BIOL398-01/S11:Week 2

This journal entry is due on Monday, January 24 at midnight PST (Sunday night/Monday morning). NOTE that the server records the time as Eastern Standard Time (EST). Therefore, midnight will register as 03:00.

Individual Assignment
The paper we will read for Journal Club 1 is:

[http://jb.asm.org/cgi/reprint/177/22/6672 ter Schure, E.G., Sillje, H.H.W., Verkleij, A.J., Boonstra, J., and Verrips, C.T. (1995) The Concentration of Ammonia Regulates Nitrogen Metabolism in Saccharomyces cerevisiae. Journal of Bacteriology 177: 6672-6675.]

Preparation for Journal Club 1
"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 four 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 their Week 2 assignment and also contribute to the shared journal page in preparation for the presentation in class on January 25.


 * 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.  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.
 * 3) *What is the main result presented in this paper?
 * 4) *What is the importance or significance of this work?
 * 5) *What were the limitations in previous studies that led them to perform this work?
 * 6) *What were the methods used in the study?
 * 7) *Briefly state the result shown in each of the figures.
 * 8) ** What do the X and Y axes represent?
 * 9) ** How were the measurements made?
 * 10) ** What trends are shown by the plots and what conclusions can you draw from the data?
 * 11) * What is the overall conclusion of the study and what are some future directions for research?
 * 12) Each group of students will be assigned one section of the paper.  The group will be responsible for explaining the section, including any tables/figures in detail to the class.  Groups will be assigned on 1/20/11 in class.  Dr. Dahlquist will prepare the PowerPoint slides this time; for future journal club assignments, you will prepare the PowerPoint.
 * 13) * Physiological parameters section, Figure 1: James, Nick
 * 14) * Northern analysis section, Figure 2: Carmen, Alondra
 * 15) * Enzyme activities section, Figure 3: Sarah

Online Biological Dictionaries

 * biology-online.org dictionary
 * Gene Ontology
 * NCI Dictionary of Cancer Terms

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:
 * 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.

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 journal entry in the shared Class Journal Week 2 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 "BIOL398-01/S11" 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 2 page after you have completed the individual assignment.


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