Team:Heidelberg

From 2009.igem.org

(Difference between revisions)

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.

Gallery

Spy on our cells or join the Heidelberg Team in the lab with our gallery tour.

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.

@@ Line 1: / Line 1: @@
 __NOTOC__
+{{Template_HD_3}}
+<html><body id="home" onload="setPageSize()">
+<div id="super_main_wrapper">
+<div id="orangeBox"><h3>Design your own promoter</h3>
+<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>
+<a href="http://igem.bioquant.uni-heidelberg.de/embperl/GUI04/index.epl">HEARTBEAT: Start Design</a>
+</div>
+<div id="greenBox"><h3>Mammalian biobricks</h3>
+<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>
+<a href="https://2009.igem.org/Team:Heidelberg/Project">Go To Project Page</a>
+</div>
+<div id="blueBox"><h3>Mission accomplished</h3>
+<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>
+<a href="https://static.igem.org/mediawiki/2009/a/a6/HD_GraphicalAbstract_high.jpg">Download Graphical Abstract</a>
+</div>
+<div class="clear"></div>
-{{Template_HD}}
+<div id="SubWrapper">
-{|
+<div id="mission_box">
-|-valign="top" border="0"
+<h2> iGEM Team Heidelberg 2009: First Runner-Up, Winner of the PoPS Prize, Finalist, Best Wiki, Best New Standard </h2>
-|width="650px" style="padding: 0 20px 0 0;"|
+<h3> Mission: Spybricks </h3>
-<!-- ***==Languages==
+<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>
- [[Image:british_flag.jpg|middle|15px]] [[Team:Heidelberg#Bacterial killers from a genetic construction kit|English]]        [[Image:German_flag_c.jpg|middle|15px]] [[Team:Heidelberg#Bakterienkiller aus dem Gen-Baukasten|Deutsch]]         [[Image:French_flag.jpg‎|middle|15px]] [[Team:Heidelberg#assasins bakterielles d'un kit construction|Français]]         [[Image:Italian_flag.jpg|middle|15px]] [[Team:Heidelberg#Un kit genetico per batteri killer|Italiano]]         [[Image:Spanish_flag.jpg|middle|15px]] [[Team:Heidelberg#Bacterias matadoras creadas a partir de un kit de construcción genética|Español]]         [[Image:Portugese_flag.jpg|middle|15px]] [[Team:Heidelberg#Bactérias predadoras a partir de um kit deconstrução genética|Português]]         [[Image:Catalonia_flag.jpg|middle|15px]] [[Team:Heidelberg#Bacteries assassines generades a partir d’ un kit de construcció genètica|Català]]         [[Image:Poland_flag.jpg|middle|15px]] [[Team:Heidelberg#Bakteryjni zabójcy z taśmy montażowej|Polski]]         [[Image:Lithuanin_flag.jpg|middle|15px]] [[Team:Heidelberg#Genetiškai sukonstruoti bakterijų žudikai|Lietuvių]]
-[[Image:Russian_flag.jpg|middle|15px]] [[Team:Heidelberg#Ликвидатор бактерий созданный из генетических материалов|Pусский]]         [[Image:China_flag.jpg|middle|15px]] [[Team:Heidelberg#由基因元件拼装的细菌杀手|中文]]         [[Image:Japanese_flag.jpg|middle|15px]] [[Team:Heidelberg#殺し屋のバクテリアを遺伝子コンストラクトキットで作る|日本語]]*** -->
+<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>
+<h3>Team</h3>
+<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>
-==Project Abstract==
+<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>
+<h3>HEARTBEAT </h3>
+<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>
-<p>Early efforts in synthetic biology have focused on using prokaryotes as an engineering
+<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>
-chassis, whereas novel developments indicate a shift towards an eukaryotic synthetic biology.
+<h3>Eukaryopedia</h3>
-The value of eukaryotic synthetic biology is manifold: in medical research, it will accomplish
+<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>
-new ways of gene therapy; in plant biotechnology, it can contribute to the struggle for a
-sustainable food and energy solution. Finally, the ability to assemble and analyze complicated
-biological systems step by step will allow a revolutionary approach to fundamental research.</p>
-<p>Establishing new standards for iGEM, the Heidelberg 2009 team will be concerned with
-developing ways for measuring promoters in mammalian cells, a default chassis and a first
-evaluation of the recently postulated BioBrick beta proposal 2 (Tom Knight).</p>
-<p>Considering the importance of controlling gene expression, our team's work will focus on
-natural and synthetic mammalian promoters. Our vision is to provide the synthetic biology
-community with a methodical library of such promoters (with different output strength and
-sensitivity to different regulatory proteins) and a model which can provide guidance for the
-development of further synthetic promoters. Our efforts will therefore, from the very
-beginning, equally entail bioinformatics and wet lab work.</p>
-<p>As an early application for such a promoter library, our team will attempt to develop an assay
-which can monitor the activity of several pathways in one cell. Such an assay is of high value
-for biological research as it can be applied for studying stem cell differentiation, tumor
-formation, apoptosis and autophagy as well as drug response. Our team will apply the assay
-towards testing several anti-cancer drugs. A computer-based model will lay the foundations
-for future work. It will help us to build a logic that integrates the promoter activities and will allow us to predict the possibilities of a single functional output.</p>
-==iGEM idea==
+<div class="clear"></div>
-<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, 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?"</p>
+<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>
-<p>The iGEM-approach to answer that question is to actually try to engineer biological systems with a proper function. Therefore 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 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.</p>
+<h3>Parts </h3>
-<p>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>
+<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>
-== Das Projekt ==
+<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>
+<h3>Gallery </h3>
+<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>
-Während sich die anfänglichen Bestrebungen der Synthetischen Biologie auf prokaryotische Systeme beschränkten, zeichnet sich gegenwärtig ein Wandel hin zu eukaryotischen Systemen ab. Die synthetische Biologie in Eukaryoten kann von vielseitigem Nutzen sein: im Bereich der medizinischen Forschung könnten neuen Ansätzen in der Gentherapie entwickelt werden; in der grünen Biotechnologie wird die Synthetische Biologie zu einer nachhaltigen Lösung der weltweiten Energie- und Nahrungsprobleme beitragen. Letztendlich wird die Möglichkeit komplexe künstliche biologische Systeme zu erschaffen und zu analysieren einen revolutionären Ansatz in der Grundlagenforschung darstellen.
+<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>
-Um neue Standards zu etablieren, wird das diesjährige iGEM Team Heidelberg sich mit der Einführung von neuen Messmethoden für Promotoren in Säugerzellen und mit der Entwicklung einer Standard-Zelllinie beschäftigen. Darüber hinaus werden wir eine erste Evaluation des kürzlich  von Tom Knight postulierten BioBrick Beta Proposal 2 Standard durchführen.
+<h3>Sponsors</h3>
-Eine kontrollierbare Genexpression ist essenziell in vielen Bereichen der synthetischen Biologie. Aus diesem Grund setzt sich unser Team die Entwicklung von natürlichen und synthetischen Promotoren zum Ziel.
+<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>
-Unser Beitrag zur internationalen Gemeinschaft der synthetischen Biologie wird eine systematische Promotorbibliothek sein (mit verschiedenen Stärken und verschiedener Sensitivität gegenüber Transkriptionsfaktoren bzw. Signalwegen). Dafür werden wir ein Modell entwickeln, welches es uns erlaubt solche synthetischen Promotoren herzustellen.
-Als eine erste Anwendung für eine derartige Promotorbibliothek werden wir versuchen einen Assay zu entwickeln, welcher die Aktivität von mehreren Signalwegen in einer Zelle visualisieren kann.  Ein solcher Assay ist für die biowissenschaftliche Forschung von höchster Bedeutung, da mit ihm Prozesse wie Stammzelldifferenzierung, Tumorentstehung,  Apoptose und Autophagie, charakterisiert und identifiziert werden können, als auch physiologische Antworten von Zellen auf Medikamente.
-== Die Idee von iGEM ==
+<div class="clear"></div>
-iGEM (international genetically engineered machines competition) ist ein internationaler Wettbewerb im Bereich der Synthetischen Biologie.  Der iGEM Wettbewerb wird jährlich von dem renommierten MIT (Massachusetts Institute of Technology ) in Cambridge, USA veranstaltet. Das Ziel ist es eine grundlegende Frage zu beantworten, die der Direktor des iGEM Wettbewerbs Randy Rettberg einst wie folgt beschrieb: „Können einfache biologische Systeme aus standardisierten und austauschbaren Komponenten aufgebaut werden? Oder ist die Biologie zu komplex, um auf diese Weise konstruiert zu werden?“
+<center>
-Um dieser Frage nachzukommen, verwirklichen mehr als 100 interdisziplinäre Studententeams unterschiedliche Projekte im Bereich der Synthetischen Biologie. Die Themen dieser Projekte reichen dabei von medizinischen Anwendungen wie z.B. Bakterien die Krebs bekämpfen, bis hin zu technischen Anwendungen. Im Gegensatz zur klassischen molekularen Biotechnologie, wo nur einzelne Gene von  einem Organismus in einen anderen eingebracht werden, ist es das Ziel der Synthetischen Biologie vollkommen artifizielle Systeme mit einer gänzlich neuen Funktion zu erschaffen.  Zu diesem Zweck besitzen alle iGEM-Teilnehmer Zugang zu einer Gen-Datenbank, die auch als Registry bezeichnet wird. In dieser Datenbank sind viele verschiedene genetische Konstrukte mit charakterisierten Funktionen verfügbar.
+<img src="https://static.igem.org/mediawiki/2009/e/e9/Igem-logo.gif"/>
-Die ständig steigende Zahl von teilnehmenden Teams und das stärker werdende Medieninteresse an iGEM legen nahe, dass die Synthetische Biologie in Zukunft eine große Auswirkung, sowohl auf die wissenschaftliche Forschung als auch auf das alltägliche Leben haben wird.
+</center>
+</div> <!-- end SubWrapper -->
-|width="250px"|
+<div id="news">
+<h3>The Team</h3>
+<center><img src="https://static.igem.org/mediawiki/2009/8/89/Team_verySmall.jpg" alt=""/></center>
+<p>This year 13 students started the Heidelberg iGEM team.</p>
-==Our Team==
+<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>
-[[Image:Team_verySmall.jpg]]
-This year 13 students are part of the [https://2009.igem.org/Team:Heidelberg/Team Heidelberg iGEM Team].
-{| class="wikitable centered" border="2" rules="rows" width="250px" style="border-color:#0000CD;"
-|- style="background-color:#009ACD;"
-|style="text-align:center"|Next Team Meeting
-|- style="background-color:#63B8FF;"
-|style="text-align:center"| 22.09.2009
-|- style="background-color:#63B8FF;"
-|style="text-align:center"| 11.00 - 15.00
-|}
+<h3> Heidelberg Jamboree Blog</h3>
 <p>
-</p>
+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>
-<html>
-<embed src="http://www.oneplusyou.com/bb/files/countdown/countdown.swf?co=8fc332&bgcolor=FFFFFF&date_month=10&date_day=30&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>
-</div>
-</div>
-</html>
-==News==
+<h3> The iGEM idea </h3>
+<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?"
+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.</p>
-''28 Aug. 2009,''    '''Generous Donation by Klaus Tschira Foundation'''
+<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>
-[[image:HD09_kts-logo.jpg|center|100px|http://www.klaus-tschira-stiftung.de/english/index.html]]
-<br>
-The Klaus Tschira Foundation GmbH is a non-profit organization and supports research in informatics, the natural sciences, and mathematics; at the same time it promotes a public understanding in these sciences. With this combination the Klaus Tschira foundation is our ideal partner in this competition.
+</div>  <!-- end news -->
-<br>
+</div> <!-- end Super_main_wrapper -->
-<br>
+<script type="text/javascript">
+function setPageSize() {
+len = document.getElementById('super_main_wrapper').offsetHeight;
+document.getElementById('bodyContent').style.height = len + 'px';
+document.getElementById('SupWrapper').style.height = len + 'px';
+document.getElementById('news').style.height = len + 'px';
+}
+</script>
-''25 Aug. 2009,'' '''Lange + Pflanz becomes Gold Sponsor'''
+</body></html>
-[[image:HD09_Lange_pflanz.gif|center|120px|http://www.lpsp.de/werbeagentur]]
-<br>
-Lange & Pflanz Werbeagentur GmbH (www.lpsp.de) have just declared the sponsorship of our team by designing a team logo, a team shirt, a website, and power-point slides for the Championship Jamboree at MIT. This positions the company - an established marketing and design company which successfully designed the website for our Bioquant Institute - right into the sponsorship Gold category. You will find soon the first results on this page!
-<br>
-<br>
-|}