Difference between revisions of "Emmatyrnauer Week 6"

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#(Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on Brightspace) and draw a graph to represent the change in transcription over time. Create your plot in Excel (or other program that can do plots) and display the image up on your wiki page. Alternately, you can do it by hand, scan or take a photo of the plot, and display the image on your wiki page.
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==Questions==
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#*
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#(See figure) [[File:Question_1_Assignment_6_Emma_Tyrnauer.png|400px|thumb|right|Question 1 Answer]]
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#(Question 6b, p. 110) Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes. These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen. Using the color scale from Figure 4.6, determine the color for each ratio in Figure 4.7b. (Use the nomenclature "bright green", "medium green", "dim green", "black", "dim red", "medium red", or "bright red" for your answers.)
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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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#*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 medium red to black to medium green. Gene Y goes from black to bright red to dim green to medium green. Finally, Gene Z goes from black to dim red to medium red and then stays at medium red.
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#Genes X and Y were transcribed similarly (had similar ratios).
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#(Question 7, p. 110) Were any of the genes in Figure 4.7b transcribed similarly? If so, which ones were transcribed similarly to which ones?
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#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.   
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#*Genes X and Y were transcribed similarly.
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#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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#(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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#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.  
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#*At time 0, no/very little change has occurred in terms of expression or repression of the gene. Spots with equal expression and repression compared to the reference sample appear yellow because red and green mix to make yellow.   
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#These genes in the common pathway could all be induced or repressed by the same transcription factor (pg. 119).
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#(Question 10, p. 118) Go to the Saccharomyces Genome Database and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4’s change in expression was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
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#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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#*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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#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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#(Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
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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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#*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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#(Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
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{{Emmatyrnauer}}
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#*These genes in the common pathway could all be induced or repressed by the same transcription factor (pg. 119).
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#(Question 13, p. 121) Consider a microarray experiment where cells deleted for the repressor TUP1 were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented glucose-repressed genes to be in the later time points of this experiment?
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==Acknowledgments==
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#*I would expect these spots to be red because since the repressor is absent, and the cells would continue to use up the glucose.
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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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#(Question 14, p. 121) Consider a microarray experiment where cells that overexpress the transcription factor Yap1p were subjected to the same experiment of a timecourse of glucose depletion where cells at t0 (plenty of glucose available) are labeled green and cells at later timepoints (glucose depleted) are labeled red. What color would you expect the spots that represented Yap1p target genes to be in the later time points of this experiment?
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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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#*I would expect the spots to be green since Yap1p target genes allow for increased resistance to environmental stresses. Therefore, a depletion of glucose in the environment would not have as significant of an effect on these cells.
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[[User:Emmatyrnauer|Emmatyrnauer]] ([[User talk:Emmatyrnauer|talk]]) 21:27, 9 October 2017 (PDT)
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#(Question 16, p. 121) Using the microarray data, how could you verify that you had truly deleted TUP1 or overexpressed YAP1 in the experiments described in questions 8 and 9?
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#*
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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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