Marmas Week 6

Purpose

The purpose of this experiment is to develop an understanding of DNA microarray experiments and their function by answering questions concerning their analysis. Additionally, a case study will be looked at that examines a violation of the standards of research ethics.

Questions

Question 1

1. 

   Question 1, based on Figure 4.6B

Question 2

Transcriptional Response of Three genes to the gradual loss of oxygen

• Gene X
  • Hour 1: Black
  • Hour 3: Medium Red
  • Hour 5: Black
  • Hour 9: Bright Green
• Gene Y
  • Hour 1: Black
  • Hour 3: Bright Red
  • Hour 5: Dim Green
  • Hour 9: Bright Green
• Gene Z
  • Hour 1: Black
  • Hour 3: Dim Red
  • Hour 5: Medium Red
  • Hour 9: Medium Red

Question 3

Genes X and Y were transcribed very similarly, except for at hour 3. However, looking at the ratio of activity, they are very similar at each hour.

Question 4

On a color spectrum, yellow is in between red and green. Thus, the color yellow, which on microarrays represents no change, shows that the gene is neither being induced or repressed. As it becomes more repressed, the color will shift to a shade of green. As it becomes more induced, it will shift to a shade of red. Looking at a microarray, there are some genes that show orange or a yellow-green color. This is an example of a less potent induction or repression as compared to a strong induction or strong repression. In an experiment, the gene expression may not change, thus showing a yellow spot.

Question 5

As the experiment progressed the expression of TEF4 was repressed. This is indicative of the yellow-green spot on the microarray at OD 3.7. An increase in OD is indicative of more yeast cells being present in the solution. This means that the glucose, which is the only available food source in the system, is being rapidly consumed by the increasing number of yeast cells. With a decrease in available glucose, the cell shifts away from the translation of proteins as it cannot afford to make more in a stressed condition. It may even be using proteins to survive in these conditions. Therefore, TEF4, which is involved in translation, is no longer needed for survival and its expression is repressed.

Question 6

As glucose levels decrease, the cell needs to survive by making its own glucose. To do this, genes associated with the TCA cycle are induced to make more glucose for the cell. In a stressed condition, this is an expected response for survivability.

Question 8

In cells where the repressor gene TUP1 were deleted, the cell would not be able to repress the expression of genes in a stressed environment. Therefore, after t = 0, it would be expected that the expression of genes would not be regulated and that spots for many genes would turn red. However, after more time, it's expected for these spots to turn back to green, as the cell would die after a short period time and genes would no longer be expressed. The cell would not able to control how its resources are used and will continue to allocate them to where is not necessary for survival.

Acknowledgements

• I would like to acknowledge my homework partner, David Ramirez, for aiding in the understanding of the analysis questions.
• I would like to acknowledge Dr. Dahlquist for her continuous help in the understanding of this field.