Peddie EXP Summer 2018

Finally done here with my experience and I wish I had more time keep researching so that I have something a little more "finalised" to present. But I guess that's what past EXP kids meant when they said that 8 weeks of research is not enough and I'll have to work with what I've got. To solve the problem of not having enough data points, we used the online TCGA database for raw data that would be used to calculate mutation rates. Mutation rates were calculated through an R coding script that Dr. Cannataro had made. Because the mutation rates were tumor specific, we had to change the proportions that were obtained from the IARC database using data from another database called cBioPortal. Basically we had to multiply the number of times a certain variant was seen in the IARC database by the percentage of tumors that have a tp53 mutation, because our mutation rates are calculated across all tumors in specific cancers (confusing, I know). After graphing the mutatio...

Bane, Joker and Penguin. On Monday, I helped David move his equipment from his car to the lab. Those were the names of the high-speed cameras he used for the Costa Rica trip. The appropriately named Batman villains, as well as the bat soft toys around the room, welcomed me into the second week of the lab.   For the first three days, I worked on more digitizing – except this time, I ran the trial from start to the final edit process. I had to calibrate the xma files before I could digitize properly. I did this by choosing around 30 good photos from the 900 from the stacked JPG of the chessboard video and digitized those on the three cameras: B, J and P. Before each set of trials, David waved a chessboard with certain black and white tiles before the cameras. This allows XMALAB to accurately represent x-y-z coordinates in relation to the points that I click for digitizing. Then, I ran 100,000 calibration iterations, which took around 4 hours. While the calibration...

Over the past two weeks, I finished processing, loading, and evaluating my final canine tail and rat tail IVD samples that I received from the vet school. Then, I used my collection of IVD load study media plates and tissue digest plates to run several different types of fluorescence and absorbance-based assays. The quantitative data gathered from the plate reader was then run through a T-Test to identify the statistically significant values. I also participated in my last study day at the Vet Med Diagnostic Lab. The vet school delivered three rat tails and three canine tails at the beginning of week 8 after their biweekly necropsy. These were my 8th set of canine/rat tail IVD samples and I breezed through the harvest and loading procedures due to my mastery of the protocols. I harvested 6 IVDs from each of the rat tails and 9 IVDs from each of the canine tails with the rongeurs and bone cutters. All of the muscle and fat surrounding the vertebral column was stripped and the IVDs w...

Despite being my last week, it was a rather busy week of a lot of different things. Kyu, my postdoc, had a lab meeting on Wednesday, and he wanted to include what I did over the summer. So, following the analysis of the brain slices, I gathered all the data and made some neat graphs to summarize all the histological work I did. I was in a bit of awe when I saw that so much work could be summarized in 2 small graphs. At the same time, it added a lot of closure and gave me a sense of accomplishment, but I digress. Regarding the code I wrote up, I continued to tweak it, annotate it, and even made 2 other versions that slightly differed in its use. For all of these, I wrote up a protocol so that the lab could use it when I’m gone L . Kyu, hoping to make my last week memorable, asked me what I wanted to do. I responded with “perfusions” (albeit how gorey, it’s really interesting). Little did I know, he had to perfuse all the mice he had been running behavior on for the past mon...

After over a month of dissecting, cleaning, bleaching, drying, and sectioning, I am finally nearing the end as I have moved on to the reading phase. You read the vertebrae almost like you would age a tree, you look for dark and light calcification bands that are deposited dude to changing water temperatures and calcium levels during different seasons. One light band signifies one year of age. I have around 150 vertebrae to read, some vertebrae's lines are very clear and distinct and other are horrendous and have little to no visible lines. After reading all the vertebrae I will do some modeling of the sizes and ages of the rays. I am also currently preparing for a week-long trip out to Orpheus Island with the lab where I will do some diving and catch and tagging of rays for some of the PhD students' projects. Although working in the lab has been incredible I can't wait to get out in the field and get my hands dirty.

The last two weeks wrap up my time testing at the Bing nursery school. The balancing toy had malfunctioned again, which meant that I had to secretly switch blocks underneath the table once again. We were able to view the data for the first time, and strangely there was a correlation in our data! It seemed that the children who were observed failing seemed to persist more in trying to balance the impossible toy than children who were observed both failing and succeeding, in contradiction to Isabel's theory that it depends on how stubborn a child is. Based on our results, we reject our earlier hypothesis that the children in the Accurate condition would attempt more than the children in the Fail condition on the impossible toy. Initially, we believed that children in the Fail condition would give up on the toy sooner because they may not wish to keep failing in front of someone who has watched them only failed. However, our results lead us to believe that perhaps children...

The past two weeks were really amazing. As I wrote in last my blog, though most of the nanorods aggregated in clusters, I have finally succeeded in coating gold nanorods on polystyrene film through drop casting. I tried to use water to wash the crystals and dissolve the nanorod clusters which, however, did not really help—several 70-80nm high nanorod clusters could still be detected by AFM (atomic force microscope). Realizing that the five times concentrated nanorod solution might be too concentrated, I then changed the solution back to stock solution and performed drop cast. Unexpectedly, the adjustment of solution concentration dramatically refined the experimental results: most of the nanorods were distributed separately as well as evenly on the polystyrene film. Moreover, the nanorod concentration this time was suitable for ellipsometer measurement. I measured the polystyrene forested glass film before dropcasting with nanords, after dropcasting (before annealing), and after anne...