Sarah Carratt: Week 9

Instructions

Formatting

• Store this journal entry as "username Week 9" (i.e., this is the text to place between the square brackets when you link to this page).
• Create the following set of links. (HINT: you can do all of this easily by adding them to your template and then using the template on your pages.)
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Link to this assignment from your journal entry.
  • Don't forget to add the "BIOL398-01/S11" category to the end of your wiki page.

Things to Read

Article

• Schade et al. (2004) Cold Adaptation in Budding Yeast. Molecular Biology of the Cell 15: 5492–5502.
  • Link to PDF version of article: use this one for printing/reading.
  • Link to full text in HTML: use this one to get the figures for your PowerPoint.

Background

• Thieringer, H.A., Jones, P.G., and Inouye, M. (1998) Cold shock and adaptation. BioEssays 20: 49–57.
• Aguilera, J., Randez-Gil, F., and Prieto, J.A. (2007) Cold Response in Saccharomyces cerevisiae: New Functions for Old Mechanisms. FEMS Microbiological Reviews 31: 327–341.
• Al-Fageeh, M.B. and Smales, C.M. (2006) Control and Regulation of the Cellular Responses to Cold Shock: the Responses in Yeast and Mammalian Systems. Biochemical Journal 397: 247–259.

Preparation for Journal Club 2

1. Make a list of at least 10 biological terms for which you did not know the definitions when you first read the article. Define each of the terms. List the citation(s) for the dictionary(s) you use, providing a URL to the page is fine.
2. Write an outline of the article and include the following questions:
   1. What is the main result presented in this paper?
   2. What is the importance or significance of this work?
   3. How did they treat the cells (what experiment were they doing?)
   4. What strain(s) of yeast did they use? Was the strain haploid or diploid?
   5. What media did they grow them in? What temperature? What type of incubator? For how long?
   6. What controls did they use?
   7. How many replicates did they perform per timepoint?
   8. What mathematical/statistical method did they use to analyze the data?
   9. What transcription factors did they talk about?
   10. Briefly state the result shown in each of the figures and tables.
3. Each group of students will be assigned one section of the paper. The group will be responsible for preparing that portion of the PowerPoint presentation and explaining the assigned section and figures in detail to the class.
   1. Introduction, Figures 1, 2: Sarah, Carmen
   2. Methods, Figures 3, 4: Alondra, Nick
   3. Discussion, Figures 5, 6: James

Online Sources

• Biology Dictionary
• Gene Ontology
• NCI Dictionary of Cancer Terms

Student Response

Biological Terms

1. transient changes: "short-lived; passing; not permanent; said of a disease or an attack" [1]
2. MIPS: "MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators" [2]
3. isoform: "any of the proteins with the same function and similar amino acid sequence, encoded by different genes (or by RNA transcript)" [3]
4. aggregation: "massing of materials together as in clumping" [4]
5. menadione: "a fat soluble vitamin that plays an important role in blood clotting" [5]
6. expression profile: "the measurement of the activity (the expression) of thousands of genes at once, to create a global picture of cellular function" [6]
7. Msn2p/Msn4p: "transciption factor that could control stress-induced expression" [7]
8. hyperosmotic shock: "shock caused or characterized by an increased osmotic pressure (typically higher than the physiological level)" [8]
9. trehalose: "also known as mycose or tremalose, is a natural alpha-linked disaccharide formed by an α,α-1,1-glucoside bond between two α-glucose units" [9]
10. glutathione/glutaredoxin system: "part of a complex regulatory network controlling defense against oxidative stress" [10]

Outline

1. What is the main result presented in this paper?
2. What is the importance or significance of this work?
3. How did they treat the cells (what experiment were they doing?)
4. What strain(s) of yeast did they use? Was the strain haploid or diploid?
5. What media did they grow them in? What temperature? What type of incubator? For how long?
6. What controls did they use?
7. How many replicates did they perform per timepoint?
8. What mathematical/statistical method did they use to analyze the data?
9. What transcription factors did they talk about?
10. Briefly state the result shown in each of the figures and tables.

Navigation Guide

Individual Assignments

Sarah Carratt: Week 2	Sarah Carratt: Week 6	Sarah Carratt: Week 11
Sarah Carratt: Week 3	Sarah Carratt: Week 7	Sarah Carratt: Week 12
Sarah Carratt: Week 4	Sarah Carratt: Week 8	Sarah Carratt: Week 13
Sarah Carratt: Week 5	Sarah Carratt: Week 9	Sarah Carratt: Week 14

Class Assignments

Shared Journal: Week 1	Shared Journal: Week 6	Shared Journal: Week 11
Shared Journal: Week 2	Shared Journal: Week 7	Shared Journal: Week 12
Shared Journal: Week 3	Shared Journal: Week 8	Shared Journal: Week 13
Shared Journal: Week 4	Shared Journal: Week 9	Shared Journal: Week 14
Shared Journal: Week 5	Shared Journal: Week 10

Class Notes

Sarah Carratt_1.18.11	Sarah Carratt_2.3.11	Sarah Carratt_2.22.11
Sarah Carratt_1.20.11	Sarah Carratt_2.8.11	Sarah Carratt_2.24.11
Sarah Carratt_1.25.11	Sarah Carratt_2.10.11	Sarah Carratt_3.1.11
Sarah Carratt_1.27.11	Sarah Carratt_2.15.11	Sarah Carratt_3.3.11
Sarah Carratt_2.1.11	Sarah Carratt_2.17.11	Sarah Carratt_3.8.11

Internal Links

BIOL398-01/S11:Assignments

BIOL398-01/S11:People

BIOL398-01/S11:Sarah Carratt