Katya Chyzhyk reports on her experiences at the Vanderbilt University Summer Institute, where she is studying “Genetic Detectives: Stray Cats Paternity and Predator Trails.” After settling in in at her dorm, Katya met with the other students over dinner and a series of ice breakers including an orientation presentation. On the first day of class, Katya met her academic proctor Caleb, a Junior at Vanderbilt University, her Professor Dr. Thomas Clements, his wife, Dr. Katie Clements, and her TA, Aiyana Cyr.
“We began with some lab basics and learned how to use micropipettes—specifically how to set them to draw different amounts of liquid and convert between microliters and milliliters. I started keeping notes in my lab notebook and downloaded the app and Chrome extension for a scientific article management platform called Zotero. It was very convenient to use for saving scientific articles, and I am sure that I will use it after this program ends,” Katya explains.
“Caleb led us to lunch at Rand, and after we got back, we started with some statistical analysis and probability work to model some of the principles of genetics. Our worksheet explained random assortment during meiosis as flipping a coin, and the law of segregation as the coin landing on only one side. Although I have had plenty of experience with these laws during Advanced Biology and AP Bio, I had never had them explained to me like this, which was an interesting perspective to consider. We then continued with some probability problems and began chi-square analysis, which I had thankfully just reviewed in my BIO 102 class at John A. We finished with goodness-of-fit and t-tests in Google Sheets, and analyzed Mendelian inheritance patterns in corn,” Katya adds.
“I knew that we would be doing some lab work in class, but I was not expecting to begin PCR (polymerase chain reaction) on the second day of class. Dr. Clements and Aiyana immediately began “PCR Boot Camp” to teach us how to compare the lengths of different DNA segments. Some DNA sequences can be different lengths, but family members would have strands of similar lengths because they are obviously related. True to half of our program name of Stray Cat Paternity, we would begin testing the lengths of DNA sequences of potentially related cats to determine paternity. Our first PCR reaction didn’t work that well since we had too much indicator in our gel solution, but the bands were visible enough that we could understand the gel electrophoresis. The PCR tubes took 2 hours to incubate and the gel electrophoresis took half an hour to run, so my class had ample downtime to play impostor and get to know each other better. We ran a second PCR/gel electrophoresis reaction after we returned from class, and that reaction was vastly more successful,” Katya reports.
“Dr. Clements introduced us to another technique on the third day: DNA extraction. This lab was essentially the common and simple strawberry DNA extraction lab, but with harsher chemicals and the possibility of extracting DNA from anything. We practiced extracting DNA from Aiyana’s dog Pipette, which involved a lot of pipetting and incubating again. However, this time something unfortunate happened: I got burnt by phenol! The DNA extraction used the chemical phenol to separate DNA from lipids and proteins. Unfortunately, the pipette had a few drops of phenol on it when I picked it up, which sprayed on my arm and lightly burned me. Although I was fine after a couple seconds, the PTY nurse was very worried and asked Vanderbilt Student Support to take me to the Vanderbilt walk-in clinic after lunch to make sure I was really okay. I ended up having to miss most of the second block of class for the clinic visit, and had to finish my DNA extraction the next morning,” Catherine explains.
When not in class, Katya and friends spent time exploring the city of Nashville, and its many restaurants. “The bus drove through Broadway on the way back to campus, and seeing that iconic part of Nashville lit up and crowded with people at night was a highlight of my evening. That night’s Community Hour activity with students from VSI and VSA (Vanderbilt’s one-week program) was tote bag decorating, so I stayed out a little later than usual to decorate a super cute tote bag with jellyfish to bring to the farmer’s market on Saturday,” Katya says.
“I finished my DNA extraction the next morning, which involved some ethanol precipitation, and then we began the actual cat paternity testing. Dr. Clements provided us a master worksheet guide of how genes influence cat fur coat patterns, which was very extensive and took multiple note-taking sessions for me to digest. However, I feel like identifying cat fur pattern genes is a pretty unique party trick that I will be using in the near future. This worksheet included a cat family tree of Dr. Clements’ friends’ stray cats, who we were were analzying for familial connections. We had to figure out if Midnight the cat was really the father of all of Fertile Myrtle’s 6 kittens by using fur pattern possibility analysis as well as paternity PCR testing. My group began PCR testing on Midnight, Winkin the kitten, and Dr. Clements’ late cat Kevin to act as a control. Class was filled with more class bonding as our PCR reactions ran,” Katya adds.
“Our final day of class this week was when I finalized my cat paternity predictions and realized that Boca and Brownie definitely couldn’t be Midnight’s children, as they had tortoiseshell fur patterns, which required at least one orange cat parents. Midnight was a black cat and Fertile Myrtle was a grey van cat, which meant that Boca and Brownie’s tortoiseshell pattern genes must have come from a different father. Our last reactions were PCR-based familial exclusion, where DNA sequences that are repeated several times are amplified and their length is noted and compared to potential familial matches. We ran 2 PCR reactions that day, each with different primers that amplified different DNA sequences, but we noted that Midnight and Winkin were very likely a genetic match because of how similar the lengths of their specific DNA sequences were. I definitely felt more comfortable pipetting into the gel wells for electrophoresis, and our PCR reaction was the most successful it ever was. We celebrated our extremely clear PCR photos by taking pictures on my friend Dhiyana’s digital camera when we had downtime during class,” Katya explains.
Weekend activities included a late breakfast and a trip to the Nashville Farmer’s Market, followed by a clay watercolor activity, and a group “lip sync battle” competition.
“This week has been exhausting but very fun and engaging—Vanderbilt PTY has definitely met and possibly exceeded my expectations for a summer program set in place by UChicago! Overall, I’ve felt very welcomed and supported by every staff member at PTY. All of the residential and academic proctors are very serious about ensuring our comfort and safety, while my professor and TA are real experts in their field and are always eager to share their knowledge and hold enriching conversations with us students. Although I do not have a lot of work outside of class, my class itself is very engaging and has a lot more hands-on lab work compared to other classes such as Physics or Neuroscience which are more demonstration and lecture-heavy,” Katya reports.
“Outside of class I’ve made great friends with almost all of the girls in my proctor group, and appreciate their constant support whenever I see them around campus and at meals. Vanderbilt PTY have done an excellent job of simulating the college experience, creating opportunities for us to connect with people during class (our academic groups), as well as connecting with people at our dorm (our residential proctor groups).I am never bored at VSI; I’m always connecting with new people and strengthening my connections with familiar friends through engaging in-class and recreational activities, and can’t wait to see how the camp continues next week!
We are so happy to hear that your experience at Vanderbilt University has been both fun and engaging and look forward to hearing more. Good job, Katya!
