BIOL398-05/S17:Week 3

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BIOL398-05: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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This journal entry is due on Thursday, February 2 at midnight PST (Monday night/Tuesday morning). NOTE that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.

Individual Journal Assignment

  • Store this journal entry as "username Week 3" (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: These links should all be in your personal template that you created for the Week 1 Assignment; you should then simply invoke your template on each new journal entry.)
    • 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 "BIOL398-05/S17" category to the end of your wiki page.
  • You can make up the points you lost on the Week 1 assignment by completing the requested changes by the Week 3 deadline, midnight Feb. 2.

Homework Partners

Please meet with your partner (either face-to-face or virtually) at least once when preparing this assignment. Even though you may work together to understand the article, your definitions and outline must be done individually. It is not acceptable to do a joint assignment and copy it over to each others' journal page.

  • Lauren, Cameron, Maggie
  • Nika, Conor

Electronic Lab Notebook

Because of the nature of the assignment this week, you need only complete the following sections of the electronic notebook:

  1. The purpose: what is the purpose of this assignment?
  2. The Acknowledgments section.
    • You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. You should include when and how you met and what content you worked on together. An appropriate statement could be (but is not limited to) the following:
      • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
    • Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist or Dr. Fitzpatrick (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
    • If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style.
    • If you need to reference content (such as the methods of a protocol) also acknowledge it here and include a formal citation in your References section (see below).
    • You must also include this statement:
      • "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
    • Sign your Acknowledgments section with your wiki signature.
  3. The References section. In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising.
    • In the case of the definitions, you will provide a citation for each definition (see below).
    • For the outline itself, state at the beginning that is is an outline of the ter Schure (1995) paper and provide the complete reference in your References section.
    • Do not include citations/references to sources that you did not use.
    • You should include a reference to this week's assignment page.
    • The references should be formatted according to the APA guidelines.
    • For more detailed instructions on how to cite journal articles, books, or web pages, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.

Preparation for Journal Club 1

The paper we will read for Journal Club 1 is:

ter Schure, E. G., Sillje, H. H., Verkleij, A. J., Boonstra, J., & Verrips, C. T. (1995). The concentration of ammonia regulates nitrogen metabolism in Saccharomyces cerevisiae. Journal of bacteriology, 177(22), 6672-6675.

"Science... is a process taking place in the minds of living scientists," (Curtis, 1983). The scientific community uses primary research articles as one method of communicating the science within the community (presentations and posters at scientific meetings are others). Primary research articles undergo a process of peer review before they are published, but the quality of papers still vary. "Journal Club" presentations are the means by which scientists with similar research interests learn about, discuss, and evaluate new research. This is the first of two journal club discussions we will have this semester. For this first journal club, the entire class will read and present the same paper referenced above. Each student will create an individual wiki journal page for his or her Week 3 assignment and also contribute to the shared journal page in preparation for the presentation in class on February 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). Cite your sources for the definitions by providing the proper citation (for a book) or the URL to the page with the definition for online sources. Each definition must have it's own citation, to a book or URL.
  2. Write an outline of the article. The length should be the equivalent of 2-3 pages of standard 8 1/2 by 11 inch paper (you can use the "Print Preview" function in your browser to judge the length). 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. It is not acceptable to copy another student's outline either. Even if you work together to understand the article, your individual entries need to be in your own words.
    • What is the main result presented in this paper?
    • What is the importance or significance of this work?
    • What were the limitations in previous studies that led them to perform this work?
    • What were the methods used in the study?
    • Briefly state the result shown in each of the figures.
      • 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?
    • What is the overall conclusion of the study?
    • What are some future directions for research?
  3. Each student will be assigned one section of the paper. You will then be responsible for discussing the assigned section and figure. Dr. Dahlquist will prepare the PowerPoint slides this time; for the second journal club assignment, you will prepare the PowerPoint.
    • Physiological parameters section, Figure 1: Lauren, Cameron, Maggie
    • Northern analysis section, Figure 2: Nika
    • Enzyme activities section, Figure 3: Conor

Online Biological Dictionaries

How to Read a Primary Research Article

A primary research article is divided into sections that each have a different purpose. Articles in Science and Nature are written in a single narrative format and do not explicitly have these headers. However, the information for each of these sections is still there. The article for the Journal Club 1 Assignment is very short and also written as a single narrative, although the information below can still be found.

Abstract

The abstract provides a brief summary of the paper. It states the significance and background, methods, major results, and conclusions from the paper. Different journals have different word limits for the abstract. The abstract is indexed on PubMed and may be the only part of the text publicly available.

Introduction

The introduction gives the background information necessary to understand the paper. The introduction should be in the form of a logical argument that “funnels” from broad to narrow:

Funnel.jpg
  • States importance of the problem
  • States what is known about the problem
  • States what is unknown about the problem
  • States clues that suggest how to approach the unknown
  • States the question the paper is trying to address
  • States the experimental approach
  • Sometimes briefly states the answer they found

Materials and Methods

Describes the experiments used in the paper with enough detail so that another investigator could reproduce the experiments. However, it is usually written in a "shorthand" style that relies heavily on references to previous literature. Articles in Science and Nature severely restrict the amount of methods that can be included in the paper. In those articles, the information is embedded in the figure legends or references or is available as supplemental online material.

Results

Describes the experiments performed and the results of the experiments. The text can take the form of question, experiment, results from that experiment, repeated several times. Each main experiment should be represented by a figure or table of results. Some people read papers by looking at the figures and reading the legends, then going back to the text for details.

Discussion

States the answer to the question the paper is trying to address. It explains and defends the answer, if necessary. It puts the results in a broader perspective by comparing with previous results or models. The implications of the results are discussed and the next steps for future research are suggested.

References

List of references cited in the main text of the paper. Different journals have different styles of references, but all the essential information should be there, authors, year of publication, journal name, volume, and page numbers. The title of the article is sometimes omitted. This list is a useful resource to look for further reading on the subject of the paper.

Caveat Emptor

Just because a paper was published does not mean that it was written well or that the experiments were sound (in a worst case scenario, data may even be fraudulent). The peer review system is designed so that only good research is published, but in practice, that may not be the case. Each paper must be approached with a critical eye. You must judge whether you believe their results and conclusions based on the evidence they give.

Shared Journal Assignment

  • Store your shared journal entry in the shared Class Journal Week 3 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 "BIOL398-05/S17" category to the end of the wiki page (if someone has not already done so).

Reflection

Answer the following questions on the Class Journal Week 3 page after you have completed the individual assignment.

  1. What aspect of this assignment came most easily to you?
  2. What aspect of this assignment was the most challenging for you?
  3. What (yet) do you not understand?