That smooth curve

"Oh, it's beautiful!" I exclaimed, "look at that smooth curve!" 

Beside me, Kharis was just as excited - although not quite as vocal. I pointed at the screen with both hands. A smooth fluorescence curve on the graph indicated that our sample contained DNA. "That means it worked!" 

"No, yeah, I get it," Kharis nodded. "Cool."

We were upstairs in a colleague's lab, using a fluorometer to measure the concentration and purity of DNA in some samples. Some of you might remember that I've struggled for a few years with methods for extracting DNA from larvae. The problem is that larvae are so small, a single individual doesn't have a lot of DNA. Any of the tried-and-true extraction methods I use for larger organisms don't really work well for larvae because they include wash steps. Of course, washing a sample is meant to carry away everything except the DNA, but a little bit inevitably gets lost with each step. When there's so little DNA to begin with, accidentally washing away even a little bit means you could lose your whole sample. 

An ascidian tadpole larva that Kharis collected and used in
the DNA extraction experiment. Photo by Kharis Schrage.

I thought I had figured out a method that worked in 2018, but I still struggled with a set of samples in 2020. [To be fair, those 2020 samples had been left sitting in a warehouse in Norway for about 4 months because of the covid pandemic, so that may have been a factor...] When my student ran into some snags processing the larvae we collected with a lander in the Arctic deep sea last summer, we knew it was time to back up and troubleshoot. We didn't want to waste any more precious Arctic samples on a method that might not work. 

My student, Kharis, came up with an experiment. She collected larvae locally - from the marine pond right next to our lab building. She divided them into groups. And she tried different extraction methods on each group. 

In the end, the fluorometer told the story: one of the methods worked very well! The DNA wasn't super clean, but it was definitely there! 

I'm excited that Kharis's experiment showed a clear path forward. Her next step is to amplify the extracted DNA using PCR and make sure she can identify the larvae using their DNA sequences. With any luck, we'll be able to charge forth with larval samples from now on!