1. SCIENTIFIC WRITING: MATERIALS AND METHODS
NURULISA ZULKIFLE (Dr.)
Cluster of Oncological & Radiological Sciences
Advanced Medical & Dental Institute
Universiti Sains Malaysia

2. ANATOMY OF A DISSERTATION
Title & Prepage
Introduction
Literature review
Materials and Methods
Results
Discussion
Summary & Conclusion
References
Appendices
On a 1000-mile journey, the hardest thing is the first step.
Make the first step easy!
The methods section is often easiest to write as it is simply descriptive.

3. CONTENT OF MATERIALS & METHODS SECTION
Description of what we did in detail – what experiments were run and how, what equipment and how they were used, how much, how often, what, where, when and why …

4. Information to include:
Subject used + handling and care
Sample preparation techniques
Origin of samples and materials
Description of the field site
Protocol for collecting data
Statistical analysis techniques used
Information on the computer programs used/written
Description of equipment set-up and function

5. Drugs: generic name, manufacturer, purity, concentration, amount administered, etc.
Culture media, buffers: components and concentrations, temperature, pH
Experimental materials: cell line, molecule, tissue, etc.
Animals: state that the research was approved by the appropriate committee at your institution
Human subjects: state that the research was approved by the appropriate committee at your institution

6. Present the experimental design.
PURPOSE
Present the experimental design.
Provide enough detail to allow (competent) readers to interpret your results.
Give enough detail for (competent) readers to replicate your work.
“The key to a successful Methods section is to include the right amount of detail - too much, and it begins to sound like a laboratory manual; too little, and no one can repeat what was done.” Successful Scientific Writing, 2nd ed.

7. Report methods in past tense (‘DNA was extracted …’)
TENSES
Report methods in past tense (‘DNA was extracted …’)
Use present tense to describe how data are presented in the thesis (‘data are summarised as means  SD….’)

8. PASSIVE VS ACTIVE VOICE
Passive (point of view of the experiment):
‘DNA was extracted from the cells…’
Passive voice, emphasises the method or variable
Active (point of view of the experimenter):
‘We extracted DNA from the cells..’
Active voice, more lively, but sacrifices having the topic as the subject of the sentence
Requires creativity to avoid starting every sentence with ‘we’:
‘Because the layers did not stick well, we processed them as small pellets.’
‘After fixing the surface layers, we then…’

9. COMMON MISTAKES!

11. (1) Method or methodology?
Materials and Method
What you do
Description of a given procedure
Tools of scientific investigation
Processes used
Experimental design
Methodology
The method and its application
The philosophical underpinnings of a particular method of investigation e.g. scientific method
Principles determining how tools used
Descriptive design

12. (2) Too much information
Long and wordy
Single action per sentence
Unnecessary details
Improved: Each plate was plated on a turntable and streaked at opposing angles with fresh overnight E. coli culture using inoculating loop. The bacteria were then incubated at 37°C for 24 hr.
Same actions in a single, concise sentence.
Delete the superfluous detail and obvious information
Add missing information
Best: Each plate was streaked with fresh overnight E. coli culture and incubated at 37°C for 24 hr.
Assuming reader has basic knowledge
Delete extra information
Combine related actions.

13. (3) Too little information

14. (4) Inappropriate use (or unuse) of table

17. (5) Reiterating published method

18. Put protocol from manufacturer in appendix.
Cite a reference for commonly used methods
Each peptide was covalently coupled to agarose and 30 to 200 ml quantities of each crude polyclonal antiserum were affinity-purified with the use of the appropriate immobilised peptide, as previously described (Woodsmith et al., 2008)
Immunoprecipitations, SDS-PAGE on 10% polyacrylamide gels, and phosphorimaging analysis were performed as described previously (Berson et al., 2000).

19. The actor implied by the infinitive is simply disappears.
(6) Dangling modifier
The actor implied by the infinitive is simply disappears.
Very common in scientific writing, sometimes unavoidable.
Due to overreliance on passive voice:
“After scraping the desired plate in four swipes, the bacteria were placed in 8 ml of media with no antibodies.”
“To determine whether pH changed through time, soil was sampled monthly.”

20. (7) Including a result/discussion
Avoid explaining
Principle
Why you have used certain method

21. (8) Other common mistakes/points to bear
Do not use different non-standard abbreviations in different places for the same materials or units, etc.
Use the correct Greek letters such as α or ß, rather a or b.
Use correct symbol such as µl not ul.
When giving the composition of reagents and referring to percentages, e.g. ‘1.0% agarose’ or ‘0.6% acrylamide’, be clear whether you are referring to either volume , volume or weight , volume percentages.
Do not capitalise the names of chemicals! Sodium Chloride and Sodium chloride are incorrect, sodium chloride is correct.
When writing formula, always to use the appropriate subscripts and superscripts, e.g. CO2 not CO2.
When writing chemical names, italicise appropriately, e.g. 1-(tert-butyldimethylsilyloxy)-1-methyl-3-(phenylsulfonyl)-4- butanol.
Do not use colloquialisms e.g. ‘hot’ when you mean ‘radioactive’.
Do not use ‘rpm’ instead of ’xg’ when describing centrifugation protocols. This is because every centrifuge is different and the force on the sample depends on revolutions per minute (rpm) and the radius of the centrifuge. The x gravity (xg) is the measure of centrifugal force, and is commonly understood by everyone. The only time it is ever correct to refer to ‘rpm’ is when you also give the exact make and model number of the centrifuge and the rotor, so that people can replicate your conditions precisely.
When describing centrifugation protocols, use xg instead of simply g; ‘xg’ is times the constant for gravity and refers to the force on your sample, ‘g’ is grams.
When you are trying to describe actions, use the correct word, e.g. do not use the word ‘spin’ if you mean ‘centrifuge’.
Learn about the conventions of notation in your field. For example, human gene names should be written in italicised capital letters (OTUB1, UBE2D2) whereas mouse gene names should be written in italicised letters, only the first one of which is capitalised (Otub1, Ube2d2).

22. Minimize complexity by
TIPS
Minimize complexity by
Breaking into smaller sections with informative subheads
Display in a map/diagram/flow chart where possible

23. Title: The effect of OTUB1 overexpression on human cervical cancer cells HeLa.

24. Title: Prevalence and causative agents of superficial mycoses in UKMMC.

25. Title: Construction and cloning of reporter-tagged replicon system for in vitro replication study of murine norovirus-1 (MNV-1).

26. Title: Investigation on the effect of fig and date vinegar on HT-29 human colon cancer cells.

27. 3.1 Materials 3.2 Methods 3.2.1 Preparation of C. roseus extract
3.2.2 Synthesis of C. roseus-AgNPs
3.2.3 Preparation of complete media
3.2.4 Freezing cells
3.2.5 Thawing cells
3.2.6 Subculturing cells
3.2.7 MTS assay
3.2.8 Annexin V-FITC/Propidium Iodide Assay
3.2.9 Cell cycle Analysis
Statistical Analysis

29. From:
Oral topiramate for treatment of alcohol dependence: a randomised controlled trial
Johnson et al. The Lancet 361;17 May 2003

30. Week
Morning dose
Afternoon dose
Total daily dose 1
0 mg
1x25 mg tablet
25 mg 2
2x25 mg tablets
50 mg 3
75 mg 4
100 mg 5
1x100 mg tablet
150 mg 6
200 mg 7
1x100 mg and 2x25 mg tablets
250 mg 8
300 mg 9 10 11 12
Schedule is similar to that provided in the Physicians' Desk Reference (2000). The placebo and topiramate groups received the same number of tablets; placebo tablets were inactive.
Table 1: Topiramate dose-escalation schedule

31. From:
Medicine & Science in Sports & Exercise 2003; 35(5):

32. From: Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Tufarelli et al. Nature Genetics. 5 May 2003.

33. Methods
From: Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Tufarelli et al. Nature Genetics. 5 May 2003.