Week 4

Hi everyone! I know my last posts have been gone into the background and initial results of my project in some detail, so this week I want to give you a better idea of what my typical day at Mayo looks like.

On Monday, I double-checked the primers I had designed earlier and mapped out where they are predicted to bind to the target strand. This helps me know how long the products I’m expecting should be, which lets me evaluate the success of my PCR reactions.

After a final screening for any obvious mistakes in my primer design, I ordered the VJ rearrangement primers on Tuesday. It takes the company about one day to synthesize them and one day to ship them, so they were delivered Thursday morning. In retrospect, I probably should’ve just ordered the primers as soon as I’d designed them because they only cost ~$5 each. I did appreciate having plenty of time to  organize my lab book and the files on my computer so the experiments I’ve planned will be well-documented even after I leave. My notes never turn out quite as neat as I’d like, but I’ve slowly gotten better at remembering to write down all the relevant details. Some advice for Honors/AP Chemistry students: recording procedures, data, and observations in lab notebooks aren’t skills you’ll need only in high school. If you plan to do any research in science, you won’t get far without keeping a diligent record of what you’re doing—and it’s always easier to maintain a good habit than to change a bad one.

While waiting for the primers, I attended two incredibly interesting seminars (along with one lab group presentation). In the lab group presentation, a professor from another lab on our floor that studies chronic myeloid leukemia. Even though there were plenty of gene, protein, and cell line names that I did not recognize, I always enjoy the opportunity to hear different approaches to answering scientific questions.

The first seminar I attended focused on viroimmunotherapy. I had no idea this existed, but apparently a new therapeutic approach is using genetic engineering to create “oncolytic” viruses, which directly attack and kill cancer cells while leaving healthy cells unaffected. And an even more promising treatment strategy is using viruses that help the immune system target cancer cells. If anyone’s interested, here’s a few papers on viroimmunotherapy by the Mayo Clinic doctor who presented at the seminar.

The second seminar I attended focused on dietary and behavioral modifications to avoid cancer, diabetes, and other obesity-related diseases. I honestly expected the seminary to be just a boring reminder to eat healthy foods and to get plenty of exercise. I couldn’t have been more wrong. Dr. Ruth Patterson, a UCSD professor, began by showing us her finding were nearly entirely independent of obesity, caloric intake, and exercise. Her research provided some strong evidence that the incidence of cancer, diabetes, and other obesity-related illnesses is instead correlated to mean sitting time and temporal patterns of food consumption. At this point, her research is too preliminary for her to make any lifestyle recommendations, but she noticed the biggest drops in insulin resistance among patients who stood in place for 2 minutes out of every hour along with patients who fasted for at least 12 hours after their last meal of the day. These seminars were a nice reminder of the many fields of research that intersect with oncology.

On Thursday, my primers finally arrived. This week, I only had time to set up one PCR reaction and gel electrophoresis. I'm still interpreting the results, but I think they are very promising so far. I can't wait to mess around with the reaction conditions next week, but for now here are some photos of the process! 

The bench I work at.

The PCR I set up Thursday afternoon. Everything is kept on ice to protect the enzyme used to amplify DNA. Just behind the ice bucket you can see four pipettes, which are used to move small volumes of liquid.

The thermal cycler I used to run my PCRs.

My gel just before I turned on the power supply. Each well is filled with a different sample from my PCR mixed with a blue loading dye that makes it easier to load the wells and visually check how quickly the gel is running. 

The same gel after 30 minutes at 100V. The loading dye has separated into blue and purple bands, indicating the gel is almost done.