Difference between revisions of "Team:KU Leuven/Description"

 
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<link rel="shortcut icon" href="https://static.igem.org/mediawiki/2015/9/9c/Ku_Leuven_Favicon.gif" /
 
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<h2>Project</h2>
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<h2>Our project</h2>
 
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<p> 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 clear. We, the KU Leuven iGEM 2015 team, decided to work on the fundamental mechanisms behind pattern formation. The way 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.</p>
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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.
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</p></br>
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<p>
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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.
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</p></br>
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<p>
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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.
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<p>
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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.
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</p></br>
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<p>
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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.
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<h3>Approach</h3>
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<p> We plan to engineer two different cell types of bacteria to form a desired pattern on a petri dish. We aim to control the cell behaviour and the motility by stimuli originating from engineered bacteria. Our design focuses on creating a construct that stimulates bacterial cells of the same type to adhere to each other and to repel the other type. After fine-tuning the plasmid constructions, the exact details will appear in the wet lab section.
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We will extract results from the wet lab for generating precise models to theoretically represent the pattern-forming bacteria. We will use techniques like Western blotting, chemiluminescence, fluorescence and biological assays coupled to image analysis to quantify certain gene products.
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Different levels of production of certain proteins will affect the shape and size of patterns that the bacteria form. Therefore we will control promoter induction and experiment runtime to study the resulting effects. Additionally, this will give the modeling team more data to fit their models to different conditions. Concurrently, simulations from the cyber lab will aid in tuning the experimental conditions that lead to the desirable patterns. In conclusion, the interaction between wet lab and cyber lab will be crucial to the successful design of our experiments. </p>
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<h3>Applications</h3>
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<p> First of all, our project has the goal to unravel the secrets of nature according to pattern formation. A better understanding of the pattern formation process in combination with the appropriate and detailed predictive mathematical models will also be advantageous in many different fields. Tumor formation and tissue regeneration are a few among the many examples where the <b>medical</b> world could benefit from a deeper knowledge of pattern formation. The generation of patterns in a controlled way will also allow the production of novel <b>biomaterials</b>. After forming a pattern, the cells can be engineered to precipitate or deposit networked biominerals, opening up exciting new avenues for the production of microstructured biocomposite materials. In the long term, the ability to construct predesigned patterns of bacteria could lead to applications in miniature electrical conductors and/or <b>electrical</b> circuits as well.
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<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.
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</p>
 
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<a href="https://2015.igem.org/Team:KU_Leuven/InterLabStudy">
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<h2>Interlab</h2>
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<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.
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<br/>
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</p>
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<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
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<h2>Modeling</h2>
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<p>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.
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<div id="more">
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<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="100%" width="85%" alt="Read more">
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<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="100%" width="85%" alt="Read more">
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<img src="https://static.igem.org/mediawiki/2015/8/84/KU_Leuven_Wiki_Button_-_Outreach2.png" width="100%">
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<a href="https://2015.igem.org/Team:KU_Leuven/Future">
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<img src="https://static.igem.org/mediawiki/2015/4/41/KU_Leuven_Wiki_Button_-_Future2.png" width="100%">
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<a href="https://2015.igem.org/Team:KU_Leuven/Team">
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<img src="https://static.igem.org/mediawiki/2015/2/23/KUL_Wiki_Button_-_Team.png" width="100%">
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<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
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<img src="https://static.igem.org/mediawiki/2015/5/59/Wiki_Button_-_Notebook2.png" width="100%">
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</a>
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<div class="subtextrow">
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<div class="subtext">
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<a href="https://2015.igem.org/Team:KU_Leuven/Practices">
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<h2>Outreach</h2>
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<p>Teaching students, other iGEM teams and the Belgian public more about synthetic biology and our project.
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<br/>
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</p>
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</a>
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</div>
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<div class="whitespace">
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<div class="subtext">
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<a href="https://2015.igem.org/Team:KU_Leuven/Future">
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<h2>Future</h2>
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<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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</p>
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</a>
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</div>
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<div class="whitespace">
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<div class="subtext">
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<a href="https://2015.igem.org/Team:KU_Leuven/Team">
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<h2>Team</h2>
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<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/>
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</p>
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</a>
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<div class="whitespace">
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<div class="subtext">
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<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
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<h2>Notebook</h2>
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<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.
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<br/>
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</p>
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</a>
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</div>
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</div>
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<div class="subimgreadmore">
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<div class="subimgrm">
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<a href="https://2015.igem.org/Team:KU_Leuven/Practices">
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<div id="more">
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<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="100%" width="85%" alt="Read more">
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<div id="more">
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<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 id="more">
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<img src="https://static.igem.org/mediawiki/2015/7/73/KUL_Wiki_Button_-_Read_more.png" height="100%" width="85%" alt="Read more">
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</a>
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<div class="subimgrowm">
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<b>Research</b>
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<a href="https://2015.igem.org/Team:KU_Leuven/Research">
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<img src="https://static.igem.org/mediawiki/2015/6/63/Wiki_Button_-_Research2.png" width="100%"></a>
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<a href="https://2015.igem.org/Team:KU_Leuven/Research">
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<p> Each experimental step requires a theoretical background.  This background, the protocols and the results of our experiments can be found in this subsection.
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</a>
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<div class="subimgm">
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<b>Interlab</b>
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<a href="https://2015.igem.org/Team:KU_Leuven/InterLabStudy">
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<img src="https://static.igem.org/mediawiki/2015/c/c3/KU_Leuven_Wiki_Button_-_Interlab_measurement2.png" width="100%">
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<div class="whitespace">
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<div class="subtextm">
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<a href="https://2015.igem.org/Team:KU_Leuven/InterLabStudy">
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<p>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.
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</p>
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</a>
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</div>
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<div class="subimgrowm">
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<div class="whiterow"></div>
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<div class="subimgrowm">
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<div class="subimgm">
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<b>Modeling</b>
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<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
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<img src="https://static.igem.org/mediawiki/2015/a/aa/Wiki_Button_-_Modelling2.png" width="100%">
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<div class="subtextm">
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<a href="https://2015.igem.org/Team:KU_Leuven/Modeling">
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<p>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.
 +
</p>
 +
</a>
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</div>
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<div class="subimgrowm">
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<div class="subimgrowm">
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<b>Outreach</b>
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<a href="https://2015.igem.org/Team:KU_Leuven/Practices">
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<img src="https://static.igem.org/mediawiki/2015/8/84/KU_Leuven_Wiki_Button_-_Outreach2.png" width="100%">
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</a>
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</div>
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<div class="whitespace">
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</div>
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<div class="subtextm">
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<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>
 +
</a>
 +
</div>
 +
 +
<div class="subimgrowm">
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<div class="whiterow"></div>
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</div>
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</div>
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<div class="subimgrowm">
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<div class="subimgm">
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<b>Future</b>
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Future">
 +
<img src="https://static.igem.org/mediawiki/2015/4/41/KU_Leuven_Wiki_Button_-_Future2.png" width="100%">
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</a>
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</div>
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<div class="whitespace">
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</div>
 +
 +
 +
<div class="subtextm">
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Future">
 +
<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>
 +
</a>
 +
</div>
 +
 +
<div class="subimgrowm">
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<div class="whiterow"></div>
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</div>
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</div>
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<div class="subimgrowm">
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<div class="subimgm">
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<b>Team</b>
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<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%">
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</a>
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</div>
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<div class="whitespace">
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</div>
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<div class="subtextm">
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<a href="https://2015.igem.org/Team:KU_Leuven/Team">
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<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>
 +
</a>
 +
</div>
 +
 +
<div class="subimgrowm">
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<div class="whiterow"></div>
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</div>
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</div>
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<div class="subimgrowm">
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<div class="subimgm">
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<b>Notebook</b>
 +
<a href="https://2015.igem.org/Team:KU_Leuven/Notebook">
 +
<img src="https://static.igem.org/mediawiki/2015/5/59/Wiki_Button_-_Notebook2.png" width="100%">
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</a>
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</div>
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<div class="whitespace">
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</div>
 +
 +
<div class="subtextm">
 +
<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>
 +
</a>
 +
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Latest revision as of 18:02, 18 September 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. 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.


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.


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.


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.


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.

Research

Swift and smart in actions to design the plasmids, quantify the parameters and to create the patterns. Join us in our exciting journey.

Interlab

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.

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.

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Outreach

Teaching 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

Each experimental step requires a theoretical background. This background, the protocols and the results of our experiments can be found in this subsection.

Interlab

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.

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

Teaching 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