Angela C Abarquez Week 2
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.
- 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.
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.
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