Coral crusher

I selected Hanny's name and then typed with my thumbs on the screen of my cell phone: "Alright, I'm going to take a short break and then get back to crushing."

Her text response came a few seconds later: "Metaphor for life!"

A bit of coral tissue about to be crushed

Friends, my first two weeks back at WHOI have been very full. I am now an Assistant Scientist (yay!), but to be honest, the past two weeks, I have felt more like a lab technician. As you may remember, Hanny and I collected hundreds of coral samples in Palau last fall. The quantitative part of our analysis involves population genetics - basically, examining the corals' DNA to see how their populations are connected. As you may imagine, extracting DNA from hundreds of coral samples is a tedious, repetitive process that takes a lot of time at the lab bench. 

To start the process, I removed each sample from its tube, broke off a piece with a razor blade, and crushed it up. The razor blades and forceps I was using had to be sterilized between each sample, so I dipped them in ethanol and then burned the ethanol off with a lighter. Yes, sometimes science involves fire! The crushed coral bits then get incubated overnight with an enzyme that breaks open the cells and sets the DNA free. 

Crushed-up tissue ready to be incubated

The next day, I retrieve the samples from the incubator and set about the long process of cleaning the DNA. A good analysis requires DNA with nothing else hanging onto it or swimming around in the solution, so we're being very careful and doing three different wash steps. The bread-and-butter tool of molecular biology is the centrifuge, a machine that spins sample tubes at high velocity. Over and over, I pipetted a solution onto the filter with the DNA, placed it into a collection tube, spun the tube at 8,000 rmp, and discarded the flow-through. Pipet, tube, spin, discard. Over and over.

The last step is called elution, and this step separates the DNA from the filter. I pipetted the solution onto the filter, placed it into a tube, and spun it in the centrifuge, but this time, I kept the tube. A small volume of clear liquid rested at the bottom. In that liquid was the corals’ DNA.

The extractions have been a lot of work, and we’re only about halfway done. Ok, enough blogging - now back to crushing corals!