Difference between revisions of "Bklein7 Week 7"

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(Added answers to questions 1-3)
(Answered question 4)
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#*(note to self: improve x-axis scale?)
 
#*(note to self: improve x-axis scale?)
 
# (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 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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[[File:Bklein7 Week7 Question2.png]]
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#*[[File:Bklein7 Week7 Question2.png]]
 
# (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?
 
#*The transcription of genes X and Y from Figure 4.7b exhibited similar patterns in response to the gradual loss of oxygen. The transcription of both genes was induced at the 3 hour mark (90% of normal oxygen level), showed very little or no change when compared to the control at the 5 hour mark (~62% of normal oxygen level), and finally was repressed at the 9 hour mark (10% of normal oxygen level). Despite these similar patterns of up and down-regulation, the magnitudes of the transcriptional changes did vary between the two genes. Gene Y was both more dramatically induced at the 3 hour mark and more dramatically repressed at the 9 hour mark. Additionally, gene Y was very slightly down-regulated at the 5 hour mark whereas gene X showed no change from its transcription at a normal oxygen level.
 
#*The transcription of genes X and Y from Figure 4.7b exhibited similar patterns in response to the gradual loss of oxygen. The transcription of both genes was induced at the 3 hour mark (90% of normal oxygen level), showed very little or no change when compared to the control at the 5 hour mark (~62% of normal oxygen level), and finally was repressed at the 9 hour mark (10% of normal oxygen level). Despite these similar patterns of up and down-regulation, the magnitudes of the transcriptional changes did vary between the two genes. Gene Y was both more dramatically induced at the 3 hour mark and more dramatically repressed at the 9 hour mark. Additionally, gene Y was very slightly down-regulated at the 5 hour mark whereas gene X showed no change from its transcription at a normal oxygen level.
 
# (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?
 +
#*At the first time point, the experimental group was the least glucose-limited when compared to all other time points, and therefore these experimental conditions were most similar to that of the control (glucose rich environment). Spots on a DNA microarray appear yellow when approximately equal amounts of cDNA from the control group, labelled green, and the experimental group, labelled red, bind to a specific spot. Thus, yellow spots indicate no change in the transcription rates of genes when comparing the experimental and control groups. Because the first time point was the time at which the experimental conditions best matched the control conditions (little/no glucose limitation), there consequentially was very little transcriptional change, resulting 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 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, 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 12, p. 120)  What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?

Revision as of 02:51, 19 October 2015

Introduction to DNA Microarrays

Discovery Questions from Campbell & Heyer 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:

  1. (Question 5, p. 110) Choose two genes from Figure 4.6b (PDF of figures on MyLMUConnect) 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 in hard copy and turn it in in class.
    • Bklein7 Week7 Question1.png
    • Disclaimer: I am red-green colorblind, so assessing the red-green color scale for changes in transcription (Figure 4.5) proved difficult. In correlating the colors from Figure 4.6b to values, I made my best guesses using the aid of pixel color analysis tools.
    • (note to self: improve x-axis scale?)
  2. (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.)
    • Bklein7 Week7 Question2.png
  3. (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?
    • The transcription of genes X and Y from Figure 4.7b exhibited similar patterns in response to the gradual loss of oxygen. The transcription of both genes was induced at the 3 hour mark (90% of normal oxygen level), showed very little or no change when compared to the control at the 5 hour mark (~62% of normal oxygen level), and finally was repressed at the 9 hour mark (10% of normal oxygen level). Despite these similar patterns of up and down-regulation, the magnitudes of the transcriptional changes did vary between the two genes. Gene Y was both more dramatically induced at the 3 hour mark and more dramatically repressed at the 9 hour mark. Additionally, gene Y was very slightly down-regulated at the 5 hour mark whereas gene X showed no change from its transcription at a normal oxygen level.
  4. (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?
    • At the first time point, the experimental group was the least glucose-limited when compared to all other time points, and therefore these experimental conditions were most similar to that of the control (glucose rich environment). Spots on a DNA microarray appear yellow when approximately equal amounts of cDNA from the control group, labelled green, and the experimental group, labelled red, bind to a specific spot. Thus, yellow spots indicate no change in the transcription rates of genes when comparing the experimental and control groups. Because the first time point was the time at which the experimental conditions best matched the control conditions (little/no glucose limitation), there consequentially was very little transcriptional change, resulting in most spots being yellow.
  5. (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).


  1. (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
  2. (Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
  3. (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?
  4. (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?
  5. (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?

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