Eyoung20 journal week 11
Contents
Purpose
Team and Journal Information
- Team 1: Kitagawa, E., Takahashi, J., Momose, Y., & Iwahashi, H. (2002). Effects of the pesticide thiuram: genome-wide screening of indicator genes by yeast DNA microarray. Environmental science & technology, 36(18), 3908-3915. DOI: 10.1021/es015705v
- Project Manager: Mike
- Quality Assurance: Iliana
- Data Analysis: Emma, Kaitlyn
- Coder: Mike
Definitions of terms
- 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. Make an in text citation of the (name, year) format next to the definition, and then list the full citation in the References section of your journal page.
- Online Biological Dictionaries
Outline
- 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?
- How did they treat the yeast cells (what experiment were they doing?)
- What strain(s) of yeast did they use? Were the strain(s) haploid or diploid?
- What media did they grow them in? What temperature? What type of incubator? For how long?
- What controls did they use?
- How many replicates did they perform per treatment or timepoint?
- What method did they use to prepare the RNA, label it and hybridize it to the microarray?
- What mathematical/statistical method did they use to analyze the data?
- Are the data publicly available for download? From which web site?
- Briefly state the result shown in each of the figures and tables, not just the ones you are presenting.
- 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?
- How does this work compare with previous studies?
- What are the important implications of this work?
- What future directions should the authors take?
- Give a critical evaluation of how well you think the authors supported their conclusions with the data they showed. Are there any major flaws to the paper?
Annotated Bibliography
APA + DOI number
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- Did LMU pay a fee for this article:
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APA + DOI number
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APA + DOI number
- PubMed Abstract:
- PubMed Central:
- Publisher Full Text (HTML):
- Publisher Full Text (PDF):
- Copyright:
- Publisher:
- Availability:
- Did LMU pay a fee for this article:
APA + DOI number
- PubMed Abstract:
- PubMed Central:
- Publisher Full Text (HTML):
- Publisher Full Text (PDF):
- Copyright:
- Publisher:
- Availability:
- Did LMU pay a fee for this article:
APA + DOI number
- PubMed Abstract:
- PubMed Central:
- Publisher Full Text (HTML):
- Publisher Full Text (PDF):
- Copyright:
- Publisher:
- Availability:
- Did LMU pay a fee for this article:
Conclusion
Acknowledgements
References
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.
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.
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.
