Work Is Good, Work on Fridays Are Even Better

Today was the most productive day of class I have had so far! It wasn’t that we don’t normally get things done; we obviously do a lot of labs and lectures everyday – it was just we did so much today. I’m very proud of both myself and our whole class. Even though it was a Friday, everybody was cool with staying late to finish work, and I didn’t even notice the time until I went back to the dorms.

To begin with the morning, we went to the lab first to continue yesterday’s DNA sequencing and modeling experiment. Everything that we had left to do was all virtual, so we did not do any actual experiment lab work in the entirety of the morning. However, as with yesterday, tinkering with the software was still somewhat of a struggle, even for our TA, Rebecca, so I guess one day really wasn’t enough for everything to sink in just yet.

Elaine and I had a lot of trouble identifying information about our specific mutation looking at the program’s model. Eventually, we called Rebecca over, and she was confused by our mutation as well. From a reference chart previously provided to us, we were told to expect our mutation to interact directly with the rifampicin. Yet, Rebecca agreed with us that it looked like the modeling showed a slight gap between the electron clouds of rifampicin and that of the mutated amino acids, which was contradictory of what we should see. There appeared to be no rotamers, steric hindrance, nor other interactions happening directly with rifampicin, puzzling all three of us greatly.

DNA modeling

With Rebecca’s guiding, Elaine and I were able to determine that our mutation does interact and form hydrogen bond with other amino acids around it, but that still did not explain other unexpected characteristics of our mutation, so we had Dawn take a look at our model as well.  

As it turned out, our group’s mutation did not make sense because it was a semi-novel mutation. This means that our mutation for rifampicin resistance on the bacterial gene was found where it was expected to be found, but the gene did not mutate to a known sequence, which was why the reference sheet did not match our actual modeling results exactly. Because this mutation was new or perhaps just rare, we had a bit of ambiguity and anomaly within our results.

For one, Dawn thought the electron clouds in our model were connected and overlapped. However, after we discussed it with her, we rotated the model several ways and we eventually found the gap between the clouds that Elaine and I saw. Dawn agreed the gap did seem large enough to be considered indirect, but the electronegativity and proximity of the clouds also make it possible for the mutated amino acid and rifampicin to interact directly. It was something we could argue either way in our lab report.

By the time we got all this figured out, it was time for lecture. We had a five minute break to walk to the class, and then we began our lecture on HIV. It was very interesting as usual; we covered the origins of the HIV virus and how it spread to become the epidemic it is today. What stood out to me the most was that some people were naturally resistant to HIV. They lacked CCR5, a kind of receptor on white blood cells, and the lack of this receptor renders HIV unable to infect any host cell in a human. I hadn’t known about this before, which was why it was especially interesting to me. There was actually someone who was cured of HIV after a bone marrow transplant, which is a phenomenon. However, during the lecture, we also discussed the reasons why bone marrow transplants will not work as a viable option for cure.

After lunch

We were allowed to go on our lunch break at 12:15 PM, which was much later than we usually get out for lunch, but honestly, I was so enthralled by the lecture that I didn’t notice the time (nor did I get hungry). We went back to the lab at 1:45 PM, where we preformed the ELISA test, which tests for HIV. Rest assured, we did not work with actual HIV samples; it was all fake.

The ELISA test was not actually that complicated; however, it was a lot of pipetting and waiting for reagents to be incubated, which was why it took very long for us to complete; our class didn’t get out until 4:30 today. During this time, the class worked on lab questions as we waited.

Unfortunately, some of my samples did not turn out right, which might have been due to contamination when I forgot to change the tip on the pipet for one of the steps. It stilled worked somewhat, and we took a picture of one of the only two groups whose samples came out right, so Elain and I are set for answering lab questions.

My results for the ELISA test

After we were done with the lab, I stayed behind a bit to talk with Dr. Fineschi. I found out that she came from Italy, where she went to college in, until she moved to the United States to get her master’s, not knowing much English. I think that it was incredible she worked so hard from barely knowing a word of English to getting into UChicago, getting her PhD, and now, she teaches at UChicago.

After I went back to my dorm, I was completely exhausted, but I still went to the gym at 5:50 PM, although I wasn’t up for anything too rigorous. I ate dinner, then returned to the dorms and I caught up with some friends. I then accidentally napped a bit before I wrote my blog.

Tomorrow, we will be meeting Ms. Sciacca for our weekly meet ups, and if I’m not wrong, Kara and Michelle will coming with us again – the more the merrier, I suppose, and with so many people, we’ll be sure to have lots fun!