Sarah Carratt: Week 8: Difference between revisions
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[[Image:carratt_microarray.jpg|thumb|upright=5|left|'''DNA Microarray Expression Over Time:''' four genes shown with negative values representing repressed expression and positive values representing induced expression in proportion according to brightness]] | |||
'''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 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b. | '''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 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b. | ||
Revision as of 21:39, 16 March 2011
Individual Journal Assignment
Formatting
- Store this journal entry as "username Week 8" (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: you can do all of this easily by adding them to your template and then using the template on your pages.)
- 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 "BIOL398-01/S11" category to the end of your wiki page.
Discovery Questions from Chapter 4
- (p. 110) Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time. *Note: Dr. Dahlquist said that this will be done on a seperate piece of paper to be submitted in class on Thursday.
- (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 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b.
- (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
- (p. 118) Why would most spots be yellow at the first time point?
- (p. 118) Go to http://www.yeastgenome.org 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 gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
- (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
- (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
- (p. 121) Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?
- (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
- (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
- (p. 121) What types of control spots would you like to see in this type of experiment? How could you verify that you had truly deleted or overexpressed a particular gene?
Online Sources
- 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 MyLMUConnect; the color figures are also posted there)
- 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.
- This animation from Malcolm Campbell may also be helpful.
Student Response
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 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b.
7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
9. (p. 118) Why would most spots be yellow at the first time point?
10. (p. 118) Go to http://www.yeastgenome.org 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 gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
13. (p. 121) Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?
14. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
15. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
16. (p. 121) What types of control spots would you like to see in this type of experiment? How could you verify that you had truly deleted or overexpressed a particular gene?
Individual Assignments
Class Assignments
Class Notes
Internal Links
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