Team:KULeuven

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Welcome to the KULeuven 2008 iGEM team page!

Welcome on the homepage of the iGEM 2008 team of the Katholieke Universiteit Leuven. We are the first Belgian team that takes part in this exciting competition and are supported by the newly founded BioSCENTer research institute. You can take a look at our team and project on the (what did you think) The Team and The Project pages, you'll find respectively our pictures and a detailed project description there. If you have some time, also take a look at the Modelling tab, where you can find some very good examples of how biological systems can and should be correctly modelled in CellDesigner or Matlab. Every day, you can find an update of that day's work on the reports in the Notebook tab.

Synthetic biology is a new challenge in biosciences. It combines biology and engineering principles to design and build new biological functions and systems. Examples are abound: cancer cell invading bacteria, microbes that take pictures, antimalarial drug producers,... The advantage of using living systems for these purposes is that, once they are designed and built, they are self-reproducible. The challenge, however lies exactly within the design and construction: making biological circuits and devices as robust and predictive as their electrical counterparts. ...

Read the whole page

The international Genetically Engineered Machine competition (iGEM) or iGEM competition is a synthetic biology competition for multidisciplinary teams of undergraduate students. It was first organized in 2004 by Drew Endy, Randy Rettberg and Tom Knight of MIT with two goals in mind: to yield new ideas in synthetic biology and to form the future researchers in this new scientific community. Whereas 5 US teams competed in 2004, the 2007 edition already had 750 students and advisors grouped in 54 teams from 19 countries. This year, the competition already counts 83 teams!

The core of the iGEM competition is to design and build a “new genetic machine” with BioBricks. BioBricks are standardized, off the shelf biological parts that are used by genetic network designers. All BioBricks that were made during previous iGEM competitions are registered and documented in the Registry of Standard Biological Parts. Each iGEM competition thus starts from the efforts of the previous years.

Leuven

KULeuven

The University of Leuven was founded almost six hundred years ago. Throughout the centuries people have always occupied center stage at the Catholic University of Leuven. The University's academic fame has attracted scholars and scientists as Justus Lipsius, Gerard Mercator and Andreas Vesalius who have all made valuable contribution to the European intellectual life. The University of Leuven can look back on a glorious past, but it also moves with the times. The University's educational concept is modern, with research activities focused on the needs and aspirations of contemporary people and society. The University of Leuven is famous not just within the borders of Belgium, but far beyond as well. Being a very lively city of and for students, Leuven aspires to maintain that reputation. In contrast to most university cities, Leuven does not have a closed campus. The University buildings are spread throughout the city and were originally built for completely different purposes.

The Team

Meet the team

The KULeuven team consists of 12 enthusiastic students selected out of three faculties, 4 civil engineers, 4 bio-engineers and 4 biochemists.

Maarten Breckpot: Maarten Breckpot

Studies:
1st Master of Applied Sciences and Engineering – Mathematical Engineering
Country:
Belgium
Nick Van Damme: Nick Van Damme

Studies:
1st Master of Applied Sciences and Engineering – Mathematical Engineering
Country:
Belgium
Benjamien Moeyaert: Benjamien Moeyaert

Studies:
3rd Bachelor of Biochemistry and Biotechnology
Country:
Belgium
Stefanie Roberfroid: Stefanie Roberfroid

Studies:
3rd Bachelor of Bioscience Engineering – Biomolecular Engineering
Country:
Belgium
Dries Vercruysse: Dries Vercruysse

Studies:
1st Master of Applied Sciences and Engineering - Nanoscience and Nanotechnology
Country:
Belgium
Andim Doldurucu: Andim Doldurucu

Studies:
1st Master of Bioscience Engineering – Nanoscience and Nanotechnology
Country:
Turkey
Hanne Tytgat: Hanne Tytgat

Studies:
3rd Bachelor of Biochemistry and Biotechnology
Country:
Belgium
Elke Van Assche: Elke Van Assche

Studies:
3rd Bachelor of Bioscience Engineering – Biomolecular Engineering
Country:
Belgium
Jan Mertens: Jan Mertens

Studies:
1st Master of Bioscience Engineering – Biomolecular Engineering
Country:
Belgium
Nathalie Busschaert: Nathalie Busschaert

Studies:
3rd Bachelor of Chemistry
Country:
Belgium
Jonas Demeulemeester: Jonas Demeulemeester

Studies:
1st Master of Biochemistry and Biotechnology
Country:
Belgium
Antoine Vandermeersch: Antoine Vandermeersch

Studies:
2nd and 3rd Bachelor of Applied Sciences and Engineering – Electrical and Materials Engineering
Country:
Belgium

The Project

Project

Our project consists of several subsystems. A detailed description about every subsystem can be found by clicking on one of the following pictograms

scroll over the pictograms to get a short description or click on them to go to the corresponding page

Modeling

Introducing engineering
Quest for parameters
Building the model

The most important assets of our project are the different control mechanisms. Since these are very much dependent on kinetic and other constants, Dr. Coli heavily relies on proper modeling. Our Dry-Lab team has spend its summer setting up a computational model of Dr. Coli to completely simulate his actions. We constructed models of all the subsystems (components) in both CellDesigner and Matlab. All these subsystems have been characterised by their ODE's and have been simulated thoroughly. Together they form our full model of Dr. Coli. These models are only capable of simulating the behaviour of 1 Dr. Coli cell, so we implemented our own Software Tool that can work with multi cellular models.

Nr of visitors:

@@ Line 133: / Line 133: @@
 <img class="floatright" width="300" heigth="300" src="https://static.igem.org/mediawiki/2008/5/59/Leuven_by_night.jpg" />
 <p>
-The University of Leuven was founded almost six hundred years ago. Throughout the centuries people have always occupied center stage at the Catholic University of Leuven.
+The University of Leuven was founded almost six hundred years ago. Throughout the centuries people have always occupied center stage at the <a href="http://www.kuleuven.be/english">Catholic University of Leuven</a>.
 The University's academic fame has attracted scholars and scientists as Justus Lipsius, Gerard Mercator and Andreas Vesalius who have all made valuable contribution to the European intellectual life.
 The University of Leuven can look back on a glorious past, but it also moves with the times.
@@ Line 259: / Line 259: @@
 <center>
 <a href="https://2008.igem.org/Team:KULeuven/Project/Input">
-<img src="https://static.igem.org/mediawiki/2008/a/a9/Pictogram_input.png" width="40" height="40"
+<img src="https://static.igem.org/mediawiki/2008/a/a9/Pictogram_input.png" width="50" height="50"
 onmouseover="CngTxt('Txt','<b>INPUT:</b> <br> The input mechanism makes use of the red light detector, used because of the possibility of easy and rapid switching between ON and OFF state. This input serves as a dummy input for e.g. inflammation signaling molecules.')"
 onmouseout="CngTxt('Txt')"
 ></a>
 <a href="https://2008.igem.org/Team:KULeuven/Project/Output">
-<img src="https://static.igem.org/mediawiki/2008/d/db/Pictogram_output.png" width="40" height="40"
+<img src="https://static.igem.org/mediawiki/2008/d/db/Pictogram_output.png" width="50" height="50"
 onmouseover="CngTxt('Txt','<b>OUTPUT:</b> <br> GFP is an easy-to-measure output mechanism. To lower the stability of GFP, the C-terminal LVA tag is applied. This output serves as a dummy output for e.g. peptide drugs.')"
 onmouseout="CngTxt('Txt')"
@@ Line 270: / Line 270: @@
 </a>
 <a href="href="https://2008.igem.org/Team:KULeuven/Project/Filter">
-<img src="https://static.igem.org/mediawiki/2008/e/ed/Pictogram_filter.png" width="40" height="40"
+<img src="https://static.igem.org/mediawiki/2008/e/ed/Pictogram_filter.png" width="50" height="50"
 onmouseover="CngTxt('Txt','<b>FILTER:</b> <br> The filter system is made to make the system irresponsive to background input. We do not want Dr. Coli to react on noise signals. The filter makes use of a coherent feed-forward loop with AND-gate, based on T7 RNA polymerase and the RiboKey/-Lock system.')"
 onmouseout="CngTxt('Txt')"
@@ Line 276: / Line 276: @@
 </a>
 <a href="https://2008.igem.org/Team:KULeuven/Project/Inverter">
-<img src="https://static.igem.org/mediawiki/2008/e/e7/Pictogram_inverter.png" width="40" height="40"
+<img src="https://static.igem.org/mediawiki/2008/e/e7/Pictogram_inverter.png" width="50" height="50"
 onmouseover="CngTxt('Txt','<b>INVERTIMER:</b> <br> For some of the following subsystems, an inverter is needed. It is based on a promoter repressor and also makes use of a C-terminal LVA tag for better responsiveness of the system. This was proven necessary by rigorous modelling.')"
 onmouseout="CngTxt('Txt')"
@@ Line 282: / Line 282: @@
 </a>
 <a href="https://2008.igem.org/Team:KULeuven/Project/Reset">
-<img src="https://static.igem.org/mediawiki/2008/e/ed/Pictogram_reset.png" width="40" height="40"
+<img src="https://static.igem.org/mediawiki/2008/e/ed/Pictogram_reset.png" width="50" height="50"
 onmouseover="CngTxt('Txt','<b>RESET:</b> <br> When input re-emerges during the self-elimination process, the dying process is stopped and reset. This will allow Dr. Coli to come back from its decision of no longer being needed.')"
 onmouseout="CngTxt('Txt')"
@@ Line 288: / Line 288: @@
 </a>
 <a href="https://2008.igem.org/Team:KULeuven/Project/CellDeath">
-<img src="https://static.igem.org/mediawiki/2008/c/c6/Pictogram_celldeath.png" width="40" height="40"
+<img src="https://static.igem.org/mediawiki/2008/c/c6/Pictogram_celldeath.png" width="50" height="50"
 onmouseover="CngTxt('Txt','<b>CELL DEATH:</b> <br> After a longer period without input signal, Dr. Coli decides to stop living because he feels himself no longer necessary. And in fact, as the patient is now cured, he is no longer of any need to the patient.')"
 onmouseout="CngTxt('Txt')"
@@ Line 294: / Line 294: @@
 </a>
 <a href="https://2008.igem.org/Team:KULeuven/Project/Memory">
-<img src="https://static.igem.org/mediawiki/2008/c/c2/Pictogram_memory.png" width="40" height="40"
+<img src="https://static.igem.org/mediawiki/2008/c/c2/Pictogram_memory.png" width="50" height="50"
 onmouseover="CngTxt('Txt','<b>MEMORY:</b> <br> As Dr. Coli does not want to die from the moment he is born, he can memorize whether he has already been active or not. If not, he will not die without input signal, thus being able to live previous to encoutering illness.')"
 onmouseout="CngTxt('Txt')"
@@ Line 334: / Line 334: @@
 <!-- 2.5.3. MODELING: ENGINEERING -->
 <div id="modeling-3">
+<img class="floatright" width="140" heigth="170" src="https://static.igem.org/mediawiki/2008/4/4e/Model_homepage.PNG" />
 <p>
-The most important assets of our project are the different control mechanisms. Since these are very much dependent on kinetic and other constants, Dr. Coli heavily relies on proper modeling.
+The most important assets of our project are the different control mechanisms. Since these are very much dependent on kinetic and other constants, Dr. Coli heavily relies on proper <a href="https://2008.igem.org/Team:KULeuven/Modeling/Overview">modeling</a>. Our Dry-Lab team has spend its summer setting up a computational model of Dr. Coli to completely simulate his actions. We constructed models of all the subsystems (components) in both CellDesigner and Matlab. All these subsystems have been characterised by their ODE's and have been simulated thoroughly. Together they form our <a href="https://2008.igem.org/Team:KULeuven/Model/FullModel">full model</a> of Dr. Coli. These models are only capable of simulating the behaviour of 1 Dr. Coli cell, so we implemented our own Software Tool that can work with <a href="https://2008.igem.org/Team:KULeuven/Model/MultiCell">multi cellular models</a>.
 </p>
 </div>

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