Peddie EXP Summer 2018

We finally did it: an optimized IHC protocol. Peering into the microscope to see the bright red below was an amazing feeling. The SERT was glowing like a Christmas tree. Our procedure incorporated two new elements that helped us achieve the finished procedure: pre-heating of the slide and antigen retrieval. Before beginning the slide washes, we heat the slide in a 55 o C water bath. This makes the slide more susceptible to the treatments we use. To complete antigen retrieval, we place the slides in .1 M citrate buffer and then heat it, using a 100 o C water bath. This exposes epitopes that were covered in the making of the slide. Therefore, the tissue is more susceptible to antigens. With these two new steps, we were finally able to see the SERT, in Cy3, and the background staining, in DAPI. However, one pitfall of our microscope is we can only look at one contrast at a time. This forces us to take separate pictures of each contrast and overlay them in photo editing (picture of inf...

Hello good people! Are you ready to read lots of science? Because today I'll be describing my research in more detail. So, let’s get right to it. These past two weeks I’ve been working with a grad student, Nengyi, on the more advanced section of my project. In this part, I’m looking at the data that’s been gathered and trying to find interesting trends. Specifically, I’m finding an approximation of the total redshift at specific points based on spectrograph data, which tells us how the plasma at that point is moving. By studying this redshift we can see how the flare loops move, and whether there’s anything interesting to analyze there. This involves the data from the IRIS satellite, which has a built in spectrograph. A spectrograph separates light by its frequency. Because different elements put out different wavelengths of light when energized, we can isolate specific elements and analyze their bands. Here’s an example of the different bands for some random elements ...

It’s official. I am halfway done with my EXP trip, and I don’t think I could have fit many more activities and work into the three weeks I’ve been here so far. Things are going wonderfully. Michigan has been treating me well, and the weather has been immaculate. Science-wise, not a ton has changed with the laser experiment. This week, Grace and I finalized our optics setup by installing the Rubidium cell (basically an enclosed glass tube with Rubidium) in line with the laser’s path, as well as place a photodetector at the end of the optics setup to get readings on the interactions with the laser and the cell. I will get a picture next week when everything is aligned once again since this week was full of pain-staking laser alignment. The caveat of using a Fabry-Perot involves SUPER precise alignment. There is a very small point of entry that the laser beam can enter and exit through the cavity within the optic. Thankfully, Grace taught me the most efficient and useful me...

I was given the project of web development. I would create simulations of various search algorithms such as Dijsktra, A*, and Weighted A*, and in the end, hopefully upload them to my lab's website. Over the past week, I spent a lot of time reading articles on the inner workings of these algorithms and even more complex extensions of them- algorithms like ARA* and Multi-Heuristic A*. Once understood, these algorithms all seem very intuitive in nature and follow a clear logical process (like Djisktra is just repetitively adding the closest neighboring node to a final set of nodes and then updating the neighboring nodes' distance values), but writing them in code isn't simple for me. I've also been using data structures that I haven't touched before, such as priority queues. I tried my hand at implementing A* and Djisktra in Java, and will soon convert my code into Javascript so that it can work as part of a Javascript applet and be used on the web.

This past week I began my data exporting from the NIDA database CDW (which I frankly have no definition of) which is a compilation of clinical subjects that have been a part of past protocols. While many of the interns I'm working with are dealing with one or two protocol groups at a time, I'm dealing with all of the neuroimaging branch data. To compile this data, I learned VLOOKUP, an excel function, which isn't a huge feat but sometimes I think a computer is broken when really the monitor is just off. I would also like to thank Dr. Cags for boosting my excel confidence during all of calculus this year. So I get excited, VLOOKUP all my data points, delete the missing data/persons for which they belong, and feel like an absolute #boss. I was mildly concerned by the fact that I had pared 1,000+ persons to a concise 64, but generally overlooked it and straight away emailed my PI ready to export some more. Well, needless to say, 64 was not the right number. Parsing through s...

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...

During my third week in the lab, I got the chance to do some work instead of just learning techniques. On Monday, I got to make the media for the HepG2 cells myself. This is media contains all the things the cells need in order to grow and proliferate for a few days. On Tuesday, both the grad students I follow were out sick. However, this was a problem because Danyelle, one of the students, needed to be in the lab to finish her western blot. This left Dara, a masters student, and I to finish it for her. Although it wasn’t a lot of work, Danyelle believed we were capable enough to finish her work for her. Later in the week, I started to do more and more things by myself. I got to run my own western blot (just with old samples), and I was excited to see that it worked (mostly). I also got to do a transfection with two plasmids, which also worked well. I’ve learned so much in my 3 weeks here, and I can’t wait for 3 more. Western Blot GFP transfection after 3 days