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

  • 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

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

  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

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

Societal Impact

  • Surveillance – International Consortium for Polynucleotide Synthesis (ICPS)

Other Related Items

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