This assignment begins a several-week long exercise in finding, reading and understanding the primary cell biology literature. The primary literature reports the results of original research by scientists.  Papers of this type usually contain an abstract, materials and methods, results, discussion, and literature cited sections, and are peer reviewed meaning they are reviewed anonymously by experts in the field prior to publication. The library holds subscriptions (paper and on-line) for many journals of this type.  Review articles summarize many primary literature articles and are generally restricted to a specific topic.  Reading review articles is a good way to learn about a topic, but they should not be cited as the source of a particular idea.  Articles about the primary literature such as those found in newspapers, books, and journals like Scientific American are not considered the primary literature since they contain secondary accounts of the primary literature and are written for a general audience.

Publishers of journals containing the primary literature usually maintain websites where you can read the table of contents and often abstracts of papers, or perhaps download the full-length papers. JMU subscribes to many of these electronic journals so while you may think they are free, they actually cost hundreds to thousands of dollars per year.

The assignment

This week you will use an Internet database to find 5 papers from the primary literature that are 1) relevant to this course, 2) available on-line, 3) of interest to you, and 4) are not on a medical topic or involve human subjects..  Because the titles of journal papers may not contain general terms, we recommend using your textbook to find technical terms likely to occur in a title or abstract.  Search the database using those technical terms.  For this first assignment each of you will simply make a list of five papers with full references (authors, year, title, journal, volume, pages).  All five papers should relate to one topic of interest.  Again, avoid clinical studies or papers on humans. 

Before adding a reference to your list make sure the journal is available on-line from JMU.  If you can't tell this from the database, use the Periodical Locator through Carrier Library.  Once you are ready to print a paper you must obtain the PDF file since it will take less paper to print and will include all of the figures as they appear in the printed journal.  You may need to download a (free) copy of Adobe Acrobat Reader if you are not using a JMU computer.  HTML files will not be acceptably.  Please don't print the HTML versions of articles - they use much more paper and may not contain full-sized images.

Searching Using PubMed

There are now various databases on the web with which to search the primary literature on a particular topic.  The library maintains a page with resources that Biologists often use called the Research Guide.  One database that we use frequently is called PubMed.  PubMed is a project developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), located at the National Institutes of Health (NIH). It was developed in conjunction with publishers as a search tool for accessing literature citations and linking to full-text journals at Web sites of participating publishers.  In addition to providing abstracts, PubMed also maintains links to relevant DNA and protein sequences in the sequence databases.

Try the following practice search to learn how to use PubMed. Suppose you wanted to find a paper describing promoter elements in the rubisco gene from spinach.  Rubisco is the carboxylase enzyme in photosynthesis.

• Link to PubMed after reading this list of commands
• Type "rubisco" in the blank provided and press the "search" button (or use the return key).
• Notice the number of hits; 3062 as of 0ct '08!  This is really too many to find one paper.
  
• Now type "rubisco promoter".  Only 229 hits - still too many.
• Lastly, try "rubisco promoter spinach."   With only 11 hits you can easily browse this list for potentially interesting papers.
  
• Click on the paper by Gruissem and Zurawski (EMBO Journal 1985...).  Notice that you can obtain the full reference, abstract, and by clicking on the button, you see the fill text and download the PDF.  Sometimes you will see other buttons under the reference line but if no buttons are visible the library probably doesn't subscribe to the journal.
  
• Once you find one potentially interesting paper look through the list of Related Articles in the box on the right to identify four other papers related to the first one.
  
• If you have trouble with any of this, check out the PubMed Tutorial.
  
• Now link to PubMed and go searching!

Turn in one typewritten page containing:

1. Your name and section number.
2. 1-2 sentences describing the topic you chose and why you found it interesting.
   
3. A list of the search terms you used to find these references.
4. A list of five references from the primary literature that you found using PubMed.  You could copy five references from the literature cited section of one paper, but that's too easy.  Use different search terms and the "Related Articles" button in PubMed to find five references that you know JMU will have access to.
5. Copy and paste the references from PubMed into your document but DO NOT stop there.  Reformat them to the following style (see Pechenik, 2007).

[Authors (last names and initials), year, title, complete journal name, volume number (no month or issue number), beginning and ending pages.  Punctuate as in the example.]

10/1/08 Copyright (C) 2008, Jonathan Monroe, monroejd@jmu.edu. All rights reserved.
URL: http://csm.jmu.edu/biology/courses/bio220/aotw8.html