Sarah's Assignment - Revision history

Sapyfrom at 15:58, 22 October 2009

2009-10-22T15:58:46Z

Sapyfrom: /* Questions */

2009-10-01T15:24:48Z

‎Questions

Sapyfrom: /* From JGI */

2009-10-01T15:23:12Z

‎From JGI

Sapyfrom at 15:20, 1 October 2009

2009-10-01T15:20:15Z

Sapyfrom: /* From JGI */

2009-10-01T15:15:49Z

‎From JGI

Sapyfrom: /* From JGI */

2009-10-01T15:14:15Z

‎From JGI

Sapyfrom: /* From JGI */

2009-10-01T15:11:17Z

‎From JGI

Sapyfrom: /* From JGI */

2009-10-01T15:10:51Z

‎From JGI

Sapyfrom: /* Comparison of RAST and JGI */

2009-10-01T14:50:33Z

‎Comparison of RAST and JGI

Sapyfrom: /* From RAST */

2009-10-01T14:45:09Z

‎From RAST

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	What does it say about RAST and JGI that they annotated completely different genes?		What does it say about RAST and JGI that they annotated completely different genes?
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		+	[[GAH!]]

← Older revision		Revision as of 15:24, 1 October 2009
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	Which sections of the DDP protein are highly conserved among halophiles?		Which sections of the DDP protein are highly conserved among halophiles?
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		+	What section of the protein does the conserved sequence reside in?
		+
		+	What differences/similarities are there between halophilic and non-halophilic photolyases?

	How does halophilic (specifically our organism's) DNA repair differ from the repair processes of other organisms?		How does halophilic (specifically our organism's) DNA repair differ from the repair processes of other organisms?

← Older revision		Revision as of 15:23, 1 October 2009
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	It's clear that there are some highly-conserved areas across all of the DDPs in these halophiles. I would like to look at these conserved regions in greater detail and compare them to non-halophiles to determine how these areas of the protein differ and how that might affect their effectiveness.		It's clear that there are some highly-conserved areas across all of the DDPs in these halophiles. I would like to look at these conserved regions in greater detail and compare them to non-halophiles to determine how these areas of the protein differ and how that might affect their effectiveness.
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		+	I tried to figure out what structures these form in the folded protein but the process is proving difficult.

@@ Line 6: / Line 6: @@
 [[Image:UV1.jpg]][http://p53.free.fr/Database/p53_cancer/p53_skin.html Source]
 Cyclobutane dimers consist of either T to T (most common), C to T or (less common) C to C. UV light creates covalent bonds between adjacent thymidines or cytosines, which can inhibit transcription or replication of DNA. Cytosines that are part of a dimer are also more likely to be deaminated and changed to uracil. This can cause errors in either transcription or replication [http://en.wikipedia.org/wiki/Pyrimidine_dimers] [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T2B-3W317X6-3&_user=2665120&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1015468107&_rerunOrigin=scholar.google&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=cd636cb6e6c4198454faaf4a1d419316].
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 [[Image:BER.png]] [http://en.wikipedia.org/wiki/Base_excision_repair Source]

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 Our gene was only matched to its own genome.
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 [[Image:photolyase3aa.png]]
 Most of the organisms that showed significant similarity with our organism's DDP were also halophiles found in salt flats around the world. This suggests that maybe the changes which make our organism's DNA-repair process so efficient have developed independently in many halophiles, while the differences show how different environmental pressures have tweaked the enzymes to fit precise needs.
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 It's clear that there are some highly-conserved areas across all of the DDPs in these halophiles. I would like to look at these conserved regions in greater detail and compare them to non-halophiles to determine how these areas of the protein differ and how that might affect their effectiveness.
 '''To edit''': Found several papers that discuss halophiles and their mutational rates in response to UV light or radiation [http://genome.cshlp.org/content/14/6/1025.full].

← Older revision		Revision as of 15:14, 1 October 2009
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−	It's clear that there are some highly-conserved areas across all of the DDPs in these halophiles.	+	It's clear that there are some highly-conserved areas across all of the DDPs in these halophiles. I would like to look at these conserved regions in greater detail and compare them to non-halophiles to determine how these areas of the protein differ and how that might affect their effectiveness.

	Strangely, when the amino acid sequences from the DDPs found in our species' genome were BLASTed against one another, very little similarity was found.		Strangely, when the amino acid sequences from the DDPs found in our species' genome were BLASTed against one another, very little similarity was found.

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 glycosylases
-I considered focusing on all of these genes but decided a focus was necessary for the most concise and effective results. I chose to pursue DDP because it is a one-enzyme pathway. I thought a simpler protein would allow me to more easily make comparisons to other genomes. As a secondary step, I wanted to look at the glycosylases as well since it is there job to recognize certain mutations in the genome and their increased performance may assist in our species' ability to combat the negative effects of UV radiation.
+I considered focusing on all of these genes but decided a more specific focus was necessary for the most concise and effective results. I chose to pursue DDP because it is a one-enzyme pathway. I thought a simpler protein would allow me to more easily make comparisons to other genomes. As a secondary step, I wanted to look at the glycosylases as well since it is there job to recognize certain mutations in the genome and their increased performance may assist in our species' ability to combat the negative effects of UV radiation.
 '''BLASTn'''

← Older revision		Revision as of 15:10, 1 October 2009
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	According to JGI our species also has the following genes associated with DNA repair:		According to JGI our species also has the following genes associated with DNA repair:
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−	~~3 deoxyribodipyrimidine photolyases (DDPs)~~

	5 DNA mismatch repair enzymes		5 DNA mismatch repair enzymes

← Older revision		Revision as of 14:50, 1 October 2009
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	I find it very interesting that, so far, I have not found any similar genes between RAST and JGI. I would like to probe further into this issue and try to find common endonucleases and photolyases in both annotations. I am open to suggestions as to which specific endonucleases (or other genes) I should compare.		I find it very interesting that, so far, I have not found any similar genes between RAST and JGI. I would like to probe further into this issue and try to find common endonucleases and photolyases in both annotations. I am open to suggestions as to which specific endonucleases (or other genes) I should compare.
		+
		+	While both JGI and RAST recognize endonucleases in the genome, RAST recognizes only Endonuclease III and a flap structure-specific nuclease. whereas JGI recognizes endonucleases IV and V.

	I [[BLASTed]] the first photolyase gene against the entire ''H. mukohaetaei'' genome in the RAST portal and found alignment, but RAST did not identify this section of the genome as a gene.		I [[BLASTed]] the first photolyase gene against the entire ''H. mukohaetaei'' genome in the RAST portal and found alignment, but RAST did not identify this section of the genome as a gene.

← Older revision		Revision as of 14:45, 1 October 2009
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−	in BER, glycosylases recognize errors in DNA base-pairing. Endonucleases cleave the 3' end of the error and endonucleases cleave the 5' end. DNA polymerase starts re-building the correct complementary strand and flips the excised bases away from the double helix so that the endonuclease can recognize and cleave it. In single base-pair excisions, ~~the endonuclease~~ removes the entire incorrect base and DNA polymerase fills in the gap. In both cases, ligases create the covalent bond between the old DNA strand and the last nucleotide placed by DNA polymerase.[http://en.wikipedia.org/wiki/Base_excision_repair#AP_endonucleases]	+	in BER, glycosylases recognize errors in DNA base-pairing. Endonucleases cleave the 3' end of the error and endonucleases cleave the 5' end. DNA polymerase starts re-building the correct complementary strand and flips the excised bases away from the double helix so that the endonuclease can recognize and cleave it. In single base-pair excisions, lyase removes the entire incorrect base and DNA polymerase fills in the gap. In both cases, ligases create the covalent bond between the old DNA strand and the last nucleotide placed by DNA polymerase.[http://en.wikipedia.org/wiki/Base_excision_repair#AP_endonucleases]

	One of the endonucleases is a flap structure-specific endonuclease. These enzymes are used during the excision of longer sequences of DNA suggesting that our species is capable of more than single-nucleotide excision repair.		One of the endonucleases is a flap structure-specific endonuclease. These enzymes are used during the excision of longer sequences of DNA suggesting that our species is capable of more than single-nucleotide excision repair.