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Chassis

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. Chassis Goals.

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Chassis

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  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/ 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 vitro151 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. Not minimal:High speed & accuracy requires a few extra genes(E.coli 20 min. doubling) Reconstituted ribosomes:Jewett & Church 113 kbp DNA 151 genes Pure translation: Forster & Church MSB ’05 GenomeRes.’06 Shimizu, Ueda ’01

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

  9. 50S and 30S ribosomal subunits simultaneously reconstituted at 37°C and constant [Mg2+] express active luciferase

  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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