Aporras1 Week 6 - Revision history

Aporras1: edit to question 10

2017-10-10T06:05:07Z

edit to question 10

Aporras1: /* Discovery Questions */ edit to question 6

2017-10-10T06:04:35Z

‎Discovery Questions: edit to question 6

Aporras1: /* Discovery Questions */ edit to question 10

2017-10-10T06:00:45Z

‎Discovery Questions: edit to question 10

Aporras1: /* Discovery Questions */ answer to question 10

2017-10-10T06:00:00Z

‎Discovery Questions: answer to question 10

Aporras1: question 9 answer

2017-10-10T05:10:24Z

question 9 answer

Aporras1: /* Discovery Questions */ question 8 answer

2017-10-10T05:03:02Z

‎Discovery Questions: question 8 answer

Aporras1: /* Discovery Questions */ answer to question 7

2017-10-10T04:49:20Z

‎Discovery Questions: answer to question 7

Aporras1: /* Acknowledgements */ added dondi and dalquist

2017-10-10T04:37:57Z

‎Acknowledgements: added dondi and dalquist

Aporras1: /* Discovery Questions */ question 6 answer

2017-10-09T07:28:53Z

‎Discovery Questions: question 6 answer

Aporras1: /* References */ added all references

2017-10-09T07:03:04Z

‎References: added all references

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 '''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 could perform the same experiment with glucose depletion and compare that to a normal microarray of TUP1 and Yap1p. You would specifically look at the target genes of these transcription factors and the dots would be red in the presence of glucose thus confirming TUP1 deletion. On the other hand, one would expect the dots of targets genes of Yap1p to be bright red as glucose concentration decreased to confirm it's over expression.
+You could perform the same experiment with glucose depletion and compare that to a normal microarray of TUP1 and Yap1p. You would specifically look at the target genes of these transcription factors and the dots would be red in the presence of glucose thus confirming TUP1 deletion. On the other hand, one would expect the dots of targets genes of Yap1p to be bright red as glucose concentration decreased to confirm its overexpression.
 ==Acknowledgements==

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 '''6. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?'''
-TCA cycle, also known as Kreb's cycle, genes would be induced because those genes are associated with energy metabolism which are induced as glucose is consumed. On the other hand, protein production genes are repressed during consumption of glucose. Overall, the cells would turn towards storage sugars to metabolize when the supply is running out.
+TCA cycle, also known as Kreb's cycle, genes would be induced because those genes are associated with energy metabolism which are induced as glucose is consumed. On the other hand, protein production genes are repressed during consumption of glucose. The primary reason for the induction of these genes is because of the increase of acetyl-COA entering the cycle from alcohol dehydrogenase.
 '''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?'''
-The genome could use common promoters to ensure genes for enzymes in a common pathway are induced or repressed simultaneously.
+The genome could use common promoters or transcription factors 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?'''

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 '''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 could perform the same experiment with glucose depletion and compare that to a normal microarray of TUP1 and Yap1p. You would specifically look at the target genes of these transcription factors and the dots would be red in the presence of glucose thus confirming TUP1 deletion. On the other hand, one would expect the dots of targets genes of Yap1p to be bright red as glucose concentration decreased to confirm it's deletion.
+You could perform the same experiment with glucose depletion and compare that to a normal microarray of TUP1 and Yap1p. You would specifically look at the target genes of these transcription factors and the dots would be red in the presence of glucose thus confirming TUP1 deletion. On the other hand, one would expect the dots of targets genes of Yap1p to be bright red as glucose concentration decreased to confirm it's over expression.
 ==Acknowledgements==

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 '''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 could perform the same experiment with glucose depletion and compare that to a normal microarray of TUP1 and Yap1p. You would specifically look at the target genes of these transcription factors and the dots would be red in the presence of glucose thus confirming TUP1 deletion. On the other hand, one would expect the dots of targets genes of Yap1p to be bright red as glucose concentration decreased to confirm it's deletion.
 ==Acknowledgements==

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 '''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 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?'''
 ==Acknowledgements==

← Older revision		Revision as of 05:03, 10 October 2017
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	'''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?'''
		+
		+	TUP1 acts as a repressor for glucose-repressed genes which are repressed by the presence of glucose. Without TUP1, these genes wouldn't be repressed by the presence of glucose and would continue transcription and thus produce red colored spots.

	'''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?'''

← Older revision		Revision as of 04:49, 10 October 2017
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	'''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?'''
		+
		+	The genome could use common promoters 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?'''		'''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?'''

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 ==Acknowledgements==
 #Met outside of class with [[User:Ebachour|Eddie Bachoura]] to discuss any questions we had prior to meeting and throughout the process of completing the Week 6 assignment.
 '''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''

← Older revision		Revision as of 07:03, 9 October 2017
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	==References==		==References==
		+	#Alberts B, Johnson A, Lewis J, et al. Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002. Studying Gene Expression and Function. Available from: https://www.ncbi.nlm.nih.gov/books/NBK26818/
		+	#Ashe, M. P., De Long, S. K., & Sachs, A. B. (2000). Glucose Depletion Rapidly Inhibits Translation Initiation in Yeast. Molecular Biology of the Cell, 11(3), 833–848.
		+	#Brown, P. O., & Botstein, D. (1999). Exploring the new world of the genome with DNA microarrays. Nature genetics, 21.
		+	#Campbell, A. M., Heyer, L. J., & Laurie, J. H. (2007). Discovering genomics, proteomics, and bioinformatics (No. 04; QH447, C3 2007.).
		+	#DeRisi, J. L., Iyer, V. R., & Brown, P. O. (1997). Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278(5338), 680-686.
		+	#LMU BioDB 2017. (2017). Week 5. Retrieved October 09, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_6

	[[Category:Journal Entry]]		[[Category:Journal Entry]]