Kasey E. O'Connor Week 8 Journal: Difference between revisions

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==Introduction to Microarrays==
==Introduction to Microarrays==
====Discovery Questions from Chapter 4====
====Discovery Questions from Chapter 4====
5. (p. 110) Choose two genes from Figure 4.6 https://mylmuconnect.lmu.edu/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_57614_1%26url%3D (PDF of figures on MyLMUConnect)] and draw a graph to represent the change in transcription over time.
*
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.
*
*In the first hour, genes X, Y, and Z are all black because they have a ratio of 1. At hour 3, X would be dim red, Y medium red, and Z dim red. At hour 5, X is black, Y is very dim green (almost black), and Z is dim red. Lastly, at hour 9 X is medium green, Y is bright green, and Z remains dim red.
7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
*
*All three gene transcriptions went from a ratio of 1 and then increased at hour 3. However, X and Y went back to about 1 at hour 5, while Z continued to increase. Gene X and Y also both decreased at hour 9, but Y decreased at a large ratio.
9. (p. 118) Why would most spots be yellow at the first time point?
9. (p. 118) Why would most spots be yellow at the first time point?
*
*At the first time point, there has been little change to the gene expression. This is due to the fact that it is going to take the yeast some time to begin to respond to the changes in the environment and change their gene expression.
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).
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).
*
*Looking at the figures in the chapter, it is clear that the TEF4 expression was repressed in the experiment by the fact that the spot is green, meaning there was more expressed in the control. Because TEF4 is used in translation, it makes sense that the cell represses the expression since it was hypothesized that cells respond to starvation through repressing genes involved in protein synthesis. Without glucose for the cells to consume, there is no energy for protein synthesis, and therefore no need to express genes used in translation.
11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
11. (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
*
*As the glucose supply runs low, the cells are going to want to produce as much energy as possible to continue functioning. The TCA cycle produces the ATP needed for cellular energy, so the genes involved with the TCA cycle would be induced to make sure that the cell can produce the all the ATP before there is no other food source for an extended time period.
12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
*
*One mechanism that the genome can use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously is the guilt by association method. With this method, genes with similar profiles will have similar promoters. Gene expression for enzymes in a common pathway would also be able to be induced or repressed with the same promoter.
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?
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?
*
*I would expect to see the DNA chip is more red when the cells repressor gene is deleted. This is because the experimental population will not be repressed and there is going to be a greater amount of gene expression.
14. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
14. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
*
*When Yap1p is overexpressed, there is going to be more red spots on the chip since overexpression of the transcription factor will cause more expression of genes to react to the stress.
15. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
15. (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
*
*It is definitely possible for a gene to be repressed if a different repressor is lost or a transcription factor is overexpressed. Due to the way that some genes work together,  the repression of one gene could result in an overexpression of a paired gene. In this same fashion, an overexpressed transcription factor can cause certain genes to be express that would alter and repress other genes.
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?
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?
*
*The control spots should be genes that are not affected by any of the deleted genes or overexpressed transcription factors. Looking at the microarray chip to make sure that no gene appears can be used to verify that it has been truly deleted. If the gene is overexpressed, the spot would be bright red on the microarray chip.


====Useful Links====
==Useful Links==
{{Kasey E. O'Connor}}
{{Kasey E. O'Connor}}

Latest revision as of 18:46, 14 March 2013

Introduction to Microarrays

Discovery Questions from Chapter 4

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.

  • In the first hour, genes X, Y, and Z are all black because they have a ratio of 1. At hour 3, X would be dim red, Y medium red, and Z dim red. At hour 5, X is black, Y is very dim green (almost black), and Z is dim red. Lastly, at hour 9 X is medium green, Y is bright green, and Z remains dim red.

7. (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?

  • All three gene transcriptions went from a ratio of 1 and then increased at hour 3. However, X and Y went back to about 1 at hour 5, while Z continued to increase. Gene X and Y also both decreased at hour 9, but Y decreased at a large ratio.

9. (p. 118) Why would most spots be yellow at the first time point?

  • At the first time point, there has been little change to the gene expression. This is due to the fact that it is going to take the yeast some time to begin to respond to the changes in the environment and change their gene expression.

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).

  • Looking at the figures in the chapter, it is clear that the TEF4 expression was repressed in the experiment by the fact that the spot is green, meaning there was more expressed in the control. Because TEF4 is used in translation, it makes sense that the cell represses the expression since it was hypothesized that cells respond to starvation through repressing genes involved in protein synthesis. Without glucose for the cells to consume, there is no energy for protein synthesis, and therefore no need to express genes used in translation.

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

  • As the glucose supply runs low, the cells are going to want to produce as much energy as possible to continue functioning. The TCA cycle produces the ATP needed for cellular energy, so the genes involved with the TCA cycle would be induced to make sure that the cell can produce the all the ATP before there is no other food source for an extended time period.

12. (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?

  • One mechanism that the genome can use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously is the guilt by association method. With this method, genes with similar profiles will have similar promoters. Gene expression for enzymes in a common pathway would also be able to be induced or repressed with the same promoter.

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?

  • I would expect to see the DNA chip is more red when the cells repressor gene is deleted. This is because the experimental population will not be repressed and there is going to be a greater amount of gene expression.

14. (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?

  • When Yap1p is overexpressed, there is going to be more red spots on the chip since overexpression of the transcription factor will cause more expression of genes to react to the stress.

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

  • It is definitely possible for a gene to be repressed if a different repressor is lost or a transcription factor is overexpressed. Due to the way that some genes work together, the repression of one gene could result in an overexpression of a paired gene. In this same fashion, an overexpressed transcription factor can cause certain genes to be express that would alter and repress other genes.

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?

  • The control spots should be genes that are not affected by any of the deleted genes or overexpressed transcription factors. Looking at the microarray chip to make sure that no gene appears can be used to verify that it has been truly deleted. If the gene is overexpressed, the spot would be bright red on the microarray chip.

Useful Links

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