April 2011

Reading the scientific literature: a step-by-step process

An online-only reprint of an article from Enzymatic discussing the use of Journal of Biological Chemistry article figures as a teaching aid.

Cytotoxicity induced by IR or BLM in Ape1-deficient TK6 and HCT116 cells.

When teaching a senior level molecular biology lecture course, there is, in my case, an attempt to balance discussion of the core material with an introduction to the current research. The former provides much needed background but lacks perspective on the cutting edge research currently underway. Equally problematic, however, is a format that relies solely on primary research literature without ensuring that the students have a fundamental understanding of the core principles. In previous courses, I have tried to maintain this balance by covering core material in a relatively standard course structure (lecture, discussion, question/answer sessions and problem solving) while introducing the students to research papers throughout the semester. With respect to the core content, we discuss both the mechanisms of replication, transcription and translation as well as the experimental techniques used to study these mechanisms. Scientific literature is introduced by asking the students to read topical, up-to-date research articles that touch on the content under discussion. Students are also required to summarize a primary research article by the end of the semester that they themselves have chosen.

Although the students generally appreciate the mix of current research and general background, I have discovered that, while the students enjoy learning about the current research, many still have difficulty linking the core concepts to the research itself. Students may have difficulty interpreting the figures, identifying the key facts of the paper or explaining how the data supports the author’s conclusions. In order to assist in this transition, I have begun to incorporate article figures that relate to the lecture topic under discussion. Shown below is a description of this approach.

Student population: The molecular biology course is a required course for all molecular biology and biochemistry majors. Pre-requisites for the course include genetics, cell biology, microbiology and biochemistry. The course is generally taken at the end of a student’s junior year or beginning of his/her senior year. For molecular biology majors, this course is a pre-requisite for the molecular biology laboratory course.

Course topic: During this section of the course the discussion has focused on DNA repair.

Assignment: During class, students were asked to interpret figure 2 in the article by Fung et al., titled “Distinct Roles of Ape1 in the Repair of DNA Damage Induced by Ionizing Radiation or Bleomycin,” in the February 2011 issue of the Journal of Biological Chemistry (see figure). In this assignment, students were asked to first extract the key ideas of the figure and then progress to a more detailed and sophisticated interpretation of the data. Finally, the students were asked to then relate the experimental results to the content topic currently being discussed.

Level 1: Correlation- When asked to summarize the figure, the students were first able to identify a reverse-correlation between survival and level of treatment (X-ray or Bleomycin). This first level discussion allowed the students to gain confidence in their own interpretation while also emphasizing the key point of the experiment.

Level 2: Comparison- Once the basic correlation was established, the students began to consider the differences between cells treated with the APE1 suppressor compared to the other suppressor and the control. Comparisons were also made between the two treatment conditions and the two cell types used and the differences noted. This provided an opportunity to discuss why the authors repeated the experiments under different conditions with different cell types.

Level 3: Significance- While this class did not discuss statistical significance at this point, students were asked to determine their confidence in the data presented. This discussion was initiated to introduce the controls performed (untreated vs. treatment with an unrelated suppressor, for example) and the importance of these controls in interpreting the data.

Level 4: Relevance- Once the data had been analyzed, it was then possible to discuss the significance of the experimental results with respect to DNA repair and to connect these experimental results with the information the students had learned previously.

By breaking down the figure from less complex to more complex, the students were given an opportunity to slowly bring complicated data into focus, gain a better appreciation for how a good experiment is designed and connect current research with core concepts.

Quinn Vega (vegaq@mail.montclair.edu) is a professor in the department of biology and molecular biology at Montclair State University.

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