SynBERC:MIT/Calendar/2008-6-18

Agenda for SB

(6/18/08)

Thanks to Scott Mohr for taking down the notes we generated! Here they are (lightly edited by Scott)

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1. “Domestication of Parts” Bringing in new parts from nature/biotech.
   1. Are there obvious industrially relevant stuff that’s outside drugs/biotech (flavor/scents)?
   2. Reliable F plasmid system.
   3. Many compatible plasmid origins. We should never have to worry about having incompatible origins
   4. More sensitive reporters that work at low copy number. (Could work with high-copy number until assembly is complete, then “drop” the construct into the genome.)
   5. Process of domestication.
   6. Inducible expression systems (< 10) -- characterization not well done; not applicable across systems (and on the chromosome).
   7. Repressible expression systems.
   8. Inducible degradation not currently standardized.
   9. Autotrophic markers (?)
   10. More antibiotics.
   11. RNA...
   12. Recode genes so that they can be easily expressed in E. coli.
2. Make the work easier.
   1. BioBricks in general.
   2. DNA synthesis.
   3. Genome integration for BBs (λ-rel).
   4. CAD tools/Registry tool for assembly.
      1. (Articulate in detail and this might just happen!)
   5. Number of systems built.
   6. Sequence analysis after construction.
   7. E. coli that grows way faster.
   8. Cheaper growth medium etc.
   9. Naturally competent strain (on the wishlist for a SB model organism).
3. Engineering infrastructure and theory.
   1. How to measure.
   2. How to design scalable parts (specs.).
   3. Interoperability.
   4. Re-usability of pafrts in different contexts.
   5. What is the most reproducible system?
      1. -- low copy, high copy.
      2. -- strain.
   6. Benchmarks for interoperability or anything else.
   7. Protein fusions.
   8. Reliable RNA stability.
4. Industry relevance.
   1. Typical in engineering, SB lacking.
   2. Scale-up to industrial level.
   3. Corn steep liquor or high OD media used in industry.
   4. No antibiotics in industry.
   5. (c) and (d) cut costs and are differences with academic labs.
5. Public policy
   1. Safe chassis.
   2. Get Ken on retainer!
6. Action items.
   1. Compare list with MIT’s intellectual assets.
   2. Push MIT to fill gaps.
   3. Reach out to other fields.
   4. Start a “Manhattan Project” aimed at some clear, important target and involving development of all the preceding SB technology categories.
      1. Do you mean a Manhattan Project (i.e., classified production of weapons) or an Apollo Project (i.e., open production of some constructive artifact or capability)? Endy 18:56, 20 June 2008 (UTC)
         • BC 22:30, 20 June 2008 (UTC):I believe the project was intended to be open and for the good of all, the idea was that people from many disciplines (or at least all sub-fields within Synthetic Biology) would be need to contribute (a hallmark of the Manhattan Project).