1. Chassis Parts jukebox : Meta-device : few strains Focus of system designs & integration Standardization, composability, abstraction Interface with environment, power supply Interface with computers: CAD, measurements Human practice: Safety & process engineering

2. Chassis Goals Genome Engineering - Multiplex Automation Accelerated evolution (GE-MASS targeting) Decelerated evolution in production (e.g. Tn- & antimutators) Data > model > CAD for efficient allele replacement Why genome-wide chassis engineering? Codon changes for multi-virus resistance Eliminate transposons (Tn-) Change restriction sites Orthogonal expression systems & compartments

3. Synergy with Thrusts & Testbeds Parts & Devices – chassis for surface display devices, eliminate restriction sites (CTAG); Construction Optimization Group (COG) meetings; IGEM Human Practices – motivation for genome isolation (via codons), ecological-testing, http://www.ia-sb.eu/ http://www.ia-sb.eu/ Tumor-killing bacterium (TKB) – inherent release hence safety features – metabolic “disabling tech” Microbial Chemical Factory (MCF) – multi-promoter & multi-RBS tuning via GE-MASS; Tn- stability

4. Thrust 3: Chassis Design & Characterization 11:00-11:20 AM Tue 4-Mar-2008 Carlos Bustamente, Anton Vila-Sanjurjo – mt-minigenome Drew Endy, Barry Canton – orthogonal expression Tom Knight – Mesoplasma florum Farren Isaacs, Harris Wang – MAGE & new codes Duhee Bang, Mike Jewett - in vitro & chiral engineering

5. Thrust 3: Chassis Design & Characterization 10:00-10:30 AM Tue 21-Sep-2008 Brad Zamft, Carlos Bustamante, Natalie Kuldell– The Mitochondria as a Minimal Chassis: Expanding the Toolkit for Mitochondrial Genomic Engineering Farren Isaacs &Harris Wang – GEMASS & new codes Mike Jewett - in vitro chassis

6. Why Minigenomes Tom Knight Mesoplasma florum ~750 genes Carlos Bustamante Mitochondrion ~1500 genes Mike Jewett E.coli in vitro 151 genes Ease of synthesis More radical designs Existing applications -Roche Rapid Translation System (RTS) -Ambion ActivePro In Vitro Translation Kit -Novagen, Promega, Invitrogen, Qiagen Stratagene, Paragon, Amersham

7. 113 kbp DNA 151 genes Pure translation: Forster & Church MSB ’05 GenomeRes.’06 Shimizu, Ueda ’01 Not minimal: High speed & accuracy requires a few extra genes (E.coli 20 min. doubling) Reconstituted ribosomes: Jewett & Church

8. Despite early success in 1968, assembly of ribosomes under conditions compatible with protein synthesis has been elusive (until Aug 2008)

10. Improving process yield & safety: trade-off or win-win? What do most biological systems fear? What do all viruses have in common?

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