Difference between revisions of "Lauren & Puneet"

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1. Determine sequence homology <br>
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1. Determine sequence homology between blueberry, cranberry,grapefruit (contains flavonoids) etc. <br>
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It would be nice to find conserved motifs  between these fruits which contain athnocyanins and flavonoids and discount the ones that are putatively involved in essential functions. Theoretically, this would leave us with candidate genes for athnocyanin/flavonoid activity. We would be limited by available genomes.
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2. Myb transcription factor expression in various fruits (containing anthocynanins) <br>
 
2. Myb transcription factor expression in various fruits (containing anthocynanins) <br>
 
3. Repeats in the blueberry genome (WGDs?) <br>
 
3. Repeats in the blueberry genome (WGDs?) <br>
 
4. The different expression patterns: in the fruit vs root; different times of the day; different seasons; various environmental factors <br>
 
4. The different expression patterns: in the fruit vs root; different times of the day; different seasons; various environmental factors <br>
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5. What phenolic compounds are regulated by myb <br>
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5. What is the BAHD family of phenolic ATs (mentioned in proposal); check out cytochrome p450s and o-methyl-transferases. <br>
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6. What is the BAHD family of phenolic ATs (mentioned in proposal) and what are the exceptions <br>
 
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7. ATP synthesis and glucose metabolism in blueberries. <br>
 
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8. The amount of t-RNA genes expressed in the blueberry <br>
 
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9. The number of introns, exons, transposable elements? What’s conserved? <br>
 
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'''Acid invertase'''
 
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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]
 
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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.
 
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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'''.
 
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[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]
 
  
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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.
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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>
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[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]
 
  
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These observations have led to speculations that '''suc hydrolysis primarily by acid invertase may determine the rate and extent of SUC storage''' in tomato
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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>
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fruit (Walker et al., 1978). In contrast, low levels of acid invertase are associated with high levels of SUC accumulation in L. hirsutum (Miron
 
  
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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.
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6. ATP synthesis and glucose metabolism in blueberries. <br>
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[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]
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7. The amount of t-RNA genes expressed in the blueberry <br>
 +
8. The number of introns, exons, transposable elements? What’s conserved? <br>

Latest revision as of 07:24, 27 January 2011

1. Determine sequence homology between blueberry, cranberry,grapefruit (contains flavonoids) etc.
It would be nice to find conserved motifs between these fruits which contain athnocyanins and flavonoids and discount the ones that are putatively involved in essential functions. Theoretically, this would leave us with candidate genes for athnocyanin/flavonoid activity. We would be limited by available genomes.

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 is the BAHD family of phenolic ATs (mentioned in proposal); check out cytochrome p450s and o-methyl-transferases.

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.

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?

6. ATP synthesis and glucose metabolism in blueberries.
7. The amount of t-RNA genes expressed in the blueberry
8. The number of introns, exons, transposable elements? What’s conserved?

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