Hivanson Week 5 - Revision history

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 *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 Brightspace)
 *CBS News. (2012, February 12). Deception at Duke. https://www.youtube.com/watch?v=eV9dcAGaVU8
 *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. DOI: https://doi.org/10.1126/science.278.5338.680
 *11.7: Gene Regulation - Operon Theory. (2016, July 10). Biology LibreTexts. https://bio.libretexts.org/Bookshelves/Microbiology/Microbiology_(OpenStax)/11%3A_Mechanisms_of_Microbial_Genetics/11.07%3A_Gene_Regulation_-_Operon_Theory

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 *Brown, P.O. & Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays Nature Genetics 21: 33-37. https://doi.org/10.1038/4462
 *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 Brightspace)
 *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. DOI: https://doi.org/10.1126/science.278.5338.680
 *11.7: Gene Regulation - Operon Theory. (2016, July 10). Biology LibreTexts. https://bio.libretexts.org/Bookshelves/Microbiology/Microbiology_(OpenStax)/11%3A_Mechanisms_of_Microbial_Genetics/11.07%3A_Gene_Regulation_-_Operon_Theory

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 ===Acknowledgments===
 I worked with my homework partner, [[User:Kmill104 | Katie Miller]] to complete this assignment. [[User:Kmill104 | Katie]] and I communicated via text message on 2/14/2024, and she helped me understand the logic behind answering Question 6b in this assignment.
 Except for what is noted above, this individual journal entry was completed by me and not copied from another source

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 ===Acknowledgments===
 I worked with my homework partner, [[User:Kmill104 | Katie Miller]] to complete this assignment. [[User:Kmill104 | Katie]] and I communicated via text message on 2/14/2024, and she helped me understand the logic behind answering Question 6b in this assignment.
 ===References===

← Older revision		Revision as of 06:49, 15 February 2024
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	===Purpose===		===Purpose===
		+	The purpose of the week 5 individual journal assignment was to familiarize us with microarrays, their purpose, and how to analyze their results. We were provided with different ways that microarrays could be used, and the Campbell textbook and questions were provided in order to deepen our understanding of microarrays through critical thinking and knowledge application about DNA microarrays.

	===Questions===		===Questions===

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 *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 Brightspace)
 *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. DOI: https://doi.org/10.1126/science.278.5338.680
 *LMU BioDB 2024. (2024). Week 5. Retrieved February 14, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_5
 *Saccharomyces Genome Database. (n.d.) TEF4 / YKL081W. Retrieved February 14, 2024, from https://www.yeastgenome.org/locus/S000001564
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← Older revision		Revision as of 06:25, 15 February 2024
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	Deletion of TUP1 and overexpression of Yap1 would both lead to red spots at later time points. TUP1 should immediately begin transcription, turning red sooner in the experiment and staying red throughout the glucose depletion, theoretically not increasing or decreasing. Yap1 overexpression should show up in later time spots, as the Yap1 will not transcribe until the yeast cell begins to respond to low glucose as an environmental stressor; Yap1 will turn red at later time points, but stay black or even green at earlier time points.		Deletion of TUP1 and overexpression of Yap1 would both lead to red spots at later time points. TUP1 should immediately begin transcription, turning red sooner in the experiment and staying red throughout the glucose depletion, theoretically not increasing or decreasing. Yap1 overexpression should show up in later time spots, as the Yap1 will not transcribe until the yeast cell begins to respond to low glucose as an environmental stressor; Yap1 will turn red at later time points, but stay black or even green at earlier time points.

		+	===Acknowledgments===
		+	I worked with my homework partner, [[User:Kmill104 \| Katie Miller]] to complete this assignment. [[User:Kmill104 \| Katie]] and I communicated via text message on 2/14/2024, and she helped me understand the logic behind answering Question 6b in this assignment.
		+
		+	===References===
		+	*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. https://doi.org/10.1038/4462
		+	*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 Brightspace)
		+	*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. DOI: https://doi.org/10.1126/science.278.5338.680
		+	*LMU BioDB 2024. (2024). Week 5. Retrieved February 14, 2024, from https://xmlpipedb.cs.lmu.edu/biodb/spring2024/index.php/Week_5
		+	*Saccharomyces Genome Database. (n.d.) TEF4 / YKL081W. Retrieved February 14, 2024, from https://www.yeastgenome.org/locus/S000001564
	{{Hivanson}}		{{Hivanson}}

← Older revision		Revision as of 06:19, 15 February 2024
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	* (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 the above questions?		* (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 the above questions?
	Deletion of TUP1 and overexpression of Yap1 would both lead to red spots at later time points. TUP1 should immediately begin transcription, turning red sooner in the experiment and staying red throughout the glucose depletion, theoretically not increasing or decreasing. Yap1 overexpression should show up in later time spots, as the Yap1 will not transcribe until the yeast cell begins to respond to low glucose as an environmental stressor; Yap1 will turn red at later time points, but stay black or even green at earlier time points.		Deletion of TUP1 and overexpression of Yap1 would both lead to red spots at later time points. TUP1 should immediately begin transcription, turning red sooner in the experiment and staying red throughout the glucose depletion, theoretically not increasing or decreasing. Yap1 overexpression should show up in later time spots, as the Yap1 will not transcribe until the yeast cell begins to respond to low glucose as an environmental stressor; Yap1 will turn red at later time points, but stay black or even green at earlier time points.
		+
		+	{{Hivanson}}

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 * (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?
 Yap1p enables resistance to environmental distress. Glucose depletion could be a form of distress for a yeast cell and therefore would trigger transcription of Yap1p target genes. The induced transcription of these target genes would lead to the spots showing as red in later time points of the 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?
+* (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 the above questions?

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 The genome could use an operon system; a group of genes, typically involved in a common pathway, that are transcribed (or not transcribed) 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?
-Glucose-repressed genes will not be repressed in the absence of repressor TUP1. These glucose-repressed genes will stay green throughout the experiment, as they will be transcribed the same in glucose-depletion conditions as in glucose-rich conditions.
+Glucose-repressed genes will not be repressed in the absence of repressor TUP1. These glucose-repressed genes will turn red throughout the experiment, as they will be transcribed the same in glucose-depletion conditions as in glucose-rich conditions (transcription will continue), marking the spots for these genes as red as transcription is induced at later time points of the 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 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?