This journal entry is due on Thursday, January 31 at midnight PST (Monday night/Tuesday morning).
The purpose of this assignment is:
- To learn about how DNA microarray experiments work.
- To reason through some DNA microarray analysis problems.
- To discuss a case where standards of research ethics were violated.
Individual Journal Assignment
- Store this journal entry as "username Week 2" (i.e., this is the text to place between the square brackets when you link to this page).
- Create the following set of links. (HINT: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.)
- Link to your journal entry from your user page.
- Link back from your journal entry to your user page.
- Link to this assignment from your journal entry.
- Don't forget to add the "BIOL388/S19" category to the end of your wiki page.
Please meet with your partner (either face-to-face or virtually) at least once when preparing this assignment. Even though you may work together to understand the article, your definitions and outline must be done individually. It is not acceptable to do a joint assignment and copy it over to each others' journal page.
- Angela and Edward
- Fatimah and Austin
- Desiree and Alison
- Leanne and Ava
- Sahil and Brianna
Electronic Lab Notebook
Because of the nature of the assignment this week, you will have four sections of the electronic notebook:
- The purpose: what is the purpose of this assignment?
- Answers to the questions posed in the assignment.
- The Acknowledgments section.
- You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. You should include when and how you met and what content you worked on together. An appropriate statement could be (but is not limited to) the following:
- I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
- Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist or Dr. Fitzpatrick (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
- If you copied
wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style.
- If you need to reference content, include the formal citation in your References section (see below).
- You must also include this statement:
- "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
- Sign your Acknowledgments section with your wiki signature.
- The References section. In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising.
- Do not include citations/references to sources that you did not use.
- You should include a reference to this week's assignment page.
- The references should be formatted according to the APA guidelines.
- For more detailed instructions on how to cite journal articles, books, or web pages, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.
Introduction to DNA Microarrays
- Alberts et al. (2002) Molecular Biology of the Cell, Ch. 8: Microarrays
- Microarray animation
- Brown, P.O. & Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays Nature Genetics 21: 33-37.
- 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. (Available on Brightspace)
- 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.
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:
- (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. You can either create your plot in Excel and put the image up on your wiki page or you can do it by hand and upload a picture or scan.
- (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.)
- (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?
- (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?
- (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).
- (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
- (Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
- (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?
- (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?
- (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?
- Store your shared journal entry in the shared Class Journal Week 2 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 "BIOL388/S19" category to the end of the wiki page (if someone has not already done so).
- Answer the following questions:
- Were you aware of this case of research fraud before viewing this video?
- What are your initial reactions to hearing about this case?
- What role did data sharing play in uncovering this fraud?
- 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.