Team:DTU Denmark

From 2009.igem.org

(Difference between revisions)
 
(92 intermediate revisions not shown)
Line 1: Line 1:
 +
[[image:wiki banner_967px.png]]
 +
<html>
<html>
-
<h1><BLINK>Page under construction! Stay tuned for bio-engineering awesomeness!</BLINK></h1>
+
<head>
 +
<title>Welcome to the DTU iGEM wiki!</title>
 +
<style>
 +
#globalWrapper {
 +
background-image: "" !important;
 +
background-repeat: repeat;
 +
 
 +
}
 +
 
 +
.ideasList{
 +
margin-bottom:30px
 +
}
 +
 
 +
ul#sub {
 +
margin:0px;
 +
padding:0px;
 +
font-size:11px;
 +
list-style-image:none;
 +
list-style-type:none;
 +
 
 +
}
 +
 
 +
#sub li { margin-bottom:20px;}
 +
 
 +
#sub li a {
 +
color:#3300FF;
 +
text-decoration:underline;
 +
}
 +
 
 +
#sub li a:hover {
 +
text-decoration:none;
 +
}
 +
 
 +
.links {
 +
width:967px;
 +
background-color:white;
 +
margin-bottom:0px;
 +
}
 +
 
 +
.links tr {
 +
background-color:#660066;
 +
height:30px;
 +
}
 +
 
 +
.links td {
 +
padding: 0;
 +
}
 +
 
 +
 
 +
.links a{
 +
display: block;
 +
width: 130px;
 +
height: 100%;
 +
margin: 0;
 +
text-align: center;
 +
text-decoration: none;
 +
font-size: 15px;
 +
color: #fff;
 +
}
 +
 
 +
.links a:active {
 +
}
 +
 
 +
.links a:hover {
 +
background-color: #660066;
 +
}
 +
 
 +
 
 +
 
 +
#header {
 +
width: 100%;
 +
text-align: left;
 +
}
 +
 
 +
h4 {
 +
font-size: 13pt;
 +
font-weight: normal;
 +
}
 +
 
 +
dt {
 +
font-size: 12pt;
 +
}
 +
 
 +
#projectnav h4 {
 +
padding: .4ex;
 +
}
 +
 
 +
#projectnav dt {
 +
font-weight: normal;
 +
margin: 1.5ex 0 0 0;
 +
}
 +
 
 +
#projectnav h4, #projectnav dt, #projectnav dd {
 +
text-align: left;
 +
text-indent: 0;
 +
margin-left: 0;
 +
}
 +
 
 +
#hbnav dd {
 +
padding: .8ex;
 +
}
 +
 
 +
#denav dd{
 +
padding: 1ex;
 +
margin-top: 0;
 +
}
 +
 
 +
#projectnav a {
 +
color: #696969;
 +
}
 +
 
 +
#pagecontent p {
 +
text-indent: 1.25em;
 +
}
 +
 
 +
p.start:first-line {
 +
font-weight: bold;
 +
letter-spacing: 1.2;
 +
}
 +
 
 +
.greybox {
 +
background-color: #DDDDDD;
 +
}
 +
 
 +
</style>
 +
<! -- END of style sheet -->
 +
 
 +
</head>
 +
<body>
 +
 
 +
<!-- First table displays centered iGEM 2009 Logo --> 
 +
<div id="header">
 +
<img src="wikibanner.jpg" />
 +
</div>
 +
 
 +
<!-- Table displaying top row of links -->
 +
<table class="links" >
 +
  <tr>
 +
    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark" >Home</a></font> </td>
 +
    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark/team" >The Team</a> </font></td>
 +
    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark/project" >The Project</a> </font></td>
 +
    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark/parts" >Parts submitted</a> </font></td>
 +
    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark/modelling">Modelling</a></font> </td>
 +
    <td align="center" ><font face="arial" size="3"><a class="mainLinks" href="https://2009.igem.org/Team:DTU_Denmark/notebook" title="Day to day lab activity">Notebook</a>
 +
 
 +
</font></td>
 +
  </tr>
 +
</table>
 +
 
 +
<table> <!-- Table for content area -->
 +
 
 +
 
 +
<!-- Main content area -->
 +
 
 +
<table cellpadding=10px>
 +
<tr>
 +
  <td width="163px" height="100%" valign="top">
 +
  <font color="#990000" face="arial" size="3">
 +
  <br>
 +
    Sponsors and acknowledgements<br><br>
 +
  <font color="DDDDDD" face="arial" size="2">
 +
    <a href="https://2009.igem.org/Team:DTU_Denmark/sponsors" CLASS=leftbar>- List of sponsors</a><br>
 +
    <a href="https://2009.igem.org/Team:DTU_Denmark/acknowledgement" CLASS=leftbar>- Acknowledgement</a><br>
 +
  </font>
 +
<br>
 +
<font color="#990000" face="arial" size="3">
 +
<br>   
 +
Also check out our Danish website<br><br>
 +
  </font>
 +
  <font color="DDDDDD" face="arial" size="2">
 +
    <a href="http://www.bio.dtu.dk/igem.aspx" target="_blank" CLASS=leftbar>- DTU iGEM 2009</a><br>
 +
    <br>
 +
  </font>
 +
  </td>
 +
  <td width="556px" height="100%" valign="top">
 +
  <font color="#990000" face="arial" size="5">
 +
<br> 
 +
<b>DTU DENMARK</b><br><br>
 +
  </font>
 +
  <font color="#333333" face="arial" size="2.5">
 +
 
 +
 
 +
<!-- INSERT MAIN TEXT HERE! (formatting: <b>bold</> <i>italic> <h4>header</h4>) -->
 +
 
 +
<p align="justify">Welcome to the DTU-DENMARK iGEM team wiki. Here we present everything about our project, the team, how we have contributed to improve the registry of standard biological parts, and much more.
 +
<br><br>
 +
 
 +
<font size="3"><b>The Project</b></font><br>
 +
 
 +
In <a href="https://2009.igem.org/Team:DTU_Denmark/project"> this project</a> we have<br>
 +
</html>
 +
*Designed and constructed a redox sensing device: The Redoxilator<br>
 +
*Performed extensive mathematical modelling on the operation of the Redoxilator device<br>
 +
*Written and submitted a novel biobrick assembly standard based on USER fusion that allows the assembly of several biobricks at once<br>
 +
*Made a program for the design of primers needed for USER fusion online: PHUSER<br>
 +
<html>
 +
 
 +
<br>
 +
Furthermore we have constructed and submitted <a href="https://2009.igem.org/Team:DTU_Denmark/parts">four very useful biobricks</a> to the registry.
 +
<br><br>
 +
 
 +
 
 +
</p>
 +
<p align="justify"><font size="3"><b>The Team</b></font><br>
 +
Our team consists of six students in biotechnology and systems biology engineering, and we are the first team from the Technical University of Denmark. Please check out our <a href="https://2009.igem.org/Team:DTU_Denmark/team">team page</a> to read more about us and our advisors.
 +
 
 +
</html>
 +
[[Image:Front_figure-v5.png|512px|frameless|center|]]
 +
<html>
 +
 
 +
</p>
 +
<p align="justify"><i>The project has been done by a synthetic biology approach, and genetic components from diverse organisms have been assembled to build a genetic device. Synthetic biology is an increasingly significant area of research that can broadly be defined as an engineering approach to biology, with the goal of designing and implementing new cellular behaviors.</i>
 +
 
 +
 
 +
 
 +
 
 +
  </font>
 +
</td>
 +
<td width="182px" height="100%" valign="top" class="greybox">
 +
  <font face="arial" size="2">
 +
 
 +
<!-- INSERT GREY BOX TEXT HERE! (formatting: <b>bold</> <i>italic> <h4>header</h4>) -->
 +
 
 +
<p>
 +
<font size="3"><strong>Achievements</strong></font><br>
 +
<br>
 +
<strong>Redox sensing device</strong><br>
 +
Two novel genes have been designed and synthesized each comprised of 5 genetic elements. Together they function as a device termed the Redoxilator that can sense the internal redox state of a yeast cell, and output a reporter signal. Extensive mathematical modelling was performed to simulate how the construct would operate <i>in vivo</i>.<br>
 +
<br>
 +
<strong>Biobricks</strong><br>
 +
DNA of several new biobricks have been designed and submitted including a yeast optimized GFP reporter protein, a protein degradation sequence and a fast degradable yeast GFP. (Bronze medal)<br>
 +
<br>
 +
We have demonstrated that our USER fusion biobrick works as expected and documented it (silver medal)<br>
 +
<br>
 +
<strong>USER fusion Assembly standard</strong><br>
 +
A new biobrick assembly standard that allows the rapid construction of multi-part devices have been developed and documented. The assembly standard offers many benefits: All restriction sites are allowed, multiple biobricks can be joined in one step, the result is scar-free making it ideal for protein fusions and more. (Gold medal)<br>
 +
<br>
 +
<strong>USER-fusion primer design software</strong><br>
 +
A novel and very useful software tool have been developed that can automatically design the optimal primers for USER fusion assembly of 2-9 biobricks, taking several parameters into account.
 +
</p>
 +
 
 +
  </font>
 +
</td>
 +
</table>
 +
 
 +
<table>
 +
 
 +
<tr height="25px">
 +
<td width="967px" valign="center" align="center">
 +
 
 +
<font face="arial" size="1">
 +
Comments or questions to the team? Please <a href="mailto:igem@bio.dtu.dk" CLASS=email>Email us</a> -- Comments of questions to webmaster? Please <a href="mailto:lronn@bio.dtu.dk" CLASS=email>Email us</a>
 +
</font>
-
<h2>Project description:</h2>
 
-
<h3>The Redoxilator</h3>
+
</td>
 +
</tr>
-
The aim of this project is to model and construct a molecular NAD<sup>+</sup>/NADH ratio sensing system in Saccharomyces cerevisiae by a synthetic biology approach. The sensor will work as an inducible transcription factor, being active only at certain levels of the NAD<sup>+</sup>/NADH ratios. By coupling the sensor to the expression of a yeast optimized fast degradable GFP, the system can be used for monitoring the NAD<sup>+</sup>/NADH redox poise in vivo. Other applications of the system could be heterologous redox coupled protein production in yeast.
+
</table>
-
<h3>The USER fusion standard</h3>
+
</body>
-
Another part of our project is the proposal of a new parts-assembly standard for Biobricks based on USER<sup>TM</sup> cloning. With this technique, not based on restriction enzymes, all parts independent of function can be assembled without leaving any ‘scars’ from the restriction enzyme digestions. Furthermore we will provide a software for easing the process of designing primers for the purpose of USER fusion.
 
</html>
</html>

Latest revision as of 00:32, 22 October 2009

Wiki banner 967px.png

Welcome to the DTU iGEM wiki!

Home The Team The Project Parts submitted Modelling Notebook

Sponsors and acknowledgements

- List of sponsors
- Acknowledgement

Also check out our Danish website

 - DTU iGEM 2009
DTU DENMARK

Welcome to the DTU-DENMARK iGEM team wiki. Here we present everything about our project, the team, how we have contributed to improve the registry of standard biological parts, and much more.

The Project
In this project we have

  • Designed and constructed a redox sensing device: The Redoxilator
  • Performed extensive mathematical modelling on the operation of the Redoxilator device
  • Written and submitted a novel biobrick assembly standard based on USER fusion that allows the assembly of several biobricks at once
  • Made a program for the design of primers needed for USER fusion online: PHUSER


Furthermore we have constructed and submitted four very useful biobricks to the registry.

The Team
Our team consists of six students in biotechnology and systems biology engineering, and we are the first team from the Technical University of Denmark. Please check out our team page to read more about us and our advisors.

Front figure-v5.png

The project has been done by a synthetic biology approach, and genetic components from diverse organisms have been assembled to build a genetic device. Synthetic biology is an increasingly significant area of research that can broadly be defined as an engineering approach to biology, with the goal of designing and implementing new cellular behaviors.

Achievements

Redox sensing device
Two novel genes have been designed and synthesized each comprised of 5 genetic elements. Together they function as a device termed the Redoxilator that can sense the internal redox state of a yeast cell, and output a reporter signal. Extensive mathematical modelling was performed to simulate how the construct would operate in vivo.

Biobricks
DNA of several new biobricks have been designed and submitted including a yeast optimized GFP reporter protein, a protein degradation sequence and a fast degradable yeast GFP. (Bronze medal)

We have demonstrated that our USER fusion biobrick works as expected and documented it (silver medal)

USER fusion Assembly standard
A new biobrick assembly standard that allows the rapid construction of multi-part devices have been developed and documented. The assembly standard offers many benefits: All restriction sites are allowed, multiple biobricks can be joined in one step, the result is scar-free making it ideal for protein fusions and more. (Gold medal)

USER-fusion primer design software
A novel and very useful software tool have been developed that can automatically design the optimal primers for USER fusion assembly of 2-9 biobricks, taking several parameters into account.

Comments or questions to the team? Please -- Comments of questions to webmaster? Please

Retrieved from "http://2009.igem.org/Team:DTU_Denmark"