IGEM:MIT/2006/System brainstorming

Post your project ideas here.

See the brainstorming of last year's team.

Rough Ideas

1. Living Lamp (RS)
2. Bacterial scents (RS)
3. Diagnostic Bacteria (BC)
4. Analog Clock (AC)
5. Square Bacteria (JK)
6. Maze (JK)
7. Algae (JK)
8. Mitochondrial Liberation & Synthetic organelle(BC)
9. genome transfer (DE)
10. meso laundry list (DE)
11. rhodopsin (AC)
12. scrapped
13. wood eater (SS)
14. wood-o-genesis(SS)

Living lamp

According to this site, most homemade lava lamps are built using a mixture of mineral oil and 70-90% isopropyl alcohol (with possibly some supplemented chemicals to help the lamp work better.) Obviously such a method wouldn't work for us.

However, according the lava lamp patent descriptions, "The clear liquid is roughly 70/30% (by volume) water and a liquid which will raise the coefficient of cubic thermal expansion and encourage the movement. The patent recommends slip agents such as propylene glycol for this. However, glycerol, ethylene glycol, and polyethylene glycol (aka PEG) are also mentioned as being sufficient." This sentence implies that we ought to be able to use something other than alcohol.

The other relevant patent says, "A display device comprising a container having two substances therein, with one of the substances being of a heavier specific gravity and immiscible with the other substance, with the first substance being of such a nature that it is either substantially solid at room temperature or is so viscous at room temperature that neither will emulsify with the other liquid, and when heat is applied to the container, the first substance will become flowable and move about in the other substance.

...The liquid in which the globule is suspended is usually dyed water, but not necessarily so. The other liquid is chosen with very many considerations in mind, including the relative densities of the liquids at the desired operating temperature; the fact that the liquids must be immiscible; the fact that the surface tension must be such that the globule does not adhere to the walls of the container; the relative coefficients of thermal expansion of the liquids; and the shapes that are obtained during operation. A suitable liquid for the globule has been found to comprise mineral oil, paraffin, carbon tetrachloride and a dye or dyes. However, undue shaking or sharp impacts, especially during transport of the display device, can cause total or partial emulsification of the globule." My guess is that most homemade lava lamps are made from an alcohol mixture because it is cheaper and possibly also easier to achieve the lava effect.

Also note that they recommend putting a dimmer switch on the bulb below the lamp to be able to regulate the heat output.

We'd have to do some research to see if media or media supplemented with something would be

1. nontoxic to cells
2. have the necessary properties to achieve the lava effect at ~37°C

References

1. Lava Lamp how-to
2. US Patent #3,570,156
3. US Patent #3,387,396

Bacterial scents

Precursor	Enzyme	Compound	Scent	References
benzoic acid & S-adenosyl-L-methionine (SAM)	S-adenosyl-L-methionine:benzoic acid carboxyl methyltransferase (BAMT)	methyl benzoate	pleasant smell	[1]
trans-cinnamic acid & S-adenosyl-L-methionine (SAM)	?	methyl cinnamate	cinnamon?
jasmonic acid & S-adenosyl-L-methionine (SAM)	S-adenosyl-L-methionine:jasmonic acid carboxyl methyltransferase (JMT)	methyl jasmonate	jasmine
salicylic acid (SA) & S-adenosyl-L-methionine (SAM)	S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase (SAMT)	methyl salicylate	wintergreen	[2, 3, 4]

Expert advice

From Natalia Dudareva, Purdue University: "I don't remember exactly, but my memory tells me that I was able to smell the compound in E. coli, although the smell was not very strong. I have also BAMT from snapdragon and BSMT from petunia, but SAMT can make both compounds, methylsalycilate and methylbenzoate, depending on provided substrate, so you don't really need different enzymes. Yes, I can provide you a construct expressing the SAMT."

From Eran Pichersky, University of Michigan: "If you feed E. coli expressing SAMT salicylic acid, they will make methylsalicylate and you will be able to smell it. In fact, we have shown the production of several scent compounds in E. coli by expressing plant scent genes. In some cases, you do not even need to feed the E. coli cells anything, because the substrates are already made by the bacteria (for example, in the case of the enzyme that makes benzyl acetate). Most of it is published, and we will be happy to provide the plant genes under an MTA. The major component of the "bad" E. coli smell is indole. It might be beneficial to inactivate the pathway that makes indole, so that the nelwy synthesized scents will be even more noticeable. P.S. You may get more informationby looking up our publications at our website ([1])"

SAMT

• C. breweri
  • DNA and protein sequence known
  • Expressed in E. coli
  • Methyl salicylate has been extracted from spent medium of E. coli cells when medium was supplemented with salicylic acid
  • Genbank AF133053
  • also can use benzoic acid as a substrate but with lower efficiency
  • crystal structure available
• A. majus (Snapdragon)
  • DNA and protein sequence known
  • Expressed in E. coli
  • Methyl salicylate has been extracted from spent medium of E. coli cells when medium was supplemented with salicylic acid
  • also can use benzoic acid as a substrate but with lower efficiency
  • Methyl benzoate has been extracted from spent medium of E. coli cells when medium was supplemented with benzoic acid
• S. floribunda
  • Genbank AJ308570
• A belladonna
  • Genbank AB049752

JMT

• A. thaliana AY008434

BAMT

• Snapdragon AF198492

References

1. Pott MB, Hippauf F, Saschenbrecker S, Chen F, Ross J, Kiefer I, Slusarenko A, Noel JP, Pichersky E, Effmert U, and Piechulla B. Biochemical and structural characterization of benzenoid carboxyl methyltransferases involved in floral scent production in Stephanotis floribunda and Nicotiana suaveolens. Plant Physiol. 2004 Aug;135(4):1946-55. DOI:10.1104/pp.104.041806 |
2. Ross JR, Nam KH, D'Auria JC, and Pichersky E. S-Adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme involved in floral scent production and plant defense, represents a new class of plant methyltransferases. Arch Biochem Biophys. 1999 Jul 1;367(1):9-16. DOI:10.1006/abbi.1999.1255 |
3. Negre F, Kolosova N, Knoll J, Kish CM, and Dudareva N. Novel S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme responsible for biosynthesis of methyl salicylate and methyl benzoate, is not involved in floral scent production in snapdragon flowers. Arch Biochem Biophys. 2002 Oct 15;406(2):261-70. DOI:10.1016/s0003-9861(02)00458-7 |
4. Zubieta C, Ross JR, Koscheski P, Yang Y, Pichersky E, and Noel JP. Structural basis for substrate recognition in the salicylic acid carboxyl methyltransferase family. Plant Cell. 2003 Aug;15(8):1704-16. DOI:10.1105/tpc.014548 |

Terpenes and terpenoids

• Terpenes are hydrocarbons: combinations of several isoprenes. (Sometimes encompasses terpenoids.)
• Terpernoids are modified terpenes with methyl groups added/removed or oxygens added
• From Wikipedia: "Terpenoids contribute to the scent of eucalyptus, the flavors of cinnamon, cloves and ginger and the color of yellow flowers. Well-known terpenoids include citral, menthol, camphor and the cannabinoids found in the Cannabis plant."

Diagnostic bacteria

I'd like to be able to add a small number of diagnostic bacteria into a larger culture to detect the presence of cells containing engineered devices in the culture. Presumably there would be BB DNA floating around from lysed bacteria (does it get cut up?). The diagnostic bacteria would need to responsd to BB DNA by glowing green or smelling minty fresh:) The response might be mediated by uptake of DNA into the diagnostic bacteria and then use the mixed connective site as a riboregulator or maybe have a membrane protein that binds specific DNA sequences and triggers a two component system. Very sketchy proposal right now. Unless we could find easy ways of doing this it would be a protein engineering project.