matandmeth



Materials and methods

This section must be clear and detailed enough for another person in your field to repeat the experiments and reproduce the results. Previously described protocols may be referenced but you must clearly outline any changes made to the previous approach. Referencing must be very accurate, referring to the original description of a technique. Only provide full details of a technique if your methods are new (unpublished).

example:

“The FISH method was modified from that previously described by Callen et al (1990) in that chromosomes were stained prior to analysis with both propidium iodide and DAPI.”

The materials and Methods section should be written in the past tense, and usually in the passive voice.

example:

“Melanoma cells were washed twice with medium and fresh medium containing sense or antisense oligomers (5 µm) was added.

Do not use the imperative form, that you may use for laboratory notes.

example:

Wash cells twice with medium and then add antisense oligomers (5 µM).”

The sources of all materials, except routine chemicals and laboratory equipment, should be given. This includes whether they were purchased from a company, or donated by a company or another research laboratory. Where materials are purchased, the complete name of the company is required, and the location of the company is also often needed. The source of important equipment is also given.

example:

“Nucleosides were resolved on a Varian Vista 5500 Liquid chromatograph.”

“…tablets were provided by Rhone-Poulenc Rorer (Antony, France).”

Most journals require a statement indicating that patients consent was obtained, and that the study was conducted according to the appropriate clinical or experimental ethical guidelines, which is included in the methods.

In clinical studies, full details of study design, data collection, and statistical anaysis must be included in a paper, and these can largely be given in the Methods section. All appropriate patient details, including eligibility or ineligibility for inclusion must be given. Details of study design such as how patients were randomized, both primary and secondary endpoints, full definitions of patient groups and disease states, matching of patients and controls etc., should be given.

example:

“Randomization was stratified by center and according to the site of disease onset…”

“The study was designed as a two-arm comparison of fludarabine with CAP.”

“Secondary endpoints were treatment-associated side effects and overall survival.”

“The definition of remission due to successful treatment was defined as a reduction of more than 80% in the baseline PASI scores.”

By including these kinds of details in the Methods section, a clearer and shorter outline of the study design and aims may be given in the important text of the Results and the Introduction.

The statistical methods should include:

1.  statements regarding sample size choice based on statistical power calculations.

2. delineation of dependent and independent variables, covariates, and subgroups of key interest.

3. steps taken to prevent study biases.

4. extent of patient follow-up.

5. statistical methods used for the analysis of different variables.

6. confidence intervals and their derivation.


Models (e.g, analysis of variance, covariance, multiple regression) should be described. In the presentation of summary statistics, authors must be especially careful in the use of the notation “a ± b”, to ensure that both a and b are specified and used appropriately. For example, if a and b represent mean and standard deviation, respectively, this expression should be written as “a ± b (SD)” the first time it appears; if b is the standard error of the mean, then “a ± b (SEM)” is written the first time.

If you are in doubt about which statistical analyses to use, or how to correctly express your results, then consult a statistician. Poor or incorrect statistical analysis of results will prejudice your paper in the review process for publication.

A few major journals, including Scienceand Nature,require only abbreviated details of Materials and Methods, encouraging referencing wherever possible. In these journals, the Methods may be largely described in the final “References and Notes” section, or in the figure legends. Always check the exact layout of an article required by the journal you are submitting to.

A lot of space is often wasted on descriptions of basic molecular cloning methods. Methods that every molecular biologist in the world uses, such as gel electrophoresis, can be kept very short. You usually do not usually need to include the electrophoresis conditions or the subsequent transfer of nucleic acids or proteins to a membrane.


avoid

Amplification products were loaded onto a 6% polyacrylamide gel run at 150V for 1 hour and then the gel was dried and exposed to Fuji x-ray film overnight at -700C.

better

Amplification products were resolved on 6% polyacrylamide sequencing gels and visualized by autoradiography.


avoid

PCR products were loaded and separated on a 1% agarose gel, stained with ethidium bromide, and photographed under UV illumination.

better

PCR products were fractionated through a 1% agarose gel and visualized by UV fluorescence.


avoid

Proteins were transferred to a Hyalon membrane for 90 minutes at 120 mA in 1X Transfer buffer using a Protrans apparatus.

better

Proteins were electrophoretically transferred to a membrane.

As with other methods, commonly used molecular cloning methods such as blotting should be abbreviated with only the important details (such as the probe or antibody used) given.

Note that every reader understands that Southern blots show genomic DNA, northern blots show RNA and Western blots show protein.


avoid

To detect RAS RNA expression, total RNA was run on a 1% agarose gel containing formamide, transferred to a membrane, and the membrane was hybridised with a RAS-specific RNA probe overnight, followed by 3 washes in 2-SSC…

better

RAS expression was determined by northern blotting with a RAS-specific probe