Dbashour Week 6 - Revision history

Dbashour: added template

2017-10-10T06:26:57Z

added template

2017-10-10T06:25:55Z

fixed syntax

2017-10-10T06:25:27Z

‎References

2017-10-10T06:25:00Z

added signature

2017-10-10T06:24:10Z

fixed syntax

2017-10-10T06:21:17Z

fixed question 1

2017-10-10T06:17:35Z

answered question 10

2017-10-10T05:52:18Z

added acknowledgements and question 8

2017-10-09T17:30:02Z

added question 7

2017-10-09T04:52:34Z

answered question 6

← Older revision		Revision as of 06:26, 10 October 2017
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	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		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
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 ==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.
 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

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 ==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.
+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.
-#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
+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

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 ==Acknowledgments==
 I worked with my partner [[User: Bhamilton18 | Blair Hamilton]] this week to complete the questions from Chapter 4 of Campbell's book. We met in person on Sunday to go over the assignment and help each other with whatever questions we both had. We communicated via text on Monday to help each other with any last minute questions or clarification.
 '''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
 ==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.
 #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 14: / Line 14: @@
 ==Acknowledgments==
-#This week I worked with my partner [[User: Bhamilton18 | Blair Hamilton]] 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.
+I worked with my partner [[User: Bhamilton18 | Blair Hamilton]] this week to complete the questions from Chapter 4 of Campbell's book. We met in person on Sunday to go over the assignment and help each other with whatever questions we both had. We communicated via text on Monday to help each other with any last minute questions or clarification.
-#'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
+'''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
 ==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.
 #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

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 ==Answered Questions From Chapter 4==
+#[[File:graphofdata.png]]
 # [[File:tableofgenecolors.png]]
 # Genes X and Y are similar due to their similar folding pattern under their respective hours.

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 # Since these genes are in a common pathway already, the reaction can be catalyzed by a common transcription factor. This allows for each gene in the pathway to be controlled simultaneously.
 # Because TUP1 is a repressor for glucose-repressed genes, the absence of TUPI would cause the genes to no longer be repressed with the presence of glucose. Consequently, the spots would be red because transcription would be taking place.
+# Yap1p is a transcription factor that confers resistance to environmental stress, according to Campbell. Knowing this, I would predict the spots to be red because it is under a stressful environment due to the depletion of glucose, therefore undergoing high levels of transcription.
+# In order to determine if TUP1 was truly deleted, you would have to look at the microarray data from question 8 over time and it would show a red spot because glucose is being transcribed, meaning that the glucose repressor, TUP1, was not present. To determine if Yap1p was truly overexpressed, you would look at the microarray data from question 9 over time and because glucose levels were decreased and Yap1p was resistant to that, there were high transcription rates meaning that it would show a bright red spot.
 ==Acknowledgments==

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 # The gene TEF4 was repressed, as shown in Figure 4.12. Because glucose was the only available form of energy, the depletion of it caused the cell to not have enough energy to perform the transcription of the gene, causing it to be repressed. Campbell mentions that specifically, genes involved in protein synthesis are reduced in environments of low energy.
 # As stated above, the cell is in an energy saving mode. When this occurs, genes begin to change their expression in order to compensate for this change in energy. Some genes reduce their expression, TEF4, and some induce their expression. Because TCA is an energy metabolic gene, it was induced in order to produce more energy for the cell.
+# Since these genes are in a common pathway already, the reaction can be catalyzed by a common transcription factor. This allows for each gene in the pathway to be controlled simultaneously.
+#
+#

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 #* The technical reason is that red and green would be mixed, making yellow.
 #* The biological reason is that this indicates the beginning of transcription, meaning that no change has occurred.
-# The gene TEF4 was repressed, as shown in Figure 4.12. Because glucose was the only available form of energy, the depletion of it caused the cell to not have enough energy to perform the transcription of the gene, causing it to be repressed.
+# The gene TEF4 was repressed, as shown in Figure 4.12. Because glucose was the only available form of energy, the depletion of it caused the cell to not have enough energy to perform the transcription of the gene, causing it to be repressed. Campbell mentions that specifically, genes involved in protein synthesis are reduced in environments of low energy.
+#
+#
+#