Week 7: Finished in the City

Tibra Wheeler

Seven weeks down, zero to go. Here we are at the end of the road. This point of the summer came waaaaay too fast. Over the weekend, I went to Queens to celebrate national cheesecake day at the Cheesecake Factory with half price slices. I also enjoyed catching up with old friends and exploring the lower east side of Manhattan. This week was mostly spent wrapping things up in lab as well as checking more things off my “things to do while in NYC” list.

Monday was a very laid back day. That morning, I worked more on the segmentations in ITK-Snap. Once I got to a stopping point with the segmentations, Kirsty gave me the RNA expression data that we collected last week so that I could make different plots in Graph Pad Prism (this really nice software that allows you to create really pretty graphs of your data). Our plots graphed the Ct value ratios of the housekeeping gene we chose against the particular gene of interest for each of the groups. The Ct value is the cycle threshold, which is the number of cycles required for the fluorescent signal to cross the threshold; the Ct value is proportional to the amount of target nucleic acid in the sample. After plotting the data, I met with Kirsty and Tony to go over the plots as well as to talk about my presentation for lab meeting. They both gave me slides that I could include in my presentation as well as feedback as to what I could add and what I could talk about. For the rest of the day, I worked more on the segmentations, but with the Seg-3D software.

That evening, we went to dinner at the Burger Joint. I had a great tasting burger and followed with some gelato for dessert. I got gelato from Amorino, the place where they serve the gelato in the shape of a flower in a cone. I went with two classic flavors – vanilla and strawberry. After dinner and dessert, we went to see the musical Chicago on Broadway. This was my third (and probably final) Broadway show since my time in NYC. Chicago was definitely a great “last show” with all of its great songs, witty lines, and humor.

Tuesday turned out to be another “chill” work day. In the early part of the day, I focused on putting together slides for my presentation for lab meeting. At first, it was a little challenging because there was so much that I wanted to talk about and include, but had to keep in mind that I have a time limit to present. Once I figured out the story that I wanted to tell with my slides, they came together nicely. That afternoon, I met with Tony and Kirsty to go through my presentation and get more feedback as to what I chose to include in the presentation. It was very helpful to go through all the slides with them and get clarification on some of the techniques and reasoning behind why we use those techniques. They also gave good input on how I could organize my slides to make the “story” flow better. After I went through my slides, I briefly met with Mehdi to get some help with the Seg-3D software as well as to show him the segmentations I had done in that software so far. 

No fancy dinner or dessert Tuesday night because I went to the J. Cole concert in Brooklyn shortly after my meeting. We grabbed burgers from Shake Shack (because it’s so close to Barclays Center) & headed to the arena. This is only my second major concert in my life and it was amazing. J. Cole is one of my favorite music artists so it was perfect that his tour was stopping in Brooklyn while I was going to be in the city. It was so much fun singing along with all the songs I knew and watching him perform live. That night was definitely one for the books. I ended the night going back to the dorm to implement Tony and Kirsty’s suggestions in my presentation because I had a meeting with Dr. Maher the next morning for her input as well (to play hard you have to work even harder).

Wednesday morning, I met with Dr. Maher to show her my presentation and get feedback from her about my slides. Overall, she was pleased with the presentation and only had a few minor suggestions. She gave me some background slides that I could use in the MRI segmentation section of my presentation. She also suggested that I get some papers from Kirsty about the gene expression primers that were chosen as next steps for that project. This would help me to incorporate some literature review in my presentation. After my meeting, I decided to work the rest of the day from home. Kirsty sent me the papers to read so I read over them and worked more on my slides. I also did some more segmenting and worked on exporting my segmentations into 3D models so that I could also add those to my presentation.

For dinner that night, we went down to East Village to Tacos Morelos. I’m more of a quesadilla person than a taco person so naturally, I got a quesadilla. After a tough decision, I decided on pork carnitas as my meat. The quesadilla was filled with so much cheese and had cheese sauce on the top, but it was really tasty. It was also a pretty big quesadilla so I was only able to eat 2 triangles of it (plus we had eaten chips and salsa). The waiter said he would box it for me so he took the plate. I totally forgot about getting the box from him before we left so I was a little bummed that I wasn’t going to have my leftovers. But to make up for it, we decided to go get dessert from Odd Fellows Ice Cream Company. We decided to get an ice cream flight which came with six scoops of varying flavors of ice cream – Olive Oil Strawberry, Peanut Butter & Jelly, Pineapple Ginger Lemonade, Thai Iced Tea, Saffron Passion Fruit, and Milk Chocolate Peanut. My favorite was the Olive Oil Strawberry. I wish we would have tried this ice cream place sooner because they have so many fun flavors that they change daily.

Finally, the big day came – presentation day! Thursday morning, I gave my presentation in lab meeting. It was nice to be able to sum up my summer work and present it to the lab. It’s a little nerve-wracking presenting to a room full of MD’s and PhD’s because you never know what kind of questions you’ll get asked. Everything went well, but I was glad when I was done and could sit back and listen to the other presentation. After lab meeting, we went to our program meeting where more summer students presented their summer research followed by a “farewell” lunch for us as thanks from the department. That afternoon, I met with Mehdi and Farrah; Farrah is going to be taking over the segmentation project that I was working on. We went through the Seg-3D software so that we could both be more familiar with it. We decided that I should continue doing the rest of my segmentations in Seg-3D for the data that I have. Shortly after, Kirsty went over the primer optimization PCR plates that another student had done earlier this week with me so that I could better understand what was done and what the data means. Then, she gave me the data to organize in Excel.

That evening, our immersion group had dinner with Dr. Min and Dr. Prince at Petaluma. It was great to be able to interact with them in a more casual setting. It also gave us the opportunity to talk about ourselves a little more outside of our research. The restaurant had great appetizers which were served family style – salad, Margherita pizza, and linguine. There were a few entrees that we could choose from so I decided on the Hanger Steak (& per Dr. Min, it’s a rare cut of meat so it was treat). The steak was delicious and came with a wonderful au jus. Dr. Prince then ordered dessert for everyone so he must know we’re a dessert kind of group. The dessert platter came with varying cakes, cheesecakes, cannolis, and fruit. We ended the night celebrating the close of immersion.

Today is my official last day working at HSS in Dr. Maher’s lab. It’s very bittersweet because I have really enjoyed my time in this lab and learning some new techniques. Tony and Kirsty were amazing researchers to work under this summer. Like the last day of school, there wasn’t much planned for today as far as lab work was concerned. We went to get lunch together at Felice 83. It’s still restaurant week here in NYC so we got a three-course meal there so we were all very full after. We decided to walk along the river on the way back to lab so it was a nice change of scenery. When we got back, another student in the lab was working on the primer optimization so I offered to help. Once that was done, it was time to say my goodbyes as my last day at HSS came to an end.

My summer immersion experience was one for the books. I found a good balance between learning new things in lab, getting some clinical exposure, and finding out what the city life had to offer. I’m looking forward to possibly working with Dr. Maher (along with Tony and Kirsty) in the future on possible collaborations.

This summer has been so fast paced in the city and I will miss that once I get back to Ithaca. I will most definitely miss all the great food and desserts that came along with NYC. However, I will not miss all the traffic, all the honking cars, all the construction, and most importantly all the expensive boxes of cereal.

Thank you, NYC for showing me a great time. You will be missed but all good things must come to an end. It’s time for this girl to go back home to South Carolina for a couple weeks to get rejuvenated to head back to Ithaca because the real work is just starting.

Catch me back in upstate NY, how bout that?

Sidenote: I guess the longer I was in the city, the fewer pictures I remembered to save from Snapchat. So unfortunately some things will have to just stay memories.