Angela C Abarquez Week 2

Purpose

The purpose of this week's assignment is to understand the process of DNA microarray experiments through readings and analysis problems. In addition, research ethics will be explored through a review of a case where standards were violated.

Reading Questions

Gene X is black after 1 hour, dim red after 3 hours, black after 5 hours, and dim green after 9 hours. Gene Y is after black 1 hour, medium red after 3 hours, black after 5 hours, and medium green after 9 hours. Gene Z is black after 1 hour, dim red after 3 hours, dim red after 5 hours, and dim red after 9 hours.
Genes X and Y were transcribed similarly as seen through their similar changes in color (see #2). Over time, they both started out black, then moved to red, then black, and lastly green.
Regarding color coding, the red dots show increased transcription and the green show repressed gene transcription. The yellow dot, being a blend of red and green, represents the reading at the first time point, which is the 'baseline' that has not yet been repressed or increased.
TEF4 had a green spot, so it was therefore repressed. A possible explanation for this could be a decrease in glucose, which is a vital source of energy. As a result, negative feedback could cause a decrease in the TEF4 gene.
If glucose is running out, the cell must turn to a different process than glycolysis to continue ATP production. This signals an increase of the TCA cycle genes in order to maintain ATP production.
A possible mechanism that the genome could use is guilt be association. Genes with similar expression patterns would have similar promoters.
The spots should be red because the TUP1 gene represses genes that are glucose-repressed. Therefore removing this gene would not cause a repression of glucose-repressed genes.
The Yap1p spots should be red because transcription would still occur due to its high resistance to environmental factors.
Performing and comparing microarrays of the mutated and wild-type genes could help confirm the predictions made in numbers 8 and 9 above. If the experiments were successful, the microarrays should be red.

Acknowledgments

I referenced Edward Talatala's References section for the citation of the readings.

I met with my homework partner Edward Talatala on Wednesday, January 30th to discuss the Week 2 assignment questions.

Except for what is noted above, this individual journal entry was completed by me and not copied from another source.

Angela C Abarquez (talk) 19:02, 30 January 2019 (PST)

References

Campbell, A.M. & Heyer, L.J. (2003), “Chapter 4: Basic Research with DNA Microarrays”, in Discovering Genomics, Proteomics, and Bioinformatics, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 107-124.

Davidson College Department of Biology (2001) DNA Microarray Methodology - Flash Animation. Retrieved from http://www.bio.davidson.edu/courses/genomics/chip/chip.html on 29 January 2019.

Dahlquist, K. and Fitzpatrick, B. (2019). BIOL388/S19:Week 2. [online] openwetware.org. Available at:Week 2 Assignment Page [Accessed 30 Jan. 2019].

User Page: Angela Abarquez

Course Homepage:BIOL388/S19

Assignments:

Week 1: Instructions and Class Journal

Week 2: Instructions and Class Journal and Individual Journal

Week 3: Instructions and Class Journal and Individual Journal

Week 4/5: Instructions and Class Journal and Individual Journal

Week 6: Instructions and Class Journal and Individual Journal

Week 7/8: Instructions and Class Journal and Individual Journal

Week 9: Instructions and Class Journal and Individual Journal

Week 10: Instructions and Class Journal and Individual Journal