Week 6 - Revision history

Dondi: Remove Under Construction message.

2017-10-09T04:59:46Z

Remove Under Construction message.

Kdahlquist: /* Answer the following Discovery Questions from Chapter 4 */ clarified how to do plots

2017-10-04T00:04:35Z

‎Answer the following Discovery Questions from Chapter 4: clarified how to do plots

Kdahlquist: /* Homework Partners */ set up homework partners

2017-10-04T00:02:46Z

‎Homework Partners: set up homework partners

Kdahlquist: /* Objectives */ added purposes

2017-10-03T20:44:53Z

‎Objectives: added purposes

Kdahlquist: add category

2017-10-03T20:40:53Z

add category

Kdahlquist: /* Shared Journal Assignment */ added note about template and length of video

2017-10-03T20:39:17Z

‎Shared Journal Assignment: added note about template and length of video

Kdahlquist: /* Shared Journal Assignment */ fixed link

2017-10-03T20:35:39Z

‎Shared Journal Assignment: fixed link

Kdahlquist: /* Introduction to DNA Microarrays */ change mylmuconnect to brightspace

2017-10-03T20:34:30Z

‎Introduction to DNA Microarrays: change mylmuconnect to brightspace

Kdahlquist: pasted in from Biomath Modeling

2017-10-03T20:33:07Z

pasted in from Biomath Modeling

Kdahlquist: pasted in from previous weeks to start

2017-10-03T20:31:40Z

pasted in from previous weeks to start

New page

{{Under_Construction}}

'''This journal entry is due on Tuesday, October 10, at 12:01 AM PDT.'''

== Objectives ==

The purpose of this assignment is:

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week 6" (i.e., this is the text to place between the square brackets when you link to this page).
* Link from your user page to this Assignment page.
* Link to your journal entry from your user page.
* Link back from your journal entry to your user page.
* Don't forget to add the "Journal Entry" category to the end of your wiki page.
**'''''Note: You can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
* For your assignment this week, and this week only, the requirement for the '''''electronic laboratory notebook''''' is waived.
* You '''''do''''' have to include both the Acknowledgments and References section as specified by the [[Week_1#Academic_Honesty | Week 1]] assignment.

=== Homework Partners ===

For most weeks in the semester, you will be assigned a "homework partner" from a complementary discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). You must give the details of the interaction with your partner in the [[Week_1#Acknowledgments | Acknowledgments section]] of your journal assignment. Homework partners for this week are:

*

← Older revision		Revision as of 04:59, 9 October 2017
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−	~~{{Under_Construction}}~~
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	'''This journal entry is due on Tuesday, October 10, at 12:01 AM PDT.'''		'''This journal entry is due on Tuesday, October 10, at 12:01 AM PDT.'''

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 Answer the following questions related to Chapter 4 of Campbell & Heyer (2003).  Note that some of the questions below have been reworded from the Discovery Questions in the book:
-# (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.
+# (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.  Create your plot in Excel (or other program that can do plots) and display the image up on your wiki page.  Alternately, you can do it by hand, scan or take a photo of the plot, and display the image on your wiki page.
 # (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?

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 For most weeks in the semester, you will be assigned a "homework partner" from a complementary discipline. You will be expected to consult with your partner, sharing your domain expertise, in order to complete the assignment. However, unless otherwise stated, each partner must submit his or her own work as the individual journal entry (direct copies of each other's work is not allowed). You must give the details of the interaction with your partner in the [[Week_1#Acknowledgments | Acknowledgments section]] of your journal assignment.  Homework partners for this week are:
+* Eddie A. and Quinn L.
 === Introduction to DNA Microarrays ===

← Older revision		Revision as of 20:40, 3 October 2017
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	*# What additional information would you like to know about this case? (We will be visiting it again in subsequent weeks in the course.)		*# What additional information would you like to know about this case? (We will be visiting it again in subsequent weeks in the course.)
	* Please feel free to respond or comment on your classmates' reflections.		* Please feel free to respond or comment on your classmates' reflections.
		+
		+	[[Category:Assignment]]

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 * Link back from the journal entry to your user page.
 * Sign your portion of the journal with the standard wiki signature shortcut (<code><nowiki>~~~~</nowiki></code>).
-* Add the "Shared" category to the end of the wiki page (if someone has not already done so).
+* Add the "Journal Entry" and "Shared" categories to the end of the wiki page (if someone has not already done so).
 === View ===
-* Watch the video [https://www.youtube.com/watch?v=eV9dcAGaVU8 "Deception at Duke" from CBS ''60 Minutes''].
+* Watch the video [https://www.youtube.com/watch?v=eV9dcAGaVU8 "Deception at Duke" from CBS ''60 Minutes''] (13:45 minutes).
 === Reflection ===

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 The purpose of this assignment is:
+* To understand how the DNA microarray biotechnology works as a foundation for data analyses we will conduct later in the course.
 == Individual Journal Assignment ==

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 == Shared Journal Assignment ==
-* Store your shared journal entry in the shared [[BIOL398-05/S17:Class Journal Week 9 | Class Journal Week 9]] page.  If this page does not exist yet, go ahead and create it (congratulations on getting in first&nbsp;''':)'''&nbsp;)
+* Store your shared journal entry in the shared [[Class Journal Week 9]] page.  If this page does not exist yet, go ahead and create it (congratulations on getting in first&nbsp;''':)'''&nbsp;)
 * Link to your journal entry from your user page.
 * Link back from the journal entry to your user page.
 * Sign your portion of the journal with the standard wiki signature shortcut (<code><nowiki>~~~~</nowiki></code>).
-* Add the "BIOL398-05/S17" category to the end of the wiki page (if someone has not already done so).
+* Add the "Shared" category to the end of the wiki page (if someone has not already done so).
 === View ===

@@ Line 32: / Line 32: @@
 * [http://www.bio.davidson.edu/courses/genomics/chip/chip.html Microarray animation]
 * Brown, P.O. & Botstein, D. (1999) [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html 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. ([https://mylmuconnect.lmu.edu/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_33586_1%26url%3D Available on MyLMUConnect])
+* 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. ([http://brightspace.lmu.edu Available on Brightspace])
 * DeRisi, J.L., Iyer, V.R., and Brown, P.O.  (1997)  [http://www.sciencemag.org/content/278/5338/680.full Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale.]  ''Science'' 278: 680-686.

← Older revision		Revision as of 20:33, 3 October 2017
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	*		*
		+
		+	=== Introduction to DNA Microarrays ===
		+
		+	==== Read ====
		+
		+	* [http://www.ncbi.nlm.nih.gov/books/NBK26818/#A1633 Alberts ''et al''. (2002) ''Molecular Biology of the Cell'', Ch. 8: Microarrays]
		+	* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html Microarray animation]
		+	* Brown, P.O. & Botstein, D. (1999) [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html 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. ([https://mylmuconnect.lmu.edu/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_33586_1%26url%3D Available on MyLMUConnect])
		+	* DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997) [http://www.sciencemag.org/content/278/5338/680.full Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale.] ''Science'' 278: 680-686.
		+
		+	==== Answer the following Discovery Questions from Chapter 4 ====
		+
		+	Answer the following questions related to Chapter 4 of Campbell & Heyer (2003). Note that some of the questions below have been reworded from the Discovery Questions in the book:
		+
		+	# (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.
		+	# (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?
		+	# (Question 10, p. 118) Go to the [http://www.yeastgenome.org ''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).
		+	# (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?
		+	# (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?
		+
		+	== Shared Journal Assignment ==
		+
		+	* Store your shared journal entry in the shared [[BIOL398-05/S17:Class Journal Week 9 \| Class Journal Week 9]] page. If this page does not exist yet, go ahead and create it (congratulations on getting in first ''':)''' )
		+	* Link to your journal entry from your user page.
		+	* Link back from the journal entry to your user page.
		+	* Sign your portion of the journal with the standard wiki signature shortcut (<code><nowiki>~~~~</nowiki></code>).
		+	* Add the "BIOL398-05/S17" category to the end of the wiki page (if someone has not already done so).
		+
		+	=== View ===
		+
		+	* Watch the video [https://www.youtube.com/watch?v=eV9dcAGaVU8 "Deception at Duke" from CBS ''60 Minutes''].
		+
		+	=== Reflection ===
		+
		+	* Answer the following questions:
		+	*# Were you aware of this case of research fraud before viewing this video?
		+	*# What are your initial reactions to hearing about this case?
		+	*# What role did data sharing play in uncovering this fraud?
		+	*# What additional information would you like to know about this case? (We will be visiting it again in subsequent weeks in the course.)
		+	* Please feel free to respond or comment on your classmates' reflections.