SynBERC:Chassis:13Dec06Call

(back to SynBERC Chassis)
12 December 2006 conference call

Agenda

1. Review of Chassis Research Thrust Goals
2. Chassis Specifications : Phage resistance levels, mutation rate assays, recombination efficiency, sepsis assays
3. Interface of Chasses with Devices, Practice & Testbeds

Goal 1 Components to be changed

1. 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.
2. 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

1. Anti-mutator alleles of: dam, dnaEQ, mutDHLMRSTY, oxyR, polAC, recAG, ssb, topB, ung, uvrD, or vsr -- STATUS: sequence CAD not initiated
2. Mutationally inactivate insertion elements & transposons -- STATUS: CAD initiated.

Goal 3 Dedicated DNA, RNA & protein synthetic systems

1. 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)
2. Update on Dedicated RNA & protein systems & Virtual Machines & Demand specifications?

Goal 4 Safety controls on the chassis

1. Specifications for lab development vs real-world use chassis (and interconversion) e.g. low and high conjugation and mutability
2. Alter surface(Lps & ) -- STATUS from Adam & Chris?
3. Add complicated or rare auxotrophies to prevent survival outside the lab

Chassis Models

1. Translational fidelity and pausing in novel genetic codes
2. Recombination and DNA synthesis forks
3. Minimal Cells
4. Maximal Cells -- combinatorial selections

Chassis support for Testbeds

1. Tumor Destroying Bacteria
2. Microbial Drug Factories

Chassis Characterization, Screening & Tuning

1. Test Constructs for Characterization
2. Models that Support Data Analysis
3. Scaleable Parts & Devices Screening & Selection Platforms
4. Sequencing Platforms : Polonies

Topics Arising

1. Follow up from last week on characterization of gene expression & biosynthetic devices, especially in the context of Chasiss supprot.
2. OpenWetWare Needs (lower IP incumberance): conjugation, recombination, Tn-minus, others?
3. Human Practice (Thrust 4) Surveillance and best practices – International Consortium for Polynucleotide Synthesis (ICPS) was announced at the Sloan workshop 4-Dec-2006.
4. Support for Mammalian Chassis?

Action Items

1. Chassis goals for SynBERC site visit 22/23-Feb-2007.
2. Prioritized list of "year 1" chassis needs. Can the chassis be specified in the Registry with DNA sequence information?
3. Chris & Kris, The two testbeds projects need to define a lead point of contact for testbed chassis development issues.