Team:Heidelberg

From 2009.igem.org

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Early efforts in synthetic biology have focused on using prokaryotes as an engineering
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<div id="orangeBox"><h3>Design your own promoter</h3>
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chassis, whereas novel developments indicate a shift towards an eukaryotic synthetic biology.
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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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The value of eukaryotic synthetic biology is manifold: in medical research, it will accomplish
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<a href="http://igem.bioquant.uni-heidelberg.de/embperl/GUI04/index.epl">HEARTBEAT: Start Design</a>
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new ways of gene therapy; in plant biotechnology, it can contribute to the struggle for a
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sustainable food and energy solution. Finally, the ability to assemble and analyze complicated
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<div id="greenBox"><h3>Mammalian biobricks</h3>
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biological systems step by step will allow a revolutionary approach to fundamental research.
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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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Establishing new standards for iGEM, the Heidelberg 2009 team will be concerned with
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<a href="https://2009.igem.org/Team:Heidelberg/Project">Go To Project Page</a>
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developing ways for measuring promoters in mammalian cells, a default chassis and a first
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evaluation of the recently postulated BioBrick beta proposal 2 (Tom Knight).
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<div id="blueBox"><h3>Mission accomplished</h3>
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Considering the importance of controlling gene expression, our team's work will focus on
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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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natural and synthetic mammalian promoters. Our vision is to provide the synthetic biology
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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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community with a methodical library of such promoters (with different output strength and
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sensitivity to different regulatory proteins) and a model which can provide guidance for the
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development of further synthetic promoters. Our efforts will therefore, from the very
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beginning, equally entail bioinformatics and wet lab work.
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As an early application for such a promoter library, our team will attempt to develop an assay
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which can monitor the activity of several pathways in one cell. Such an assay is of high value
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for biological research as it can be applied for studying stem cell differentiation, tumor
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formation, apoptosis and autophagy as well as drug response. Our team will apply the assay
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towards testing several anti-cancer drugs. A computer-based model will lay the foundations
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for future work. It will help us to build a logic that integrates the promoter activities and will
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allow us to predict the possibilities of a single functional output.</div>
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<h2> iGEM Team Heidelberg 2009: First Runner-Up, Winner of the PoPS Prize, Finalist, Best Wiki, Best New Standard </h2>
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<h3> Mission: 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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<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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<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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|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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''Tell us more about your project.  Give us background.  Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)''
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|align="center"|[[Team:Heidelberg | Team Example]]
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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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!align="center"|[[Team:Heidelberg|Home]]
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<h3>Gallery </h3>
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!align="center"|[[Team:Heidelberg/Team|The Team]]
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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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!align="center"|[[Team:Heidelberg/Project|The Project]]
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!align="center"|[[Team:Heidelberg/Parts|Parts Submitted to the Registry]]
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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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!align="center"|[[Team:Heidelberg/Modeling|Modeling]]
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<h3>Sponsors</h3>
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!align="center"|[[Team:Heidelberg/Notebook|Notebook]]
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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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<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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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 10:13, 25 October 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 Team Heidelberg 2009: First Runner-Up, Winner of the PoPS Prize, Finalist, Best Wiki, Best New Standard

Mission: 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://2009.igem.org/Team:Heidelberg"