Peddie EXP Summer 2018

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...

During Week 5, I worked on connecting the two equipments: the hydra harp and the stages. The hydra harp is the equipment that counts the photons when the sample is excited, and the stages is a moving microscope that examines the sample. Therefore, in my code, I inputted the movement of the stages, which is 3 dimensional, then I allowed it to count photons while it moves to different locations. Dr. Peretz visited me this week, and it was really nice for me to show her what I’ve been doing so far and how the lab environment is. I can’t believe 5 weeks have already passed and I only have one more week.

My third week started with me having to make sure that my hematopoietic mouse stem cells completely differentiated into macrophages, which should have taken five days to occur. Once I had the macrophages, I treated them with different ligands (low-density lipoproteins (LDL), lipopolysaccharide (LPS), and dimethyl sulfoxide (DMSO).) The goal of this experiment was to recreate the environment where the expression of a Cyclooxygenase (COX) 2 gene would become over expressed. (The COX-2 gene is induced by the LPS and LDL.) In a real life application, the environment where the cells are kept, is similar to a patient that has atherosclerosis (a cardiovascular disease where macrophages consume oxidized LDL and form plaques in blood vessels). Eventually, to observe any potential changes to the phenotype I was told to use a fluorescent microscope. Hence, from the name, I needed to take the COX-2 protein with a fluorescent that would show the presence of the COX-2 protein in the cells. (By the w...

The past few weeks in the lab were really fun. About 2 weeks ago, the lab welcomed 3 more summer students, which was nice because I wasn’t the newest one around anymore. It was cool to both be learning from my grad students and to be teaching the new student things, even if they were small. I started to truly enjoy coming to work everyday, not only because of the science, but because my lab became a little community and I was a part of it. Lab members weren’t just lab members— they were friends now too. I am really going to miss being here. One issue I faced was not knowing when I would start my project. As time went on, my project kept changing so that it would be something I could complete in my remaining time. I am currently working on determining if there is a difference in the localization of AKT (a protein kinase that has many functions in the cell) if the presence of HBV. To do this, I will be transfecting cells under different conditions, and then counting cells to see whe...

The First Two Weeks Are Complicated, Even on the Sunny Shores of San Diego As the sixth EXP student to intern under Dr. Ballatore, I have never felt more welcome when introduced to a new working environment. On the first day, I was in awe of the campus. The buildings were/are huge, the university is verdant as ever, and the student population is quite noticeable. This may be because I showed up at 9:30 AM on the first day. Similar to Peddie's campus life, it is quite lively later in the day rather than in the morning. After entering what I thought was the lobby of the daunting Skaggs School of Pharmacy, Ms. Cremonese, my PI's HR, came herself to greet me. After taking an elevator to the first floor, she made me go through a short process of regulations and requirements that are necessary for obtaining the right to work in a laboratory setting. Soon, I took the elevator back to the main floor and met with Dr. Ballatore. He decided to take me on a tour of the campus: wher...

Hey everyone! It’s been a while since my last blog post – I’ll chalk that up to being so busy these past couple of weeks with lab work and other things. Going into my fourth week at the Roy lab, it’s hard to believe that my time here is flying by so quickly already, but here we are.  After my first week at the lab, I started working on my independent project. As I mentioned before, my lab works with creating bioartificial organ devices, specifically an implantable artificial pancreas. Once implanted, the patients blood goes through the device and through diffusion, an ultrafiltrate is produced by passing the blood across a silicon nanopore membrane (SNM). (here’s a picture of one of those silicon nanopore membranes I keep talking about - the rainbow is from refracted light, not actual coloring)  This ultrafiltrate is mostly just blood plasma, but it has a couple of key ingredients: dissolved oxygen, glucose, and other nutrients. The ultrafiltrate is then fed thro...

The third week of my lab started with a testing with Elizabeth at a participant’s house. Testing was something that I always wanted to do since learning about this lab in the late fall. When I skyped with my lab PI and graduate student in December, I was told that most of the testing would be done in March, and I might only have a few leftovers to finish with a research assistant. Thus coming into the lab, I had three testing to go to. The first one was last Sunday at 12. My undergrad student Elizabeth drove an hour to get to the participant’s house, where a pair of twins and their parents welcomed us. I watched Elizabeth set up equipment (a lab laptop for the flanker test, a think binder for other cognitive tests, and a recorder). Then I sat and watched kids to play games that were designed to be cognitive tests. On Wednesday, Elizabeth and I went to a sketchy neighborhood for testing. The participant and her family were very kind to us as well, and I look forward to my last testing ...

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...

Week 3 and Week 4 After somewhat settling down in the new lab, the first couple of days were more of getting the finishing touches on the new lab. I helped the graduate students to get all the machines working such as the laser. After doing mostly basic stuff for the first two weeks, I actually started to work on my project for the summer, which is the program a machine that connects the laser and the laser platform, which moves around, to collect data from the samples. Through week 3 and week 4, I mostly went in and out on this project. I did a lot of coding, but I also helped other graduate students with their own projects. For instance, I helped Anu, a graduate student in my lab, collecting graphs and peaks of samples using spectroscopy. While doing this, we had to use liquid nitrogen in the process. Therefore, we played around with liquid nitrogen. I also helped other graduate students collecting data. We also had a lot of fun. Since I am a really big soccer fan and I ha...

My lab centers their research around the study of Giardia, a parasite that infects the small intestine. Giardiasis, the disease caused by Giardia, often leads to Irritable Bowel Syndrome (IBS). In the late stages of Giardia and in IBS, high levels of serotonin (5-HTT) are present. We are confident that this is what links the two diseases together. Our first step in answering all of our questions is determining what causes high levels of serotonin in Giardia. One theory we have is that high expression and presence of the serotonin transport protein (SERT) causes higher levels of 5-HTT. To do this, we are trying to stain difference cross sections of small intestine of infected and non-infected mice to determine the changes in levels. To do this, we must use the art of IHC. Immunohistochemistry (IHC) is about finding the perfect blend of antibodies, chemical washes, bead baths, and various other factors to produce the result you want. Over my two weeks here, I have been told constantly t...

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...

My first week at the Center for Solar-Terrestrial Research at NJIT went (luckily) almost exactly according to plan. After moving in to my room less than a block away from my lab, I had a weekend to contemplate my new home. I would say explore, except, being in Newark, there hasn’t really been that much wandering around. Newark is honestly a rather boring city. Nobody wants to visit, all the stores are closed on weekends and after 6 pm, and pretty much everyone flees to New York City on the weekends. Luckily, a light rail station a block away from my dorm makes that very convenient. I had already gotten an overview of my research over email, and that was confirmed by my PI, Dr. Wang, upon my arrival to the lab. I would be working under Dr. Jing, a research professor, for the first part of my research, when I looked at H-alpha images. These are the emissions from a specific spectral line created by hydrogen. By comparing red- and blue-shifted images, I created a dopplergram. This is an...

I have actually visited my lab two times previously, and the last time I went was around the beginning of May when they gave me the materials to use for data collection. Since my project has to do with measuring facial recognition abilities in adolescents, I have to do a lot of work from home to meet with people around our age. So, last week I did data collection from home (didn't think it would be very interesting to blog about since I didn't get to actually to into the lab) and this week I had a substantial amount of data to go into the lab and enter into the program. The first thing I did when I got to the lab was meet with the secretary, Stacey, who showed me where to sit and then began showing me how to enter data into the master spreadsheets. Each individual has to fill out two personality questionnaires and then complete a facial recognition “game” on my laptop. She got me settled into my desk and gave me instructions on how to enter all the information from the questi...

As I entered my lab at 9:30 on Monday morning, I was surprised to see only one other person in the lab, an undergraduate student.  After introducing myself, getting my Penn ID, and taking a tour of the lab, the undergraduate student gave me literature to read and basic mat lab tasks. Overall, my first week at the lab consisted mainly of reading literature.  In fact, the first assignment that my Post Doc had given me was to read 10-15 literature articles on past studies that studied creativity, found different areas of the brain associated with creativity, or were able to increase creativity.  Then, I had to present a PowerPoint on Friday based on my findings.  Initially, I was upset since I felt like I would be reading literature for the entirety of my time at the lab.  However, in expressing my desire to do more “hands-on” research, he explained that after thoroughly researching past studies, I would be conducting my own similar experiment in relation to m...

**Sorry for the weird format, Blogger did some weird stuff to my post that I had to fix** After an action-packed first week, it was time to get down to business. When I walked into the office on Monday morning, nobody was there. I made efficient use of my morning by reviewing additional safety modules. The second module was a laser-focused course, so I completed it within the hour, making me eligible to attain a lab key. I submitted my request for a key and by noon I was completely finished with my orientation-related tasks. Being fully acclimated to the lab, I made productive use of my time. Each morning, I worked with Chris on coding and developing some models to depict the behavior of the MDCS Analog. Each afternoon, I worked with Grace on the laser experiment. I am surprised at how my knowledge of Python has increased 10-fold in just these short two weeks. My confidence is soaring, enabling my ability to contribute to the project. Cesar has been monumentally helpful...