Team:KULeuven

   



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Our wiki has been frozen. For future updates we advise you to redirect to iGEM's Main Page. To follow our adventure at the Jamboree in Boston, keep an eye on our online BLOG</a>.

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Welcome to the KULeuven IGEM 2008 Homepage! Enjoy the hard work we delivered, feel free to contact us at igem@kuleuven.be</a> and visit our university/sponsor (BioSCENTer</a>) iGEM page</a>!

Synthetic Biology: BioSCENTer and iGEM <ul> <li> On Synthetic Biology </a></li> <li> On IGEM </a></li> </ul>

Synthetic biology</a> 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. ...</a> <li>Read the whole page</a></li> </ul>

<img class="floatright" src="http://2008.igem.org/wiki/images/1/1e/IGEM_logo_1.png" /> The international Genetically Engineered Machine competition (iGEM) or iGEM competition</a> 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</a>. 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. <li>Read the whole page</a></li> <li>More on our team</a></li> </ul>

Leuven <ul> <li> KULeuven </a></li> </ul>

<img class="floatright" width="300" heigth="300" src="http://2008.igem.org/wiki/images/5/59/Leuven_by_night.jpg" /> The University of Leuven was founded almost six hundred years ago. Throughout the centuries people have always occupied center stage at the Katholieke Universiteit 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. 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 <ul> <li> Meet the team </a></li> </ul>

The KULeuven team consists of 12 enthusiastic students selected out of three faculties, 4 civil engineers, 4 bio-engineers and 4 biochemists. More information on the team members can be found on the Students page</a> or by scrolling over the heads of the students. function haxbackground{ document.getElementById('cartoonmap').style.backgroundImage='url(http://2008.igem.org/wiki/images/1/17/StudentsKULBlackWhite.JPG)'; } function unhaxbackground{ document.getElementById('cartoonmap').style.backgroundImage="url('http://2008.igem.org/wiki/images/5/57/StudentsKUL.JPG')"; }

<dt>Maarten Breckpot</dt> <a href="http://2008.igem.org/User:Maarten" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Maarten Breckpot <font size="2.5">Studies:  1st Master of Applied Sciences and Engineering – Mathematical Engineering <font size="2.5">Country:  Belgium </a></dd>

<dt>Nick Van Damme</dt> <a href="http://2008.igem.org/User:Nickvd" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Nick Van Damme <font size="2.5">Studies:  1st Master of Applied Sciences and Engineering – Mathematical Engineering <font size="2.5">Country:  Belgium </a></dd>

<dt>Benjamien Moeyaert</dt> <a href="http://2008.igem.org/User:Bmoeyaert" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Benjamien Moeyaert <font size="2.5">Studies:  3rd Bachelor of Biochemistry and Biotechnology <font size="2.5">Country:  Belgium </a></dd>

<dt>Stefanie Roberfroid</dt> <a href="http://2008.igem.org/User:Stefanie" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Stefanie Roberfroid <font size="2.5">Studies:  3rd Bachelor of Bioscience Engineering – Biomolecular Engineering <font size="2.5">Country:  Belgium </a></dd>

<dt>Dries Vercruysse</dt> <a href="http://2008.igem.org/User:Dries" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Dries Vercruysse <font size="2.5">Studies:  1st Master of Applied Sciences and Engineering - Nanoscience and Nanotechnology <font size="2.5">Country:  Belgium </a></dd>

<dt>Andim Doldurucu</dt> <a href="http://2008.igem.org/User:Andim" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Andim Doldurucu <font size="2.5">Studies:  1st Master of Bioscience Engineering – Nanoscience and Nanotechnology <font size="2.5">Country:  Turkey </a></dd>

<dt>Hanne Tytgat</dt> <a href="http://2008.igem.org/User:Hanne" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Hanne Tytgat <font size="2.5">Studies:  3rd Bachelor of Biochemistry and Biotechnology <font size="2.5">Country:  Belgium </a></dd>

<dt>Elke Van Assche</dt> <a href="" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Elke Van Assche <font size="2.5">Studies:  3rd Bachelor of Bioscience Engineering – Biomolecular Engineering <font size="2.5">Country:  Belgium </a></dd>

<dt>Jan Mertens</dt> <a href="http://2008.igem.org/User:Jotaro" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Jan Mertens <font size="2.5">Studies:  1st Master of Bioscience Engineering – Biomolecular Engineering <font size="2.5">Country:  Belgium </a></dd>

<dt>Nathalie Busschaert</dt> <a href="http://2008.igem.org/User:BNathalie" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Nathalie Busschaert <font size="2.5">Studies:  3rd Bachelor of Chemistry <font size="2.5">Country:  Belgium </a></dd>

<dt>Jonas Demeulemeester</dt> <a href="http://2008.igem.org/User:Zeunas" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Jonas Demeulemeester <font size="2.5">Studies:  1st Master of Biochemistry and Biotechnology <font size="2.5">Country:  Belgium </a></dd>

<dt>Antoine Vandermeersch</dt> <a href="http://2008.igem.org/User:Avdmeers" onmouseover="haxbackground;" onmouseout="unhaxbackground;"> Antoine Vandermeersch <font size="2.5">Studies:  2nd and 3rd Bachelor of Applied Sciences and Engineering – Electrical and Materials Engineering <font size="2.5">Country:  Belgium </a></dd> </dl>

The Project <ul> <li><a href="#project-1"> Project </a></li> </ul>

Our team’s project is Dr. Coli, an E. coli bacterium that produces a drug when and where it is needed in the human body. It does this in an intelligent way, such that the drug production meets the individual patient’s needs. And when the patient is cured, Dr. Coli eliminates itself from the body. To achieve this goal we divided our project into several subsystems. A detailed description about every subsystem can be found by clicking on one of the following pictograms. <a href="http://2008.igem.org/Team:KULeuven/Project/Input"> <img src="http://2008.igem.org/wiki/images/a/a9/Pictogram_input.png" width="50" height="50" onmouseover="CngTxt('Txt','INPUT: 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="http://2008.igem.org/Team:KULeuven/Project/Output"> <img src="http://2008.igem.org/wiki/images/d/db/Pictogram_output.png" width="50" height="50" onmouseover="CngTxt('Txt','OUTPUT: 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')" > </a> <a href="href="http://2008.igem.org/Team:KULeuven/Project/Filter"> <img src="http://2008.igem.org/wiki/images/e/ed/Pictogram_filter.png" width="50" height="50" onmouseover="CngTxt('Txt','FILTER: 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')" > </a> <a href="http://2008.igem.org/Team:KULeuven/Project/Inverter"> <img src="http://2008.igem.org/wiki/images/e/e7/Pictogram_inverter.png" width="50" height="50" onmouseover="CngTxt('Txt','INVERTIMER: 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')" > </a> <a href="http://2008.igem.org/Team:KULeuven/Project/Reset"> <img src="http://2008.igem.org/wiki/images/e/ed/Pictogram_reset.png" width="50" height="50" onmouseover="CngTxt('Txt','RESET: 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')" > </a> <a href="http://2008.igem.org/Team:KULeuven/Project/CellDeath"> <img src="http://2008.igem.org/wiki/images/c/c6/Pictogram_celldeath.png" width="50" height="50" onmouseover="CngTxt('Txt','CELL DEATH: 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')" > </a> <a href="http://2008.igem.org/Team:KULeuven/Project/Memory"> <img src="http://2008.igem.org/wiki/images/c/c2/Pictogram_memory.png" width="50" height="50" onmouseover="CngTxt('Txt','MEMORY: 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')" > </a>

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Modeling <ul> <li><a href="#modeling-1"> Introducing engineering </a></li> <li><a href="#modeling-2"> Adding reality </a></li> <li><a href="#modeling-3"> Assembling the model </a></li> </ul>

<img class="floatright" width="140" heigth="170" src="http://2008.igem.org/wiki/images/4/4e/Model_homepage.PNG" /> 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="http://2008.igem.org/Team:KULeuven/Model/Overview">modeling</a>. Our Dry-Lab team has spent 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="http://2008.igem.org/Team:KULeuven/Model/FullModel">full model</a> of Dr. Coli. These models are only capable of simulating the behaviour of one Dr. Coli cell, so we implemented our own Software Tool that can work with <a href="http://2008.igem.org/Team:KULeuven/Model/MultiCell">multi cellular models</a>.

<p style="text-align:center"> <img src="http://2008.igem.org/wiki/images/8/86/5652strip.gif" border="0" alt="Parameters are everything" /> After building the model frame, it was time to add the physical relevance to it. Kinetic constants were searched for and investigated by means of previous iGEM teams (e.g. <a href="http://2007.igem.org/title=ETHZ/Parameters">ETHZ 2007</a>), the parts characterizations on the Registry of Standard Biological Parts and popular biological literature databases such as <a href="http://www.hubmed.org">Hubmed</a>, ... Our own contribution would revolve around <a href="http://2008.igem.org/Team:KULeuven/Data/Overview">data analysis</a> of the produced parts.

<p style="text-align:center"> <img src="http://2008.igem.org/wiki/images/f/f8/10797strip.gif" border="0" alt="Dilbert.com" /> Working with concepts as modularity and abstraction, we worked out every subsystem (Output, Memory, Filter, ...) to eventually merge them all in our <a href="http://2008.igem.org/Team:KULeuven/Model/FullModel">full model</a>. By trial and error the system was adapted to achieve desired output quantities (amount of molecules, proteins, ...) given a representative input. To take it a step further, a <a href="http://2008.igem.org/Team:KULeuven/Model/MultiCell">multi-cell model</a> was build, to analyse crucial steps in cell division (e.g. Memory inheritance). A <a href="http://2008.igem.org/Team:KULeuven/Model/Diffusion">diffusion model</a> was made to investigate HSL diffusion towards neighbouring cells and see what effects this generated on their <a href="http://2008.igem.org/Team:KULeuven/Project/Inverter">Invertimer</a> system.

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Interesting Links <ul class="external-links"> <li>Synthetic Biology comic</li> <li>Registry of Standard Biological Parts</li> <li>BioSCENTer</li> </ul> <ul class="general-links"> <li>KUL MultiCell Toolbox</li> <li>KUL Simbiology2LaTeX Toolbox</li> <li>KUL Dropdown (utility)</li> <li>KUL Notebook (utility)</li> </ul>

Fun Stuff

<a href="http://2008.igem.org/wiki/images/5/50/Microbe-kombat.swf" onClick="return popup(this,'notes')"><img src="http://2008.igem.org/wiki/images/a/aa/Microbe-kombat.png">Microbe Kombat</a>

<a href="http://2008.igem.org/wiki/images/8/81/Bacteria.swf" onClick="return popup(this,'notes')"><img src="http://2008.igem.org/wiki/images/1/10/Bacteria_Cannibals.png">Bacteria Cannibals</a>

<a href="http://2008.igem.org/wiki/images/4/46/Dna-double_helix.swf" onClick="return popup(this,'notes')"><img src="http://2008.igem.org/wiki/images/1/1b/Helix-intro.png">Double Helix</a>

<a href="http://2008.igem.org/wiki/images/f/f6/Bacteria_pairs.swf" onClick="return popup(this,'notes')"><img src="http://2008.igem.org/wiki/images/e/e5/Bacteria_pairs.PNG">Bacteria Pairs</a>

<a href="http://2008.igem.org/wiki/images/8/85/Bacteria_solitaire.swf" onClick="return popup(this,'notes')"><img src="http://2008.igem.org/wiki/images/d/d9/Bacteria_solitaire.PNG">Bacteria Solitaire</a>

<a href="http://2008.igem.org/wiki/images/1/12/MathAttack.swf" onClick="return popup(this,'notes')"><img src="http://2008.igem.org/wiki/images/e/e7/Math_Attack.png">Math Attack</a>

<ul class="general-links"> <li><a href="http://www.youtube.com/watch?v=x5yPkxCLads" target="blank">PCR song</a></li> </ul>

Notebook (August)

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