Difference between revisions of "Bhamilton18 Week 6"

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=Discovery Questions=
 
=Discovery Questions=
 
#[[File:Blairtransciptiongraph.png| 500px]]
 
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*(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.)
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#*'''Gene X:''' ''Hour 1:'' Black ''Hour 3:'' Dim Red ''Hour 5:'' Black ''Hour 9:'' Dim Green
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#*'''Gene Y:''' ''Hour 1:'' Black ''Hour 3:'' Medium Red ''Hour 5:'' Black ''Hour 9:'' Bright Green
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#*'''Gene Z:''' ''Hour 1:'' Black ''Hour 3:'' Black ''Hour 5:'' Dim Red ''Hour 9:'' Dim Red
 
*(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 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 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?

Revision as of 04:00, 9 October 2017

Discovery Questions

  1. Blairtransciptiongraph.png
    • Gene X: Hour 1: Black Hour 3: Dim Red Hour 5: Black Hour 9: Dim Green
    • Gene Y: Hour 1: Black Hour 3: Medium Red Hour 5: Black Hour 9: Bright Green
    • Gene Z: Hour 1: Black Hour 3: Black Hour 5: Dim Red Hour 9: Dim Red
  • (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 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?


Category Links
User Page Blair Hamilton
Weekly Assignments Bhamilton18 Week 2   Bhamilton18 Week 3   Bhamilton18 Week 4  Animal QTL  Bhamilton18 Week 6  Bhamilton18 Week 7  Bhamilton18 Week 8  Bhamilton18 Week 9  Bhamilton18 Week 10  Bhamilton18 Week 11  Bhamilton18 Week 12  Bhamilton18 Week 14  Bhamilton18 Week 15
Weekly Assignment
Instructions		 Week 1   Week 2   Week 3   Week 4   Week 5   Week 6   Week 7   Week 8   Week 9   Week 10   Week 11   Week 12   Week 14   Week 15
Class Journals Class Journal Week 1   Class Journal Week 2   Class Journal Week 3   Class Journal Week 4   Class Journal Week 5   Class Journal Week 6   Class Journal Week 7   Class Journal Week 8   Class Journal Week 9   Class Journal Week 10
Final Project Lights, Camera, InterACTION!  Lights, Camera, InterACTION! Deliverables

Acknowledgments

  1. This week I worked with my partnerDina 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.
  2. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.

References

  1. 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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