Team:British Columbia

From 2010.igem.org

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<div id="orangeBox"><h3>Design your own promoter</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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<a href="http://igem.bioquant.uni-heidelberg.de/embperl/GUI04/index.epl">HEARTBEAT: Start Design</a>
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<div id="greenBox"><h3>Mammalian biobricks</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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<a href="https://2009.igem.org/Team:Heidelberg/Project">Go To Project Page</a>
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<div id="blueBox"><h3>Mission accomplished</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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<a href="https://static.igem.org/mediawiki/2009/a/a6/HD_GraphicalAbstract_high.jpg">Download Graphical Abstract</a>
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!align="center"|[[Team:British_Columbia|Home]]
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!align="center"|[[Team:British_Columbia/Team|Team]]
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!align="center"|[https://igem.org/Team.cgi?year=2010&team_name=British_Columbia Official Team Profile]
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!align="center"|[[Team:British_Columbia/Project|Project]]
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!align="center"|[[Team:British_Columbia/Parts|Parts Submitted to the Registry]]
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!align="center"|[[Team:British_Columbia/Modeling|Modeling]]
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!align="center"|[[Team:British_Columbia/Notebook|Notebook]]
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!align="center"|[[Team:British_Columbia/Safety|Safety]]
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|You can write a background of your team here. Give us a background of your team, the members, etc.  Or tell us more about something of your choosing.
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<h2>Project Description</h2>
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With the aim of dispersing Staphylococcus aureus biofilms, the 2010 UBC iGEM Team is working to express an endogenous bacteriophage and biofilm matrix-degrading enzyme DspB under the control of the Agr quorum-sensing system. We will be using existing BioBrick parts (the P2 promoter and AgrCA genes) as well as creating our own DspB Biobrick part. In addition, we plan to develop a new standard for working with bacteriophages that are 15-50kbp in length.
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<div id="mission_box"> <h3> iGEM Heidelberg Mission 2009: Spybricks </h3>
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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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Our team is composed of 9 undergradate students, 2 graduate advisors and 3 faculty advisors. We are a diverse team from various disciplines including Pharmacology, Life Sciences, Physiology, Chemical and Biological Engineering, Materials Engineering, Engineering Physics and Computer Science.
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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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<h3>Team</h3>
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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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Our project will include all 3 components of an iGEM endeavor.
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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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The core of our project will be the design and engineering of a bacteriophage that disintegrates a S. aureus biofilm under the control of quorum sensing molecules. The quorum sensing will control when the phage switches from a lysogenic to lytic. The matrix-degrading enzyme will be part of the phage genome, putting it under the control of quorum sensing as well.
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<div id="parts_box"> <center><a href="https://2009.igem.org/Team:Heidelberg/Parts"><img src="https://static.igem.org/mediawiki/2009/c/c0/Parts_HD.jpg" alt=""/></a></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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<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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<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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The modeling component will produce a model that describes the population dynamics of the engineered bacteriophage and the affected biofilm. Simulations of our model will be implemented in MATLAB. The goals of the model are threefold: 1) Write a functional math model of the system, 2) Provide numerical simulations that may predict the outcome of the system  3) Use what we learn from making the model to make hypotheses that we can test with our system.
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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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<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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The human practices project will be a compilation of creative works from each of our team members that addresses different issues and problems and conveys thoughts and ideas regarding the diverse aspects of synthetic biology and genetic engineering.
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This component will encourage thinking about modern biotechnology from different perspectives and promote the synthesis of viewpoints and notions of people from a broad range of backgrounds and disciplines.
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<img src="https://static.igem.org/mediawiki/2009/e/e9/Igem-logo.gif"/>
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<h3>The Team</h3>
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<center><img src="https://static.igem.org/mediawiki/2009/8/89/Team_verySmall.jpg" alt=""/></center>
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<p>This year 13 students started the Heidelberg iGEM team.</p>
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<center><embed src="http://www.oneplusyou.com/bb/files/countdown/countdown.swf?co=8fc332&bgcolor=FFFFFF&date_month=11&date_day=09&date_year=0&un=IGEM JAMBOREE 2009&size=normal&mo=10&da=31&yr=2009" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" width="240" height="80" wmode="transparent"></embed></center>
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<h3> Heidelberg Jamboree Blog</h3>
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<p>
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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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Revision as of 01:21, 3 September 2010

Design your own promoter

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.

HEARTBEAT: Start Design

Mammalian biobricks

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.

Go To Project Page

Mission accomplished

We developed two novel, in silico 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.

Download Graphical Abstract

iGEM Heidelberg Mission 2009: Spybricks

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. Go to Project Abstract

Team

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 Team page and let's get to know each other better at the Jamboree in Boston.

HEARTBEAT

Our team worked on a computational approach for the rational design of promoter libraries. 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.

Eukaryopedia

You are working in bacteria and never heard of U2-OS, SREBP or CYP1A1? Don't worry! Browse our Eukaryopedia and enter the world of mammalian BioBricks.

Parts

Our team submits a library of thoroughly characterized and standardized parts. Therefore contributing towards the establishment of a new standard for eukaryotic cells in the iGEM context.

Sponsors

We thank our great sponsors, who supported us financially and made this project a success. Go here to find out more about them.

The Team

This year 13 students started the Heidelberg iGEM team.

Heidelberg Jamboree Blog

We will report all important news during the jamboree right away from Cambridge here.

The iGEM idea

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?" 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. 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.

The contents and design of this wiki are published under the GNU Free Documentation License 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.

Retrieved from "http://2010.igem.org/Team:British_Columbia"