This past week and a half of life in the Perry lab has been rather exciting. We've recently welcomed a new Ph.D.-track Biology grad student, Cory Henderson, as well as a visiting undergrad student from Howard University, NaTazah O'Neil, who will spend the summer with the Perry lab to get some bioinformatics experience. I've been working with Cory for the past few days on a rather interesting task: how best to extract the DNA from a body louse (plural = lice). |
Cory is attempting to get lice DNA because he is broadly interested in the evolutionary relationship between humans and their parasites. PJ and Cory will be working closely with Professor John Marshall Clark's lab up at UMass Amherst, where they maintain colonies of head and body lice. For those who are unfamiliar, lice are parasitic insects that feed on human blood. They can infect any human population worldwide, and are easily transmitted in crowded living conditions with poor hygiene. For more info, visit the CDC's website.
One of the first steps to beginning a new wet lab experiment is optimizing your protocols for your lab space, or vice versa. I say vice versa because sometimes the best way to ensure the success of your protocol is to buy a fancy new piece of equipment - one recent example from the Perry lab was a new speed vac concentrator :) In the world of DNA sequencing, you have three essential components to figure out in the first stages of your project: 1) how to get the DNA out of your sample, 2) how to prepare your DNA libraries for sequencing, and 3) how to do both 1 and 2 in a cost-effective manner. Dr. Clark's lab mailed us 50 body lice last week so we could begin optimizing Cory's DNA extraction protocols. |
Most DNA extraction protocols for tissues will have you prepare said tissue by grinding it up in a buffer solution (AKA "homogenizing" it) then digesting it in proteinase K (which breaks down proteins to release more DNA) for a specified amount of time. I have previously ground up a few tapeworms in the Perry modern lab with plastic pestles, and we also have a fancy electronic homogenizer (that I nicknamed the nose-hair trimmer) that essentially makes a smoothie of your tissue. But Dr. Clark's lab's favorite homogenizing tool is this glass-glass homogenizer.
Since we really wanted to try a few extractions this week and Cory's leaving for a conference in Zanzibar tomorrow, we decided to test our plastic pestles and electronic homogenizer to see how they'd get the job done. Pictured on the left are Cory's lice. Using sterile lab techniques, he would fish one out, wash it off, then add it to some buffer in a neatly labeled microtube for homogenization. |
Long story short, our fancy homogenizer failed completely and our pestles worked sort of okay. The lice were small enough that they wouldn't get sucked into the homogenizer; they'd just spin around in the buffer solution, which eventually became so foamy that we couldn't even tell if the bug was getting ground up or not. The plastic pestles were a bit better at breaking up the lice, but weren't as effective as we hoped. So here we are, trying to get these silly little dead bugs to cooperate with our various grinding techniques, when another grad student in the Anth department, Kelsey Kjosness, saved the day with a scalpel. Simply cutting up the louse a bit before trying to pulverize it with a pestle yielded much more DNA than mashing alone. Sometimes old school = best school.
Cory will continue refining his louse extraction techniques upon his return from Zanzibar, probably with the help of a glass-glass homogenizer or two. While the first stages of a new project may seem tedious, it is also a rather exciting time as a researcher. It is so completely satisfying to finally have "this is the best way to do this step" checked off on your project to-do list. I hope to be checking off my own extraction to-do list rather soon, and I will keep y'all updated on that! Cheers :)