Jaewon Oh - Week 2 and 3

So there still hasn't been any updates on the shortage of ALK data on neuroblastoma. So instead of moving forward with this project, I focused on the TP53 project. As I mentioned in my previous post, I have been learning how to use the coding language "R" in order to manage and analyse large sets of data. The data I have been looking at contains functional assessments of mutations at specific codons and their resulting amino acid change. I was looking into whether the mutations resulted in a gain or loss of function in the TP53 gene and was aiming to eventually compare these results to the selection intensity data my lab had provided for me. However, before I did the final step, Dr. Cannataro had sent me another paper to look at. (End of week 2)

Now when week 3 began, I began reading another p53 paper. This paper, however, focused on RFS values. RFS values, short for relative fitness scores, represents the survival rate of different p53 variants when they were cultured together. Data on these RFS values were found in the supplementary information section. I then proceeded to compare these RFS values with the data provided by my lab (selection intensity, frequency of mutation, and proportion of mutations in specific tumors). There is not significant overlap that occurs between these two data sets, but when there is, there are positive correlations between the values. But there is a problem. With the lack of data, some values may repeat themselves. For example, a data set may include multiple RFS values for the same codon number and mutation, but because the other data set only contains one selection intensity, Rstudio (platform for "R"), will input the same value for each data point. This is an issue that will have to be addressed next week.

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Evan Bradley, Week 3 at the Missouri Orthopaedic Institute

As mentioned in my previous blog, I have been awaiting ligament, menisci, and cartilage tissue from a canine or human knee joint for (interleukin) IL-1B tissue culture. IL-1B is an inflammatory cytokine that has been proven to increase rates of tissue degeneration and osteoarthritis development in the Thompson Lab. Dr. Stoker wants me to experiment with different types of knee tissues in a co-culture with varying levels of this cytokine to determine its effects on the entire knee joint. This co-culture uses an insert permeable to the media to separate the two tissue samples from physical contact, while allowing them to share the same media. This creates an extremely accurate model for knee tissues in their native environment due to their exposure to the same synovial fluid in the joint. This model would then be treated with the IL-1B and cultured for 21 days. During these 21 days, the media would be collected every three days for biomarker evaluation at the end of the stu...

Kylie Heering, Week 2 at the Goldstein Lab

We started off our week with a congratulatory acai bowl trip to celebrate Preston’s acceptance into a training grant program. Acai bowls in California top Playa Bowls (no question about it). From what I can tell, its a pretty huge honor to be recognized by this grant, but he’s really humble about it. On Monday, Preston and I decided that testing antibodies that have never been tested on prostate epithelial cells before would be a good objective for my first Western blot on my own. We needed to probe for ASCT2, a glutamine transporter, and GLS in order to determine if their corresponding antibodies are functional. Antibodies are crucial for Western blots because they bind to the protein of interest (POI), allowing for us to qualify its expression after imaging. As such, Preston wanted to make sure they worked by probing for ASCT2 and GLS on three different cell lines. Cell lines are commercially purchased human cells that have been immortalized (modified to grow indefinitely) by telome...

Daniel Cheng, In My Own Room

I had no idea that Pennsylvania is this wide. Within the first hour, my train had reached Philly. But to Pittsburgh, it took another seven. Even before I stepped foot into the Search-Based Planning Lab, I was waylaid by some anxious news. The PhD student assigned to be my mentor, Dhruv, texted me that he, Dr. Likhachev, and most of the lab would be out of town for the entire week. So that was that. Fortunately, it was my first week, the week to be spent learning new material, and Dhruv provided me with plenty to digest. I already had ROS (Robot Operating System) installed, so I looked towards the tutorials that ROS provided. I copied commands into my Linux laptop's terminal to run ROS features. I learned the basic structure of ROS: packages, services and clients, publishers and subscribers, messages, nodes, and topics (which nodes communicate messages over). There was one simple yet interesting program I came across in the tutorials called turtlesim, for which using only 2 comm...

Peddie EXP Summer 2018

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