This blog post addresses technical problems that might arise when writing molecular biology articles if not properly proofread.
Once the long-awaited moment of writing the last sentence of the manuscript arrives, many scientists fail to proofread their work closely. This may result from overexposure to one’s own text to the point where some of the mistakes simply become invisible. By that point, scientists might even dream about their research at night. Although it might sometimes feel like you can no longer look at your manuscript, there are a few important points that should be double-checked before the final submission.
“I was working on the proof of one of my poems all the morning and took out a comma. In the afternoon I put it back again.”
― Oscar Wilde
Is it ok to cut blots horizontally? How about vertically?
It is common practice to cut blots horizontally as well as crop them to reduce their overall size in order to save space in publications1. However, if you choose to do that, make sure you haven’t removed the product of interest by mistake or any of the data without a clear label informing the reader of doing so.
Cutting blots vertically to present two blots side by side is a completely different story though. To avoid being suspected of misconduct, be mindful of a newly developed screening algorithm for the detection of unnatural patterns on gel electrophoresis images as well as skilled researchers, reviewers, and editors2. Research misconduct is defined by The Office of Research Integrity (U.S. Department of Health & Human Services) as “fabrication, falsification, or plagiarism in proposing, performing, or reviewing research, or in reporting research results”3. To stay in line with usual guidelines and/or etiquette, any alterations need to be designated.
The splicing of numerous gels together requires clear indication of such, otherwise, the topic of fabricated or falsified data will naturally arise. Furthermore, vertical gel alignment is not only problematic for quantitative evaluation but also because bands, more often than not, run with a certain degree of distortion (“frown” or “smile”)4. It is more advisable to re-design and re-run the experiment with the samples that are supposed to appear next to each other and/or on the same gel and omit all the cut-and-paste steps that may lead to speculations. It is good scientific conduct to disclose in the figure legend or Materials and Methods the type of (electronic) manipulation that was carried out as well as the software/tools used5.
Don’t doubt my primer sequences!
Designing oligonucleotides is an important step in securing successful DNA amplification. Some scientists might have still designed them by hand before primer design tools became freely available.
When reviewing manuscripts, I have encountered many primer sequences that have not been checked for their correctness. More often than not, primers are either recorded in the wrong direction or flipped. Sometimes bases are omitted due to cut-and-paste errors or exchanged due to simple typos. In rare cases, complete primer sequences have been swapped for sequences that target genes or even pseudogenes unrelated to the content of the document. Most of these mistakes stem from the fact that all scientists work very quickly and on a few projects in parallel and do not “waste” time on reviewing primer sequences. The easiest way to catch those mistakes is by blasting and running an in-silico polymerase chain reaction (PCR) on the primer sequences that are shown in the document.
In the best-case scenario, you will waste 5 minutes reviewing your data. In the worst case, a reviewer or reader of the article will catch your mistake and point it out to you. The price for such mistakes can at times be higher than you bargained for!
Errors introduced by autoformatting functions
The autoformatting function in spreadsheet programs like Microsoft Excel has driven many of us crazy before. Typical errors are gene names, tRNA synthetase symbols, and identifiers. SEPT1 and MARCH1 are changed by default to the dates Sep-01 and Mar-01, respectively, or some form of it depending on the formatting settings, while RIKEN identifiers are automatically converted to exponential numbers (2310009E13 to 2.31E+13)6. The HUGO Gene Nomenclature Committee (HGNC) is trying to solve this problem by changing gene symbols that are auto-converted to dates (SEPT1 is now SEPTIN1; MARCH1 is now MARCHF1)7. The easiest solution to this problem is replacing the old with the new gene symbols and in the case of identifiers, to double-check the spreadsheet settings.
Have you ever come up short in proofreading your manuscript? Share your stories in the comments!
Literature
- Bass JJ, Wilkinson DJ, Rankin D, et al. An overview of technical considerations for Western blotting applications to physiological research. Scand J Med Sci Sports 2017; 27: 4–25.
- Shao H-C, Cheng Y-J, Duh M-Y, et al. Forgery Blind Inspection for Detecting Manipulations of Gel Electrophoresis Images. 2018 IEEE Glob Conf Signal Inf Process Glob 2018; 534–538.
- Definition of Research Misconduct | ORI – The Office of Research Integrity, https://ori.hhs.gov/definition-misconduct (accessed 17 November 2020).
- Gel slicing and dicing: a recipe for disaster. Nat Cell Biol 2004; 6: 275–275.
- Rossner M, Yamada KM. What’s in a picture? The temptation of image manipulation. J Cell Biol 2004; 166: 11–15.
- Ziemann M, Eren Y, El-Osta A. Gene name errors are widespread in the scientific literature. Genome Biol 2016; 17: 177.
- Bruford EA, Braschi B, Denny P, et al. Guidelines for human gene nomenclature. Nat Genet 2020; 52: 754–758.
Written by:
Daniela Kamir, Ph.D.
Medical Writer