Cdomin12 Week 6 - Revision history

Cdomin12: answer

2019-10-09T05:37:05Z

answer

Cdomin12: answer

2019-10-09T05:30:48Z

answer

Cdomin12: /* Acknowledgments */ added user

2019-10-09T05:20:09Z

‎Acknowledgments: added user

Cdomin12: added image

2019-10-09T05:18:59Z

added image

Cdomin12: invoke template

2019-10-08T20:12:41Z

invoke template

Cdomin12: added answer

2019-10-08T20:09:29Z

added answer

Cdomin12: answer

2019-10-07T16:03:19Z

answer

Cdomin12: answer

2019-10-07T15:53:07Z

answer

Cdomin12: /* 6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out? */ answer

2019-10-07T15:42:54Z

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

Cdomin12: /* Gene Y */ change color

2019-10-07T15:38:49Z

‎Gene Y: change color

← Older revision		Revision as of 05:37, 9 October 2019
Line 59:		Line 59:

	===10. (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?===		===10. (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?===
		+	You can compare a previous microarray that contains the original genes that did not delete TUP1 or overexposes YAP1. By comparing this to the deleted TUP1 and over expressed YAP1, you can see the change in color mentioned above that would show that it is complete and verified.

	==Acknowledgments==		==Acknowledgments==

← Older revision		Revision as of 05:30, 9 October 2019
Line 50:		Line 50:

	===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?===		===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?===
		+	If these genes have the same operon and a single promoter, it would ensure that they are transcribed together and thus they will be 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?===		===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?===

@@ Line 60: / Line 60: @@
 ==Acknowledgments==
-. I worked with
+. I worked with [[User:Msamdars]] for this assignment.
 ."Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

@@ Line 6: / Line 6: @@
 ==Questions==
 ===1. (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.===
 ===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.)===

← Older revision		Revision as of 20:12, 8 October 2019
Line 1:		Line 1:
		+	{{template:cdomin12}}
		+
	==Purpose==		==Purpose==
	To use microarray data and analysis in order to uncover more about gene regulation and expression in different environments, including various glucose and oxygen levels.		To use microarray data and analysis in order to uncover more about gene regulation and expression in different environments, including various glucose and oxygen levels.

@@ Line 34: / Line 34: @@
 ===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?===
-Gene X and Y were transcribed similarly in increase in oxygen and than loss in oxygen.
+Gene X and Y were transcribed similarly in increase in oxygen and than loss in oxygen due to its consumption.
 ===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?===

← Older revision		Revision as of 16:03, 7 October 2019
Line 51:		Line 51:

	===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?===		===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?===
		+	I would expect the spots to be green. Since the Yap1p gene is overexpressed and glucose is depleted, there would be less expression due to the lack of glucose as it was overexpressed and quickly used.

	===10. (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?===		===10. (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?===

← Older revision		Revision as of 15:53, 7 October 2019
Line 48:		Line 48:

	===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?===		===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?===
		+	I would expect the spots to be red. Since the repressor TUP1 is turned off (and thus not repressing), the glucose- repressed genes will be induced during glucose depletion and thus red.

	===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?===		===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?===

@@ Line 43: / Line 43: @@
 ===6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?===
-TCA cycle genes would be induced due to
+The TCA cycle can be induced as it can break down various other components such as proteins, in order to produce energy. When they are broken down, they can feed into the TCA cycle so that the cells can get the energy they need without starting with an initial glucose supply.
 ===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?===

@@ Line 20: / Line 20: @@
 hours:medium red
-hours:medium green
+hours:dim green
-hours:bright green
+hours:dim green
 ====Gene Z====