IGEM:Harvard/2007/Brainstorming/ - Revision history

GeorgeXu at 02:56, 26 June 2007

GeorgeXu — Tue, 26 Jun 2007 02:56:37 GMT

←Older revision		Revision as of 02:56, 26 June 2007
Line 1:		Line 1:
	== Quorum Sensing ==		== Quorum Sensing ==

-	Basically all of the parts that are available ~~come~~ from the [http://www.che.caltech.edu/groups/fha/quorum.html LuxI/LuxR system] found in ''V. fishcheri''. The Voigt paper that we read a long time ago used this system to demonstrate cell-density dependent expression of invasin ([[Media:Voigt.pdf]]).	+	Basically all of the parts that are available are derived from the [http://www.che.caltech.edu/groups/fha/quorum.html LuxI/LuxR system] found in ''V. fishcheri''. The Voigt paper that we read a long time ago used this system to demonstrate a cell-density dependent expression of invasin in E. Coli ([[Media:Voigt.pdf]]).

	The basic idea that Perry and I discussed requires two basic parts which Perry transformed into three separate tubes of Top10 cells this afternoon:		The basic idea that Perry and I discussed requires two basic parts which Perry transformed into three separate tubes of Top10 cells this afternoon:

GeorgeXu at 02:53, 26 June 2007

GeorgeXu — Tue, 26 Jun 2007 02:53:41 GMT

←Older revision		Revision as of 02:53, 26 June 2007
Line 1:		Line 1:
	== Quorum Sensing ==		== Quorum Sensing ==

-	Basically all of the parts that are available come from the [[LuxI/LuxR system]] found in ''V. fishcheri''. The Voigt paper that we read a long time ago used this system to demonstrate cell-density dependent expression of invasin ([[Media:Voigt.pdf]]).	+	Basically all of the parts that are available come from the [http://www.che.caltech.edu/groups/fha/quorum.html LuxI/LuxR system] found in ''V. fishcheri''. The Voigt paper that we read a long time ago used this system to demonstrate cell-density dependent expression of invasin ([[Media:Voigt.pdf]]).

	The basic idea that Perry and I discussed requires two basic parts which Perry transformed into three separate tubes of Top10 cells this afternoon:		The basic idea that Perry and I discussed requires two basic parts which Perry transformed into three separate tubes of Top10 cells this afternoon:

GeorgeXu at 02:45, 26 June 2007

GeorgeXu — Tue, 26 Jun 2007 02:45:49 GMT

←Older revision		Revision as of 02:45, 26 June 2007
Line 4:		Line 4:

	The basic idea that Perry and I discussed requires two basic parts which Perry transformed into three separate tubes of Top10 cells this afternoon:		The basic idea that Perry and I discussed requires two basic parts which Perry transformed into three separate tubes of Top10 cells this afternoon:
-	# An HSL signal sender ([http://parts.mit.edu/registry/index.php/Part:BBa_F1610])	+	# An HSL signal sender ([http://parts.mit.edu/registry/index.php/Part:BBa_F1610 BBa_F1610])
	# An HSL signal receiver attached to a report		# An HSL signal receiver attached to a report
-	([http://parts.mit.edu/registry/index.php/Part:BBa_I13263] or	+	([http://parts.mit.edu/registry/index.php/Part:BBa_I13263 BBa_I13263] or
-	[http://parts.mit.edu/registry/index.php/Part:BBa_I13272])	+	[http://parts.mit.edu/registry/index.php/Part:BBa_I13272 BBa_I13272])
	The only difference between the two signal receivers is a different YFP reporter protein.		The only difference between the two signal receivers is a different YFP reporter protein.

-	A quick rundown of how it will work: we will stick some sort of promoter in front of the [http://parts.mit.edu/registry/index.php/Part:BBa_F1610] in order to produce constitutive expression of HSL. We can play around with which promoter we want to use in order to tweak the sensitivity of the system. This HSL will normally diffuse quickly. Meanwhile, there is constitutive expression of the protein produced after transcription and translation of luxR (called R from now on) is continually going on in the bacteria with the receiver. The HSL will bind to the R and these bound complexes will dimerize and activate transcription of the YFP reporter. However, normally the concentration of HSL is too low and the equilibrium highly favors unbound HSL and R. In areas of high cell concentration, the concentration of HSL will be great enough to shift the equilibrium toward the bound complex. This bound complex will then activate the transcription of the reporter gene. An interesting note is that the bound complex supposedly also represses the luxR gene according to the Biobricks parts list. However, I haven't found any confirmation of this. If it is true, then it means that along with the activation of transcription of the reporter gene the amount of luxR will decrease and transcription of the YFP reporter would probably decrease.	+	A quick rundown of how it will work: we will stick some sort of promoter in front of the [http://parts.mit.edu/registry/index.php/Part:BBa_F1610 BBa_F1610] in order to produce constitutive expression of HSL. We can play around with which promoter we want to use in order to tweak the sensitivity of the system. This HSL will normally diffuse quickly. Meanwhile, there is constitutive expression of the protein produced after transcription and translation of luxR (called R from now on) is continually going on in the bacteria with the receiver. The HSL will bind to the R and these bound complexes will dimerize and activate transcription of the YFP reporter. However, normally the concentration of HSL is too low and the equilibrium highly favors unbound HSL and R. In areas of high cell concentration, the concentration of HSL will be great enough to shift the equilibrium toward the bound complex. This bound complex will then activate the transcription of the reporter gene. An interesting note is that the bound complex supposedly also represses the luxR gene according to the Biobricks parts list. However, I haven't found any confirmation of this. If it is true, then it means that along with the activation of transcription of the reporter gene the amount of luxR will decrease and transcription of the YFP reporter would probably decrease.

	There are a few ways we could approach this:		There are a few ways we could approach this:

GeorgeXu at 02:40, 26 June 2007

GeorgeXu — Tue, 26 Jun 2007 02:40:50 GMT

←Older revision		Revision as of 02:40, 26 June 2007
Line 4:		Line 4:

	The basic idea that Perry and I discussed requires two basic parts which Perry transformed into three separate tubes of Top10 cells this afternoon:		The basic idea that Perry and I discussed requires two basic parts which Perry transformed into three separate tubes of Top10 cells this afternoon:
-	# An HSL signal sender ([[BBa_F1610]])	+	# An HSL signal sender ([http://parts.mit.edu/registry/index.php/Part:BBa_F1610])
-	# An HSL signal receiver attached to a report ([[BBa_I13263]] or [[BBa_I13272]])	+	# An HSL signal receiver attached to a report
		+	([http://parts.mit.edu/registry/index.php/Part:BBa_I13263] or
		+	[http://parts.mit.edu/registry/index.php/Part:BBa_I13272])
	The only difference between the two signal receivers is a different YFP reporter protein.		The only difference between the two signal receivers is a different YFP reporter protein.

-	A quick rundown of how it will work: we will stick some sort of promoter in front of the [[BBa_F1610]] in order to produce constitutive expression of HSL. We can play around with which promoter we want to use in order to tweak the sensitivity of the system. This HSL will normally diffuse quickly. Meanwhile, there is constitutive expression of the protein produced after transcription and translation of luxR (called R from now on) is continually going on in the bacteria with the receiver. The HSL will bind to the R and these bound complexes will dimerize and activate transcription of the YFP reporter. However, normally the concentration of HSL is too low and the equilibrium highly favors unbound HSL and R. In areas of high cell concentration, the concentration of HSL will be great enough to shift the equilibrium toward the bound complex. This bound complex will then activate the transcription of the reporter gene. An interesting note is that the bound complex supposedly also represses the luxR gene according to the Biobricks parts list. However, I haven't found any confirmation of this. If it is true, then it means that along with the activation of transcription of the reporter gene the amount of luxR will decrease and transcription of the YFP reporter would probably decrease.	+	A quick rundown of how it will work: we will stick some sort of promoter in front of the [http://parts.mit.edu/registry/index.php/Part:BBa_F1610] in order to produce constitutive expression of HSL. We can play around with which promoter we want to use in order to tweak the sensitivity of the system. This HSL will normally diffuse quickly. Meanwhile, there is constitutive expression of the protein produced after transcription and translation of luxR (called R from now on) is continually going on in the bacteria with the receiver. The HSL will bind to the R and these bound complexes will dimerize and activate transcription of the YFP reporter. However, normally the concentration of HSL is too low and the equilibrium highly favors unbound HSL and R. In areas of high cell concentration, the concentration of HSL will be great enough to shift the equilibrium toward the bound complex. This bound complex will then activate the transcription of the reporter gene. An interesting note is that the bound complex supposedly also represses the luxR gene according to the Biobricks parts list. However, I haven't found any confirmation of this. If it is true, then it means that along with the activation of transcription of the reporter gene the amount of luxR will decrease and transcription of the YFP reporter would probably decrease.

	There are a few ways we could approach this:		There are a few ways we could approach this:

GeorgeXu at 02:38, 26 June 2007

GeorgeXu — Tue, 26 Jun 2007 02:38:11 GMT

←Older revision		Revision as of 02:38, 26 June 2007
Line 1:		Line 1:
		+	== Quorum Sensing ==
		+
		+	Basically all of the parts that are available come from the [[LuxI/LuxR system]] found in ''V. fishcheri''. The Voigt paper that we read a long time ago used this system to demonstrate cell-density dependent expression of invasin ([[Media:Voigt.pdf]]).
		+
		+	The basic idea that Perry and I discussed requires two basic parts which Perry transformed into three separate tubes of Top10 cells this afternoon:
		+	# An HSL signal sender ([[BBa_F1610]])
		+	# An HSL signal receiver attached to a report ([[BBa_I13263]] or [[BBa_I13272]])
		+	The only difference between the two signal receivers is a different YFP reporter protein.
		+
		+	A quick rundown of how it will work: we will stick some sort of promoter in front of the [[BBa_F1610]] in order to produce constitutive expression of HSL. We can play around with which promoter we want to use in order to tweak the sensitivity of the system. This HSL will normally diffuse quickly. Meanwhile, there is constitutive expression of the protein produced after transcription and translation of luxR (called R from now on) is continually going on in the bacteria with the receiver. The HSL will bind to the R and these bound complexes will dimerize and activate transcription of the YFP reporter. However, normally the concentration of HSL is too low and the equilibrium highly favors unbound HSL and R. In areas of high cell concentration, the concentration of HSL will be great enough to shift the equilibrium toward the bound complex. This bound complex will then activate the transcription of the reporter gene. An interesting note is that the bound complex supposedly also represses the luxR gene according to the Biobricks parts list. However, I haven't found any confirmation of this. If it is true, then it means that along with the activation of transcription of the reporter gene the amount of luxR will decrease and transcription of the YFP reporter would probably decrease.
		+
		+	There are a few ways we could approach this:
		+	# Have both the signaller and receiver+reporter parts in the same plasmid
		+	# Have the signaller part in one plasmid and the receiver+reporter part in another plasmid, both in the same bacterium
		+	# Have two different bacteria: one with the signaller part and one with the receiver+reporter part
		+
		+	Perry asked Mike about the first two possibilities and confirmed that both should be doable. The last possibility was demonstrated in the Voigt paper.
		+
		+	I'm not completely sure what the advantages/disadvantages of each system is, but I think we should try all three possibilities.
		+
		+	Also, if we can get this to work, we could potentially build more complex systems that involve logical gates. One example paper ([[Media:Pulse.pdf]]) used two bacteria and five separate parts controlled by inducible/repressible promoters two create a pulse of fluorescence.
		+
	== Signal Transduction ==		== Signal Transduction ==

Sambu: /* Adhesion Targets */

Sambu — Mon, 25 Jun 2007 23:53:34 GMT

Adhesion Targets

←Older revision		Revision as of 23:53, 25 June 2007
Line 23:		Line 23:
	*polyester		*polyester
	*nylon fibres		*nylon fibres
-	*Could ~~use the MIT idea to~~ clone E coli that secrete pleasant smells and similarly bind to these fibers -- a living deodorant!	+	*Could clone E coli that secrete pleasant smells and similarly bind to these fibers -- a living deodorant!

Sambu: /* Adhesion Targets */

Sambu — Mon, 25 Jun 2007 23:53:09 GMT

Adhesion Targets

←Older revision		Revision as of 23:53, 25 June 2007
Line 15:		Line 15:
	Brainstorming of Possible Adhesion Targets (feel free to add/reorganize/whatever--I just thought I'd get this started):		Brainstorming of Possible Adhesion Targets (feel free to add/reorganize/whatever--I just thought I'd get this started):

-	*Keratins -- was thinking of new lines of "hair conditioners" --> these tend to add body to the hair shaft by using bonding polymers; ~~I was thinking that~~ bacteria could be the new line of "bonding polyproteinecious entities" etc etc	+	*Keratins -- was thinking of new lines of "hair conditioners" --> these tend to add body to the hair shaft by using bonding polymers; bacteria could be the new line of "bonding polyproteinecious entities" etc etc

Perry: /* 2 Component Systems */

Perry — Fri, 22 Jun 2007 15:58:58 GMT

2 Component Systems

←Older revision		Revision as of 15:58, 22 June 2007
Line 86:		Line 86:
	* Maybe look over the light sensitive bacteria paper again, they use a 2 component system there.		* Maybe look over the light sensitive bacteria paper again, they use a 2 component system there.
	<biblio>		<biblio>
-	# ~~sb2~~ pmid=16306980	+	# sb1 pmid=16306980
	</biblio>		</biblio>
-	~~<br>~~

	*Controlled spider-silk production in the presence of calcium ions or vitamin K		*Controlled spider-silk production in the presence of calcium ions or vitamin K

Shlo at 16:11, 20 June 2007

Shlo — Wed, 20 Jun 2007 16:11:52 GMT

←Older revision		Revision as of 16:11, 20 June 2007
Line 10:		Line 10:
	*Papers of Interest		*Papers of Interest
	** [[http://www.hhmi.org/research/investigators/stock.html OmpR/PhoB Overview See Figure 1]		** [[http://www.hhmi.org/research/investigators/stock.html OmpR/PhoB Overview See Figure 1]
-		+	** A common dimerization interface in bacterial response regulators KdpE and TorR (OmpR family members) PMID: 16322582 Protein Sci. 2005 Dec;14(12):3077-88.
	== Adhesion Targets ==		== Adhesion Targets ==

Shlo: /* Signal Transduction */

Shlo — Wed, 20 Jun 2007 15:52:58 GMT

Signal Transduction

←Older revision		Revision as of 15:52, 20 June 2007
Line 7:		Line 7:
	*Nick refined this idea by suggesting that we use a protein with clearly defined C-terminal and N-terminal domains as a target. We could use a protease to snip the C-terminal and N-terminal domains apart, then separately select for libraries that bind to each. Once we have sequences that bind to the C-terminal and N-terminal domains separately, we can combine those two sequences in the same plasmid. This would ensure that the two OmpR genes target different portions of the bacteria, and hopefully that they'll be brought close enough to dimerize.		*Nick refined this idea by suggesting that we use a protein with clearly defined C-terminal and N-terminal domains as a target. We could use a protease to snip the C-terminal and N-terminal domains apart, then separately select for libraries that bind to each. Once we have sequences that bind to the C-terminal and N-terminal domains separately, we can combine those two sequences in the same plasmid. This would ensure that the two OmpR genes target different portions of the bacteria, and hopefully that they'll be brought close enough to dimerize.
	-Alex		-Alex
		+
		+	*Papers of Interest
		+	** [[http://www.hhmi.org/research/investigators/stock.html OmpR/PhoB Overview See Figure 1]

	== Adhesion Targets ==		== Adhesion Targets ==