Genetically identifying nematodes with a portable lab

I’m so happy my first first-author scientific paper (which you can find here, if you’re up for the challenge) is published! Here’s a summary of what I have been doing these last four years, beautifully illustrated by my friend Rachel Glover.

The bottom line is that we combined a portable molecular biology lab, the Bento Lab, with a portable DNA sequencer, the MinION. With these two techniques combined we can now genetically identify nematodes all over the world, even in remote field sites.

Im my paper I looked at the DNA of nematodes, microscopically small worms. DNA is made up of letters, and the combinations of these letters create codons (like words) and genes (like sentences). Nematodes are common parasites of humans, great apes and other animals, they are a crucial component of soil ecosystems and are abundant in marine environments. Many researchers are interested in learning which species of nematodes are present in different environments.

Genes can be used to differentiate between different nematode species, because each species has a different sequence of letters. To be able to read which letters are present in a nematode species, we have to multiply the gene to create a lot of identical parts of DNA. This is scientifically known as ‘amplification’. In our paper we proved we can do this amplification process on the fully portable molecular biology lab, the Bento Lab. This lab combines three lab techniques in one, bringing the price of a basic molecular lab down from ~$7000* to ~$2000.

Then I used a new, portable DNA sequencer – the MinION – to read the biological information stored in the DNA. In the MinION the DNA is passed through a membrane. This passage creates differences in electric current, where different letters in the DNA (A, C, G, or T) create a different current.

These differences in current are stored in a digital file, which we need to translate to the corresponding letters. After all, I want to be able to read the information to find those different sequences I talked about earlier, with which we can identify species.

I used an analysis called ONTrack, which can be compared to a real-life Pokédex. It translates my digital files, and as a result shows me the letters of the gene on my computer screen. I can then compare the gene to a biological database with lots of species, to know which species my gene represents. I did this for four different species, and we could identify them all as the correct species!

* Estimated cost based on BioRad equipment (rounded down): PCR ~$5000, centrifuge ~$120, electrophoresis chamber ~$400, electrophoresis power supply ~$500, UV transilluminator ~$1250.