Team:ETH Zurich

From 2008.igem.org

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[[Image:ETH_Logo.JPG|center|850px]]
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== Project Abstract ==
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''''''Random walks towards the minimal genome''''''<br>
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"This year's ETH Zurich project tackles a fundamental problem of synthetic biology: the minimal genome.
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Exploring the minimal set of genes that is able to support life is not only a question of significant biological interest, it is also a crucial step towards the implementation of orthogonal functionalities into a rationally designed complex biological system. An organism carrying a minimal genome would provide a simple chassis for biological engineering.
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We attempted to exploit the power of accelerated evolution for a genome reduction strategy. Our approach is based on an iterative cycle of genome reduction and strain selection.
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We propose a novel method to randomly delete chromosomal DNA fragments by controlled expression of restriction enzymes and ligases in vivo. Furthermore, we develop a chemostat-based condition to select for cells with a smaller genome size by constraining nucleotide availability. Computationally, we analyze the genome for the optimal restriction enzyme, and perform flux balance analysis on a genome scale model to predict growth of reduced genome strains. Finally, we simulate the restriction enzyme expression and the progression of selection."<br>
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=="Meet us" video==
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== The Team ==
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[[Image:Team_eth.JPG|left|thumb|150px|Team ETH]]
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The iGEM team 2008 follows the tradition of the ETH teams before, and consits of students from very diverse scientific backgrounds.
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If you'd like to know more about the team, you will find more information in the [https://2008.igem.org/Team:ETH_Zurich/Team/Members Team Section].<br>
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<strong>Undergraduate Students</strong><br>
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Julia Slipantschuk, Sebastian Giese, Nico Hensgens, Rebecca Herbst, Reine Byun, [http://www.facebook.com/profile.php?id=804108753&ref=profile Georg Ofenbeck].
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<br><strong>Graduate Students</strong><br>
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[https://2008.igem.org/User:snev Sven Lucas Dietz], [https://2007.igem.org/User:Luca.Gerosa  Luca Gerosa], [http://www.biol.ethz.ch/IMB/groups/ban_group/members/jrabl Julius Rabl].
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<br><strong>Advisors</strong><br>
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    <tr><td width=5px></td><td>[[Team:ETH_Zurich|Home]]</td></tr><tr><td width=5px></td><td><table><tr><td width=5px></td><td>[[Team:ETH_Zurich/Design_and_Implementation|Design & Implementation]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Background|Background]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Applications|Applications]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Introduction|Introduction]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Wet%20Lab|Wet Lab]]</td></tr><tr><td width=5px></td><td><table><tr><td width=5px></td><td>[[Team:ETH_Zurich/Wet%20Lab/PoC%20Reducing%20Genome|PoC Reducing Genome]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Wet%20Lab/PoC%20Selection%20in%20Chemostat|PoC Selection in Chemostat]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Wet%20Lab/Pulse%20Generator|Pulse Generator]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Wet%20Lab/Materials_Methods|Materials & Methods]]</td></tr><tr><td width=5px></td><td><table><tr><td width=5px></td><td>[[Team:ETH_Zurich/Wet%20Lab/Materials_Methods/MDS42|MDS42]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Wet%20Lab/Materials_Methods/MG1655|MG1655]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Wet%20Lab/Materials_Methods/pKD46|pKD46]]</td></tr></table></td></tr></table></td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Modelling|Modelling]]</td></tr><tr><td width=5px></td><td><table><tr><td width=5px></td><td>[[Team:ETH_Zurich/Modelling/RE%20Cutting%20Distribution|RE Cutting Distribution]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Modelling/Analysis%20of%20RE%20generated%20Knockout%20via%20FBA|Analysis of RE generated Knockout via FBA]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Modelling/Dynamics%20in%20Chemostat|Dynamics in Chemostat]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Modelling/Dynamics%20of%20Puls%20Generator|Dynamics of Puls Generator]]</td></tr></table></td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Conclusions|Conclusions]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Team%20Page|Team Page]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Organization|Organization]]</td></tr><tr><td width=5px></td><td>[[Team:ETH_Zurich/Introduction|Introduction]]</td></tr></table></td></tr>
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[http://www.ipe.ethz.ch/laboratories/bpl/people/panke Sven Panke], [http://www.ipe.ethz.ch/laboratories/bpl/people/meyer Andreas J&ouml;rg Meyer], [http://www.csb.ethz.ch/people/joergs J&ouml;rg Stelling].
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== Achievements ==
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[[Image:Results_seal_gold.jpg‎]][[Image:Results_seal_silver.jpg‎]][[Image:Results_seal_bronze.jpg‎]]
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For all the award relevant issues that had to be addressed, check out our [https://2008.igem.org/Team:ETH_Zurich/Project/Medal_Relevant Medal Relevant Section] in which we listed how we strived for our goals.
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<h2 style="text-align: center">Welcome to the Wiki of the ETH&nbsp;iGEM Team!</h2>
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== Site Map  ==
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! Home !! Team !! Project !! Wetlab !! Modeling !! Tools
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|-
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| [https://2008.igem.org/Team:ETH_Zurich Overview] 
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| [https://2008.igem.org/Team:ETH_Zurich/Team/Overview Overview]
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| [https://2008.igem.org/Team:ETH_Zurich/Project/Overview Overview]
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| [https://2008.igem.org/Team:ETH_Zurich/Wetlab/Overview Overview]
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| [https://2008.igem.org/Team:ETH_Zurich/Modeling/Overview Overview]
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| [https://2008.igem.org/Team:ETH_Zurich/Tools/Wiki_Templates Wiki Templates]
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| [https://2008.igem.org/Team:ETH_Zurich ETH Zuerich]  
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| [https://2008.igem.org/Team:ETH_Zurich/Team/Members Members]
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| [https://2008.igem.org/Team:ETH_Zurich/Project/Motivation Motivation]
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| [https://2008.igem.org/Team:ETH_Zurich/Wetlab/Genome_Reduction Genome Reduction]
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| [https://2008.igem.org/Team:ETH_Zurich/Modeling/Framework Framework]
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[http://www4.clustrmaps.com/user/d1a56e05 http://www4.clustrmaps.com/stats/maps-no_clusters/2008.igem.org-Team-ETH_Zurich-thumb.jpg]
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| [https://2008.igem.org/Team:ETH_Zurich/Tools/Automated_Wiki Automated Wiki]
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| [https://2008.igem.org/Team:ETH_Zurich/Credits Credits]
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| [https://2008.igem.org/Team:ETH_Zurich/Team/Pictures Pictures]
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<ref>Excel For Dummies, First Edition, Hungry Minds, Inc., 1980.</ref>
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| [https://2008.igem.org/Team:ETH_Zurich/Project/Background Background]
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| [https://2008.igem.org/Team:ETH_Zurich/Wetlab/Chemostat_Selection Chemostat Selection]
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| [https://2008.igem.org/Team:ETH_Zurich/Modeling/Genome_Static_Analysis Genome Restriction Enzyme Analysis]
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| [https://2008.igem.org/Team:ETH_Zurich/Project/Applications Applications]
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| [https://2008.igem.org/Team:ETH_Zurich/Wetlab/Switch_Circuit Switch Circuit]
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| [https://2008.igem.org/Team:ETH_Zurich/Modeling/Genome-Scale_Model Genome Scale Model]
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| [https://2008.igem.org/Team:ETH_Zurich/Project/Conclusions Conclusions]
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| [https://2008.igem.org/Team:ETH_Zurich/Wetlab/Submitted_Parts Submitted Parts]
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| [https://2008.igem.org/Team:ETH_Zurich/Modeling/Chemostat_Selection Chemostat Selection]
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| [https://2008.igem.org/Team:ETH_Zurich/Project/Medal_Relevant Medal Relevant]
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| [https://2008.igem.org/Team:ETH_Zurich/Wetlab/Safety Lab Safety]
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| [https://2008.igem.org/Team:ETH_Zurich/Modeling/Switch_Circuit Switch Circuit]
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| [https://2008.igem.org/Team:ETH_Zurich/Modeling/Download Download]
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Latest revision as of 03:14, 30 October 2008


ETH Logo.JPG

Contents

Project Abstract

'Random walks towards the minimal genome'

"This year's ETH Zurich project tackles a fundamental problem of synthetic biology: the minimal genome. Exploring the minimal set of genes that is able to support life is not only a question of significant biological interest, it is also a crucial step towards the implementation of orthogonal functionalities into a rationally designed complex biological system. An organism carrying a minimal genome would provide a simple chassis for biological engineering. We attempted to exploit the power of accelerated evolution for a genome reduction strategy. Our approach is based on an iterative cycle of genome reduction and strain selection. We propose a novel method to randomly delete chromosomal DNA fragments by controlled expression of restriction enzymes and ligases in vivo. Furthermore, we develop a chemostat-based condition to select for cells with a smaller genome size by constraining nucleotide availability. Computationally, we analyze the genome for the optimal restriction enzyme, and perform flux balance analysis on a genome scale model to predict growth of reduced genome strains. Finally, we simulate the restriction enzyme expression and the progression of selection."

"Meet us" video

The Team

Team ETH

The iGEM team 2008 follows the tradition of the ETH teams before, and consits of students from very diverse scientific backgrounds. If you'd like to know more about the team, you will find more information in the Team Section.

Undergraduate Students
Julia Slipantschuk, Sebastian Giese, Nico Hensgens, Rebecca Herbst, Reine Byun, [http://www.facebook.com/profile.php?id=804108753&ref=profile Georg Ofenbeck].


Graduate Students
Sven Lucas Dietz, Luca Gerosa, [http://www.biol.ethz.ch/IMB/groups/ban_group/members/jrabl Julius Rabl].


Advisors
[http://www.ipe.ethz.ch/laboratories/bpl/people/panke Sven Panke], [http://www.ipe.ethz.ch/laboratories/bpl/people/meyer Andreas Jörg Meyer], [http://www.csb.ethz.ch/people/joergs Jörg Stelling].

Achievements

Results seal gold.jpgResults seal silver.jpgResults seal bronze.jpg For all the award relevant issues that had to be addressed, check out our Medal Relevant Section in which we listed how we strived for our goals.

Site Map

Home Team Project Wetlab Modeling Tools
Overview Overview Overview Overview Overview Wiki Templates
ETH Zuerich Members Motivation Genome Reduction Framework Automated Wiki
Credits Pictures Background Chemostat Selection Genome Restriction Enzyme Analysis
Applications Switch Circuit Genome Scale Model
Conclusions Submitted Parts Chemostat Selection
Medal Relevant Lab Safety Switch Circuit
Download



Retrieved from "http://2008.igem.org/Team:ETH_Zurich"