Week 6

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This journal entry is due on Tuesday, October 10, at 12:01 AM PDT.

Objectives

The purpose of this assignment is:

  • To understand how the DNA microarray biotechnology works as a foundation for data analyses we will conduct later in the course.
  • To further understand how yeast is used as a model organism in biology.
  • To reflect upon a case of academic fraud related to microarray technology and the role of data sharing in uncovering the fraud.

Individual Journal Assignment

  • Store this journal entry as "username Week 6" (i.e., this is the text to place between the square brackets when you link to this page).
  • Link from your user page to this Assignment page.
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Don't forget to add the "Journal Entry" category to the end of your wiki page.
    • Note: You can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
  • For your assignment this week, and this week only, the requirement for the electronic laboratory notebook is waived.
  • You do have to include both the Acknowledgments and References section as specified by the Week 1 assignment.

Homework Partners

For most weeks in the semester, you will be assigned a "homework partner" from a complementary discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). You must give the details of the interaction with your partner in the Acknowledgments section of your journal assignment. Homework partners for this week are:

  • Eddie A. and Quinn L.
  • Eddie B. and Antonio P.
  • Mary B. and John L.
  • Dina B. and Blair H.
  • Hayden H. and Corinne W.
  • Nicole K. and Katie W.
  • Arash L. and Emma T.
  • Zach V. and Simon W.

Introduction to DNA Microarrays

Read

Answer the following Discovery Questions from Chapter 4

Answer the following questions related to Chapter 4 of Campbell & Heyer (2003). Note that some of the questions below have been reworded from the Discovery Questions in the book:

  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.
  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?
  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?
  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).
  6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
  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?
  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?
  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?
  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?

Shared Journal Assignment

  • Store your shared journal entry in the shared Class Journal Week 9 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).
  • Note that if the class is using a template for the shared journal entry, please just copy and paste the text onto this page instead of actually invoking the template. Since the text of the shared reflection is changing from week to week, invoking a template makes it difficult for the instructors to grade the weekly work.

View

Reflection

  • Answer the following questions:
    1. Were you aware of this case of research fraud before viewing this video?
    2. What are your initial reactions to hearing about this case?
    3. What role did data sharing play in uncovering this fraud?
    4. What additional information would you like to know about this case? (We will be visiting it again in subsequent weeks in the course.)
  • Please feel free to respond or comment on your classmates' reflections.