding region that has been optimized for expression in E. coli. Additionally, we created a functional dCas9 operon (http://parts.igem.org/Part:BBa_K1795001) that, when transformed into E. coli is constitutively expressed.  
 +
</p><p>
  
−
<p>Most genetically-encoded functions have not yet been converted to BioBrick parts. Thus, there are <b>many</b> opportunities to find new, cool, and important genetically encoded functions, and refine and convert the DNA encoding these functions into BioBrick standard biological parts. </p>
+
<div><p><IMG SRC="https://static.igem.org/mediawiki/2015/6/6f/WMdcasIm.jpeg"></p><p>(ABOVE) This part has been functionally validated by showing 97% repression of R0010-driven (http://parts.igem.org/Part:BBa_R0010) expression of RFP when co-transformed with BBa_K1795002.</p></div></p>
 +
 
 +
<div><p>Once individual cell measurements have been taken for both CFP and YFP expression using confocal microscopy, the intrinsic noise measurements can be calculated (link to John’s part about this) and further analyzed.</p></div>
  
 
</div>
 
</div>
  
−
</html>
+
<div>
 +
 
 +
<p>References UPDATE THESE:</p>
 +
 
 +
<p>1: Elowitz, Michael B., et al. "Stochastic gene expression in a single cell." Science 297.5584 (2002): 1183-1186.</p>
 +
 
 +
<p>2: Raser, Jonathan M., and Erin K. O'Shea. "Noise in gene expression: origins, consequences, and control." Science 309.5743 (2005): 2010-2013.
 +
</p>
 +
 
 +
                </div>
 +
            </div>
 +
        </div>
 +
    </div>
 +
</div>
 +
 
 +
<footer class="footer footer-color-black" data-color="black">
 +
                            <div class="container">
 +
                                <nav class="pull-left navbar-burger">
 +
                                    <ul>
 +
                                        <li>
 +
                                            <a href="#">
 +
                                                Home
 +
                                            </a>
 +
                                        </li>
 +
                                        <li>
 +
                                            <a href="#">
 +
                                                Contact
 +
                                            </a>
 +
                                        </li>
 +
                                        <li>
 +
                                            <a href="#">
 +
                                              Blog
 +
                                            </a>
 +
                                        </li>
 +
                                    </ul>
 +
                                </nav>
 +
                                <div class="social-area pull-right">               
 +
                                    <a class="btn btn-social btn-facebook btn-simple">
 +
                                        <i class="fa fa-facebook-square"></i>
 +
                                    </a>
 +
                                    <a class="btn btn-social btn-twitter btn-simple">
 +
                                        <i class="fa fa-twitter"></i>
 +
                                    </a>
 +
                                </div>
 +
                                <div class="copyright">
 +
                                    © 2015 William & Mary iGEM
 +
                                </div>
 +
                            </div>
 +
                        </footer>                       
 +
               
 +
    </body>
 +
   
 +
   
 +
 +
   
 +
    <script type="text/javascript" src="https://2015.igem.org/Template:William_and_Mary/jquery1112minJS?
 +
action=raw&ctype=text/javascript"></script>
 +
   
 +
    <script type="text/javascript" src="https://2015.igem.org/Template:William_and_Mary/bootstrapJS?
 +
action=raw&ctype=text/javascript"></script>
 +
 
 +
 
 +
    <script type="text/javascript" src="https://2015.igem.org/Template:William_and_Mary/jquerywaypointsminJS?
 +
action=raw&ctype=text/javascript"></script>
 +
 
 +
    <script type="text/javascript" src="http://presentation.paperplane.io/assets/js/modernizr.js"></script>
 +
 
 +
    <script type="text/javascript" src="https://2015.igem.org/Template:William_and_Mary/rubickJS?
 +
action=raw&ctype=text/javascript"></script>

Revision as of 12:39, 18 September 2015

NOISE - W&M iGEM

Basic Part

Despite the extensive characterization of the average strength of the promoters available on the Biobrick registry, very few have information pertaining to the variability in their expression. This variability, also commonly referred to as stochasticity or noise, in gene expression can be split into two components: extrinsic and intrinsic noise.

CRISPR/Cas9 has seen an explosion in use over the last five years, both within and outside of iGEM. Recent developments have extended the functionality of the Cas9 protein by modifying the nuclease domain to remove its catalytic function. This Cas9 variant, dCas9, can be used to simply target and bind to DNA. If dCas9 is targeted to a promoter, this binding causes steric hindrance, preventing RNAP from binding to and activating transcription. (Bikard, David, et al. "Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system." Nucleic acids research41.15 (2013): 7429-7437.Gilbert, Luke A., et al. "Genome-scale CRISPR-mediated control of gene repression and activation." Cell 159.3 (2014): 647-661. Qi, Lei S., et al. "Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression." Cell 152.5 (2013): 1173-1183.)

However, despite several iGEM teams using both Cas9 and dCas9 variants in previous years, there have been no codon-optimized versions of the Cas9 protein made for E. coli. Part BBa_K1795000 is a dCas9 protein-coding region that has been optimized for expression in E. coli. Additionally, we created a functional dCas9 operon (http://parts.igem.org/Part:BBa_K1795001) that, when transformed into E. coli is constitutively expressed.

(ABOVE) This part has been functionally validated by showing 97% repression of R0010-driven (http://parts.igem.org/Part:BBa_R0010) expression of RFP when co-transformed with BBa_K1795002.

Once individual cell measurements have been taken for both CFP and YFP expression using confocal microscopy, the intrinsic noise measurements can be calculated (link to John’s part about this) and further analyzed.

References UPDATE THESE:

1: Elowitz, Michael B., et al. "Stochastic gene expression in a single cell." Science 297.5584 (2002): 1183-1186.

2: Raser, Jonathan M., and Erin K. O'Shea. "Noise in gene expression: origins, consequences, and control." Science 309.5743 (2005): 2010-2013.