Difference between revisions of "Team:KU Leuven"

 
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<div id="center">
 
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<h2>Our project</h2>
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<h2>Our Project</h2>
 
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<div class="summary">
 
<div class="summary">
 
<p>
 
<p>
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Patterns are fascinating, from the veins of a leaf to the stripes of a zebra. Patterns are found everywhere in nature, but how they are formed is not entirely understood. We, the KU Leuven 2015 iGEM team, decided to work on the fundamental mechanisms behind pattern formation. The way the cells of multicellular organisms interact to generate a specific pattern has triggered our curiosity. Our mission is to create astonishing biological patterns with engineered bacteria on a petri dish to unravel the secrets of nature. We will design a ‘proof of principle’ which can form the basis for fundamental research.<br>
+
Patterns are fascinating, from the veins of a leaf to the stripes of a zebra. They are everywhere in nature, but why and how they are formed is not entirely understood. The way cells of multicellular organisms interact to generate a specific pattern has triggered our curiosity. We, the KU Leuven 2015 iGEM team, engaged in a project on the regulatory mechanisms of motif formation. Our mission is to engineer bacteria able to communicate and influence each other’s behaviour resulting in the assembly of predictable visible patterns.
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<a href="https://2015.igem.org/Team:KU_Leuven/Project/About"><img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" alt="Read more" height="2.5%" width="10%"></a>
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</p><br />
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<p>
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We designed a system in which two different <i>E. coli</i> cell types A and B, when mixed on an agar plate, organize themselves in a complex pattern. The regulatory circuit controls and steers two bacterial properties: cell-cell interaction and motility. This circuit makes bacterial cells of type A to produce an adherent protein and at the same time repel B-type cells. We expect the development of a pattern, where A-cells are clumping together and B-cells form circles around A-cells. This synthetic bacterial system will provide us with a platform to study the fundamentals of pattern formation. Such synthetic circuits will be useful, e.g., for engineering complex tissues consisting of different cell types.
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</p><br />
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<p>
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A big part of our project is its three layer structure modeling. The colony level considers the bacteria a large group of cells, described by partial differential equations. On the other hand, the internal level describes the interactions within the single cells. Finally, our hybrid model merges both colony and internal level to define the cell-cell interactions of our pattern forming cells. Those models give us even more potential to explain, plan and explore the fascinating, fundamental research of patterns.
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</p><br />
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<!--
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<p>
 +
Patterns are fascinating, from the veins of a leaf to the stripes of a zebra. They are everywhere in nature, but why and how they are formed is not entirely understood. We, the KU Leuven 2015 iGEM team, decided to work on the fundamental mechanisms behind pattern formation. The way the cells of multicellular organisms interact to generate a specific pattern has triggered our curiosity. Our mission is to create astonishing biological patterns with engineered bacteria on a petri dish to unravel the secrets of nature. We design a ‘proof of principle’ which can form the basis for further research.
 +
</p></br>
 +
<p>
 +
We devise a system in which two different cell types A and B of E.Coli form a complex pattern on a petri dish. Our main goal is to design a circuit capable of controlling and steering two bacterial properties essential for pattern formation, namely cell-cell interaction and motility. After a heat induced stimulus, this circuit makes bacterial cells of one type adhere and at the same time these cells repel the other type. We expect to see a pattern where cells A are clumping together and cells B, which are repelled by A, form circles around cells A. Together with possible modulation of certain experimental conditions, this circuit allows the study of pattern formation using synthetic biology in a more general way.
 +
</p></br>
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<p>
 +
In order to give our modeling team the necessary data and parameters, we also create the possibility to get exact numbers by introducing different tags for protein purifications. From recent literature, we also adapt some new measurement techniques in order to better parameterize our models.
 +
</p></br>
 +
<p>
 +
Next to this, we also model the patterns in a three layer structure. The colony level considers the bacteria as a large group of cells, described by partial differential equations. On the other hand, the internal level describes the interactions within the single cells. Finally, our hybrid model merges both colony and internal level to define the cell-cell interactions of our pattern forming cells.
 +
</p></br>
 +
<p>
 +
Simulations from the cyber lab aid the wet lab in tuning the experimental conditions that lead to the desirable patterns. At the same time, results from the lab give the modeling team more data and parameters to fit their models to different conditions. Interaction between wet lab and cyber lab is clearly a crucial factor to the successful design our experiments.
 
</p>
 
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<div class="whiterow">
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<div class="center">
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        <div class="quote" style="width:95%;">
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<p><h2>A last message of the team</h2></p>
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<div class="achieftable'>
 +
<div class="achiefrow">
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<img src="https://static.igem.org/mediawiki/2015/3/39/IGEMKUL.jpeg" style="width:225px;height:400px;overflow:hidden;bottom: 30px;margin:0px 30px 20px 30px" align="left">
 +
</div>
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<p>
 +
<b> We are back from the Jamboree!!! <br> <br>
 +
We were very eager to present our hard work to the jury and we received positive feedback: <br> <br>
 +
First of all, we won a gold medal!!! <br> <br>
 +
And we were nominated for 4 prizes in the Overgrad section: Best Poster, Best Education and Public Engagement, Best Model, and Best New Application Project, for which we were the runner-up! On top of that, we received the Interlab Study Award!<br> <br>
 +
We are very happy with these results and we want to thank everybody who helped us achieve this! Thank you very much for giving us the summer of a lifetime!!! </b> </p>
 +
 +
<p>To view all our achievements press the medal! </p>
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Notebook/Achievements"><img src="https://static.igem.org/mediawiki/2015/8/89/KU_Leuven_Medal_Gold.png" style="margin:20px;width:20%"></a>
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</div>
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</div>
  
 
<div class="whiterow">
 
<div class="whiterow">
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Browsing through iGEM team wiki’s can be a time consuming job. To make this easier and fun we invented a wiki game to help you discover the nook and corner of our wiki. It allows you to get a simple overview of our wiki. <a href="https://2015.igem.org/Team:KU_Leuven/Secret">Play our wiki game!</a>
 
Browsing through iGEM team wiki’s can be a time consuming job. To make this easier and fun we invented a wiki game to help you discover the nook and corner of our wiki. It allows you to get a simple overview of our wiki. <a href="https://2015.igem.org/Team:KU_Leuven/Secret">Play our wiki game!</a>
 
</p>
 
</p>
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</div>
 
  
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</div>
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</div>
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<div class="nontransparent">
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<div class="nonpart">
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<h3><a href="https://2015.igem.org/Team:KU_Leuven/Team">Meet our team</a></h3>
 +
<p>We made a movie to introduce to you our team and our project. Check it out!</p>
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<!-- Video start-->
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            <video id="video" preload="auto" tabindex="0" controls="" type="audio/mpeg" >
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              <source type="video/mp4" src="https://static.igem.org/mediawiki/2015/5/5e/KU_Leuven_TeamVid.mp4">
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              Sorry, your browser does not support HTML5 video.
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            </video>
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      <br/>
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</div>
 
<div class="whiterow">
 
<div class="whiterow">
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</div>
 
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</div>
 
</div>
  
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<a href="https://2015.igem.org/Team:KU_Leuven/Research">
 
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
 
  <h2>Research</h2>
 
  <h2>Research</h2>
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  <p>Swift and smart in actions to design the plasmids, quantify the parameters and to create the patterns. Join us in our exciting journey.
+
  <p>Swift and smart in constructing our gene interaction scheme, plasmids and protein quantification methods. All of this to obtain and understand pattern formation.
 
<br/>
 
<br/>
 
</p>
 
</p>
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<a href="https://2015.igem.org/Team:KU_Leuven/InterLabStudy">
 
<a href="https://2015.igem.org/Team:KU_Leuven/InterLabStudy">
 
  <h2>Interlab</h2>
 
  <h2>Interlab</h2>
−
  <p>Many small steps need to be taken to achieve our goal. We like to keep you informed and welcome you to discover our newsfeed and history.
+
  <p>We decided to contribute to the worldwide fluorescence database. Click here to find more information about the InterLab Study.
 
<br/>
 
<br/>
 
</p>
 
</p>
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<div class="subimg">
 
<div class="subimg">
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<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
+
<a href="https://2015.igem.org/Team:KU_Leuven/Future">
−
  <img src="https://static.igem.org/mediawiki/2015/1/1a/KUL_Wiki_Button_-_Project.png" width="100%">
+
  <img src="https://static.igem.org/mediawiki/2015/4/41/KU_Leuven_Wiki_Button_-_Future2.png" width="100%">
 
</a>
 
</a>
 
</div>
 
</div>
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<a href="https://2015.igem.org/Team:KU_Leuven/Practices">
 
<a href="https://2015.igem.org/Team:KU_Leuven/Practices">
 
  <h2>Outreach</h2>
 
  <h2>Outreach</h2>
−
  <p>Teaching students, iGEM teams and the Belgian public more about synthetic biology and our project.
+
  <p> We informed students, other iGEM teams and the Belgian public more about synthetic biology and our project.
 
<br/>
 
<br/>
 
</p>
 
</p>
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<div class="subtext">
 
<div class="subtext">
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<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
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<a href="https://2015.igem.org/Team:KU_Leuven/Future">
−
  <h2>Project</h2>
+
  <h2>Future</h2>
−
  <p>We decided to work on the fundamental mechanisms behind pattern formation. Our preliminary idea is to design two bacterial strains that can interact with each other.
+
  <p>Does Spot E.Shape only impact the academic environment, or is it likely to be picked up by industry? Click here to find out more about its future potential and applications.  
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<br/>
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</p>  
−
</p>
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</a>
 
</a>
 
</div>
 
</div>
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<div class="subimgrm">
 
<div class="subimgrm">
−
<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
+
<a href="https://2015.igem.org/Team:KU_Leuven/Future">
 
<div id="more">
 
<div id="more">
 
<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="40%" width="85%" alt="Read more">
 
<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="40%" width="85%" alt="Read more">
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</div>
 
</div>
 
</div>
 
</div>
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−
 
−
 
−
 
−
 
−
 
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<div class="subimgrowm">
 
<div class="subimgrowm">
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  <b>Research</b>
 
  <b>Research</b>
 
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
 
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
−
<img src="https://static.igem.org/mediawiki/2015/archive/c/ca/20150807120732%21KU_Leuven_Wiki_Button_-_Wetlab.png" width="100%">
+
<img src="https://static.igem.org/mediawiki/2015/6/63/Wiki_Button_-_Research2.png" width="100%"></a>
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</a>
+
 
</div>
 
</div>
  
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<div class="subtextm">
 
<div class="subtextm">
 
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
 
<a href="https://2015.igem.org/Team:KU_Leuven/Research">
−
<p style='text-align:left'> Each experimental step requires a theoretical background.  This background, the protocols and the results of our experiments can be found in this subsection.
+
<p> Swift and smart in constructing our gene interaction scheme, plasmids and protein quantification methods. All of this to obtain and understand pattern formation.
 
<br/>
 
<br/>
 
</p>
 
</p>
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<div class="subimgm">
 
<div class="subimgm">
 
  <b>Interlab</b>
 
  <b>Interlab</b>
−
<a href="https://2015.igem.org/Team:KU_Leuven/InterladStudy">
+
<a href="https://2015.igem.org/Team:KU_Leuven/InterLabStudy">
 
  <img src="https://static.igem.org/mediawiki/2015/c/c3/KU_Leuven_Wiki_Button_-_Interlab_measurement2.png" width="100%">
 
  <img src="https://static.igem.org/mediawiki/2015/c/c3/KU_Leuven_Wiki_Button_-_Interlab_measurement2.png" width="100%">
 
</a>
 
</a>
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<div class="subtextm">
 
<div class="subtextm">
−
<a href="https://2015.igem.org/Team:KU_Leuven/InterlabStudy">
+
<a href="https://2015.igem.org/Team:KU_Leuven/InterLabStudy">
−
<p style='text-align:left'>We decided to work on the fundamental mechanisms behind pattern formation. To achieve our goal, the link between wet lab and modeling will be crucial to the successful design of our experiments.
+
<p>We decided to contribute to the worldwide fluorescence database. Click here to find more information about the InterLab Study.
 
</p>
 
</p>
 
</a>
 
</a>
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<b>Modeling</b>
 
<b>Modeling</b>
 
<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
 
<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
−
<img src="https://static.igem.org/mediawiki/2015/archive/d/db/20150807120714%21KU_Leuven_Wiki_Button_-_Modelling.png" width="100%">
+
<img src="https://static.igem.org/mediawiki/2015/a/aa/Wiki_Button_-_Modelling2.png" width="100%">
 
</a>
 
</a>
 
</div>
 
</div>
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<div class="whitespace">
 
<div class="whitespace">
 
</div>
 
</div>
−
 
  
 
<div class="subtextm">
 
<div class="subtextm">
 
<a href="https://2015.igem.org/Team:KU_Leuven/Practices">
 
<a href="https://2015.igem.org/Team:KU_Leuven/Practices">
−
<p>Teaching students, iGEM teams and the Belgian public more about synthetic biology and our project.
+
<p>We informed students, iGEM teams and the Belgian public more about synthetic biology and our project.
 
</p>
 
</p>
 
</a>
 
</a>
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<div class="subimgrowm">
 
<div class="subimgrowm">
 
<div class="subimgm">
 
<div class="subimgm">
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  <b>Project</b>
+
  <b>Future</b>
−
<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
+
<a href="https://2015.igem.org/Team:KU_Leuven/Future">
−
  <img src="https://static.igem.org/mediawiki/2015/1/1a/KUL_Wiki_Button_-_Project.png" width="100%">
+
  <img src="https://static.igem.org/mediawiki/2015/4/41/KU_Leuven_Wiki_Button_-_Future2.png" width="100%">
 
</a>
 
</a>
 
</div>
 
</div>
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<div class="subtextm">
 
<div class="subtextm">
−
<a href="https://2015.igem.org/Team:KU_Leuven/Project/About">
+
<a href="https://2015.igem.org/Team:KU_Leuven/Future">
−
<p style='text-align:left'>We decided to work on the fundamental mechanisms behind pattern formation. To achieve our goal, the link between wet lab and modeling will be crucial to the successful design of our experiments.
+
<p>Does Spot E.Shape only impact the academic environment, or is it likely to be picked up by industry? Click here to find out more about its future potential and applications.
 
</p>
 
</p>
 
</a>
 
</a>
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</div>
 
</div>
 
</div>
 
</div>
 +
  
 
<div class="subimgrowm">
 
<div class="subimgrowm">
 
<div class="subimgm">
 
<div class="subimgm">
 
  <b>Team</b>
 
  <b>Team</b>
−
<a href="https://2015.igem.org/Team:KU_Leuven/Team/Members">
+
<a href="https://2015.igem.org/Team:KU_Leuven/Team">
 
  <img src="https://static.igem.org/mediawiki/2015/2/23/KUL_Wiki_Button_-_Team.png" width="100%">
 
  <img src="https://static.igem.org/mediawiki/2015/2/23/KUL_Wiki_Button_-_Team.png" width="100%">
 
</a>
 
</a>
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<div class="subtextm">
 
<div class="subtextm">
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<a href="https://2015.igem.org/Team:KU_Leuven/Team/Members">
+
<a href="https://2015.igem.org/Team:KU_Leuven/Team">
 
<p>Diverse with respect to thoughts, perspectives, nationalities and languages, yet bound together by our enthusiasm for science and research. Would you like to know more about us?
 
<p>Diverse with respect to thoughts, perspectives, nationalities and languages, yet bound together by our enthusiasm for science and research. Would you like to know more about us?
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<br/>
 
 
</p>
 
</p>
 
</a>
 
</a>
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<div class="subimgrowm">
 
<div class="subimgrowm">
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<div class="subimgm">
 
<div class="subimgm">
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<b>Notebook</b>
+
<b>Notebook</b>
 
<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
 
<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
−
  <img src="https://static.igem.org/mediawiki/2015/archive/8/82/20150807120658%21KU_Leuven_Wiki_Button_-_Literature.png" width="100%">
+
  <img src="https://static.igem.org/mediawiki/2015/5/59/Wiki_Button_-_Notebook2.png" width="100%">
 
</a>
 
</a>
 
</div>
 
</div>
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<div class="subtextm">
 
<div class="subtextm">
 
<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
 
<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
−
<p>Many small steps need to be taken to achieve our goal. We like to keep you informed and welcome you to discover our newsfeed and history!
+
<p>Many small steps need to be taken to achieve our goal. We like to keep you informed and welcome you to discover our newsfeed and history.
 
</p>
 
</p>
 
</a>
 
</a>
 
</div>
 
</div>
 +
 +
<div class="subimgrowm">
 +
<div class="whiterow"></div>
 
</div>
 
</div>
 
</div>
 
</div>
 
</div>
 
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</div>
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   <div id="eppendorf">
 
   <div id="eppendorf">
 
       <a href="https://www.eppendorf.com/BE-en/"><img src="https://static.igem.org/mediawiki/2015/9/96/KU_Leuven_Logo_Eppendorf_transparant.png" alt="Eppendorf" width="95%"></a>
 
       <a href="https://www.eppendorf.com/BE-en/"><img src="https://static.igem.org/mediawiki/2015/9/96/KU_Leuven_Logo_Eppendorf_transparant.png" alt="Eppendorf" width="95%"></a>
 +
  </div>
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<div id="saillart">
 +
      <a href="http://www.glasatelier-saillart.be/English/english.html"><img src="https://static.igem.org/mediawiki/2015/c/ce/KU_Leuven_Sponsor_Saillard.png" alt="Glasatelier Saillart" width="95%"></a>
 
   </div>
 
   </div>
 
<div id="kuleuven">
 
<div id="kuleuven">
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       <a><img src="https://static.igem.org/mediawiki/2015/1/15/KUL_Ko-Lo_Instruments_logo_transparant.png" alt="Ko-Lo Instruments" width="95%"></a>
 
       <a><img src="https://static.igem.org/mediawiki/2015/1/15/KUL_Ko-Lo_Instruments_logo_transparant.png" alt="Ko-Lo Instruments" width="95%"></a>
 
     </div>
 
     </div>
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<div id="regensys">
 
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      <a href="http://regenesys.eu/"><img src="https://static.igem.org/mediawiki/2015/e/eb/KU_Leuven_Logo_Regenesys_Transparant.png" alt="Regenesys" width="95%"></a>
 
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       <a href="https://www.bioke.com/"><img src="https://static.igem.org/mediawiki/2015/e/e1/KUL_Biok%C3%A9_logo_transparant.png" alt="Bioké" width="95%"></a>
 
       <a href="https://www.bioke.com/"><img src="https://static.igem.org/mediawiki/2015/e/e1/KUL_Biok%C3%A9_logo_transparant.png" alt="Bioké" width="95%"></a>
 
   </div>
 
   </div>
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<div class="logonormal">
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<div id="regensys">
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      <a href="http://regenesys.eu/"><img src="https://static.igem.org/mediawiki/2015/e/eb/KU_Leuven_Logo_Regenesys_Transparant.png" alt="Regenesys" width="95%"></a>
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  </div>
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<div class="whiterow"></div>
 
   <div id="thermofisher">
 
   <div id="thermofisher">
 
       <a href="https://www.fishersci.com/us/en/home.html"><img src="https://static.igem.org/mediawiki/2015/a/aa/KUL_Fischer_Scientific_logo_transparant.png" alt="Thermo Fisher Scientific" width="95%"></a>
 
       <a href="https://www.fishersci.com/us/en/home.html"><img src="https://static.igem.org/mediawiki/2015/a/aa/KUL_Fischer_Scientific_logo_transparant.png" alt="Thermo Fisher Scientific" width="95%"></a>
 
   </div>
 
   </div>
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</div>
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<div class="logonormal2">
 
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Latest revision as of 01:39, 21 November 2015

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Our Project

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Patterns are fascinating, from the veins of a leaf to the stripes of a zebra. They are everywhere in nature, but why and how they are formed is not entirely understood. The way cells of multicellular organisms interact to generate a specific pattern has triggered our curiosity. We, the KU Leuven 2015 iGEM team, engaged in a project on the regulatory mechanisms of motif formation. Our mission is to engineer bacteria able to communicate and influence each other’s behaviour resulting in the assembly of predictable visible patterns.


We designed a system in which two different E. coli cell types A and B, when mixed on an agar plate, organize themselves in a complex pattern. The regulatory circuit controls and steers two bacterial properties: cell-cell interaction and motility. This circuit makes bacterial cells of type A to produce an adherent protein and at the same time repel B-type cells. We expect the development of a pattern, where A-cells are clumping together and B-cells form circles around A-cells. This synthetic bacterial system will provide us with a platform to study the fundamentals of pattern formation. Such synthetic circuits will be useful, e.g., for engineering complex tissues consisting of different cell types.


A big part of our project is its three layer structure modeling. The colony level considers the bacteria a large group of cells, described by partial differential equations. On the other hand, the internal level describes the interactions within the single cells. Finally, our hybrid model merges both colony and internal level to define the cell-cell interactions of our pattern forming cells. Those models give us even more potential to explain, plan and explore the fascinating, fundamental research of patterns.


A last message of the team

We are back from the Jamboree!!!

We were very eager to present our hard work to the jury and we received positive feedback:

First of all, we won a gold medal!!!

And we were nominated for 4 prizes in the Overgrad section: Best Poster, Best Education and Public Engagement, Best Model, and Best New Application Project, for which we were the runner-up! On top of that, we received the Interlab Study Award!

We are very happy with these results and we want to thank everybody who helped us achieve this! Thank you very much for giving us the summer of a lifetime!!!

To view all our achievements press the medal!

Wiki Game

Browsing through iGEM team wiki’s can be a time consuming job. To make this easier and fun we invented a wiki game to help you discover the nook and corner of our wiki. It allows you to get a simple overview of our wiki. Play our wiki game!

Meet our team

We made a movie to introduce to you our team and our project. Check it out!


Research

Swift and smart in constructing our gene interaction scheme, plasmids and protein quantification methods. All of this to obtain and understand pattern formation.

Interlab

We decided to contribute to the worldwide fluorescence database. Click here to find more information about the InterLab Study.

Modeling

The modeling team will fit models to the data obtained by the wet lab. Continuous and hybrid models will be used. Hybrid models are models which have a discrete and continuous part.

Read more
Read more
Read more

Outreach

We informed students, other iGEM teams and the Belgian public more about synthetic biology and our project.

Future

Does Spot E.Shape only impact the academic environment, or is it likely to be picked up by industry? Click here to find out more about its future potential and applications.

Team

Diverse with respect to thoughts, perspectives, nationalities and languages, yet bound together by our enthusiasm for science and research. Would you like to know more about us?

Notebook

Many small steps need to be taken to achieve our goal. We like to keep you informed and welcome you to discover our newsfeed and history.

Read more
Read more
Read more
Read more
Research

Swift and smart in constructing our gene interaction scheme, plasmids and protein quantification methods. All of this to obtain and understand pattern formation.

Interlab

We decided to contribute to the worldwide fluorescence database. Click here to find more information about the InterLab Study.

Modeling

The modeling team fits models to the data obtained by the wet lab. Synergically, simulations from the cyber lab will aid tuning the experimental conditions that lead to the desirable patterns.

Outreach

We informed students, iGEM teams and the Belgian public more about synthetic biology and our project.

Future

Does Spot E.Shape only impact the academic environment, or is it likely to be picked up by industry? Click here to find out more about its future potential and applications.

Team

Diverse with respect to thoughts, perspectives, nationalities and languages, yet bound together by our enthusiasm for science and research. Would you like to know more about us?

Notebook

Many small steps need to be taken to achieve our goal. We like to keep you informed and welcome you to discover our newsfeed and history.

Contact

Address: Celestijnenlaan 200G room 00.08 - 3001 Heverlee
Telephone: +32(0)16 32 73 19
Email: igem@chem.kuleuven.be