IGEM:MIT/2007/Ideas

Ideas to chew on

Some ideas from 4/23/07 meeting

M1. Bacteria with squid reflecting protein (reflectin)

• comments:
  • Brian: 6 family members, all highly homologous
  • Brian: biggest issue could be solubility problems (E. Coli)
  • Brian: try expression in different systems where folding more likely to be correct (yeast, streptomyces, etc)
  • Brian: only 1 major publication, so very little known about possible chaperones (see reference)

M2. Self mini-prepping bacteria

• comments: once triggered, will lyse, express RNases, and precipitate proteins and genomic DNA

M3. Bacteria with limited lifetime (telomeres)

• comments:
  • Brian: streptomyces bacteria have linear genome
  • Brian: e. coli w/ linear genomes have been constructed (see reference)

M4. Bacteria with removed/non-functional DNA

• comments: "minicells" will grow for several weeks

M5. Incorporating biobrick parts into minicell

• comments: difficult to produce in large quatities

M6. Magnetic alignment of bacteria

• comments:
  • Brian: surface display of peptide which binds magnetic nanoparticles (iron oxide, cobalt oxide)
  • Brian: can we control number of bound nanoparticles via concentration (i.e. one NP per bacteria)?
  • Brian: feasibility: can we generate enough force and torque on NP to align bacteria (calculations)

M7. Bacteria that illuminate when dark

• comments:

M8. Bacteria which synthesize vitamins

• comments:

M9. Sensing pH

• comments:
  • Brian: idea -- use anthocyanins as pH sensor (expressed in plants such as red cabbage)
  • Brian: E. Coli have been metabolically engineered to produce anthocyanin (see reference)

M10. Bacteria with kill switch

• comments:

M11. Bacteria battle

• comments:
  • Forrest: Austin mentioned during the 4/23/07 meeting that this could be done in 2-D (on a dish)
  • Forrest: Environmental conditions/stimuli can skew the outcome (e.g. shinning light or lowering pH causes on colony to have advantage over another)
  • Brian: Could use F factor (bacterial conjugation) as the "weapon", where Strain A delivers a repressor gene lethal to Strain B and so on.
  • Brian: Could have multiple fighting strains (e.g., A kills B, B kills C, C kills A)
  • Brian: Possible to see population oscillations? Could easily model the system...

M12. Plastic binding bacteria

• comments: credit to Reshma
  • Brian: bacteria bind to polymer plastic via surface display peptides
  • Brian: one idea: couple to growth phase -- bacteria in stationary phase bind to side of plastic tube, which those still growing can be poured out (easy separation)

M13. Luciferase Lava Lamp

• comments: credit to Reshma

M14. Organic Transistore?

• comments: using conductive M13 phage nanowires?

Random ideas from Superphage (Forrest)

F1. Engineering bacteria to operate in extreme environment (extremophiles)

• bacteria that die when not in artificially harsh environments (i.e. bacteria that 'escaped' from lab would not thrive)

http://environment.newscientist.com/article/dn11614-extremeliving-bacteria-has-genome-sequenced.html

• comments:

F2. High protein bacteria/fungus

• Easy to grow, and highly-nutritious
• To be made into bread spread for poor or disaster-striken communities
• comments:

F3. Blood clotting phage/bacteria

• function like Chitosan bandaids

http://en.wikipedia.org/wiki/Chitosan

• comments:

F4. Bacteria that process animal waste to recover nutrients

• Recover proteins and other substances from pool of farm animal waste (e.g. the edible stuff floats to the top) and add back to animal feed
• comments:

F5. Food spoilage detection

• Add non-harmful bacteria to milk, meat packaging, etc; these bacteria grow slightly more easily that the usual bacteria that make people sick, and are highly visible (e.g. bright purple) when they grow
• If consumer sees purple, if means that the food is possibly spoiled
• comments:

Random ideas from Cookb (Brian)

B1. RNA oligo synthesizing bacteria

• bacteria that produce and secrete RNA (mRNA, siRNA, RNAi, microRNA, etc)
• could be used to mass produce RNA-based therapies
• benefit from high-fidelity biological production (no error-prone commercial synthesis)
• commercial synthesis is limited to <20 bp (maybe 50 bp max)
• purification by HPLC later (and analyze by MS)
• protect RNA (chemicals protect 2'OH, could secrete as dsRNA)
• F factor secretion?