Difference between revisions of "BIOL398-03/S13:Week 11"

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(pasted in from previos/changed ref to 308-03/S13)
(Read: link to Tai paper)
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The class will make a Journal Club Presentation on the following article:
The class will make a Journal Club Presentation on the following article:
* Schade ''et al.'' (2004) Cold Adaptation in Budding Yeast. ''Molecular Biology of the Cell'' 15: 5492–5502.
* Tai ''et al.'' (2007) Acclimation of ''Saccharomyces cerevisiae'' to Low Temperature: A Chemostat-based Transcriptome Analysis. ''Molecular Biology of the Cell'' 18: 5100–5112.
** [http://www.molbiolcell.org/cgi/reprint/15/12/5492 Link to PDF version of article]: use this one for printing/reading.
** [http://www.molbiolcell.org/content/18/12/5100.full.pdf Link to PDF version of article]
** [http://www.molbiolcell.org/cgi/content/full/15/12/5492 Link to full text in HTML]: use this one to get the figures for your PowerPoint.
** [http://www.molbiolcell.org/content/18/12/5100.full Link to full text in HTML]
==== Background Reading on Cold Stress ====
==== Background Reading on Cold Stress ====

Revision as of 09:44, 21 March 2013

BIOL398-03: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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This journal entry is due on Thursday, April 4 at midnight PDT (Wednesday night/Thursday morning). NOTE new due date and that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Individual Journal Assignment

  • Store this journal entry as "username Week 11" (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 "BIOL398-03/S13" category to the end of your wiki page.


The class will make a Journal Club Presentation on the following article:

Background Reading on Cold Stress

Review articles on cold stress that may be helpful:

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. You can use the glossary in any molecular biology, cell biology, or genetics text book as a source for definitions, or you can use one of many available online biological dictionaries (links below). 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. The length should be the equivalent of 2 pages of standard 8 1/2 by 11 inch paper (you can check this by clicking on "Print preview" in your browser). Your outline can be in any form you choose, but you should utilize the wiki syntax of headers and either numbered or bulleted lists to create it. The text of the outline does not have to be complete sentences, but it should answer the questions listed below and have enough information so that others can follow it. However, your outline should be in YOUR OWN WORDS, not copied straight from the article.
    • What is the main result presented in this paper?
    • What is the importance or significance of this work?
    • How did they treat the cells (what experiment were they doing?)
    • What strain(s) of yeast did they use? Was the strain haploid or diploid?
    • What media did they grow them in? What temperature? What type of incubator? For how long?
    • What controls did they use?
    • How many replicates did they perform per timepoint?
    • What mathematical/statistical method did they use to analyze the data?
    • What transcription factors did they talk about?
    • 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. Groups will be assigned on 3/10/11 in class.
    • Introduction, Figures 1, 2: Sarah, Carmen
    • Methods, Figures 3, 4: Alondra, Nick
    • Discussion, Figures 5, 6: James

Tips for your PowerPoint Presentation

  • Please follow the Presentation Guidelines when preparing your PowerPoint slides.
  • Each slide needs to have a title that is a sentence that says the main take-home message for the slide. Do not use the words "Introduction", "Methods", "Results", or "Discussion" as titles for your slides.
  • Your outline should be a "mini-talk" that actually makes the points of your talk (not just what the talk is "about").
  • When putting the figures into your PowerPoint presentation, do the following:
    1. First download the image as a file to your computer's hard drive. (Right-clicking the image in most web browsers will open a menu with "Save image as" as one of the options.
    2. Then in PowerPoint, select "Insert image from file" and browse to your file. If you just copy/paste the image, this could lead to problems when showing a PowerPoint presentation made on a Mac on a Windows PC.
    3. When enlarging images, be careful to not change the aspect ratio of the image.
    4. You may choose to crop large figures into smaller pieces to facilitate your presentation.
    5. Save your file as a .ppt compatible with Microsoft Office 97-2003 instead of .pptx.

Online Biological Dictionaries

Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 11 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL398-03/S13" category to the end of the wiki page (if someone has not already done so).


Critically evaluate the Schade et al. (2004) paper.

  1. Overall, do you think this paper was clearly written? Why or why not?
  2. Based on what is written in the methods section, do you think you could reproduce their experiments and data analysis?
  3. What else would you like to know about their methods, results, and future directions?