Dmadere Week 11

Definitions

1. Hematological Cancer
   • Cancer that begins in blood-forming tissue, like bone marrow or in the cells of the immune system.
   • https://www.cancer.gov/publications/dictionaries/cancer-terms/def/hematologic-cancer
2. Aquaglyceroporin
   • Membrane channel involved in urea transport and osmotic water permeability functions in specialized leukocyte as immunological and bactericidal response.
   • https://www.biology-online.org/dictionary/Aquaporin-9
3. Hexamer
   • A molecule made up of six structural subunits, such as an oligomer (or polymer) having six monomers.
   • https://www.biology-online.org/dictionary/Hexamer
4. Proteolytic activity
   • An enzyme that promotes proteolysis (the splitting of proteins by hydrolysis of the peptide bonds with formation of smaller polypeptides).
   • https://www.biology-online.org/dictionary/Proteolytic
5. Chelation
   • The combination of a metal ion with a chemical compound, forming a ring.
   • https://www.biology-online.org/dictionary/Chelation
6. Flux
   • The rate of passage of energy or matter (usually in crossing a given area or passing through a given volume) under steady‐state conditions.
   • https://www.oxfordreference.com/view/10.1093/acref/9780198529170.001.0001/acref-9780198529170-e-7217?rskey=6x4y0R&result=7101
7. Promyelocytic leukemia
   • Is an aggressive type of acute myeloid leukemia in which there are too many immature blood-forming cells (promyelocytes) in the blood and bone marrow.
   • https://rarediseases.info.nih.gov/diseases/538/acute-promyelocytic-leukemia
8. Metabolite
   • A substance that is a product of metabolic action or that is involved in a metabolic process.
   • https://www.biology-online.org/dictionary/Metabolite
9. Biosynthesis
   • The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes and energy.
   • https://www.biology-online.org/dictionary/Biosynthesis
10. Isoenzyme
    • Enzymes that differ in amino acid sequence but catalyze the same chemical reaction.
    • https://www.biology-online.org/dictionary/Isoenzyme
11. Assimilation
    • The conversion of nutriment into a useable form (e.g. liquid or solid) that is incorporated into the tissues and organs following the processes of digestion.
    • https://www.biology-online.org/dictionary/Assimilation

Article Outline

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?

Data & Files

DM_Yeast_Undergoes_Arsenic_Stress.pdf

Annotated Bibliography

Ibstedt, S., Sideri, T. C., Grant, C. M., & Tamás, M. J. (2014). Global analysis of protein aggregation in yeast during physiological conditions and arsenite stress. Biology open, 3(10), 913-923. doi: 10.1242/bio.20148938

1. PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/?term=Global+analysis+of+protein+aggregation+in+yeast+during+physiological+conditions+and+arsenite+stress
2. PubMed Central Full Text: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4197440/
3. Publisher Full Text (HTML): https://bio.biologists.org/content/3/10/913.short
4. Publisher Full Text (PDF): https://bio.biologists.org/content/biolopen/3/10/913.full.pdf
5. Copyright:2014. Published by The Company of Biologists Ltd (information found on PDF version of article)
6. Article is Open Access.
7. Article is available only online. The journal website allows for a subscription, but only for access to online content.
8. Publisher: The Company of Biologists Ltd (not a scientific society), non-profit, OAPA member, United Kingdom
9. The journal began in 2012.
10. The articles in the journal are peer-reviewed.
11. Editors and Board: https://bio.biologists.org/content/edboard
12. Journal Impact Factor: 1.962
13. The article is a primary research article.
14. Data from article: https://bio.biologists.org/content/3/10/913.supplemental

Sanchez, Y., Taulien, J., Borkovich, K. A., & Lindquist, S. (1992). Hsp104 is required for tolerance to many forms of stress. The EMBO journal, 11(6), 2357-2364. doi: 10.1002/j.1460-2075.1992.tb05295.x

1. PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/1600951
2. PubMed Central Full Text: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC556703/
3. Publisher Full Text: https://www.embopress.org/doi/abs/10.1002/j.1460-2075.1992.tb05295.x