Over the course of the next few weeks, we’re going to introduce you to the undergraduate students and recent grads who work hard behind-the-scenes to keep Your Wild Life ticking.
Today, sophomore Justin Hills explains the in’s and out’s of DNA extraction.
Cotton swab? Check. Belly button? Check. Three seconds of wondering, “What am I doing?” Check. But finally, you just did it. You swabbed your belly button (or door sill or armpit…) and returned your samples back to the Dunn Lab at NC State University. So what happens now? What classified operations will take place in the lab to unlock the secrets of the microbes living in your navel?
In order for us to identify who’s who among your belly buddies, we have to crack the microbes’ genetic code – we need to read their DNA. Today, we’re going to give you a backstage pass to the first step in this process – DNA extraction.
The goal of DNA extractions is to lyse, or break-up, cells and separate out the DNA from other material in the cells and the environmental debris that might be floating around in the sample. We use a soapy, detergent solution to break apart the cell membrane (because it’s largely made up of fat molecules), and tiny glass beads to grab hold of the DNA inside. Then, through a series of chemical washes and high-speed spins, we’re able to get rid of all the other stuff from the busted up cells (particularly the proteins). In the end, we’re left with just a tube of DNA.
Here’s a slide show of the steps we take in the lab:
But we’re actually not interested in every bit of DNA we extract – we want to zoom in on one specific gene to help us identify the bacteria in your belly button, the 16S rRNA gene. This gene is found in all bacteria, and codes for a part of the ribosome (the important machinery in every cell responsible for translating the genetic code into proteins). There’s a region within the 16S rRNA gene that is extremely variable among strains of bacteria; in essence, this hypervariable region provides a species-specific DNA “fingerprint.”
Recall, however, that the tube of DNA we isolated above contains lots of different genes, including the 16S rRNA gene. And often, these DNA sequences we’re most interested in are present in low concentrations, too low for our DNA sequencing machines to detect. So we need to boost the numbers of 16S rRNA in the sample. To do that, we use a DNA-copying procedure called Polymerase Chain Reaction (or PCR).
And for how that process works, I’ll let the Science Rapper explain:
So whether we’re interested in the bacteria living in your belly button or the microbes in the dust atop your doorframe, Your Wild Life Team uses the molecular biology procedures I outlined above to extract, isolate and copy DNA. The most exciting part is yet to come – analyzing the 16S rRNA gene sequences to uncover the identities of those microbes living on us and around us.
Justin Hills is a sophomore at NC State University majoring in Biological Sciences with a concentration in Human Biology and a minor in Africana Studies. Always fascinated by the many ways in which our personal lives can be shaped by the little guys who live on and around us, Justin especially loves working with the Your Wild Life Team. Originally from Charlotte, NC, Justin is a Park Scholar in the Class of 2014 and enjoys sharing his time as both a University Ambassador and executive board member for the Minority Association of Pre-Health Students.