Template:Individual Journal Instructions - Revision history

Kdahlquist: /* Individual Journal Assignment */ added category "Assignment"

2013-10-18T18:40:03Z

‎Individual Journal Assignment: added category "Assignment"

Kdahlquist: Undo revision 1829 by Kdahlquist (talk)

2013-09-19T19:56:24Z

Undo revision 1829 by Kdahlquist (talk)

Kdahlquist: /* Individual Journal Assignment */ pasted in from OpenWetware/Biomath modeling class

2013-09-19T19:54:14Z

‎Individual Journal Assignment: pasted in from OpenWetware/Biomath modeling class

Kdahlquist: /* Individual Journal Assignment */ added note about using template

2013-09-17T16:17:40Z

‎Individual Journal Assignment: added note about using template

Kdahlquist: added that they need to link to the assignment page

2013-08-28T23:03:43Z

added that they need to link to the assignment page

Dondi: Transcribe individual journal assignment template.

2013-06-25T17:36:26Z

Transcribe individual journal assignment template.

New page

== Individual Journal Assignment ==

* Store this journal entry as "''username'' Week {{{week}}}" (i.e., this is the text to place between the square brackets when you link to this page).
* Link to this 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.

← Older revision		Revision as of 18:40, 18 October 2013
Line 7:		Line 7:
	* Don't forget to add the "Journal Entry" category to the end of your wiki 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.'''''		**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
		+
		+	[[Category:Assignment]]

← Older revision		Revision as of 19:56, 19 September 2013
Line 7:		Line 7:
	* Don't forget to add the "Journal Entry" category to the end of your wiki 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.'''''		**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
−
−	~~=== Introduction to Microarrays ===~~
−
−	~~==== Read ====~~
−
−	* 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. (Available on MyLMUConnect; the color figures are also posted there)
−	* [http://www.sciencemag.org/content/278/5338/680.full?sid=542f6cc5-016c-4cea-83af-1ea62867993e 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.]
−	* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html This animation from Malcolm Campbell may also be helpful.]
−
−	~~==== Answer the following Discovery Questions from Chapter 4====~~
−
−	~~'''5.''' (p. 110) Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time.~~
−	~~'''<nowiki>*</nowiki>Note: Dr. Dahlquist said that this will be done on a seperate piece of paper to be submitted in class on Thursday.'''~~
−
−	'''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 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b.
−
−	~~'''7.''' (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?~~
−
−	~~'''9.''' (p. 118) Why would most spots be yellow at the first time point?~~
−
−	'''10.''' (p. 118) Go to http://www.yeastgenome.org 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 gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
−
−	~~'''11.''' (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?~~
−
−	~~'''12.''' (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?~~
−
−	~~'''13.''' (p. 121) Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?~~
−
−	~~'''14.''' (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?~~
−
−	~~'''15.''' (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?~~
−
−	~~'''16.''' (p. 121) What types of control spots would you like to see in this type of experiment? How could you verify that you had truly deleted or overexpressed a particular gene?~~

← Older revision		Revision as of 19:54, 19 September 2013
Line 7:		Line 7:
	* Don't forget to add the "Journal Entry" category to the end of your wiki 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.'''''		**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
		+
		+	=== Introduction to Microarrays ===
		+
		+	==== Read ====
		+
		+	* 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. (Available on MyLMUConnect; the color figures are also posted there)
		+	* [http://www.sciencemag.org/content/278/5338/680.full?sid=542f6cc5-016c-4cea-83af-1ea62867993e 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.]
		+	* [http://www.bio.davidson.edu/courses/genomics/chip/chip.html This animation from Malcolm Campbell may also be helpful.]
		+
		+	==== Answer the following Discovery Questions from Chapter 4====
		+
		+	'''5.''' (p. 110) Choose two genes from Figure 4.6 (PDF of figures on MyLMUConnect) and draw a graph to represent the change in transcription over time.
		+	'''<nowiki>*</nowiki>Note: Dr. Dahlquist said that this will be done on a seperate piece of paper to be submitted in class on Thursday.'''
		+
		+	'''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 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b.
		+
		+	'''7.''' (p. 110) Were any of the genes in Figure 4.7b transcribed similarly?
		+
		+	'''9.''' (p. 118) Why would most spots be yellow at the first time point?
		+
		+	'''10.''' (p. 118) Go to http://www.yeastgenome.org 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 gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).
		+
		+	'''11.''' (p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
		+
		+	'''12.''' (p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
		+
		+	'''13.''' (p. 121) Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?
		+
		+	'''14.''' (p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?
		+
		+	'''15.''' (p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?
		+
		+	'''16.''' (p. 121) What types of control spots would you like to see in this type of experiment? How could you verify that you had truly deleted or overexpressed a particular gene?

← Older revision		Revision as of 16:17, 17 September 2013
Line 6:		Line 6:
	* Link back from your journal entry to 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.		* 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.'''''

@@ Line 2: / Line 2: @@
 * Store this journal entry as "''username'' Week {{{week}}}" (i.e., this is the text to place between the square brackets when you link to this page).
-* Link to this journal entry from your user page.
+* Link from your user page to this Assignment 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.