Round the Clock

Shannon He is a freshman from Glenview, Illinois studying neurobiology on the pre-medicine track in Weinberg College of Arts and Sciences. She is an executive member (publicity chair) of the Biology Students Association and volunteers at Campus Kitchens. Outside of school, she enjoys writing scripts and is currently working with her friends on a startup comic production company, Helion Comics. She is a script writer on their project: a science fiction, superhero comic titled The Misfits. This summer, she will be studying circadian rhythms in mice in the Turek Lab.

Newcomer’s Nerves

As with anything, approaching something new is always difficult; whether you welcome the difficulty is a different matter. I, for one, was anxious for essentially an entire quarter about starting science research. So anxious in fact that I came in a few days before I was supposed to start to fill out two sheets of paperwork that easily could have been handled in the first hour. My friends had already began research during the school year and felt comfortable in their labs, taking their own lunch breaks, doing whatever processes were necessary for their experiments. But, I still had/have worries over beginning my experiment. Where do I begin? Where do I order mice from? Where do I order their chow from? How do I weigh them? I haven’t even touched a mouse yet.

The thing is, the people in my lab, and any lab, are extremely great resources. Though I still have all those questions, they make sure I practice techniques (such as using the micropipette), learn new processes I am unfamiliar with (PCR and qPCR), and they continue to make sure I am going in the right direction. After all, I have 8 weeks to learn everything I need to for my experiment. I have my first in-person animal training tomorrow and though I am nervous the mice won’t like me, I have come to terms with the fact that I probably won’t be the next mouse-whisperer because I know I am in good hands no matter what I’m doing.

On a different note, I feel like I would enjoy writing about the different processes I learn. After all, it is a science blog. For any prospective researchers, maybe this will give you an idea of the things you might learn in lab, and labs you might be interested in. This past week has consisted mostly of learning how to do several processes, mainly PCR and real-time PCR. For anyone who has taken the genetics course in the biology sequence, PCR is used to amplify DNA. In my case, we amplified the DNA in mice tail tips to determine their genotype.

First, we have to extract the DNA from the tips. Then, once we have the DNA, we can run either a PCR or a real-time PCR (qPCR). qPCR differs from PCR in that we can detect amplification much earlier (thus, real time) rather than after the entire process is completed. Both use primers, dNTP’s, a buffer solution, and DNA polymerase. For regular PCR, we use master mix (DNA polymerase), a forward primer and reverse primer (to initiate replication of both strands), and water. Another very important part of any science research is concentrations of the solutions you are using. After putting our solution together, we pipette the master mix solution into each DNA sample. After vortexing and centrifuging the DNA samples, we let it run in the thermal cycler, which actually carries out the amplification process. While that’s happening, we make the gel for the gel electrophoresis. Something I realized very quickly was that we have to actually make most of the things we simply read about in the textbook. We use a previous gel and heat it up until it is a clear liquid and add in ethidium bromide (carcinogen, aka use gloves!). Then, we pour the gel into the electrophoresis apparatus with two plastic combs with teeth to create wells. After a lot of waiting, we take out the combs and add the buffer and DNA. We let the machine run voltage through our samples to separate the DNA into strands of different sizes and, again, wait. After that’s done, we have the completed product. Now, all that’s left is to look at the gel with a UV light to see the bands and from there we can determine the genotypes of each sample. Though qPCR is very similar, it presents its own learning curve and challenges, so I’ll probably write about this next time. For now, I am going to take a lunch break with my friends and fellow summer science researchers.

Agarose Gel Electrophoresis

Introduction

The circadian rhythm is a mechanism that allow organisms to synchronize their internal physiological systems to their external environment. Our brain has an internal biological clock that synchronizes other biological clocks in our bodies, such as in our heart, pancreas, fat tissue, kidney, and liver. In 2009, researchers in the Turek Lab discovered that mice fed a high-fat diet during the light phase (mice’s irregular feeding phase since mice are nocturnal) gain significantly more weight than mice fed a high-fat diet during the dark phase. However, the experiment only tested male mice. In 2015, researchers found no significant difference in weight gain between daytime-fed female mice and night-time fed female mice. My project aims to identify a cause for the difference in how male and female mice gain weight by testing the effect of estrogen. Estrogen is a hormone that reduces food intake and body adiposity while increasing energy expenditure. Previous research has shown that a decline in estrogen levels may be associated with irregular internal circadian rhythms. Furthermore, studies have shown that ovariectomies have shown an increase in body weight while estrogen treatment after an ovariectomy showed a decrease in body weight. To study the effect of estrogen, I will study the weight gain in normal female mice compared to ovariectomized female mice on different feeding times to see how estrogen and circadian timing of feeding affect weight gain together.

This blog will likely be a place for me to share experiences of working in a science lab for the first time, learning new procedures, and any other challenges that may come my way.