Materials and Methods

Writing Tips

Writing materials and methods for a research paper is very different from keeping a logbook. While you want to record all details in your notebook, the method section in your paper is a summary of what you did and should not include every minor detail.
The method section should contain the information that someone, with a similar amount of lab experience as yourself, would need to replicate your study.

Some reasons that people struggle with writing good/succinct materials and methods are

they:

  • want to write the methods in chronological order – this leads to a lot of repetition because the same methods were used repeatedly (if you were writing bread-making cookbook – would you want to describe the details of how to knead the bread with every recipe?)
  • don’t know how to deal with small variances in the way methods were applied – so they describe the entire method more than once – with only minor changes in implementation
  • reproduce protocols rather than describing what they did
  • list all materials separately and then restate the materials used as they describe the related method
  • include too many general knowledge details – for example, should you need to tell your peers what pipetter was used for each volume – or could you assume that given a volume they could figure out how to obtain it themselves?

To avoid these problems

  • describe each method as a discrete unit (use clear descriptive subtitles)
  • describe a method’s details only once – if some parts of the method were altered depending on the specific application, explain the adjustments as you describe that part of the method
  • where applicable, give final component concentrations, not the starting component concentration and the volume used
  • don’t separately list materials which you will need to refer to when you describe the method anyway
  • don’t reproduce easily accessible methods such as kit protocols
  • USE SUBTITLES – I can’t emphasize this enough – subtitles will help you organize your methods so that they are not only easier to write, but are easier for your reader to follow

An example of a single method description you might need in your paper follows (my notes are in italics).

Plasmid isolation (this title clearly indicates what method is described)
Plasmids were isolated using the Fermentas GeneJet™ Plasmid Isolation kit (the kit name is included here, not in a separate materials list) according to the manufacture’s instructions (Fermentas 2007).
That’s it for this method as all other details are described in the manual that is available online.

Plasmid isolation (an alternate okay method – I don't recommend this one because this is an easily accessible method and so many words are needed)
All plasmids were isolated using the Fermentas GeneJet™ Plasmid Isolation kit (Fermentas 2007). Stationary E. coli cultures were harvested by centrifugation at 6800 g (8 ml for pKC7, 2 ml for pUC18 and 3 ml for recombinant plasmids). Pellets were resuspended in 250 µl of Resuspension Solution. The cells were lysed by adding 250 µl of Lysis Solution and mixing by inversion. Cell debris was precipitated by adding 350 µl of Neutralization Solution, mixing by inversion and pelleted by centrifugation for 5 min at 12000 g, the supernatant was transferred to a GeneJET™ column. Columns were processed by centrifugation for 1 min at 12000g. After passing the crude plasmid prep over the column it was washed 2 times with 500 µl of Wash Solution. After the final wash, the column was centrifuged for an additional minute and then transferred to a new tube. Plasmid DNA was eluted in 50 µl of Elution (the column was incubated with elution buffer for 2 min at room temperature).

A BAD example for describing digest (my notes are in italics).

Restriction enzyme digestions
We used Fast Digest BamH I and Hind III from Thermoscientic. For the first digest to check the concentration of the purified plasmids, we digested 2 uL of pUC18 with 1 uL of BamH I and 1 uL of 10X buffer with 6 ul of H2O. We digested 5 uL of pKC7 with 1 uL of BamH I and 1 uL of 10X buffer and 4 uL of H20.
In preparation for ligation, we digested 5 uL of pUC18 with 1 uL of BamH I and 1 uL of Hind III and 2 uL of 10x buffer and 11 uL of H2O.
In preparation for gel purification of Gene A, we digested….
Do you see the problem here? I am already at 7 lines of text and I haven’t even got to the final recombinant screening. Additionally, because we are using everyone's data in the final report, I would need to list the specific conditions of everyone's digest. This will take even more space. And, in the end, this level of detail is not helpful for someone who is going to try and follow what we did (it is next to impossible to even follow) or for someone to try and repeat what we did (the amounts of plasmid they will want to digest will depend on their plasmid concentrations and they may not want to purchase their enzymes from the same company).

A better way to describe the digests

Restriction enzyme digestions
Thermoscientific Fast Digest Enzymes according to the manufacturer’s instructions. Generally, 10 to 500 ng of purified plasmid DNA was digested in a final volume of 10 – 20 uL.

Here in one sentence, we have given the reader an idea of the scale of our digests and then referred them to the manufacturer's protocol. It is not necessary to name the specific enzymes here, it would be more appropriate to name them when we describe the overall cloning strategy.

Describing the overall cloning strategies

After describing the individual methods briefly (in one or two paragraphs) describe the overall strategy used to create the recombinant plasmids. Don't forget that identifying the final recombinants is part of the strategy.
Since one of your goals is to compare two strategies, make sure you clarify how the strategies differ.

Remember – when writing a research paper for publication – WORDS COST MONEY.
They cost money in the page charges paid to the journal. They also cost time. Scientists are very busy people with massive amounts of material to read on a weekly basis. They don’t want to waste their time reading long convoluted papers in which unimportant details are included and the information is unnecessarily repeated.

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