Dramir36 Week 11

Purpose

• To learn how to search the primary literature.
• To prepare and give a journal club presentation.

10 definitions of biological terms

• retrograde pathway: The mechanism of moving backward or against the usual direction of flow. Biology Dictionary (2019)
• septin: A protein involved in cytokinesis and also functions in maintaining cell morphology Biology Dictionary (2019)
• β‐galactosidase: One of a class of enzymes which cuts the glycosidic bond between the sugar galactose and another sugar molecule (of a different type than galactose). Biology Dictionary (2019)
• oxidoreductase: An enzyme that catalyzes the transfer of electrons from an electron donor (reductant) to an electron acceptor (oxidant) in a redox reaction Biology Dictionary (2019)
• trehalose: A disaccharide made up of two α-glucose molecules, and serves as an energy source in certain fungi, bacteria, plants, and invertebrates Biology Dictionary (2019)
• supernatant: The soluble liquid fraction of a sample after centrifugation or precipitation of insoluble solids. Biology Dictionary (2019)
• biosynthesis: The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes (to catalyze the reaction) and energy source (such as ATP) Biology Dictionary (2019)
• assimilation: The act of absorption or incorporation into the biological tissue. Biology Dictionary (2019)
• isoform: Any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript). Biology Dictionary (2019)
• attenuate: Tapering gradually. Biology Dictionary (2019)

Outline of Journal Article

1. 1. What is the main result presented in this paper?
   2. What is the importance or significance of this work?
   3. What were the limitations in previous studies that led them to perform this work?
   4. How did they treat the yeast cells (what experiment were they doing?)
   5. What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
   6. What media did they grow them in? What temperature? What type of incubator? For how long?
   7. What controls did they use?
   8. How many replicates did they perform per treatment or timepoint?
   9. What method did they use to prepare the RNA, label it and hybridize it to the microarray?
   10. What mathematical/statistical method did they use to analyze the data?
   11. Are the data publicly available for download? From which web site?
   12. Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
       • What do the X and Y axes represent?
       • How were the measurements made?
       • What trends are shown by the plots and what conclusions can you draw from the data?
   13. How does this work compare with previous studies?
   14. What are the important implications of this work?
   15. What future directions should the authors take?
   16. Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?

References

• Barreto, L., Canadell, D., Valverde-Saubí, D., Casamayor, A., & Ariño, J. (2012). The short-term response of yeast to potassium starvation. Environmental Microbiology, 14(11), 3026–3042. doi: 10.1111/j.1462-2920.2012.02887.x, https://sfamjournals.onlinelibrary.wiley.com/doi/full/10.1111/j.1462-2920.2012.02887.x
• Biology Online. (2019). Biology Dictionary. https://www.biology-online.org/dictionary/Main_Page