Bhamilton18 Week 6 - Revision history

Bhamilton18: answered final question and added reference

2017-10-10T01:32:02Z

answered final question and added reference

Bhamilton18: Answered question 9

2017-10-10T01:15:46Z

Answered question 9

Bhamilton18: answered question 8

2017-10-10T00:58:13Z

answered question 8

Bhamilton18: Answered question 7

2017-10-10T00:27:15Z

Answered question 7

Bhamilton18: Changed some of my answers for #2

2017-10-09T23:19:26Z

Changed some of my answers for #2

Bhamilton18: answer question 6

2017-10-09T05:00:04Z

answer question 6

Bhamilton18: answered question 5

2017-10-09T04:33:56Z

answered question 5

Bhamilton18: Answered question 4

2017-10-09T04:22:12Z

Answered question 4

Bhamilton18: Answered question 3

2017-10-09T04:07:55Z

Answered question 3

Bhamilton18: Inserted ene X,Y,Z color transciption

2017-10-09T04:00:31Z

Inserted ene X,Y,Z color transciption

@@ Line 14: / Line 14: @@
 #According to Campbell, TUP1 is responsible for the repression of glucose-repressed genes. Given this information I would expect the spots to be red, because the TUP1 and glucose would be depleted at said time period.
 #I would expect Yap1p to be colored red as it is "a transcription factor known to confer resistance to environmental stress"(121). During glucose depletion a cell in under stress, there Yap1p would increase expressed target genes and therefore be overly expressed and turn bright red.
-*(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?
+#To see if TUP1 has been deleted you can look at the change in time and see the coloring of the dot. If TUP! has been deleted it will turn black and not light up at all. To see if YAP1 has been overexpressed you can see once the gene turns bright red it is most likely highly induced.
 {{Bhamilton18}}
@@ Line 22: / Line 22: @@
 #'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
 ==References==
 #LMU BioDB 2017. (2017). Week 6. Retrieved October 5, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_6#Individual_Journal_Assignment

@@ Line 13: / Line 13: @@
 #The best mechanism a genome can use is a transcription factor to ensure genes for enzymes have a common induced or repressed pathway.
 #According to Campbell, TUP1 is responsible for the repression of glucose-repressed genes. Given this information I would expect the spots to be red, because the TUP1 and glucose would be depleted at said time period.
-*(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 Yap1p to be colored red as it is "a transcription factor known to confer resistance to environmental stress"(121). During glucose depletion a cell in under stress, there Yap1p would increase expressed target genes and therefore be overly expressed and turn bright red.
 *(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?

@@ Line 11: / Line 11: @@
 #TEF4, or "translational elongation factor", was repressed, as the dot on the figure corresponded to bright green. The TEF4 could be reacting to the low amounts of glucose which provides energy to the cell. The TEF4 resorts to, according to Campbell, an energy saving mode therefore the genes were repressed.
 #During high stress environments genes are repressed and induced according to their energy levels. Due to TCA being a energy metabolic gene, it becomes induced in order to make energy efficiently and effectively.
-#The genome can use a transcription factor to ensure genes for enzymes have a common induced or repressed pathway.
+#The best mechanism a genome can use is a transcription factor to ensure genes for enzymes have a common induced or repressed pathway.
-*(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?
+#According to Campbell, TUP1 is responsible for the repression of glucose-repressed genes. Given this information I would expect the spots to be red, because the TUP1 and glucose would be depleted at said time period.
 *(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?
 *(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?

@@ Line 11: / Line 11: @@
 #TEF4, or "translational elongation factor", was repressed, as the dot on the figure corresponded to bright green. The TEF4 could be reacting to the low amounts of glucose which provides energy to the cell. The TEF4 resorts to, according to Campbell, an energy saving mode therefore the genes were repressed.
 #During high stress environments genes are repressed and induced according to their energy levels. Due to TCA being a energy metabolic gene, it becomes induced in order to make energy efficiently and effectively.
-*(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 can use a transcription factor to ensure genes for enzymes have a common induced or repressed pathway.
 *(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?
 *(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 19: / Line 19: @@
 ==Acknowledgments==
-#This week I worked with my partner[[User: Dbashour|Dina Bashoura]] on the discovery questions segment of the homework. We met in person as well as messaged each other if we were stuck on a question or needed more explanation.
+#This week I worked with my partner [[User: Dbashour|Dina Bashoura]] on the discovery questions segment of the homework. We met in person as well as messaged each other if we were stuck on a question or needed more explanation.
 #'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
 ==References==
 #LMU BioDB 2017. (2017). Week 6. Retrieved October 5, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_6#Individual_Journal_Assignment

@@ Line 2: / Line 2: @@
 #[[File:Blairtransciptiongraph.png| 500px]]
+#
-#*'''Gene X:''' ''Hour 1:'' Black ''Hour 3:'' Dim Red ''Hour 5:'' Black ''Hour 9:'' Dim Green
+#*'''Gene X:''' ''Hour 1:'' Black ''Hour 3:'' Dim Red ''Hour 5:'' Black ''Hour 9:'' Medium Green
-#*'''Gene Y:''' ''Hour 1:'' Black ''Hour 3:'' Medium Red ''Hour 5:'' Black ''Hour 9:'' Bright Green
+#*'''Gene Y:''' ''Hour 1:'' Black ''Hour 3:'' Medium Red ''Hour 5:'' Dim Green ''Hour 9:'' Bright Green
-#*'''Gene Z:''' ''Hour 1:'' Black ''Hour 3:'' Black ''Hour 5:'' Dim Red ''Hour 9:'' Dim Red
+#*'''Gene Z:''' ''Hour 1:'' Black ''Hour 3:'' Dim Red ''Hour 5:'' Dim Red ''Hour 9:'' Dim Red
 #Gene X and Y were similar. Both had similar fold induction increase then deplete to 1:1 then proceed to fold repression.
+#

@@ Line 9: / Line 9: @@
 #*The technical reason these spots come up yellow is that there are equal amounts of green and red dye and when mixed they create yellow.
 #* The biological reason a majority were unchanged, i.e yellow, was because of the conditions that the experiment placed on the DNA slides.
-*(Question 10, p. 118) Go to the Saccharomyces Genome Database 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 change in expression was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
+#TEF4, or "translational elongation factor", was repressed, as the dot on the figure corresponded to bright green. The TEF4 could be reacting to the low amounts of glucose which provides energy to the cell. The TEF4 resorts to, according to Campbell, an energy saving mode therefore the genes were repressed.
 *(Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
 *(Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
 *(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 1: / Line 1: @@
 =Discovery Questions=
 #[[File:Blairtransciptiongraph.png| 500px]]
-*(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.)
 *(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?
 *(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?