Peddie EXP Summer 2018

The past two weeks at the MOI have been packed full of 12 hour days due to the influx of rat and canine models from the vet school. The vet school students practiced their necropsy techniques and sent over 8 rat models at the beginning of week 6 and 3 canine tails on week 7. With the arrival of these new rat models and canine tissues, I had to harvest all of the available tail IVDs, place them in the flexcell plates and vacuum system, culture them under load for 6 days each, and perform media changes and the end-of-culture procedure. The lab also had an MOI organized study day this week in which I was one of the first five people in the world to evaluate a successful ACL to ACL allograft! I received the 8 rat tail models on Monday of Week 6 and immediately started the harvesting procedure. All of the harvesting procedures for IVDs have to be performed sterilely, so I had to lay sterile mats in the hood, gather all the necessary sterile equipment, and use sterile gloves. I used a sc...

Throughout the 7 weeks that I've been at the lab so far, I have helped dissect a litter of mice approximately once a week. Since my lab is half-spinal-cord and half-gut, I have learned how to dissect everything from the small intestine to the cerebellum, which is pretty cool. The process for each is quite different and I'm grateful to have had the opportunity to learn and practice both. Today, Anna and I perfused and dissected a litter of P6 mice for the spinal cord and cerebellum, and we have definitely come a long way since my first dissection in the lab. If you read my post on week 4, you'll know that I was sorta stunned by seeing a living being die before me. Seeing a mouse go from running around in its cage to pinned down and getting cut open is something I definitely had to take time to adjust to. But at this point, I've become so used to it, I wasn't even phased when I ripped out the organs from a headless mouse and cut off its limbs. Although I'm not ent...

Week 1 (6/25/18) and Week 2 (7/2/18) This marks the end of my official second week in the lab. The first few days that I came to NJIT I was only watching my mentor, Purva, complete the experiments because my paperwork hadn’t yet cleared. In order to work at the New Jersey Institute of Technology as a high school student, one must also apply for and take part in their Provost Summer Research High School Internship Program. This program is very similar to EXP: we will learn lab safety, how to find and read primary literature, and at the end must write a research summary accompanied by a powerpoint presentation. Luckily for me, through EXP I have already done most of the legwork when writing the research proposal, so finding sources will be no issue. I feel prepared, if not, overprepared, to complete these requirements. In the lab, however, I immediately felt uncomfortable – unprepared, even – while standing there, watching Purva complete the experimental routine. I felt gawky and bu...

I feel like there are two essential parts of coding. One is coding, and the other is the shameless act of talking to an inanimate object. During the past four weeks I have learnt that coding can be overly frustrating because a single punctation mark may cause your code not to work. In order to get things working, you need to be able to look through your code meticulously. But sometimes that doesn't always work. This week, I tried the "rubber ducking" method, a funny concept where you explain your code line by line to a duck or object of your choice. By doing so you may eventually locate the bug/error in your code. I've been talking to my stapler all week! The past week and a half, the lab has simply consisted of me, my stapler, and Dr. Cannataro. The three of us worked together to tackle the problem I mentioned in my previous post about gaining multiple RFS values for the same codon numbers + mutations. We decided to average out the RFS values for each mutation bef...

At the start of my fourth week, I was given an independent project to do along with an undergraduate student there, Sarah. Our job would be to perform immunohistochemistry (IHC) on mice brains to delineate regions in the striatum, a region in the brain. IHC utilizes the specificity of antibodies to attach to epitopes on specific antigens. This allows certain cells of a tissue section (with a certain antigen) to be “selected” by a certain antibody. By adding a secondary antibody with a fluorescent tag, target cells can be selectively labeled, imaged, and analyzed. We sought to mark regions in the striatum based on cellular count intensity.   The procedure begins with perfusing the mice.   This is a gory procedure that involves anaesthetizing a live mouse, pumping out the blood from its circulatory system, injecting a preservative solution into it heart, pumping this solution throughout its circulatory system, chopping its head off, and dissecting out the whole brain. This...

This week I finished my data collection! Getting 50 subjects seemed easy-ish at first but it actually turned out to be a lot harder than I thought. I finished Wednesday night and Thursday was one of the busiest days I’ve had so far. Dr. Peretz visited me and took me out to lunch (!!!) and then I got to show her around my lab and introduce her to Nick (the postdoc) and Dr. Lewis (even though we had to interrupt his meeting to say hi). Then I got to meet with Dr. Lewis and Nick and we discussed what the next steps of data analysis would be. We ended up talking for over an hour which was great because they both helped me a lot and genuinely wanted me to understand what I was doing. We worked together to categorize the questions in the surveys into “social behaviors” and “non-social behaviors” and then we discussed how to give each individual a score for how “social” they are. Kinda hard to explain without showing it but basically as I sort of explained in an earlier blog post each answer ...

Pittsburgh is a beautiful city, at least the part I'm living in. The streets of my neighborhood, lined with stores, a mix of antique restaurants and contemporary fashion salons, feel so fresh, clean, and perhaps even a little romantic at dusk. That's what I felt about my project when I finally created a working animation of my grid, minus the romantic part. I took Mr. Corica's suggestion on repeatedly drawing the graph during the algorithm's execution to simulate live animation. New versions of the graph would draw over previous versions so quickly that to the human eye, it would seem as if every iteration of my code's draw function only adds newer elements to the graph. To make this happen would, of course, also require a wait function that runs in between iterations, as otherwise only the final state of the graph would be observable. Javascript is a single-threaded language, so it doesn't offer a built-in sleep function that pauses the code without killing t...