Difference between revisions of "Emmatyrnauer Week 6"

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#[[File:Question_1_Assignment_6_Emma_Tyrnauer.png|200px|thumb|right]]
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==Questions==
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#The ratio is calculated by dividing one gene’s activity in cells gradually consuming all the available oxygen by its activity in control cells with unlimited oxygen. Therefore, Gene X goes from black to dim red to black to medium green. Gene Y goes from black to medium red to dim green to bright green. Finally, Gene Z goes from black to dim red and stays at dim red. (In the order of 1 hour, 2 hour, 3 hour, and 4 hour, respectively)
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#(See figure) [[File:Question_1_Assignment_6_Emma_Tyrnauer.png|400px|thumb|right|Question 1 Answer]]
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#Genes X and Y were transcribed similarly.
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#The ratio is calculated by dividing one gene’s activity in cells gradually consuming all the available oxygen by its activity in control cells with unlimited oxygen. Therefore, Gene X goes from black to dim red to black to medium green. Gene Y goes from black to medium red to dim green to bright green. Finally, Gene Z goes from black to dim red and stays at dim red (in the order of 1 hour, 2 hour, 3 hour, and 4 hour, respectively).
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#(Question 9, p. 118) Why would most spots be yellow at the first time point? I.e., what is the technical reason that spots show up as yellow - where does the yellow color come from? And, what would be the biological reason that the experiment resulted in most spots being yellow?
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#Genes X and Y were transcribed similarly (had similar ratios).
 
#At time 0, no/very little change has occurred in terms of expression or repression of the gene because the cells have just been exposed to the experimental growth conditions. Spots with equal expression and repression compared to the control sample appear yellow because red and green mix to make yellow.   
 
#At time 0, no/very little change has occurred in terms of expression or repression of the gene because the cells have just been exposed to the experimental growth conditions. Spots with equal expression and repression compared to the control sample appear yellow because red and green mix to make yellow.   
 
#TEF4 was repressed over the course of the experiment indicated by the green color. TEF4's change in expression was part of the cell's response to a reduction in available glucose. Glucose is the source of energy for cells and in the absence of glucose, actions that expend the cells energy (such as translation) may be limited.
 
#TEF4 was repressed over the course of the experiment indicated by the green color. TEF4's change in expression was part of the cell's response to a reduction in available glucose. Glucose is the source of energy for cells and in the absence of glucose, actions that expend the cells energy (such as translation) may be limited.
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#The TCA cycle does not use glucose directly--glucose is converted into pyruvic acid prior to its entrance into the TCA cycle.
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#The TCA cycle does not use glucose directly--glucose is converted into pyruvic acid. When glucose levels are low, pyruvic acid is modified and converted into acetyl-CoA, which then enters the TCA cycle.  
 
#These genes in the common pathway could all be induced or repressed by the same transcription factor (pg. 119).
 
#These genes in the common pathway could all be induced or repressed by the same transcription factor (pg. 119).
 
#I would expect these spots to be red because since the repressor is absent, the cells would continue to express the gene even in the absence of glucose.
 
#I would expect these spots to be red because since the repressor is absent, the cells would continue to express the gene even in the absence of glucose.
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#I would expect the spots to be red since Yap1p target genes allow for increased resistance to environmental stresses. Therefore, a depletion of glucose in the environment would induce more expression of these genes.  
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#I would expect the spots to be red since Yap1p target genes allow for increased resistance to environmental stresses. Therefore, a depletion of glucose in the environment (i.e. an environmental stress) would induce more expression of these genes.  
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#Deletion of TUP1 and YAP1 would result in a red spot on the microarray for Tup1p compared to a green spot and a brighter red spot for Yap1p (indicating more expression).
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#Deletion of TUP1 and YAP1 would result in a red spot on the microarray for Tup1p compared to a green spot (expression compared to repression) and a brighter red spot for Yap1p (indicating more expression).
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{{Emmatyrnauer}}
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==Acknowledgments==
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#I worked with my homework partner [[User:ArashLari|Arash Lari]] over text. We were available for one another for questions about the assignment.
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#While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.
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[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 21:27, 9 October 2017 (PDT)
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==References==
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#LMU BioDB 2017. (2017). Week 6. Retrieved October 9, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_6
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#Campbell, A.M. and Heyer, L.J. (2003), “Chapter 4: Basic Research with DNA Microarrays”, in Discovering Genomics, Proteomics, and Bioinformatics, Cold Spring Harbor Laboratory Press, pp. 107-124.
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[[Category:Journal Entry]]

Latest revision as of 06:11, 10 October 2017

Questions

  1. (See figure)
    Question 1 Answer
  2. The ratio is calculated by dividing one gene’s activity in cells gradually consuming all the available oxygen by its activity in control cells with unlimited oxygen. Therefore, Gene X goes from black to dim red to black to medium green. Gene Y goes from black to medium red to dim green to bright green. Finally, Gene Z goes from black to dim red and stays at dim red (in the order of 1 hour, 2 hour, 3 hour, and 4 hour, respectively).
  3. Genes X and Y were transcribed similarly (had similar ratios).
  4. At time 0, no/very little change has occurred in terms of expression or repression of the gene because the cells have just been exposed to the experimental growth conditions. Spots with equal expression and repression compared to the control sample appear yellow because red and green mix to make yellow.
  5. TEF4 was repressed over the course of the experiment indicated by the green color. TEF4's change in expression was part of the cell's response to a reduction in available glucose. Glucose is the source of energy for cells and in the absence of glucose, actions that expend the cells energy (such as translation) may be limited.
  6. The TCA cycle does not use glucose directly--glucose is converted into pyruvic acid. When glucose levels are low, pyruvic acid is modified and converted into acetyl-CoA, which then enters the TCA cycle.
  7. These genes in the common pathway could all be induced or repressed by the same transcription factor (pg. 119).
  8. I would expect these spots to be red because since the repressor is absent, the cells would continue to express the gene even in the absence of glucose.
  9. I would expect the spots to be red since Yap1p target genes allow for increased resistance to environmental stresses. Therefore, a depletion of glucose in the environment (i.e. an environmental stress) would induce more expression of these genes.
  10. Deletion of TUP1 and YAP1 would result in a red spot on the microarray for Tup1p compared to a green spot (expression compared to repression) and a brighter red spot for Yap1p (indicating more expression).

Links

  1. My User Page
  2. List of Assignments
  3. List of Journal Entries
  4. List of Shared Journal Entries

Acknowledgments

  1. I worked with my homework partner Arash Lari over text. We were available for one another for questions about the assignment.
  2. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Emmatyrnauer (talk) 21:27, 9 October 2017 (PDT)

References

  1. LMU BioDB 2017. (2017). Week 6. Retrieved October 9, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_6
  2. Campbell, A.M. and Heyer, L.J. (2003), “Chapter 4: Basic Research with DNA Microarrays”, in Discovering Genomics, Proteomics, and Bioinformatics, Cold Spring Harbor Laboratory Press, pp. 107-124.
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