SynBERC:Chassis: Difference between revisions
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==Goal 4 Safety controls on the chassis == | ==Goal 4 Safety controls on the chassis == | ||
* Delete phage lysogens & receptors (e.g. LamB) : resistance level (x100) | * Delete phage lysogens & receptors (e.g. LamB) : resistance level (x100) | ||
* Delete surface toxins ( | * Delete surface toxins (Lps) : quant sepsis, innate imm. (x0.1) | ||
* Low conjugation (Express | * 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) | * 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) | * Remove antibiotic resistance genes : MIC (x0.1) | ||
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#Maximal Cells -- combinatorial selections | #Maximal Cells -- combinatorial selections | ||
=Chasses support for [[Testbeds]]= | =Chasses support for [[SynBERC:Testbeds|Testbeds]]= | ||
#[[Tumor Destroying Bacteria]] | #[[Tumor Destroying Bacteria]] | ||
#[[Microbial Drug Factories]] | #[[Microbial Drug Factories]] | ||
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# Test Constructs for Characterization | # Test Constructs for Characterization | ||
# Models that Support Data Analysis | # Models that Support Data Analysis | ||
# Scaleable [[Parts]] & [[Devices]] Screening & Selection Platforms | # Scaleable [[SynBERC:Parts|Parts]] & [[SynBERC:Devices|Devices]] Screening & Selection Platforms | ||
# Sequencing Platforms : [http://arep.med.harvard.edu/Polonator/ Polonies] | # Sequencing Platforms : [http://arep.med.harvard.edu/Polonator/ Polonies] | ||
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* Surveillance – International Consortium for Polymer Synthesis (ICPS): [http://www.codondevices.com/ Codon Devices], [http://www.blueheronbio.com/ Blue Heron], etc. | * Surveillance – International Consortium for Polymer Synthesis (ICPS): [http://www.codondevices.com/ Codon Devices], [http://www.blueheronbio.com/ Blue Heron], etc. | ||
=Other Related Projects= | =Other Related Projects= | ||
[http://arep.med.harvard.edu/SBP/ Harvard Constructive Biology Projects] | [http://arep.med.harvard.edu/SBP/ Harvard Constructive Biology Projects] | ||
Revision as of 23:18, 29 August 2006
The is a draft list of research topics that the SynBERC Chasses Thrust is considering for support.
Please feel free to contribute & edit.
Chasses 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 Chasses robust to change & minimizing mutation rates
- dam, dnaEQ, mutDHLMRSTY, oxyR, polAC, recAG, ssb, topB, ung, uvrD, vsr : mutation rate (x0.5)
- insertion elements & transposons : mutation rate (x0.1)
Goal 3 Additional chromosome(s)
- 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)
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)
Chasses Models
- Translational fidelity and pausing in novel genetic codes
- Recombination and DNA synthesis forks
- Minimal Cells
- Maximal Cells -- combinatorial selections
Chasses support for Testbeds
Chasses 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.
