BIOL368/F14:Week 10

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BIOL368: Bioinformatics Laboratory

Loyola Marymount University

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This journal entry is due on Wednesday, November 5 at midnight PST (Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.

Individual Journal Assignment

  • Store this journal entry as "username Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. These links should all be in your personal template; then use the template on your 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 "BIOL368/F14" category to the end of your wiki page.

HIV Structure Redux

  • For each of the amino acid substitutions that you talked about in your HIV Structure Project Presentation, use StarBiochem or Cn3D to locate the positions of those amino acids on the structure..
  • Take a screenshot showing a view that shows the amino acid(s) in question. You may choose to do one substitution at a time or show all of them on the same screenshot. Save your screenshot(s) in a PowerPoint slide and use an arrow or circle to point to the amino acid. Label each with the amino acid it is in the structure and what the substitutions were in the subjects you studied.
  • Interpret whether the amino acids are in a location that should affect the function of gp120.

Introduction to DNA Microarrays


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 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?
  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 15, p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
  11. (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?

Finding a Journal Club Article/Microarray Dataset

  • You may choose to work ahead towards your Week 11 Assignment and Journal Club 3 presentation by finding your article and corresponding microarray dataset with which you will perform your final project in the course. Your task is to find a published microarray dataset that fulfills the following criteria:
    • The data are from a micraorray experiment that measures changes in gene expression (also known as transcription profiling by array).
    • A minimum of three biological replicates have been performed for each condition measured.
    • The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye.
    • The control sample needs to be derived from mRNA and not genomic DNA.
    • The experiment was performed on one of the following species:
      • Arabidopsis thaliana
      • Chlamydia trachomatis
      • Escherichia coli K12
      • Helicobacter pylori
      • Mycobacterium smegmatis
      • Mycobacterium tuberculosis H37Rv
      • Plasmodium falciparum
      • Pseudomonas aerugenosa
      • Saccharomyces cerevisiae (budding yeast)
      • Salmonella typhimurium
      • Sinorhizobium meliloti
      • Staphylococcus aureus COL
      • Staphylococcus aureus MRSA252
      • Streptococcus pneumoniae
      • Vibrio cholerae
  • Microarray data are not centrally located on the web. Some major sources are:
  • You learned how to use PubMed, GoogleScholar, and Web of Science for your Week 3 Assignment. In this case, it will be likely be easier to search for the data first in one of the databases listed above and then retrieve the article corresponding to the data.
  • You must make a list of five potential articles/datasets on your Week 11 journal page by the end of class on Wednesday, November 5. The instructor will notify you as to which article(s) are approved for your Journal Club presentation and final project.

Shared Journal Assignment

  • Store your journal entry in the shared BIOL368/F14:Class Journal Week 10 page. If this page does not exist yet, go ahead and create it.
  • Link to the shared journal entry from your user page; this should be part of your template.
  • Link the shared journal page to this assignment page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL368/F14" category to the end of the wiki page (if someone has not already done so).


After reading the Brown & Botstein (1999), Campbell & Heyer (2003), and DeRisi et al. (1997) readings, reflect on the following:

  1. What was the purpose of these readings?
  2. What did I learn from these readings?
  3. What did I not understand (yet) about the readings?