Dylan - Revision history

Dycoughtreydavenport at 01:30, 29 March 2011

2011-03-29T01:30:51Z

Dycoughtreydavenport: /* Additional Sources */

2011-03-22T14:56:58Z

‎Additional Sources

Dycoughtreydavenport: /* Update */

2011-02-24T15:53:15Z

‎Update

Dycoughtreydavenport: /* Update */

2011-02-24T15:52:15Z

‎Update

Dycoughtreydavenport: /* Update */

2011-02-13T20:45:19Z

‎Update

Dycoughtreydavenport: /* Potential Directions */

2011-02-13T20:43:18Z

‎Potential Directions

10.40.209.19: /* Additional Sources */

2011-02-13T19:48:35Z

‎Additional Sources

Dycoughtreydavenport: /* Potential Directions */

2011-02-10T15:58:42Z

‎Potential Directions

Dycoughtreydavenport: /* Additional Sources */

2011-02-10T15:04:55Z

‎Additional Sources

Dycoughtreydavenport: /* Potential Directions */

2011-02-09T18:14:57Z

‎Potential Directions

← Older revision		Revision as of 01:30, 29 March 2011
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		+	[[Media:Super Myb.ppt]]
		+
	== Myb Transcription Factors ==		== Myb Transcription Factors ==
	'''Myb''' is actually an acronym taken from “myeloblastosis,” an old name for a certain type of leukemia. Studies have established that the absence of Myb proteins causes an increase in mitotic arrest, abnormal chromosome number, and faulty spindle formation. The protein localizes to recently replicated DNA in mitotically cycling and endocycling cells, regulating gene expression by binding directly to the DNA. The graphic representation below shows the helical structure of the protein (light blue) as it works in the cell: fitting into the major groove of the DNA double helix (red and yellow).[http://www.stanford.edu/group/lipsick/whatsmyb%20long.htm]		'''Myb''' is actually an acronym taken from “myeloblastosis,” an old name for a certain type of leukemia. Studies have established that the absence of Myb proteins causes an increase in mitotic arrest, abnormal chromosome number, and faulty spindle formation. The protein localizes to recently replicated DNA in mitotically cycling and endocycling cells, regulating gene expression by binding directly to the DNA. The graphic representation below shows the helical structure of the protein (light blue) as it works in the cell: fitting into the major groove of the DNA double helix (red and yellow).[http://www.stanford.edu/group/lipsick/whatsmyb%20long.htm]

← Older revision		Revision as of 14:56, 22 March 2011
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	[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507771/?tool=pubmed Conserved Grape Myb]		[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507771/?tool=pubmed Conserved Grape Myb]
		+
		+	[http://www.jbc.org/content/267/8/5656.full.pdf Myb binding to DNA]

← Older revision		Revision as of 15:53, 24 February 2011
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−	[[File:Myb Consensus Sequence.jpg]]	+	<center>[[File:Myb Consensus Sequence.jpg]]</center>
	::'''Multiple alignment of 20 representative R2R3 MYB domains from Arabidopsis and six MYB domains from characterised grape MYB genes.''' Identical amino acid residues are shaded in yellow and the blue and white boxes indicate the extent of the R2 and R3 repeats. The consensus sequence shown under the alignment was used to search for MYB homologues in the Grape Genome. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507771/?tool=pubmed#S1]		::'''Multiple alignment of 20 representative R2R3 MYB domains from Arabidopsis and six MYB domains from characterised grape MYB genes.''' Identical amino acid residues are shaded in yellow and the blue and white boxes indicate the extent of the R2 and R3 repeats. The consensus sequence shown under the alignment was used to search for MYB homologues in the Grape Genome. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507771/?tool=pubmed#S1]

← Older revision		Revision as of 15:52, 24 February 2011
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−	[[File:Myb Consensus Sequence]]	+	[[File:Myb Consensus Sequence.jpg]]
	::'''Multiple alignment of 20 representative R2R3 MYB domains from Arabidopsis and six MYB domains from characterised grape MYB genes.''' Identical amino acid residues are shaded in yellow and the blue and white boxes indicate the extent of the R2 and R3 repeats. The consensus sequence shown under the alignment was used to search for MYB homologues in the Grape Genome. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507771/?tool=pubmed#S1]		::'''Multiple alignment of 20 representative R2R3 MYB domains from Arabidopsis and six MYB domains from characterised grape MYB genes.''' Identical amino acid residues are shaded in yellow and the blue and white boxes indicate the extent of the R2 and R3 repeats. The consensus sequence shown under the alignment was used to search for MYB homologues in the Grape Genome. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507771/?tool=pubmed#S1]

← Older revision		Revision as of 20:45, 13 February 2011
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	[[File:Myb Consensus Sequence]]		[[File:Myb Consensus Sequence]]
		+	::'''Multiple alignment of 20 representative R2R3 MYB domains from Arabidopsis and six MYB domains from characterised grape MYB genes.''' Identical amino acid residues are shaded in yellow and the blue and white boxes indicate the extent of the R2 and R3 repeats. The consensus sequence shown under the alignment was used to search for MYB homologues in the Grape Genome. [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507771/?tool=pubmed#S1]

	== Additional Sources ==		== Additional Sources ==

@@ Line 72: / Line 72: @@
 === Update ===
 The ''tblastn'' tool works!  I ran a control by copying a nucleotide sequence from the genome and translating it into an amino acid sequence.  I then blasted that back against the database and got a hit within the expected scaffold.  Now I just have to find the amino acid sequence for the Myb domain (hopefully as highly conserved as the literature is insinuating) and BLAST it using the tblastn command.
 == Additional Sources ==

← Older revision		Revision as of 19:48, 13 February 2011
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	[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC553695/pdf/emboj00249-0208.pdf Myb DNA binding domain]		[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC553695/pdf/emboj00249-0208.pdf Myb DNA binding domain]
		+
		+	[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2507771/?tool=pubmed Conserved Grape Myb]

← Older revision		Revision as of 15:58, 10 February 2011
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	This new tool should allow users to search within a nucleotide sequence database for a given amino acid sequence. Hopefully, once I can find the protein sequence of the Myb binding domain, I can search for it within the genome. Myb, here we come!		This new tool should allow users to search within a nucleotide sequence database for a given amino acid sequence. Hopefully, once I can find the protein sequence of the Myb binding domain, I can search for it within the genome. Myb, here we come!
		+
		+
		+	=== Update ===
		+	The ''tblastn'' tool works! I ran a control by copying a nucleotide sequence from the genome and translating it into an amino acid sequence. I then blasted that back against the database and got a hit within the expected scaffold. Now I just have to find the amino acid sequence for the Myb domain (hopefully as highly conserved as the literature is insinuating) and BLAST it using the tblastn command.

	== Additional Sources ==		== Additional Sources ==

← Older revision		Revision as of 15:04, 10 February 2011
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	[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025947/?tool=pubmed Transcriptional Regulation of Flavonoid Biosynthesis]		[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025947/?tool=pubmed Transcriptional Regulation of Flavonoid Biosynthesis]
		+
		+	[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC553695/pdf/emboj00249-0208.pdf Myb DNA binding domain]

← Older revision		Revision as of 18:14, 9 February 2011
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	== Potential Directions ==		== Potential Directions ==
−	An attempt will be made to find the '''amino acid sequence''' of the highly conserved '''Myb domain''' in the Myb transcription factor. This will require a new ~~blast~~ technique, as described below in this section of the [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide#tblastn NCBI Blast Program Selection Guide].	+	An attempt will be made to find the '''amino acid sequence''' of the highly conserved '''Myb domain''' in the Myb transcription factor. This will require a new BLAST technique, as described below in this section of the [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=ProgSelectionGuide#tblastn NCBI Blast Program Selection Guide].