BIOL398-03/S13:Week 11

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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.

Contents

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.

Read

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

  • Tai et al. (2007) Acclimation of Saccharomyces cerevisiae to Low Temperature: A Chemostat-based Transcriptome Analysis. Molecular Biology of the Cell 18: 5100–5112.

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? Under what conditions and temperatures?
    • What controls did they use?
    • How many replicates did they perform per condition?
    • 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 student will be assigned one figure or table from the paper to explain in class. You will prepare one PowerPoint slide about your figure. Your slide must contain the figure from the paper, a title that describes the main message of the figure, and any other information required to explain your slide (legend information, summary information, etc.) Upload your slide file and link to it on your individual journal page and on this page here.

Tips for your PowerPoint Slide

  • When putting the figures into your PowerPoint slide, do the following:
    1. First download the image as a file to your computer's hard drive from the HTML version of the article. (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; in this casse it would be acceptable to submit two or even three slides if you need to do this. Each slide needs to have a descriptive title and summary information on the slide.
    5. Save your file as a .ppt compatible with Microsoft Office 97-2003 instead of .pptx.
  • When putting the tables into your PowerPoint slide, do the following:
    1. Capture the image from the PDF version of the article. In the full version of Adobe Acrobat (available on most LMU lab computers) use the "camera" icon to draw a marquee around the table. This will capture the table to your computers's clipboard. You can then paste this into the PowerPoint slide.
    2. When enlarging or reducing the table to fit the slide, be careful to not change the aspect ratio.
    3. You may choose to crop large tables into smaller pieces to facilitate your presentation; in this casse it would be acceptable to submit two or even three slides if you need to do this. Each slide needs to have a descriptive title and summary information on the slide.

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).

Reflection

Critically evaluate the Tai et al. (2007) 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?


Personal tools
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