Lauren & Puneet - Revision history

Pulakhmani at 07:24, 27 January 2011

2011-01-27T07:24:01Z

Laivey at 03:08, 27 January 2011

2011-01-27T03:08:06Z

Laivey at 02:54, 27 January 2011

2011-01-27T02:54:16Z

Laivey at 02:45, 27 January 2011

2011-01-27T02:45:12Z

Laivey at 02:44, 27 January 2011

2011-01-27T02:44:41Z

Laivey at 02:43, 27 January 2011

2011-01-27T02:43:50Z

Pulakhmani at 16:01, 25 January 2011

2011-01-25T16:01:36Z

Pulakhmani at 15:58, 25 January 2011

2011-01-25T15:58:12Z

New page

1. Determine sequence homology
2. Myb transcription factor expression in various fruits (containing anthocynanins)
3. Repeats in the blueberry genome (WGDs?)
4. The different expression patterns: in the fruit vs root; different times of the day; different seasons; various environmental factors
5. What phenolic compounds are regulated by myb
6. What is the BAHD family of phenolic ATs (mentioned in proposal) and what are the exceptions
7. ATP synthesis and glucose metabolism in blueberries.
8. The amount of t-RNA genes expressed in the blueberry
9. The number of introns, exons, transposable elements? What’s conserved?

@@ Line 1: / Line 1: @@
-.	Determine sequence homology  <br>
+.	Determine sequence homology between blueberry, cranberry,grapefruit (contains flavonoids) etc. <br>
 .	Myb transcription factor expression in various fruits (containing anthocynanins) <br>
 .	Repeats in the blueberry genome (WGDs?) <br>
 .	The different expression patterns: in the fruit vs root; different times of the day; different seasons; various environmental factors <br>
-.	What phenolic compounds are regulated by myb <br>
+.	What is the BAHD family of phenolic ATs (mentioned in proposal); check out cytochrome p450s and o-methyl-transferases. <br>
-.	What is the BAHD family of phenolic ATs (mentioned in proposal) and what are the exceptions <br>
-.	ATP synthesis and glucose metabolism in blueberries. <br>
+The BAHD family of ATs are acyltransferases and contain, according to the grant proposal, the f2 conserved domain; apparently, researchers have found 94 putative BAHDs in Populis and 64 in Arabidopsis. It would be interesting to see if these sequences are conserved throughout athnocynanin containing fruits (of course, this would require obtaining the lignin, cranberry, etc. genome). Additionally, they talked about how there is some evidence that these enzymes are related to malonating athnocynanins. <br>
-.	The amount of t-RNA genes expressed in the blueberry <br>
-.	The number of introns, exons, transposable elements? What’s conserved? <br>
+In the proposal, they use grape to identify possible candidate genes for OMTs, ATs, Mybs, etc. in the blueberry using the grape genome (because they haven't diverged too much evolutionarily). This seems like a good strategy to do for other proteins/genes that are worth checking out e.g. ones involved in glucose metabolism and ATP sythesis? <br>

← Older revision		Revision as of 03:08, 27 January 2011
Line 8:		Line 8:
	8. The amount of t-RNA genes expressed in the blueberry <br>		8. The amount of t-RNA genes expressed in the blueberry <br>
	9. The number of introns, exons, transposable elements? What’s conserved? <br>		9. The number of introns, exons, transposable elements? What’s conserved? <br>
−
−
−	~~'''Inhibition of mitochondrial proton F0F1-ATPase/ATP synthase by polyphenolic phytochemicals'''~~
−
−	'''inhibition of mitochondrial F0F1-ATPase/ATP synthase could be a potential mechanism contributing to the many effects of dietary polyphenolics'''. It has been shown that the same ''ATP synthase is localized also on the plasma membranes of several tumour cell lines'' (Das et al., 1994) and human umbilical vein endothelial cells, and that it is a binding protein for angiostatin, a potent protein inhibitor of angiogenesis and cell proliferation (Moser et al., 1999). Therefore, phytoestrogens could also play a similar role by binding the ATP synthase on the plasma membrane. In fact, genistein has been shown to be a potent inhibitor of angiogenesis (Fotsis et al., 1993). Moreover, '''resveratrol and genistein also inhibit the bovine mitochondrial NADH:ubiquinone oxidoreductase and induce ornithine decarboxylase, a marker for cancer chemopreventive potency,''' with IC50=30μM (Fang & Casida, 1998). The simultaneous effects of these phytochemicals on NADH:ubiquinone oxidoreductase and F0F1-ATPase/ATP synthase could significantly affect mitochondrial function and '''alter ATP level, mitochondrial transmembrane potential and generation of reactive oxygen species, which have been implicated in many cellular processes such as cellular protection, apoptosis, O2 sensing and ageing.'''[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1572158/]
−
−
−
−	~~'''Acid invertase'''~~
−
−	Invertase (EC 3.2.1.26 ) (systematic name: beta-fructofuranosidase) is an enzyme that '''catalyzes the hydrolysis (breakdown) of sucrose (table sugar)'''. The resulting mixture of fructose and glucose is called inverted sugar syrup. Related to invertases are sucrases. Invertases and sucrases hydrolyze sucrose to give the same mixture of glucose and fructose. Invertases cleave the O-C(fructose) bond, whereas the sucrases cleave the O-C(glucose) bond.[1]
−
−	~~AI appears to be the key enzyme induced by root restriction that '''explains the higher sugar content found in grape berry''' produced under root restriction.~~
−
−	~~The characteristic rapid '''rise in the rate of sugar accumulation''' by the berries about halfway through development was '''preceded by an increase in the activity of invertase'''.~~
−
−	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TH7-42HX9BK-FB&_user=2665120&_origUdi=B6TC3-4X1GG3H-2&_fmt=high&_coverDate=01%2F31%2F1969&_rdoc=1&_orig=article&_origin=article&_zone=related_art&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=2058330cf33d2fc8a9948cf5093dc6fc]
−
−	In fact, the protein fraction retrieved from a buffered medium after incubation of ripening berry slices contained a soluble invertase of presumably vacuolar origin with an acid pH-activity profile and a pI of about 4.
−	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRD-3WC440P-4&_user=2665120&_origUdi=B6TH7-42HX9BK-FB&_fmt=high&_coverDate=12%2F31%2F1998&_rdoc=1&_orig=article&_origin=article&_zone=related_art&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=2ab0f5006b9242edde3dc6e11bf4e9fe]
−
−	~~These observations have led to speculations that '''suc hydrolysis primarily by acid invertase may determine the rate and extent of SUC storage''' in tomato~~
−	~~fruit (Walker et al., 1978). In contrast, low levels of acid invertase are associated with high levels of SUC accumulation in L. hirsutum (Miron~~
−
−	The levels of invertase activity were found to vary significantly among 14 varieties of grapes tested. The crude invertases were, however, similar in both pH and temperature optima, as well as pH and thermal stabilities. The '''enzymes showed a high degree of thermostability and were also stable at acidic pH''' and high concentration of alcohol. A significant level of invertase activity persisted in several white table wines. The optimum activity of the enzyme purified from Semillon grape was observed at about 75°C and it was stable up to 70°C. Although the enzyme was stable between the pH 2 and 8, the optimum pH for its activity was about 4. The enzyme, whose molecular weight was estimated to be 65,000 by SDS polyacrylamide slab gel electrophoresis, was found to be a glycoprotein with a total carbohydrate content of 33%. This enzyme showed activity toward sucrose and raffinose, but was inactive on the other disaccharides tested.
−	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T8G-4865FF4-4&_user=2665120&_coverDate=12%2F31%2F1990&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1621200458&_rerunOrigin=google&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=55f72f60edb45c0e17e43713aa759cef&searchtype=a]

← Older revision	Revision as of 02:54, 27 January 2011
Line 10:	Line 10:


	+	'''Inhibition of mitochondrial proton F0F1-ATPase/ATP synthase by polyphenolic phytochemicals'''

−	+	'''inhibition of mitochondrial F0F1-ATPase/ATP synthase could be a potential mechanism contributing to the many effects of dietary polyphenolics'''. It has been shown that the same ''ATP synthase is localized also on the plasma membranes of several tumour cell lines'' (Das et al., 1994) and human umbilical vein endothelial cells, and that it is a binding protein for angiostatin, a potent protein inhibitor of angiogenesis and cell proliferation (Moser et al., 1999). Therefore, phytoestrogens could also play a similar role by binding the ATP synthase on the plasma membrane. In fact, genistein has been shown to be a potent inhibitor of angiogenesis (Fotsis et al., 1993). Moreover, '''resveratrol and genistein also inhibit the bovine mitochondrial NADH:ubiquinone oxidoreductase and induce ornithine decarboxylase, a marker for cancer chemopreventive potency,''' with IC50=30μM (Fang & Casida, 1998). The simultaneous effects of these phytochemicals on NADH:ubiquinone oxidoreductase and F0F1-ATPase/ATP synthase could significantly affect mitochondrial function and '''alter ATP level, mitochondrial transmembrane potential and generation of reactive oxygen species, which have been implicated in many cellular processes such as cellular protection, apoptosis, O2 sensing and ageing.'''[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1572158/]

@@ Line 8: / Line 8: @@
 .	The amount of t-RNA genes expressed in the blueberry <br>
 .	The number of introns, exons, transposable elements? What’s conserved? <br>
 '''Acid invertase'''

@@ Line 20: / Line 20: @@
 In fact, the protein fraction retrieved from a buffered medium after incubation of ripening berry slices contained a soluble invertase of presumably vacuolar origin with an acid pH-activity profile and a pI of about 4.
-h[ttp://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRD-3WC440P-4&_user=2665120&_origUdi=B6TH7-42HX9BK-FB&_fmt=high&_coverDate=12%2F31%2F1998&_rdoc=1&_orig=article&_origin=article&_zone=related_art&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=2ab0f5006b9242edde3dc6e11bf4e9fe]
+[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRD-3WC440P-4&_user=2665120&_origUdi=B6TH7-42HX9BK-FB&_fmt=high&_coverDate=12%2F31%2F1998&_rdoc=1&_orig=article&_origin=article&_zone=related_art&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=2ab0f5006b9242edde3dc6e11bf4e9fe]
 These observations have led to speculations that '''suc hydrolysis primarily by acid invertase may determine the rate and extent of SUC storage''' in tomato
@@ Line 26: / Line 26: @@
 The levels of invertase activity were found to vary significantly among 14 varieties of grapes tested. The crude invertases were, however, similar in both pH and temperature optima, as well as pH and thermal stabilities. The '''enzymes showed a high degree of thermostability and were also stable at acidic pH''' and high concentration of alcohol. A significant level of invertase activity persisted in several white table wines. The optimum activity of the enzyme purified from Semillon grape was observed at about 75°C and it was stable up to 70°C. Although the enzyme was stable between the pH 2 and 8, the optimum pH for its activity was about 4. The enzyme, whose molecular weight was estimated to be 65,000 by SDS polyacrylamide slab gel electrophoresis, was found to be a glycoprotein with a total carbohydrate content of 33%. This enzyme showed activity toward sucrose and raffinose, but was inactive on the other disaccharides tested.
-[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T8G-4865FF4-4&_user=2665120&_coverDate=12%2F31%2F1990&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1621200458&_rerunOrigin=google&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=55f72f60edb45c0e17e43713aa759cef&searchtype=a
+[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T8G-4865FF4-4&_user=2665120&_coverDate=12%2F31%2F1990&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1621200458&_rerunOrigin=google&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=55f72f60edb45c0e17e43713aa759cef&searchtype=a]

← Older revision		Revision as of 02:43, 27 January 2011
Line 8:		Line 8:
	8. The amount of t-RNA genes expressed in the blueberry <br>		8. The amount of t-RNA genes expressed in the blueberry <br>
	9. The number of introns, exons, transposable elements? What’s conserved? <br>		9. The number of introns, exons, transposable elements? What’s conserved? <br>
		+
		+	'''Acid invertase'''
		+
		+	Invertase (EC 3.2.1.26 ) (systematic name: beta-fructofuranosidase) is an enzyme that '''catalyzes the hydrolysis (breakdown) of sucrose (table sugar)'''. The resulting mixture of fructose and glucose is called inverted sugar syrup. Related to invertases are sucrases. Invertases and sucrases hydrolyze sucrose to give the same mixture of glucose and fructose. Invertases cleave the O-C(fructose) bond, whereas the sucrases cleave the O-C(glucose) bond.[1]
		+
		+	AI appears to be the key enzyme induced by root restriction that '''explains the higher sugar content found in grape berry''' produced under root restriction.
		+
		+	The characteristic rapid '''rise in the rate of sugar accumulation''' by the berries about halfway through development was '''preceded by an increase in the activity of invertase'''.
		+
		+	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TH7-42HX9BK-FB&_user=2665120&_origUdi=B6TC3-4X1GG3H-2&_fmt=high&_coverDate=01%2F31%2F1969&_rdoc=1&_orig=article&_origin=article&_zone=related_art&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=2058330cf33d2fc8a9948cf5093dc6fc]
		+
		+	In fact, the protein fraction retrieved from a buffered medium after incubation of ripening berry slices contained a soluble invertase of presumably vacuolar origin with an acid pH-activity profile and a pI of about 4.
		+	h[ttp://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRD-3WC440P-4&_user=2665120&_origUdi=B6TH7-42HX9BK-FB&_fmt=high&_coverDate=12%2F31%2F1998&_rdoc=1&_orig=article&_origin=article&_zone=related_art&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=2ab0f5006b9242edde3dc6e11bf4e9fe]
		+
		+	These observations have led to speculations that '''suc hydrolysis primarily by acid invertase may determine the rate and extent of SUC storage''' in tomato
		+	fruit (Walker et al., 1978). In contrast, low levels of acid invertase are associated with high levels of SUC accumulation in L. hirsutum (Miron
		+
		+	The levels of invertase activity were found to vary significantly among 14 varieties of grapes tested. The crude invertases were, however, similar in both pH and temperature optima, as well as pH and thermal stabilities. The '''enzymes showed a high degree of thermostability and were also stable at acidic pH''' and high concentration of alcohol. A significant level of invertase activity persisted in several white table wines. The optimum activity of the enzyme purified from Semillon grape was observed at about 75°C and it was stable up to 70°C. Although the enzyme was stable between the pH 2 and 8, the optimum pH for its activity was about 4. The enzyme, whose molecular weight was estimated to be 65,000 by SDS polyacrylamide slab gel electrophoresis, was found to be a glycoprotein with a total carbohydrate content of 33%. This enzyme showed activity toward sucrose and raffinose, but was inactive on the other disaccharides tested.
		+	[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T8G-4865FF4-4&_user=2665120&_coverDate=12%2F31%2F1990&_rdoc=1&_fmt=high&_orig=search&_origin=search&_sort=d&_docanchor=&view=c&_searchStrId=1621200458&_rerunOrigin=google&_acct=C000058476&_version=1&_urlVersion=0&_userid=2665120&md5=55f72f60edb45c0e17e43713aa759cef&searchtype=a
		+	]