Zvanysse Week 6 - Revision history

Zvanysse: added acknowledgements/references/category

2017-10-10T02:39:03Z

added acknowledgements/references/category

Zvanysse: Finishing up homework

2017-10-09T19:03:37Z

Finishing up homework

Zvanysse: answering and tweaking questions

2017-10-09T18:50:20Z

answering and tweaking questions

Zvanysse: updated graph

2017-10-09T18:31:28Z

updated graph

Zvanysse: fixed formatting

2017-10-08T23:46:38Z

fixed formatting

Zvanysse: Answered numbers 7-9

2017-10-08T23:42:22Z

Answered numbers 7-9

Zvanysse: Answering questions 3,5,7

2017-10-08T22:59:52Z

Answering questions 3,5,7

Zvanysse: uploaded graph

2017-10-08T22:28:39Z

uploaded graph

New page

==Biological Databases Bookwork==
# [[Image:Graph1Week6.png | 600px]]

← Older revision		Revision as of 02:39, 10 October 2017
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	===Question 10===		===Question 10===
	With mostly all scientific experiments, there should be a control test cell that depicts normal levels. Then, one can compare and see if the Tup1p related genes were red in the presence of glucose. If it is red - then one can verify that there has been a deletion of Tup1p. Similarly, if Yap1p related genes were brighter red as glucose diminished, this would indicate an over expression of YAP1.		With mostly all scientific experiments, there should be a control test cell that depicts normal levels. Then, one can compare and see if the Tup1p related genes were red in the presence of glucose. If it is red - then one can verify that there has been a deletion of Tup1p. Similarly, if Yap1p related genes were brighter red as glucose diminished, this would indicate an over expression of YAP1.
		+	==Acknowledgments==
		+	#I would like to acknowledge Simon as we both worked on the assignment together.
		+	#I would like to acknowledge Quinn for explaining to me some of the biological terminologies.
		+
		+	==References==
		+	#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.
		+	#https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_6
		+	#https://www.yeastgenome.org/locus/S000001564
		+
		+	[[Category:Journal Entry]]

@@ Line 30: / Line 30: @@
 If all the genes for enzymes in a common pathway are regulated by a similar transcription factor, the genome is able to ensure induction or repression simultaneously.
 ===Question 8===
+Tup1p is a repressor. Without this, the glucose-repressed genes wouldn't be able to be repressed with the presence or absence of glucose. This means that the rate of transcription would increase causing red spots.
 ===Question 9===
-Assuming that cells that over express the transcription factor of Yap1p were subjected to the same experiment of a timecourse of glucose depletion, the spots that represented Yap1p target genes would show up as green the later the time points of this experiment. This is because Yap1p confers environmental stress. I am assuming that glucose depletion is an environmental stress factor.
+Assuming that cells that over express the transcription factor of Yap1p were subjected to the same experiment of a timecourse of glucose depletion, the spots that represented Yap1p target genes would show up as red the later the time points of this experiment. This is because Yap1p confers environmental stress and of course, glucose depletion is an environmental stress factor.
 ===Question 10===

@@ Line 22: / Line 22: @@
 Yes, genes X and Y were transcribed similarly. They both have a spike in transcriptions and then quickly fall nearing 0 by the end of hour 9.
 ===Question 4===
 ===Question 5===
-According to OD 3.7 in Figure 4.12, TEF4 is depicted as repressed. This is possibly because TEF4 needs glucose to be able to transcribe, so as glucose supplies are reduced, the TEF4 gene's ability to transcribe reduce as well. It is shown in figure 4.10 that as glucose levels drop, cell density increases.
+According to OD 3.7 in Figure 4.12, TEF4 is depicted as repressed. This is possibly because TEF4 needs glucose to be able to transcribe, so as glucose supplies are reduced, the TEF4 gene's ability to transcribe reduce as well, as it must save it's energy. It is shown in figure 4.10 that as glucose levels drop, cell density increases.
 ===Question 6===
 ===Question 7===
-The gene can use the "guilt by association" mechanism to ensure genes for enzymes in a common pathway are induced or repressed simultaneously.
+If all the genes for enzymes in a common pathway are regulated by a similar transcription factor, the genome is able to ensure induction or repression simultaneously.
 ===Question 8===
 ===Question 9===
 Assuming that cells that over express the transcription factor of Yap1p were subjected to the same experiment of a timecourse of glucose depletion, the spots that represented Yap1p target genes would show up as green the later the time points of this experiment. This is because Yap1p confers environmental stress. I am assuming that glucose depletion is an environmental stress factor.
 ===Question 10===

@@ Line 1: / Line 1: @@
 ==Biological Databases Bookwork==
 ===Question 1===
-[[Image:Graph1Week6.png | 600px]]
+[[Image:induction2genegraphweek6.png | 600px]]
 ===Question 2===
 '''Gene X'''

@@ Line 1: / Line 1: @@
 ==Biological Databases Bookwork==
-# [[Image:Graph1Week6.png | 600px]]
+===Question 1===
 [[Image:Graph1Week6.png | 600px]]
-# Yes, genes X and Y were transcribed similarly. They both have a spike in transcriptions and then quickly fall nearing 0 by the end of hour 9.
+===Question 2===
+'''Gene X'''
-#According to OD 3.7 in Figure 4.12, TEF4 is depicted as repressed. This is possibly because TEF4 needs glucose to be able to transcribe, so as glucose supplies are reduced, the TEF4 gene's ability to transcribe reduce as well. It is shown in figure 4.10 that as glucose levels drop, cell density increases.
+*Hour 1: 1.0 ratio, black.
+*Hour 3: 2.2 ratio, very dim red.
-#The gene can use the "guilt by association" mechanism to ensure genes for enzymes in a common pathway are induced or repressed simultaneously.
+*Hour 5: 1.0 ratio, black.
+*Hour 9: 0.15 ratio, medium green.
-#Assuming that cells that over express the transcription factor of Yap1p were subjected to the same experiment of a timecourse of glucose depletion, the spots that represented Yap1p target genes would show up as green the later the time points of this experiment. This is because Yap1p confers environmental stress. I am assuming that glucose depletion is an environmental stress factor.
+'''Gene Y'''
+*Hour 1: 1.0 ratio, black.

← Older revision		Revision as of 22:59, 8 October 2017
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	==Biological Databases Bookwork==		==Biological Databases Bookwork==
	# [[Image:Graph1Week6.png \| 600px]]		# [[Image:Graph1Week6.png \| 600px]]
		+	#
		+	# Yes, genes X and Y were transcribed similarly. They both have a spike in transcriptions and then quickly fall nearing 0 by the end of hour 9.
		+	#
		+	#According to OD 3.7 in Figure 4.12, TEF4 is depicted as repressed. This is possibly because TEF4 needs glucose to be able to transcribe, so as glucose supplies are reduced, the TEF4 gene's ability to transcribe reduce as well.
		+	#
		+	#The gene can use the "guilt by association" mechanism to ensure genes for enzymes in a common pathway are induced or repressed simultaneously.
		+	#
		+	#