Week 6 Individual Journal - Revision history

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Ymesfin: /* 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; changed answer

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/* 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; changed answer

Jnimmers: Revert back to original, mistake in overlapping page names

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Ymesfin: /* 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? */

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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?

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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?===
 In order to verify whether Tup1 had been deleted or whether Yap1 had been overexpressed, one can either use a microarray experiment and locate the spots associated with both genes. If the mutated Tup1 appears green, then its expression has been reduced, and if the mutated Yap1 appears red, then its expression has been induced. Similarly, one could also observe the spots associated with the target genes of the mutated Tup1 and Yap1. Since Tup1 is a repressor, it can be expected that its deletion would induce the expression of its target genes, and since Yap1 is a transcription factor, its overexpression would also be expected to induce the expression of its target genes.
 ==Acknowledgements==

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	Except for what is noted above, this individual journal entry was completed by me and not copied from another source.		Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
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	[[User:Ymesfin\|Ymesfin]] ([[User talk:Ymesfin\|talk]]) 20:45, 9 October 2019 (PDT)		[[User:Ymesfin\|Ymesfin]] ([[User talk:Ymesfin\|talk]]) 20:45, 9 October 2019 (PDT)

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	John Nimmers-Minor; Homework Partner		John Nimmers-Minor; Homework Partner
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		+	Except for what is noted above, this individual journal entry was completed by me and not copied from another source.
		+	[[User:Ymesfin\|Ymesfin]] ([[User talk:Ymesfin\|talk]]) 20:45, 9 October 2019 (PDT)

	==References==		==References==

@@ Line 11: / Line 11: @@
 **1 Hr: YELLOW
 **3 Hr:BRIGHT RED
-**5 Hr: BLACK
+**5 Hr: YELLOW
 **9 Hr:DIM GREEN
 *Gene Y

@@ 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.===
-[[File:JnimmersChart1.png]]
+[[File: Ymesfin q1 graph.PNG]]
 ===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.)===
 *Gene X
-**1 Hr: Yellow
+**1 Hr: YELLOW
-**3 Hr:Bright Red
+**3 Hr:BRIGHT RED
-**5 Hr: Black
+**5 Hr: BLACK
-**9 Hr:Dim Green
+**9 Hr:DIM GREEN
 *Gene Y
-**1 Hr: Yellow
+**1 Hr: YELLOW
-**3 Hr: Bright Red
+**3 Hr: BRIGHT RED
-**5 Hr: Dim Green
+**5 Hr: DIM GREEN
-**9 Hr: Bright Green
+**9 Hr: BRIGHT GREEN
 *Gene Z
-**1 Hr: Yellow
+**1 Hr: YELLOW
-**3 Hr: Medium Red
+**3 Hr: MEDIUM RED
-**5 Hr: Bright Red
+**5 Hr: BRIGHT RED
-**9 Hr: Dim Red
+**9 Hr: DIM RED
 ===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?===
-* Genes X and Y were both transcribed similarly. Both genes started at 1.0 as their ratio of transcription, in hour 3, hit their peak, and then declined from the 3rd hour to the 9th hour.
+Gene X and Gene Y were transcribed similarly. The ratio of their transcription was the same at the first hour, peaked after the third hour, and descending with a similar negative slope in the last couple hours.
 ===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?===
 The yellow coloration at the first time point occurs because the glucose deprived cells have not yet acclimated to the lack of glucose and thus are operating in a similar manner as the control, expressing similar genes. The yellow color is an indication that the genes in question are being transcribed in both transcriptomes. In other words, the cells are operating in a biologically similar manner. The yellow color comes from the presence of both the green and red fluorescent tags from both transcriptomes in each spot which merge together to create a yellow dye.
@@ Line 46: / Line 45: @@
 ===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?===
-In order to verify whether Tup1 had been deleted or whether Yap1 had been overexpressed, one can either use a microarray experiment or locate the spots associated with both genes. If the mutated Tup1 appears green, then its expression has been reduced, and if the mutated Yap1 appears red, then its expression has been induced. Similarly, one could also observe the spots associated with the target genes of the mutated Tup1 and Yap1. Since Tup1 is a repressor, it can be expected that its deletion would induce the expression of its target genes, and since Yap1 is a transcription factor, its overexpression would also be expected to induce the expression of its target genes.
+In order to verify whether Tup1 had been deleted or whether Yap1 had been overexpressed, one can either use a microarray experiment and locate the spots associated with both genes. If the mutated Tup1 appears green, then its expression has been reduced, and if the mutated Yap1 appears red, then its expression has been induced. Similarly, one could also observe the spots associated with the target genes of the mutated Tup1 and Yap1. Since Tup1 is a repressor, it can be expected that its deletion would induce the expression of its target genes, and since Yap1 is a transcription factor, its overexpression would also be expected to induce the expression of its target genes.
 ==Acknowledgements==
-*Thank you to [[User:Kdahlquist | Dr. Kam Dahlquist]] for her assistance in this class and for helping to teach us about the topics covered in this assignment.
+Dr. Kam Dahlquist; Professor
-*Thank you to my homework partner, [[User:Ymesfin | Yeabsira (Aby) Mesfin]] for his assitance on this assignment,. We met in person and spoke over the phone to coordinate questions and answers to the individual journal assignment questions.
 ==References==
-*Alberts et al. (2002) Molecular Biology of the Cell, Ch. 8: Microarrays
+Alberts et al. (2002) Molecular Biology of the Cell, Ch. 8: Microarrays
-*Brown, P.O. & Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays Nature Genetics 21: 33-37.
-*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.
+Brown, P.O. & Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays Nature Genetics 21: 33-37.
-*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.
-*LMU BioDB 2019. (2019). Week 6. Retrieved October 10, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_6
+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.
 [[Category: Journal Entry]]