Lab 2

Objective of Lab 2: Selection of a Research Article

This week you'll select a research article for analysis.

Look at the review article you selected last week. Find a section of the review that interests you and look up cited research articles. Obtain articles that interest you AND meet the course criteria.  The article you select must:

• have been published 5 to 10 years ago (e.g. between 2006 and 2010, for students taking the course in W16). This is essential because you will later search for information on the context and outcome of the research. There will be no outcome for more recent articles!
• be a full research paper, not a review article or a "Note". To be certain that you have chosen a full research paper, verify that it includes a distinct section labeled "Methods", "Materials and Methods", "Experimental Procedures" or the equivalent, as well as distinct sections labeled "Results" and "Discussion" or "Conclusions", and discuss it with your Instructor or TA.
• help you to understand the course material.
• list the experimental techniques used by the researchers. This list should be long enough to provide a good basis for Report 1, but short enough to be manageable (e.g. not more than 5-10 methods). Beware of authors who use every method known to humanity (or at least, microbiology), or who hide methods in "supplementary material" that is only available via the journal web site. (Yes, your analysis must include all the supplementary material for your article.)

Before finalizing your selection, make sure that you understand (or can understand) the methods used by the researchers (see below).

Each research article should contain enough information to allow a suitably trained investigator to reproduce the reported experiments. Nevertheless, authors are discouraged from publishing technical details more than once. In most papers, only unusual (or newly created) methods are described in detail in the Materials and Methods (or Methods, or Experimental Procedures) section. Others are listed in that section or in Table and Figure legends by citing supplementary material or other publications, and still others are considered to be standard techniques within the discipline (for example, it's assumed that microbiologists know how to streak plates!).

Make a list of the methods employed by the researchers. Don't just reproduce the paragraph headings from the Methods section of your article. Some headings will cover groups of methods. You may need to be a sleuth to extract a complete list of methods from your article, but your effort will be rewarded later in the project. Once you've made your list, think about your knowledge of each of the listed methods. Can you visualize how each was performed, and what information it provided? It's best to choose an article in which most of the methods are familiar (e.g. cell culture, SDS-PAGE, protein assays), but a few are new, so that your work on this project will expand your technical knowledge.

Take the following steps to determine what methods were used to conduct the reported research, what background study may be necessary to understand them and which one you will describe in detail (refer to Report 1):

1. Make a list of the methods employed by the researchers. Look at the Figure and Table legends as well as the Materials and Methods section of the paper. If your authors have used a large number of complex or unfamiliar techniques, reconsider your selection.
2. Note which methods were described in detail in your article, which are not described, but for which there are literature citations and which are standard to bacterial physiology (hence neither described nor cited). The last category will include only the basic methods that you've like preparing standard media and solutions, streaking petCheck with your Instructor or TA to make sure that they agree with your designations of "standard" methods.
3. Look up references that are cited by the authors as sources of technical information. Don't be surprised if this turns into a treasure hunt! Authors may repeatedly modify basic techniques, describing one modification in each of a (chronological) series of articles. If they do this without ever describing the basic method, you must independently find that information (during Lab 3).
4. Decide whether you already understand the theory on which each method was based and how each type of experiment was performed. Will you need to seek more information from other sources?
5. Consult with your TA or Dr. Wood to assess the completeness of your list and decide which technique will be described in Report 1.

During Lab 3 you'll learn how to find information on the listed techniques, whether familiar or not.