Cwong34 Week 6

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Discovery Questions

  1. (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.
    • DMC1&SPS100 cwong34.png
  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.)
    • Gene X - hour 1: black, hour 3: dim red, hour 5: black, hour 9: bright green
    • Gene Y - hour 1: black, hour 3: medium red, hour 5: black, hour 9: bright green
    • Gene Z - hour 1: black, hour 3: dim red, hour 5: medium red, hour 9: medium red
  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?
    • Yes, gene X and gene Y were transcribed similarly. They both began induction, then reduced back to a 1:1 ratio, and then reduced even further.
  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?
    • Most spots would be yellow at the first time point because the two sets have the same promoters, so spots would contain both red and green. The spots turn yellow because it is a mix of both of the colors. If the experiment resulted in most spots being yellow, then maybe there was an error in growing the cells where one set received oxygen or vice versa. Moreover, it could mean that growing in differently oxygenated environments doesn't have a huge effect on the DNA.
  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 the experiment, TEF4 was repressed. It may have been repressed because it needed glucose to be able to help with translational elongation.
  6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
    • The genes would be induced to convert the remaining glucose into storage sugars to retain energy.
  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?
    • The genes could on the same pathway, so they are all changed together.
  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?
    • The spots would be red because there would be no TUP1 to repress the glucose-repressed genes. Thus, they would be present and red because the glucose depleted cells are labeled red.
  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?
    • The spots would be red because Yap1p is acting on the genes experiencing environmental stresses.
  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?
    • There would be a large array of red and no green at the later time points.

Acknowledgments

  1. I met with Hayden Hinsch, and we worked together for this week's assignment.
  2. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

Cwong34 (talk) 22:35, 8 October 2017 (PDT)

References

  1. Alberts et al. (2002) Molecular Biology of the Cell, Ch. 8: Microarrays
  2. Brown, P.O. & Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays Nature Genetics 21: 33-37.
  3. 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.
  4. DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997) Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale. Science 278: 680-686.
  5. LMU BioDB 2017. (2017). Week 6. Retrieved October 3, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_6

cwong34

BIOL/CMSI 367-01: Biological Databases Fall 2017

Assignments

Journal Entries:

Shared Journals:

Group Project

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