Writing Methods and Results

APS Professional Skills Course:

Writing and Reviewing for Scientific Journals

Manuscript Structure • Title• Abstract• Introduction• Methods• Results• Discussion• References• Tables• Figures• [Appendices]

Where Do You Start?

• No “correct” order

• Frequently used order:– Methods– Results– Discussion– Introduction– Title– Abstract

The Methods Section

• Purpose– Foundation for results analysis– Builds the readers’ confidence in your results

• Before you write the draft…– Review the journal requirements– Develop an outline and review with co-authors

Methods Section Components • Major Components

– Study design– Rationale– Experiments completed

• How much detail?– Don’t replicate the lab notebook– Review the journal space limitations– Detail should allow replication of your work– Cite previously published methods – Describe modifications of published methods– For new methods, provide additional detail

• Can others repeat my work based on this description?

Experimental Design

• Treatments, experimental groups, controls

• Data collection protocols

• Variables measured

• Reagents and materials

• Replicate experiments

• Statistical analyses– Power analysis– Data analysis

Experimental Subjects • Cell line

– Source and strain• Animals

– Age, size, sex, and source– Handling (diet, housing, etc.)

• Humans– Age, size, sex, pre-existing conditions

• Protocol/Procedure Review– Institutional Animal Care and Use Committee

(IACUC)– Institutional Review Board (IRB)

Sources of Reagent and Materials

• Drugs and chemicals– Supplier– Stock number– Lot number

• Antibodies or biological reagents– Describe development process– Be prepared to share

Example: Experimental Subjects

“Adult (250-350 g) male Sprague-Dawley rats (Harlan, Indianapolis, IN) were individually housed (wire-hanging cages) in a temperature- (25oC) and light-controlled environment with a 12:12-h light-dark cycle (lights off at 1800h). Rats were provided ad libitum access to standard rat chow (Purina, 5001) and water except, as indicated in the experimental procedure, when they were deprived of food but not water overnight (16h). Prior to testing, rats were adapted to experimental conditions for one week.”

Modified from: MR Hayes, et al. Serotonin type-3 receptors mediate cholecystokinin-induced satiation through gastric distension. Am J Physiol Regul Integr Comp Physiol 291: R115-R123, 2006.

Example: Protocol Review

“The experimental procedure was approved by the Animal Care Committee at the Virginia Polytechnic Institute and State University which adheres to USDA and NIH guidelines.”

From: HB Park, et al. QTL analysis of body composition and metabolic traits in an intercross between chicken lines divergently selected for growth. Physiol Genomics 25: 216-223, 2006.

Example: Reagents and Materials

“All cell culture material and supplies were purchased from Sigma (St. Louis, MO). Recombinant murine VEGF-A164 and TNF- were purchased from Calbiochem (San Diego, CA). All antibodies for flow cytometry analysis were purchased from BD Laboratories (Franklin Lakes, NJ).”

From: S. Goebel, et al. VEGF-A stimulation of leukocyte adhesion to colonic microvascular endothelium: implications for inflammatory bowel

disease. Am J Physiol Gastrointest Liver Physiol 290: G648-G654, 2006.

Example: Experimental Protocols

“Bromodeoxyuridine (BrdU) staining and cell cycle analysis were performed as described previously (10). Briefly, cells grown on coverslips were treated as indicated in the figures and labeled with 10 µM BrdU for 60 min. After fixation in ethanol, cells were permeabilized with 0.25% Triton X-100, and DNA was denatured by 4 N HCl. Cells were then immunostained with anti-BrdU monoclonal antibody and Alexa fluor 488-conjugated secondary antibody.

From: Y. Gui, et al. Endoreduplication of human smooth muscle cells induced by 2-methoxyestradiol: a role for cyclin-dependent kinase 2. Am J Physiol Heart Circ Physiol 292: H1313-H1320, 2007.

Example: Statistical Procedures

“Results are presented as means ± SE. Statistical analysis was performed with Student's t-test for unpaired groups or with ANOVA followed by Bonferroni's correction for comparisons of three or more groups. A P value <0.05 was considered a significant difference.”

From: Y. Gui, et al. Endoreduplication of human smooth muscle cells induced by 2-methoxyestradiol: a role for cyclin-dependent kinase 2. Am J Physiol Heart Circ Physiol 292: H1313-H1320, 2007.

Methods Section Should NOT Include…

• Step-by-step protocols

• Details on common statistical procedures

• Results

Results Section Tells a Story!

• Results are presented in a logical order– May not be the chronological order

• Only the relevant results are presented– Do not replicate lab notebook

• Include a brief rationale for the experiments

• Include transitions between experiments or results

• Distinguish between results and analysis

Organizing the Results Section

• Identify and highlight the important points

• Use figures and tables– Minimize the data presented in the text– Check journal guidelines

• Format– Write in past tense– Use 1st or 3rd person

Example: Using a Figure

“The percentage of fibers responsive to inflammation soup was approximately the same for each category of conduction velocity (Fig. 2).”

From: Ma, et al. Inflammatory Mediators Enhance the Excitability of Chronically Compressed

Dorsal Root Ganglion Neurons. J Neurophysiol 95: 2098-2107, 2006.

Using Figures

• To show trends or relationships in the data

• Use the right type of figure– Bar graphs for non-contiguous variables– Line graphs for contiguous variables

• Figures and legends should “stand alone”

• Discuss each figure in the text

Figure Legends

• Good legends -> Clear understanding

• Four components– Brief title– Experimental details– Definitions– Statistical information

Example: Figure and Legend “Fig. 2. Mice blood pressures measured under pentobarbital sodium anesthesia. Data are means ± SE. Both systolic and diastolic blood pressures were higher in hGRK4 A142V transgenic mice (n = 46) than in nontransgenic littermates (NT; n = 7) and hGRK4 wild-type transgenic mice (n = 37) (*P < 0.05, one-way factorial ANOVA, Duncan's test).”

From: Wang, et al. Am J Physiol Heart Circ Physiol 292: H2083-H2092, 2007

Example: Data Presented in Text

“Mean arterial pressure, measured in the carotid artery, was 85.3 ± 6.9 in female, 87.5 ± 5.5 in male, 90.3 ± 5.5 in ovx, and 96.3 ± 7.4 mmHg in eNOS–/– mice, respectively.”

From: Guo, et al. Estrogen modulates the mechanical homeostasis of mouse arterial vessels through nitric oxide. Am J Physiol Heart Circ Physiol

290: H1788-H1797, 2006.

Using Tables

• Use to compare data or values– Can use for complex variables or

measurements – Do not use to show relationships or trends

• Each table includes:– Title– Legend

• Tables and legends should “stand alone”

Example: Data Table

From: Damgaard, et al. Hemodynamic and neuroendocrine responses to changes in sodium intake in compensated heart failure. Am J Physiol Regul Integr Comp Physiol 290: R1294-R1301, 2006.

Expert Suggestions

• Be concise; don’t provide unnecessary details• Don’t over-justify your rationale• State limitations of the study clearly but without

“apology” • Use well-written papers as models• Practice!• Create an outline before writing• Solicit and use feedback from experienced

colleagues