IGEM:MIT/2006/System brainstorming - Revision history

Jagoler at 07:16, 11 July 2006

Jagoler — Tue, 11 Jul 2006 07:16:42 GMT

←Older revision		Revision as of 07:16, 11 July 2006
Line 350:		Line 350:
	Park has discovered a strain of ''Vibrio furnissii'' which produces significant quantities of long chain hydrocarbons from fatty acids <cite>Park01 Park05 Park05a </cite>. The key pathway is from the aldehyde hexadecanal to the alcohol hexadecanol to the hydrocarbon hexadecane. Remarkably, this reduction appears to take place in an oxygen environment, making the enzyme especially interesting.		Park has discovered a strain of ''Vibrio furnissii'' which produces significant quantities of long chain hydrocarbons from fatty acids <cite>Park01 Park05 Park05a </cite>. The key pathway is from the aldehyde hexadecanal to the alcohol hexadecanol to the hydrocarbon hexadecane. Remarkably, this reduction appears to take place in an oxygen environment, making the enzyme especially interesting.

-	~~A biological sensor for hexadecane could be made from the system of Holden <cite>Holden02</cite> using the hydrocarbon sensor of ''Pseudomonas aeruginosa''.~~

	The project would be to enrich for ''V. furnissii'' strains on alkaline peptone water (with 7% NaCl see [http://www.cfsan.fda.gov/~ebam/bam-9.html here]), plate out on TCBS agar, isolate Vibrio colonies, and select hydrocarbon producers. We would then shotgun clone genomic DNA into ''E. coli'', add exogenous hexadecanol, and attempt to isolate clones producing hexadecane. Sequencing selected strains might reveal the important enzyme.		The project would be to enrich for ''V. furnissii'' strains on alkaline peptone water (with 7% NaCl see [http://www.cfsan.fda.gov/~ebam/bam-9.html here]), plate out on TCBS agar, isolate Vibrio colonies, and select hydrocarbon producers. We would then shotgun clone genomic DNA into ''E. coli'', add exogenous hexadecanol, and attempt to isolate clones producing hexadecane. Sequencing selected strains might reveal the important enzyme.

-	Several diffficulties arise: potential pathogenicity of ''V. furnissii'', likelihood of obtaining a hydrocarbon producing strain, cross reaction ~~of the Holden sensor~~ between hexadecanol and hexadecane. The strain NCTC 11218 is alleged to be non-pathogenic, although the evidence for this seems thin. It is used as a validation test for TCBS agar in microbiology labs. See Taylor <cite>Taylor81</cite>.	+	Several diffficulties arise: potential pathogenicity of ''V. furnissii'', likelihood of obtaining a hydrocarbon producing strain, cross reaction between hexadecanol and hexadecane. The strain NCTC 11218 is alleged to be non-pathogenic, although the evidence for this seems thin. It is used as a validation test for TCBS agar in microbiology labs. See Taylor <cite>Taylor81</cite>.

	Wackett at the University of Minnesota has started looking at this with this short proposal:		Wackett at the University of Minnesota has started looking at this with this short proposal:

Jason R. Kelly at 16:54, 6 June 2006

Jason R. Kelly — Tue, 06 Jun 2006 16:54:32 GMT

←Older revision		Revision as of 16:54, 6 June 2006
Line 2:		Line 2:
	#[[IGEM:MIT/2006/System brainstorming/Smell-o-Rama]]		#[[IGEM:MIT/2006/System brainstorming/Smell-o-Rama]]
	#[[IGEM:MIT/2006/Other]]		#[[IGEM:MIT/2006/Other]]
-		+	#[[IGEM:MIT/2006/System brainstorming/Autotrophic bacteria]] - filed some in in case its still on the table?

	'''Post your project ideas here.'''		'''Post your project ideas here.'''

Skatebro: /* Shortlist */

Skatebro — Tue, 06 Jun 2006 14:35:47 GMT

Shortlist

←Older revision		Revision as of 14:35, 6 June 2006
Line 8:		Line 8:
	See the [[IGEM:MIT/2005/System Brainstorm\|brainstorming]] of last year's team.		See the [[IGEM:MIT/2005/System Brainstorm\|brainstorming]] of last year's team.

-	#[[/Scent ~~Subprojects~~/]]	+	#[[/Scent subprojects/]]

	==Rough Ideas==		==Rough Ideas==

Skatebro: /* Shortlist */

Skatebro — Tue, 06 Jun 2006 14:20:13 GMT

Shortlist

←Older revision		Revision as of 14:20, 6 June 2006
Line 1:		Line 1:
	==Shortlist==		==Shortlist==
	#[[IGEM:MIT/2006/System brainstorming/Smell-o-Rama]]		#[[IGEM:MIT/2006/System brainstorming/Smell-o-Rama]]
-	#[[IGEM:MIT/2006~~/System brainstorming/Autotrophic E.coli~~/Other]]	+	#[[IGEM:MIT/2006/Other]]

Skatebro: /* Shortlist */

Skatebro — Tue, 06 Jun 2006 14:14:36 GMT

Shortlist

←Older revision		Revision as of 14:14, 6 June 2006
Line 1:		Line 1:
	==Shortlist==		==Shortlist==
	#[[IGEM:MIT/2006/System brainstorming/Smell-o-Rama]]		#[[IGEM:MIT/2006/System brainstorming/Smell-o-Rama]]
-	#[[IGEM:MIT/2006/Other]]	+	#[[IGEM:MIT/2006/System brainstorming/Autotrophic E.coli/Other]]


Line 8:		Line 8:
	See the [[IGEM:MIT/2005/System Brainstorm\|brainstorming]] of last year's team.		See the [[IGEM:MIT/2005/System Brainstorm\|brainstorming]] of last year's team.

-	#[[/Scent ~~subprojects~~/]]	+	#[[/Scent Subprojects/]]

	==Rough Ideas==		==Rough Ideas==

Austin J. Che: /* Shortlist */

Austin J. Che — Tue, 06 Jun 2006 13:01:00 GMT

Shortlist

←Older revision		Revision as of 13:01, 6 June 2006
Line 8:		Line 8:
	See the [[IGEM:MIT/2005/System Brainstorm\|brainstorming]] of last year's team.		See the [[IGEM:MIT/2005/System Brainstorm\|brainstorming]] of last year's team.

-	#[[~~scent~~ subprojects]]	+	#[[/Scent subprojects/]]

	==Rough Ideas==		==Rough Ideas==

Jason R. Kelly: /* Autotrophic e.coli */

Jason R. Kelly — Tue, 06 Jun 2006 06:35:29 GMT

Autotrophic e.coli

←Older revision		Revision as of 06:35, 6 June 2006
Line 469:		Line 469:

	This project would involve "domesticating" this system by getting the relevant genes either chromosomally integrated or all on a single BioBrick plasmid. We would be able to tell its working at a first pass by just seeing that the cells turn red, and we could follow up by doing pH measurements as specified by [[DeLong Lab\|Ed Delong's group]]. We could also determine the other steps necessary to make E.coli truly autotrophic and start on those if we have time. The eventual goal is e.coli that grows on minimal media with no carbon source. bam!		This project would involve "domesticating" this system by getting the relevant genes either chromosomally integrated or all on a single BioBrick plasmid. We would be able to tell its working at a first pass by just seeing that the cells turn red, and we could follow up by doing pH measurements as specified by [[DeLong Lab\|Ed Delong's group]]. We could also determine the other steps necessary to make E.coli truly autotrophic and start on those if we have time. The eventual goal is e.coli that grows on minimal media with no carbon source. bam!
		+
		+	===Calvin Cycle (the "dark reactions")===
		+	So check [http://peds.oxfordjournals.org/cgi/content/abstract/19/3/113 this out]. In an effort to do directed evolution on RuBisCO, these folks partially reconstructed the Calvin cycle in E.Coli (wt E.coli naturally expresses 8 of 11 of the required calvin cycle enzymes), by adding RuBisCO & phosphoribulokinase from cyanobacteria PCC6301 and PCC7492, respectively. Anyway, these cells needed CO2 to grow (as well as a pentose C-source), so this looks to be something close to the other piece of the puzzle. I have to do my e.coli metabolism HWK, but it seems like it might be possible to fill in the other calvin cycle genes, hook up the light-driven proton pump and then grow on minimal media.
		+
		+	===Organization===
		+	I think this project divides up nicely into the two areas outlined above (assuming those make sense, more hwk reqd). It would also provide 2 intermediate goals - i.e. get proton pump/calvin cycle working, as well as a final goal -- integrate and grow on minimal. shezam!
		+
		+
		+

	===References===		===References===
	[[Image:PACCAR16.JPG\|thumb\|left\|pACCAR16 plasmid structure]]		[[Image:PACCAR16.JPG\|thumb\|left\|pACCAR16 plasmid structure]]

Skatebro: /* Shortlist */

Skatebro — Tue, 06 Jun 2006 05:28:19 GMT

Shortlist

←Older revision		Revision as of 05:28, 6 June 2006
Line 1:		Line 1:
	==Shortlist==		==Shortlist==
	#[[IGEM:MIT/2006/System brainstorming/Smell-o-Rama]]		#[[IGEM:MIT/2006/System brainstorming/Smell-o-Rama]]
-	#[[IGEM:MIT/2006/~~System brainstorming/Autotrophic bacteria~~]]	+	#[[IGEM:MIT/2006/Other]]

Skatebro: /* Shortlist */

Skatebro — Tue, 06 Jun 2006 02:57:53 GMT

Shortlist

←Older revision		Revision as of 02:57, 6 June 2006
Line 7:		Line 7:

	See the [[IGEM:MIT/2005/System Brainstorm\|brainstorming]] of last year's team.		See the [[IGEM:MIT/2005/System Brainstorm\|brainstorming]] of last year's team.
		+
		+	#[[scent subprojects]]

	==Rough Ideas==		==Rough Ideas==

Boyuanzhu: /* Shortlist */

Boyuanzhu — Mon, 05 Jun 2006 20:31:21 GMT

Shortlist

←Older revision		Revision as of 20:31, 5 June 2006
Line 1:		Line 1:
	==Shortlist==		==Shortlist==
	#[[IGEM:MIT/2006/System brainstorming/Smell-o-Rama]]		#[[IGEM:MIT/2006/System brainstorming/Smell-o-Rama]]
-	~~#[[IGEM:MIT/2006/System brainstorming/Power supply florum]]~~
	#[[IGEM:MIT/2006/System brainstorming/Autotrophic bacteria]]		#[[IGEM:MIT/2006/System brainstorming/Autotrophic bacteria]]