SynBERC:Chassis

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This is a draft list of research topics that the SynBERC Chassis Thrust is considering for support.
Please feel free to contribute & edit.

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Contents

Conference Calls

  1. 13 December 2006 SynBERC Devices Call

Chassis Goals

Quantitative specs/measures/milestones

Goal 1 Components to be changed (quantitative goals in parens)

  • Pathway removal to free up more promoter types : (# paths = 2)
  • Cell heterogeneity -- e.g., ara transporter  : (variance x0.7)
  • Genetic code changes
    • # of codon changes (314 UAG to UAA)
    • # of novel phage restistances (10) & resistance level (x100)
  • Introduce novel chemistries into cells :
    • Amber suppressor efficiency (x1.5)
    • # of additional amino acids beyond 21 (+2)


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) Kristala

Goal 3 Dedicated DNA, RNA & protein synthetic systems

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) ChrisV
  • Remove antibiotic resistance genes : MIC (x0.1)


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 and iGEM

  1. Tumor Destroying Bacteria
  2. Microbial Drug Factories
  3. iGEM: SpeI/XbaI sites TK

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
  5. Assembly Platform: COG
  6. Programming Cells Instrumentation: GE-MASS

Societal Impact

  • Surveillance – International Consortium for Polynucleotide Synthesis (ICPS)

Other Related Items

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