Week 6: Pipetted in the City

Tibra Wheeler

Flashbacking to the 90’s this past weekend was really fun but back to the 21st century for this girl this week. Over the weekend, we also went to Coney Island. We ate “The Original” Nathan’s Hotdogs, rode the 90-year old wooden roller coaster the Cyclone, visited the New York Aquarium, and walked along the boardwalk. The end of immersion is quickly approaching so this week was time to really focus on what goals I wanted to reach by the end of next week. It also means trying to fit in every tourist thing, every restaurant, and every dessert I want to do before I leave NYC.




Monday was a day for me to do some more touristy things with some friends. We decided to take the Statue Cruises to Liberty Island and Ellis Island. I was really excited to go see Lady Liberty as well as visit the Ellis Island Immigration Museum. Unfortunately, tickets were sold out to go inside the Statue of Liberty, but it was still an experience. I’m also pretty sure we picked the windiest day of the summer to go on the ferry to the island, so we had to do a lot of hair adjusting for pictures. Nonetheless, we made the best of our time. It was really interesting to walk through the immigration museum and see the process that the immigrants had to go through when coming to the United States. While walking through, we saw a historical poster that was announcing the sale of slaves. The poster was something that had come out of a newspaper in Charleston, South Carolina, which is basically home for me. I thought it was cool that even all the way on Ellis Island, there was a piece of history that I could relate to. That evening, we had dinner at Nocello which is a cozy little Italian restaurant. The food was AMAZING – homemade fettuccine noodles in a from scratch alfredo sauce with grilled chicken. We followed dinner with dessert from Buttercup Bakery. I decided on their infamous sea salt caramel cupcake and I wasn’t disappointed.



It was back to the grind on Tuesday. I picked up continuing with the RNA isolation protocol. The steps in the part of the protocol we did that day were to help isolate the RNA from things we don’t want in our final RNA product like proteoglycans. This consisted of adding chemicals to the RNA “smoothie” that we had homogenized on last week, centrifuging the mixtures in columns, and repeating. Lastly, we had to clean-up the RNA and freeze thaw the samples to use the next day.

After lab, some of us decided to get dessert before dinner. We went to the Doughnut Project and I got a lemon love letter doughnut. It was the perfect mix of lemon with an original glazed doughnut. For dinner, we got falafel from Taïm. This was my first time having falafel so I got the sampler to taste the three flavors they had. I was not a fan of their green or olive falafel, but their harissa falafel was tasty.

Wednesday was a day full of pipetting. We began by running reverse transcription on the isolated RNA samples from the day before. This is the same process we did last week, in which the RNA is converted into cDNA. After the reverse transcription, the real pipetting began. We made two PCR plates to run six different primers on the newly synthesized cDNA. To put this into perspective, each plate has 96 wells, each well gets the cDNA and a master mix of primers, water, and dye – so that pipetting into each well twice or 192 times of pipetting for each plate! Needless to say, my thumb was a little sore after the two plates were done, but I was very efficient with the process once I got to the second plate. That afternoon we ran the first plate on the PCR machine.




I finally got to try Luke’s Lobster for dinner. Because I’m so indecisive and love seafood so much, I got the Trio which came with three half rolls each filled with lobster, shrimp, or crab. If that lobster roll was really indicative of lobster rolls in Maine, then I’m definitely going to have to take a trip up there soon. After dinner, we wanted to get cupcakes. We decided on Baked by Melissa which serves mini-cupcakes in fun flavors. I chose the caramel cone, cookie dough, tye-dye, and love is blue (filled with vanilla cake batter!) flavors. Although they were very good, they were gone way too fast.




Thursday morning was filled with our weekly lab meetings and floor meetings. That afternoon, we started the second PCR plate on the PCR machine. While that plate was running, Kirsty showed me how to export the data from the first plate off the computer and how to start sorting through it. She showed me how to edit the plate plan to match up with the wells of the plate that was run. She also showed me some key things to look at initially to make sure there wasn’t contamination with the primers. Once we did these initial things, I went in Excel and organized the data by the primer that had been run and the values returned from the PCR. Also, that afternoon, I had a meeting with Medhi about the segmentation mini-project I’m working on. I showed him some of the segmentations I had done using ITK-Snap and he gave me feedback on how I could improve them. He also showed me another program that he just learned about that is good for segmenting biomedical images. The program is called Seg-3D so I’m going to do some segmentations using that program to see how it compares to the segmentations that I have done in ITK-Snap.

For dinner, we ventured up to Harlem to go to Amy Ruth’s. The restaurant is known for their chicken and waffles, but they serve all the southern comfort food that I basically grew up. I reluctantly ordered a sweet tea, but to my surprise, it was probably some of the sweetest sweet tea I’ve ever had (and yes that’s including tea I’ve had in the South). The food was sooooo good and the dessert was even better – a warm sweet potato pie. This meal made me feel like I was home again.




This morning we had our final weekly immersion meeting with Dr. Min and Dr. Prince. We got some good insight on the patent process from the two of them so it was interesting to get a clinical view of inventions and patents. After the meeting, I met back with Kirsty to get the data from the second PCR plate to organize it in the Excel spreadsheet with the other data. I also had a meeting with Dr. Maher to just update her and get her input for a presentation I’m giving next week. We talked about which project I should focus on for the presentation and the message that I should try to convey. We’re going to meet next week as well to go over the slides I put together.


I’m not sure what is in store for this weekend, but I’m sure the city won’t let me down. Here’s to hoping time slows down a little before my last week is here!




*images taken from http://www.biorad.com/webroot/web/images/lsr/products/amplification_pcr/sku_view/global/HSP9601_view.jpg and http://media.biocompare.com/m/37/product/3132623-400x300.jpg

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