SynBERC:Chassis
From OpenWetWare
The is a draft list of research topics that the SynBERC Chassis Thrust is considering for support.
Please feel free to contribute & edit.
Chassis Goals
Quantitative specs/measures/milestones
Goal 1 Components to be changed
- Pathway removal (for more promoters) : # paths = 2
- Cell heterogeneity (e.g., ara transporter) : variance (x0.7)
- Code changes : #aa (2), # phage (10) & resistance level (x100)
- Introduce novel chemistries into cells : sup efficiency (x1.5)
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 : mutation rate (x0.5)
- Mutationally inactivate insertion elements & transposons : mutation rate (x0.1)
Goal 3 Dedicated DNA, RNA & protein synthetic systems
- Isolate exogenous gene function from native chromosome: I/O transfer function for main/plasmid/BAC
- Origin: Partition, Addiction : loss rate (x0.3)
- Improved recombination (x2)
- Dedicated RNA & protein systems: efficiency >10%, crosstalk <10%
- Virtual Machines & Demand specifications
Goal 4 Safety controls on the chassis
- Delete phage lysogens & receptors (e.g. LamB) : resistance level (x100)
- Delete surface toxins (Lps) : quant sepsis, innate imm. (x0.1)
- Low conjugation (Express TraS and TraT) : escape rate (x0.1)
- Add complicated or rare auxotrophies to prevent survival outside the lab (aTc-tetR, Dap) : t1/2 = 1 to 90hr; escape % (x0.01)
- Remove antibiotic resistance genes : MIC (x0.1)
Chassis Models
- 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
Societal Impact
- Safety – clinical, accidental, threat A Synthetic Biohazard Non-proliferation Proposal
- Surveillance – International Consortium for Polymer Synthesis (ICPS): Codon Devices, Blue Heron, etc.
