http://2013.igem.org/wiki/index.php?title=Special:Contributions/Bkaptur&feed=atom&limit=50&target=Bkaptur&year=&month=2013.igem.org - User contributions [en]2024-03-28T21:17:46ZFrom 2013.igem.orgMediaWiki 1.16.5http://2013.igem.org/File:Badgel.JPGFile:Badgel.JPG2013-10-29T03:58:54Z<p>Bkaptur: </p>
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<div></div>Bkapturhttp://2013.igem.org/Team:Penn/SponsorsTeam:Penn/Sponsors2013-10-29T03:58:03Z<p>Bkaptur: </p>
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<div><html lang="en"><br />
<head><br />
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<h1> <center><b>Thank you to all of our sponsors!</b></center> </h1><br />
<!-- <div class="container marketing" style="margin-top: -20px; padding: 30px;">--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<!--MACK INSTITUTE--> <br />
<div class="row"><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('https://dl.dropboxusercontent.com/sh/11iqct3rfv0z3i8/gtn68O7nLE/PNG%20-%20Onscreen%20and%20PDF/large/L_mackinstitute_stacked_color.png?token_hash=AAFVJoJ_oJ-6AVIVHnQ76irVa73dyAs_2KYKcdrLBbjt6w');"> <br />
</div><br />
<h2>William and Phyllis Mack Institute</h2><br />
<p>In 2011, and again in 2013, the Mack Institute has co-sponsored the University of Pennsylvania’s undergraduate student team in the annual International Genetically Engineered Machine competition (iGEM).<br />
<a class="btn" id="wrap-btn" href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/"></a></p><br />
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<!--NEB--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2012/d/d6/Austin_Texas_NEB_logo.jpeg');"></div><br />
<h2> NEB</h2><br />
<p>New England Biolabs has been more than generous with our team this year (as in previous years) and we are extremely appreciative of their support!</p><br />
<br />
</div><!-- /.span4 --> <br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<!--ADDGENE--><br />
<div class="img-wrap" style="background-image: url('http://dmsbulletin.hms.harvard.edu/images/NovDec11/addgene.jpg')"></div><br />
<h2>Addgene</h2><br />
<p>We are thrilled to have Addgene supporting our team this year, they have been a great resource for our project.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
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<!----END OF BLOCK--><br />
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<!--textwrap--><br />
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<!--PENN M&T--><br />
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<div class="span4" style = "float: left;"><br />
<div class="img-wrap" style="background-image: url('https://si0.twimg.com/profile_images/799689415/m_t_logo_stackedcopy.jpg'); background-position: 0px 10px"></div><br />
<h2> Penn M&T </h2><br />
<p>Penn's M&T department has been very generous to support our team for several years now, we hope that they continue to support us in the future.</p><br />
<br />
</div><!-- /.span4 --></div><br />
<br />
<!--Penn CURF--><br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://secure.www.upenn.edu/themeyear/proof/images/stories/curf.jpg')"></div><br />
<h2> Penn CURF </h2><br />
<p>CURF has offered our team numerous outreach opportunities and financial support, we are happy that they connect with our mission of educating the community about synthetic biology.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--IDT--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('http://bitesizebio.s3.amazonaws.com/content/uploads/2011/04/IDT-Logo-2010_3-578x240.jpg')"></div><br />
<h2> IDT </h2><br />
<p>IDT's service and support has been a cornerstone of our team for years, we truly appreciate their corporate sponsorship.</p><br />
<br />
<br />
<br />
</div></div><br />
<br />
<div class="text-wrap"><br />
</div><!-- /.span4 --><br />
<br />
<!--Biomatters--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://s10.postimg.org/twfinment/geneiouslogo.png')"></div><br />
<h2> Biomatters</h2><br />
<p>For the duration of iGEM 2013 competition Biomatters has provided us with a license to use Geneious for every team-member. This software has been crucial to our team for designing and simulating experiments in silico.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('http://s8.postimg.org/w4oxbbcj9/penn_logo.jpg')"></div><br />
<h2> The University of Pennsylvania</h2><br />
<p>We would like to thank the University of Pennsylvania for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn Engineering--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://fling.seas.upenn.edu/~edab/dynamic/edab/wordpress/wp-content/uploads/2012/09/pennEngFrontPage-960x400.png')"></div><br />
<h2> Penn Engineering</h2><br />
<p>We would like to thank the SEAS for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--pgfi--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://published.genomics.upenn.edu/2009/PGFI_logo_2008-12-11-small.png')"></div><br />
<h2> PGFI</h2><br />
<p>We would like to thank the PGFI for providing training support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Penn Epigenetics--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/1/1f/Perelman_Logo.jpg')"></div><br />
<h2> Penn Epigenetics</h2><br />
<p>We would like to thank the Penn Epigenetics department, specifically the Bartomlei and Simmons labs, for providing reagents, advice, and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Qiagen--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/5/51/QLogo.jpg')"></div><br />
<h2>Qiagen</h2><br />
<p>We would like to thank Qiagen for providing reagents and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
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</div>--><br />
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</div><br />
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Copy the formatting starting from span4 to /span4<br />
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<div class="span4"><br />
<div class="img-wrap" style="background-image: url('image.jpg)"/><br />
<h2>Title</h2><br />
<p>description</p><br />
<p><a href="link">read more &raquo;</a><br />
</div>--><br />
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<div class="span4"> <br />
~~~up to 3 sponsors can go in here~~~<br />
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<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
</center> <br />
<br><br />
Penn iGem &copy; 2013<br />
</div><br />
<br />
</body><br />
</html></div>Bkapturhttp://2013.igem.org/Team:Penn/SponsorsTeam:Penn/Sponsors2013-10-29T03:57:38Z<p>Bkaptur: </p>
<hr />
<div><html lang="en"><br />
<head><br />
<br />
<title>Penn iGEM</title><br />
<link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/> <!--css--><br />
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<br />
<script><br />
$(document).ready(function($) {<br />
<br />
$('.nav_wrap').load('https://googledrive.com/host/0B4ZBZOYYKBzEclFHMmpZcVlydmc');<br />
});<br />
</script><br />
<br />
<style><br />
<br />
/*Page specific*/<br />
/*fonts/headings*/<br />
h4 {<br />
text-align: center;<br />
}<br />
<br />
/*logos*/<br />
<br />
.span4 {<br />
background-color: white; /*background color white and slightly transparent*/<br />
width: 200px;<br />
height: 400px;<br />
padding: 10px;<br />
display: inline-block;<br />
overflow: hidden;<br />
margin: 10px;<br />
}<br />
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.span4 img {<br />
border-radius: 0px;<br />
bottom: 0px;<br />
}<br />
<br />
<br />
#break {<br />
height: 50px;<br />
width: 100%;<br />
background-color: gray;<br />
}<br />
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.img {<br />
border-radius: 0px;<br />
position: absolute;<br />
bottom: 0px;<br />
height: 600px;<br />
}<br />
<br />
.img-wrap {<br />
height: 150px;<br />
width: 200px;<br />
overflow: hidden;<br />
position: relative;<br />
margin-top: 0px;<br />
background-size: 200px;<br />
background-position: center;<br />
background-repeat: no-repeat;<br />
}<br />
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/*fix margins on button (lines them up better)*/<br />
#wrap-btn {<br />
margin-bottom: 16px;<br />
}<br />
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</head><br />
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<div id = "nav_holder"><br />
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</div><br />
</div><br />
<div id="text"><br />
<div class = "textwrap"><br />
<br />
<br />
<h1> <center><b>Thank you to all of our sponsors!</b></center> </h1><br />
<!-- <div class="container marketing" style="margin-top: -20px; padding: 30px;">--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<!--MACK INSTITUTE--> <br />
<div class="row"><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('https://dl.dropboxusercontent.com/sh/11iqct3rfv0z3i8/gtn68O7nLE/PNG%20-%20Onscreen%20and%20PDF/large/L_mackinstitute_stacked_color.png?token_hash=AAFVJoJ_oJ-6AVIVHnQ76irVa73dyAs_2KYKcdrLBbjt6w');"> <br />
</div><br />
<h2>William and Phyllis Mack Institute</h2><br />
<p>In 2011, and again in 2013, the Mack Institute has co-sponsored the University of Pennsylvania’s undergraduate student team in the annual International Genetically Engineered Machine competition (iGEM).<br />
<a class="btn" id="wrap-btn" href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/"></a></p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--NEB--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2012/d/d6/Austin_Texas_NEB_logo.jpeg');"></div><br />
<h2> NEB</h2><br />
<p>New England Biolabs has been more than generous with our team this year (as in previous years) and we are extremely appreciative of their support!</p><br />
<br />
</div><!-- /.span4 --> <br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<!--ADDGENE--><br />
<div class="img-wrap" style="background-image: url('http://dmsbulletin.hms.harvard.edu/images/NovDec11/addgene.jpg')"></div><br />
<h2>Addgene</h2><br />
<p>We are thrilled to have Addgene supporting our team this year, they have been a great resource for our project.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
<br />
<!----END OF BLOCK--><br />
<br />
<!--textwrap--><br />
<br />
<div class="text-wrap"><br />
<br />
<br />
<br />
<br />
<!--PENN M&T--><br />
<div class="row"><br />
<div class="span4" style = "float: left;"><br />
<div class="img-wrap" style="background-image: url('https://si0.twimg.com/profile_images/799689415/m_t_logo_stackedcopy.jpg'); background-position: 0px 10px"></div><br />
<h2> Penn M&T </h2><br />
<p>Penn's M&T department has been very generous to support our team for several years now, we hope that they continue to support us in the future.</p><br />
<br />
</div><!-- /.span4 --></div><br />
<br />
<!--Penn CURF--><br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://secure.www.upenn.edu/themeyear/proof/images/stories/curf.jpg')"></div><br />
<h2> Penn CURF </h2><br />
<p>CURF has offered our team numerous outreach opportunities and financial support, we are happy that they connect with our mission of educating the community about synthetic biology.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--IDT--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('http://bitesizebio.s3.amazonaws.com/content/uploads/2011/04/IDT-Logo-2010_3-578x240.jpg')"></div><br />
<h2> IDT </h2><br />
<p>IDT's service and support has been a cornerstone of our team for years, we truly appreciate their corporate sponsorship.</p><br />
<br />
<br />
<br />
</div></div><br />
<br />
<div class="text-wrap"><br />
</div><!-- /.span4 --><br />
<br />
<!--Biomatters--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://s10.postimg.org/twfinment/geneiouslogo.png')"></div><br />
<h2> Biomatters</h2><br />
<p>For the duration of iGEM 2013 competition Biomatters has provided us with a license to use Geneious for every team-member. This software has been crucial to our team for designing and simulating experiments in silico.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('http://s8.postimg.org/w4oxbbcj9/penn_logo.jpg')"></div><br />
<h2> The University of Pennsylvania</h2><br />
<p>We would like to thank the University of Pennsylvania for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn Engineering--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://fling.seas.upenn.edu/~edab/dynamic/edab/wordpress/wp-content/uploads/2012/09/pennEngFrontPage-960x400.png')"></div><br />
<h2> Penn Engineering</h2><br />
<p>We would like to thank the SEAS for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--pgfi--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://published.genomics.upenn.edu/2009/PGFI_logo_2008-12-11-small.png')"></div><br />
<h2> PGFI</h2><br />
<p>We would like to thank the PGFI for providing training support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Penn Epigenetics--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/1/1f/Perelman_Logo.jpg')"></div><br />
<h2> Penn Epigenetics</h2><br />
<p>We would like to thank the Penn Epigenetics department, specifically the Bartomlei and Simmons labs, for providing reagents, advice, and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Qiagen--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/5/51/QLogo.jpg')"></div><br />
<h2>Qiagen</h2><br />
<p>We would like to thank Qiagen for providing reagents and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<div class="text-wrap"><br />
<div class="row" style="margin-top: 35px;"><br />
<div class="span4"> <br />
<div class="span4" ><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/7/77/Redbullsponsor.jpg')"/><br />
<h2>Redbull</h2><br />
<p>description</p><br />
</div><br />
<br />
<br />
</div>--><br />
<br />
</div><br />
<br />
<br />
<br />
<!--here is where you would add another sponsor.<br />
Copy the formatting starting from span4 to /span4<br />
So something like:<br />
<br />
<div class="span4"><br />
<div class="img-wrap" style="background-image: url('image.jpg)"/><br />
<h2>Title</h2><br />
<p>description</p><br />
<p><a href="link">read more &raquo;</a><br />
</div>--><br />
<br />
<br />
<!--make sure your new sponsors go before these /divs--><br />
</div><!--/row--><br />
</div><!--text-wrap--><br />
<br />
<!-- if you have to add more than 2 sponsors, wrap the new sponsors like this:<br />
<br />
<div class="text-wrap"><br />
<div class="row" style="margin-top: 35px;"><br />
<div class="span4"> <br />
~~~up to 3 sponsors can go in here~~~<br />
</div><br />
</div>--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div id ="pagefooter"><br />
<br><br />
<br><br />
<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
</center> <br />
<br><br />
Penn iGem &copy; 2013<br />
</div><br />
<br />
</body><br />
</html></div>Bkapturhttp://2013.igem.org/Team:Penn/SponsorsTeam:Penn/Sponsors2013-10-29T03:54:25Z<p>Bkaptur: </p>
<hr />
<div><html lang="en"><br />
<head><br />
<br />
<title>Penn iGEM</title><br />
<link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/> <!--css--><br />
<br />
<script src="https://googledrive.com/host/0B4ZBZOYYKBzETkFqdnhMeV9fMzA" ></script> <!--jquery--><br />
<br />
<script><br />
$(document).ready(function($) {<br />
<br />
$('.nav_wrap').load('https://googledrive.com/host/0B4ZBZOYYKBzEclFHMmpZcVlydmc');<br />
});<br />
</script><br />
<br />
<style><br />
<br />
/*Page specific*/<br />
/*fonts/headings*/<br />
h4 {<br />
text-align: center;<br />
}<br />
<br />
/*logos*/<br />
<br />
.span4 {<br />
background-color: white; /*background color white and slightly transparent*/<br />
width: 200px;<br />
height: 400px;<br />
padding: 10px;<br />
display: inline-block;<br />
overflow: hidden;<br />
margin: 10px;<br />
}<br />
<br />
.span4 img {<br />
border-radius: 0px;<br />
bottom: 0px;<br />
}<br />
<br />
<br />
#break {<br />
height: 50px;<br />
width: 100%;<br />
background-color: gray;<br />
}<br />
<br />
.img {<br />
border-radius: 0px;<br />
position: absolute;<br />
bottom: 0px;<br />
height: 600px;<br />
}<br />
<br />
.img-wrap {<br />
height: 150px;<br />
width: 200px;<br />
overflow: hidden;<br />
position: relative;<br />
margin-top: 0px;<br />
background-size: 200px;<br />
background-position: center;<br />
background-repeat: no-repeat;<br />
}<br />
<br />
<br />
<br />
/*fix margins on button (lines them up better)*/<br />
#wrap-btn {<br />
margin-bottom: 16px;<br />
}<br />
<br />
<br />
<br />
</style><br />
</head><br />
<body><br />
<br />
<body><br />
<div id = "banner_wrap"><br />
<div class = "banner"></div><br />
</div><br />
<div id = "nav_holder"><br />
<div class = "nav_wrap"></div><br />
</div><br />
</div><br />
<div id="text"><br />
<div class = "textwrap"><br />
<br />
<br />
<h1> <center><b>Thank you to all of our sponsors!</b></center> </h1><br />
<!-- <div class="container marketing" style="margin-top: -20px; padding: 30px;">--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<!--MACK INSTITUTE--> <br />
<div class="row"><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('https://dl.dropboxusercontent.com/sh/11iqct3rfv0z3i8/gtn68O7nLE/PNG%20-%20Onscreen%20and%20PDF/large/L_mackinstitute_stacked_color.png?token_hash=AAFVJoJ_oJ-6AVIVHnQ76irVa73dyAs_2KYKcdrLBbjt6w');"> <br />
</div><br />
<h2>William and Phyllis Mack Institute</h2><br />
<p>In 2011, and again in 2013, the Mack Institute has co-sponsored the University of Pennsylvania’s undergraduate student team in the annual International Genetically Engineered Machine competition (iGEM).<br />
<a class="btn" id="wrap-btn" href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/"></a></p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--NEB--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2012/d/d6/Austin_Texas_NEB_logo.jpeg');"></div><br />
<h2> NEB</h2><br />
<p>New England Biolabs has been more than generous with our team this year (as in previous years) and we are extremely appreciative of their support!</p><br />
<br />
</div><!-- /.span4 --> <br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<!--ADDGENE--><br />
<div class="img-wrap" style="background-image: url('http://dmsbulletin.hms.harvard.edu/images/NovDec11/addgene.jpg')"></div><br />
<h2>Addgene</h2><br />
<p>We are thrilled to have Addgene supporting our team this year, they have been a great resource for our project.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
<br />
<!----END OF BLOCK--><br />
<br />
<!--textwrap--><br />
<br />
<div class="text-wrap"><br />
<br />
<br />
<br />
<br />
<!--PENN M&T--><br />
<div class="row"><br />
<div class="span4" style = "float: left;"><br />
<div class="img-wrap" style="background-image: url('https://si0.twimg.com/profile_images/799689415/m_t_logo_stackedcopy.jpg'); background-position: 0px 10px"></div><br />
<h2> Penn M&T </h2><br />
<p>Penn's M&T department has been very generous to support our team for several years now, we hope that they continue to support us in the future.</p><br />
<br />
</div><!-- /.span4 --></div><br />
<br />
<!--Penn CURF--><br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://secure.www.upenn.edu/themeyear/proof/images/stories/curf.jpg')"></div><br />
<h2> Penn CURF </h2><br />
<p>CURF has offered our team numerous outreach opportunities and financial support, we are happy that they connect with our mission of educating the community about synthetic biology.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--IDT--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('http://bitesizebio.s3.amazonaws.com/content/uploads/2011/04/IDT-Logo-2010_3-578x240.jpg')"></div><br />
<h2> IDT </h2><br />
<p>IDT's service and support has been a cornerstone of our team for years, we truly appreciate their corporate sponsorship.</p><br />
<br />
<br />
<br />
</div></div><br />
<br />
<div class="text-wrap"><br />
</div><!-- /.span4 --><br />
<br />
<!--Biomatters--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://s10.postimg.org/twfinment/geneiouslogo.png')"></div><br />
<h2> Biomatters</h2><br />
<p>For the duration of iGEM 2013 competition Biomatters has provided us with a license to use Geneious for every team-member. This software has been crucial to our team for designing and simulating experiments in silico.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('http://s8.postimg.org/w4oxbbcj9/penn_logo.jpg')"></div><br />
<h2> The University of Pennsylvania</h2><br />
<p>We would like to thank the University of Pennsylvania for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn Engineering--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://fling.seas.upenn.edu/~edab/dynamic/edab/wordpress/wp-content/uploads/2012/09/pennEngFrontPage-960x400.png')"></div><br />
<h2> Penn Engineering</h2><br />
<p>We would like to thank the SEAS for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--pgfi--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://published.genomics.upenn.edu/2009/PGFI_logo_2008-12-11-small.png')"></div><br />
<h2> PGFI</h2><br />
<p>We would like to thank the PGFI for providing training support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Penn Epigenetics--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/1/1f/Perelman_Logo.jpg')"></div><br />
<h2> Penn Epigenetics</h2><br />
<p>We would like to thank the Penn Epigenetics department, specifically the Bartomlei and Simmons labs, for providing reagents, advice, and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Qiagen--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/5/51/QLogo.jpg')"></div><br />
<h2>Qiagen</h2><br />
<p>We would like to thank Qiagen for providing reagents and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<div class="span4" ><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/7/77/Redbullsponsor.jpg')"/><br />
<h2>Redbull</h2><br />
<p>description</p><br />
<br />
</div>--><br />
<br />
</div><br />
<br />
<br />
<br />
<!--here is where you would add another sponsor.<br />
Copy the formatting starting from span4 to /span4<br />
So something like:<br />
<br />
<div class="span4"><br />
<div class="img-wrap" style="background-image: url('image.jpg)"/><br />
<h2>Title</h2><br />
<p>description</p><br />
<p><a href="link">read more &raquo;</a><br />
</div>--><br />
<br />
<br />
<!--make sure your new sponsors go before these /divs--><br />
</div><!--/row--><br />
</div><!--text-wrap--><br />
<br />
<!-- if you have to add more than 2 sponsors, wrap the new sponsors like this:<br />
<br />
<div class="text-wrap"><br />
<div class="row" style="margin-top: 35px;"><br />
<div class="span4"> <br />
~~~up to 3 sponsors can go in here~~~<br />
</div><br />
</div>--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div id ="pagefooter"><br />
<br><br />
<br><br />
<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
</center> <br />
<br><br />
Penn iGem &copy; 2013<br />
</div><br />
<br />
</body><br />
</html></div>Bkapturhttp://2013.igem.org/Team:Penn/SponsorsTeam:Penn/Sponsors2013-10-29T03:53:23Z<p>Bkaptur: </p>
<hr />
<div><html lang="en"><br />
<head><br />
<br />
<title>Penn iGEM</title><br />
<link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/> <!--css--><br />
<br />
<script src="https://googledrive.com/host/0B4ZBZOYYKBzETkFqdnhMeV9fMzA" ></script> <!--jquery--><br />
<br />
<script><br />
$(document).ready(function($) {<br />
<br />
$('.nav_wrap').load('https://googledrive.com/host/0B4ZBZOYYKBzEclFHMmpZcVlydmc');<br />
});<br />
</script><br />
<br />
<style><br />
<br />
/*Page specific*/<br />
/*fonts/headings*/<br />
h4 {<br />
text-align: center;<br />
}<br />
<br />
/*logos*/<br />
<br />
.span4 {<br />
background-color: white; /*background color white and slightly transparent*/<br />
width: 200px;<br />
height: 400px;<br />
padding: 10px;<br />
display: inline-block;<br />
overflow: hidden;<br />
margin: 10px;<br />
}<br />
<br />
.span4 img {<br />
border-radius: 0px;<br />
bottom: 0px;<br />
}<br />
<br />
<br />
#break {<br />
height: 50px;<br />
width: 100%;<br />
background-color: gray;<br />
}<br />
<br />
.img {<br />
border-radius: 0px;<br />
position: absolute;<br />
bottom: 0px;<br />
height: 600px;<br />
}<br />
<br />
.img-wrap {<br />
height: 150px;<br />
width: 200px;<br />
overflow: hidden;<br />
position: relative;<br />
margin-top: 0px;<br />
background-size: 200px;<br />
background-position: center;<br />
background-repeat: no-repeat;<br />
}<br />
<br />
<br />
<br />
/*fix margins on button (lines them up better)*/<br />
#wrap-btn {<br />
margin-bottom: 16px;<br />
}<br />
<br />
<br />
<br />
</style><br />
</head><br />
<body><br />
<br />
<body><br />
<div id = "banner_wrap"><br />
<div class = "banner"></div><br />
</div><br />
<div id = "nav_holder"><br />
<div class = "nav_wrap"></div><br />
</div><br />
</div><br />
<div id="text"><br />
<div class = "textwrap"><br />
<br />
<br />
<h1> <center><b>Thank you to all of our sponsors!</b></center> </h1><br />
<!-- <div class="container marketing" style="margin-top: -20px; padding: 30px;">--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<!--MACK INSTITUTE--> <br />
<div class="row"><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('https://dl.dropboxusercontent.com/sh/11iqct3rfv0z3i8/gtn68O7nLE/PNG%20-%20Onscreen%20and%20PDF/large/L_mackinstitute_stacked_color.png?token_hash=AAFVJoJ_oJ-6AVIVHnQ76irVa73dyAs_2KYKcdrLBbjt6w');"> <br />
</div><br />
<h2>William and Phyllis Mack Institute</h2><br />
<p>In 2011, and again in 2013, the Mack Institute has co-sponsored the University of Pennsylvania’s undergraduate student team in the annual International Genetically Engineered Machine competition (iGEM).<br />
<a class="btn" id="wrap-btn" href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/"></a></p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--NEB--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2012/d/d6/Austin_Texas_NEB_logo.jpeg');"></div><br />
<h2> NEB</h2><br />
<p>New England Biolabs has been more than generous with our team this year (as in previous years) and we are extremely appreciative of their support!</p><br />
<br />
</div><!-- /.span4 --> <br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<!--ADDGENE--><br />
<div class="img-wrap" style="background-image: url('http://dmsbulletin.hms.harvard.edu/images/NovDec11/addgene.jpg')"></div><br />
<h2>Addgene</h2><br />
<p>We are thrilled to have Addgene supporting our team this year, they have been a great resource for our project.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
<br />
<!----END OF BLOCK--><br />
<br />
<!--textwrap--><br />
<br />
<div class="text-wrap"><br />
<br />
<br />
<br />
<br />
<!--PENN M&T--><br />
<div class="row"><br />
<div class="span4" style = "float: left;"><br />
<div class="img-wrap" style="background-image: url('https://si0.twimg.com/profile_images/799689415/m_t_logo_stackedcopy.jpg'); background-position: 0px 10px"></div><br />
<h2> Penn M&T </h2><br />
<p>Penn's M&T department has been very generous to support our team for several years now, we hope that they continue to support us in the future.</p><br />
<br />
</div><!-- /.span4 --></div><br />
<br />
<!--Penn CURF--><br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://secure.www.upenn.edu/themeyear/proof/images/stories/curf.jpg')"></div><br />
<h2> Penn CURF </h2><br />
<p>CURF has offered our team numerous outreach opportunities and financial support, we are happy that they connect with our mission of educating the community about synthetic biology.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--IDT--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('http://bitesizebio.s3.amazonaws.com/content/uploads/2011/04/IDT-Logo-2010_3-578x240.jpg')"></div><br />
<h2> IDT </h2><br />
<p>IDT's service and support has been a cornerstone of our team for years, we truly appreciate their corporate sponsorship.</p><br />
<br />
<br />
<br />
</div></div><br />
<br />
<div class="text-wrap"><br />
</div><!-- /.span4 --><br />
<br />
<!--Biomatters--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://s10.postimg.org/twfinment/geneiouslogo.png')"></div><br />
<h2> Biomatters</h2><br />
<p>For the duration of iGEM 2013 competition Biomatters has provided us with a license to use Geneious for every team-member. This software has been crucial to our team for designing and simulating experiments in silico.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('http://s8.postimg.org/w4oxbbcj9/penn_logo.jpg')"></div><br />
<h2> The University of Pennsylvania</h2><br />
<p>We would like to thank the University of Pennsylvania for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn Engineering--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://fling.seas.upenn.edu/~edab/dynamic/edab/wordpress/wp-content/uploads/2012/09/pennEngFrontPage-960x400.png')"></div><br />
<h2> Penn Engineering</h2><br />
<p>We would like to thank the SEAS for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--pgfi--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://published.genomics.upenn.edu/2009/PGFI_logo_2008-12-11-small.png')"></div><br />
<h2> PGFI</h2><br />
<p>We would like to thank the PGFI for providing training support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Penn Epigenetics--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/1/1f/Perelman_Logo.jpg')"></div><br />
<h2> Penn Epigenetics</h2><br />
<p>We would like to thank the Penn Epigenetics department, specifically the Bartomlei and Simmons labs, for providing reagents, advice, and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Qiagen--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/5/51/QLogo.jpg')"></div><br />
<h2>Qiagen</h2><br />
<p>We would like to thank Qiagen for providing reagents and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<div class="span4"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/7/77/Redbullsponsor.jpg')"/><br />
<h2>Redbull</h2><br />
<p>description</p><br />
<p><a href="link">read more &raquo;</a><br />
</div>--><br />
<br />
</div><br />
<br />
<br />
<br />
<!--here is where you would add another sponsor.<br />
Copy the formatting starting from span4 to /span4<br />
So something like:<br />
<br />
<div class="span4"><br />
<div class="img-wrap" style="background-image: url('image.jpg)"/><br />
<h2>Title</h2><br />
<p>description</p><br />
<p><a href="link">read more &raquo;</a><br />
</div>--><br />
<br />
<br />
<!--make sure your new sponsors go before these /divs--><br />
</div><!--/row--><br />
</div><!--text-wrap--><br />
<br />
<!-- if you have to add more than 2 sponsors, wrap the new sponsors like this:<br />
<br />
<div class="text-wrap"><br />
<div class="row" style="margin-top: 35px;"><br />
<div class="span4"> <br />
~~~up to 3 sponsors can go in here~~~<br />
</div><br />
</div>--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div id ="pagefooter"><br />
<br><br />
<br><br />
<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
</center> <br />
<br><br />
Penn iGem &copy; 2013<br />
</div><br />
<br />
</body><br />
</html></div>Bkapturhttp://2013.igem.org/Team:Penn/SponsorsTeam:Penn/Sponsors2013-10-29T03:52:21Z<p>Bkaptur: </p>
<hr />
<div><html lang="en"><br />
<head><br />
<br />
<title>Penn iGEM</title><br />
<link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/> <!--css--><br />
<br />
<script src="https://googledrive.com/host/0B4ZBZOYYKBzETkFqdnhMeV9fMzA" ></script> <!--jquery--><br />
<br />
<script><br />
$(document).ready(function($) {<br />
<br />
$('.nav_wrap').load('https://googledrive.com/host/0B4ZBZOYYKBzEclFHMmpZcVlydmc');<br />
});<br />
</script><br />
<br />
<style><br />
<br />
/*Page specific*/<br />
/*fonts/headings*/<br />
h4 {<br />
text-align: center;<br />
}<br />
<br />
/*logos*/<br />
<br />
.span4 {<br />
background-color: white; /*background color white and slightly transparent*/<br />
width: 200px;<br />
height: 400px;<br />
padding: 10px;<br />
display: inline-block;<br />
overflow: hidden;<br />
margin: 10px;<br />
}<br />
<br />
.span4 img {<br />
border-radius: 0px;<br />
bottom: 0px;<br />
}<br />
<br />
<br />
#break {<br />
height: 50px;<br />
width: 100%;<br />
background-color: gray;<br />
}<br />
<br />
.img {<br />
border-radius: 0px;<br />
position: absolute;<br />
bottom: 0px;<br />
height: 600px;<br />
}<br />
<br />
.img-wrap {<br />
height: 150px;<br />
width: 200px;<br />
overflow: hidden;<br />
position: relative;<br />
margin-top: 0px;<br />
background-size: 200px;<br />
background-position: center;<br />
background-repeat: no-repeat;<br />
}<br />
<br />
<br />
<br />
/*fix margins on button (lines them up better)*/<br />
#wrap-btn {<br />
margin-bottom: 16px;<br />
}<br />
<br />
<br />
<br />
</style><br />
</head><br />
<body><br />
<br />
<body><br />
<div id = "banner_wrap"><br />
<div class = "banner"></div><br />
</div><br />
<div id = "nav_holder"><br />
<div class = "nav_wrap"></div><br />
</div><br />
</div><br />
<div id="text"><br />
<div class = "textwrap"><br />
<br />
<br />
<h1> <center><b>Thank you to all of our sponsors!</b></center> </h1><br />
<!-- <div class="container marketing" style="margin-top: -20px; padding: 30px;">--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<!--MACK INSTITUTE--> <br />
<div class="row"><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('https://dl.dropboxusercontent.com/sh/11iqct3rfv0z3i8/gtn68O7nLE/PNG%20-%20Onscreen%20and%20PDF/large/L_mackinstitute_stacked_color.png?token_hash=AAFVJoJ_oJ-6AVIVHnQ76irVa73dyAs_2KYKcdrLBbjt6w');"> <br />
</div><br />
<h2>William and Phyllis Mack Institute</h2><br />
<p>In 2011, and again in 2013, the Mack Institute has co-sponsored the University of Pennsylvania’s undergraduate student team in the annual International Genetically Engineered Machine competition (iGEM).<br />
<a class="btn" id="wrap-btn" href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/"></a></p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--NEB--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2012/d/d6/Austin_Texas_NEB_logo.jpeg');"></div><br />
<h2> NEB</h2><br />
<p>New England Biolabs has been more than generous with our team this year (as in previous years) and we are extremely appreciative of their support!</p><br />
<br />
</div><!-- /.span4 --> <br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<!--ADDGENE--><br />
<div class="img-wrap" style="background-image: url('http://dmsbulletin.hms.harvard.edu/images/NovDec11/addgene.jpg')"></div><br />
<h2>Addgene</h2><br />
<p>We are thrilled to have Addgene supporting our team this year, they have been a great resource for our project.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
<br />
<!----END OF BLOCK--><br />
<br />
<!--textwrap--><br />
<br />
<div class="text-wrap"><br />
<br />
<br />
<br />
<br />
<!--PENN M&T--><br />
<div class="row"><br />
<div class="span4" style = "float: left;"><br />
<div class="img-wrap" style="background-image: url('https://si0.twimg.com/profile_images/799689415/m_t_logo_stackedcopy.jpg'); background-position: 0px 10px"></div><br />
<h2> Penn M&T </h2><br />
<p>Penn's M&T department has been very generous to support our team for several years now, we hope that they continue to support us in the future.</p><br />
<br />
</div><!-- /.span4 --></div><br />
<br />
<!--Penn CURF--><br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://secure.www.upenn.edu/themeyear/proof/images/stories/curf.jpg')"></div><br />
<h2> Penn CURF </h2><br />
<p>CURF has offered our team numerous outreach opportunities and financial support, we are happy that they connect with our mission of educating the community about synthetic biology.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--IDT--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('http://bitesizebio.s3.amazonaws.com/content/uploads/2011/04/IDT-Logo-2010_3-578x240.jpg')"></div><br />
<h2> IDT </h2><br />
<p>IDT's service and support has been a cornerstone of our team for years, we truly appreciate their corporate sponsorship.</p><br />
<br />
<br />
<br />
</div></div><br />
<br />
<div class="text-wrap"><br />
</div><!-- /.span4 --><br />
<br />
<!--Biomatters--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://s10.postimg.org/twfinment/geneiouslogo.png')"></div><br />
<h2> Biomatters</h2><br />
<p>For the duration of iGEM 2013 competition Biomatters has provided us with a license to use Geneious for every team-member. This software has been crucial to our team for designing and simulating experiments in silico.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('http://s8.postimg.org/w4oxbbcj9/penn_logo.jpg')"></div><br />
<h2> The University of Pennsylvania</h2><br />
<p>We would like to thank the University of Pennsylvania for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn Engineering--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://fling.seas.upenn.edu/~edab/dynamic/edab/wordpress/wp-content/uploads/2012/09/pennEngFrontPage-960x400.png')"></div><br />
<h2> Penn Engineering</h2><br />
<p>We would like to thank the SEAS for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--pgfi--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://published.genomics.upenn.edu/2009/PGFI_logo_2008-12-11-small.png')"></div><br />
<h2> PGFI</h2><br />
<p>We would like to thank the PGFI for providing training support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Penn Epigenetics--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/1/1f/Perelman_Logo.jpg')"></div><br />
<h2> Penn Epigenetics</h2><br />
<p>We would like to thank the Penn Epigenetics department, specifically the Bartomlei and Simmons labs, for providing reagents, advice, and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Qiagen--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/5/51/QLogo.jpg')"></div><br />
<h2>Qiagen</h2><br />
<p>We would like to thank Qiagen for providing reagents and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<div class="span4"><br />
<div class="img-wrap" style="background-image: url('image.jpg)"/><br />
<h2>Title</h2><br />
<p>description</p><br />
<p><a href="link">read more &raquo;</a><br />
</div>--><br />
<br />
</div><br />
<br />
<br />
<br />
<!--here is where you would add another sponsor.<br />
Copy the formatting starting from span4 to /span4<br />
So something like:<br />
<br />
<div class="span4"><br />
<div class="img-wrap" style="background-image: url('image.jpg)"/><br />
<h2>Title</h2><br />
<p>description</p><br />
<p><a href="link">read more &raquo;</a><br />
</div>--><br />
<br />
<br />
<!--make sure your new sponsors go before these /divs--><br />
</div><!--/row--><br />
</div><!--text-wrap--><br />
<br />
<!-- if you have to add more than 2 sponsors, wrap the new sponsors like this:<br />
<br />
<div class="text-wrap"><br />
<div class="row" style="margin-top: 35px;"><br />
<div class="span4"> <br />
~~~up to 3 sponsors can go in here~~~<br />
</div><br />
</div>--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div id ="pagefooter"><br />
<br><br />
<br><br />
<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
</center> <br />
<br><br />
Penn iGem &copy; 2013<br />
</div><br />
<br />
</body><br />
</html></div>Bkapturhttp://2013.igem.org/Team:Penn/SponsorsTeam:Penn/Sponsors2013-10-29T03:51:56Z<p>Bkaptur: </p>
<hr />
<div><html lang="en"><br />
<head><br />
<br />
<title>Penn iGEM</title><br />
<link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/> <!--css--><br />
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$(document).ready(function($) {<br />
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$('.nav_wrap').load('https://googledrive.com/host/0B4ZBZOYYKBzEclFHMmpZcVlydmc');<br />
});<br />
</script><br />
<br />
<style><br />
<br />
/*Page specific*/<br />
/*fonts/headings*/<br />
h4 {<br />
text-align: center;<br />
}<br />
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/*logos*/<br />
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.span4 {<br />
background-color: white; /*background color white and slightly transparent*/<br />
width: 200px;<br />
height: 400px;<br />
padding: 10px;<br />
display: inline-block;<br />
overflow: hidden;<br />
margin: 10px;<br />
}<br />
<br />
.span4 img {<br />
border-radius: 0px;<br />
bottom: 0px;<br />
}<br />
<br />
<br />
#break {<br />
height: 50px;<br />
width: 100%;<br />
background-color: gray;<br />
}<br />
<br />
.img {<br />
border-radius: 0px;<br />
position: absolute;<br />
bottom: 0px;<br />
height: 600px;<br />
}<br />
<br />
.img-wrap {<br />
height: 150px;<br />
width: 200px;<br />
overflow: hidden;<br />
position: relative;<br />
margin-top: 0px;<br />
background-size: 200px;<br />
background-position: center;<br />
background-repeat: no-repeat;<br />
}<br />
<br />
<br />
<br />
/*fix margins on button (lines them up better)*/<br />
#wrap-btn {<br />
margin-bottom: 16px;<br />
}<br />
<br />
<br />
<br />
</style><br />
</head><br />
<body><br />
<br />
<body><br />
<div id = "banner_wrap"><br />
<div class = "banner"></div><br />
</div><br />
<div id = "nav_holder"><br />
<div class = "nav_wrap"></div><br />
</div><br />
</div><br />
<div id="text"><br />
<div class = "textwrap"><br />
<br />
<br />
<h1> <center><b>Thank you to all of our sponsors!</b></center> </h1><br />
<!-- <div class="container marketing" style="margin-top: -20px; padding: 30px;">--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<!--MACK INSTITUTE--> <br />
<div class="row"><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('https://dl.dropboxusercontent.com/sh/11iqct3rfv0z3i8/gtn68O7nLE/PNG%20-%20Onscreen%20and%20PDF/large/L_mackinstitute_stacked_color.png?token_hash=AAFVJoJ_oJ-6AVIVHnQ76irVa73dyAs_2KYKcdrLBbjt6w');"> <br />
</div><br />
<h2>William and Phyllis Mack Institute</h2><br />
<p>In 2011, and again in 2013, the Mack Institute has co-sponsored the University of Pennsylvania’s undergraduate student team in the annual International Genetically Engineered Machine competition (iGEM).<br />
<a class="btn" id="wrap-btn" href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/"></a></p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--NEB--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2012/d/d6/Austin_Texas_NEB_logo.jpeg');"></div><br />
<h2> NEB</h2><br />
<p>New England Biolabs has been more than generous with our team this year (as in previous years) and we are extremely appreciative of their support!</p><br />
<br />
</div><!-- /.span4 --> <br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<!--ADDGENE--><br />
<div class="img-wrap" style="background-image: url('http://dmsbulletin.hms.harvard.edu/images/NovDec11/addgene.jpg')"></div><br />
<h2>Addgene</h2><br />
<p>We are thrilled to have Addgene supporting our team this year, they have been a great resource for our project.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
<br />
<!----END OF BLOCK--><br />
<br />
<!--textwrap--><br />
<br />
<div class="text-wrap"><br />
<br />
<br />
<br />
<br />
<!--PENN M&T--><br />
<div class="row"><br />
<div class="span4" style = "float: left;"><br />
<div class="img-wrap" style="background-image: url('https://si0.twimg.com/profile_images/799689415/m_t_logo_stackedcopy.jpg'); background-position: 0px 10px"></div><br />
<h2> Penn M&T </h2><br />
<p>Penn's M&T department has been very generous to support our team for several years now, we hope that they continue to support us in the future.</p><br />
<br />
</div><!-- /.span4 --></div><br />
<br />
<!--Penn CURF--><br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://secure.www.upenn.edu/themeyear/proof/images/stories/curf.jpg')"></div><br />
<h2> Penn CURF </h2><br />
<p>CURF has offered our team numerous outreach opportunities and financial support, we are happy that they connect with our mission of educating the community about synthetic biology.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--IDT--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('http://bitesizebio.s3.amazonaws.com/content/uploads/2011/04/IDT-Logo-2010_3-578x240.jpg')"></div><br />
<h2> IDT </h2><br />
<p>IDT's service and support has been a cornerstone of our team for years, we truly appreciate their corporate sponsorship.</p><br />
<br />
<br />
<br />
</div></div><br />
<br />
<div class="text-wrap"><br />
</div><!-- /.span4 --><br />
<br />
<!--Biomatters--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://s10.postimg.org/twfinment/geneiouslogo.png')"></div><br />
<h2> Biomatters</h2><br />
<p>For the duration of iGEM 2013 competition Biomatters has provided us with a license to use Geneious for every team-member. This software has been crucial to our team for designing and simulating experiments in silico.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('http://s8.postimg.org/w4oxbbcj9/penn_logo.jpg')"></div><br />
<h2> The University of Pennsylvania</h2><br />
<p>We would like to thank the University of Pennsylvania for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn Engineering--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://fling.seas.upenn.edu/~edab/dynamic/edab/wordpress/wp-content/uploads/2012/09/pennEngFrontPage-960x400.png')"></div><br />
<h2> Penn Engineering</h2><br />
<p>We would like to thank the SEAS for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--pgfi--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://published.genomics.upenn.edu/2009/PGFI_logo_2008-12-11-small.png')"></div><br />
<h2> PGFI</h2><br />
<p>We would like to thank the PGFI for providing training support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Penn Epigenetics--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/1/1f/Perelman_Logo.jpg')"></div><br />
<h2> Penn Epigenetics</h2><br />
<p>We would like to thank the Penn Epigenetics department, specifically the Bartomlei and Simmons labs, for providing reagents, advice, and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Qiagen--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/5/51/QLogo.jpg')"></div><br />
<h2>Qiagen</h2><br />
<p>We would like to thank Qiagen for providing reagents and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
<br />
<div class="span4"><br />
<div class="img-wrap" style="background-image: url('image.jpg)"/><br />
<h2>Title</h2><br />
<p>description</p><br />
<p><a href="link">read more &raquo;</a><br />
</div>--><br />
<br />
<!--here is where you would add another sponsor.<br />
Copy the formatting starting from span4 to /span4<br />
So something like:<br />
<br />
<div class="span4"><br />
<div class="img-wrap" style="background-image: url('image.jpg)"/><br />
<h2>Title</h2><br />
<p>description</p><br />
<p><a href="link">read more &raquo;</a><br />
</div>--><br />
<br />
<br />
<!--make sure your new sponsors go before these /divs--><br />
</div><!--/row--><br />
</div><!--text-wrap--><br />
<br />
<!-- if you have to add more than 2 sponsors, wrap the new sponsors like this:<br />
<br />
<div class="text-wrap"><br />
<div class="row" style="margin-top: 35px;"><br />
<div class="span4"> <br />
~~~up to 3 sponsors can go in here~~~<br />
</div><br />
</div>--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div id ="pagefooter"><br />
<br><br />
<br><br />
<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
</center> <br />
<br><br />
Penn iGem &copy; 2013<br />
</div><br />
<br />
</body><br />
</html></div>Bkapturhttp://2013.igem.org/Team:Penn/SponsorsTeam:Penn/Sponsors2013-10-29T03:28:55Z<p>Bkaptur: </p>
<hr />
<div><html lang="en"><br />
<head><br />
<br />
<title>Penn iGEM</title><br />
<link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/> <!--css--><br />
<br />
<script src="https://googledrive.com/host/0B4ZBZOYYKBzETkFqdnhMeV9fMzA" ></script> <!--jquery--><br />
<br />
<script><br />
$(document).ready(function($) {<br />
<br />
$('.nav_wrap').load('https://googledrive.com/host/0B4ZBZOYYKBzEclFHMmpZcVlydmc');<br />
});<br />
</script><br />
<br />
<style><br />
<br />
/*Page specific*/<br />
/*fonts/headings*/<br />
h4 {<br />
text-align: center;<br />
}<br />
<br />
/*logos*/<br />
<br />
.span4 {<br />
background-color: white; /*background color white and slightly transparent*/<br />
width: 200px;<br />
height: 400px;<br />
padding: 10px;<br />
display: inline-block;<br />
overflow: hidden;<br />
margin: 10px;<br />
}<br />
<br />
.span4 img {<br />
border-radius: 0px;<br />
bottom: 0px;<br />
}<br />
<br />
<br />
#break {<br />
height: 50px;<br />
width: 100%;<br />
background-color: gray;<br />
}<br />
<br />
.img {<br />
border-radius: 0px;<br />
position: absolute;<br />
bottom: 0px;<br />
height: 600px;<br />
}<br />
<br />
.img-wrap {<br />
height: 150px;<br />
width: 200px;<br />
overflow: hidden;<br />
position: relative;<br />
margin-top: 0px;<br />
background-size: 200px;<br />
background-position: center;<br />
background-repeat: no-repeat;<br />
}<br />
<br />
<br />
<br />
/*fix margins on button (lines them up better)*/<br />
#wrap-btn {<br />
margin-bottom: 16px;<br />
}<br />
<br />
<br />
<br />
</style><br />
</head><br />
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<br />
<body><br />
<div id = "banner_wrap"><br />
<div class = "banner"></div><br />
</div><br />
<div id = "nav_holder"><br />
<div class = "nav_wrap"></div><br />
</div><br />
</div><br />
<div id="text"><br />
<div class = "textwrap"><br />
<br />
<br />
<h1> <center><b>Thank you to all of our sponsors!</b></center> </h1><br />
<!-- <div class="container marketing" style="margin-top: -20px; padding: 30px;">--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<!--MACK INSTITUTE--> <br />
<div class="row"><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('https://dl.dropboxusercontent.com/sh/11iqct3rfv0z3i8/gtn68O7nLE/PNG%20-%20Onscreen%20and%20PDF/large/L_mackinstitute_stacked_color.png?token_hash=AAFVJoJ_oJ-6AVIVHnQ76irVa73dyAs_2KYKcdrLBbjt6w');"> <br />
</div><br />
<h2>William and Phyllis Mack Institute</h2><br />
<p>In 2011, and again in 2013, the Mack Institute has co-sponsored the University of Pennsylvania’s undergraduate student team in the annual International Genetically Engineered Machine competition (iGEM).<br />
<a class="btn" id="wrap-btn" href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/"></a></p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--NEB--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2012/d/d6/Austin_Texas_NEB_logo.jpeg');"></div><br />
<h2> NEB</h2><br />
<p>New England Biolabs has been more than generous with our team this year (as in previous years) and we are extremely appreciative of their support!</p><br />
<br />
</div><!-- /.span4 --> <br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<!--ADDGENE--><br />
<div class="img-wrap" style="background-image: url('http://dmsbulletin.hms.harvard.edu/images/NovDec11/addgene.jpg')"></div><br />
<h2>Addgene</h2><br />
<p>We are thrilled to have Addgene supporting our team this year, they have been a great resource for our project.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
<br />
<!----END OF BLOCK--><br />
<br />
<!--textwrap--><br />
<br />
<div class="text-wrap"><br />
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<br />
<br />
<!--PENN M&T--><br />
<div class="row"><br />
<div class="span4" style = "float: left;"><br />
<div class="img-wrap" style="background-image: url('https://si0.twimg.com/profile_images/799689415/m_t_logo_stackedcopy.jpg'); background-position: 0px 10px"></div><br />
<h2> Penn M&T </h2><br />
<p>Penn's M&T department has been very generous to support our team for several years now, we hope that they continue to support us in the future.</p><br />
<br />
</div><!-- /.span4 --></div><br />
<br />
<!--Penn CURF--><br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://secure.www.upenn.edu/themeyear/proof/images/stories/curf.jpg')"></div><br />
<h2> Penn CURF </h2><br />
<p>CURF has offered our team numerous outreach opportunities and financial support, we are happy that they connect with our mission of educating the community about synthetic biology.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--IDT--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('http://bitesizebio.s3.amazonaws.com/content/uploads/2011/04/IDT-Logo-2010_3-578x240.jpg')"></div><br />
<h2> IDT </h2><br />
<p>IDT's service and support has been a cornerstone of our team for years, we truly appreciate their corporate sponsorship.</p><br />
<br />
<br />
<br />
</div></div><br />
<br />
<div class="text-wrap"><br />
</div><!-- /.span4 --><br />
<br />
<!--Biomatters--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://s10.postimg.org/twfinment/geneiouslogo.png')"></div><br />
<h2> Biomatters</h2><br />
<p>For the duration of iGEM 2013 competition Biomatters has provided us with a license to use Geneious for every team-member. This software has been crucial to our team for designing and simulating experiments in silico.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('http://s8.postimg.org/w4oxbbcj9/penn_logo.jpg')"></div><br />
<h2> The University of Pennsylvania</h2><br />
<p>We would like to thank the University of Pennsylvania for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn Engineering--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://fling.seas.upenn.edu/~edab/dynamic/edab/wordpress/wp-content/uploads/2012/09/pennEngFrontPage-960x400.png')"></div><br />
<h2> Penn Engineering</h2><br />
<p>We would like to thank the SEAS for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--pgfi--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://published.genomics.upenn.edu/2009/PGFI_logo_2008-12-11-small.png')"></div><br />
<h2> PGFI</h2><br />
<p>We would like to thank the PGFI for providing training support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Penn Epigenetics--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/1/1f/Perelman_Logo.jpg')"></div><br />
<h2> Penn Epigenetics</h2><br />
<p>We would like to thank the Penn Epigenetics department, specifically the Bartomlei and Simmons labs, for providing reagents, advice, and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Qiagen--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/5/51/QLogo.jpg')"></div><br />
<h2>Qiagen</h2><br />
<p>We would like to thank Qiagen for providing reagents and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
<br />
<!--here is where you would add another sponsor.<br />
Copy the formatting starting from span4 to /span4<br />
So something like:<br />
<br />
<div class="span4"><br />
<div class="img-wrap" style="background-image: url('image.jpg)"/><br />
<h2>Title</h2><br />
<p>description</p><br />
<p><a href="link">read more &raquo;</a><br />
</div>--><br />
<br />
<br />
<!--make sure your new sponsors go before these /divs--><br />
</div><!--/row--><br />
</div><!--text-wrap--><br />
<br />
<!-- if you have to add more than 2 sponsors, wrap the new sponsors like this:<br />
<br />
<div class="text-wrap"><br />
<div class="row" style="margin-top: 35px;"><br />
<div class="span4"> <br />
~~~up to 3 sponsors can go in here~~~<br />
</div><br />
</div>--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div id ="pagefooter"><br />
<br><br />
<br><br />
<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
</center> <br />
<br><br />
Penn iGem &copy; 2013<br />
</div><br />
<br />
</body><br />
</html></div>Bkapturhttp://2013.igem.org/Team:Penn/SponsorsTeam:Penn/Sponsors2013-10-29T03:28:29Z<p>Bkaptur: </p>
<hr />
<div><html lang="en"><br />
<head><br />
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<title>Penn iGEM</title><br />
<link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/> <!--css--><br />
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h4 {<br />
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background-color: white; /*background color white and slightly transparent*/<br />
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position: absolute;<br />
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height: 150px;<br />
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position: relative;<br />
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background-position: center;<br />
background-repeat: no-repeat;<br />
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</head><br />
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<div id = "banner_wrap"><br />
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<div id="text"><br />
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<br />
<h1> <center><b>Thank you to all of our sponsors!</b></center> </h1><br />
<!-- <div class="container marketing" style="margin-top: -20px; padding: 30px;">--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<!--MACK INSTITUTE--> <br />
<div class="row"><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('https://dl.dropboxusercontent.com/sh/11iqct3rfv0z3i8/gtn68O7nLE/PNG%20-%20Onscreen%20and%20PDF/large/L_mackinstitute_stacked_color.png?token_hash=AAFVJoJ_oJ-6AVIVHnQ76irVa73dyAs_2KYKcdrLBbjt6w');"> <br />
</div><br />
<h2>William and Phyllis Mack Institute</h2><br />
<p>In 2011, and again in 2013, the Mack Institute has co-sponsored the University of Pennsylvania’s undergraduate student team in the annual International Genetically Engineered Machine competition (iGEM).<br />
<a class="btn" id="wrap-btn" href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/"></a></p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--NEB--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2012/d/d6/Austin_Texas_NEB_logo.jpeg');"></div><br />
<h2> NEB</h2><br />
<p>New England Biolabs has been more than generous with our team this year (as in previous years) and we are extremely appreciative of their support!</p><br />
<br />
</div><!-- /.span4 --> <br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<!--ADDGENE--><br />
<div class="img-wrap" style="background-image: url('http://dmsbulletin.hms.harvard.edu/images/NovDec11/addgene.jpg')"></div><br />
<h2>Addgene</h2><br />
<p>We are thrilled to have Addgene supporting our team this year, they have been a great resource for our project.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
<br />
<!----END OF BLOCK--><br />
<br />
<!--textwrap--><br />
<br />
<div class="text-wrap"><br />
<br />
<br />
<br />
<br />
<!--PENN M&T--><br />
<div class="row"><br />
<div class="span4" style = "float: left;"><br />
<div class="img-wrap" style="background-image: url('https://si0.twimg.com/profile_images/799689415/m_t_logo_stackedcopy.jpg'); background-position: 0px 10px"></div><br />
<h2> Penn M&T </h2><br />
<p>Penn's M&T department has been very generous to support our team for several years now, we hope that they continue to support us in the future.</p><br />
<br />
</div><!-- /.span4 --></div><br />
<br />
<!--Penn CURF--><br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://secure.www.upenn.edu/themeyear/proof/images/stories/curf.jpg')"></div><br />
<h2> Penn CURF </h2><br />
<p>CURF has offered our team numerous outreach opportunities and financial support, we are happy that they connect with our mission of educating the community about synthetic biology.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--IDT--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('http://bitesizebio.s3.amazonaws.com/content/uploads/2011/04/IDT-Logo-2010_3-578x240.jpg')"></div><br />
<h2> IDT </h2><br />
<p>IDT's service and support has been a cornerstone of our team for years, we truly appreciate their corporate sponsorship.</p><br />
<br />
<br />
<br />
</div></div><br />
<br />
<div class="text-wrap"><br />
</div><!-- /.span4 --><br />
<br />
<!--Biomatters--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://s10.postimg.org/twfinment/geneiouslogo.png')"></div><br />
<h2> Biomatters</h2><br />
<p>For the duration of iGEM 2013 competition Biomatters has provided us with a license to use Geneious for every team-member. This software has been crucial to our team for designing and simulating experiments in silico.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('http://s8.postimg.org/w4oxbbcj9/penn_logo.jpg')"></div><br />
<h2> The University of Pennsylvania</h2><br />
<p>We would like to thank the University of Pennsylvania for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--Penn Engineering--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://fling.seas.upenn.edu/~edab/dynamic/edab/wordpress/wp-content/uploads/2012/09/pennEngFrontPage-960x400.png')"></div><br />
<h2> Penn Engineering</h2><br />
<p>We would like to thank the SEAS for providing monetary support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--pgfi--><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('http://published.genomics.upenn.edu/2009/PGFI_logo_2008-12-11-small.png')"></div><br />
<h2> PGFI</h2><br />
<p>We would like to thank the PGFI for providing training support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Penn Epigenetics--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/1/1f/Perelman_Logo.jpg')"></div><br />
<h2> Penn Epigenetics</h2><br />
<p>We would like to thank the Penn Epigenetics department, specifically the Bartomlei and Simmons labs, for providing reagents, advice, and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<br />
<br />
<!--Qiagen--><br />
<div class="span4" style="margin-left:50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2013/5/51/QLogo.jpg')"></div><br />
<h2>Qiagen</h2><br />
<p>We would like to thank Qiagen for providing reagents and support for the team.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
<br />
<!--here is where you would add another sponsor.<br />
Copy the formatting starting from span4 to /span4<br />
So something like:<br />
<br />
<div class="span4"><br />
<div class="img-wrap" style="background-image: url('image.jpg)"/><br />
<h2>Title</h2><br />
<p>description</p><br />
<p><a href="link">read more &raquo;</a><br />
</div>--><br />
<br />
<br />
<!--make sure your new sponsors go before these /divs--><br />
</div><!--/row--><br />
</div><!--text-wrap--><br />
<br />
<!-- if you have to add more than 2 sponsors, wrap the new sponsors like this:<br />
<br />
<div class="text-wrap"><br />
<div class="row" style="margin-top: 35px;"><br />
<div class="span4"> <br />
~~~up to 3 sponsors can go in here~~~<br />
</div><br />
</div>--><br />
<br />
<!-- BLOCK OF 3 SPONSORS--><br />
<br />
<!--MACK INSTITUTE--> <br />
<div class="row"><br />
<div class="span4" style="float: left;"><br />
<div class="img-wrap" style="background-image: url('https://dl.dropboxusercontent.com/sh/11iqct3rfv0z3i8/gtn68O7nLE/PNG%20-%20Onscreen%20and%20PDF/large/L_mackinstitute_stacked_color.png?token_hash=AAFVJoJ_oJ-6AVIVHnQ76irVa73dyAs_2KYKcdrLBbjt6w');"> <br />
</div><br />
<h2>William and Phyllis Mack Institute</h2><br />
<p>In 2011, and again in 2013, the Mack Institute has co-sponsored the University of Pennsylvania’s undergraduate student team in the annual International Genetically Engineered Machine competition (iGEM).<br />
<a class="btn" id="wrap-btn" href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/"></a></p><br />
<br />
</div><!-- /.span4 --><br />
<br />
<!--NEB--><br />
<div class="span4" style="margin-left: 50px;"><br />
<div class="img-wrap" style="background-image: url('https://static.igem.org/mediawiki/2012/d/d6/Austin_Texas_NEB_logo.jpeg');"></div><br />
<h2> NEB</h2><br />
<p>New England Biolabs has been more than generous with our team this year (as in previous years) and we are extremely appreciative of their support!</p><br />
<br />
</div><!-- /.span4 --> <br />
<br />
<div class="span4" style="margin-left: 50px;"><br />
<!--ADDGENE--><br />
<div class="img-wrap" style="background-image: url('http://dmsbulletin.hms.harvard.edu/images/NovDec11/addgene.jpg')"></div><br />
<h2>Addgene</h2><br />
<p>We are thrilled to have Addgene supporting our team this year, they have been a great resource for our project.</p><br />
<br />
</div><!-- /.span4 --><br />
</div><br />
<br />
<!----END OF BLOCK--><br />
<br />
<br />
<br />
<br />
<br />
<br />
</div><br />
<br />
<div id ="pagefooter"><br />
<br><br />
<br><br />
<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
</center> <br />
<br><br />
Penn iGem &copy; 2013<br />
</div><br />
<br />
</body><br />
</html></div>Bkapturhttp://2013.igem.org/Team:Penn/AbstractTeam:Penn/Abstract2013-10-29T03:24:15Z<p>Bkaptur: </p>
<hr />
<div><html lang="en"><br />
<head><br />
<br />
<title>Penn iGEM</title><br />
<link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/> <!--css--><br />
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<p><br />
The code of life is more than a sequence of A’s, C’s, T’s, and G’s. Heart cells in the human body contain the same DNA as skin cells in the foot, yet these two cell types behave in radically different ways. Both contain the DNA for every one of over 20,000 human genes but express only the ones needed for their own form and function. These differences are due to epigenetic controls. Epigenetics refers to any regulation of gene expression and phenotype that is not based on the sequence of bases in DNA. In addition to governing cellular differentiation, epigenetic mechanisms facilitate the proper functioning of a cell. When these mechanisms go awry, neurodevelopmental disorders, immunodeficiency, and cancer can result. Epigenetic phenomena are amongst the primary ways gene expression is regulated; yet, our current understanding of them is limited, especially due to the challenge of studying them in noisy mammalian systems. By virtue of its emphasis on the isolation and testing of biological networks in engineered systems with reduced complexity, synthetic biology offers the promise of fostering understanding of phenomena difficult to study in their native environments. It is thus an ideal forum for epigenetic studies. At its core, synthetic biology also involves the engineering of non-native networks for useful purposes. Well-tuned gene expression is essential to the proper functioning of synthetic biological circuitry, yet epigenetics has not yet been fully explored as a tool for this application. <br />
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</p><br />
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<div id ="pagefooter"><br />
<br><br />
<br><br />
<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
</center> <br />
<br><br />
Penn iGem &copy; 2013<br />
</div><br />
<br />
</body><br />
<script><br />
</script><br />
</html></div>Bkapturhttp://2013.igem.org/Team:Penn/AbstractTeam:Penn/Abstract2013-10-29T03:23:38Z<p>Bkaptur: </p>
<hr />
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<head><br />
<br />
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<link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/> <!--css--><br />
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<p><br />
The code of life is more than a sequence of A’s, C’s, T’s, and G’s. Heart cells in the human body contain the same DNA as skin cells in the foot, yet these two cell types behave in radically different ways. Both contain the DNA for every one of over 20,000 human genes but express only the ones needed for their own form and function. These differences are due to epigenetic controls. Epigenetics refers to any regulation of gene expression and phenotype that is not based on the sequence of bases in DNA. In addition to governing cellular differentiation, epigenetic mechanisms facilitate the proper functioning of a cell. When these mechanisms go awry, neurodevelopmental disorders, immunodeficiency, and cancer can result. Epigenetic phenomena are amongst the primary ways gene expression is regulated; yet, our current understanding of them is limited, especially due to the challenge of studying them in noisy mammalian systems. By virtue of its emphasis on the isolation and testing of biological networks in engineered systems with reduced complexity, synthetic biology offers the promise of fostering understanding of phenomena difficult to study in their native environments. It is thus an ideal forum for epigenetic studies. At its core, synthetic biology also involves the engineering of non-native networks for useful purposes. Well-tuned gene expression is essential to the proper functioning of synthetic biological circuitry, yet epigenetics has not yet been fully explored as a tool for this application. <br />
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The code of life is more than a sequence of A’s, C’s, T’s, and G’s. Heart cells in the human body contain the same DNA as skin cells in the foot, yet these two cell types behave in radically different ways. Both contain the DNA for every one of over 20,000 human genes but express only the ones needed for their own form and function. These differences are due to epigenetic controls. Epigenetics refers to any regulation of gene expression and phenotype that is not based on the sequence of bases in DNA. In addition to governing cellular differentiation, epigenetic mechanisms facilitate the proper functioning of a cell. When these mechanisms go awry, neurodevelopmental disorders, immunodeficiency, and cancer can result. Epigenetic phenomena are amongst the primary ways gene expression is regulated; yet, our current understanding of them is limited, especially due to the challenge of studying them in noisy mammalian systems. By virtue of its emphasis on the isolation and testing of biological networks in engineered systems with reduced complexity, synthetic biology offers the promise of fostering understanding of phenomena difficult to study in their native environments. It is thus an ideal forum for epigenetic studies. At its core, synthetic biology also involves the engineering of non-native networks for useful purposes. Well-tuned gene expression is essential to the proper functioning of synthetic biological circuitry, yet epigenetics has not yet been fully explored as a tool for this application. <br />
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<h2>Laboratory Information Management Systems</h2> <!--title--><br />
<br><p><b>What's LIMS and Why Use It?</b><br><br />
LIMS stands for Laboratory Information Management System. It's a way of managing data involved in working in a lab. The definition of LIMS has expanded recently to include assay management, data mining, and a lot of other complicated features available in expensive commercial programs. However, one core, indispensable feature is sample management: A key feature of a good lab information system is that it will tell you where you put your tube after you've long forgotten. To fill this need for an electronic sample management system, Penn iGEM created LIMS systems using the Google Spreadsheet and Forms platform. The LIMS forms and spreadsheets provided on this page are updated versions of the same ones that Penn iGEM used to manage its samples all summer.<br><center><br />
<br> <img src="https://static.igem.org/mediawiki/2013/5/56/AdfadfsIMG_0540.JPG" width="500"><figcaption>Have you ever tried to find an old primer or glycerol stock from unlabeled tubes such as in the box above? It can be a pain, so we adopted the rigorous Laboratory Information Management System (LIMS).</figcaption><br><br></center><br />
<br><p><b>How to Copy and Edit Penn iGEM’s Google Doc LIMS Forms:</b><br><br />
1. Sign into Google using your Gmail account.<br><br />
2. Open one of our forms that you wish to copy using the links on our website.<br><br />
3. Here you will be able to view our spreadsheet, but not able to edit it.<br><br />
4. To make a copy for yourself, go to “File” -> “Make a Copy.”<br><br />
5. Enter the document name you wish to use.<br><br />
6. You now have a copy of our form and spreadsheet for your own use.<br><br />
7. To edit the form, go to “Form” -> “Edit Form.”<br><br />
8. From here, you have the option to change any of the data entry options on our form. For instructions on editing specifics, consult Google’s help documentation under “Help” -> “Forms Help.”<br><br />
9. After you have adjusted the form to your liking, add entries to the spreadsheet by going to “Form” -> “Go to Live Form.”<br><br />
10. Note: While you may edit the spreadsheet directly, using the form can streamline data entry by using radio buttons and checkboxes that you have pre-set. Additionally, it adds consistency and makes finding data later much easier.<br />
</p><br />
<br><br />
<div align="center"><br />
<br />
<object width="640" height="480"><param name="movie" value="//www.youtube.com/v/yAvCx_qjJDk?hl=en_US&amp;version=3"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="//www.youtube.com/v/yAvCx_qjJDk?hl=en_US&amp;version=3" type="application/x-shockwave-flash" width="640" height="480" allowscriptaccess="always" allowfullscreen="true"></embed></object><br />
<br />
</div><br />
<br />
<p><b>Download Your Own LIMS Forms (Version 1.0) Here:</b><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdEpuU3dvYmpibU9TdkpTRU1KUGdzQWc&usp=sharing">DNA LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdERNUHRiREhqWkdmOVN1MXlnMXBJYlE&usp=sharing">Glycerol Stock LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdHM3S2RvaWJxbHJzNGtlYzZidVJSMVE&usp=sharing">Primers LIMS</a><br><br />
</p><br />
<br />
<h1>Updates:</h1><br />
<p>In our continuous efforts to improve our sample management, we've found that when there's dozens or even hundreds of samples within a Google Documents-generated spreadsheet, Control+F can be an inefficient way to search your data. We're in the process of generating a Javascript-based query system that builds upon Google Spreadsheets, allowing the user to search using useful parameters. Users can search based on a range of dates when their sample may have been entered, partial sample sequence information, and more. We've also updated our forms and merged the DNA LIMS and Primers LIMS into one. Our new forms are available and ready to be downloaded. While we have a working copy of our query system, we're working out a few kinks associated with other users making copies. Once we have a solution for the distribution of our query, we'll be sure to post links for that as well.</p><br />
<p><b>Download Your Own LIMS Forms (Version 2.0) with Queries Here:</b><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dG5aeDl0bnNQa0pqSnlHSnQ2bHhTNFE&usp=drive_web#gid=5">DNA LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dExJOGo2Y0s2RTlqNk5GaktJZW1zQVE&usp=drive_web#gid=2">Strains LIMS</a><br><br />
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<h2>Laboratory Information Management Systems</h2> <!--title--><br />
<br><p><b>What's LIMS and Why Use It?</b><br><br />
LIMS stands for Laboratory Information Management System. It's a way of managing data involved in working in a lab. The definition of LIMS has expanded recently to include assay management, data mining, and a lot of other complicated features available in expensive commercial programs. However, one core, indispensable feature is sample management: A key feature of a good lab information system is that it will tell you where you put your tube after you've long forgotten. To fill this need for an electronic sample management system, Penn iGEM created LIMS systems using the Google Spreadsheet and Forms platform. The LIMS forms and spreadsheets provided on this page are updated versions of the same ones that Penn iGEM used to manage its samples all summer.<br><center><br />
<br> <img src="https://static.igem.org/mediawiki/2013/5/56/AdfadfsIMG_0540.JPG" width="500"><figcaption>Have you ever tried to find an old primer or glycerol stock from unlabeled tubes such as in the box above? It can be a pain, so we adopted the rigorous Laboratory Information Management System (LIMS).</figcaption><br><br></center><br />
<br><p><b>How to Copy and Edit Penn iGEM’s Google Doc LIMS Forms:</b><br><br />
1. Sign into Google using your Gmail account.<br><br />
2. Open one of our forms that you wish to copy using the links on our website.<br><br />
3. Here you will be able to view our spreadsheet, but not able to edit it.<br><br />
4. To make a copy for yourself, go to “File” -> “Make a Copy.”<br><br />
5. Enter the document name you wish to use.<br><br />
6. You now have a copy of our form and spreadsheet for your own use.<br><br />
7. To edit the form, go to “Form” -> “Edit Form.”<br><br />
8. From here, you have the option to change any of the data entry options on our form. For instructions on editing specifics, consult Google’s help documentation under “Help” -> “Forms Help.”<br><br />
9. After you have adjusted the form to your liking, add entries to the spreadsheet by going to “Form” -> “Go to Live Form.”<br><br />
10. Note: While you may edit the spreadsheet directly, using the form can streamline data entry by using radio buttons and checkboxes that you have pre-set. Additionally, it adds consistency and makes finding data later much easier.<br />
</p><br />
<br><br />
<div align="center"><br />
<br />
<object width="640" height="480"><param name="movie" value="//www.youtube.com/v/yAvCx_qjJDk?hl=en_US&amp;version=3"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="//www.youtube.com/v/yAvCx_qjJDk?hl=en_US&amp;version=3" type="application/x-shockwave-flash" width="640" height="480" allowscriptaccess="always" allowfullscreen="true"></embed></object><br />
<br />
</div><br />
<br />
<p><b>Download Your Own LIMS Forms (Version 1.0) Here:</b><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdEpuU3dvYmpibU9TdkpTRU1KUGdzQWc&usp=sharing">DNA LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdERNUHRiREhqWkdmOVN1MXlnMXBJYlE&usp=sharing">Glycerol Stock LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdHM3S2RvaWJxbHJzNGtlYzZidVJSMVE&usp=sharing">Primers LIMS</a><br><br />
</p><br />
<br />
<h1>Updates:</h1><br />
<p>In our continuous efforts to improve our sample management, we've found that when there's dozens or even hundreds of samples within a Google Documents-generated spreadsheet, Control+F can be an inefficient way to search your data. We're in the process of generating a Javascript-based query system that builds upon Google Spreadsheets, allowing the user to search using useful parameters. Users can search based on a range of dates when their sample may have been entered, partial sample sequence information, and more. We've also updated our formed and merged the DNA LIMS and Primers LIMS into one. Our new forms are available and ready to be downloaded. While we have a working copy of our query system, we're working out a few kinks associated with other users making copies. Once we have a solution for the distribution of our query, we'll be sure to post links for that as well.</p><br />
<p><b>Download Your Own LIMS Forms (Version 2.0) with Queries Here:</b><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dG5aeDl0bnNQa0pqSnlHSnQ2bHhTNFE&usp=drive_web#gid=5">DNA LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dExJOGo2Y0s2RTlqNk5GaktJZW1zQVE&usp=drive_web#gid=2">Strains LIMS</a><br><br />
<br><br />
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<h2>WEEK 1</h2><br />
<div class="box"><br />
<h2>June 4 2013 - June 11 2013</h2><br />
<img src="https://static.igem.org/mediawiki/2013/2/22/BE_LynchLabGroup_DSC2796.jpg" width = "600px" class="image"/><br />
<p><b>Goals:<br></b><br />
<p> This was our first week setting foot in the lab as the Penn iGEM team. We wanted to become more acquainted with the lab and start transforming and growing parts that would be useful in our future project ideas. This week we wanted to brainstorm our project ideas further as well as being more competent in basic molecular biology techniques.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We learned how to make competent cells and performed our first transformations of the summer. We continued to brainstorm potential projects and thought about directions we would like to pursue for the summer. Our idea for a project that would revolve around quorum sensing systems is currently being put into motion. We continued brainstorming for our idea about uses for DNA binding domains like TALE, Cas9, and zinc fingers. We grew up and miniprepped our transformations of various quorum sensing parts and learned how to use a plate reader.</p><br><br />
</div><br />
<br />
<br />
<div><br />
<h2>WEEK 2</h2><br />
<br />
<div class="box"><br />
<h2>June 11 2013 - June 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/3e/Photo-8.JPG" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> This week we wanted to transform some parts for our methylation idea that we ordered from addgene. We also wanted to attempt a bisulfite conversion to test methylation. We had some problems transforming some biobrick parts the previous week, so we wanted to troubleshoot our transformations as well. Another goal of ours was to make more competent DH5-alpha and Dam- cells as well as figure out methylation assays for our promoters.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We worked out the details of one of our potential projects: creating DNA binding domain-methyltransferase fusions. Like last week, we transformed and miniprepped parts that we would need for the quorum sensing project, like the LuxI system. We also transformed and miniprepped the standard biobrick backbones psb1A3, psb1C3, and psb1K3, which would be useful in almost any project we decide to pursue. We pinned down and ordered exactly the DNA binding domains that we thought we would be using and ordered the gene blocks from addgene. We methylated a biobrick part, c0051, with an M.sssI, and used our bisulfite conversion kit for the first time. </p><br> </div><br />
<br />
<br />
<div><br />
<br />
<h2>WEEK 3</h2><br />
<div class="box"> <h2>June 18 2013 - June 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/2/21/Aaathermopcrlala.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> It was increasingly important that we decide on our project. At this point we were considering a quorum sensing/cell signaling project that would build upon previously created quorum sensing parts submitted in the registry. We were also considering a methyltransferase-DNA binding domain fusion project with the goal of creating a new methyltransferase. We wanted to begin cloning t9002, a GFP producer controlled by an AHL signaling molecule receiver into psb1C3 from psb1A3 in order to use it in a quorum sensing device we were imagining.<br></b><p><b>Achievements:</b><br><br />
<p>This week we got all of our minipreps submitted for sequencing, and we made headway on our first cloning reaction. We figured out how to add restriction sites for cloning reactions using PCR and completed our first cloning reaction according to our successful colony PCR. We experimented with different thermocycler conditions and polymerases for our PCRs that had previously failed, and began to perform PCR with more success.</p><br></div><br />
</div><br />
<br />
<br />
<div><br />
<h2>WEEK 4</h2><br />
<div class="box"> <h2>June 25 2013 - July 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Device_photo.jpg" width = "600px"><p><b>Goals:<br></b><br />
<p> This week we wanted to think about applications for selective methylation in E. coli and figure out how our project could be useful for future research. We brainstormed how we wanted to create our constructs and began thinking about the cloning reactions that would be required to create them. We also wanted to begin creating our wiki and start generating useful content.<br></b><p><b>Achievements:</b></p><br />
<p>We confirmed that we completed our first successful cloning reaction. We transformed and miniprepped the biobrick parts for the quorum sensing system that we envisioned creating, with one cell having a light-induced AHL producer, and another cell having a AHL producer downstream of an AHL activated promoter. We thought about creating a device that would spatially separate the cells, as opposed to having them in the same media. We used a simple restriction digest assay to test how BstUI, a methylation sensitive promoter, would behave. </p><br></div><!--/box--><br />
</div><br />
<br />
<div><br />
<h2>WEEK 5</h2><br />
<div class="box"> <h2>July 2 2013 - July 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/95/IMG_2175.JPG" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> We wanted to experiment with USER cloning for assembling our gene blocks and minigenes. We also wanted to characterize pdawn and mcherry, parts we got from a lab at the University that we could use in our quorum sensing project. We wanted to attempt to PCR assemble our MsssI and begin fabricating a device for our quorum sensing project. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We practiced measuring fluorescence using our pDawn and mcherry constructs. We successfully completed PCR assembly of our M.sssI. We performed our first cotransformation with I751250, an AHL sender that was downstream of pDawn and T9002. We redesigned primers for PCR reactions that had been giving us trouble, paying more attention to the annealing temperatures of the primers we were designing.</p><br></div><br />
</div><br />
<br />
<div><br />
<h2>WEEK 6</h2><br />
<div class="box"> <h2>July 10 2013 - July 17 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b6/PennigemPic4.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> As the summer was nearing its halfway mark, we wanted to decide on the relative merits of the two projects and reach a decision. We also wanted to continue our cloning for the two projects and troubleshoot cloning-related problems. We now had all the parts we needed for Cas9, TALE, and zinc finger methylase constructs and wanted to begin assembling them into constructs that we envisioned. These constructs would have a two-plasmid system. One plasmid would have the DNA binding domain downstream of a T7 promoter activated by tetracycline, and the other would be a reporter plasmid to detect methylation. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We decided on the constructs that we would create and began the restriction digest and gel extract steps of our miniprepped components. We planned an experiment we could do with tetracycline induction to test whether our hypothetical methyltransferase-DNA binding domain fusions were actually being expressed.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 7</h2><br />
<div class="box"> <h2>July 18 2013 - July 24 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/6/61/Pennnotebook3pic.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week our main goals were to attempt our tetracycline induction experiment, order primers for performing a COBRA assay, and refine our LIMS and retroactively manage our samples. We also wanted to finish the cloning experiments we began the previous week.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We completed our construct for our zinc finger fusion plasmid after a successful colony PCR and sequencing result. We performed our first induction experiment by inoculating cultures with a tetracycline-activated promoter. We redid a PCR assembly of our TALE and Cas9 systems that had been failed before. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 8</h2><br />
<div class="box"> <h2>July 25 2013 - July 31 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/9e/IMG_2173.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to finish our remaining fusion protein constructs and begin thinking about an SDS PAGE to measure protein expression. We also wanted to dedicate more time to pursuing drylab—making advances on our human practices and continue reading the literature on selective methylation. We also wanted to look into trying out different biobrick parts for our quorum sensing system.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We made advances on our cloning of the constructs for both projects. We completed a LIMS system on a Google spreadsheet that would be used to manage our increasingly overwhelming primers box as well as fixing our minipreps and glycerol stock LIMS and retroactively adding samples. We performed a new induction experiment, inducing our cultures with aTc. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 9</h2><br />
<div class="box"> <h2>Aug 1 2013 - Aug 7 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/59/IMG_0382.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make advances toward generating our device for the quorum sensing project. We wanted to better budget our remaining resources and stock up on supplies that we would need throughout the rest of the summer. We also wanted to use our zinc finger clone in an induction experiment, similar to the ones we had performed earlier for the quorum sensing project. Additionally, we aimed to generate a growth curve and see how the zinc finger cells would respond to induction. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We met with various professors at the University and made contacts who had knowledge about areas in both projects. We ordered more reagents and created the abstract for our project. We designed primers to attempt to Gibson assemble the Cas construct that had been giving us trouble during USER cloning. We hoped that the new cloning strategy would yield better results. We aliquoted our antibiotics, making boxes full of Kan, Chlor, and Amp to last us the entire summer and well into the year. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 10</h2><br />
<div class="box"> <h2>Aug 8 2013 - Aug 14 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/a5/IMG_0501.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to use our restriction digest-based test to analyze how our constructs were working with regards to methylation. We needed to decide on which project we were going to pursue as soon as possible, and we decided this week would be the deadline. We wanted to perform our first SDS Page, which had been in the brainstorming stage for a while. Additionally, we wanted to consult experts about designing better primers and see how we could improve our protocols. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We finally decided to fully pursue the project of constructing targeted methyltransferase fusions. While it was a hard decision, it was necessary to commit our efforts to one project. We also finished our TALE clone and began the induction experiment for testing the methyltransferase fusion. We consulted with designers from the School of Design about making our website and better presentations. We began transforming promoters for an additional screen for methyltransferases that we had envisioned, with the belief that methyltransferases could silence promoters.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 11</h2><br />
<div class="box"> <h2>Aug 15 2013 - Aug 21 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/be/Pennnotebook1pic.jpg" width = "600px" ><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to get our Cas construct working after additional drylab work in designing better assembly reactions. We needed to make a detailed plan of where our funds were going to go for the rest of the summer and begin planning our slides for our iGEM presentation. We wanted to decide where we wanted to be by the competition and what we needed to do to get there.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began creating a plan for creating a video about methylation in general and our project specifically. After consulting with our advisors we decided to change the direction of our methyltransferase-DNA binding domain fusion from a two-plasmid to a one-plasmid system that would incorporate a digestion-based assay within the plasmid.</p><br><br />
<br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 12</h2><br />
<div class="box"> <h2>Aug 22 2013 - Aug 28 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/bd/PennigemPic12.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal for this week was to finalize our ideal cloning constructs and figure out how to port what we had already created into the one-plasmid system. We wanted to elaborate more on the assay, as our advisors had emphasized that as one of the more important contributions that our project could make to the synthetic biology community.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We focused on drylab this week, as we needed to get our plans for the rest of the summer set. We worked on a human practices essay about the ethics of targeted methylation in medical therapies. We also began work designing new primers for our revised cloning strategy.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 13</h2><br />
<div class="box"> <h2>Aug 29 2013 - Sep 4 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/f/f7/IMG_2180.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal was to once again begin a new cloning strategy focused on assembling our one-plasmid systems. We needed our cloning strategy finalized as soon as possible, and we dedicated the majority of our time this week to streamlining our cloning process.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began setting up our travel plans to get to the Jamboree. We began the initial stages of cloning our new systems and made substantial progress on cloning our zinc finger and TALE. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 14</h2><br />
<div class="box"> <h2>Sep 5 2013 - Sep 11 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/ad/IMG_0495.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal for this week was to make further progress on cloning our constructs. We also wanted to continue our work on the human practices essay, and begin creating a poster presentation for presenting at University research conferences. We also wanted to begin thinking about designing a computer application for analyzing gels.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>During a marathon weekend coding session, we created a program that we called MaGellin that was designed to analyze our gels and characterize the amount of methylation. We attempted to improve our cloning efficiency by utilizing Antarctic Phosphatase within our reactions. We made substantial progress on finishing our TALE and zinc finger constructs, and selected and grew colonies that would be used to test our assay the following week. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 15</h2><br />
<div class="box"> <h2>Sep 12 2013 - Sep 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/d/d0/Pennigempic1.jpg" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make substantial progress on the website this week. We also wanted to run our assay and test how well our methyltransferase-DNA binding domain fusions had worked. We wanted to work on animation for our video as well as make progress on our human practices essay.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran the assay on the TALE and zinc finger clones, and it yielded promising results. The expression of our fusion protein was a definite achievement. We made substantial progress on the website and essay as well. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 16</h2><br />
<div class="box"> <h2>Sep 19 2013 - Sep 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/5e/DSC_0482.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We needed to finish our website and various forms this week, as well as run our assay in triplicate on the constructs we had created thus far. We needed to plan our remaining time up to the Jamboree, and practice our presentation skills at various outreach events.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We attended several events aimed at recruiting future team members that showed substantial interest in our research and iGEM in general. Our assay returned promising results about the state of our methyltransferase-DNA binding domain fusions. Additionally, we finished the website and filled out all the forms we needed. We have a few experiments still in progress, but our time now is spent preparing for the Jamboree and being ready to present our results. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<br />
<h2>WEEK 17</h2><br />
<div class="box"> <h2>Sep 26 2013 - Oct 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/c/c8/Momomomomomomo.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> In the week before the Jamboree, we wanted to compile all our last-minute data as well as create our poster and Powerpoint presentation for the competition.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We gathered a ton of last-minute data this week. The solid deadline put upon us by the Jamboree motivated us all to work as hard as possible to get data worthy of our presentation at the Jamboree. While there's still a lot that we wish to accomplish with our project, we're proud of how far we've made it and hope our hard work pays off at the Jamboree. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 18 (North America Regionals)</h2><br />
<div class="box"> <h2>Oct 3 2013 - Oct 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/31/Pennigempic3.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We just became the Regional Winners for North America for iGEM 2013, but there's no time to rest. Now it's time to get back in the lab and prepare for the World Jamboree. We want to make a game plan for what we are going to accomplish before the World Jamboree at MIT in early November and gather data in areas where we needed more work. We're taking the judge's comments from the regional Jamboree very seriously and attempting to improve our project as much as possible in the coming month. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran our MaGellin assay in a preliminary screening of our cas-methylase fusion and got some activity. We re-ran some previous experiments in triplicate to make the data more compelling. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 19 </h2><br />
<div class="box"> <h2>Oct 10 2013 - Oct 16 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Pennnotebook2pic.jpg" width = "600px"><br />
<br />
<p><b>Goals: <br></b><br />
<p> We wanted to look further into the possibility of transcriptional silencing using targeted methylation. Additionally, we planned to run the full assay to screen our potential Cas-methylase fusion. Another major priority is to perform bisulfite sequencing to look at the target site for our TALE methylase. </p><br><br />
<p><b>Achievements: <br></b><br />
<p>We continued to reach out to underclassmen and recruit members for the upcoming team. At the same time, we were hard at work in lab, performing our assay and trying to further quantify the extent of methylation in our fusion constructs. We got our bisulfite sequencing for our TALE submitted and are eagerly awaiting the results. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 20</h2><br />
<div class="box"> <h2>Oct 17 2013 - Oct 23 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/0/08/PennigemPic11.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week we wat to begin utilizing a cell-free system to test our targeted TALE methylase. It is imperative that we give the Wiki a complete design overhaul. We also want to make a plan for the couple weeks. </p><br><br />
<p><b>Achievements:<br></b><br />
<p> This week we were screening our cas methylase and found noticeable activity when done in triplicate with all the proper controls. We experimented with various induction times as well. We re-ran some experiments that had previous flaws or were missing controls in triplicate. We had some additional cloning to do to modify our constructs as well. We gathered data for our 3D plot of induction for our methylase fusion, which was perhaps the most time-consuming experiment we have done all year. </p><br><br />
</div><br />
</div><br />
<div><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 21</h2><br />
<div class="box"> <h2>Oct 24 2013 - Oct 30 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/4/42/Dannygel.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal is to finalize Wiki for World Jamboree and to collect data for any major experiments we still need to wrap up. We also need to begin our poster for the Jamboree and work on our presentation. At the same time, there is a ton of wetlab and experiments that we have planned, all of which are unlikely to get done in the next couple weeks, but that won't stop us from trying. We have several presentations with various labs at Penn, including the epigenetics department this week. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>This week we finished the Wiki for World Competition. Additionally, we began our last set of experiments, for which the data will be revealed at the World Jamboree. </p><br><br />
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</html></div>Bkapturhttp://2013.igem.org/Team:Penn/NotebookTeam:Penn/Notebook2013-10-29T01:45:40Z<p>Bkaptur: </p>
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<h2>WEEK 1</h2><br />
<div class="box"><br />
<h2>June 4 2013 - June 11 2013</h2><br />
<img src="https://static.igem.org/mediawiki/2013/2/22/BE_LynchLabGroup_DSC2796.jpg" width = "600px" class="image"/><br />
<p><b>Goals:<br></b><br />
<p> This was our first week setting foot in the lab as the Penn iGEM team. We wanted to become more acquainted with the lab and start transforming and growing parts that would be useful in our future project ideas. This week we wanted to brainstorm our project ideas further as well as being more competent in basic molecular biology techniques.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We learned how to make competent cells and performed our first transformations of the summer. We continued to brainstorm potential projects and thought about directions we would like to pursue for the summer. Our idea for a project that would revolve around quorum sensing systems is currently being put into motion. We continued brainstorming for our idea about uses for DNA binding domains like TALE, Cas9, and zinc fingers. We grew up and miniprepped our transformations of various quorum sensing parts and learned how to use a plate reader.</p><br><br />
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<h2>WEEK 2</h2><br />
<br />
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<h2>June 11 2013 - June 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/3e/Photo-8.JPG" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> This week we wanted to transform some parts for our methylation idea that we ordered from addgene. We also wanted to attempt a bisulfite conversion to test methylation. We had some problems transforming some biobrick parts the previous week, so we wanted to troubleshoot our transformations as well. Another goal of ours was to make more competent DH5-alpha and Dam- cells as well as figure out methylation assays for our promoters.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We worked out the details of one of our potential projects: creating DNA binding domain-methyltransferase fusions. Like last week, we transformed and miniprepped parts that we would need for the quorum sensing project, like the LuxI system. We also transformed and miniprepped the standard biobrick backbones psb1A3, psb1C3, and psb1K3, which would be useful in almost any project we decide to pursue. We pinned down and ordered exactly the DNA binding domains that we thought we would be using and ordered the gene blocks from addgene. We methylated a biobrick part, c0051, with an M.sssI, and used our bisulfite conversion kit for the first time. </p><br> </div><br />
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<h2>WEEK 3</h2><br />
<div class="box"> <h2>June 18 2013 - June 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/2/21/Aaathermopcrlala.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> It was increasingly important that we decide on our project. At this point we were considering a quorum sensing/cell signaling project that would build upon previously created quorum sensing parts submitted in the registry. We were also considering a methyltransferase-DNA binding domain fusion project with the goal of creating a new methyltransferase. We wanted to begin cloning t9002, a GFP producer controlled by an AHL signaling molecule receiver into psb1C3 from psb1A3 in order to use it in a quorum sensing device we were imagining.<br></b><p><b>Achievements:</b><br><br />
<p>This week we got all of our minipreps submitted for sequencing, and we made headway on our first cloning reaction. We figured out how to add restriction sites for cloning reactions using PCR and completed our first cloning reaction according to our successful colony PCR. We experimented with different thermocycler conditions and polymerases for our PCRs that had previously failed, and began to perform PCR with more success.</p><br></div><br />
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<h2>WEEK 4</h2><br />
<div class="box"> <h2>June 25 2013 - July 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Device_photo.jpg" width = "600px"><p><b>Goals:<br></b><br />
<p> This week we wanted to think about applications for selective methylation in E. coli and figure out how our project could be useful for future research. We brainstormed how we wanted to create our constructs and began thinking about the cloning reactions that would be required to create them. We also wanted to begin creating our wiki and start generating useful content.<br></b><p><b>Achievements:</b></p><br />
<p>We confirmed that we completed our first successful cloning reaction. We transformed and miniprepped the biobrick parts for the quorum sensing system that we envisioned creating, with one cell having a light-induced AHL producer, and another cell having a AHL producer downstream of an AHL activated promoter. We thought about creating a device that would spatially separate the cells, as opposed to having them in the same media. We used a simple restriction digest assay to test how BstUI, a methylation sensitive promoter, would behave. </p><br></div><!--/box--><br />
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<h2>WEEK 5</h2><br />
<div class="box"> <h2>July 2 2013 - July 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/6/61/Pennnotebook3pic.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> We wanted to experiment with USER cloning for assembling our gene blocks and minigenes. We also wanted to characterize pdawn and mcherry, parts we got from a lab at the University that we could use in our quorum sensing project. We wanted to attempt to PCR assemble our MsssI and begin fabricating a device for our quorum sensing project. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We practiced measuring fluorescence using our pDawn and mcherry constructs. We successfully completed PCR assembly of our M.sssI. We performed our first cotransformation with I751250, an AHL sender that was downstream of pDawn and T9002. We redesigned primers for PCR reactions that had been giving us trouble, paying more attention to the annealing temperatures of the primers we were designing.</p><br></div><br />
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<h2>WEEK 6</h2><br />
<div class="box"> <h2>July 10 2013 - July 17 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b6/PennigemPic4.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> As the summer was nearing its halfway mark, we wanted to decide on the relative merits of the two projects and reach a decision. We also wanted to continue our cloning for the two projects and troubleshoot cloning-related problems. We now had all the parts we needed for Cas9, TALE, and zinc finger methylase constructs and wanted to begin assembling them into constructs that we envisioned. These constructs would have a two-plasmid system. One plasmid would have the DNA binding domain downstream of a T7 promoter activated by tetracycline, and the other would be a reporter plasmid to detect methylation. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We decided on the constructs that we would create and began the restriction digest and gel extract steps of our miniprepped components. We planned an experiment we could do with tetracycline induction to test whether our hypothetical methyltransferase-DNA binding domain fusions were actually being expressed.</p><br><br />
</div><br />
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<div><br />
<br />
<h2>WEEK 7</h2><br />
<div class="box"> <h2>July 18 2013 - July 24 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/95/IMG_2175.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week our main goals were to attempt our tetracycline induction experiment, order primers for performing a COBRA assay, and refine our LIMS and retroactively manage our samples. We also wanted to finish the cloning experiments we began the previous week.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We completed our construct for our zinc finger fusion plasmid after a successful colony PCR and sequencing result. We performed our first induction experiment by inoculating cultures with a tetracycline-activated promoter. We redid a PCR assembly of our TALE and Cas9 systems that had been failed before. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 8</h2><br />
<div class="box"> <h2>July 25 2013 - July 31 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/9e/IMG_2173.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to finish our remaining fusion protein constructs and begin thinking about an SDS PAGE to measure protein expression. We also wanted to dedicate more time to pursuing drylab—making advances on our human practices and continue reading the literature on selective methylation. We also wanted to look into trying out different biobrick parts for our quorum sensing system.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We made advances on our cloning of the constructs for both projects. We completed a LIMS system on a Google spreadsheet that would be used to manage our increasingly overwhelming primers box as well as fixing our minipreps and glycerol stock LIMS and retroactively adding samples. We performed a new induction experiment, inducing our cultures with aTc. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 9</h2><br />
<div class="box"> <h2>Aug 1 2013 - Aug 7 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/59/IMG_0382.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make advances toward generating our device for the quorum sensing project. We wanted to better budget our remaining resources and stock up on supplies that we would need throughout the rest of the summer. We also wanted to use our zinc finger clone in an induction experiment, similar to the ones we had performed earlier for the quorum sensing project. Additionally, we aimed to generate a growth curve and see how the zinc finger cells would respond to induction. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We met with various professors at the University and made contacts who had knowledge about areas in both projects. We ordered more reagents and created the abstract for our project. We designed primers to attempt to Gibson assemble the Cas construct that had been giving us trouble during USER cloning. We hoped that the new cloning strategy would yield better results. We aliquoted our antibiotics, making boxes full of Kan, Chlor, and Amp to last us the entire summer and well into the year. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 10</h2><br />
<div class="box"> <h2>Aug 8 2013 - Aug 14 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/a5/IMG_0501.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to use our restriction digest-based test to analyze how our constructs were working with regards to methylation. We needed to decide on which project we were going to pursue as soon as possible, and we decided this week would be the deadline. We wanted to perform our first SDS Page, which had been in the brainstorming stage for a while. Additionally, we wanted to consult experts about designing better primers and see how we could improve our protocols. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We finally decided to fully pursue the project of constructing targeted methyltransferase fusions. While it was a hard decision, it was necessary to commit our efforts to one project. We also finished our TALE clone and began the induction experiment for testing the methyltransferase fusion. We consulted with designers from the School of Design about making our website and better presentations. We began transforming promoters for an additional screen for methyltransferases that we had envisioned, with the belief that methyltransferases could silence promoters.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 11</h2><br />
<div class="box"> <h2>Aug 15 2013 - Aug 21 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/be/Pennnotebook1pic.jpg" width = "600px" ><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to get our Cas construct working after additional drylab work in designing better assembly reactions. We needed to make a detailed plan of where our funds were going to go for the rest of the summer and begin planning our slides for our iGEM presentation. We wanted to decide where we wanted to be by the competition and what we needed to do to get there.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began creating a plan for creating a video about methylation in general and our project specifically. After consulting with our advisors we decided to change the direction of our methyltransferase-DNA binding domain fusion from a two-plasmid to a one-plasmid system that would incorporate a digestion-based assay within the plasmid.</p><br><br />
<br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 12</h2><br />
<div class="box"> <h2>Aug 22 2013 - Aug 28 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/bd/PennigemPic12.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal for this week was to finalize our ideal cloning constructs and figure out how to port what we had already created into the one-plasmid system. We wanted to elaborate more on the assay, as our advisors had emphasized that as one of the more important contributions that our project could make to the synthetic biology community.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We focused on drylab this week, as we needed to get our plans for the rest of the summer set. We worked on a human practices essay about the ethics of targeted methylation in medical therapies. We also began work designing new primers for our revised cloning strategy.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 13</h2><br />
<div class="box"> <h2>Aug 29 2013 - Sep 4 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/f/f7/IMG_2180.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal was to once again begin a new cloning strategy focused on assembling our one-plasmid systems. We needed our cloning strategy finalized as soon as possible, and we dedicated the majority of our time this week to streamlining our cloning process.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began setting up our travel plans to get to the Jamboree. We began the initial stages of cloning our new systems and made substantial progress on cloning our zinc finger and TALE. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 14</h2><br />
<div class="box"> <h2>Sep 5 2013 - Sep 11 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/ad/IMG_0495.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal for this week was to make further progress on cloning our constructs. We also wanted to continue our work on the human practices essay, and begin creating a poster presentation for presenting at University research conferences. We also wanted to begin thinking about designing a computer application for analyzing gels.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>During a marathon weekend coding session, we created a program that we called MaGellin that was designed to analyze our gels and characterize the amount of methylation. We attempted to improve our cloning efficiency by utilizing Antarctic Phosphatase within our reactions. We made substantial progress on finishing our TALE and zinc finger constructs, and selected and grew colonies that would be used to test our assay the following week. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 15</h2><br />
<div class="box"> <h2>Sep 12 2013 - Sep 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/d/d0/Pennigempic1.jpg" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make substantial progress on the website this week. We also wanted to run our assay and test how well our methyltransferase-DNA binding domain fusions had worked. We wanted to work on animation for our video as well as make progress on our human practices essay.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran the assay on the TALE and zinc finger clones, and it yielded promising results. The expression of our fusion protein was a definite achievement. We made substantial progress on the website and essay as well. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 16</h2><br />
<div class="box"> <h2>Sep 19 2013 - Sep 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/5e/DSC_0482.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We needed to finish our website and various forms this week, as well as run our assay in triplicate on the constructs we had created thus far. We needed to plan our remaining time up to the Jamboree, and practice our presentation skills at various outreach events.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We attended several events aimed at recruiting future team members that showed substantial interest in our research and iGEM in general. Our assay returned promising results about the state of our methyltransferase-DNA binding domain fusions. Additionally, we finished the website and filled out all the forms we needed. We have a few experiments still in progress, but our time now is spent preparing for the Jamboree and being ready to present our results. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<br />
<h2>WEEK 17</h2><br />
<div class="box"> <h2>Sep 26 2013 - Oct 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/c/c8/Momomomomomomo.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> In the week before the Jamboree, we wanted to compile all our last-minute data as well as create our poster and Powerpoint presentation for the competition.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We gathered a ton of last-minute data this week. The solid deadline put upon us by the Jamboree motivated us all to work as hard as possible to get data worthy of our presentation at the Jamboree. While there's still a lot that we wish to accomplish with our project, we're proud of how far we've made it and hope our hard work pays off at the Jamboree. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 18 (North America Regionals)</h2><br />
<div class="box"> <h2>Oct 3 2013 - Oct 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/31/Pennigempic3.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We just became the Regional Winners for North America for iGEM 2013, but there's no time to rest. Now it's time to get back in the lab and prepare for the World Jamboree. We want to make a game plan for what we are going to accomplish before the World Jamboree at MIT in early November and gather data in areas where we needed more work. We're taking the judge's comments from the regional Jamboree very seriously and attempting to improve our project as much as possible in the coming month. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran our MaGellin assay in a preliminary screening of our cas-methylase fusion and got some activity. We re-ran some previous experiments in triplicate to make the data more compelling. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 19 </h2><br />
<div class="box"> <h2>Oct 10 2013 - Oct 16 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Pennnotebook2pic.jpg" width = "600px"><br />
<br />
<p><b>Goals: <br></b><br />
<p> We wanted to look further into the possibility of transcriptional silencing using targeted methylation. Additionally, we planned to run the full assay to screen our potential Cas-methylase fusion. Another major priority is to perform bisulfite sequencing to look at the target site for our TALE methylase. </p><br><br />
<p><b>Achievements: <br></b><br />
<p>We continued to reach out to underclassmen and recruit members for the upcoming team. At the same time, we were hard at work in lab, performing our assay and trying to further quantify the extent of methylation in our fusion constructs. We got our bisulfite sequencing for our TALE submitted and are eagerly awaiting the results. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 20</h2><br />
<div class="box"> <h2>Oct 17 2013 - Oct 23 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/0/08/PennigemPic11.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week we wat to begin utilizing a cell-free system to test our targeted TALE methylase. It is imperative that we give the Wiki a complete design overhaul. We also want to make a plan for the couple weeks. </p><br><br />
<p><b>Achievements:<br></b><br />
<p> This week we were screening our cas methylase and found noticeable activity when done in triplicate with all the proper controls. We experimented with various induction times as well. We re-ran some experiments that had previous flaws or were missing controls in triplicate. We had some additional cloning to do to modify our constructs as well. We gathered data for our 3D plot of induction for our methylase fusion, which was perhaps the most time-consuming experiment we have done all year. </p><br><br />
</div><br />
</div><br />
<div><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 21</h2><br />
<div class="box"> <h2>Oct 24 2013 - Oct 30 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/4/42/Dannygel.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal is to finalize Wiki for World Jamboree and to collect data for any major experiments we still need to wrap up. We also need to begin our poster for the Jamboree and work on our presentation. At the same time, there is a ton of wetlab and experiments that we have planned, all of which are unlikely to get done in the next couple weeks, but that won't stop us from trying. We have several presentations with various labs at Penn, including the epigenetics department this week. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>This week we finished the Wiki for World Competition. Additionally, we began our last set of experiments, for which the data will be revealed at the World Jamboree. </p><br><br />
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</html></div>Bkapturhttp://2013.igem.org/Team:Penn/NotebookTeam:Penn/Notebook2013-10-29T01:44:35Z<p>Bkaptur: </p>
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<h2>WEEK 1</h2><br />
<div class="box"><br />
<h2>June 4 2013 - June 11 2013</h2><br />
<img src="https://static.igem.org/mediawiki/2013/2/22/BE_LynchLabGroup_DSC2796.jpg" width = "600px" class="image"/><br />
<p><b>Goals:<br></b><br />
<p> This was our first week setting foot in the lab as the Penn iGEM team. We wanted to become more acquainted with the lab and start transforming and growing parts that would be useful in our future project ideas. This week we wanted to brainstorm our project ideas further as well as being more competent in basic molecular biology techniques.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We learned how to make competent cells and performed our first transformations of the summer. We continued to brainstorm potential projects and thought about directions we would like to pursue for the summer. Our idea for a project that would revolve around quorum sensing systems is currently being put into motion. We continued brainstorming for our idea about uses for DNA binding domains like TALE, Cas9, and zinc fingers. We grew up and miniprepped our transformations of various quorum sensing parts and learned how to use a plate reader.</p><br><br />
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<h2>WEEK 2</h2><br />
<br />
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<h2>June 11 2013 - June 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/3e/Photo-8.JPG" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> This week we wanted to transform some parts for our methylation idea that we ordered from addgene. We also wanted to attempt a bisulfite conversion to test methylation. We had some problems transforming some biobrick parts the previous week, so we wanted to troubleshoot our transformations as well. Another goal of ours was to make more competent DH5-alpha and Dam- cells as well as figure out methylation assays for our promoters.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We worked out the details of one of our potential projects: creating DNA binding domain-methyltransferase fusions. Like last week, we transformed and miniprepped parts that we would need for the quorum sensing project, like the LuxI system. We also transformed and miniprepped the standard biobrick backbones psb1A3, psb1C3, and psb1K3, which would be useful in almost any project we decide to pursue. We pinned down and ordered exactly the DNA binding domains that we thought we would be using and ordered the gene blocks from addgene. We methylated a biobrick part, c0051, with an M.sssI, and used our bisulfite conversion kit for the first time. </p><br> </div><br />
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<h2>WEEK 3</h2><br />
<div class="box"> <h2>June 18 2013 - June 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/2/21/Aaathermopcrlala.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> It was increasingly important that we decide on our project. At this point we were considering a quorum sensing/cell signaling project that would build upon previously created quorum sensing parts submitted in the registry. We were also considering a methyltransferase-DNA binding domain fusion project with the goal of creating a new methyltransferase. We wanted to begin cloning t9002, a GFP producer controlled by an AHL signaling molecule receiver into psb1C3 from psb1A3 in order to use it in a quorum sensing device we were imagining.<br></b><p><b>Achievements:</b><br><br />
<p>This week we got all of our minipreps submitted for sequencing, and we made headway on our first cloning reaction. We figured out how to add restriction sites for cloning reactions using PCR and completed our first cloning reaction according to our successful colony PCR. We experimented with different thermocycler conditions and polymerases for our PCRs that had previously failed, and began to perform PCR with more success.</p><br></div><br />
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<h2>WEEK 4</h2><br />
<div class="box"> <h2>June 25 2013 - July 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Device_photo.jpg" width = "600px"><p><b>Goals:<br></b><br />
<p> This week we wanted to think about applications for selective methylation in E. coli and figure out how our project could be useful for future research. We brainstormed how we wanted to create our constructs and began thinking about the cloning reactions that would be required to create them. We also wanted to begin creating our wiki and start generating useful content.<br></b><p><b>Achievements:</b></p><br />
<p>We confirmed that we completed our first successful cloning reaction. We transformed and miniprepped the biobrick parts for the quorum sensing system that we envisioned creating, with one cell having a light-induced AHL producer, and another cell having a AHL producer downstream of an AHL activated promoter. We thought about creating a device that would spatially separate the cells, as opposed to having them in the same media. We used a simple restriction digest assay to test how BstUI, a methylation sensitive promoter, would behave. </p><br></div><!--/box--><br />
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<h2>WEEK 5</h2><br />
<div class="box"> <h2>July 2 2013 - July 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/6/61/Pennnotebook3pic.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> We wanted to experiment with USER cloning for assembling our gene blocks and minigenes. We also wanted to characterize pdawn and mcherry, parts we got from a lab at the University that we could use in our quorum sensing project. We wanted to attempt to PCR assemble our MsssI and begin fabricating a device for our quorum sensing project. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We practiced measuring fluorescence using our pDawn and mcherry constructs. We successfully completed PCR assembly of our M.sssI. We performed our first cotransformation with I751250, an AHL sender that was downstream of pDawn and T9002. We redesigned primers for PCR reactions that had been giving us trouble, paying more attention to the annealing temperatures of the primers we were designing.</p><br></div><br />
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<h2>WEEK 6</h2><br />
<div class="box"> <h2>July 10 2013 - July 17 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b6/PennigemPic4.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> As the summer was nearing its halfway mark, we wanted to decide on the relative merits of the two projects and reach a decision. We also wanted to continue our cloning for the two projects and troubleshoot cloning-related problems. We now had all the parts we needed for Cas9, TALE, and zinc finger methylase constructs and wanted to begin assembling them into constructs that we envisioned. These constructs would have a two-plasmid system. One plasmid would have the DNA binding domain downstream of a T7 promoter activated by tetracycline, and the other would be a reporter plasmid to detect methylation. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We decided on the constructs that we would create and began the restriction digest and gel extract steps of our miniprepped components. We planned an experiment we could do with tetracycline induction to test whether our hypothetical methyltransferase-DNA binding domain fusions were actually being expressed.</p><br><br />
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<h2>WEEK 7</h2><br />
<div class="box"> <h2>July 18 2013 - July 24 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/95/IMG_2175.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week our main goals were to attempt our tetracycline induction experiment, order primers for performing a COBRA assay, and refine our LIMS and retroactively manage our samples. We also wanted to finish the cloning experiments we began the previous week.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We completed our construct for our zinc finger fusion plasmid after a successful colony PCR and sequencing result. We performed our first induction experiment by inoculating cultures with a tetracycline-activated promoter. We redid a PCR assembly of our TALE and Cas9 systems that had been failed before. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 8</h2><br />
<div class="box"> <h2>July 25 2013 - July 31 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/9e/IMG_2173.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to finish our remaining fusion protein constructs and begin thinking about an SDS PAGE to measure protein expression. We also wanted to dedicate more time to pursuing drylab—making advances on our human practices and continue reading the literature on selective methylation. We also wanted to look into trying out different biobrick parts for our quorum sensing system.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We made advances on our cloning of the constructs for both projects. We completed a LIMS system on a Google spreadsheet that would be used to manage our increasingly overwhelming primers box as well as fixing our minipreps and glycerol stock LIMS and retroactively adding samples. We performed a new induction experiment, inducing our cultures with aTc. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 9</h2><br />
<div class="box"> <h2>Aug 1 2013 - Aug 7 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/59/IMG_0382.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make advances toward generating our device for the quorum sensing project. We wanted to better budget our remaining resources and stock up on supplies that we would need throughout the rest of the summer. We also wanted to use our zinc finger clone in an induction experiment, similar to the ones we had performed earlier for the quorum sensing project. Additionally, we aimed to generate a growth curve and see how the zinc finger cells would respond to induction. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We met with various professors at the University and made contacts who had knowledge about areas in both projects. We ordered more reagents and created the abstract for our project. We designed primers to attempt to Gibson assemble the Cas construct that had been giving us trouble during USER cloning. We hoped that the new cloning strategy would yield better results. We aliquoted our antibiotics, making boxes full of Kan, Chlor, and Amp to last us the entire summer and well into the year. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 10</h2><br />
<div class="box"> <h2>Aug 8 2013 - Aug 14 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/a5/IMG_0501.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to use our restriction digest-based test to analyze how our constructs were working with regards to methylation. We needed to decide on which project we were going to pursue as soon as possible, and we decided this week would be the deadline. We wanted to perform our first SDS Page, which had been in the brainstorming stage for a while. Additionally, we wanted to consult experts about designing better primers and see how we could improve our protocols. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We finally decided to fully pursue the project of constructing targeted methyltransferase fusions. While it was a hard decision, it was necessary to commit our efforts to one project. We also finished our TALE clone and began the induction experiment for testing the methyltransferase fusion. We consulted with designers from the School of Design about making our website and better presentations. We began transforming promoters for an additional screen for methyltransferases that we had envisioned, with the belief that methyltransferases could silence promoters.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 11</h2><br />
<div class="box"> <h2>Aug 15 2013 - Aug 21 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/be/Pennnotebook1pic.jpg" width = "600px" ><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to get our Cas construct working after additional drylab work in designing better assembly reactions. We needed to make a detailed plan of where our funds were going to go for the rest of the summer and begin planning our slides for our iGEM presentation. We wanted to decide where we wanted to be by the competition and what we needed to do to get there.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began creating a plan for creating a video about methylation in general and our project specifically. After consulting with our advisors we decided to change the direction of our methyltransferase-DNA binding domain fusion from a two-plasmid to a one-plasmid system that would incorporate a digestion-based assay within the plasmid.</p><br><br />
<br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 12</h2><br />
<div class="box"> <h2>Aug 22 2013 - Aug 28 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/bd/PennigemPic12.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal for this week was to finalize our ideal cloning constructs and figure out how to port what we had already created into the one-plasmid system. We wanted to elaborate more on the assay, as our advisors had emphasized that as one of the more important contributions that our project could make to the synthetic biology community.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We focused on drylab this week, as we needed to get our plans for the rest of the summer set. We worked on a human practices essay about the ethics of targeted methylation in medical therapies. We also began work designing new primers for our revised cloning strategy.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 13</h2><br />
<div class="box"> <h2>Aug 29 2013 - Sep 4 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/f/f7/IMG_2180.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal was to once again begin a new cloning strategy focused on assembling our one-plasmid systems. We needed our cloning strategy finalized as soon as possible, and we dedicated the majority of our time this week to streamlining our cloning process.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began setting up our travel plans to get to the Jamboree. We began the initial stages of cloning our new systems and made substantial progress on cloning our zinc finger and TALE. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 14</h2><br />
<div class="box"> <h2>Sep 5 2013 - Sep 11 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/ad/IMG_0495.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal for this week was to make further progress on cloning our constructs. We also wanted to continue our work on the human practices essay, and begin creating a poster presentation for presenting at University research conferences. We also wanted to begin thinking about designing a computer application for analyzing gels.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>During a marathon weekend coding session, we created a program that we called MaGellin that was designed to analyze our gels and characterize the amount of methylation. We attempted to improve our cloning efficiency by utilizing Antarctic Phosphatase within our reactions. We made substantial progress on finishing our TALE and zinc finger constructs, and selected and grew colonies that would be used to test our assay the following week. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 15</h2><br />
<div class="box"> <h2>Sep 12 2013 - Sep 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/5e/DSC_0482.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make substantial progress on the website this week. We also wanted to run our assay and test how well our methyltransferase-DNA binding domain fusions had worked. We wanted to work on animation for our video as well as make progress on our human practices essay.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran the assay on the TALE and zinc finger clones, and it yielded promising results. The expression of our fusion protein was a definite achievement. We made substantial progress on the website and essay as well. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 16</h2><br />
<div class="box"> <h2>Sep 19 2013 - Sep 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/d/d0/Pennigempic1.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We needed to finish our website and various forms this week, as well as run our assay in triplicate on the constructs we had created thus far. We needed to plan our remaining time up to the Jamboree, and practice our presentation skills at various outreach events.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We attended several events aimed at recruiting future team members that showed substantial interest in our research and iGEM in general. Our assay returned promising results about the state of our methyltransferase-DNA binding domain fusions. Additionally, we finished the website and filled out all the forms we needed. We have a few experiments still in progress, but our time now is spent preparing for the Jamboree and being ready to present our results. </p><br><br />
</div><br />
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<div><br />
<br />
<br />
<h2>WEEK 17</h2><br />
<div class="box"> <h2>Sep 26 2013 - Oct 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/c/c8/Momomomomomomo.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> In the week before the Jamboree, we wanted to compile all our last-minute data as well as create our poster and Powerpoint presentation for the competition.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We gathered a ton of last-minute data this week. The solid deadline put upon us by the Jamboree motivated us all to work as hard as possible to get data worthy of our presentation at the Jamboree. While there's still a lot that we wish to accomplish with our project, we're proud of how far we've made it and hope our hard work pays off at the Jamboree. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 18 (North America Regionals)</h2><br />
<div class="box"> <h2>Oct 3 2013 - Oct 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/31/Pennigempic3.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We just became the Regional Winners for North America for iGEM 2013, but there's no time to rest. Now it's time to get back in the lab and prepare for the World Jamboree. We want to make a game plan for what we are going to accomplish before the World Jamboree at MIT in early November and gather data in areas where we needed more work. We're taking the judge's comments from the regional Jamboree very seriously and attempting to improve our project as much as possible in the coming month. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran our MaGellin assay in a preliminary screening of our cas-methylase fusion and got some activity. We re-ran some previous experiments in triplicate to make the data more compelling. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 19 </h2><br />
<div class="box"> <h2>Oct 10 2013 - Oct 16 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Pennnotebook2pic.jpg" width = "600px"><br />
<br />
<p><b>Goals: <br></b><br />
<p> We wanted to look further into the possibility of transcriptional silencing using targeted methylation. Additionally, we planned to run the full assay to screen our potential Cas-methylase fusion. Another major priority is to perform bisulfite sequencing to look at the target site for our TALE methylase. </p><br><br />
<p><b>Achievements: <br></b><br />
<p>We continued to reach out to underclassmen and recruit members for the upcoming team. At the same time, we were hard at work in lab, performing our assay and trying to further quantify the extent of methylation in our fusion constructs. We got our bisulfite sequencing for our TALE submitted and are eagerly awaiting the results. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 20</h2><br />
<div class="box"> <h2>Oct 17 2013 - Oct 23 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/0/08/PennigemPic11.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week we wat to begin utilizing a cell-free system to test our targeted TALE methylase. It is imperative that we give the Wiki a complete design overhaul. We also want to make a plan for the couple weeks. </p><br><br />
<p><b>Achievements:<br></b><br />
<p> This week we were screening our cas methylase and found noticeable activity when done in triplicate with all the proper controls. We experimented with various induction times as well. We re-ran some experiments that had previous flaws or were missing controls in triplicate. We had some additional cloning to do to modify our constructs as well. We gathered data for our 3D plot of induction for our methylase fusion, which was perhaps the most time-consuming experiment we have done all year. </p><br><br />
</div><br />
</div><br />
<div><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 21</h2><br />
<div class="box"> <h2>Oct 24 2013 - Oct 30 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/4/42/Dannygel.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal is to finalize Wiki for World Jamboree and to collect data for any major experiments we still need to wrap up. We also need to begin our poster for the Jamboree and work on our presentation. At the same time, there is a ton of wetlab and experiments that we have planned, all of which are unlikely to get done in the next couple weeks, but that won't stop us from trying. We have several presentations with various labs at Penn, including the epigenetics department this week. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>This week we finished the Wiki for World Competition. Additionally, we began our last set of experiments, for which the data will be revealed at the World Jamboree. </p><br><br />
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</html></div>Bkapturhttp://2013.igem.org/Team:Penn/NotebookTeam:Penn/Notebook2013-10-29T01:42:09Z<p>Bkaptur: </p>
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<h2>WEEK 1</h2><br />
<div class="box"><br />
<h2>June 4 2013 - June 11 2013</h2><br />
<img src="https://static.igem.org/mediawiki/2013/2/22/BE_LynchLabGroup_DSC2796.jpg" width = "600px" class="image"/><br />
<p><b>Goals:<br></b><br />
<p> This was our first week setting foot in the lab as the Penn iGEM team. We wanted to become more acquainted with the lab and start transforming and growing parts that would be useful in our future project ideas. This week we wanted to brainstorm our project ideas further as well as being more competent in basic molecular biology techniques.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We learned how to make competent cells and performed our first transformations of the summer. We continued to brainstorm potential projects and thought about directions we would like to pursue for the summer. Our idea for a project that would revolve around quorum sensing systems is currently being put into motion. We continued brainstorming for our idea about uses for DNA binding domains like TALE, Cas9, and zinc fingers. We grew up and miniprepped our transformations of various quorum sensing parts and learned how to use a plate reader.</p><br><br />
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<h2>WEEK 2</h2><br />
<br />
<div class="box"><br />
<h2>June 11 2013 - June 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/3e/Photo-8.JPG" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> This week we wanted to transform some parts for our methylation idea that we ordered from addgene. We also wanted to attempt a bisulfite conversion to test methylation. We had some problems transforming some biobrick parts the previous week, so we wanted to troubleshoot our transformations as well. Another goal of ours was to make more competent DH5-alpha and Dam- cells as well as figure out methylation assays for our promoters.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We worked out the details of one of our potential projects: creating DNA binding domain-methyltransferase fusions. Like last week, we transformed and miniprepped parts that we would need for the quorum sensing project, like the LuxI system. We also transformed and miniprepped the standard biobrick backbones psb1A3, psb1C3, and psb1K3, which would be useful in almost any project we decide to pursue. We pinned down and ordered exactly the DNA binding domains that we thought we would be using and ordered the gene blocks from addgene. We methylated a biobrick part, c0051, with an M.sssI, and used our bisulfite conversion kit for the first time. </p><br> </div><br />
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<h2>WEEK 3</h2><br />
<div class="box"> <h2>June 18 2013 - June 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/2/21/Aaathermopcrlala.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> It was increasingly important that we decide on our project. At this point we were considering a quorum sensing/cell signaling project that would build upon previously created quorum sensing parts submitted in the registry. We were also considering a methyltransferase-DNA binding domain fusion project with the goal of creating a new methyltransferase. We wanted to begin cloning t9002, a GFP producer controlled by an AHL signaling molecule receiver into psb1C3 from psb1A3 in order to use it in a quorum sensing device we were imagining.<br></b><p><b>Achievements:</b><br><br />
<p>This week we got all of our minipreps submitted for sequencing, and we made headway on our first cloning reaction. We figured out how to add restriction sites for cloning reactions using PCR and completed our first cloning reaction according to our successful colony PCR. We experimented with different thermocycler conditions and polymerases for our PCRs that had previously failed, and began to perform PCR with more success.</p><br></div><br />
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<h2>WEEK 4</h2><br />
<div class="box"> <h2>June 25 2013 - July 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Device_photo.jpg" width = "600px"><p><b>Goals:<br></b><br />
<p> This week we wanted to think about applications for selective methylation in E. coli and figure out how our project could be useful for future research. We brainstormed how we wanted to create our constructs and began thinking about the cloning reactions that would be required to create them. We also wanted to begin creating our wiki and start generating useful content.<br></b><p><b>Achievements:</b></p><br />
<p>We confirmed that we completed our first successful cloning reaction. We transformed and miniprepped the biobrick parts for the quorum sensing system that we envisioned creating, with one cell having a light-induced AHL producer, and another cell having a AHL producer downstream of an AHL activated promoter. We thought about creating a device that would spatially separate the cells, as opposed to having them in the same media. We used a simple restriction digest assay to test how BstUI, a methylation sensitive promoter, would behave. </p><br></div><!--/box--><br />
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<h2>WEEK 5</h2><br />
<div class="box"> <h2>July 2 2013 - July 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/6/61/Pennnotebook3pic.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> We wanted to experiment with USER cloning for assembling our gene blocks and minigenes. We also wanted to characterize pdawn and mcherry, parts we got from a lab at the University that we could use in our quorum sensing project. We wanted to attempt to PCR assemble our MsssI and begin fabricating a device for our quorum sensing project. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We practiced measuring fluorescence using our pDawn and mcherry constructs. We successfully completed PCR assembly of our M.sssI. We performed our first cotransformation with I751250, an AHL sender that was downstream of pDawn and T9002. We redesigned primers for PCR reactions that had been giving us trouble, paying more attention to the annealing temperatures of the primers we were designing.</p><br></div><br />
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<h2>WEEK 6</h2><br />
<div class="box"> <h2>July 10 2013 - July 17 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b6/PennigemPic4.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> As the summer was nearing its halfway mark, we wanted to decide on the relative merits of the two projects and reach a decision. We also wanted to continue our cloning for the two projects and troubleshoot cloning-related problems. We now had all the parts we needed for Cas9, TALE, and zinc finger methylase constructs and wanted to begin assembling them into constructs that we envisioned. These constructs would have a two-plasmid system. One plasmid would have the DNA binding domain downstream of a T7 promoter activated by tetracycline, and the other would be a reporter plasmid to detect methylation. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We decided on the constructs that we would create and began the restriction digest and gel extract steps of our miniprepped components. We planned an experiment we could do with tetracycline induction to test whether our hypothetical methyltransferase-DNA binding domain fusions were actually being expressed.</p><br><br />
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<h2>WEEK 7</h2><br />
<div class="box"> <h2>July 18 2013 - July 24 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/95/IMG_2175.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week our main goals were to attempt our tetracycline induction experiment, order primers for performing a COBRA assay, and refine our LIMS and retroactively manage our samples. We also wanted to finish the cloning experiments we began the previous week.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We completed our construct for our zinc finger fusion plasmid after a successful colony PCR and sequencing result. We performed our first induction experiment by inoculating cultures with a tetracycline-activated promoter. We redid a PCR assembly of our TALE and Cas9 systems that had been failed before. </p><br><br />
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<h2>WEEK 8</h2><br />
<div class="box"> <h2>July 25 2013 - July 31 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/9e/IMG_2173.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to finish our remaining fusion protein constructs and begin thinking about an SDS PAGE to measure protein expression. We also wanted to dedicate more time to pursuing drylab—making advances on our human practices and continue reading the literature on selective methylation. We also wanted to look into trying out different biobrick parts for our quorum sensing system.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We made advances on our cloning of the constructs for both projects. We completed a LIMS system on a Google spreadsheet that would be used to manage our increasingly overwhelming primers box as well as fixing our minipreps and glycerol stock LIMS and retroactively adding samples. We performed a new induction experiment, inducing our cultures with aTc. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 9</h2><br />
<div class="box"> <h2>Aug 1 2013 - Aug 7 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/59/IMG_0382.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make advances toward generating our device for the quorum sensing project. We wanted to better budget our remaining resources and stock up on supplies that we would need throughout the rest of the summer. We also wanted to use our zinc finger clone in an induction experiment, similar to the ones we had performed earlier for the quorum sensing project. Additionally, we aimed to generate a growth curve and see how the zinc finger cells would respond to induction. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We met with various professors at the University and made contacts who had knowledge about areas in both projects. We ordered more reagents and created the abstract for our project. We designed primers to attempt to Gibson assemble the Cas construct that had been giving us trouble during USER cloning. We hoped that the new cloning strategy would yield better results. We aliquoted our antibiotics, making boxes full of Kan, Chlor, and Amp to last us the entire summer and well into the year. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 10</h2><br />
<div class="box"> <h2>Aug 8 2013 - Aug 14 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/a5/IMG_0501.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to use our restriction digest-based test to analyze how our constructs were working with regards to methylation. We needed to decide on which project we were going to pursue as soon as possible, and we decided this week would be the deadline. We wanted to perform our first SDS Page, which had been in the brainstorming stage for a while. Additionally, we wanted to consult experts about designing better primers and see how we could improve our protocols. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We finally decided to fully pursue the project of constructing targeted methyltransferase fusions. While it was a hard decision, it was necessary to commit our efforts to one project. We also finished our TALE clone and began the induction experiment for testing the methyltransferase fusion. We consulted with designers from the School of Design about making our website and better presentations. We began transforming promoters for an additional screen for methyltransferases that we had envisioned, with the belief that methyltransferases could silence promoters.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 11</h2><br />
<div class="box"> <h2>Aug 15 2013 - Aug 21 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/be/Pennnotebook1pic.jpg" width = "600px" ><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to get our Cas construct working after additional drylab work in designing better assembly reactions. We needed to make a detailed plan of where our funds were going to go for the rest of the summer and begin planning our slides for our iGEM presentation. We wanted to decide where we wanted to be by the competition and what we needed to do to get there.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began creating a plan for creating a video about methylation in general and our project specifically. After consulting with our advisors we decided to change the direction of our methyltransferase-DNA binding domain fusion from a two-plasmid to a one-plasmid system that would incorporate a digestion-based assay within the plasmid.</p><br><br />
<br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 12</h2><br />
<div class="box"> <h2>Aug 22 2013 - Aug 28 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/bd/PennigemPic12.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal for this week was to finalize our ideal cloning constructs and figure out how to port what we had already created into the one-plasmid system. We wanted to elaborate more on the assay, as our advisors had emphasized that as one of the more important contributions that our project could make to the synthetic biology community.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We focused on drylab this week, as we needed to get our plans for the rest of the summer set. We worked on a human practices essay about the ethics of targeted methylation in medical therapies. We also began work designing new primers for our revised cloning strategy.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 13</h2><br />
<div class="box"> <h2>Aug 29 2013 - Sep 4 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/f/f7/IMG_2180.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal was to once again begin a new cloning strategy focused on assembling our one-plasmid systems. We needed our cloning strategy finalized as soon as possible, and we dedicated the majority of our time this week to streamlining our cloning process.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began setting up our travel plans to get to the Jamboree. We began the initial stages of cloning our new systems and made substantial progress on cloning our zinc finger and TALE. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 14</h2><br />
<div class="box"> <h2>Sep 5 2013 - Sep 11 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/ad/IMG_0495.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal for this week was to make further progress on cloning our constructs. We also wanted to continue our work on the human practices essay, and begin creating a poster presentation for presenting at University research conferences. We also wanted to begin thinking about designing a computer application for analyzing gels.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>During a marathon weekend coding session, we created a program that we called MaGellin that was designed to analyze our gels and characterize the amount of methylation. We attempted to improve our cloning efficiency by utilizing Antarctic Phosphatase within our reactions. We made substantial progress on finishing our TALE and zinc finger constructs, and selected and grew colonies that would be used to test our assay the following week. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 15</h2><br />
<div class="box"> <h2>Sep 12 2013 - Sep 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/c/c8/Momomomomomomo.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make substantial progress on the website this week. We also wanted to run our assay and test how well our methyltransferase-DNA binding domain fusions had worked. We wanted to work on animation for our video as well as make progress on our human practices essay.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran the assay on the TALE and zinc finger clones, and it yielded promising results. The expression of our fusion protein was a definite achievement. We made substantial progress on the website and essay as well. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 16</h2><br />
<div class="box"> <h2>Sep 19 2013 - Sep 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/d/d0/Pennigempic1.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We needed to finish our website and various forms this week, as well as run our assay in triplicate on the constructs we had created thus far. We needed to plan our remaining time up to the Jamboree, and practice our presentation skills at various outreach events.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We attended several events aimed at recruiting future team members that showed substantial interest in our research and iGEM in general. Our assay returned promising results about the state of our methyltransferase-DNA binding domain fusions. Additionally, we finished the website and filled out all the forms we needed. We have a few experiments still in progress, but our time now is spent preparing for the Jamboree and being ready to present our results. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<br />
<h2>WEEK 17</h2><br />
<div class="box"> <h2>Sep 26 2013 - Oct 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/5e/DSC_0482.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> In the week before the Jamboree, we wanted to compile all our last-minute data as well as create our poster and Powerpoint presentation for the competition.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We gathered a ton of last-minute data this week. The solid deadline put upon us by the Jamboree motivated us all to work as hard as possible to get data worthy of our presentation at the Jamboree. While there's still a lot that we wish to accomplish with our project, we're proud of how far we've made it and hope our hard work pays off at the Jamboree. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 18 (North America Regionals)</h2><br />
<div class="box"> <h2>Oct 3 2013 - Oct 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/31/Pennigempic3.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We just became the Regional Winners for North America for iGEM 2013, but there's no time to rest. Now it's time to get back in the lab and prepare for the World Jamboree. We want to make a game plan for what we are going to accomplish before the World Jamboree at MIT in early November and gather data in areas where we needed more work. We're taking the judge's comments from the regional Jamboree very seriously and attempting to improve our project as much as possible in the coming month. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran our MaGellin assay in a preliminary screening of our cas-methylase fusion and got some activity. We re-ran some previous experiments in triplicate to make the data more compelling. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 19 </h2><br />
<div class="box"> <h2>Oct 10 2013 - Oct 16 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Pennnotebook2pic.jpg" width = "600px"><br />
<br />
<p><b>Goals: <br></b><br />
<p> We wanted to look further into the possibility of transcriptional silencing using targeted methylation. Additionally, we planned to run the full assay to screen our potential Cas-methylase fusion. Another major priority is to perform bisulfite sequencing to look at the target site for our TALE methylase. </p><br><br />
<p><b>Achievements: <br></b><br />
<p>We continued to reach out to underclassmen and recruit members for the upcoming team. At the same time, we were hard at work in lab, performing our assay and trying to further quantify the extent of methylation in our fusion constructs. We got our bisulfite sequencing for our TALE submitted and are eagerly awaiting the results. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 20</h2><br />
<div class="box"> <h2>Oct 17 2013 - Oct 23 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/0/08/PennigemPic11.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week we wat to begin utilizing a cell-free system to test our targeted TALE methylase. It is imperative that we give the Wiki a complete design overhaul. We also want to make a plan for the couple weeks. </p><br><br />
<p><b>Achievements:<br></b><br />
<p> This week we were screening our cas methylase and found noticeable activity when done in triplicate with all the proper controls. We experimented with various induction times as well. We re-ran some experiments that had previous flaws or were missing controls in triplicate. We had some additional cloning to do to modify our constructs as well. We gathered data for our 3D plot of induction for our methylase fusion, which was perhaps the most time-consuming experiment we have done all year. </p><br><br />
</div><br />
</div><br />
<div><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 21</h2><br />
<div class="box"> <h2>Oct 24 2013 - Oct 30 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/4/42/Dannygel.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal is to finalize Wiki for World Jamboree and to collect data for any major experiments we still need to wrap up. We also need to begin our poster for the Jamboree and work on our presentation. At the same time, there is a ton of wetlab and experiments that we have planned, all of which are unlikely to get done in the next couple weeks, but that won't stop us from trying. We have several presentations with various labs at Penn, including the epigenetics department this week. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>This week we finished the Wiki for World Competition. Additionally, we began our last set of experiments, for which the data will be revealed at the World Jamboree. </p><br><br />
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<h2>WEEK 1</h2><br />
<div class="box"><br />
<h2>June 4 2013 - June 11 2013</h2><br />
<img src="https://static.igem.org/mediawiki/2013/2/22/BE_LynchLabGroup_DSC2796.jpg" width = "600px" class="image"/><br />
<p><b>Goals:<br></b><br />
<p> This was our first week setting foot in the lab as the Penn iGEM team. We wanted to become more acquainted with the lab and start transforming and growing parts that would be useful in our future project ideas. This week we wanted to brainstorm our project ideas further as well as being more competent in basic molecular biology techniques.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We learned how to make competent cells and performed our first transformations of the summer. We continued to brainstorm potential projects and thought about directions we would like to pursue for the summer. Our idea for a project that would revolve around quorum sensing systems is currently being put into motion. We continued brainstorming for our idea about uses for DNA binding domains like TALE, Cas9, and zinc fingers. We grew up and miniprepped our transformations of various quorum sensing parts and learned how to use a plate reader.</p><br><br />
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<h2>WEEK 2</h2><br />
<br />
<div class="box"><br />
<h2>June 11 2013 - June 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/3e/Photo-8.JPG" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> This week we wanted to transform some parts for our methylation idea that we ordered from addgene. We also wanted to attempt a bisulfite conversion to test methylation. We had some problems transforming some biobrick parts the previous week, so we wanted to troubleshoot our transformations as well. Another goal of ours was to make more competent DH5-alpha and Dam- cells as well as figure out methylation assays for our promoters.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We worked out the details of one of our potential projects: creating DNA binding domain-methyltransferase fusions. Like last week, we transformed and miniprepped parts that we would need for the quorum sensing project, like the LuxI system. We also transformed and miniprepped the standard biobrick backbones psb1A3, psb1C3, and psb1K3, which would be useful in almost any project we decide to pursue. We pinned down and ordered exactly the DNA binding domains that we thought we would be using and ordered the gene blocks from addgene. We methylated a biobrick part, c0051, with an M.sssI, and used our bisulfite conversion kit for the first time. </p><br> </div><br />
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<h2>WEEK 3</h2><br />
<div class="box"> <h2>June 18 2013 - June 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/2/21/Aaathermopcrlala.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> It was increasingly important that we decide on our project. At this point we were considering a quorum sensing/cell signaling project that would build upon previously created quorum sensing parts submitted in the registry. We were also considering a methyltransferase-DNA binding domain fusion project with the goal of creating a new methyltransferase. We wanted to begin cloning t9002, a GFP producer controlled by an AHL signaling molecule receiver into psb1C3 from psb1A3 in order to use it in a quorum sensing device we were imagining.<br></b><p><b>Achievements:</b><br><br />
<p>This week we got all of our minipreps submitted for sequencing, and we made headway on our first cloning reaction. We figured out how to add restriction sites for cloning reactions using PCR and completed our first cloning reaction according to our successful colony PCR. We experimented with different thermocycler conditions and polymerases for our PCRs that had previously failed, and began to perform PCR with more success.</p><br></div><br />
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<h2>WEEK 4</h2><br />
<div class="box"> <h2>June 25 2013 - July 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Device_photo.jpg" width = "600px"><p><b>Goals:<br></b><br />
<p> This week we wanted to think about applications for selective methylation in E. coli and figure out how our project could be useful for future research. We brainstormed how we wanted to create our constructs and began thinking about the cloning reactions that would be required to create them. We also wanted to begin creating our wiki and start generating useful content.<br></b><p><b>Achievements:</b></p><br />
<p>We confirmed that we completed our first successful cloning reaction. We transformed and miniprepped the biobrick parts for the quorum sensing system that we envisioned creating, with one cell having a light-induced AHL producer, and another cell having a AHL producer downstream of an AHL activated promoter. We thought about creating a device that would spatially separate the cells, as opposed to having them in the same media. We used a simple restriction digest assay to test how BstUI, a methylation sensitive promoter, would behave. </p><br></div><!--/box--><br />
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<h2>WEEK 5</h2><br />
<div class="box"> <h2>July 2 2013 - July 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/6/61/Pennnotebook3pic.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> We wanted to experiment with USER cloning for assembling our gene blocks and minigenes. We also wanted to characterize pdawn and mcherry, parts we got from a lab at the University that we could use in our quorum sensing project. We wanted to attempt to PCR assemble our MsssI and begin fabricating a device for our quorum sensing project. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We practiced measuring fluorescence using our pDawn and mcherry constructs. We successfully completed PCR assembly of our M.sssI. We performed our first cotransformation with I751250, an AHL sender that was downstream of pDawn and T9002. We redesigned primers for PCR reactions that had been giving us trouble, paying more attention to the annealing temperatures of the primers we were designing.</p><br></div><br />
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<h2>WEEK 6</h2><br />
<div class="box"> <h2>July 10 2013 - July 17 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b6/PennigemPic4.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> As the summer was nearing its halfway mark, we wanted to decide on the relative merits of the two projects and reach a decision. We also wanted to continue our cloning for the two projects and troubleshoot cloning-related problems. We now had all the parts we needed for Cas9, TALE, and zinc finger methylase constructs and wanted to begin assembling them into constructs that we envisioned. These constructs would have a two-plasmid system. One plasmid would have the DNA binding domain downstream of a T7 promoter activated by tetracycline, and the other would be a reporter plasmid to detect methylation. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We decided on the constructs that we would create and began the restriction digest and gel extract steps of our miniprepped components. We planned an experiment we could do with tetracycline induction to test whether our hypothetical methyltransferase-DNA binding domain fusions were actually being expressed.</p><br><br />
</div><br />
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<h2>WEEK 7</h2><br />
<div class="box"> <h2>July 18 2013 - July 24 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/95/IMG_2175.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week our main goals were to attempt our tetracycline induction experiment, order primers for performing a COBRA assay, and refine our LIMS and retroactively manage our samples. We also wanted to finish the cloning experiments we began the previous week.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We completed our construct for our zinc finger fusion plasmid after a successful colony PCR and sequencing result. We performed our first induction experiment by inoculating cultures with a tetracycline-activated promoter. We redid a PCR assembly of our TALE and Cas9 systems that had been failed before. </p><br><br />
</div><br />
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<h2>WEEK 8</h2><br />
<div class="box"> <h2>July 25 2013 - July 31 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/9e/IMG_2173.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to finish our remaining fusion protein constructs and begin thinking about an SDS PAGE to measure protein expression. We also wanted to dedicate more time to pursuing drylab—making advances on our human practices and continue reading the literature on selective methylation. We also wanted to look into trying out different biobrick parts for our quorum sensing system.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We made advances on our cloning of the constructs for both projects. We completed a LIMS system on a Google spreadsheet that would be used to manage our increasingly overwhelming primers box as well as fixing our minipreps and glycerol stock LIMS and retroactively adding samples. We performed a new induction experiment, inducing our cultures with aTc. </p><br><br />
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<h2>WEEK 9</h2><br />
<div class="box"> <h2>Aug 1 2013 - Aug 7 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/59/IMG_0382.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make advances toward generating our device for the quorum sensing project. We wanted to better budget our remaining resources and stock up on supplies that we would need throughout the rest of the summer. We also wanted to use our zinc finger clone in an induction experiment, similar to the ones we had performed earlier for the quorum sensing project. Additionally, we aimed to generate a growth curve and see how the zinc finger cells would respond to induction. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We met with various professors at the University and made contacts who had knowledge about areas in both projects. We ordered more reagents and created the abstract for our project. We designed primers to attempt to Gibson assemble the Cas construct that had been giving us trouble during USER cloning. We hoped that the new cloning strategy would yield better results. We aliquoted our antibiotics, making boxes full of Kan, Chlor, and Amp to last us the entire summer and well into the year. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 10</h2><br />
<div class="box"> <h2>Aug 8 2013 - Aug 14 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/a5/IMG_0501.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to use our restriction digest-based test to analyze how our constructs were working with regards to methylation. We needed to decide on which project we were going to pursue as soon as possible, and we decided this week would be the deadline. We wanted to perform our first SDS Page, which had been in the brainstorming stage for a while. Additionally, we wanted to consult experts about designing better primers and see how we could improve our protocols. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We finally decided to fully pursue the project of constructing targeted methyltransferase fusions. While it was a hard decision, it was necessary to commit our efforts to one project. We also finished our TALE clone and began the induction experiment for testing the methyltransferase fusion. We consulted with designers from the School of Design about making our website and better presentations. We began transforming promoters for an additional screen for methyltransferases that we had envisioned, with the belief that methyltransferases could silence promoters.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 11</h2><br />
<div class="box"> <h2>Aug 15 2013 - Aug 21 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/be/Pennnotebook1pic.jpg" width = "600px" ><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to get our Cas construct working after additional drylab work in designing better assembly reactions. We needed to make a detailed plan of where our funds were going to go for the rest of the summer and begin planning our slides for our iGEM presentation. We wanted to decide where we wanted to be by the competition and what we needed to do to get there.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began creating a plan for creating a video about methylation in general and our project specifically. After consulting with our advisors we decided to change the direction of our methyltransferase-DNA binding domain fusion from a two-plasmid to a one-plasmid system that would incorporate a digestion-based assay within the plasmid.</p><br><br />
<br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 12</h2><br />
<div class="box"> <h2>Aug 22 2013 - Aug 28 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/bd/PennigemPic12.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal for this week was to finalize our ideal cloning constructs and figure out how to port what we had already created into the one-plasmid system. We wanted to elaborate more on the assay, as our advisors had emphasized that as one of the more important contributions that our project could make to the synthetic biology community.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We focused on drylab this week, as we needed to get our plans for the rest of the summer set. We worked on a human practices essay about the ethics of targeted methylation in medical therapies. We also began work designing new primers for our revised cloning strategy.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 13</h2><br />
<div class="box"> <h2>Aug 29 2013 - Sep 4 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/f/f7/IMG_2180.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal was to once again begin a new cloning strategy focused on assembling our one-plasmid systems. We needed our cloning strategy finalized as soon as possible, and we dedicated the majority of our time this week to streamlining our cloning process.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began setting up our travel plans to get to the Jamboree. We began the initial stages of cloning our new systems and made substantial progress on cloning our zinc finger and TALE. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 14</h2><br />
<div class="box"> <h2>Sep 5 2013 - Sep 11 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/ad/IMG_0495.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal for this week was to make further progress on cloning our constructs. We also wanted to continue our work on the human practices essay, and begin creating a poster presentation for presenting at University research conferences. We also wanted to begin thinking about designing a computer application for analyzing gels.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>During a marathon weekend coding session, we created a program that we called MaGellin that was designed to analyze our gels and characterize the amount of methylation. We attempted to improve our cloning efficiency by utilizing Antarctic Phosphatase within our reactions. We made substantial progress on finishing our TALE and zinc finger constructs, and selected and grew colonies that would be used to test our assay the following week. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 15</h2><br />
<div class="box"> <h2>Sep 12 2013 - Sep 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/5e/DSC_0482.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make substantial progress on the website this week. We also wanted to run our assay and test how well our methyltransferase-DNA binding domain fusions had worked. We wanted to work on animation for our video as well as make progress on our human practices essay.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran the assay on the TALE and zinc finger clones, and it yielded promising results. The expression of our fusion protein was a definite achievement. We made substantial progress on the website and essay as well. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 16</h2><br />
<div class="box"> <h2>Sep 19 2013 - Sep 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/c/c8/Momomomomomomo.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We needed to finish our website and various forms this week, as well as run our assay in triplicate on the constructs we had created thus far. We needed to plan our remaining time up to the Jamboree, and practice our presentation skills at various outreach events.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We attended several events aimed at recruiting future team members that showed substantial interest in our research and iGEM in general. Our assay returned promising results about the state of our methyltransferase-DNA binding domain fusions. Additionally, we finished the website and filled out all the forms we needed. We have a few experiments still in progress, but our time now is spent preparing for the Jamboree and being ready to present our results. </p><br><br />
</div><br />
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<div><br />
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<br />
<h2>WEEK 17</h2><br />
<div class="box"> <h2>Sep 26 2013 - Oct 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/d/d0/Pennigempic1.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> In the week before the Jamboree, we wanted to compile all our last-minute data as well as create our poster and Powerpoint presentation for the competition.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We gathered a ton of last-minute data this week. The solid deadline put upon us by the Jamboree motivated us all to work as hard as possible to get data worthy of our presentation at the Jamboree. While there's still a lot that we wish to accomplish with our project, we're proud of how far we've made it and hope our hard work pays off at the Jamboree. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 18 (North America Regionals)</h2><br />
<div class="box"> <h2>Oct 3 2013 - Oct 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/31/Pennigempic3.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We just became the Regional Winners for North America for iGEM 2013, but there's no time to rest. Now it's time to get back in the lab and prepare for the World Jamboree. We want to make a game plan for what we are going to accomplish before the World Jamboree at MIT in early November and gather data in areas where we needed more work. We're taking the judge's comments from the regional Jamboree very seriously and attempting to improve our project as much as possible in the coming month. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran our MaGellin assay in a preliminary screening of our cas-methylase fusion and got some activity. We re-ran some previous experiments in triplicate to make the data more compelling. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 19 </h2><br />
<div class="box"> <h2>Oct 10 2013 - Oct 16 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Pennnotebook2pic.jpg" width = "600px"><br />
<br />
<p><b>Goals: <br></b><br />
<p> We wanted to look further into the possibility of transcriptional silencing using targeted methylation. Additionally, we planned to run the full assay to screen our potential Cas-methylase fusion. Another major priority is to perform bisulfite sequencing to look at the target site for our TALE methylase. </p><br><br />
<p><b>Achievements: <br></b><br />
<p>We continued to reach out to underclassmen and recruit members for the upcoming team. At the same time, we were hard at work in lab, performing our assay and trying to further quantify the extent of methylation in our fusion constructs. We got our bisulfite sequencing for our TALE submitted and are eagerly awaiting the results. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 20</h2><br />
<div class="box"> <h2>Oct 17 2013 - Oct 23 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/0/08/PennigemPic11.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week we wat to begin utilizing a cell-free system to test our targeted TALE methylase. It is imperative that we give the Wiki a complete design overhaul. We also want to make a plan for the couple weeks. </p><br><br />
<p><b>Achievements:<br></b><br />
<p> This week we were screening our cas methylase and found noticeable activity when done in triplicate with all the proper controls. We experimented with various induction times as well. We re-ran some experiments that had previous flaws or were missing controls in triplicate. We had some additional cloning to do to modify our constructs as well. We gathered data for our 3D plot of induction for our methylase fusion, which was perhaps the most time-consuming experiment we have done all year. </p><br><br />
</div><br />
</div><br />
<div><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 21</h2><br />
<div class="box"> <h2>Oct 24 2013 - Oct 30 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/4/42/Dannygel.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal is to finalize Wiki for World Jamboree and to collect data for any major experiments we still need to wrap up. We also need to begin our poster for the Jamboree and work on our presentation. At the same time, there is a ton of wetlab and experiments that we have planned, all of which are unlikely to get done in the next couple weeks, but that won't stop us from trying. We have several presentations with various labs at Penn, including the epigenetics department this week. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>This week we finished the Wiki for World Competition. Additionally, we began our last set of experiments, for which the data will be revealed at the World Jamboree. </p><br><br />
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<h2>WEEK 1</h2><br />
<div class="box"><br />
<h2>June 4 2013 - June 11 2013</h2><br />
<img src="https://static.igem.org/mediawiki/2013/2/22/BE_LynchLabGroup_DSC2796.jpg" width = "600px" class="image"/><br />
<p><b>Goals:<br></b><br />
<p> This was our first week setting foot in the lab as the Penn iGEM team. We wanted to become more acquainted with the lab and start transforming and growing parts that would be useful in our future project ideas. This week we wanted to brainstorm our project ideas further as well as being more competent in basic molecular biology techniques.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We learned how to make competent cells and performed our first transformations of the summer. We continued to brainstorm potential projects and thought about directions we would like to pursue for the summer. Our idea for a project that would revolve around quorum sensing systems is currently being put into motion. We continued brainstorming for our idea about uses for DNA binding domains like TALE, Cas9, and zinc fingers. We grew up and miniprepped our transformations of various quorum sensing parts and learned how to use a plate reader.</p><br><br />
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<h2>WEEK 2</h2><br />
<br />
<div class="box"><br />
<h2>June 11 2013 - June 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/3e/Photo-8.JPG" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> This week we wanted to transform some parts for our methylation idea that we ordered from addgene. We also wanted to attempt a bisulfite conversion to test methylation. We had some problems transforming some biobrick parts the previous week, so we wanted to troubleshoot our transformations as well. Another goal of ours was to make more competent DH5-alpha and Dam- cells as well as figure out methylation assays for our promoters.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We worked out the details of one of our potential projects: creating DNA binding domain-methyltransferase fusions. Like last week, we transformed and miniprepped parts that we would need for the quorum sensing project, like the LuxI system. We also transformed and miniprepped the standard biobrick backbones psb1A3, psb1C3, and psb1K3, which would be useful in almost any project we decide to pursue. We pinned down and ordered exactly the DNA binding domains that we thought we would be using and ordered the gene blocks from addgene. We methylated a biobrick part, c0051, with an M.sssI, and used our bisulfite conversion kit for the first time. </p><br> </div><br />
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<h2>WEEK 3</h2><br />
<div class="box"> <h2>June 18 2013 - June 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/2/21/Aaathermopcrlala.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> It was increasingly important that we decide on our project. At this point we were considering a quorum sensing/cell signaling project that would build upon previously created quorum sensing parts submitted in the registry. We were also considering a methyltransferase-DNA binding domain fusion project with the goal of creating a new methyltransferase. We wanted to begin cloning t9002, a GFP producer controlled by an AHL signaling molecule receiver into psb1C3 from psb1A3 in order to use it in a quorum sensing device we were imagining.<br></b><p><b>Achievements:</b><br><br />
<p>This week we got all of our minipreps submitted for sequencing, and we made headway on our first cloning reaction. We figured out how to add restriction sites for cloning reactions using PCR and completed our first cloning reaction according to our successful colony PCR. We experimented with different thermocycler conditions and polymerases for our PCRs that had previously failed, and began to perform PCR with more success.</p><br></div><br />
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<br />
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<h2>WEEK 4</h2><br />
<div class="box"> <h2>June 25 2013 - July 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Device_photo.jpg" width = "600px"><p><b>Goals:<br></b><br />
<p> This week we wanted to think about applications for selective methylation in E. coli and figure out how our project could be useful for future research. We brainstormed how we wanted to create our constructs and began thinking about the cloning reactions that would be required to create them. We also wanted to begin creating our wiki and start generating useful content.<br></b><p><b>Achievements:</b></p><br />
<p>We confirmed that we completed our first successful cloning reaction. We transformed and miniprepped the biobrick parts for the quorum sensing system that we envisioned creating, with one cell having a light-induced AHL producer, and another cell having a AHL producer downstream of an AHL activated promoter. We thought about creating a device that would spatially separate the cells, as opposed to having them in the same media. We used a simple restriction digest assay to test how BstUI, a methylation sensitive promoter, would behave. </p><br></div><!--/box--><br />
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<h2>WEEK 5</h2><br />
<div class="box"> <h2>July 2 2013 - July 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/6/61/Pennnotebook3pic.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> We wanted to experiment with USER cloning for assembling our gene blocks and minigenes. We also wanted to characterize pdawn and mcherry, parts we got from a lab at the University that we could use in our quorum sensing project. We wanted to attempt to PCR assemble our MsssI and begin fabricating a device for our quorum sensing project. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We practiced measuring fluorescence using our pDawn and mcherry constructs. We successfully completed PCR assembly of our M.sssI. We performed our first cotransformation with I751250, an AHL sender that was downstream of pDawn and T9002. We redesigned primers for PCR reactions that had been giving us trouble, paying more attention to the annealing temperatures of the primers we were designing.</p><br></div><br />
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<h2>WEEK 6</h2><br />
<div class="box"> <h2>July 10 2013 - July 17 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b6/PennigemPic4.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> As the summer was nearing its halfway mark, we wanted to decide on the relative merits of the two projects and reach a decision. We also wanted to continue our cloning for the two projects and troubleshoot cloning-related problems. We now had all the parts we needed for Cas9, TALE, and zinc finger methylase constructs and wanted to begin assembling them into constructs that we envisioned. These constructs would have a two-plasmid system. One plasmid would have the DNA binding domain downstream of a T7 promoter activated by tetracycline, and the other would be a reporter plasmid to detect methylation. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We decided on the constructs that we would create and began the restriction digest and gel extract steps of our miniprepped components. We planned an experiment we could do with tetracycline induction to test whether our hypothetical methyltransferase-DNA binding domain fusions were actually being expressed.</p><br><br />
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<h2>WEEK 7</h2><br />
<div class="box"> <h2>July 18 2013 - July 24 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/95/IMG_2175.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week our main goals were to attempt our tetracycline induction experiment, order primers for performing a COBRA assay, and refine our LIMS and retroactively manage our samples. We also wanted to finish the cloning experiments we began the previous week.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We completed our construct for our zinc finger fusion plasmid after a successful colony PCR and sequencing result. We performed our first induction experiment by inoculating cultures with a tetracycline-activated promoter. We redid a PCR assembly of our TALE and Cas9 systems that had been failed before. </p><br><br />
</div><br />
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<h2>WEEK 8</h2><br />
<div class="box"> <h2>July 25 2013 - July 31 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/9e/IMG_2173.JPG" width = "600px"><br />
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<p><b>Goals:<br></b><br />
<p> We wanted to finish our remaining fusion protein constructs and begin thinking about an SDS PAGE to measure protein expression. We also wanted to dedicate more time to pursuing drylab—making advances on our human practices and continue reading the literature on selective methylation. We also wanted to look into trying out different biobrick parts for our quorum sensing system.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We made advances on our cloning of the constructs for both projects. We completed a LIMS system on a Google spreadsheet that would be used to manage our increasingly overwhelming primers box as well as fixing our minipreps and glycerol stock LIMS and retroactively adding samples. We performed a new induction experiment, inducing our cultures with aTc. </p><br><br />
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<h2>WEEK 9</h2><br />
<div class="box"> <h2>Aug 1 2013 - Aug 7 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/59/IMG_0382.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make advances toward generating our device for the quorum sensing project. We wanted to better budget our remaining resources and stock up on supplies that we would need throughout the rest of the summer. We also wanted to use our zinc finger clone in an induction experiment, similar to the ones we had performed earlier for the quorum sensing project. Additionally, we aimed to generate a growth curve and see how the zinc finger cells would respond to induction. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We met with various professors at the University and made contacts who had knowledge about areas in both projects. We ordered more reagents and created the abstract for our project. We designed primers to attempt to Gibson assemble the Cas construct that had been giving us trouble during USER cloning. We hoped that the new cloning strategy would yield better results. We aliquoted our antibiotics, making boxes full of Kan, Chlor, and Amp to last us the entire summer and well into the year. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 10</h2><br />
<div class="box"> <h2>Aug 8 2013 - Aug 14 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/a5/IMG_0501.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to use our restriction digest-based test to analyze how our constructs were working with regards to methylation. We needed to decide on which project we were going to pursue as soon as possible, and we decided this week would be the deadline. We wanted to perform our first SDS Page, which had been in the brainstorming stage for a while. Additionally, we wanted to consult experts about designing better primers and see how we could improve our protocols. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We finally decided to fully pursue the project of constructing targeted methyltransferase fusions. While it was a hard decision, it was necessary to commit our efforts to one project. We also finished our TALE clone and began the induction experiment for testing the methyltransferase fusion. We consulted with designers from the School of Design about making our website and better presentations. We began transforming promoters for an additional screen for methyltransferases that we had envisioned, with the belief that methyltransferases could silence promoters.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 11</h2><br />
<div class="box"> <h2>Aug 15 2013 - Aug 21 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/be/Pennnotebook1pic.jpg" width = "600px" ><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to get our Cas construct working after additional drylab work in designing better assembly reactions. We needed to make a detailed plan of where our funds were going to go for the rest of the summer and begin planning our slides for our iGEM presentation. We wanted to decide where we wanted to be by the competition and what we needed to do to get there.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began creating a plan for creating a video about methylation in general and our project specifically. After consulting with our advisors we decided to change the direction of our methyltransferase-DNA binding domain fusion from a two-plasmid to a one-plasmid system that would incorporate a digestion-based assay within the plasmid.</p><br><br />
<br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 12</h2><br />
<div class="box"> <h2>Aug 22 2013 - Aug 28 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/bd/PennigemPic12.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal for this week was to finalize our ideal cloning constructs and figure out how to port what we had already created into the one-plasmid system. We wanted to elaborate more on the assay, as our advisors had emphasized that as one of the more important contributions that our project could make to the synthetic biology community.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We focused on drylab this week, as we needed to get our plans for the rest of the summer set. We worked on a human practices essay about the ethics of targeted methylation in medical therapies. We also began work designing new primers for our revised cloning strategy.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 13</h2><br />
<div class="box"> <h2>Aug 29 2013 - Sep 4 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/f/f7/IMG_2180.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal was to once again begin a new cloning strategy focused on assembling our one-plasmid systems. We needed our cloning strategy finalized as soon as possible, and we dedicated the majority of our time this week to streamlining our cloning process.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began setting up our travel plans to get to the Jamboree. We began the initial stages of cloning our new systems and made substantial progress on cloning our zinc finger and TALE. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 14</h2><br />
<div class="box"> <h2>Sep 5 2013 - Sep 11 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/ad/IMG_0495.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal for this week was to make further progress on cloning our constructs. We also wanted to continue our work on the human practices essay, and begin creating a poster presentation for presenting at University research conferences. We also wanted to begin thinking about designing a computer application for analyzing gels.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>During a marathon weekend coding session, we created a program that we called MaGellin that was designed to analyze our gels and characterize the amount of methylation. We attempted to improve our cloning efficiency by utilizing Antarctic Phosphatase within our reactions. We made substantial progress on finishing our TALE and zinc finger constructs, and selected and grew colonies that would be used to test our assay the following week. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 15</h2><br />
<div class="box"> <h2>Sep 12 2013 - Sep 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/c/c8/Momomomomomomo.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make substantial progress on the website this week. We also wanted to run our assay and test how well our methyltransferase-DNA binding domain fusions had worked. We wanted to work on animation for our video as well as make progress on our human practices essay.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran the assay on the TALE and zinc finger clones, and it yielded promising results. The expression of our fusion protein was a definite achievement. We made substantial progress on the website and essay as well. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 16</h2><br />
<div class="box"> <h2>Sep 19 2013 - Sep 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/5e/DSC_0482.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We needed to finish our website and various forms this week, as well as run our assay in triplicate on the constructs we had created thus far. We needed to plan our remaining time up to the Jamboree, and practice our presentation skills at various outreach events.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We attended several events aimed at recruiting future team members that showed substantial interest in our research and iGEM in general. Our assay returned promising results about the state of our methyltransferase-DNA binding domain fusions. Additionally, we finished the website and filled out all the forms we needed. We have a few experiments still in progress, but our time now is spent preparing for the Jamboree and being ready to present our results. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<br />
<h2>WEEK 17</h2><br />
<div class="box"> <h2>Sep 26 2013 - Oct 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/d/d0/Pennigempic1.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> In the week before the Jamboree, we wanted to compile all our last-minute data as well as create our poster and Powerpoint presentation for the competition.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We gathered a ton of last-minute data this week. The solid deadline put upon us by the Jamboree motivated us all to work as hard as possible to get data worthy of our presentation at the Jamboree. While there's still a lot that we wish to accomplish with our project, we're proud of how far we've made it and hope our hard work pays off at the Jamboree. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 18 (North America Regionals)</h2><br />
<div class="box"> <h2>Oct 3 2013 - Oct 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/31/Pennigempic3.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We just became the Regional Winners for North America for iGEM 2013, but there's no time to rest. Now it's time to get back in the lab and prepare for the World Jamboree. We want to make a game plan for what we are going to accomplish before the World Jamboree at MIT in early November and gather data in areas where we needed more work. We're taking the judge's comments from the regional Jamboree very seriously and attempting to improve our project as much as possible in the coming month. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran our MaGellin assay in a preliminary screening of our cas-methylase fusion and got some activity. We re-ran some previous experiments in triplicate to make the data more compelling. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 19 </h2><br />
<div class="box"> <h2>Oct 10 2013 - Oct 16 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Pennnotebook2pic.jpg" width = "600px"><br />
<br />
<p><b>Goals: <br></b><br />
<p> We wanted to look further into the possibility of transcriptional silencing using targeted methylation. Additionally, we planned to run the full assay to screen our potential Cas-methylase fusion. Another major priority is to perform bisulfite sequencing to look at the target site for our TALE methylase. </p><br><br />
<p><b>Achievements: <br></b><br />
<p>We continued to reach out to underclassmen and recruit members for the upcoming team. At the same time, we were hard at work in lab, performing our assay and trying to further quantify the extent of methylation in our fusion constructs. We got our bisulfite sequencing for our TALE submitted and are eagerly awaiting the results. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 20</h2><br />
<div class="box"> <h2>Oct 17 2013 - Oct 23 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/0/08/PennigemPic11.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week we wat to begin utilizing a cell-free system to test our targeted TALE methylase. It is imperative that we give the Wiki a complete design overhaul. We also want to make a plan for the couple weeks. </p><br><br />
<p><b>Achievements:<br></b><br />
<p> This week we were screening our cas methylase and found noticeable activity when done in triplicate with all the proper controls. We experimented with various induction times as well. We re-ran some experiments that had previous flaws or were missing controls in triplicate. We had some additional cloning to do to modify our constructs as well. We gathered data for our 3D plot of induction for our methylase fusion, which was perhaps the most time-consuming experiment we have done all year. </p><br><br />
</div><br />
</div><br />
<div><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 21</h2><br />
<div class="box"> <h2>Oct 24 2013 - Oct 30 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/4/42/Dannygel.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal is to finalize Wiki for World Jamboree and to collect data for any major experiments we still need to wrap up. We also need to begin our poster for the Jamboree and work on our presentation. At the same time, there is a ton of wetlab and experiments that we have planned, all of which are unlikely to get done in the next couple weeks, but that won't stop us from trying. We have several presentations with various labs at Penn, including the epigenetics department this week. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>This week we finished the Wiki for World Competition. Additionally, we began our last set of experiments, for which the data will be revealed at the World Jamboree. </p><br><br />
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</html></div>Bkapturhttp://2013.igem.org/Team:Penn/NotebookTeam:Penn/Notebook2013-10-29T01:33:25Z<p>Bkaptur: </p>
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<h2>WEEK 1</h2><br />
<div class="box"><br />
<h2>June 4 2013 - June 11 2013</h2><br />
<img src="https://static.igem.org/mediawiki/2013/2/22/BE_LynchLabGroup_DSC2796.jpg" width = "600px" class="image"/><br />
<p><b>Goals:<br></b><br />
<p> This was our first week setting foot in the lab as the Penn iGEM team. We wanted to become more acquainted with the lab and start transforming and growing parts that would be useful in our future project ideas. This week we wanted to brainstorm our project ideas further as well as being more competent in basic molecular biology techniques.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We learned how to make competent cells and performed our first transformations of the summer. We continued to brainstorm potential projects and thought about directions we would like to pursue for the summer. Our idea for a project that would revolve around quorum sensing systems is currently being put into motion. We continued brainstorming for our idea about uses for DNA binding domains like TALE, Cas9, and zinc fingers. We grew up and miniprepped our transformations of various quorum sensing parts and learned how to use a plate reader.</p><br><br />
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<br />
<div><br />
<h2>WEEK 2</h2><br />
<br />
<div class="box"><br />
<h2>June 11 2013 - June 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/3e/Photo-8.JPG" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> This week we wanted to transform some parts for our methylation idea that we ordered from addgene. We also wanted to attempt a bisulfite conversion to test methylation. We had some problems transforming some biobrick parts the previous week, so we wanted to troubleshoot our transformations as well. Another goal of ours was to make more competent DH5-alpha and Dam- cells as well as figure out methylation assays for our promoters.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We worked out the details of one of our potential projects: creating DNA binding domain-methyltransferase fusions. Like last week, we transformed and miniprepped parts that we would need for the quorum sensing project, like the LuxI system. We also transformed and miniprepped the standard biobrick backbones psb1A3, psb1C3, and psb1K3, which would be useful in almost any project we decide to pursue. We pinned down and ordered exactly the DNA binding domains that we thought we would be using and ordered the gene blocks from addgene. We methylated a biobrick part, c0051, with an M.sssI, and used our bisulfite conversion kit for the first time. </p><br> </div><br />
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<h2>WEEK 3</h2><br />
<div class="box"> <h2>June 18 2013 - June 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/2/21/Aaathermopcrlala.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> It was increasingly important that we decide on our project. At this point we were considering a quorum sensing/cell signaling project that would build upon previously created quorum sensing parts submitted in the registry. We were also considering a methyltransferase-DNA binding domain fusion project with the goal of creating a new methyltransferase. We wanted to begin cloning t9002, a GFP producer controlled by an AHL signaling molecule receiver into psb1C3 from psb1A3 in order to use it in a quorum sensing device we were imagining.<br></b><p><b>Achievements:</b><br><br />
<p>This week we got all of our minipreps submitted for sequencing, and we made headway on our first cloning reaction. We figured out how to add restriction sites for cloning reactions using PCR and completed our first cloning reaction according to our successful colony PCR. We experimented with different thermocycler conditions and polymerases for our PCRs that had previously failed, and began to perform PCR with more success.</p><br></div><br />
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<br />
<div><br />
<h2>WEEK 4</h2><br />
<div class="box"> <h2>June 25 2013 - July 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Device_photo.jpg" width = "600px"><p><b>Goals:<br></b><br />
<p> This week we wanted to think about applications for selective methylation in E. coli and figure out how our project could be useful for future research. We brainstormed how we wanted to create our constructs and began thinking about the cloning reactions that would be required to create them. We also wanted to begin creating our wiki and start generating useful content.<br></b><p><b>Achievements:</b></p><br />
<p>We confirmed that we completed our first successful cloning reaction. We transformed and miniprepped the biobrick parts for the quorum sensing system that we envisioned creating, with one cell having a light-induced AHL producer, and another cell having a AHL producer downstream of an AHL activated promoter. We thought about creating a device that would spatially separate the cells, as opposed to having them in the same media. We used a simple restriction digest assay to test how BstUI, a methylation sensitive promoter, would behave. </p><br></div><!--/box--><br />
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<h2>WEEK 5</h2><br />
<div class="box"> <h2>July 2 2013 - July 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/6/61/Pennnotebook3pic.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> We wanted to experiment with USER cloning for assembling our gene blocks and minigenes. We also wanted to characterize pdawn and mcherry, parts we got from a lab at the University that we could use in our quorum sensing project. We wanted to attempt to PCR assemble our MsssI and begin fabricating a device for our quorum sensing project. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We practiced measuring fluorescence using our pDawn and mcherry constructs. We successfully completed PCR assembly of our M.sssI. We performed our first cotransformation with I751250, an AHL sender that was downstream of pDawn and T9002. We redesigned primers for PCR reactions that had been giving us trouble, paying more attention to the annealing temperatures of the primers we were designing.</p><br></div><br />
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<h2>WEEK 6</h2><br />
<div class="box"> <h2>July 10 2013 - July 17 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b6/PennigemPic4.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> As the summer was nearing its halfway mark, we wanted to decide on the relative merits of the two projects and reach a decision. We also wanted to continue our cloning for the two projects and troubleshoot cloning-related problems. We now had all the parts we needed for Cas9, TALE, and zinc finger methylase constructs and wanted to begin assembling them into constructs that we envisioned. These constructs would have a two-plasmid system. One plasmid would have the DNA binding domain downstream of a T7 promoter activated by tetracycline, and the other would be a reporter plasmid to detect methylation. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We decided on the constructs that we would create and began the restriction digest and gel extract steps of our miniprepped components. We planned an experiment we could do with tetracycline induction to test whether our hypothetical methyltransferase-DNA binding domain fusions were actually being expressed.</p><br><br />
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<h2>WEEK 7</h2><br />
<div class="box"> <h2>July 18 2013 - July 24 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/95/IMG_2175.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week our main goals were to attempt our tetracycline induction experiment, order primers for performing a COBRA assay, and refine our LIMS and retroactively manage our samples. We also wanted to finish the cloning experiments we began the previous week.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We completed our construct for our zinc finger fusion plasmid after a successful colony PCR and sequencing result. We performed our first induction experiment by inoculating cultures with a tetracycline-activated promoter. We redid a PCR assembly of our TALE and Cas9 systems that had been failed before. </p><br><br />
</div><br />
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<h2>WEEK 8</h2><br />
<div class="box"> <h2>July 25 2013 - July 31 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/9e/IMG_2173.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to finish our remaining fusion protein constructs and begin thinking about an SDS PAGE to measure protein expression. We also wanted to dedicate more time to pursuing drylab—making advances on our human practices and continue reading the literature on selective methylation. We also wanted to look into trying out different biobrick parts for our quorum sensing system.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We made advances on our cloning of the constructs for both projects. We completed a LIMS system on a Google spreadsheet that would be used to manage our increasingly overwhelming primers box as well as fixing our minipreps and glycerol stock LIMS and retroactively adding samples. We performed a new induction experiment, inducing our cultures with aTc. </p><br><br />
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<h2>WEEK 9</h2><br />
<div class="box"> <h2>Aug 1 2013 - Aug 7 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/59/IMG_0382.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make advances toward generating our device for the quorum sensing project. We wanted to better budget our remaining resources and stock up on supplies that we would need throughout the rest of the summer. We also wanted to use our zinc finger clone in an induction experiment, similar to the ones we had performed earlier for the quorum sensing project. Additionally, we aimed to generate a growth curve and see how the zinc finger cells would respond to induction. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We met with various professors at the University and made contacts who had knowledge about areas in both projects. We ordered more reagents and created the abstract for our project. We designed primers to attempt to Gibson assemble the Cas construct that had been giving us trouble during USER cloning. We hoped that the new cloning strategy would yield better results. We aliquoted our antibiotics, making boxes full of Kan, Chlor, and Amp to last us the entire summer and well into the year. </p><br><br />
</div><br />
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<div><br />
<br />
<h2>WEEK 10</h2><br />
<div class="box"> <h2>Aug 8 2013 - Aug 14 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/a5/IMG_0501.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to use our restriction digest-based test to analyze how our constructs were working with regards to methylation. We needed to decide on which project we were going to pursue as soon as possible, and we decided this week would be the deadline. We wanted to perform our first SDS Page, which had been in the brainstorming stage for a while. Additionally, we wanted to consult experts about designing better primers and see how we could improve our protocols. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We finally decided to fully pursue the project of constructing targeted methyltransferase fusions. While it was a hard decision, it was necessary to commit our efforts to one project. We also finished our TALE clone and began the induction experiment for testing the methyltransferase fusion. We consulted with designers from the School of Design about making our website and better presentations. We began transforming promoters for an additional screen for methyltransferases that we had envisioned, with the belief that methyltransferases could silence promoters.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 11</h2><br />
<div class="box"> <h2>Aug 15 2013 - Aug 21 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/0/08/PennigemPic11.JPG" width = "600px" ><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to get our Cas construct working after additional drylab work in designing better assembly reactions. We needed to make a detailed plan of where our funds were going to go for the rest of the summer and begin planning our slides for our iGEM presentation. We wanted to decide where we wanted to be by the competition and what we needed to do to get there.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began creating a plan for creating a video about methylation in general and our project specifically. After consulting with our advisors we decided to change the direction of our methyltransferase-DNA binding domain fusion from a two-plasmid to a one-plasmid system that would incorporate a digestion-based assay within the plasmid.</p><br><br />
<br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 12</h2><br />
<div class="box"> <h2>Aug 22 2013 - Aug 28 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/bd/PennigemPic12.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal for this week was to finalize our ideal cloning constructs and figure out how to port what we had already created into the one-plasmid system. We wanted to elaborate more on the assay, as our advisors had emphasized that as one of the more important contributions that our project could make to the synthetic biology community.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We focused on drylab this week, as we needed to get our plans for the rest of the summer set. We worked on a human practices essay about the ethics of targeted methylation in medical therapies. We also began work designing new primers for our revised cloning strategy.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 13</h2><br />
<div class="box"> <h2>Aug 29 2013 - Sep 4 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/f/f7/IMG_2180.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal was to once again begin a new cloning strategy focused on assembling our one-plasmid systems. We needed our cloning strategy finalized as soon as possible, and we dedicated the majority of our time this week to streamlining our cloning process.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began setting up our travel plans to get to the Jamboree. We began the initial stages of cloning our new systems and made substantial progress on cloning our zinc finger and TALE. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 14</h2><br />
<div class="box"> <h2>Sep 5 2013 - Sep 11 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/ad/IMG_0495.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal for this week was to make further progress on cloning our constructs. We also wanted to continue our work on the human practices essay, and begin creating a poster presentation for presenting at University research conferences. We also wanted to begin thinking about designing a computer application for analyzing gels.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>During a marathon weekend coding session, we created a program that we called MaGellin that was designed to analyze our gels and characterize the amount of methylation. We attempted to improve our cloning efficiency by utilizing Antarctic Phosphatase within our reactions. We made substantial progress on finishing our TALE and zinc finger constructs, and selected and grew colonies that would be used to test our assay the following week. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 15</h2><br />
<div class="box"> <h2>Sep 12 2013 - Sep 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/c/c8/Momomomomomomo.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make substantial progress on the website this week. We also wanted to run our assay and test how well our methyltransferase-DNA binding domain fusions had worked. We wanted to work on animation for our video as well as make progress on our human practices essay.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran the assay on the TALE and zinc finger clones, and it yielded promising results. The expression of our fusion protein was a definite achievement. We made substantial progress on the website and essay as well. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 16</h2><br />
<div class="box"> <h2>Sep 19 2013 - Sep 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/5e/DSC_0482.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We needed to finish our website and various forms this week, as well as run our assay in triplicate on the constructs we had created thus far. We needed to plan our remaining time up to the Jamboree, and practice our presentation skills at various outreach events.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We attended several events aimed at recruiting future team members that showed substantial interest in our research and iGEM in general. Our assay returned promising results about the state of our methyltransferase-DNA binding domain fusions. Additionally, we finished the website and filled out all the forms we needed. We have a few experiments still in progress, but our time now is spent preparing for the Jamboree and being ready to present our results. </p><br><br />
</div><br />
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<div><br />
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<br />
<h2>WEEK 17</h2><br />
<div class="box"> <h2>Sep 26 2013 - Oct 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/d/d0/Pennigempic1.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> In the week before the Jamboree, we wanted to compile all our last-minute data as well as create our poster and Powerpoint presentation for the competition.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We gathered a ton of last-minute data this week. The solid deadline put upon us by the Jamboree motivated us all to work as hard as possible to get data worthy of our presentation at the Jamboree. While there's still a lot that we wish to accomplish with our project, we're proud of how far we've made it and hope our hard work pays off at the Jamboree. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 18 (North America Regionals)</h2><br />
<div class="box"> <h2>Oct 3 2013 - Oct 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/31/Pennigempic3.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We just became the Regional Winners for North America for iGEM 2013, but there's no time to rest. Now it's time to get back in the lab and prepare for the World Jamboree. We want to make a game plan for what we are going to accomplish before the World Jamboree at MIT in early November and gather data in areas where we needed more work. We're taking the judge's comments from the regional Jamboree very seriously and attempting to improve our project as much as possible in the coming month. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran our MaGellin assay in a preliminary screening of our cas-methylase fusion and got some activity. We re-ran some previous experiments in triplicate to make the data more compelling. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 19 </h2><br />
<div class="box"> <h2>Oct 10 2013 - Oct 16 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Pennnotebook2pic.jpg" width = "600px"><br />
<br />
<p><b>Goals: <br></b><br />
<p> We wanted to look further into the possibility of transcriptional silencing using targeted methylation. Additionally, we planned to run the full assay to screen our potential Cas-methylase fusion. Another major priority is to perform bisulfite sequencing to look at the target site for our TALE methylase. </p><br><br />
<p><b>Achievements: <br></b><br />
<p>We continued to reach out to underclassmen and recruit members for the upcoming team. At the same time, we were hard at work in lab, performing our assay and trying to further quantify the extent of methylation in our fusion constructs. We got our bisulfite sequencing for our TALE submitted and are eagerly awaiting the results. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 20</h2><br />
<div class="box"> <h2>Oct 17 2013 - Oct 23 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/be/Pennnotebook1pic.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week we wat to begin utilizing a cell-free system to test our targeted TALE methylase. It is imperative that we give the Wiki a complete design overhaul. We also want to make a plan for the couple weeks. </p><br><br />
<p><b>Achievements:<br></b><br />
<p> This week we were screening our cas methylase and found noticeable activity when done in triplicate with all the proper controls. We experimented with various induction times as well. We re-ran some experiments that had previous flaws or were missing controls in triplicate. We had some additional cloning to do to modify our constructs as well. We gathered data for our 3D plot of induction for our methylase fusion, which was perhaps the most time-consuming experiment we have done all year. </p><br><br />
</div><br />
</div><br />
<div><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 21</h2><br />
<div class="box"> <h2>Oct 24 2013 - Oct 30 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/4/42/Dannygel.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal is to finalize Wiki for World Jamboree and to collect data for any major experiments we still need to wrap up. We also need to begin our poster for the Jamboree and work on our presentation. At the same time, there is a ton of wetlab and experiments that we have planned, all of which are unlikely to get done in the next couple weeks, but that won't stop us from trying. We have several presentations with various labs at Penn, including the epigenetics department this week. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>This week we finished the Wiki for World Competition. Additionally, we began our last set of experiments, for which the data will be revealed at the World Jamboree. </p><br><br />
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</html></div>Bkapturhttp://2013.igem.org/Team:Penn/NotebookTeam:Penn/Notebook2013-10-29T01:23:45Z<p>Bkaptur: </p>
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<h2>WEEK 1</h2><br />
<div class="box"><br />
<h2>June 4 2013 - June 11 2013</h2><br />
<img src="https://static.igem.org/mediawiki/2013/2/22/BE_LynchLabGroup_DSC2796.jpg" width = "600px" class="image"/><br />
<p><b>Goals:<br></b><br />
<p> This was our first week setting foot in the lab as the Penn iGEM team. We wanted to become more acquainted with the lab and start transforming and growing parts that would be useful in our future project ideas. This week we wanted to brainstorm our project ideas further as well as being more competent in basic molecular biology techniques.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We learned how to make competent cells and performed our first transformations of the summer. We continued to brainstorm potential projects and thought about directions we would like to pursue for the summer. Our idea for a project that would revolve around quorum sensing systems is currently being put into motion. We continued brainstorming for our idea about uses for DNA binding domains like TALE, Cas9, and zinc fingers. We grew up and miniprepped our transformations of various quorum sensing parts and learned how to use a plate reader.</p><br><br />
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<div><br />
<h2>WEEK 2</h2><br />
<br />
<div class="box"><br />
<h2>June 11 2013 - June 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/3e/Photo-8.JPG" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> This week we wanted to transform some parts for our methylation idea that we ordered from addgene. We also wanted to attempt a bisulfite conversion to test methylation. We had some problems transforming some biobrick parts the previous week, so we wanted to troubleshoot our transformations as well. Another goal of ours was to make more competent DH5-alpha and Dam- cells as well as figure out methylation assays for our promoters.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We worked out the details of one of our potential projects: creating DNA binding domain-methyltransferase fusions. Like last week, we transformed and miniprepped parts that we would need for the quorum sensing project, like the LuxI system. We also transformed and miniprepped the standard biobrick backbones psb1A3, psb1C3, and psb1K3, which would be useful in almost any project we decide to pursue. We pinned down and ordered exactly the DNA binding domains that we thought we would be using and ordered the gene blocks from addgene. We methylated a biobrick part, c0051, with an M.sssI, and used our bisulfite conversion kit for the first time. </p><br> </div><br />
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<h2>WEEK 3</h2><br />
<div class="box"> <h2>June 18 2013 - June 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/2/21/Aaathermopcrlala.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> It was increasingly important that we decide on our project. At this point we were considering a quorum sensing/cell signaling project that would build upon previously created quorum sensing parts submitted in the registry. We were also considering a methyltransferase-DNA binding domain fusion project with the goal of creating a new methyltransferase. We wanted to begin cloning t9002, a GFP producer controlled by an AHL signaling molecule receiver into psb1C3 from psb1A3 in order to use it in a quorum sensing device we were imagining.<br></b><p><b>Achievements:</b><br><br />
<p>This week we got all of our minipreps submitted for sequencing, and we made headway on our first cloning reaction. We figured out how to add restriction sites for cloning reactions using PCR and completed our first cloning reaction according to our successful colony PCR. We experimented with different thermocycler conditions and polymerases for our PCRs that had previously failed, and began to perform PCR with more success.</p><br></div><br />
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<br />
<div><br />
<h2>WEEK 4</h2><br />
<div class="box"> <h2>June 25 2013 - July 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b6/PennigemPic4.JPG" width = "600px"><p><b>Goals:<br></b><br />
<p> This week we wanted to think about applications for selective methylation in E. coli and figure out how our project could be useful for future research. We brainstormed how we wanted to create our constructs and began thinking about the cloning reactions that would be required to create them. We also wanted to begin creating our wiki and start generating useful content.<br></b><p><b>Achievements:</b></p><br />
<p>We confirmed that we completed our first successful cloning reaction. We transformed and miniprepped the biobrick parts for the quorum sensing system that we envisioned creating, with one cell having a light-induced AHL producer, and another cell having a AHL producer downstream of an AHL activated promoter. We thought about creating a device that would spatially separate the cells, as opposed to having them in the same media. We used a simple restriction digest assay to test how BstUI, a methylation sensitive promoter, would behave. </p><br></div><!--/box--><br />
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<h2>WEEK 5</h2><br />
<div class="box"> <h2>July 2 2013 - July 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/6/61/Pennnotebook3pic.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> We wanted to experiment with USER cloning for assembling our gene blocks and minigenes. We also wanted to characterize pdawn and mcherry, parts we got from a lab at the University that we could use in our quorum sensing project. We wanted to attempt to PCR assemble our MsssI and begin fabricating a device for our quorum sensing project. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We practiced measuring fluorescence using our pDawn and mcherry constructs. We successfully completed PCR assembly of our M.sssI. We performed our first cotransformation with I751250, an AHL sender that was downstream of pDawn and T9002. We redesigned primers for PCR reactions that had been giving us trouble, paying more attention to the annealing temperatures of the primers we were designing.</p><br></div><br />
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<h2>WEEK 6</h2><br />
<div class="box"> <h2>July 10 2013 - July 17 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Device_photo.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> As the summer was nearing its halfway mark, we wanted to decide on the relative merits of the two projects and reach a decision. We also wanted to continue our cloning for the two projects and troubleshoot cloning-related problems. We now had all the parts we needed for Cas9, TALE, and zinc finger methylase constructs and wanted to begin assembling them into constructs that we envisioned. These constructs would have a two-plasmid system. One plasmid would have the DNA binding domain downstream of a T7 promoter activated by tetracycline, and the other would be a reporter plasmid to detect methylation. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We decided on the constructs that we would create and began the restriction digest and gel extract steps of our miniprepped components. We planned an experiment we could do with tetracycline induction to test whether our hypothetical methyltransferase-DNA binding domain fusions were actually being expressed.</p><br><br />
</div><br />
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<h2>WEEK 7</h2><br />
<div class="box"> <h2>July 18 2013 - July 24 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/95/IMG_2175.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week our main goals were to attempt our tetracycline induction experiment, order primers for performing a COBRA assay, and refine our LIMS and retroactively manage our samples. We also wanted to finish the cloning experiments we began the previous week.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We completed our construct for our zinc finger fusion plasmid after a successful colony PCR and sequencing result. We performed our first induction experiment by inoculating cultures with a tetracycline-activated promoter. We redid a PCR assembly of our TALE and Cas9 systems that had been failed before. </p><br><br />
</div><br />
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<h2>WEEK 8</h2><br />
<div class="box"> <h2>July 25 2013 - July 31 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/9e/IMG_2173.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to finish our remaining fusion protein constructs and begin thinking about an SDS PAGE to measure protein expression. We also wanted to dedicate more time to pursuing drylab—making advances on our human practices and continue reading the literature on selective methylation. We also wanted to look into trying out different biobrick parts for our quorum sensing system.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We made advances on our cloning of the constructs for both projects. We completed a LIMS system on a Google spreadsheet that would be used to manage our increasingly overwhelming primers box as well as fixing our minipreps and glycerol stock LIMS and retroactively adding samples. We performed a new induction experiment, inducing our cultures with aTc. </p><br><br />
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<h2>WEEK 9</h2><br />
<div class="box"> <h2>Aug 1 2013 - Aug 7 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/59/IMG_0382.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make advances toward generating our device for the quorum sensing project. We wanted to better budget our remaining resources and stock up on supplies that we would need throughout the rest of the summer. We also wanted to use our zinc finger clone in an induction experiment, similar to the ones we had performed earlier for the quorum sensing project. Additionally, we aimed to generate a growth curve and see how the zinc finger cells would respond to induction. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We met with various professors at the University and made contacts who had knowledge about areas in both projects. We ordered more reagents and created the abstract for our project. We designed primers to attempt to Gibson assemble the Cas construct that had been giving us trouble during USER cloning. We hoped that the new cloning strategy would yield better results. We aliquoted our antibiotics, making boxes full of Kan, Chlor, and Amp to last us the entire summer and well into the year. </p><br><br />
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<div><br />
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<h2>WEEK 10</h2><br />
<div class="box"> <h2>Aug 8 2013 - Aug 14 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/a5/IMG_0501.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to use our restriction digest-based test to analyze how our constructs were working with regards to methylation. We needed to decide on which project we were going to pursue as soon as possible, and we decided this week would be the deadline. We wanted to perform our first SDS Page, which had been in the brainstorming stage for a while. Additionally, we wanted to consult experts about designing better primers and see how we could improve our protocols. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We finally decided to fully pursue the project of constructing targeted methyltransferase fusions. While it was a hard decision, it was necessary to commit our efforts to one project. We also finished our TALE clone and began the induction experiment for testing the methyltransferase fusion. We consulted with designers from the School of Design about making our website and better presentations. We began transforming promoters for an additional screen for methyltransferases that we had envisioned, with the belief that methyltransferases could silence promoters.</p><br><br />
</div><br />
</div><br />
<div><br />
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<h2>WEEK 11</h2><br />
<div class="box"> <h2>Aug 15 2013 - Aug 21 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/0/08/PennigemPic11.JPG" width = "600px" ><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to get our Cas construct working after additional drylab work in designing better assembly reactions. We needed to make a detailed plan of where our funds were going to go for the rest of the summer and begin planning our slides for our iGEM presentation. We wanted to decide where we wanted to be by the competition and what we needed to do to get there.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began creating a plan for creating a video about methylation in general and our project specifically. After consulting with our advisors we decided to change the direction of our methyltransferase-DNA binding domain fusion from a two-plasmid to a one-plasmid system that would incorporate a digestion-based assay within the plasmid.</p><br><br />
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<div><br />
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<h2>WEEK 12</h2><br />
<div class="box"> <h2>Aug 22 2013 - Aug 28 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/bd/PennigemPic12.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal for this week was to finalize our ideal cloning constructs and figure out how to port what we had already created into the one-plasmid system. We wanted to elaborate more on the assay, as our advisors had emphasized that as one of the more important contributions that our project could make to the synthetic biology community.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We focused on drylab this week, as we needed to get our plans for the rest of the summer set. We worked on a human practices essay about the ethics of targeted methylation in medical therapies. We also began work designing new primers for our revised cloning strategy.</p><br><br />
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<h2>WEEK 13</h2><br />
<div class="box"> <h2>Aug 29 2013 - Sep 4 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/f/f7/IMG_2180.JPG" width = "600px"><br />
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<p><b>Goals:<br></b><br />
<p> Our goal was to once again begin a new cloning strategy focused on assembling our one-plasmid systems. We needed our cloning strategy finalized as soon as possible, and we dedicated the majority of our time this week to streamlining our cloning process.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began setting up our travel plans to get to the Jamboree. We began the initial stages of cloning our new systems and made substantial progress on cloning our zinc finger and TALE. </p><br><br />
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<div><br />
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<h2>WEEK 14</h2><br />
<div class="box"> <h2>Sep 5 2013 - Sep 11 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/ad/IMG_0495.JPG" width = "600px""><br />
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<p><b>Goals:<br></b><br />
<p> Our goal for this week was to make further progress on cloning our constructs. We also wanted to continue our work on the human practices essay, and begin creating a poster presentation for presenting at University research conferences. We also wanted to begin thinking about designing a computer application for analyzing gels.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>During a marathon weekend coding session, we created a program that we called MaGellin that was designed to analyze our gels and characterize the amount of methylation. We attempted to improve our cloning efficiency by utilizing Antarctic Phosphatase within our reactions. We made substantial progress on finishing our TALE and zinc finger constructs, and selected and grew colonies that would be used to test our assay the following week. </p><br><br />
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<h2>WEEK 15</h2><br />
<div class="box"> <h2>Sep 12 2013 - Sep 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/c/c8/Momomomomomomo.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make substantial progress on the website this week. We also wanted to run our assay and test how well our methyltransferase-DNA binding domain fusions had worked. We wanted to work on animation for our video as well as make progress on our human practices essay.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran the assay on the TALE and zinc finger clones, and it yielded promising results. The expression of our fusion protein was a definite achievement. We made substantial progress on the website and essay as well. </p><br><br />
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<div><br />
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<h2>WEEK 16</h2><br />
<div class="box"> <h2>Sep 19 2013 - Sep 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/5e/DSC_0482.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We needed to finish our website and various forms this week, as well as run our assay in triplicate on the constructs we had created thus far. We needed to plan our remaining time up to the Jamboree, and practice our presentation skills at various outreach events.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We attended several events aimed at recruiting future team members that showed substantial interest in our research and iGEM in general. Our assay returned promising results about the state of our methyltransferase-DNA binding domain fusions. Additionally, we finished the website and filled out all the forms we needed. We have a few experiments still in progress, but our time now is spent preparing for the Jamboree and being ready to present our results. </p><br><br />
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<h2>WEEK 17</h2><br />
<div class="box"> <h2>Sep 26 2013 - Oct 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/d/d0/Pennigempic1.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> In the week before the Jamboree, we wanted to compile all our last-minute data as well as create our poster and Powerpoint presentation for the competition.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We gathered a ton of last-minute data this week. The solid deadline put upon us by the Jamboree motivated us all to work as hard as possible to get data worthy of our presentation at the Jamboree. While there's still a lot that we wish to accomplish with our project, we're proud of how far we've made it and hope our hard work pays off at the Jamboree. </p><br><br />
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<h2>WEEK 18 (North America Regionals)</h2><br />
<div class="box"> <h2>Oct 3 2013 - Oct 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/31/Pennigempic3.jpg" width = "600px"><br />
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<p><b>Goals:<br></b><br />
<p> We just became the Regional Winners for North America for iGEM 2013, but there's no time to rest. Now it's time to get back in the lab and prepare for the World Jamboree. We want to make a game plan for what we are going to accomplish before the World Jamboree at MIT in early November and gather data in areas where we needed more work. We're taking the judge's comments from the regional Jamboree very seriously and attempting to improve our project as much as possible in the coming month. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran our MaGellin assay in a preliminary screening of our cas-methylase fusion and got some activity. We re-ran some previous experiments in triplicate to make the data more compelling. </p><br><br />
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<div><br />
<h2>WEEK 19 </h2><br />
<div class="box"> <h2>Oct 10 2013 - Oct 16 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Pennnotebook2pic.jpg" width = "600px"><br />
<br />
<p><b>Goals: <br></b><br />
<p> We wanted to look further into the possibility of transcriptional silencing using targeted methylation. Additionally, we planned to run the full assay to screen our potential Cas-methylase fusion. Another major priority is to perform bisulfite sequencing to look at the target site for our TALE methylase. </p><br><br />
<p><b>Achievements: <br></b><br />
<p>We continued to reach out to underclassmen and recruit members for the upcoming team. At the same time, we were hard at work in lab, performing our assay and trying to further quantify the extent of methylation in our fusion constructs. We got our bisulfite sequencing for our TALE submitted and are eagerly awaiting the results. </p><br><br />
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<div><br />
<h2>WEEK 20</h2><br />
<div class="box"> <h2>Oct 17 2013 - Oct 23 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/be/Pennnotebook1pic.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week we wat to begin utilizing a cell-free system to test our targeted TALE methylase. It is imperative that we give the Wiki a complete design overhaul. We also want to make a plan for the couple weeks. </p><br><br />
<p><b>Achievements:<br></b><br />
<p> This week we were screening our cas methylase and found noticeable activity when done in triplicate with all the proper controls. We experimented with various induction times as well. We re-ran some experiments that had previous flaws or were missing controls in triplicate. We had some additional cloning to do to modify our constructs as well. We gathered data for our 3D plot of induction for our methylase fusion, which was perhaps the most time-consuming experiment we have done all year. </p><br><br />
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<div><br />
<h2>WEEK 21</h2><br />
<div class="box"> <h2>Oct 24 2013 - Oct 30 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/4/42/Dannygel.jpg" width = "600px"><br />
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<p><b>Goals:<br></b><br />
<p> Our main goal is to finalize Wiki for World Jamboree and to collect data for any major experiments we still need to wrap up. We also need to begin our poster for the Jamboree and work on our presentation. At the same time, there is a ton of wetlab and experiments that we have planned, all of which are unlikely to get done in the next couple weeks, but that won't stop us from trying. We have several presentations with various labs at Penn, including the epigenetics department this week. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>This week we finished the Wiki for World Competition. Additionally, we began our last set of experiments, for which the data will be revealed at the World Jamboree. </p><br><br />
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</html></div>Bkapturhttp://2013.igem.org/File:Aaathermopcrlala.jpgFile:Aaathermopcrlala.jpg2013-10-29T01:20:26Z<p>Bkaptur: </p>
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<h1><b><center>About the Team</center></b></h1><br />
<div align="left">The Penn iGEM 2013 team is made up of 5 undergraduate students and various advisors and mentors at the University of Pennsylvania. The team comes from various academic disciplines such as math, bioengineering, and computer science. The team works out of the undergraduate bioengineering laboratory and is rumored to live there. <br />
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<h2>Brad "Big Dark" Kaptur</h2><p>Bioengineering</p><br />
<p>"Screw minipreps, gotta get big."</p> <br />
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<h2>Josh Tycko</h2><p>Mathematics and Biology</p><br />
<p> "Don't worry, I know a guy."</p> <br />
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<h2>Danielle Fields</h2><p>Bioengineering</p><br />
<p>"I have a Starbucks Gold Card. Literally."</p> <br />
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<h2>Danny Cabrera</h2><p>Computational Biology</p><br />
<p>"Yo, [mumble] you pour [mumble] that gel yet?"</p> <br />
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<div class="member_divide"><h2>Mahamad "Dusty" Charawi</h2><p>Management and Computer Science</p><br />
<p>"Hi my name Mahamad, from Penn iGEM."</p> <br />
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<h3>The Advisors</h3> <!--title of section--><br />
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<div class="member_divide_text"><h2><a href='http://www.seas.upenn.edu/directory/profile.php?ID=178'>Brian Chow, Ph.D</a></h2><p>Assistant Professor</p><br />
<p>Chow's laboratory aims to create technological innovations to enhance therapeutic interventions in CNS disorders, and to this end, focuses on engineering tools to elucidate, diagnose and treat the diseased brain. He was instrumental in the direction of the team, teaching us science, organization, and leadership.</p> <br />
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<div class="member_divide_text"><h2>Spencer "STG" Glantz</h2><p>Bioengineering (PhD Student)</p><br />
<p>Spencer helped found the first iGEM team at the University of Pennsylvania and has been lending us his deep knowledge and experience with synthetic biology ever since. He helped us every day and truly made this project possible.</p> <br />
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<div class="member_divide_text"><h2><a href='http://www.orkantelhan.com/'>Orkan Telhan, Ph.D</a></h2><p>Assistant Professor</p><br />
<p> Interdisciplinary artist, designer, and researcher whose investigations focus on the design of interrogative objects, interfaces, and media, engaging with critical issues in social, cultural, and environmental responsibility. He greatly assisted the team with our efforts to properly communicate synthetic biology to the public.</p> <br />
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<div class="member_divide_text"><h2><a href='http://bioengineering.rice.edu/Content.aspx?id=4294967626'>Jordan Miller, Ph.D</a></h2><p>Assistant Professor of Bioengineering at Rice</p><br />
<p>Jordan has been an advisor to Penn iGEM teams for the last three years. He has given us insightful scientific advice and words of wisdom, and he sends the best emails.</p> <br />
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<div class="member_divide_text"><h2>Avin "Shiii" Veerakumar </h2><p>iGEM Guru</p><br />
<p>The Penn iGEM Godfather. He sent us great GIFs and drew a computer.</p> <br />
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<div class="member_divide_text"><h2>Michael Salvatore "Gumbaicci Margaricci" Magaraci</h2><p>iGEM Guru</p><br />
<p>Cloning Master. Diagram Master. He was a huge help.</p> <br />
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<h3>Nothing would be possible without these guys</h3> <!--title of section--><br />
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<div class="member_divide_text"><h2>Sevile Mannickarottu</h2><p>Director of Bioengineering Instructional Laboratories</p><br />
<p>The 2013 Penn iGEM team would like to thank Sevile for providing his facilities and equipment for use during the project.</p> <br />
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<div class="member_divide_text"><h2>Henry "HMFM" Ma </h2><p>Bioengineering (Masters Student)</p><br />
<br />
<p>"Coffee?"</p> <br />
<p>Thank you to Henry for his wonderful support throughout this whole process.</p><br />
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<p style="text-align: center"><b>We could not have succeeded without the help of all these incredibly talented people. We are extremely grateful for their help.</b></p><br />
<p style="text-align: center">Generously donated interesting organisms and scientific expertise by <a href='http://www.bio.upenn.edu/people/mark-goulian'>Dr. Mark Goulian</a></p><br />
<p style="text-align: center">Advice on epigenetics by Drs <a href='http://www.med.upenn.edu/apps/faculty/index.php/g20000320/p13534'>Marisa Bartolomei</a> and <a href='http://www.med.upenn.edu/apps/faculty/index.php/g361/p11818'>Rebecca Simmons</a></p><br />
<p style="text-align: center">Advice on methylation assays by Chris Krapp</p><br />
<p style="text-align: center">Computer Vision algorithm by Eric Kauderer Abrams</p><br />
<p style="text-align: center">Graphic Design by Micah Kaats</p><br />
<p style="text-align: center">Assistance developing MaGellin user interface by Morgan Snyder</p><br />
<p style="text-align: center">Video editing and Animation by Dylan Petro</p><br />
<p style="text-align: center">Cinematography and Photography by Jake Whritner</p><br />
<p style="text-align: center">Music by Ben Brodie</p><br />
<p style="text-align: center">Photography by Erica Sacshe</p><br />
<p style="text-align: center">Web development by Dylan Petro and Stefanie Alfonso</p><br />
<p style="text-align: center">We would also like to thank <a href='http://davidgdula.com'>David Gdula</a> of NEB for being so personally invested in the team's success</p><br />
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<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
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<h1><b><center>About the Team</center></b></h1><br />
<div align="left">The Penn iGEM 2013 team is made up of 5 undergraduate students and various advisors and mentors at the University of Pennsylvania. The team comes from various academic disciplines such as math, bioengineering, and computer science. The team works out of the undergraduate bioengineering laboratory and is rumored to live there. <br />
<br />
<h3>The Team Members</h3> <!--title of section--><br />
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<div class = "member_divide_text"><br />
<h2>Brad "Big Dark" Kaptur</h2><p>Bioengineering</p><br />
<p>"Screw minipreps, gotta get big."</p> <br />
</div><br />
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<h2>Josh Tycko</h2><p>Mathematics and Biology</p><br />
<p> "Don't worry, I know a guy."</p> <br />
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<h2>Danielle Fields</h2><p>Bioengineering</p><br />
<p>"I have a Starbucks Gold Card. Literally."</p> <br />
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<h2>Danny Cabrera</h2><p>Computational Biology</p><br />
<p>"Yo, [mumble] you pour [mumble] that gel yet?"</p> <br />
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<div class="member_divide"><h2>Mahamad "Dusty" Charawi</h2><p>Management and Computer Science</p><br />
<p>"Hi my name Mahamad, from Penn iGEM."</p> <br />
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<h3>The Advisors</h3> <!--title of section--><br />
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<div class="member_divide_text"><h2><a href='http://www.seas.upenn.edu/directory/profile.php?ID=178'>Brian Chow, Ph.D</a></h2><p>Assistant Professor</p><br />
<p>Chow's laboratory aims to create technological innovations to enhance therapeutic interventions in CNS disorders, and to this end, focuses on engineering tools to elucidate, diagnose and treat the diseased brain. He was instrumental in the direction of the team, teaching us science, organization, and leadership.</p> <br />
</div><br />
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<div class="member_divide_text"><h2>Spencer "STG" Glantz</h2><p>Bioengineering (PhD Student)</p><br />
<p>Spencer helped found the first iGEM team at the University of Pennsylvania and has been lending us his deep knowledge and experience with synthetic biology ever since. He helped us every day and truly made this project possible.</p> <br />
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<div class="member_divide_text"><h2><a href='http://www.orkantelhan.com/'>Orkan Telhan, Ph.D</a></h2><p>Assistant Professor</p><br />
<p> Interdisciplinary artist, designer, and researcher whose investigations focus on the design of interrogative objects, interfaces, and media, engaging with critical issues in social, cultural, and environmental responsibility. He greatly assisted the team with our efforts to properly communicate synthetic biology to the public.</p> <br />
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<div class = "member_divide" style = "background: url('http://farm4.staticflickr.com/3677/10504328243_fabe132f04.jpg') center center; background-size: 120%;"></div><br />
<div class="member_divide_text"><h2><a href='http://bioengineering.rice.edu/Content.aspx?id=4294967626'>Jordan Miller, Ph.D</a></h2><p>Assistant Professor of Bioengineering at Rice</p><br />
<p>Jordan has been an advisor to Penn iGEM teams for the last three years. He has given us insightful scientific advice and words of wisdom, and he sends the best emails.</p> <br />
</div><br />
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<div class="member_divide_text"><h2>Avin "Shiii" Veerakumar </h2><p>iGEM Guru</p><br />
<p>The Penn iGEM Godfather. He sent us great GIFs and drew a computer.</p> <br />
</div><br />
<div class = "member_divide" style = "background: url('http://farm8.staticflickr.com/7429/10546067283_d794d49cf6.jpg') center center; background-size: 140%;"></div><br />
<div class="member_divide_text"><h2>Michael Salvatore "Gumbaicci Margaricci" Magarachi</h2><p>iGEM Guru</p><br />
<p>Cloning Master. Diagram Master. He was a huge help.</p> <br />
</div><br />
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<h3>Nothing would be possible without these guys</h3> <!--title of section--><br />
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<div class="member_divide_text"><h2>Sevile Mannickarottu</h2><p>Director of Bioengineering Instructional Laboratories</p><br />
<p>The 2013 Penn iGEM team would like to thank Sevile for providing his facilities and equipment for use during the project.</p> <br />
</div><br />
<div class = "member_divide" style = "background: url('https://static.igem.org/mediawiki/2013/5/55/Aaahenry.JPG') center center; background-size: 130%;"></div><br />
<div class="member_divide_text"><h2>Henry "HMFM" Ma </h2><p>Bioengineering (Masters Student)</p><br />
<br />
<p>"Coffee?"</p> <br />
<p>Thank you to Henry for his wonderful support throughout this whole process.</p><br />
</div><br />
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<p style="text-align: center"><b>We could not have succeeded without the help of all these incredibly talented people. We are extremely grateful for their help.</b></p><br />
<p style="text-align: center">Generously donated interesting organisms and scientific expertise by <a href='http://www.bio.upenn.edu/people/mark-goulian'>Dr. Mark Goulian</a></p><br />
<p style="text-align: center">Advice on epigenetics by Drs <a href='http://www.med.upenn.edu/apps/faculty/index.php/g20000320/p13534'>Marisa Bartolomei</a> and <a href='http://www.med.upenn.edu/apps/faculty/index.php/g361/p11818'>Rebecca Simmons</a></p><br />
<p style="text-align: center">Advice on methylation assays by Chris Krapp</p><br />
<p style="text-align: center">Computer Vision algorithm by Eric Kauderer Abrams</p><br />
<p style="text-align: center">Graphic Design by Micah Kaats</p><br />
<p style="text-align: center">Assistance developing MaGellin user interface by Morgan Snyder</p><br />
<p style="text-align: center">Video editing and Animation by Dylan Petro</p><br />
<p style="text-align: center">Cinematography and Photography by Jake Whritner</p><br />
<p style="text-align: center">Music by Ben Brodie</p><br />
<p style="text-align: center">Photography by Erica Sacshe</p><br />
<p style="text-align: center">Web development by Dylan Petro and Stefanie Alfonso</p><br />
<p style="text-align: center">We would also like to thank <a href='http://davidgdula.com'>David Gdula</a> of NEB for being so personally invested in the team's success</p><br />
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<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
</center> <br />
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Penn iGem &copy; 2013<br />
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</html></div>Bkapturhttp://2013.igem.org/File:Aaahenry.JPGFile:Aaahenry.JPG2013-10-29T01:09:24Z<p>Bkaptur: </p>
<hr />
<div></div>Bkapturhttp://2013.igem.org/Team:Penn/LIMSTeam:Penn/LIMS2013-10-29T00:42:07Z<p>Bkaptur: </p>
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<div><html lang="en"><br />
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<h2>Laboratory Information Management Systems</h2> <!--title--><br />
<br><p><b>What's LIMS and Why Use It?</b><br><br />
LIMS stands for Laboratory Information Management System. It's a way of managing data involved in working in a lab. The definition of LIMS has expanded recently to include assay management, data mining, and a lot of other complicated features available in expensive commercial programs. However, one core, indispensable feature is sample management: A key feature of a good lab information system is that it will tell you where you put your tube after you've long forgotten. To fill this need for an electronic sample management system, Penn iGEM created LIMS systems using the Google Spreadsheet and Forms platform. The LIMS forms and spreadsheets provided on this page are updated versions of the same ones that Penn iGEM used to manage its samples all summer.<br><center><br />
<br> <img src="https://static.igem.org/mediawiki/2013/5/56/AdfadfsIMG_0540.JPG" width="500"><figcaption>Have you ever tried to find an old primer or glycerol stock from unlabeled tubes such as in the box above? It can be a pain, so we adopted the rigorous Laboratory Information Management System (LIMS).</figcaption><br><br></center><br />
<br><p><b>How to Copy and Edit Penn iGEM’s Google Doc LIMS Forms:</b><br><br />
1. Sign into Google using your Gmail account.<br><br />
2. Open one of our forms that you wish to copy using the links on our website.<br><br />
3. Here you will be able to view our spreadsheet, but not able to edit it.<br><br />
4. To make a copy for yourself, go to “File” -> “Make a Copy.”<br><br />
5. Enter the document name you wish to use.<br><br />
6. You now have a copy of our form and spreadsheet for your own use.<br><br />
7. To edit the form, go to “Form” -> “Edit Form.”<br><br />
8. From here, you have the option to change any of the data entry options on our form. For instructions on editing specifics, consult Google’s help documentation under “Help” -> “Forms Help.”<br><br />
9. After you have adjusted the form to your liking, add entries to the spreadsheet by going to “Form” -> “Go to Live Form.”<br><br />
10. Note: While you may edit the spreadsheet directly, using the form can streamline data entry by using radio buttons and checkboxes that you have pre-set. Additionally, it adds consistency and makes finding data later much easier.<br />
</p><br />
<br><br />
<div align="center"><br />
<br />
<object width="640" height="480"><param name="movie" value="//www.youtube.com/v/yAvCx_qjJDk?hl=en_US&amp;version=3"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="//www.youtube.com/v/yAvCx_qjJDk?hl=en_US&amp;version=3" type="application/x-shockwave-flash" width="640" height="480" allowscriptaccess="always" allowfullscreen="true"></embed></object><br />
<br />
</div><br />
<br />
<p><b>Download Your Own LIMS Forms (Version 2.0) with Queries Here:</b><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dG5aeDl0bnNQa0pqSnlHSnQ2bHhTNFE&usp=drive_web#gid=5">DNA LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dExJOGo2Y0s2RTlqNk5GaktJZW1zQVE&usp=drive_web#gid=2">Strains LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dE1Iek1QNWk2cWVWSTNoVVVIT1pHQVE&usp=drive_web#gid=4">DNA LIMS Query</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dHQzd0haazFlWmUzWWFXbVN6LUJZY0E&usp=drive_web#gid=6">Strains LIMS Query</a><br><br />
</p><br />
<br />
<p><b>Download Your Own LIMS Forms (Version 1.0) Here:</b><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdEpuU3dvYmpibU9TdkpTRU1KUGdzQWc&usp=sharing">DNA LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdERNUHRiREhqWkdmOVN1MXlnMXBJYlE&usp=sharing">Glycerol Stock LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdHM3S2RvaWJxbHJzNGtlYzZidVJSMVE&usp=sharing">Primers LIMS</a><br><br />
</p><br />
<br />
<br />
<br />
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<br />
</div><br />
<br />
<br />
<br />
<div id ="pagefooter"><br />
<br><br />
<br><br />
<center><a href = "https://2013.igem.org/Team:Penn"> Home </a> <a href = "https://static.igem.org/mediawiki/2013/e/e5/Spec_Sheet.pdf" >Spec Sheet</a> <a href = "https://2013.igem.org/Team:Penn/sitemap" >Sitemap</a><br />
</center> <br />
<br><br />
Penn iGem &copy; 2013<br />
</div><br />
<br />
<br />
<br />
</body></div>Bkapturhttp://2013.igem.org/Team:Penn/LIMSTeam:Penn/LIMS2013-10-29T00:32:25Z<p>Bkaptur: </p>
<hr />
<div><html lang="en"><br />
<head><br />
<br />
<title>Penn iGEM</title><br />
<link href="https://googledrive.com/host/0B4ZBZOYYKBzEVHRaZEdUVGo5cjA" type="text/css" rel="stylesheet"/> <!--css--><br />
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<br />
<h2>Laboratory Information Management Systems</h2> <!--title--><br />
<br><p><b>What's LIMS and Why Use It?</b><br><br />
LIMS stands for Laboratory Information Management System. It's a way of managing data involved in working in a lab. The definition of LIMS has expanded recently to include assay management, data mining, and a lot of other complicated features available in expensive commercial programs. However, one core, indispensable feature is sample management: A key feature of a good lab information system is that it will tell you where you put your tube after you've long forgotten. To fill this need for an electronic sample management system, Penn iGEM created LIMS systems using the Google Spreadsheet and Forms platform. The LIMS forms and spreadsheets provided on this page are updated versions of the same ones that Penn iGEM used to manage its samples all summer.<br><center><br />
<br> <img src="https://static.igem.org/mediawiki/2013/5/56/AdfadfsIMG_0540.JPG" width="500"><figcaption>Have you ever tried to find an old primer or glycerol stock from unlabeled tubes such as in the box above? It can be a pain, so we adopted the rigorous Laboratory Information Management System (LIMS).</figcaption><br><br></center><br />
<br><p><b>How to Copy and Edit Penn iGEM’s Google Doc LIMS Forms:</b><br><br />
1. Sign into Google using your Gmail account.<br><br />
2. Open one of our forms that you wish to copy using the links on our website.<br><br />
3. Here you will be able to view our spreadsheet, but not able to edit it.<br><br />
4. To make a copy for yourself, go to “File” -> “Make a Copy.”<br><br />
5. Enter the document name you wish to use.<br><br />
6. You now have a copy of our form and spreadsheet for your own use.<br><br />
7. To edit the form, go to “Form” -> “Edit Form.”<br><br />
8. From here, you have the option to change any of the data entry options on our form. For instructions on editing specifics, consult Google’s help documentation under “Help” -> “Forms Help.”<br><br />
9. After you have adjusted the form to your liking, add entries to the spreadsheet by going to “Form” -> “Go to Live Form.”<br><br />
10. Note: While you may edit the spreadsheet directly, using the form can streamline data entry by using radio buttons and checkboxes that you have pre-set. Additionally, it adds consistency and makes finding data later much easier.<br />
</p><br />
<br><br />
<div align="center"><br />
<br />
<object width="640" height="480"><param name="movie" value="//www.youtube.com/v/yAvCx_qjJDk?hl=en_US&amp;version=3"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="//www.youtube.com/v/yAvCx_qjJDk?hl=en_US&amp;version=3" type="application/x-shockwave-flash" width="640" height="480" allowscriptaccess="always" allowfullscreen="true"></embed></object><br />
<br />
</div><br />
<br />
<p><b>Download Your Own Version 2.0 LIMS Forms with Queries Here:</b><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dG5aeDl0bnNQa0pqSnlHSnQ2bHhTNFE&usp=drive_web#gid=5">DNA LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dExJOGo2Y0s2RTlqNk5GaktJZW1zQVE&usp=drive_web#gid=2">Strains LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dE1Iek1QNWk2cWVWSTNoVVVIT1pHQVE&usp=drive_web#gid=4">DNA LIMS Query</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dHQzd0haazFlWmUzWWFXbVN6LUJZY0E&usp=drive_web#gid=6">Strains LIMS Query</a><br><br />
</p><br />
<br />
<p><b>Download Your Own Version 1.0 LIMS Forms Here:</b><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdEpuU3dvYmpibU9TdkpTRU1KUGdzQWc&usp=sharing">DNA LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdERNUHRiREhqWkdmOVN1MXlnMXBJYlE&usp=sharing">Glycerol Stock LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdHM3S2RvaWJxbHJzNGtlYzZidVJSMVE&usp=sharing">Primers LIMS</a><br><br />
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<h2>Laboratory Information Management Systems</h2> <!--title--><br />
<br><p><b>What's LIMS and Why Use It?</b><br><br />
LIMS stands for Laboratory Information Management System. It's a way of managing data involved in working in a lab. The definition of LIMS has expanded recently to include assay management, data mining, and a lot of other complicated features available in expensive commercial programs. However, one core, indispensable feature is sample management: A key feature of a good lab information system is that it will tell you where you put your tube after you've long forgotten. To fill this need for an electronic sample management system, Penn iGEM created LIMS systems using the Google Spreadsheet and Forms platform. The LIMS forms and spreadsheets provided on this page are updated versions of the same ones that Penn iGEM used to manage its samples all summer.<br><center><br />
<br> <img src="https://static.igem.org/mediawiki/2013/5/56/AdfadfsIMG_0540.JPG" width="500"><figcaption>Have you ever tried to find an old primer or glycerol stock from unlabeled tubes such as in the box above? It can be a pain, so we adopted the rigorous Laboratory Information Management System (LIMS).</figcaption><br><br></center><br />
<br><p><b>How to Copy and Edit Penn iGEM’s Google Doc LIMS Forms:</b><br><br />
1. Sign into Google using your Gmail account.<br><br />
2. Open one of our forms that you wish to copy using the links on our website.<br><br />
3. Here you will be able to view our spreadsheet, but not able to edit it.<br><br />
4. To make a copy for yourself, go to “File” -> “Make a Copy.”<br><br />
5. Enter the document name you wish to use.<br><br />
6. You now have a copy of our form and spreadsheet for your own use.<br><br />
7. To edit the form, go to “Form” -> “Edit Form.”<br><br />
8. From here, you have the option to change any of the data entry options on our form. For instructions on editing specifics, consult Google’s help documentation under “Help” -> “Forms Help.”<br><br />
9. After you have adjusted the form to your liking, add entries to the spreadsheet by going to “Form” -> “Go to Live Form.”<br><br />
10. Note: While you may edit the spreadsheet directly, using the form can streamline data entry by using radio buttons and checkboxes that you have pre-set. Additionally, it adds consistency and makes finding data later much easier.<br />
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<object width="640" height="480"><param name="movie" value="//www.youtube.com/v/yAvCx_qjJDk?hl=en_US&amp;version=3"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="//www.youtube.com/v/yAvCx_qjJDk?hl=en_US&amp;version=3" type="application/x-shockwave-flash" width="640" height="480" allowscriptaccess="always" allowfullscreen="true"></embed></object><br />
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<p><b>Download Your Own Simple LIMS Forms Here:</b><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdEpuU3dvYmpibU9TdkpTRU1KUGdzQWc&usp=sharing">DNA LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdERNUHRiREhqWkdmOVN1MXlnMXBJYlE&usp=sharing">Glycerol Stock LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0AiCIrEV11SKjdHM3S2RvaWJxbHJzNGtlYzZidVJSMVE&usp=sharing">Primers LIMS</a><br><br />
</p><br />
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<p><b>Download Your Own LIMS Forms with Queries Here:</b><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dG5aeDl0bnNQa0pqSnlHSnQ2bHhTNFE&usp=drive_web#gid=5">DNA LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dExJOGo2Y0s2RTlqNk5GaktJZW1zQVE&usp=drive_web#gid=2">Strains LIMS</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dE1Iek1QNWk2cWVWSTNoVVVIT1pHQVE&usp=drive_web#gid=4">DNA LIMS Query</a><br><br />
<a href="https://docs.google.com/spreadsheet/ccc?key=0Andg3QBGwDP7dHQzd0haazFlWmUzWWFXbVN6LUJZY0E&usp=drive_web#gid=6">Strains LIMS Query</a><br><br />
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<h2>WEEK 1</h2><br />
<div class="box"><br />
<h2>June 4 2013 - June 11 2013</h2><br />
<img src="https://static.igem.org/mediawiki/2013/2/22/BE_LynchLabGroup_DSC2796.jpg" width = "600px" class="image"/><br />
<p><b>Goals:<br></b><br />
<p> This was our first week setting foot in the lab as the Penn iGEM team. We wanted to become more acquainted with the lab and start transforming and growing parts that would be useful in our future project ideas. This week we wanted to brainstorm our project ideas further as well as being more competent in basic molecular biology techniques.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We learned how to make competent cells and performed our first transformations of the summer. We continued to brainstorm potential projects and thought about directions we would like to pursue for the summer. Our idea for a project that would revolve around quorum sensing systems is currently being put into motion. We continued brainstorming for our idea about uses for DNA binding domains like TALE, Cas9, and zinc fingers. We grew up and miniprepped our transformations of various quorum sensing parts and learned how to use a plate reader.</p><br><br />
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<h2>WEEK 2</h2><br />
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<h2>June 11 2013 - June 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/3e/Photo-8.JPG" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> This week we wanted to transform some parts for our methylation idea that we ordered from addgene. We also wanted to attempt a bisulfite conversion to test methylation. We had some problems transforming some biobrick parts the previous week, so we wanted to troubleshoot our transformations as well. Another goal of ours was to make more competent DH5-alpha and Dam- cells as well as figure out methylation assays for our promoters.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We worked out the details of one of our potential projects: creating DNA binding domain-methyltransferase fusions. Like last week, we transformed and miniprepped parts that we would need for the quorum sensing project, like the LuxI system. We also transformed and miniprepped the standard biobrick backbones psb1A3, psb1C3, and psb1K3, which would be useful in almost any project we decide to pursue. We pinned down and ordered exactly the DNA binding domains that we thought we would be using and ordered the gene blocks from addgene. We methylated a biobrick part, c0051, with an M.sssI, and used our bisulfite conversion kit for the first time. </p><br> </div><br />
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<h2>WEEK 3</h2><br />
<div class="box"> <h2>June 18 2013 - June 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/8/85/IMG_0264.JPG" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> It was increasingly important that we decide on our project. At this point we were considering a quorum sensing/cell signaling project that would build upon previously created quorum sensing parts submitted in the registry. We were also considering a methyltransferase-DNA binding domain fusion project with the goal of creating a new methyltransferase. We wanted to begin cloning t9002, a GFP producer controlled by an AHL signaling molecule receiver into psb1C3 from psb1A3 in order to use it in a quorum sensing device we were imagining.<br></b><p><b>Achievements:</b><br><br />
<p>This week we got all of our minipreps submitted for sequencing, and we made headway on our first cloning reaction. We figured out how to add restriction sites for cloning reactions using PCR and completed our first cloning reaction according to our successful colony PCR. We experimented with different thermocycler conditions and polymerases for our PCRs that had previously failed, and began to perform PCR with more success.</p><br></div><br />
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<h2>WEEK 4</h2><br />
<div class="box"> <h2>June 25 2013 - July 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b6/PennigemPic4.JPG" width = "600px"><p><b>Goals:<br></b><br />
<p> This week we wanted to think about applications for selective methylation in E. coli and figure out how our project could be useful for future research. We brainstormed how we wanted to create our constructs and began thinking about the cloning reactions that would be required to create them. We also wanted to begin creating our wiki and start generating useful content.<br></b><p><b>Achievements:</b></p><br />
<p>We confirmed that we completed our first successful cloning reaction. We transformed and miniprepped the biobrick parts for the quorum sensing system that we envisioned creating, with one cell having a light-induced AHL producer, and another cell having a AHL producer downstream of an AHL activated promoter. We thought about creating a device that would spatially separate the cells, as opposed to having them in the same media. We used a simple restriction digest assay to test how BstUI, a methylation sensitive promoter, would behave. </p><br></div><!--/box--><br />
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<h2>WEEK 5</h2><br />
<div class="box"> <h2>July 2 2013 - July 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/6/61/Pennnotebook3pic.jpg" width = "600px"><br />
<p><b>Goals:<br></b><br />
<p> We wanted to experiment with USER cloning for assembling our gene blocks and minigenes. We also wanted to characterize pdawn and mcherry, parts we got from a lab at the University that we could use in our quorum sensing project. We wanted to attempt to PCR assemble our MsssI and begin fabricating a device for our quorum sensing project. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We practiced measuring fluorescence using our pDawn and mcherry constructs. We successfully completed PCR assembly of our M.sssI. We performed our first cotransformation with I751250, an AHL sender that was downstream of pDawn and T9002. We redesigned primers for PCR reactions that had been giving us trouble, paying more attention to the annealing temperatures of the primers we were designing.</p><br></div><br />
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<h2>WEEK 6</h2><br />
<div class="box"> <h2>July 10 2013 - July 17 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Device_photo.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> As the summer was nearing its halfway mark, we wanted to decide on the relative merits of the two projects and reach a decision. We also wanted to continue our cloning for the two projects and troubleshoot cloning-related problems. We now had all the parts we needed for Cas9, TALE, and zinc finger methylase constructs and wanted to begin assembling them into constructs that we envisioned. These constructs would have a two-plasmid system. One plasmid would have the DNA binding domain downstream of a T7 promoter activated by tetracycline, and the other would be a reporter plasmid to detect methylation. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We decided on the constructs that we would create and began the restriction digest and gel extract steps of our miniprepped components. We planned an experiment we could do with tetracycline induction to test whether our hypothetical methyltransferase-DNA binding domain fusions were actually being expressed.</p><br><br />
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<h2>WEEK 7</h2><br />
<div class="box"> <h2>July 18 2013 - July 24 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/95/IMG_2175.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week our main goals were to attempt our tetracycline induction experiment, order primers for performing a COBRA assay, and refine our LIMS and retroactively manage our samples. We also wanted to finish the cloning experiments we began the previous week.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We completed our construct for our zinc finger fusion plasmid after a successful colony PCR and sequencing result. We performed our first induction experiment by inoculating cultures with a tetracycline-activated promoter. We redid a PCR assembly of our TALE and Cas9 systems that had been failed before. </p><br><br />
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<h2>WEEK 8</h2><br />
<div class="box"> <h2>July 25 2013 - July 31 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/9/9e/IMG_2173.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to finish our remaining fusion protein constructs and begin thinking about an SDS PAGE to measure protein expression. We also wanted to dedicate more time to pursuing drylab—making advances on our human practices and continue reading the literature on selective methylation. We also wanted to look into trying out different biobrick parts for our quorum sensing system.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We made advances on our cloning of the constructs for both projects. We completed a LIMS system on a Google spreadsheet that would be used to manage our increasingly overwhelming primers box as well as fixing our minipreps and glycerol stock LIMS and retroactively adding samples. We performed a new induction experiment, inducing our cultures with aTc. </p><br><br />
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<h2>WEEK 9</h2><br />
<div class="box"> <h2>Aug 1 2013 - Aug 7 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/59/IMG_0382.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make advances toward generating our device for the quorum sensing project. We wanted to better budget our remaining resources and stock up on supplies that we would need throughout the rest of the summer. We also wanted to use our zinc finger clone in an induction experiment, similar to the ones we had performed earlier for the quorum sensing project. Additionally, we aimed to generate a growth curve and see how the zinc finger cells would respond to induction. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We met with various professors at the University and made contacts who had knowledge about areas in both projects. We ordered more reagents and created the abstract for our project. We designed primers to attempt to Gibson assemble the Cas construct that had been giving us trouble during USER cloning. We hoped that the new cloning strategy would yield better results. We aliquoted our antibiotics, making boxes full of Kan, Chlor, and Amp to last us the entire summer and well into the year. </p><br><br />
</div><br />
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<div><br />
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<h2>WEEK 10</h2><br />
<div class="box"> <h2>Aug 8 2013 - Aug 14 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/a5/IMG_0501.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to use our restriction digest-based test to analyze how our constructs were working with regards to methylation. We needed to decide on which project we were going to pursue as soon as possible, and we decided this week would be the deadline. We wanted to perform our first SDS Page, which had been in the brainstorming stage for a while. Additionally, we wanted to consult experts about designing better primers and see how we could improve our protocols. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We finally decided to fully pursue the project of constructing targeted methyltransferase fusions. While it was a hard decision, it was necessary to commit our efforts to one project. We also finished our TALE clone and began the induction experiment for testing the methyltransferase fusion. We consulted with designers from the School of Design about making our website and better presentations. We began transforming promoters for an additional screen for methyltransferases that we had envisioned, with the belief that methyltransferases could silence promoters.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 11</h2><br />
<div class="box"> <h2>Aug 15 2013 - Aug 21 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/0/08/PennigemPic11.JPG" width = "600px" ><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to get our Cas construct working after additional drylab work in designing better assembly reactions. We needed to make a detailed plan of where our funds were going to go for the rest of the summer and begin planning our slides for our iGEM presentation. We wanted to decide where we wanted to be by the competition and what we needed to do to get there.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began creating a plan for creating a video about methylation in general and our project specifically. After consulting with our advisors we decided to change the direction of our methyltransferase-DNA binding domain fusion from a two-plasmid to a one-plasmid system that would incorporate a digestion-based assay within the plasmid.</p><br><br />
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<h2>WEEK 12</h2><br />
<div class="box"> <h2>Aug 22 2013 - Aug 28 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/bd/PennigemPic12.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal for this week was to finalize our ideal cloning constructs and figure out how to port what we had already created into the one-plasmid system. We wanted to elaborate more on the assay, as our advisors had emphasized that as one of the more important contributions that our project could make to the synthetic biology community.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We focused on drylab this week, as we needed to get our plans for the rest of the summer set. We worked on a human practices essay about the ethics of targeted methylation in medical therapies. We also began work designing new primers for our revised cloning strategy.</p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 13</h2><br />
<div class="box"> <h2>Aug 29 2013 - Sep 4 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/f/f7/IMG_2180.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal was to once again begin a new cloning strategy focused on assembling our one-plasmid systems. We needed our cloning strategy finalized as soon as possible, and we dedicated the majority of our time this week to streamlining our cloning process.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We began setting up our travel plans to get to the Jamboree. We began the initial stages of cloning our new systems and made substantial progress on cloning our zinc finger and TALE. </p><br><br />
</div><br />
</div><br />
<div><br />
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<h2>WEEK 14</h2><br />
<div class="box"> <h2>Sep 5 2013 - Sep 11 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/a/ad/IMG_0495.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our goal for this week was to make further progress on cloning our constructs. We also wanted to continue our work on the human practices essay, and begin creating a poster presentation for presenting at University research conferences. We also wanted to begin thinking about designing a computer application for analyzing gels.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>During a marathon weekend coding session, we created a program that we called MaGellin that was designed to analyze our gels and characterize the amount of methylation. We attempted to improve our cloning efficiency by utilizing Antarctic Phosphatase within our reactions. We made substantial progress on finishing our TALE and zinc finger constructs, and selected and grew colonies that would be used to test our assay the following week. </p><br><br />
</div><br />
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<div><br />
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<h2>WEEK 15</h2><br />
<div class="box"> <h2>Sep 12 2013 - Sep 18 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/c/c8/Momomomomomomo.JPG" width = "600px""><br />
<br />
<p><b>Goals:<br></b><br />
<p> We wanted to make substantial progress on the website this week. We also wanted to run our assay and test how well our methyltransferase-DNA binding domain fusions had worked. We wanted to work on animation for our video as well as make progress on our human practices essay.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran the assay on the TALE and zinc finger clones, and it yielded promising results. The expression of our fusion protein was a definite achievement. We made substantial progress on the website and essay as well. </p><br><br />
</div><br />
</div><br />
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<h2>WEEK 16</h2><br />
<div class="box"> <h2>Sep 19 2013 - Sep 25 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/5/5e/DSC_0482.JPG" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We needed to finish our website and various forms this week, as well as run our assay in triplicate on the constructs we had created thus far. We needed to plan our remaining time up to the Jamboree, and practice our presentation skills at various outreach events.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We attended several events aimed at recruiting future team members that showed substantial interest in our research and iGEM in general. Our assay returned promising results about the state of our methyltransferase-DNA binding domain fusions. Additionally, we finished the website and filled out all the forms we needed. We have a few experiments still in progress, but our time now is spent preparing for the Jamboree and being ready to present our results. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<br />
<h2>WEEK 17</h2><br />
<div class="box"> <h2>Sep 26 2013 - Oct 2 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/d/d0/Pennigempic1.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> In the week before the Jamboree, we wanted to compile all our last-minute data as well as create our poster and Powerpoint presentation for the competition.</p><br><br />
<p><b>Achievements:<br></b><br />
<p>We gathered a ton of last-minute data this week. The solid deadline put upon us by the Jamboree motivated us all to work as hard as possible to get data worthy of our presentation at the Jamboree. While there's still a lot that we wish to accomplish with our project, we're proud of how far we've made it and hope our hard work pays off at the Jamboree. </p><br><br />
</div><br />
</div><br />
<div><br />
<br />
<h2>WEEK 18 (North America Regionals)</h2><br />
<div class="box"> <h2>Oct 3 2013 - Oct 9 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/3/31/Pennigempic3.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> We just became the Regional Winners for North America for iGEM 2013, but there's no time to rest. Now it's time to get back in the lab and prepare for the World Jamboree. We want to make a game plan for what we are going to accomplish before the World Jamboree at MIT in early November and gather data in areas where we needed more work. We're taking the judge's comments from the regional Jamboree very seriously and attempting to improve our project as much as possible in the coming month. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>We ran our MaGellin assay in a preliminary screening of our cas-methylase fusion and got some activity. We re-ran some previous experiments in triplicate to make the data more compelling. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 19 </h2><br />
<div class="box"> <h2>Oct 10 2013 - Oct 16 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/b3/Pennnotebook2pic.jpg" width = "600px"><br />
<br />
<p><b>Goals: <br></b><br />
<p> We wanted to look further into the possibility of transcriptional silencing using targeted methylation. Additionally, we planned to run the full assay to screen our potential Cas-methylase fusion. Another major priority is to perform bisulfite sequencing to look at the target site for our TALE methylase. </p><br><br />
<p><b>Achievements: <br></b><br />
<p>We continued to reach out to underclassmen and recruit members for the upcoming team. At the same time, we were hard at work in lab, performing our assay and trying to further quantify the extent of methylation in our fusion constructs. We got our bisulfite sequencing for our TALE submitted and are eagerly awaiting the results. </p><br><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 20</h2><br />
<div class="box"> <h2>Oct 17 2013 - Oct 23 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/b/be/Pennnotebook1pic.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> This week we wat to begin utilizing a cell-free system to test our targeted TALE methylase. It is imperative that we give the Wiki a complete design overhaul. We also want to make a plan for the couple weeks. </p><br><br />
<p><b>Achievements:<br></b><br />
<p> This week we were screening our cas methylase and found noticeable activity when done in triplicate with all the proper controls. We experimented with various induction times as well. We re-ran some experiments that had previous flaws or were missing controls in triplicate. We had some additional cloning to do to modify our constructs as well. We gathered data for our 3D plot of induction for our methylase fusion, which was perhaps the most time-consuming experiment we have done all year. </p><br><br />
</div><br />
</div><br />
<div><br />
</div><br />
</div><br />
<div><br />
<h2>WEEK 21</h2><br />
<div class="box"> <h2>Oct 24 2013 - Oct 30 2013</h2><br />
<img class="image" src="https://static.igem.org/mediawiki/2013/4/42/Dannygel.jpg" width = "600px"><br />
<br />
<p><b>Goals:<br></b><br />
<p> Our main goal is to finalize Wiki for World Jamboree and to collect data for any major experiments we still need to wrap up. We also need to begin our poster for the Jamboree and work on our presentation. At the same time, there is a ton of wetlab and experiments that we have planned, all of which are unlikely to get done in the next couple weeks, but that won't stop us from trying. We have several presentations with various labs at Penn, including the epigenetics department this week. </p><br><br />
<p><b>Achievements:<br></b><br />
<p>This week we finished the Wiki for World Competition. Additionally, we began our last set of experiments, for which the data will be revealed at the World Jamboree. </p><br><br />
</div><br />
</div><br />
<div><br />
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<div></div>Bkapturhttp://2013.igem.org/File:PennigemPic11.JPGFile:PennigemPic11.JPG2013-10-27T19:24:03Z<p>Bkaptur: </p>
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<hr />
<div></div>Bkapturhttp://2013.igem.org/Team:Penn/AchievementsTeam:Penn/Achievements2013-10-27T05:47:08Z<p>Bkaptur: </p>
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<header><h1><b><center>Achievements</b></h1></header><br />
<p><!--write accomplishments here--><br />
<br />
<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed the M.sssI methylase and the M.sssI methylase with the linker we used for other teams working with methylases</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
<li><a href="https://twitter.com/NEBiolabs/statuses/390858803836502016">Invited to tour and speak at New England Biolabs about our assay and project</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/2013-penn-igem-team-on-their-regional-championship-victory/">Published on the Mack Institute for Innovation Management website for our regional success</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MethylaseCharacterization">Constructed and screened another novel methylase fusion protein--this one based on Cas9<a></li><br />
<br />
</ol><br />
</p><br />
<!--Text goes here><br />
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</div><br />
</div><br />
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<header><h1><b><center>Achievements</b></h1></header><br />
<p><!--write accomplishments here--><br />
<br />
<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed the M.sssI methylase and the M.sssI methylase with the linker we used for other teams working with methylases</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
<li><a href="https://twitter.com/NEBiolabs/statuses/390858803836502016">Invited to tour and speak at New England Biolabs about our assay and project</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/2013-penn-igem-team-on-their-regional-championship-victory/">Published on the Mack Institute for Innovation Management for our regional success</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MethylaseCharacterization">Constructed and screened another novel methylase fusion protein--this one based on Cas9<a></li><br />
<br />
</ol><br />
</p><br />
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<header><h1><b><center>Achievements</b></h1></header><br />
<p><!--write accomplishments here--><br />
<br />
<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed the M.sssI methylase and the M.sssI methylase with the linker we used for other teams working with methylases</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
<li><a href="https://www.neb.com/">Invited to tour and speak at New England Biolabs about our assay and project</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/2013-penn-igem-team-on-their-regional-championship-victory/">Published on the Mack Institute for Innovation Management for our regional success</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MethylaseCharacterization">Constructed and screened another novel methylase fusion protein--this one based on Cas9<a></li><br />
<br />
</ol><br />
</p><br />
<!--Text goes here><br />
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<header><h1><b><center>Achievements</b></h1></header><br />
<p><!--write accomplishments here--><br />
<br />
<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
<li><a href="https://www.neb.com/">Invited to tour and speak at New England Biolabs about our assay and project</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/2013-penn-igem-team-on-their-regional-championship-victory/">Published on the Mack Institute for Innovation Management for our regional success</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MethylaseCharacterization">Constructed and screened another novel methylase fusion protein--this one based on Cas9<a></li><br />
<br />
</ol><br />
</p><br />
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<title>Penn iGEM</title><br />
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<header><h1><b><center>Achievements</b></h1></header><br />
<p><!--write accomplishments here--><br />
<br />
<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
<li><a href="https://www.neb.com/">Invited to tour and speak at New England Biolabs about our assay and project</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/2013-penn-igem-team-on-their-regional-championship-victory/">Published on the Mack Institute for Innovation Management for our regional success</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MethylaseCharacterization">Constructed and screened another novel methylase fusion protein; this one is based on Cas9<a></li><br />
<br />
</ol><br />
</p><br />
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<header><h1><b><center>Achievements</b></h1></header><br />
<p><!--write accomplishments here--><br />
<br />
<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
<li><a href="https://www.neb.com/">Invited to tour and speak at New England Biolabs about our assay and project.</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/2013-penn-igem-team-on-their-regional-championship-victory/">Published on the Mack Institute for Innovation Management for our regional success.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MethylaseCharacterization">Constructed and screened another novel methylase fusion protein; this one is based on Cas9.<a></li><br />
<br />
</ol><br />
</p><br />
<!--Text goes here><br />
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</div><br />
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<header><h1><b><center>Achievements</b></h1></header><br />
<p><!--write accomplishments here--><br />
<br />
<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
<li><a href="https://www.neb.com/">Invited to tour and speak at New England Biolabs about our assay and project.</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/2013-penn-igem-team-on-their-regional-championship-victory/">Published on the Mack Institute for Innovation Management for our regional success.</a></li><br />
<br />
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<header><h1><b><center>Achievements</b></h1></header><br />
<p><!--write accomplishments here--><br />
<br />
<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
<li><a href="https://www.neb.com/">Invited to tour and speak at New England Biolabs about our assay and project.</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/2013-penn-igem-team-on-their-regional-championship-victory/">Our regional success was published on the Mack Institute website.</a></li><br />
<br />
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<!--Text goes here><br />
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<header><h1><b><center>Achievements</b></h1></header><br />
<p><!--write accomplishments here--><br />
<br />
<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
<li><a href="https://www.neb.com/">Invited to tour and speak at New England Biolabs about our assay and project.</a></li><br />
<br />
</ol><br />
</p><br />
<!--Text goes here><br />
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<header><h1><b><center>Achievements</b></h1></header><br />
<p><!--write accomplishments here--><br />
<br />
<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
<br />
</ol><br />
</p><br />
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<p><!--write accomplishments here--><br />
<h2>Achievements</h2><br />
<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
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<h2>Accomplishments:</h2><br />
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<header><h1><b><center><!--Header goes here--></center></b></h1></header><br />
<p><!--write accomplishments here--><br />
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<br/><b><br />
Our goal was to enable epigenetic engineering. We believe synthetic biological systems should be as subtle and robust as their naturally occurring counterparts. Moreover, we wanted to begin development on much-needed second-generation epigenetic therapeutics.</b><br/><br />
<br />
<ol><br />
<li><a href="https://2013.igem.org/Team:Penn/FusionMotivation">Designed a functional fusion protein to facilitate epigenetic engineering, with numerous advantages over existing technologies</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinMotivation">Validated a novel methylation assay, MaGellin, to accelerate development of epigenetic engineering tools</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/MaGellinSoftware">Built a complementary MaGellin software package to automate experimental analysis</a></li><br />
<li><a href="https://dl.dropboxusercontent.com/u/11828463/MaGellin%20Spec%20Sheet.pdf">Created a specification sheet for the MaGellin Assay workflow, to facilitate quick epigenetic assay studies.</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Biobricks">BioBrick'ed our MaGellin plasmid so other iGEM teams can build off our work</a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Too_Soon_To_Treat">Wrote an article on the ethical implications of epigenetic interventions, accepted for publication in the "nation's premier peer-reviewed undergraduate bioethics journal" </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/LIMS">Developed an open-source Laboratory Information Management System to help teams keep their labs organized </a></li><br />
<li><a href="https://2013.igem.org/Team:Penn/Outreach">Promoted iGEM, synthetic biology, and our research at numerous outreach events to inspire future scientists</a></li><br />
<li><a href="http://mackinstitute.wharton.upenn.edu/2013/its-not-all-in-the-dna-penn-team-benefits-from-mack-institute-sponsorship-in-synthetic-biology-competition/">Featured in an interview</a></li><br />
<li><a href="https://2013.igem.org/Jamborees">North American regional winners and winners of Best BioBrick Measurement Approach award for our gel-electrophoresis assay.</a></li><br />
<br />
</ol><br />
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