Difference between revisions of "Team:William and Mary/Description"

(Undo revision 336787 by Cgolino (talk))
(Undo revision 336727 by Cgolino (talk))
Line 3: Line 3:
 
<head>
 
<head>
 
<meta charset="UTF-8" />
 
<meta charset="UTF-8" />
−
<title>Team:William and Mary/Description - 2015.igem.org</title>
+
<title>Team:William and Mary/Parts - 2015.igem.org</title>
 
<meta name="generator" content="MediaWiki 1.24.1" />
 
<meta name="generator" content="MediaWiki 1.24.1" />
−
<meta name="robots" content="noindex,nofollow" />
+
<link rel="alternate" type="application/x-wiki" title="Edit" href="/wiki/index.php?title=Team:William_and_Mary/Parts&amp;action=edit" />
−
<link rel="alternate" type="application/x-wiki" title="Edit" href="/wiki/index.php?title=Team:William_and_Mary/Description&amp;action=edit" />
+
<link rel="edit" title="Edit" href="/wiki/index.php?title=Team:William_and_Mary/Parts&amp;action=edit" />
−
<link rel="edit" title="Edit" href="/wiki/index.php?title=Team:William_and_Mary/Description&amp;action=edit" />
+
 
<link rel="shortcut icon" href="/favicon.ico" />
 
<link rel="shortcut icon" href="/favicon.ico" />
 
<link rel="search" type="application/opensearchdescription+xml" href="/wiki/opensearch_desc.php" title="2015.igem.org (en)" />
 
<link rel="search" type="application/opensearchdescription+xml" href="/wiki/opensearch_desc.php" title="2015.igem.org (en)" />
 
<link rel="EditURI" type="application/rsd+xml" href="https://2015.igem.org/wiki/api.php?action=rsd" />
 
<link rel="EditURI" type="application/rsd+xml" href="https://2015.igem.org/wiki/api.php?action=rsd" />
−
<link rel="alternate" hreflang="x-default" href="/Team:William_and_Mary/Description" />
+
<link rel="alternate" hreflang="x-default" href="/Team:William_and_Mary/Parts" />
 
<link rel="copyright" href="http://creativecommons.org/licenses/by/3.0/" />
 
<link rel="copyright" href="http://creativecommons.org/licenses/by/3.0/" />
 
<link rel="alternate" type="application/atom+xml" title="2015.igem.org Atom feed" href="/wiki/index.php?title=Special:RecentChanges&amp;feed=atom" />
 
<link rel="alternate" type="application/atom+xml" title="2015.igem.org Atom feed" href="/wiki/index.php?title=Special:RecentChanges&amp;feed=atom" />
Line 21: Line 20:
 
<script src="https://2015.igem.org/wiki/load.php?debug=false&amp;lang=en&amp;modules=startup&amp;only=scripts&amp;skin=igem&amp;*"></script>
 
<script src="https://2015.igem.org/wiki/load.php?debug=false&amp;lang=en&amp;modules=startup&amp;only=scripts&amp;skin=igem&amp;*"></script>
 
<script>if(window.mw){
 
<script>if(window.mw){
−
mw.config.set({"wgCanonicalNamespace":"","wgCanonicalSpecialPageName":false,"wgNamespaceNumber":0,"wgPageName":"Team:William_and_Mary/Description","wgTitle":"Team:William and Mary/Description","wgCurRevisionId":335507,"wgRevisionId":315553,"wgArticleId":4044,"wgIsArticle":true,"wgIsRedirect":false,"wgAction":"view","wgUserName":"Cgolino","wgUserGroups":["*","user","autoconfirmed"],"wgCategories":[],"wgBreakFrames":false,"wgPageContentLanguage":"en","wgPageContentModel":"wikitext","wgSeparatorTransformTable":["",""],"wgDigitTransformTable":["",""],"wgDefaultDateFormat":"dmy","wgMonthNames":["","January","February","March","April","May","June","July","August","September","October","November","December"],"wgMonthNamesShort":["","Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec"],"wgRelevantPageName":"Team:William_and_Mary/Description","wgUserId":750,"wgUserEditCount":32,"wgUserRegistration":1427756178000,"wgUserNewMsgRevisionId":null,"wgIsProbablyEditable":true,"wgRestrictionEdit":[],"wgRestrictionMove":[],"wgWikiEditorEnabledModules":{"toolbar":false,"dialogs":false,"hidesig":true,"preview":false,"previewDialog":false,"publish":false}});
+
mw.config.set({"wgCanonicalNamespace":"","wgCanonicalSpecialPageName":false,"wgNamespaceNumber":0,"wgPageName":"Team:William_and_Mary/Parts","wgTitle":"Team:William and Mary/Parts","wgCurRevisionId":317452,"wgRevisionId":317452,"wgArticleId":4048,"wgIsArticle":true,"wgIsRedirect":false,"wgAction":"view","wgUserName":"Cgolino","wgUserGroups":["*","user","autoconfirmed"],"wgCategories":[],"wgBreakFrames":false,"wgPageContentLanguage":"en","wgPageContentModel":"wikitext","wgSeparatorTransformTable":["",""],"wgDigitTransformTable":["",""],"wgDefaultDateFormat":"dmy","wgMonthNames":["","January","February","March","April","May","June","July","August","September","October","November","December"],"wgMonthNamesShort":["","Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec"],"wgRelevantPageName":"Team:William_and_Mary/Parts","wgUserId":750,"wgUserEditCount":29,"wgUserRegistration":1427756178000,"wgUserNewMsgRevisionId":null,"wgIsProbablyEditable":true,"wgRestrictionEdit":[],"wgRestrictionMove":[],"wgWikiEditorEnabledModules":{"toolbar":false,"dialogs":false,"hidesig":true,"preview":false,"previewDialog":false,"publish":false}});
 
}</script><script>if(window.mw){
 
}</script><script>if(window.mw){
 
mw.loader.implement("user.options",function($,jQuery){mw.user.options.set({"ccmeonemails":0,"cols":80,"date":"default","diffonly":0,"disablemail":0,"editfont":"default","editondblclick":0,"editsectiononrightclick":0,"enotifminoredits":0,"enotifrevealaddr":0,"enotifusertalkpages":1,"enotifwatchlistpages":1,"extendwatchlist":0,"fancysig":0,"forceeditsummary":0,"gender":"unknown","hideminor":0,"hidepatrolled":0,"imagesize":2,"math":1,"minordefault":0,"newpageshidepatrolled":0,"nickname":"","norollbackdiff":0,"numberheadings":0,"previewonfirst":0,"previewontop":1,"rcdays":7,"rclimit":50,"rows":25,"showhiddencats":0,"shownumberswatching":1,"showtoolbar":1,"skin":"igem","stubthreshold":0,"thumbsize":5,"underline":2,"uselivepreview":0,"usenewrc":1,"watchcreations":1,"watchdefault":1,"watchdeletion":0,"watchlistdays":3,"watchlisthideanons":0,"watchlisthidebots":0,"watchlisthideliu":0,"watchlisthideminor":0,"watchlisthideown":0,"watchlisthidepatrolled":0,"watchmoves":0,"watchrollback":0,
 
mw.loader.implement("user.options",function($,jQuery){mw.user.options.set({"ccmeonemails":0,"cols":80,"date":"default","diffonly":0,"disablemail":0,"editfont":"default","editondblclick":0,"editsectiononrightclick":0,"enotifminoredits":0,"enotifrevealaddr":0,"enotifusertalkpages":1,"enotifwatchlistpages":1,"extendwatchlist":0,"fancysig":0,"forceeditsummary":0,"gender":"unknown","hideminor":0,"hidepatrolled":0,"imagesize":2,"math":1,"minordefault":0,"newpageshidepatrolled":0,"nickname":"","norollbackdiff":0,"numberheadings":0,"previewonfirst":0,"previewontop":1,"rcdays":7,"rclimit":50,"rows":25,"showhiddencats":0,"shownumberswatching":1,"showtoolbar":1,"skin":"igem","stubthreshold":0,"thumbsize":5,"underline":2,"uselivepreview":0,"usenewrc":1,"watchcreations":1,"watchdefault":1,"watchdeletion":0,"watchlistdays":3,"watchlisthideanons":0,"watchlisthidebots":0,"watchlisthideliu":0,"watchlisthideminor":0,"watchlisthideown":0,"watchlisthidepatrolled":0,"watchmoves":0,"watchrollback":0,
Line 31: Line 30:
 
}</script>
 
}</script>
 
</head>
 
</head>
−
<body class="mediawiki ltr sitedir-ltr ns-0 ns-subject page-Team_William_and_Mary_Description skin-igem action-view">
+
<body class="mediawiki ltr sitedir-ltr ns-0 ns-subject page-Team_William_and_Mary_Parts skin-igem action-view">
  
 
         <script type='text/javascript'        src ='/common/tablesorter/jquery.tablesorter.min.js'></script>
 
         <script type='text/javascript'        src ='/common/tablesorter/jquery.tablesorter.min.js'></script>
Line 41: Line 40:
 
         <div id='top_menu_14' class='noprint'>Loading menubar.....</div> <!-- Will be replaced with the jQuery.load -->
 
         <div id='top_menu_14' class='noprint'>Loading menubar.....</div> <!-- Will be replaced with the jQuery.load -->
 
<script>jQuery('#top_menu_14').load('https://2015.igem.org/cgi/top_menu_14/menubar_reply.cgi',
 
<script>jQuery('#top_menu_14').load('https://2015.igem.org/cgi/top_menu_14/menubar_reply.cgi',
−
    {  t:"Team%3AWilliam%20and%20Mary%2FDescription",
+
    {  t:"Team%3AWilliam%20and%20Mary%2FParts",
−
a:"View+%2FTeam%3AWilliam_and_Mary%2FDescription++Edit+%2Fwiki%2Findex.php%3Ftitle%3DTeam%3AWilliam_and_Mary%2FDescription%26action%3Dedit%26oldid%3D315553++History+%2Fwiki%2Findex.php%3Ftitle%3DTeam%3AWilliam_and_Mary%2FDescription%26action%3Dhistory++Move+%2FSpecial%3AMovePage%2FTeam%3AWilliam_and_Mary%2FDescription++Unwatch+%2Fwiki%2Findex.php%3Ftitle%3DTeam%3AWilliam_and_Mary%2FDescription%26action%3Dunwatch%26token%3D54a78db931e18e4480431d007de08bdb%252B%255C++Page+%2FTeam%3AWilliam_and_Mary%2FDescription++Discussion+%2Fwiki%2Findex.php%3Ftitle%3DTalk%3ATeam%3AWilliam_and_Mary%2FDescription%26action%3Dedit%26redlink%3D1++" });
+
a:"View+%2FTeam%3AWilliam_and_Mary%2FParts++Edit+%2Fwiki%2Findex.php%3Ftitle%3DTeam%3AWilliam_and_Mary%2FParts%26action%3Dedit++History+%2Fwiki%2Findex.php%3Ftitle%3DTeam%3AWilliam_and_Mary%2FParts%26action%3Dhistory++Move+%2FSpecial%3AMovePage%2FTeam%3AWilliam_and_Mary%2FParts++Watch+%2Fwiki%2Findex.php%3Ftitle%3DTeam%3AWilliam_and_Mary%2FParts%26action%3Dwatch%26token%3D000a43ce8e87773dc29e93947e9ce21b%252B%255C++Page+%2FTeam%3AWilliam_and_Mary%2FParts++Discussion+%2Fwiki%2Findex.php%3Ftitle%3DTalk%3ATeam%3AWilliam_and_Mary%2FParts%26action%3Dedit%26redlink%3D1++" });
 
 
 
</script>
 
</script>
Line 48: Line 47:
 
    <a id="top"></a>
 
    <a id="top"></a>
 
    <h1 id="firstHeading" class="firstHeading">
 
    <h1 id="firstHeading" class="firstHeading">
−
        <span dir="auto">Team:William and Mary/Description</span>
+
        <span dir="auto">Team:William and Mary/Parts</span>
 
    </h1>
 
    </h1>
 
    <div id="bodyContent">
 
    <div id="bodyContent">
Line 188: Line 187:
 
             <!--    replace this line with the code generated with the rubik-builder.html              -->
 
             <!--    replace this line with the code generated with the rubik-builder.html              -->
  
−
<div class="section section-we-are-2" id="projectdesc">
+
                   
−
                        <A NAME="whatis">
+
                        <!-- 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="text-area">
−
                                 <div class="container">
+
                                 <div class="title">
−
                                     <div class="row">
+
                                     <p class="h2WM">All Parts (By Category)</p>
−
                                        <div class="col-md-4">
+
<!--                                   <div class="separator-container">
−
                                            <div class="title">
+
                                        <div class="separator line-separator">✻</div>
−
 
+
                                    </div>-->
−
                                                <p class="h2WM">What is noise?</p>
+
                                    <p>In deciding which parts to submit to the iGEM Registry we focused on three main aspects.</p>
−
                                            </div>
+
<p>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 for simple genome integration using either 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.   </p>
−
                                        </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>
+
−
Extrinsic factors, like differing RNA polymerase concentrations and nucleotide availability, affect transcription equally within the cell, regardless of what cis-regulatory elements drive transcription of the genes in question. Intrinsic components, like DNA-protein binding kinetics, are promoter-specific contributions to noise. Our project aims to tease apart the extrinsic and intrinsic components of gene expression noise, and characterize the noise inherent to commonly used promoters in synthetic biology.
+
−
+
−
Original work done by Michael Elowitz investigated stochasticity in gene expression at the single cell level using a dual-reporter fluorescent system [1]. In this method two constructs are created that both drive expression of a fluorescent protein using the same promoter, RBS, and terminator. One of these reporter constructs uses YFP and the other CFP. This dual reporter system is what allows the investigator to differentiate between the extrinsic factors of noise, which should affect both constructs equally, and the intrinsic factors, which will result in a difference in the ratio of CFP: YFP fluorescence. These constructs are then integrated (notebook link here) into specific sites on the genome and the fluorescence output measured using fluorescent imaging.  </p> <p>
+
−
<div><p style="float: left;"><IMG SRC="https://static.igem.org/mediawiki/2015/7/74/WMraser.png"></p><p> Panel A shows an example of intrinsic and extrinsic noise; both the ratio of the fluorescence of the two reporters (intrinsic) and the absolute fluorescence of the two reporters (extrinsic) changes. Panel B shows an example of extrinsic noise only; the ratio of the fluorescence of the two reporters stays constant while the absolute fluorescence changes. Figure taken from:[2].</p></div></p>
+
−
 
+
−
<p>
+
−
 
+
−
References
+
−
 
+
−
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.
+
 
</p>
 
</p>
−
 
−
</div>                                           
 
−
</div>
 
−
                                        </div>
 
−
                                    </div>
 
 
                                 </div>
 
                                 </div>
 
                             </div>
 
                             </div>
−
 
+
                            <div class="row" id="projectsLine1">
−
             
+
                                <div class="col-md-4">
−
 
+
                                     <div class="project">
−
 
+
                                         <img alt="..." src="https://static.igem.org/mediawiki/2015/b/bf/Wm15integration.jpg">
−
                        <footer class="footer footer-color-black" data-color="black">
+
                                        <a class="over-area color-green" href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="integrator">
−
                            <div class="container">
+
                                            <div class="content">
−
                                <nav class="pull-left navbar-burger">
+
                                                <h4>Integrator Suites</h4>
−
                                     <ul>
+
                                                <p>Click for details.</p>
−
                                        <li>
+
                                            </div>
−
                                            <a href="#">
+
                                         </a>
−
                                                Home
+
                                     </div>
−
                                            </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>
−
                                 <div class="copyright">
+
                                 <div class="col-md-4">
−
                                     © 2015 William &amp; Mary iGEM
+
                                     <div class="project">
 +
                                        <img alt="..." src="https://static.igem.org/mediawiki/2015/c/cf/Wm15repression.jpg">
 +
                                        <a class="over-area color-black" href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="antibiotic">
 +
                                            <div class="content">
 +
                                                <h4>Antibiotic Operons</h4>
 +
                                                <p>Click for details.</p>
 +
                                            </div>
 +
                                        </a>
 +
                                    </div>
 +
                                </div>
 +
                                <div class="col-md-4">
 +
                                    <div class="project">
 +
                                        <img alt="dCas9 Plates" src="https://static.igem.org/mediawiki/2015/3/36/WMdCas9Plates.png">                                   
 +
                                        <a class="over-area color-blue " href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="dcas">
 +
                                            <div class="content">
 +
                                                <h4>dCas9s</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/d/dc/Wm15guide.jpg">
 +
                                        <a class="over-area color-purple" href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="grna">
 +
                                            <div class="content">
 +
                                                <h4>gRNAs</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/2015/4/4f/Wm15antibiotic.jpg">
 +
                                        <a class="over-area color-green" href="javascript:void(0)" onclick="rubik.showModal(this)" data-target="xfp">
 +
                                            <div class="content">
 +
                                                <h4>XFPs under various promoters</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/2015/3/3c/WMG2.png">
 +
                                        <a class="over-area color-gold" href="#" target="g2">
 +
                                            <div class="content">
 +
                                                <h4>G^2</h4>
 +
                                                <p>Click for details.</p>
 +
                                            </div>
 +
                                        </a>
 +
                                    </div>
 
                                 </div>
 
                                 </div>
 
                             </div>
 
                             </div>
−
                         </footer>
+
                         </div>
−
        </div>
+
                        <!-- End Section "Our Projects" example 2: 3 Columns Full Width -->
−
       
+
                     
 
          
 
          
 
          
 
          
Line 608: Line 613:
 
Expensive parser function count: 0/100
 
Expensive parser function count: 0/100
 
-->
 
-->
 +
 +
<!-- Saved in parser cache with key 2015_igem_org:pcache:idhash:4048-0!*!*!*!*!*!* and timestamp 20150918005837 and revision id 317452
 +
-->
 
</div> <div class="visualClear"></div>
 
</div> <div class="visualClear"></div>
 
    </div>
 
    </div>

Revision as of 11:22, 18 September 2015

<!DOCTYPE html> Team:William and Mary/Parts - 2015.igem.org

Loading menubar.....

Team:William and Mary/Parts

NOISE - W&M iGEM

All Parts (By Category)

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 for simple genome integration using either 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.

Integrator Suites

Detail1

Detail2

Detail3

Detail4


text

text

...
...
...
...

Antibiotic Operons

Detail1

Detail2

Detail3

Detail4


text

text

...
...
...
...

dCas9s

Detail1

Detail2

Detail3

Detail4


text

text

...
...
...
...

gRNAs

Detail1

Detail2

Detail3

Detail4


text

text

...
...
...
...

XFPs Under Various Promoters

Detail1

Detail2

Detail3

Detail4


text

text

...
...
...
...

G^2

Detail1

Detail2

Detail3

Detail4


text

text

...
...
...
...