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Electronic Lab Notebook

Purpose

The purpose of this assignment is to learn about DNA microarrays. It also is a way to learn about data and how we can organize data to derive meaningful information from experimental results.

Assignment 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.

ADD IMAGE HERE OF GRAPH

(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.)

X: Black, Dim Red, Black, Medium Green Y: Black, Medium Red, Dim Green, Bright Green Z: Black, Dim Red, Dim Red, 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?

Yes, X and Y, my explanation is this below: The genes all have ratios of 1.0 an hour in so they are not showing induction or repression yet. Then an hour in they have all been inducting but at different rates. Then 5 hours in they all split in what they are doing, Gene X is having no change in transcription, while Gene Y is starting to repress very slightly and gene Z is inducting again. Then at 9 hours, Gene X and Y are repressing a lot. All in all Gene X and Y are the most similar in terms of their transcription ratios here.

(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?

Most would be yellow in the first time point because there is no difference in levels of expression at the start. They show up yellow because one gene is using the green fluorescence and one is using the red, so they look yellow on the computer screen when they are imposed on one another. If two genes were expressed equally that would be the reason for an experiment to result 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).

At the beginning the TEF4 is yellow, this shows it is neither being induced or repressed compared to the control. As the time continues and the available glucose is reduced, we see it slowly becoming greener which means it is being more repressed than the control. According to this journal article, Translation Elongation Factors are a key part of protein synthesis. So it seems possible that with less glucose available the cells are doing less and therefore need to create less YKL081W Protein. Which is what it says the protein it creates is called on the Saccharomyces Genome Database.

(Question 11, p. 120)

Why would TCA cycle genes be induced if the glucose supply is running out? I used this online paper as my source. It looks like they might be induced to help use energy more efficiently or to use alternate energy sources.

(Question 12, p. 120)

(Question 13, p. 121)

(Question 14, p. 121)

(Question 16, p. 121)