BIOL368/F14:Isabel Gonzaga Week 10

HIV Structure Project Addendum

The Huang et. al (2005) 2B4C structure was uploaded onto the StarBiochem software. The V3 region was isolated and imaged with its contained secondary structures. The amino acid side group positions predicted to change within secondary structures of the V3 region (from the PSIPred prediction) were isolated and imaged.

Figure 1. Phenylalanine (a, position 20) and Threonine (b, position 22) residues highlighted in the context of the V3 region, as imaged by StarBiochem. These structures showed to be non conserved regions as a part of a Beta sheet, according to the original PSIPred results. Comparing this structure against StarBiochem shows the PSIPred results to be inaccurate in determining the beta sheet region. Rather, these amino acids are predicted to be between successive Beta sheets. These residues were highlighted as they showed change and non conservation amongst the progressing group sequences

Figure 2. Aspartate (a), Glutamine (b) and Histidine (c) (at positions 29, 32 and 34 on the V3 region, respectively) shown in context of the entire V3 region, as imaged by StarBiochem. PSIPred determined these residues to be components of an alpha helix, which is inconsistent with the secondary structures predicted by StarBiochem. These residues were highlighted as they showed change and non conservation amongst the progressing group sequences.

Introduction to DNA Microarrays

Discovery Questions taken from Campbell, A.M. and Heyer, L.J. (2003), Chapter 4 and can be found on the Week 10 Assignment page.

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.
   • This graph shows the change in transcription levels over time for SPS1 (blue) and DIT1 (red). SPS1 and DIT1 overlap at the same transcription level at the tree time periods between 0 and 2 hours.
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?

Week 11 Project Preparation

• Isabel Gonzaga
• BIOL 368 Fall 2014

Weekly Assignments

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Electronic Lab Notebook

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