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)
  • Forrest: We have peptide sequences that bind to an electically conducting polymer (PPyCl) (NATURE MATERIALS 4 (6): 496-502 JUN 2005)

M13. Luciferase Lava Lamp

• comments: credit to Reshma

M14. Organic Transister?

• comments:
  • using conductive M13 phage nanowires?
  • Forrest: For electrical transister, M13 phage is not suitable because it's difficult to program both the head and tail to bind to electrodes. In the past, someone has been able to bind the tail end to an electrode and play with flow to get the head to make contact with another electrode. Not sure how much more we can improve on...

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:

F6. Fungus-based sensors

• Sensing: ammonia (NH3), CO2, light, stresses (osmotic shock, temperature, salt), UV, other fungi

http://www.nature.com/nrmicro/journal/v5/n1/full/nrmicro1578.html http://www.jstor.org/view/00368075/ap003641/00a00190/0?frame=noframe&userID=123301de@mit.edu/01cc99332600501bc0a90&dpi=3&config=jstor

• 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?