Karen's Assignment - Revision history

MaCampbell at 13:21, 1 October 2009

2009-10-01T13:21:39Z

MaCampbell at 13:19, 1 October 2009

2009-10-01T13:19:58Z

MaCampbell at 13:18, 1 October 2009

2009-10-01T13:18:24Z

Kahasty at 02:26, 1 October 2009

2009-10-01T02:26:54Z

Kahasty at 02:25, 1 October 2009

2009-10-01T02:25:43Z

Kahasty at 02:23, 1 October 2009

2009-10-01T02:23:33Z

Kahasty at 16:48, 29 September 2009

2009-09-29T16:48:02Z

Kahasty at 16:39, 29 September 2009

2009-09-29T16:39:21Z

Kahasty at 16:36, 29 September 2009

2009-09-29T16:36:47Z

Kahasty at 16:16, 29 September 2009

2009-09-29T16:16:18Z

← Older revision		Revision as of 13:21, 1 October 2009
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−	'''Potassium homeostasis''' ([http://~~www~~.~~example~~.~~com~~ Download PPT Presentation)	+	'''Potassium homeostasis''' ([http://gcat.davidson.edu/GcatWiki/images/c/c6/Potassium_homeostasis_presentation.ppt Download PPT Presentation])

	'''How does our species maintain potassium homeostasis?'''		'''How does our species maintain potassium homeostasis?'''

← Older revision		Revision as of 13:19, 1 October 2009
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−	'''Potassium homeostasis''' (Download PPT Presentation)	+	'''Potassium homeostasis''' ([http://www.example.com Download PPT Presentation)

	'''How does our species maintain potassium homeostasis?'''		'''How does our species maintain potassium homeostasis?'''

← Older revision		Revision as of 13:18, 1 October 2009
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−	'''Potassium homeostasis'''	+	'''Potassium homeostasis''' (Download PPT Presentation)

	'''How does our species maintain potassium homeostasis?'''		'''How does our species maintain potassium homeostasis?'''

← Older revision		Revision as of 02:26, 1 October 2009
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	'''Other species potassium uptake systems'''		'''Other species potassium uptake systems'''
	For the 6 other species that have similar potassium related genes to our species (Halorhabdus utahensis, Halorubrum lacusprofundi, Halobacterium sp. NRC-1, Haloarcula marismortui, Natronomonas pharaonis, & Halogeometricum borinquense. Excluding Halobacterium salinarum since I already compared the KdpFABC operon), I reviewed literature and did pubmed searches trying to find anything that would relate potassium to these species. The only time I found potassium mentioned in conjunction with one of these species was when one website said that Halobacterium sp. NRC-1 has potassium uptake systems coded for in its genome [http://microbewiki.kenyon.edu/index.php/Halobacterium_sp._NRC-1 Kenyon MicrobeWiki]. Since this was the only time potassium was mentioned in conjunction with any of these species, it is unlikely that potassium is essential for the survival of these species. Because of this fact and the lack of evidence of the KdpFABC operon in our species genome, it seems unlikely that potassium homeostasis is essential for our species survival in high salinity environments.		For the 6 other species that have similar potassium related genes to our species (Halorhabdus utahensis, Halorubrum lacusprofundi, Halobacterium sp. NRC-1, Haloarcula marismortui, Natronomonas pharaonis, & Halogeometricum borinquense. Excluding Halobacterium salinarum since I already compared the KdpFABC operon), I reviewed literature and did pubmed searches trying to find anything that would relate potassium to these species. The only time I found potassium mentioned in conjunction with one of these species was when one website said that Halobacterium sp. NRC-1 has potassium uptake systems coded for in its genome [http://microbewiki.kenyon.edu/index.php/Halobacterium_sp._NRC-1 Kenyon MicrobeWiki]. Since this was the only time potassium was mentioned in conjunction with any of these species, it is unlikely that potassium is essential for the survival of these species. Because of this fact and the lack of evidence of the KdpFABC operon in our species genome, it seems unlikely that potassium homeostasis is essential for our species survival in high salinity environments.
−
−	~~[[Media:[[Image:Example.jpg]]]]~~

← Older revision		Revision as of 02:25, 1 October 2009
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	'''Other species potassium uptake systems'''		'''Other species potassium uptake systems'''
	For the 6 other species that have similar potassium related genes to our species (Halorhabdus utahensis, Halorubrum lacusprofundi, Halobacterium sp. NRC-1, Haloarcula marismortui, Natronomonas pharaonis, & Halogeometricum borinquense. Excluding Halobacterium salinarum since I already compared the KdpFABC operon), I reviewed literature and did pubmed searches trying to find anything that would relate potassium to these species. The only time I found potassium mentioned in conjunction with one of these species was when one website said that Halobacterium sp. NRC-1 has potassium uptake systems coded for in its genome [http://microbewiki.kenyon.edu/index.php/Halobacterium_sp._NRC-1 Kenyon MicrobeWiki]. Since this was the only time potassium was mentioned in conjunction with any of these species, it is unlikely that potassium is essential for the survival of these species. Because of this fact and the lack of evidence of the KdpFABC operon in our species genome, it seems unlikely that potassium homeostasis is essential for our species survival in high salinity environments.		For the 6 other species that have similar potassium related genes to our species (Halorhabdus utahensis, Halorubrum lacusprofundi, Halobacterium sp. NRC-1, Haloarcula marismortui, Natronomonas pharaonis, & Halogeometricum borinquense. Excluding Halobacterium salinarum since I already compared the KdpFABC operon), I reviewed literature and did pubmed searches trying to find anything that would relate potassium to these species. The only time I found potassium mentioned in conjunction with one of these species was when one website said that Halobacterium sp. NRC-1 has potassium uptake systems coded for in its genome [http://microbewiki.kenyon.edu/index.php/Halobacterium_sp._NRC-1 Kenyon MicrobeWiki]. Since this was the only time potassium was mentioned in conjunction with any of these species, it is unlikely that potassium is essential for the survival of these species. Because of this fact and the lack of evidence of the KdpFABC operon in our species genome, it seems unlikely that potassium homeostasis is essential for our species survival in high salinity environments.
		+
		+	[[Media:[[Image:Example.jpg]]]]

← Older revision		Revision as of 02:23, 1 October 2009
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	These hits could just be related to the ATPase function of the Kdp operon in H. salinarum and have nothing to do with potassium transport. I am going to redo this blastx with individual genes from operon Kdp compared to our species genome separately. When blasted separately, I found that the three hits from above were in the gene KdpB in the operon of H salinarum. No other similarities, however, were discovered.		These hits could just be related to the ATPase function of the Kdp operon in H. salinarum and have nothing to do with potassium transport. I am going to redo this blastx with individual genes from operon Kdp compared to our species genome separately. When blasted separately, I found that the three hits from above were in the gene KdpB in the operon of H salinarum. No other similarities, however, were discovered.
		+
		+	'''Other species potassium uptake systems'''
		+	For the 6 other species that have similar potassium related genes to our species (Halorhabdus utahensis, Halorubrum lacusprofundi, Halobacterium sp. NRC-1, Haloarcula marismortui, Natronomonas pharaonis, & Halogeometricum borinquense. Excluding Halobacterium salinarum since I already compared the KdpFABC operon), I reviewed literature and did pubmed searches trying to find anything that would relate potassium to these species. The only time I found potassium mentioned in conjunction with one of these species was when one website said that Halobacterium sp. NRC-1 has potassium uptake systems coded for in its genome [http://microbewiki.kenyon.edu/index.php/Halobacterium_sp._NRC-1 Kenyon MicrobeWiki]. Since this was the only time potassium was mentioned in conjunction with any of these species, it is unlikely that potassium is essential for the survival of these species. Because of this fact and the lack of evidence of the KdpFABC operon in our species genome, it seems unlikely that potassium homeostasis is essential for our species survival in high salinity environments.

← Older revision		Revision as of 16:48, 29 September 2009
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	[[Image:heavy metal translocating P-type ATPase-3.png]]		[[Image:heavy metal translocating P-type ATPase-3.png]]

−	These hits could just be related to the ATPase function of the Kdp operon in H. salinarum and have nothing to do with potassium transport. I am going to redo this blastx with individual genes from operon Kdp compared to our species genome separately.	+	These hits could just be related to the ATPase function of the Kdp operon in H. salinarum and have nothing to do with potassium transport. I am going to redo this blastx with individual genes from operon Kdp compared to our species genome separately. When blasted separately, I found that the three hits from above were in the gene KdpB in the operon of H salinarum. No other similarities, however, were discovered.

← Older revision		Revision as of 16:39, 29 September 2009
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	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=C4DEM387014&log%24=protalign&blast_rank=3&list_uids=257373045 heavy metal translocating P-type ATPase-3] <br>		[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=C4DEM387014&log%24=protalign&blast_rank=3&list_uids=257373045 heavy metal translocating P-type ATPase-3] <br>
	[[Image:heavy metal translocating P-type ATPase-3.png]]		[[Image:heavy metal translocating P-type ATPase-3.png]]
		+
		+	These hits could just be related to the ATPase function of the Kdp operon in H. salinarum and have nothing to do with potassium transport. I am going to redo this blastx with individual genes from operon Kdp compared to our species genome separately.

← Older revision		Revision as of 16:36, 29 September 2009
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	A paper by [http://illiad.davidson.edu/pdf/40339.pdf Oren et al.] describes another species, Salinibacter ruber, that appears to be capable of surviving in high salinity environments due to the uptake of high concentrations of potassium. The finding that potassium homeostasis seems to be the mechanism of maintaining life in a high salinity environment was determined by measuring K+, Cl+, glutamate, glycine betaine, and N-alpha-acetyllysine concentrations within the cytoplasm. High amounts of K+ and Cl+ were found within the cytoplasm but low amounts of glutamate, glycine betaine, and N-alpha-acetyllysine were discovered. These three organic solutes are often associated with maintaining osmotic equilibrium in archaic halophiles that exist in high salinity environments. It is unusual that this species does not utilize these organic solutes to maintain homeostasis but instead seems to be utilizing the inorganic molecule KCl. This paper provides another example of potassium concentrations being utilized to maintain life in high salinity environments. I need to determine if our species is using this inorganic molecule or the more common organic molecules to maintain osmotic balance in a high salinity environment.		A paper by [http://illiad.davidson.edu/pdf/40339.pdf Oren et al.] describes another species, Salinibacter ruber, that appears to be capable of surviving in high salinity environments due to the uptake of high concentrations of potassium. The finding that potassium homeostasis seems to be the mechanism of maintaining life in a high salinity environment was determined by measuring K+, Cl+, glutamate, glycine betaine, and N-alpha-acetyllysine concentrations within the cytoplasm. High amounts of K+ and Cl+ were found within the cytoplasm but low amounts of glutamate, glycine betaine, and N-alpha-acetyllysine were discovered. These three organic solutes are often associated with maintaining osmotic equilibrium in archaic halophiles that exist in high salinity environments. It is unusual that this species does not utilize these organic solutes to maintain homeostasis but instead seems to be utilizing the inorganic molecule KCl. This paper provides another example of potassium concentrations being utilized to maintain life in high salinity environments. I need to determine if our species is using this inorganic molecule or the more common organic molecules to maintain osmotic balance in a high salinity environment.
		+
		+	'''H. salinarum K+ transport mechanism comparison'''
		+	Found the nucleotide sequence for the KdpFABC operon in the species H. salinarum using NCBI. Compared this sequence to our species genome using Blastx. Found three significant hits:
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=C4DEM387014&log%24=protalign&blast_rank=1&list_uids=257372919 heavy metal translocating P-type ATPase-1] <br>
		+	[[Image:heavy metal translocating P-type ATPase-1.png]]
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=C4DEM387014&log%24=protalign&blast_rank=2&list_uids=257388732 heavy metal translocating P-type ATPase-2] <br>
		+	[[Image:heavy metal translocating P-type ATPase-2.png]]
		+
		+	[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=protein&dopt=GenPept&RID=C4DEM387014&log%24=protalign&blast_rank=3&list_uids=257373045 heavy metal translocating P-type ATPase-3] <br>
		+	[[Image:heavy metal translocating P-type ATPase-3.png]]

@@ Line 3: / Line 3: @@
 '''How does our species maintain potassium homeostasis?'''
-In JGI's list of genes with predicted functions, I found the following 10 genes related to K+:<br>
+In JGI's list of genes with predicted functions, I found the following 10 genes related to K+ (6 of which were called in RAST):<br>
 [http://img.jgi.doe.gov/cgi-bin/geba/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=644032472 K+ transport system, NAD-binding component]<br>