User:ShLo - Revision history

Shlo: Redirecting to Shlo/notebook

2007-07-12T16:48:34Z

←Older revision		Revision as of 16:48, 12 July 2007
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-	~~Stephanie Lo <br>~~	+	#redirect[[shlo/notebook]]
-	~~Harvard College 2010~~	+
-	~~<Br><Br>~~	+
-	~~c/o Harvard College PRISE<br>~~	+
-	~~Leverett Mail Center<br>~~	+
-	~~28 DeWolfe Street<br>~~	+
-	~~Cambridge, MA 02138~~	+
-	~~<br><br>~~	+
-		+
-	I have always had a passion for sciences, particularly chemistry, and hope to pursue a joint concentration in Molecular and Cellular Biology and Economics. Eventually, I plan to apply for an MD/PhD program and specialize in digestive disorders.	+
-	~~<br><br>~~	+
-		+
-	[[shlo/notebook]]	+
-		+
-		+
-		+
-		+
-	~~[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM~~]	+

Shlo at 23:43, 20 June 2007

2007-06-20T23:43:20Z

←Older revision		Revision as of 23:43, 20 June 2007
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	[[shlo/notebook]]		[[shlo/notebook]]

-	~~<br>~~
-	~~NanoDrop results (6/20) performed by Ellenor and Stephanie:<br>~~
-	~~(1.5 uL used out of a 30uL elution with nuclease free water)<br>~~

-	~~S: 10.9 ng/uL<br>~~
-	~~S2: 15.4 ng/uL<br>~~
-	~~B: 59.1 ng/uL<br>~~
-	~~B1: 25.1 ng/uL<br>~~
-
-	~~<br><br><br>~~
-	~~Brainstorming for the two-component systems (really for my own use for now - not expected to be coherent)<br>~~
-	[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=10653699&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus Structural comparison of the PhoB and OmpR DNA binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box]<br>
-	-NMR used to determine 3DE structure of PhoB DNA-binding/transactivation domain. Very similar to OmpR DNA-binding/transactivation domain, except for conformation of the long turn region of PhoB (interaction site for sigma subunit, rather than interaction with alpha subunit for OmpR)
-	~~<br><br>~~
-	~~[http://jb.asm.org.ezp1.harvard.edu/cgi/content/full/185/1/317?view=long&pmid=12486069 Interdomain linkers of homologous response regulators determine their mechanism of action]<br>~~
-	Focuses on OmpR and PhoB and, as the title suggests, supports that phosphorylation of sites (particularly N-terminus of both proteins) improves affinity to bind DNA. Isolated C terminus of OmpR is insufficient to productively interact with RNA polymerase. <br>
-	~~I've been told by some of the lab members that OmpR is an inner-membrane protein and therefore cannot be used for our assays. It seems that we'll have to find another protein ...<br>~~
-	~~<br>~~
-	[http://www.ncbi.nlm.nih.gov.ezp1.harvard.edu/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=11325944&ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum The phosphoryl transfer domain of UhpB interacts with the response regulator UhpA]
-	~~<br> UhpB = histidine kinase protein that controls production of sugar phosphate transporter UhpT<br>~~
-	~~UhpA = response regulator; when phosphate is transferred from histidine to aspartate, ability of kinase to bind to target DNA sequences and to alter gene transcription is altered.~~
-	~~<br> Major result: indication that phosphoryl, transfer-dimerization of UhpB participates in specific binding of UhpA, in control of autokinase activity, and dephosphorylation of P-UhpA<br>~~
-	... So I found this paper on a search on PubMed for e coli outer membrane protein signaling dimerization. However, I've found that UhpA resides in the cytoplasm, whereas UhpB is an inner-membrane protein. Boo.<br>
-	More thoughts: we could potentially try to target some of these inner-membrane proteins to the outer-membrane. I don't know if this is really feasible - while we can attach the appropriate signal sequence, I'm not sure the environment would allow for correct conformation and activity of said proteins.


	[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]		[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]

Shlo at 23:42, 20 June 2007

2007-06-20T23:42:50Z

←Older revision		Revision as of 23:42, 20 June 2007
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	<br><br>		<br><br>

-	[[notebook]]	+	[[shlo/notebook]]

	<br>		<br>

Shlo at 23:42, 20 June 2007

2007-06-20T23:42:30Z

←Older revision		Revision as of 23:42, 20 June 2007
Line 10:		Line 10:
	I have always had a passion for sciences, particularly chemistry, and hope to pursue a joint concentration in Molecular and Cellular Biology and Economics. Eventually, I plan to apply for an MD/PhD program and specialize in digestive disorders.		I have always had a passion for sciences, particularly chemistry, and hope to pursue a joint concentration in Molecular and Cellular Biology and Economics. Eventually, I plan to apply for an MD/PhD program and specialize in digestive disorders.
	<br><br>		<br><br>
		+
		+	[[notebook]]

	<br>		<br>

Shlo at 19:51, 20 June 2007

2007-06-20T19:51:13Z

←Older revision		Revision as of 19:51, 20 June 2007
Line 33:		Line 33:
	UhpA = response regulator; when phosphate is transferred from histidine to aspartate, ability of kinase to bind to target DNA sequences and to alter gene transcription is altered.		UhpA = response regulator; when phosphate is transferred from histidine to aspartate, ability of kinase to bind to target DNA sequences and to alter gene transcription is altered.
	<br> Major result: indication that phosphoryl, transfer-dimerization of UhpB participates in specific binding of UhpA, in control of autokinase activity, and dephosphorylation of P-UhpA<br>		<br> Major result: indication that phosphoryl, transfer-dimerization of UhpB participates in specific binding of UhpA, in control of autokinase activity, and dephosphorylation of P-UhpA<br>
-	... So I found this paper on a search on PubMed for e coli outer membrane protein signaling dimerization. However, I've found that UhpA resides in the cytoplasm, whereas UhpB is an inner-membrane protein. Boo.	+	... So I found this paper on a search on PubMed for e coli outer membrane protein signaling dimerization. However, I've found that UhpA resides in the cytoplasm, whereas UhpB is an inner-membrane protein. Boo.<br>
		+	More thoughts: we could potentially try to target some of these inner-membrane proteins to the outer-membrane. I don't know if this is really feasible - while we can attach the appropriate signal sequence, I'm not sure the environment would allow for correct conformation and activity of said proteins.


	[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]		[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]

Shlo at 19:38, 20 June 2007

2007-06-20T19:38:21Z

←Older revision		Revision as of 19:38, 20 June 2007
Line 33:		Line 33:
	UhpA = response regulator; when phosphate is transferred from histidine to aspartate, ability of kinase to bind to target DNA sequences and to alter gene transcription is altered.		UhpA = response regulator; when phosphate is transferred from histidine to aspartate, ability of kinase to bind to target DNA sequences and to alter gene transcription is altered.
	<br> Major result: indication that phosphoryl, transfer-dimerization of UhpB participates in specific binding of UhpA, in control of autokinase activity, and dephosphorylation of P-UhpA<br>		<br> Major result: indication that phosphoryl, transfer-dimerization of UhpB participates in specific binding of UhpA, in control of autokinase activity, and dephosphorylation of P-UhpA<br>
-	... So I found this paper on a search on PubMed for e coli outer membrane protein signaling dimerization. However, I'~~m not sure~~ that the ~~dimerization during this process~~ is ~~appropriate for the type of protocol we're investigating. ... I obviously have to think about this a lot more .~~..	+	... So I found this paper on a search on PubMed for e coli outer membrane protein signaling dimerization. However, I've found that UhpA resides in the cytoplasm, whereas UhpB is an inner-membrane protein. Boo.


	[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]		[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]

Shlo at 19:22, 20 June 2007

2007-06-20T19:22:16Z

←Older revision		Revision as of 19:22, 20 June 2007
Line 31:		Line 31:
	[http://www.ncbi.nlm.nih.gov.ezp1.harvard.edu/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=11325944&ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum The phosphoryl transfer domain of UhpB interacts with the response regulator UhpA]		[http://www.ncbi.nlm.nih.gov.ezp1.harvard.edu/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=11325944&ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum The phosphoryl transfer domain of UhpB interacts with the response regulator UhpA]
	<br> UhpB = histidine kinase protein that controls production of sugar phosphate transporter UhpT<br>		<br> UhpB = histidine kinase protein that controls production of sugar phosphate transporter UhpT<br>
-	UhpA = response regulator; when phosphate is transferred from histidine to aspartate, ability of kinase to bind to target DNA sequences and to alter gene transcription is altered ~~<br>~~	+	UhpA = response regulator; when phosphate is transferred from histidine to aspartate, ability of kinase to bind to target DNA sequences and to alter gene transcription is altered.
	<br> Major result: indication that phosphoryl, transfer-dimerization of UhpB participates in specific binding of UhpA, in control of autokinase activity, and dephosphorylation of P-UhpA<br>		<br> Major result: indication that phosphoryl, transfer-dimerization of UhpB participates in specific binding of UhpA, in control of autokinase activity, and dephosphorylation of P-UhpA<br>
	... So I found this paper on a search on PubMed for e coli outer membrane protein signaling dimerization. However, I'm not sure that the dimerization during this process is appropriate for the type of protocol we're investigating. ... I obviously have to think about this a lot more ...		... So I found this paper on a search on PubMed for e coli outer membrane protein signaling dimerization. However, I'm not sure that the dimerization during this process is appropriate for the type of protocol we're investigating. ... I obviously have to think about this a lot more ...

Shlo at 19:21, 20 June 2007

2007-06-20T19:21:58Z

←Older revision		Revision as of 19:21, 20 June 2007
Line 28:		Line 28:
	Focuses on OmpR and PhoB and, as the title suggests, supports that phosphorylation of sites (particularly N-terminus of both proteins) improves affinity to bind DNA. Isolated C terminus of OmpR is insufficient to productively interact with RNA polymerase. <br>		Focuses on OmpR and PhoB and, as the title suggests, supports that phosphorylation of sites (particularly N-terminus of both proteins) improves affinity to bind DNA. Isolated C terminus of OmpR is insufficient to productively interact with RNA polymerase. <br>
	I've been told by some of the lab members that OmpR is an inner-membrane protein and therefore cannot be used for our assays. It seems that we'll have to find another protein ...<br>		I've been told by some of the lab members that OmpR is an inner-membrane protein and therefore cannot be used for our assays. It seems that we'll have to find another protein ...<br>
		+	<br>
		+	[http://www.ncbi.nlm.nih.gov.ezp1.harvard.edu/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=11325944&ordinalpos=6&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum The phosphoryl transfer domain of UhpB interacts with the response regulator UhpA]
		+	<br> UhpB = histidine kinase protein that controls production of sugar phosphate transporter UhpT<br>
		+	UhpA = response regulator; when phosphate is transferred from histidine to aspartate, ability of kinase to bind to target DNA sequences and to alter gene transcription is altered <br>
		+	<br> Major result: indication that phosphoryl, transfer-dimerization of UhpB participates in specific binding of UhpA, in control of autokinase activity, and dephosphorylation of P-UhpA<br>
		+	... So I found this paper on a search on PubMed for e coli outer membrane protein signaling dimerization. However, I'm not sure that the dimerization during this process is appropriate for the type of protocol we're investigating. ... I obviously have to think about this a lot more ...


	[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]		[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]

Shlo at 19:09, 20 June 2007

2007-06-20T19:09:44Z

←Older revision		Revision as of 19:09, 20 June 2007
Line 31:		Line 31:

	[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]		[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]
-	~~[[Media:Example.ogg]]~~

Shlo at 19:09, 20 June 2007

2007-06-20T19:09:26Z

←Older revision		Revision as of 19:09, 20 June 2007
Line 22:		Line 22:
	<br><br><br>		<br><br><br>
	Brainstorming for the two-component systems (really for my own use for now - not expected to be coherent)<br>		Brainstorming for the two-component systems (really for my own use for now - not expected to be coherent)<br>
-	[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=10653699&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus Structural comparison of the PhoB and OmpR DNA binding/transactivation domains and ~~teh~~ arrangement of PhoB molecules on the phosphate box]	+	[http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=10653699&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus Structural comparison of the PhoB and OmpR DNA binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box]<br>
-	-NMR used to determine 3DE structure of PhoB DNA-binding/transactivation domain. Very similar to OmpR DNA-binding/transactivation domain, except for conformation of the long turn region of ~~∏hoB~~ (interaction site for sigma subunit, rather than interaction with alpha subunit for OmpR	+	-NMR used to determine 3DE structure of PhoB DNA-binding/transactivation domain. Very similar to OmpR DNA-binding/transactivation domain, except for conformation of the long turn region of PhoB (interaction site for sigma subunit, rather than interaction with alpha subunit for OmpR)
-		+	<br><br>
		+	[http://jb.asm.org.ezp1.harvard.edu/cgi/content/full/185/1/317?view=long&pmid=12486069 Interdomain linkers of homologous response regulators determine their mechanism of action]<br>
		+	Focuses on OmpR and PhoB and, as the title suggests, supports that phosphorylation of sites (particularly N-terminus of both proteins) improves affinity to bind DNA. Isolated C terminus of OmpR is insufficient to productively interact with RNA polymerase. <br>
		+	I've been told by some of the lab members that OmpR is an inner-membrane protein and therefore cannot be used for our assays. It seems that we'll have to find another protein ...<br>


	[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]		[http://openwetware.org/wiki/IGEM:Harvard/2007 Harvard iGEM]
		+	[[Media:Example.ogg]]