Lauren M. Magee Week 9

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  1. (Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time. You can either create your plot in Excel and put the image up on your wiki page or you can do it in hard copy and turn it in in class.
  2. (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.
  3. (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?
    • Gene X and Gene Y are transcribed similarly, because they show similar patterns of induction and repression. They both begin showing black color, moving to a dim red, then back to black, and then finally to medium green.
  4. (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?
    • Yellow dots represent no change. In the past figures, black represented no change, but because we are using a black background in this test, we must note the change in the identification to yellow. Yellow spots make up the majority of the first time point, because cells have not yet had a chance to react to their environmental pressures. Whether transcription is induced or repressed is yet to be determined.
  5. (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).
    • Over the course of this experiment, TEF4 seems to have been induced. I would hypothesize that the TEF4 gene is not depend on glucose, so when the resource is depleted, the expression of this gene increases as it becomes more essential, when other genes are no longer able to be expressed.
  6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
    • TCA cycle genes are prepared to function without the presence of glucose, because they use alternate forms of energy to feed the cell. Therefore, when the supply of glucose is low, the TCA cycle genes are induced to help facilitate the jobs that other genes are not prepared to complete without the energy provided by glucose.
  7. (Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
    • Cluster analysis is a mechanism that can be used to ensure that genes within the same pathway are induced or repressed simultaneously. This practice specifically identifies genes that are coordinately regulated and can be effectively grouped to one another to provide incite into their similarities and functionality.
  8. (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?
    • I would expect the spots that represent the glucose-repressed genes to be red, because they will be induced when the environmental supply of glucose becomes depleted. Without the presence of glucose, the genes will not have nothing in the form of repression and therefore will be overexpressed.
  9. (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?
    • I would expect the spots that represent Yap1p to be red, because if we are studying genes that characteristically overexpress the transcription factor Yap1p, we would expect to see an induced expression even after glucose has been depleted.
  10. (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?
    • To verify that TUP1 had truly been deleted, you would need to see a black coloring in your microarray data. Since the gene is no longer present, it will show no change upon resource depletion an remain black (no change) throughout. If the YAP1 gene is overexpressed, you will see a bright red coloring, indicating that the gene has been induced in a capacity of 20+ folds.

Lauren M. Magee

  1. Week 1
  2. Week 2
  3. Week 3
  4. Week 4
  5. Week 5
  6. Week 6
  7. Week 7
  8. Week 8
    • Assignment Cancelled
  9. Week 9
  10. Week 10
  11. Week 11
  12. Week 12
  13. Week 13
  14. Week 14
  15. Week 15
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