Team:PennState

Penn State University has participated in the International Genetically Engineered Machines (iGEM) competition for four years as of 2008, and we are excited to participate once more. Our team consists of 5 undergraduate students, one visiting undergrad and one high school student who work independently, coordinated through weekly meetings with our advisers. Check out our Team Page to meet us!

Our main focus for 2008 was the elimination of diauxie in E. coli to create a xylose inducible system independent of glucose regulation. This system could be used for creating more efficient bioproduction by altering the utilization of 5 and 6 carbon sugars. Please check out the links on the left to navigate through our work.

Two other projects begun this year focus on creating biosensors that use human nuclear hormone receptors to recognize potentially harmful compounds. These receptor systems occur naturally in the human body, but our goal is to retain and utilize their functions in E. coli. The links on the left should introduce you to our thought process and progress on each of these projects, and provide a fuller introduction to the topic.

Please explore our website to find out more about us and our projects! If there are any questions or comments about the information on this site please feel free to contact us at gjt5001@psu.edu.

Medal Checklist

Drew Endy On Synthetic Biology

Garrett Tobin On Diauxie Elimination

Sponsors for our team! Thanks so much!

@@ Line 1: / Line 1: @@
 <html>
-<!--
-   Landing page
-   Contains links to all other pages of the site as well as a quick introduction to the projects
-   The aim of this page was to be visually appealing and contain a very small amount of text so that the user would be given a quick introduction to the project. The   user has only to read several lines to get a good grasp of what we did. This will encourage them to explore deeper.
--->
 <head>
-<!--
-   Cascading Style Sheet (CSS) component
-   in plain html style sheets are completely independent of the HTML page but are included in this page to simplify design within a wiki script environment.
-   This section describes the layout, colors and images displayed on the page
--->
 <style>
+#globalWrapper {
+ background-image: url("https://static.igem.org/mediawiki/2008/e/e4/Bglogo.png") !important;
+ background-repeat: repeat;
+}
 .ideasList{
@@ Line 47: / Line 42: @@
 }
-.links td:hover {
+.links td {
-	background-color: rgb(37,169,113);
+ padding: 0;
 }
 .links a{
-	text-decoration:none;
+ display: block;
-	font-size:14px;
+ width: 100%;
-	color: #000;
+ height: 100%;
+ margin: 0;
+ text-align: center;
+ text-decoration: none;
+ font-size: 14px;
+ color: #000;
 }
@@ Line 62: / Line 62: @@
 .links a:hover {
+	background-color: rgb(37,169,113);
 }
 #header {
@@ Line 98: / Line 98: @@
   border-left: dashed #FFF 3px;
   border-right: dashed #FFF 3px;
-  padding: 1em;
+  padding: .8ex;
 }
@@ Line 105: / Line 105: @@
   border-left: dashed #FFF 3px;
   border-right: dashed #FFF 3px;
-  padding: 1em;
+  padding: 1ex;
   margin-top: 0;
 }
@@ Line 115: / Line 115: @@
 #pagecontent p {
   text-indent: 1.25em;
+}
+p.start:first-line {
+ font-weight: bold;
+ letter-spacing: 1.2;
 }
 </style>
@@ Line 124: / Line 129: @@
 <!-- First table displays centered iGEM 2007 Logo -->
 <div id="header">
-  <img src="https://static.igem.org/mediawiki/2008/d/df/Penn_state_igem_logo.JPG" alt="Penn State" />
+  <img src="https://static.igem.org/mediawiki/2008/a/ad/Penn_state_igem_logo2.JPG" alt="Penn State" />
 </div>
@@ Line 130: / Line 135: @@
 <table class="links" >
    <tr>
-     <td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState" >Home</a> </td>
+     <td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState" title="Welcome!">Home</a> </td>
      <td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Team" >The Team</a> </td>
-     <td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Project" >The Project</a> </td>
+     <td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Project" title="Full Abstracts.">The Project</a> </td>
      <td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Parts">Parts</a> </td>
-     <td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Modeling" >Modeling</a> </td>
+     <td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Notebook" title="Day to day lab activity">Notebook</a> </td>
-    <td align="center" ><a class="mainLinks" href="https://2008.igem.org/Team:PennState/Notebook" >Notebook</a> </td>
    </tr>
 </table>
@@ Line 147: / Line 151: @@
 -->
 <td valign="top" width="20%" id="projectnav">
-  <h4 style="margin-top: 0;">Hormone Biosensors</h4>
+  <h4>Diauxie Elimination</h4>
   <dl id="hbnav">
-   <dd><a href="hbintro" title="Intro to Endocrine Disruption, pseudoestrogens, pthalates, nuclear hormone receptors, and our goals">Introduction</a></dd>
+   <dd><a href="https://2008.igem.org/Team:PennState/diauxie/intro">Introduction</a></dd>
-  <dt>Smart Fold</dt>
+   <dd><a href="https://2008.igem.org/Team:PennState/diauxie/TheSystem">The System</a></dd>
-   <dd><a href="smartfold/overview">Overview</a></dd>
+   <dd><a href="https://2008.igem.org/Team:PennState/diauxie/Strategies">Strategies</a></dd>
-   <dd><a href="smartfold/parts" title="Parts submitted to the registry for this project">Parts</a></dd>
+   <dd><a href="https://2008.igem.org/Team:PennState/diauxie/progress">Progress</a></dd>
-   <dd><a href="smartfold/references">References</a></dd>
+   <dd><a href="https://2008.igem.org/Team:PennState/diauxie/conclusions">Conclusions</a></dd>
-  <dt>Nuclear Fusion</dt>
+   <dd><a href="https://2008.igem.org/Team:PennState/diauxie/parts" title="Parts submitted to the registry for diauxie">Parts</a></dd>
-   <dd><a href="fusion/overview">Overview</a></dd>
+   <dd><a href="https://2008.igem.org/Team:PennState/diauxie/references">References</a></dd>
-   <dd><a href="fusion/parts" title="Parts submitted to the registry for this project">Parts</a></dd>
-   <dd><a href="fusion/references">References</a></dd>
   </dl>
-  <h4>Diauxie Elimination</h4>
+  <h4><acronym title="Nuclear Hormone Receptor">NHR Biosensors</acronym><br/></h4>
   <dl id="denav">
-   <dd><a href="diauxie/intro">Introduction</a></dd>
+   <dd><a href="https://2008.igem.org/Team:PennState/NHR/introduction">NHR Introduction</a></dd>
-   <dd><a href="diauxie/overview">Overview</a></dd>
-   <dd><a href="diauxie/parts" title="Parts submitted to the registry for this project">Parts</a></dd>
+   <dd><a href="https://2008.igem.org/Team:PennState/smartfold/overview">Phthalate Biosensor</a></dd>
-  <dd><a href="diauxie/references">References</dd>
+   <dd><a href="https://2008.igem.org/Team:PennState/fusion/overview">BPA Biosensor</a></dd>
   </dl>
 </td>
 <!-- Main content area -->
-<td valign="top" id="pagecontent"><span style="font-size: 16pt">PENN STATE iGEM 2008</span>
+<td valign="top" id="pagecontent" width="80%"><span style="font-size: 16pt">Welcome to Penn State iGEM 2008</span>
   <hr />
- <p>Welcome to the Penn State iGEM 2008 team’s website.  We are currently working hard at a few different projects for this year's competition.  In early May we began brainstorming and came up with a couple of ideas to create biosensors that use human nuclear hormone receptors to recognize potentially harmful ligands. These receptor systems occur naturally in the human body, but our goal is to retain and utilize their functions in <em>Escherichia Coli</em>.  We are also finishing up one of last year's projects which is aimed at creating a more efficient bioproduction process by altering how <em>E. Coli</em> selects between the utilization of 5 and 6 carbon sugars.  Please explore our website to find out more about us and our projects!</p>
+   <p class="start"><a href="http://www.psu.edu" title="Pennsylvania State University" target="_blank">Penn State University</a> has participated in the International Genetically Engineered Machines (iGEM) competition for four years as of 2008, and we are excited to participate once more. Our team consists of 5 undergraduate students, one visiting undergrad and one high school student who work independently, coordinated through weekly meetings with our advisers. Check out our <a href="https://2008.igem.org/Team:PennState/Team" title="Penn State's 2008 iGEM team">Team Page</a> to meet us!</p>
- <p> If there are any questions or comments about the information on this site please contact us at
+  <p><strong>Our main focus for 2008 was the elimination of <a href="https://2008.igem.org/Team:PennState/diauxie/intro">diauxie</a> in <em>E. coli</em> to create a xylose inducible system independent of glucose regulation.</strong> This system could be used for creating more efficient bioproduction by altering the utilization of 5 and 6 carbon sugars. Please check out the links on the left to navigate through our work.</p>
- <a href="mailto:gjt5001@psu.edu" title="email us">gjt5001@psu.edu</a>. </p>
+   <p>Two other projects begun this year focus on creating <a href="https://2008.igem.org/Team:PennState/NHR/introduction"What kind of 'Biosensors' are we talking about?">biosensors</a> that use human nuclear hormone receptors to recognize potentially harmful compounds. These receptor systems occur naturally in the human body, but our goal is to retain and utilize their functions in <em>E. coli</em>. The links on the left should introduce you to our thought process and progress on each of these projects, and provide a fuller introduction to the topic.</p>
+   <p> Please explore our website to find out more about us and our projects! If there are any questions or comments about the information on this site please feel free to contact us at <a href="mailto:gjt5001@psu.edu" title="email us">gjt5001@psu.edu</a>. </p>
- <table style="padding-left: 0">  <!-- change padding to re-indent this content segment -->
-        <tr><td style="padding-top:30px; padding-right:30px" valign="top" width="90%"><span style="font-size:14pt">Hormone Prescreening <em>E. coli</em></span>
-      <hr />
-      <p>Two of our projects aim to construct biosensors which will ultimately serve as a water prescreening tool.  The focus of these biosensors will be to detect phthalates utilization the Peroxisome Proliferator Activated Receptor (PPAR) and detecting Bisphenol A (BPA) by the Estrogen Receptor (ER).  Recently phthalates have been shown to cause negative health effects such as damage to the liver and kidneys and cause birth defects in rodent studies.  Phthalates are introduced into our environment by their use as plastisizers in materials ranging from polyvinyl chloride to nail polish to small toys.  BPA is also found in plastics but instead is used in the synthesis of hard plastics.  Once BPA enters the human body it is confused for estrogen and parallels the effects of estrogen after attaching to the ligand binding region of the ER.  Analytical detection methods for water contamination are compound specific and very costly.  Having a simple and cheap tool to screen for phthalates or BPA as a general class of compounds would eliminate the cost and time involved in detection.</p>
-      <p> We are using two of the natural human nuclear hormone receptor proteins that recognizea large class of ligands, and attempting to express them heterologously in <em>E. Coli</em>.  The complexity of this mammalian protein makes it difficult to express it in a prokaryote.  We have two different strategies to express and use these receptors to detect compounds in <em>E. Coli</em>.  </p>
-      <table> <!-- this table separates content into column-like quadrants -->
+    <span style="font-size: 14pt"><a href="https://2008.igem.org/Team:PennState/MedalChecklist">Medal Checklist</a></span>
-        <tr>
-          <td style="padding-top:30px; padding-right:30px" valign="top" width="45%"><span style="font-size: 14pt">Smart Fold Reporter</span>
+<table>
-            <hr />
-            <img src="picture here" alt="[img]" style="float:left; margin:5px;"/>
-            <p> <em>Smart Fold Reporter</em> is the subproject for the first strategy for expressing hPPARα in <em>E. coli</em>. This project uses altered growth conditions such that this nuclear hormone receptor protein can be successfully expressed and used to transcriptionally report for the presence of phthalates.</p></td>
-          <td style="padding-top:30px; padding-right:30px" valign="top" width="45%"><span style="font-size:18px">Nuclear Fusion</span>
-            <hr />
-            <img src="picture here" alt="[img]" style="float:left; margin:5px;"/>
-            <p> <em> Nuclear Fusion</em> is our second approach to constructing a phthalate detection system in <em> E. coli</em>. In this project we use just the ligand binding domain of hPPARα fused to thymidylate synthase (TS). Binding of the phthalate ligand to this chimeric protein activates TS. When this construct is placed in a TS diffident strain, only <em>E. coli</em> in the presence of a hPPARalpha agonist will survive. </p></td>
-        </tr>
-<tr>
-    <td colspan="2" style="padding-top:30px; padding-right:30px" valign="top" width="45%"><span style="font-size: 14pt">Diauxie Elimination: <em>Two</em> spoons full of sugar.</span>
-      <hr />
-      <p><img src="picture here" alt="[img]" style="float:left; margin:5px;"/>Cellulosic biomass is an abundant and inexpensive energy source, coming from plant waste: ideal for Ethanol production through fermentation. However, biomass contains glucose and xylose sugars in relatively equal ratios, while <em>e. coli</em> preferentially metabolizes glucose before any other sugar. In this project we attempt to eliminate this phenomenon, called <em>diauxie</em>, and get our cells to utilize both sugars at the same time. Solving this problem will lead to more efficent use of cellulosic biomass including moving towards the future of bioproduction: continous processes.</p>
-   </td>
-  </tr>
    <tr>
-    <td style="padding-top:30px; padding-right:30px" valign="top" width="45%"><span style="font-size: 14pt">Quick Links</span>
+    <td style="padding-top:30px; padding-right:30px" valign="top" width="45%">
-            <hr />
+     <h3>Related Links</h3>
-            <br/>
+     <hr />
-            <p><a href="http://parts.mit.edu/igem07/index.php/PennState/final_result#contributions" title="Our Contribution To the Registry">Table of our Contributions to the Registry</a></p>
+     <ul>
-            <p><a href="http://parts.mit.edu/igem07/images/7/73/IgemDesign.swf" title="Interactive Schematic" target="_blank">Interactive <em>E. co</em>Lisa Schematic</a></p>
+       <li><a href="http://partsregistry.org/Main_Page" title="Parts Registry">Parts Registry</a></li>
-            <p> <a href="http://www.psu.edu" title="Pennsylvania State University" target="_blank">Pennsylvania State University</a> </p>
-            <p> <a href="http://www.environment.psu.edu/" title="Penn State Institutes of Energy and the Environment" target="_blank">Penn State Institutes of Energy and the Environment</a> </p>
+<li><a href="http://www.che.psu.edu/Faculty/Cirino/" title="Prof. Pat Cirino's Lab website" target="_blank">Prof. Pat Cirino's Lab website</a></li>
-            </div>
+<li><a href="http://www.abe.psu.edu/fac/Richard/Overview.htm" title="Prof. Tom Richard's Lab website" target="_blank">Prof. Tom Richard's Lab website</a></li>
-          </td>
+<li><a href="http://openwetware.org/wiki/IGEM:PennState" title="Penn State iGEM OpenWetWare" target="_blank">Penn State iGEM OpenWetWare</a></li>
-          <td style="padding-top:30px; padding-right:30px" valign="top" width="45%"><span style="font-size: 14pt">Drew Endy On Synthetic Biology</span>
-            <hr />
+       <li><a href="http://www.princeton.edu/che/people/faculty/wood/" title="David Wood" target="_blank">David Wood</a></li>
-			<!--
+       <li><a href="http://www.cmtc.psu.edu/" title="Center for Molecular Toxicology and Carcinogenesis" target="_blank">PennState Center for Molecular Toxicology and Carcinogenesis</a></li>
-			    This division block contains the code to import and display a flash object
+     </ul>
-				Specifically importing and formatting a video uploaded onto "youtube"
+   </td>
-			-->
+   <td style="padding-top:30px; padding-right:30px" valign="top" width="45%">
+     <h3>Drew Endy On Synthetic Biology</h3>
+       <hr />
+	<!--
+	   This division block contains the code to import and display a flash object
+	   Specifically importing and formatting a video uploaded onto "youtube"
+	-->
              <div style="margin:10px">
-              <object width="200">
-                <param name="movie" value="http://www.youtube.com/v/XIuh7KDRzLk&rel=1">
+<object width="205" height="200">
-                </param>
+<param name="movie" value="http://www.youtube.com/v/XIuh7KDRzLk&hl=en&fs=1"></param><param name="allowFullScreen" value="true">
-                <param name="wmode" value="transparent">
+</param>
-                </param>
+<embed src="http://www.youtube.com/v/XIuh7KDRzLk&hl=en&fs=1" type="application/x-shockwave-flash" allowfullscreen="true" width="205" height="200">
-                <embed src="http://www.youtube.com/v/XIuh7KDRzLk&rel=1" type="application/x-shockwave-flash" wmode="transparent" width="200" ></embed>
+</embed>
-              </object>
+</object>
-             </div></td>
+            </div>
-        </tr>
+    </td>
-      </table>
+<td style="padding-top:30px; padding-right:30px" valign="top" width="45%">
+     <h3>Garrett Tobin On Diauxie Elimination</h3>
+       <hr />
+	<!--
+	   This division block contains the code to import and display a flash object
+	   Specifically importing and formatting a video uploaded onto "youtube"
+	-->
+ <div style="margin:10px">
+    <object width="205" height="200">
+      <param name="movie" value="http://www.youtube.com/v/QA-tETsb3Wo&hl=en&fs=1">
+       </param>
+      <param name="allowFullScreen" value="true">
+       </param>
+      <embed src="http://www.youtube.com/v/QA-tETsb3Wo&hl=en&fs=1" type="application/x-shockwave-flash"  allowfullscreen="true" width="205" height="200">
+       </embed>
+     </object>
+             </div>
+    </td>
+ </tr>
+</table>
 </td></tr></table> <!-- end the table for content quadrants -->
 </td></tr></table> <!-- end content block that is adjacent to sidelinks -->