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(back to SynBERC Chassis)
12 December 2006 conference call
- 1 Agenda
- 2 Goal 1 Components to be changed
- 3 Goal 2 Chassis robust to change & minimizing mutation rates
- 4 Goal 3 Dedicated DNA, RNA & protein synthetic systems
- 5 Goal 4 Safety controls on the chassis
- 6 Chassis Models
- 7 Chassis support for Testbeds
- 8 Chassis Characterization, Screening & Tuning
- 9 Topics Arising
- 10 Action Items
- Review of Chassis Research Thrust Goals
- Chassis Specifications : Phage resistance levels, mutation rate assays, recombination efficiency, sepsis assays
- Interface of Chasses with Devices, Practice & Testbeds
Goal 1 Components to be changed
- Code changes (UAG to UAA) -- STATUS: CAD complete, new allele replacement method implemented and 7 of 40 essential gene UAG codons replaced using it. RF1 gene conditional alleles constructed.
- Introduce novel chemistries into cells -- STATUS: MCB100 class introducing novel amino acid for the UAG-minus strain
Goal 2 Chassis robust to change & minimizing mutation rates
- Anti-mutator alleles of: dam, dnaEQ, mutDHLMRSTY, oxyR, polAC, recAG, ssb, topB, ung, uvrD, or vsr -- STATUS: sequence CAD not initiated
- Mutationally inactivate insertion elements & transposons -- STATUS: CAD initiated.
Goal 3 Dedicated DNA, RNA & protein synthetic systems
- Replication origin, conjugation, recombination -- STATUS: Andy Tolonen has multi-Mbp conjugation working and is setting up half-genome system in recognition of lagging-strand allelereplacement stategy (above)
- Update on Dedicated RNA & protein systems & Virtual Machines & Demand specifications?
Goal 4 Safety controls on the chassis
- Specifications for lab development vs real-world use chassis (and interconversion) e.g. low and high conjugation and mutability
- Alter surface(Lps & ) -- STATUS from Adam & Chris?
- Add complicated or rare auxotrophies to prevent survival outside the lab
- Translational fidelity and pausing in novel genetic codes
- Recombination and DNA synthesis forks
- Minimal Cells
- Maximal Cells -- combinatorial selections
Chassis support for Testbeds
Chassis Characterization, Screening & Tuning
- Test Constructs for Characterization
- Models that Support Data Analysis
- Scaleable Parts & Devices Screening & Selection Platforms
- Sequencing Platforms : Polonies
- Follow up from last week on characterization of gene expression & biosynthetic devices, especially in the context of Chasiss supprot.
- OpenWetWare Needs (lower IP incumberance): conjugation, recombination, Tn-minus, others?
- Human Practice (Thrust 4) Surveillance and best practices – International Consortium for Polynucleotide Synthesis (ICPS) was announced at the Sloan workshop 4-Dec-2006.
- Support for Mammalian Chassis?
- Chassis goals for SynBERC site visit 22/23-Feb-2007.
- Prioritized list of "year 1" chassis needs. Can the chassis be specified in the Registry with DNA sequence information?
- Chris & Kris, The two testbeds projects need to define a lead point of contact for testbed chassis development issues.