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[[SynBERC | back to SynBERC on OWW]] | [[SynBERC | back to SynBERC on OWW]] | ||
''' | '''This is a draft list of research topics that the SynBERC Chassis Thrust is considering for support.''' <br> | ||
<font color="red">'''Please feel free to contribute & edit.'''</font><br> | <font color="red">'''Please feel free to contribute & edit.'''</font><br> | ||
Join the [[List:Synberc-chassis|mailing list]]! | |||
=Conference Calls= | |||
#[[SynBERC:Chassis:13Dec06Call|13 December 2006 SynBERC Devices Call]] | |||
=Chassis Goals= | =Chassis Goals= | ||
Quantitative specs/measures/milestones | Quantitative specs/measures/milestones | ||
==Goal 1 Components to be changed== | ==Goal 1 Components to be changed (quantitative goals in parens)== | ||
* Pathway removal | * Pathway removal to free up more promoter types : (# paths = 2) | ||
* Cell heterogeneity | * Cell heterogeneity -- e.g., ara transporter : (variance x0.7) | ||
* | * Genetic code changes | ||
* Introduce novel chemistries into cells : | ** # 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 == | ==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 | * 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 | * Mutationally inactivate insertion elements & transposons : (mutation rate x0.1) Kristala | ||
==Goal 3 | ==Goal 3 Dedicated DNA, RNA & protein synthetic systems == | ||
* Isolate exogenous gene function from native chromosome: I/O transfer function for main/plasmid/BAC | * Isolate exogenous gene function from native chromosome: I/O transfer function for main/plasmid/BAC | ||
* Origin: Partition, Addiction : loss rate | * Origin: Partition, Addiction : (loss rate x0.3) | ||
* Improved recombination (x2) | * Improved recombination (x2) | ||
* [[Endy:Dedicated_systems|Dedicated RNA & protein systems]]: (efficiency >10%, crosstalk <10%) | |||
* [[Endy:Dedicated_systems/Virtual_machines| Virtual Machines]] & [[Endy:Translation_demand|Demand specifications]] | |||
==Goal 4 Safety controls on the chassis == | ==Goal 4 Safety controls on the chassis == | ||
| Line 27: | Line 39: | ||
* Delete surface toxins (Lps) : quant sepsis, innate imm. (x0.1) | * Delete surface toxins (Lps) : quant sepsis, innate imm. (x0.1) | ||
* Low conjugation (Express TraS and TraT) : escape rate (x0.1) | * Low conjugation (Express TraS and TraT) : escape rate (x0.1) | ||
* Add complicated or rare auxotrophies to prevent survival outside the lab | * 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) | * Remove antibiotic resistance genes : [http://en.wikipedia.org/wiki/Minimum_inhibitory_concentration MIC] (x0.1) | ||
| Line 37: | Line 49: | ||
#Maximal Cells -- combinatorial selections | #Maximal Cells -- combinatorial selections | ||
=Chassis support for [[SynBERC:Testbeds|Testbeds]]= | =Chassis support for [[SynBERC:Testbeds|Testbeds]] and [[iGEM]]= | ||
#[[Tumor Destroying Bacteria]] | #[[Tumor Destroying Bacteria]] | ||
#[[Microbial Drug Factories]] | #[[SynBERC:Drugs | Microbial Drug Factories]] | ||
#iGEM: [[Tk:E._coli_cut_sites|SpeI/XbaI sites]] TK | |||
=Chassis Characterization, Screening & Tuning= | =Chassis Characterization, Screening & Tuning= | ||
| Line 46: | Line 59: | ||
# Scaleable [[SynBERC:Parts|Parts]] & [[SynBERC:Devices|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] | ||
# Assembly Platform: COG | |||
# Programming Cells Instrumentation: GE-MASS | |||
=Societal Impact= | =Societal Impact= | ||
* Safety – clinical, accidental, threat [http://arep.med.harvard.edu/SBP/Church_Biohazard04c.htm A Synthetic Biohazard Non-proliferation Proposal] | * Safety – clinical, accidental, threat [http://arep.med.harvard.edu/SBP/Church_Biohazard04c.htm A Synthetic Biohazard Non-proliferation Proposal] | ||
* Surveillance – International Consortium for | * Surveillance – International Consortium for Polynucleotide Synthesis ([http://pgen.us/ICPS.htm ICPS]) | ||
=Other Related Items= | =Other Related Items= | ||
*[http://arep.med.harvard.edu/SBP/ Harvard Constructive Biology Projects] | *[http://arep.med.harvard.edu/SBP/ Harvard Constructive Biology Projects] | ||
*[[SynBERC:Chassis/Team]] | *[[SynBERC:Chassis/Team]] | ||
*[[Standard_E._coli_Strain_for_BioBricks|Standard ''E. coli'' Strain for BioBricks]] | |||
Latest revision as of 05:37, 9 July 2008
This is a draft list of research topics that the SynBERC Chassis Thrust is considering for support.
Please feel free to contribute & edit.
Join the mailing list!
Conference Calls
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
- 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) ChrisV
- 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 and iGEM
Chassis Characterization, Screening & Tuning
- Test Constructs for Characterization
- Models that Support Data Analysis
- Scaleable Parts & Devices Screening & Selection Platforms
- Sequencing Platforms : Polonies
- Assembly Platform: COG
- Programming Cells Instrumentation: GE-MASS
Societal Impact
- Safety – clinical, accidental, threat A Synthetic Biohazard Non-proliferation Proposal
- Surveillance – International Consortium for Polynucleotide Synthesis (ICPS)
