College Writing 161: Writing in the Biological Sciences: Read scientific articles

The structure of scientific articles

Primary scientific research articles generally contain the following sections (though not always in the order given below):

1. Title: A brief descriptive statement of the article topic.
    
2. Abstract: A brief summary of the content of an article, answering the questions:
   1.  What is the problem domain (system under investigation)?
   2.  What is the specific research question? 
   3.  What were the methods and results? 
   4.  What are the conclusions? 
   
   Example: Nunez JK, Bai L, Harrington LB, Hinder TL, Doudna JA. 2016. CRISPR immunological memory requires a host factor for specificity. Molecular Cell 62: 824-833. DOI: https://doi.org/10.1016/j.molcel.2016.04.027
   Abstract:
   Bacteria and archaea employ adaptive immunity against foreign genetic elements using CRISPR-Cas systems. To generate immunological memory, the Cas1-Cas2 protein complex captures 30-40 base pair segments of foreign DNA and catalyzes their integration into the host genome as unique spacer sequences.  Although spacers are inserted strictly at the A-T-rich leader end of CRISPR loci in vivo, the molecular mechanism of leader-specific spacer integration remains poorly understood.  Here we show that the E. coli integration host factor (IHF) protein is required for spacer acquisition in vivo and for integration into linear DNA in vitro. IHF binds to the leader sequence and induces a sharp DNA bend, allowing the Cas1-Cas2 integrase to catalyze the first integration reaction at the leader-repeat border.  Together, these results reveal that Cas1-Cas2-mediated spacer integration requires IHF-induced target DNA bending and explain the elusive role of CRISPR leader sequences during spacer acquisition. 
    
3. Introduction: The question or system investigated and the findings of previous relevant scientific studies.
    
4. Methods and materials: A description of the reagents, cell lines, model organisms, sampling techniques, equipment and experimental protocols used in gathering data; should provide enough detail to enable the experiment to be reproduced by another researcher in the field.
    
5. Results: The data gathered, presented and analyzed. Often this section will include figures and tables.
    
6. Discussion: Explains the meaning and significance of the results (how do they advance the field?) and how they relate to the research question; describes limitations and further work suggested by study.
    
7. Acknowledgements: The funding sources, potential competing interests, other contributors, ethics statements for human- and animal-subject research (if there isn't a separate section), etc.
    
8. References/Literature/Works cited: The previous scientific studies and other sources cited in the paper.
    
9. Supplementary information: supporting technical information (figures, protocols, methods, tables, additional data) too long or detailed to fit into the body of the paper.

Literature reviews generally do not present original data (that is, data that has not been previously published). As a result literature reviews don't generally have Methods or Results sections.

How to read a primary scientific research article

To read primary scientific articles effectively requires dedicated time. If you encounter unfamiliar words or undefined acronyms, pause and look them up immediately. If you are struggling to understand the paper's context, finding a relevant encyclopedia entry, textbook chapter or review article can provide helpful background.

Your reading should answer the following questions:

1. What is the major research area of this study? What system is it investigating?
2. What is the specific research question being investigated by the authors? Why is it important? Are the authors testing a hypothesis?
3. How did the authors try to answer the research question? What experiments did they perform? (You don't necessarily have to understand the experiment in close detail, but it is important to understand the basic steps and methods involved.)
4. What data were collected by the authors? How did they analyze and present the data?
5. Do the results seem to support the authors' conclusions?
6. What are the limitations of the study?
7. Does the paper suggest any follow-up studies, additional experiments, or future areas of inquiry?

To get a general sense of the question or system studied and the conclusions drawn:

1. Read the Title: Does it seem relevant to your topic? If so,
2. Read the Abstract: This will give you a summary of the content of the paper. If it seems relevant,
3. Read the Introduction: This will give you more detail about the question or system studied. If it still seems relevant,
4. Read the Discussion/conclusion: This will describe the scope and significance of the results; at this point you may also want to look for any potential conflicts of interest in the Acknowledgements.

To get more detail about the experimental results and methods,

5. Read the Results: This will detail the data and analysis used by the authors to draw their conclusions.
6. Look carefully at the figures and data tables and read the captions: These will show you what data was gathered and how it was analyzed and interpreted. Additional figures and data may be included in the supplementary or supporting information.
7. Read the Methods: This will provide the specifics of the experimental procedures followed such as where samples were gathered and how measurements were taken.

To find additional relevant resources,

8. Look at the References.

The first four steps will give you a good picture of what the paper is about and what conclusions can be drawn from the study. Steps 5 through 7 provide essential details for in-depth understanding. Step 8 will point you to the earlier work on which this study was based.

How to read a literature review

1. Read the Title: Does it seem relevant to your topic? If so,
2. Read the Abstract: This will give you a summary of the content of the paper. If it seems relevant,
3. Read the Introduction: This will give you more detail about the topic under review, with citations to earlier relevant studies. If it still seems relevant,
4. Read the conclusion for a summary of the findings and suggestions about future research directions.
5. Read the sections of interest to get more detail.
6. For additional resources, note citations to specific references that seem especially relevant.