Jcowan4 Journal Week 6
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Contents
- 1 Purpose
- 2 Questions
- 2.1 (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.
- 2.2 (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.)
- 2.3 (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?
- 2.4 (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?
- 2.5 (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).
- 2.6 (Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
- 2.7 (Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
- 2.8 (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?
- 2.9 (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?
- 2.10 (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?
- 3 Acknowledgements
- 4 References
Purpose
The purpose is to check our knowledge and answer questions posted for us. We need to know about how DNA microarray experiments work, be able to understand DNA microarrays analysis problems and discuss cases where standards of research ethics were violated.
Questions
(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.)
Gene X: 1 hour = Black, 3 hours = Bright Red, 5 hours = Black, 9 hours = Dark Green
Gene Y: 1 hour = Black, 3 hours = Bright Red, 5 hours = Dark Green, 9 hours = Bright Green
Gene Z: 1 hour = Black, 3 hours = Red, 5 hours = Bright Red, 9 hours = Bright 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?
Gene X and Y are very similar in their transcriptional response.
(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?
The mixture of genes from both the red and green gene expressions.
(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).
TEF4 appears green. It is also repressed because of the reduction in glucose production.
(Question, 11, p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?
TCA genes would be induced because of a lack of glucose. As a result, TCA makes ATP without glucose and oxygen.
(Question 12, p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?
Guilt by association identifies similar genes and genes with similar expressions.
(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?
TUP1 is a repressor and so less glucose causes more repressed genes to appear. Repressed genes are associated with red, so there would be red dots.
(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?
It would be more green due to decreased protein production.
(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?
If TUP1 was deleted then green spots would be scene and vice versa with YAP1. YAP1 you would see red spots.
Acknowledgements
- To my Homework Partner, User:ntesfaio. We met during class and quickly talked about the assignment.
- Except with what is noted above, this individual journal entry was completed by me and not copied from another source.
References
- TEF4 Background by SGD. (2019), TEF4/YKL081W Overview, in Saccharymyces Genome Database. Retrieved October 8, 2019 from [https://www.yeastgenome.org/locus/S000001564].
- LMU BioDB 2019. (2019). Week 6. Retrieved October 9, 2019 from [https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_6].
