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Synthetic Biology 3.0 Conference Proceedings Design of Parts, Devices and Systems Synthetic Biology 3.0 June 24–26, 2007 ETH Zurich, Switzerland Conference Proceedings June, 24-26, 2007 1 7^dX]^eh7^dWg^X`h I]Z7Zhid[IldLdgaYh SYNTHETIC BIOLOGY EMPOWERED BY GENIOM® HeZZYjendjggZhZVgX]i]gdj\]^bbZY^ViZVcVan" 7ZndcYb^XgdVggVnVeea^XVi^dch/<Zc^dbÉh]^\]an h^hd[cZlanZc\^cZZgZYeVgihVcYeVi]lVnhl^i] eVgVaaZa9C6hnci]Zh^hiZX]cdad\nVaadlhi]Z Xjhidb^oZYb^Xgd[aj^Y^Xb^XgdVggVnh#9Vn"id"YVn W^dX]^e"WVhZYegdYjXi^dcd[VcnYZh^gZY9C6 VggVnYZh^\cVaadlhgVe^YVYVeiVi^dcd[b^XgdÓj^Y^X hZfjZcXZÄbVYZiddgYZg[gdb[ZW^ihncW^d\bW]# W^dX]^ehidndjgegd\gZhh^ci]ZlZiaVW# EaZVhZ^cfj^gZ[dgbdgZ^c[dgbVi^dc BIOCHIPS ·b^Xgd[aj^Y^XW^dX]^eh ·ZconbVi^XgZVXi^dch hjeedgiZY ·\ZcZZmegZhh^dcegd[^a^c\ www.geniom.com ·b^XgdGC6egd[^a^c\ ·VcYbVcnbdgZ ANALYSIS SYNTHESIS BIOBRICKS ·hnci]Zi^X\ZcZh www.synbio.com ·X9C6!egdbdidgh ·da^\da^WgVg^Zh ·W^dWg^X`h GET IN CONTACT WITH US febit synbio gmbh (Heidelberg) · phone +49 6221 6510-300 · www.febit-synbio.com · info febit-synbio.com febit inc. (Boston) · phone +1 781 391 4360 · www.febit.com · info febit.com Welcome to the Synthetic Biology Conference 3.0 in Zurich! It is great that you are here to share your science, your ideas, and your visions for the progress of Synthetic Biology with a rapidly growing community of scientists and engineers that are enthusiastic about the field. We, the organizers, feel that Synthetic Biology is about to truly change our perception how we will do bioengineering in the future, and that the Synthetic Biology conference series is the adequate place to make this change visible. Synthetic Biology is still a nascent field – many of the achievements only hint at possible paths for the future, technological foundations still need to be clarified and implemented, and social implications need to be thoroughly evaluated. We tried to put together a program that reflects these requirements, but at the same time emphasizes the great enthusiasm we feel for the development of the field. We hope that you enjoy your stay here in Zurich at the conference, can get all the possible benefit out of the various sessions and discussions, and can expand your network within our community. Have fun! The SB3.0 Organizing Committee. June, 24-26, 2007 3 springer.com Call for Papers Systems and Synthetic Biology Systems and Synthetic Biology is a new biomedical journal publishing original papers and articles on all aspects of Systems and Synthetic Biology. Systems biology is an integrated approach to study collective behaviour of biological interactions. The grand challenge is to connect molecular topography with physiological responses. The systems biology fi eld will realize its fullest potential once individual contributions are tied to variations in the NEW system level behavior. The emerging fi eld of synthetic biology combines knowledge from various disciplines including molecular biology, engineering, mathematics, and physics to design and implement new cellular behaviors. The goal of synthetic biology is both to improve our quantitative understanding of natural phenomenon as well as to foster an engineering discipline for obtaining new complex cell behaviors in a predictable and reliable fashion. Systems and Synthetic Biology publishes research articles that either advance this fi eld as an engineering discipline or use synthetic biology to improve our scientifi c knowledge of existing phenomena. Systems and Synthetic Biology is accepting submissions of the following types of articles: Editorials Orginal research articles Review articles Methodology articles Software articles Commentaries Editors-in-Chief Pawan K. Dhar RIKEN Genomic Sciences Center, Yokohama, Japan Ron Weiss Princeton University, New Jersey, USA Submit online at editorialmanager.com/ssbj submit Springer off ers authors, editors and reviewers the use of its full web-enabled online manuscript ONLINE submission and review system, Editorial Manager. This off ers authors the option to track the progress of the review process of manuscripts in real time. Manuscripts should be submitted to: www.editorialmanager.com/ssbj Easy Ways to Order for the Americas Write: Springer Order Department, PO Box 2485, Secaucus, NJ 07096-2485, USA Call: (toll free) 1-800-SPRINGER Fax: +1(201)348-4505 Email: [email protected] or for outside the Americas Write: Springer Distribution Center GmbH, Haberstrasse 7, 69126 Heidelberg, Germany Call: +49 (0) 6221-345-4303 Fax: +49 (0) 6221-345-4229 Email: [email protected] 013124x Table of Contents Welcome to the Synthetic Biology Conference 3.0 in Zurich! 3 SB3.0 Conference Committee 7 General Information 9 Program at a Glance 11 Sunday, June 24: Oral Presentations 16 Monday, June 25: Oral Presentations 26 Tuesday, June 26: Oral Presentations 52 Poster Session 1 & 2 68 Participant List 187 We gratefully thank our two main sponsors: June, 24-26, 2007 5 www.theiet.org/synbio IET Synthetic Biology IET Synthetic Biology is a new journal INSIDE: The application of engineering principles to biological systems from the Institution of Engineering and Technology covering the application of Published by The Institution of Engineering and Technology | Volume 1 | Number 1 | March 2007 | ISSN 1752-1394 engineering principles to biological systems. I Worldwide readership and The journal will host an online repository Editor-in-Chief database coverage of video resources through the iet.tv Dr. Jim Haseloff I Fast publication with advance platform , specialised University of Cambridge (www.iet.tv) Editorial Board online publication review material and research information Dr. Jim Ajioka I University of Cambridge Free access to web resources for synthetic biology. Dr. Jason Chin I Online open peer review for MRC Laboratory of Molecular Biology Dr. Alistair Elfick initial short reports In the early stages of the journal’s University of Edinburgh I Prof. Andy Ellington Prompt and rigorous peer review development, all published content will University of Texas, Austin I Online submission and be freely available online. In particular, Prof. Paul Freemont Imperial College London tracking platform we wish to support the activities of Dr. Alfonso Jaramillo I No page charges young workers entering the synthetic Ecole Polytechnique, CNRS Dr. Sven Panke biology field. We currently invite the ETH, Zurich Prof. Ron Weiss submission of research and review Princeton University papers as well as short reports. For further information contact: [email protected] SB3.0 Conference Committee Local Scientific Board & Organization Committee (ETH Zurich) Sven Panke, Institute for Process Engineering Matthias Heinemann, Institute of Molecular Systems Biology Jörg Stelling, Institute of Computational Science Martin Fussenegger, Institute for Chemical and Bio-Engineering Local Organizing Committee (ETH Zurich) Frauke Greve, Institute for Process Engineering Agnes Rupacher, Institute for Process Engineering International scientific advisory board Tom Knight, Massachusetts Institute of Technology, USA Jay Keasling, UC Berkeley, USA George Church, Harvard University, USA Luis Serrano, Centre for Genomic Regulation, Spain George Attard, Southampton University, UK Phil Holliger, MRC Cambridge, UK Helmut Grubmüller, MPI Göttingen, G Frank Breitling, DKFZ Heidelberg, G Vitor Martins dos Santos, Helmholtz Centre for Infection Research, G Ruedi Aebersold, ETH Zurich, CH Markus Schmidt, IDC, Vienna, AU June, 24-26, 2007 7 Over the past three years ITI Life Sciences has committed over £50 ITI has a successful track record of working with entrepreneurial million ($98 million) to fund innovative R&D programmes ranging companies and is committed to achieving success and ensuring the from biomarkers and point-of-care diagnostics to text-mining and onward profitable commercialisation of programme outputs. stem cell technologies. So, whoever you are, if you’ve got an innovative idea, let’s see if we We actively manage funding with a long-term view and look to can make a success of it, together. transcend traditional scientific boundaries. With our research providers and commercial partners we aim to generate market-focused intellectual assets for exploitation by existing and new companies. Life Sciences real possibilities To learn more about building a successful partnership with us, please visit www.itilifesciences.com General Information Conference Location ETH Hönggerberg, Building HCI, Room G3 Wireless LAN in the HCI Building x Choose the wireless 'unsecured public network' (Windows: Click on 'view available wireless networks') x Open your browser (Firefox, Internet Explorer, ...) x Enter any external URL, e.g. 'google.com' (ETH login page will be displayed) x Username: sb3_0; password: SynBio Additionally, there is a computer room (HCI G174) available on Monday and Tuesday for the SB3.0 participants. Please use the username and password above. June, 24-26, 2007 9 Program at a Glance Sunday, June 24, 2007 Workshops 09:00 – 10:30 D2 Tutorial 1: Yeast for Synthetic Biology Stefan Hohmann, Göteborg University D8 Tutorial 2: Mathematical Models for SB Diego di Bernardo, TIGEM & Jörg Stelling, ETH Zurich 10:45 – 12:15 D2 Tutorial 3: Introduction to Microfluidics Nicolas Szita, UCL J3 Tutorial 4: iGEM and the MIT Registry Randy Rettberg, MIT 08:00 – 13:00 Foyer Registration 13:00 – 13:05 G3 Welcome Sven Panke, ETH Zurich Keynote 1 13:05 – 13:55 G3 Reading, Writing and Evolving Genomes George Church, Harvard Medical School Design of Parts, Devices and Systems 13:55 – 14:20 G3 I. CoLi Team Project iGEM Imperial 14:20 – 14:45 G3
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