Team:British Columbia

From 2010.igem.org

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<div id="orangeBox"><h3>Design your own promoter</h3>
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<div id="orangeBox"><h3>Blasting Away Biofilms</h3>
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<p>Here we present a new approach to synthesize synthetic promoters using a database that predicts the position of conserved promoter binding sequences. We coded an easy to use interface that is available for public use. </p>
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<p>To disperse <i>Staphylococcus aureus</i> biofilms, our team is working to express a bacteriophage and biofilm-degrading enzyme under the control of the agr quorum-sensing system.</p>
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<a href="http://igem.bioquant.uni-heidelberg.de/embperl/GUI04/index.epl">HEARTBEAT: Start Design</a>
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<a href="https://2010.igem.org/Team:British_Columbia/Project">Our Project Page</a>
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<div id="greenBox"><h3>Mammalian biobricks</h3>
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<div id="greenBox"><h3>And The Award Goes To...</h3>
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<p>Mammalian synthetic biology has huge potential, but it is in need of new standards and of systematic construction of comprehensive part libraries. Learn more about our new mission on the project page. </p>
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<p>Here's a list of the things we've accomplished according to iGEM judging and awards criteria.</p>
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<a href="https://2009.igem.org/Team:Heidelberg/Project">Go To Project Page</a>
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<a href="https://2010.igem.org/Team:British_Columbia/Project_Outlook">Our Accomplishments</a>
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<div id="blueBox"><h3>Mission accomplished</h3>
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<div id="blueBox"><h3>It's Human!</h3>
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<p>We developed two novel, <i>in silico</i> guided methods for the rational construction of synthetic promoters and experimentally validated the predicted results. View our graphical abstract and get an overview of the achievements of our team.</p>
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<p>Wonder what people on the streets think about synthetic biology? Come take a look at our quirky promoter maps, fabulous art gallery, NaNoWriMo synthetic biology novels, and live forum!</p>
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<a href="https://static.igem.org/mediawiki/2009/a/a6/HD_GraphicalAbstract_high.jpg">Download Graphical Abstract</a>
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<a href="https://2010.igem.org/Team:British_Columbia/HumanPractices">Talk Play Love</a>
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<center><a href="https://2010.igem.org/Team:British_Columbia/Team"><img src="https://static.igem.org/mediawiki/2010/c/c5/Teambox.jpg" alt=""/></center>
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<p>We are 9 undergraduate students, 2 graduate advisors and 3 faculty advisors from various disciplines including Pharmacology, Physiology, the Life Sciences, Materials Engineering, Chemical and Biological Engineering, and Engineering Physics.</p><p><a href="https://2010.igem.org/Team:British_Columbia/Team">Get up close and personal!</a></p></div>
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<div id="mission_box"> <h3> iGEM Heidelberg Mission 2009: Spybricks </h3>
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<div id="project_box"> <center><a href="https://2010.igem.org/Team:British_Columbia/Project"><img src="https://static.igem.org/mediawiki/2010/a/a8/Projectbox.jpg" alt=""/></center>
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<p> The Heidelberg 2009 team attempts to take Synthetic Biology a step further by introducing novel concepts for the work with mammalian cells, defining Synthetic Mammalian Biology (SMB). We are the first-ever team at iGEM trying to systematically develop a BioBrick library for use in mammalian cells. Being the first team of Heidelberg's "SMB initiative", we emphasize the central position of gene regulation. Our team's work therefore focused on synthetic mammalian promoters. We provide the foundations of a methodical library of such promoters, together with novel standards for their characterization. We have developed an avant-garde method for the synthesis of mammalian promoters, and a bioinformatical model predicting such promoters which we test in vivo. <a href="https://2009.igem.org/Team:Heidelberg/Project">Go to Project Abstract</a></p></div>
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<p>With the aim of dispersing Staphylococcus aureus biofilms, our team is working to express an endogenous bacteriophage and biofilm matrix-degrading enzyme DspB under the control of the agr quorum-sensing system. We are using existing BioBrick parts (e.g. the P2 promoter) as well as our own new DspB Biobrick part. We have also developd a new standard for working with bacteriophages.</p><p><a href="https://2010.igem.org/Team:British_Columbia/Team">Learn more at our Project page!</a>  
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<div id="team_box"><center><a href="https://2009.igem.org/Team:Heidelberg/Team"><img src="https://static.igem.org/mediawiki/2009/0/06/HD09_Team_180px.png" alt=""/></a></center>
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<div id="parts_box"> <center><a href="https://2010.igem.org/Team:British_Columbia/Parts"><img src="https://static.igem.org/mediawiki/2010/3/30/Partsbox.jpg" alt=""/></center></a>
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<h3>Team</h3>  
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<p>Our new and characterized Biobrick part is the biofilm matrix-degrading enzyme DspB. In addition, we have further characterized the existing promoter Biobrick parts, P2 (BBa_I174106) and Pcon (BBa_J23100) in Staphylococcus aureus.</p><p><a href="https://2010.igem.org/Team:British_Columbia/Parts">For more details, visit our Parts page!</a> </p> </div>
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<p>Thirteen students and nine advisors are working on this four month project. We split up into several subgroups whose focus and results you can follow on the Notebook and Project pages. If you want to know more about the subgroups and the people involved, meet us on our <a href="https://2009.igem.org/Team:Heidelberg/Team">Team page </a> and let's get to know each other better at the Jamboree in Boston. </p></div>
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<div id="heartbeat_box"> <center><a href="https://2009.igem.org/Team:Heidelberg/HEARTBEAT"><img src="https://static.igem.org/mediawiki/2009/3/37/Heartbeat_small.gif" alt=""/></a></center>
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<h3>HEARTBEAT </h3>
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<p> Our team worked on a computational approach for the rational <a href="https://2009.igem.org/Team:Heidelberg/HEARTBEAT">design of promoter libraries</a>. Similar to existing methods which predict spatial preferences of transcription factor binding sites (TFBS) by detecting statistically overrepresented motives we used Promotersweep to analyze and process the information of over 4000 human promoter sequences.</p></div>
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<div id="notebook_box"> <center><a href="https://2009.igem.org/Team:Heidelberg/Eukaryopedia"><img src="https://static.igem.org/mediawiki/2009/d/dc/Brockhauscells.jpg" alt=""/></a></center>
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<h3>Eukaryopedia</h3>
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<p>You are working in bacteria and never heard of U2-OS, SREBP or CYP1A1? Don't worry! Browse our <a href="https://2009.igem.org/Team:Heidelberg/Eukaryopedia">Eukaryopedia</a> and enter the world of mammalian BioBricks.</p> </div>
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<div id="modeling_box"> <center><a href="https://2010.igem.org/Team:British_Columbia/modeling_description"><img src="https://static.igem.org/mediawiki/2010/b/b6/Modelingbox.jpg" alt=""/></center>
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<h3>Parts </h3>
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<p>Our team <a href="https://2009.igem.org/Team:Heidelberg/Parts">submits a library </a> of thoroughly characterized and standardized parts. Therefore contributing towards the establishment of a new standard for eukaryotic cells in the iGEM context.</p> </div>
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<p>We have developed a model of biofilm population dynamics as affected by our engineered bacteriophage. Using this model, we are able to run simulations that predict outcomes of the system and construct informed hypotheses to test with our system.</p><p><a href="https://2010.igem.org/Team:British_Columbia/modeling_description">Visit our Modeling page!</a>  
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<div id="gallery_box"><center><a href="https://2009.igem.org/Team:Heidelberg/Gallery"><img src="https://static.igem.org/mediawiki/2009/d/d9/Leopardeye.png" alt=""/></a></center>
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<div id="humanpractices_box"><center><a href="https://2010.igem.org/Team:British_Columbia/HumanPractices"><img src="https://static.igem.org/mediawiki/2010/e/eb/Hpbox.jpg" alt=""/></center>
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<h3>Gallery </h3>
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<p>Spy on our cells or join the Heidelberg Team in the lab with our <a href="https://2009.igem.org/Team:Heidelberg/Gallery">gallery tour</a>.</p></div>
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<p>What are human practices? What are its goals? Gaze upon our promoter maps to see what people on the streets think "Synthetic Biology" means. Browse through our art gallery, read NaNoWriMo novels, and be inspired to think more deeply about the diverse issues of synthetic biology. Share your thoughts at our forum discussions about synthetic biology and its applications.</p><p><a href="https://2010.igem.org/Team:British_Columbia/HumanPractices">What are you waiting for?</a> </p>
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<div id="sponsors_box"> <center><a href="https://2009.igem.org/Team:Heidelberg/Sponsors"><img src="https://static.igem.org/mediawiki/2009/9/91/Handschlag.png" alt=""/></a></center>
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<div id="notebook_box"> <center><a href="https://2010.igem.org/Team:British_Columbia/Notebook"><img src="https://static.igem.org/mediawiki/2010/e/ec/Notebookbox.jpg" alt=""/></center>
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<h3>Sponsors</h3>
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<p>We thank our great sponsors, who supported us financially and made this project a success. <a href="https://2009.igem.org/Team:Heidelberg/Sponsors">Go here </a> to find out more about them.</p> </div>  
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<p>Every sub-team has its unique story of success and heartbreak. What are most important are the invaluable lessons learned, the extensive trouble-shooting expertise gained, the bonds of friendship formed, and of course... the victories!</p><p><a href="https://2010.igem.org/Team:British_Columbia/Notebook">Come trace our steps...</a> </p></div>  
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<h3>The Team</h3>
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<p>This year 13 students started the Heidelberg iGEM team.</p>
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<br></br><p>The International Genetically Engineered Machine competition (iGEM) is the premiere undergraduate synthetic biology competition. Student teams world-wide are given a set of biological parts from the Registry of Standard Biological Parts. Over the summer, the teams use these parts and create new parts of their own to build biological systems and operate them in living cells to achieve various creative purposes. To complement their wet lab findings, the teams also endeavour to design and carry out computer modeling and human practices projects. Through this experience, undergraduate students gain insight into the research process of seeking out information and protocols to come up with their own novel project (not to mention all the re-searching and trouble-shooting expertise gained!). Graduate student advisors also get a taste of what it feels like to be a principal investigator or lab manager in terms of providing for and guiding the undergraduate students. Finally, in November, hundreds of iGEM teams gather at MIT to compete at the annual Jamboree!</p>
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<h3> Heidelberg Jamboree Blog</h3>
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We will report all important news during the jamboree right away from Cambridge <a href="http://www.bioquant.uni-heidelberg.de/igem/jamboree-blog"> here</a>.</p>
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<h3> The iGEM idea </h3>
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<p>iGEM (international genetically engineered machines competition) is an international competition in synthetic biology, hosted by the MIT in Boston. The aim of this competition is to answer a basic question that Randy Rettberg, the director of iGEM, once described as follows: "Can simple biological systems be built from standard, interchangeable parts and operated in living cells? Or is biology just too complicated to be engineered in this way?"
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The iGEM-approach to answer that question is to actually try to engineer biological systems with a proper function. To this end, more than 100 interdisciplinary student teams from all over the world, mainly consisting of undergraduate students in biology, biochemistry, engineering, informatics and mathematics, carry out different projects during the Summer. These projects reach from medical applications, i.e. genetically modified bacteria used in cancer-treatment to environmental and manufacturing projects, i.e. the construction of a watch-like counter consisting of living cells. In contrast to classical genetic engineering where only one gene is transferred from organism A to organism B, synthetic biology goes forward into the construction of whole new systems with a completely new function. Therefore, all iGEM-Teams get access to a gene- Database called registry, where hundreds of different genetic parts with characterized functions are available in a “plug-and-play” –like format. These parts can be simply stuck together to build functional systems.
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The rising number of iGEM-Teams over the last years as well as the upcoming public interest in iGEM, the iGEM-Teams’ projects and synthetic biology in general shows, that synthetic biology will for sure have a great impact in many different fields of both scientific research and every-day life.</p>
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<p>The contents and design of this wiki are published under the <a href="http://commons.wikimedia.org/wiki/Commons:GNU_Free_Documentation_License">GNU Free Documentation License</a> You are granted the right to copy and modify our work, but you must publish your work under the same type of license while recognizing us the authors.</p>
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Latest revision as of 15:11, 27 October 2010

Blasting Away Biofilms

To disperse Staphylococcus aureus biofilms, our team is working to express a bacteriophage and biofilm-degrading enzyme under the control of the agr quorum-sensing system.

Our Project Page

And The Award Goes To...

Here's a list of the things we've accomplished according to iGEM judging and awards criteria.

Our Accomplishments

It's Human!

Wonder what people on the streets think about synthetic biology? Come take a look at our quirky promoter maps, fabulous art gallery, NaNoWriMo synthetic biology novels, and live forum!

Talk Play Love


We are 9 undergraduate students, 2 graduate advisors and 3 faculty advisors from various disciplines including Pharmacology, Physiology, the Life Sciences, Materials Engineering, Chemical and Biological Engineering, and Engineering Physics.

Get up close and personal!

With the aim of dispersing Staphylococcus aureus biofilms, our team is working to express an endogenous bacteriophage and biofilm matrix-degrading enzyme DspB under the control of the agr quorum-sensing system. We are using existing BioBrick parts (e.g. the P2 promoter) as well as our own new DspB Biobrick part. We have also developd a new standard for working with bacteriophages.

Learn more at our Project page!

Our new and characterized Biobrick part is the biofilm matrix-degrading enzyme DspB. In addition, we have further characterized the existing promoter Biobrick parts, P2 (BBa_I174106) and Pcon (BBa_J23100) in Staphylococcus aureus.

For more details, visit our Parts page!

We have developed a model of biofilm population dynamics as affected by our engineered bacteriophage. Using this model, we are able to run simulations that predict outcomes of the system and construct informed hypotheses to test with our system.

Visit our Modeling page!

What are human practices? What are its goals? Gaze upon our promoter maps to see what people on the streets think "Synthetic Biology" means. Browse through our art gallery, read NaNoWriMo novels, and be inspired to think more deeply about the diverse issues of synthetic biology. Share your thoughts at our forum discussions about synthetic biology and its applications.

What are you waiting for?

Every sub-team has its unique story of success and heartbreak. What are most important are the invaluable lessons learned, the extensive trouble-shooting expertise gained, the bonds of friendship formed, and of course... the victories!

Come trace our steps...





The International Genetically Engineered Machine competition (iGEM) is the premiere undergraduate synthetic biology competition. Student teams world-wide are given a set of biological parts from the Registry of Standard Biological Parts. Over the summer, the teams use these parts and create new parts of their own to build biological systems and operate them in living cells to achieve various creative purposes. To complement their wet lab findings, the teams also endeavour to design and carry out computer modeling and human practices projects. Through this experience, undergraduate students gain insight into the research process of seeking out information and protocols to come up with their own novel project (not to mention all the re-searching and trouble-shooting expertise gained!). Graduate student advisors also get a taste of what it feels like to be a principal investigator or lab manager in terms of providing for and guiding the undergraduate students. Finally, in November, hundreds of iGEM teams gather at MIT to compete at the annual Jamboree!

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