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.