Peddie EXP Summer 2018

EXP has finally come to an end. Considering that silicon wafer should be better for dropcasting, I then created PS film embedded with gold nanorod on silicon substrate and measured it with ellipsometer. Besides, I finally got the chance to perform SEM imaging to sample films to see the overall dispersion and out-of–plane orientation of nanorods. As a result, nanorods were mostly evenly distributed all over the film; however, they are distributed in small nanorod clusters, suggesting that I can still dilute the nanorod solution for future adjustment of this research. As my 7-week research came to an end, I would like to thank all my group mates, especially Subarna and Lexi, for supporting my summer research throughout last two months. In addition to broadening my theoretical knowledge, gaining lots of hand on experience with all these fantastic facilities, and gradually growing up towards a real researcher, I am really grateful for being a part of the group. It was a pleasure to wat...

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...

Week 6 and 7 These two weeks were really busy. Sarah - an undergraduate - and I continued on the IHC project and I perfused 3 more mice so we could do IHC on them. I’m getting better and better at perfusions (and more desensitized to the gore). Though, I always remember to say a little prayer for the mice before I cut it open and thank it for its scientific contribution. Hopefully they are all doing fine in mice heaven. Because mice brains are sliced and sectioned off into 6 wells, we were able to perform IHC on 6 batches of brain slices, 2 from each mice, (the other 4 batches are preserved and saved in case they need to be used in the future). Of these two batches, one was stained for the somatostatin receptor, and the other one was stained for the parvalbumin receptor. After IHC, we mounted the slices and then viewed them under a microscope. Unfortunately, the slices were a little beat up, but overall the entire staining went well. During this process, I continued on my sem...

As I was wrapping up my time at the lab, Claire was also wrapping up some of her work to present to her thesis committee.  My seventh week was a continuation of probing western blots with different antibodies after extracting protein from the heart, lung, and brain of each of the mice which had been genotyped before.  This allowed for the comparison of heterozygous, homozygous, and wild type mice.  The results from the antibodies were unexpected, leading to some confusion.  Thus, we had to go back and redo the genotyping in order to confirm the original conclusions from the gel electrophoresis.  The genotyping was correct, but there were a variety of other factors which could have led to the unexpected results. My 8th and final week was spent doing some lab work, but mostly reading some primary literature in order to prepare for my poster.  I took some notes and discussed what I read with Claire in order to gain confidence in my knowledge of the topic. ...

The last two weeks of EXP went by quickly. I planned to stay at Penn until July 31 st , but since Dr. Plante gave me a new section in my project about two weeks ago I decided to stay until August 3 rd to make sure I can finish everything I needed to work on. I spent the last two weeks of my EXP experience finishing up the alkali extractions and doing data analysis. With the TOC concentrations I got from the two different extraction methods, I was able to calculate the mass of carbon extracted out of one gram of soil. Then I compared these results with the total organic carbon data Dr. Plante keeps in his lab and was able to calculate the percentage of carbon extracted. I did not finish further steps of data analysis when I left the lab, but I will be working on these data and discussing with Dr. Plante through email next week. My EXP experience overall has been wonderful. I learned much about research. I met some awesome people. I learned some life lessons both from living a...

    Week 7 has certainly been a whirlwind. For our experiment, we essentially wanted to compare the DNA damage in the muscle stem cells (MuSCs) of injured mice with those of non-injured mice. However, our experiment which tested for DNA damage using the biomarker 53BP1 didn't quite work out. When my postdoc Elisia imaged the MuSCs in the microscope room, she looked at the DAPI (nuclei) staining and the 53BP1 staining to see if they overlapped; an overlap of the two stains would indicate DNA damage. While the DAPI staining successfully indicated the nuclei of the MuSCs, the biomarker 53BP1 had stained both the cells and their background. 53BP1 therefore proved to be ineffective at indicating the DNA damage we were looking for. Subsequently, Elisia decided to perform this experiment using a different biomarker, one that would reliably indicate DNA damage. I then spent the first half of Week 7 repeating this experiment using the biomarker Gamma-H2AX, which stains for double-...

For the first two days of last week, I finished my last batch of hot-water extraction. My data turned out well for the majority of the samples, but there were some samples that had TOC concentrations over the measuring range and one sample that had a negative number. I planned to dilute the over-range samples but had no idea what to do with the negative one. I might rerun the negative sample just to see if it's an analysis error. It is unsatisfying to see such a result, but as Dr. Dmochowski said during our lunch meeting: no progress is progress, so I hope to learn something from this negative number. Since both Kyle and I were using mid-range kits for our TOC analysis, we ran out of kits and needed to wait for more to come, and I used this time to do some data calculation. I used the total carbon amount/percentage data from Liz and calculated the percentages of TOC that were extracted by hot-water extraction. The results turned out interesting: even though there is more ...

I began week 5 by using the microscope to view the cell plates that I had previously stained.  It was really exciting both to have results and to also see that I had followed the procedure correctly.  I was a little bit nervous that something that gone wrong along the way and that the microscope but be unable to see the neurons, but I was able to view the red, blue, and green stains.  I then had to set points in the center of each well and then focus the image and change the brightness, in order for the microscope to, hopefully, capture.  However, I was a little unlucky and had to keep restarting the process because the microscope kept crashing, and was not able to take the 25 images needed of each well.  Instead,  Claire was able to take a single image of each well by zooming out, leading to a larger picture.  We were happy to find that the results were as expected, with cell death occurring in wells in which it was predicted, and the cells in the veh...

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...

I spent the last two weeks conducting 3 batches of hot-water extractions and testing total organic carbon concentrations on my soil samples. After spending almost two weeks consolidating my protocol, I officially began working on the soil samples from the Luquillo Critical Zone Observatory. Instead of 3 samples that I used in each of my practice trial, I have 12 samples per batch for 4 batches in total, which required much more time and attention. For my first and third batch of hot-water extractions, my data turned out well, and I could see some differences of TOC concentrations between surface and subsurface samples even though I only had half of the complete data. However, the same problem that happened in my practice trials occurred in my second batch—I got some negative numbers, which means that the TOC concentrations of certain samples are lower than that of distilled water. In order to fix this problem, Dr. Plante told me to rerun these samples after I finish all 4 batche...

Going into this week, I was a little bit terrified.  My grad student, being away this week, had left me a list of tasks to complete and some protocols.  I really did not want to have to send a text to her saying, "Please help.  I messed up a lot!"  (spoiler alert: I didn't have to) My first job on Monday was to rinse a primary antibody off of western blots and to then put on a secondary.  I was in charge of four westerns which had different lid covers and were all slightly different from each other.  Two westerns followed one protocol and the other two followed another protocol.  When I put the westerns down, I oriented them in a certain way so that I would not accidentally switch the lids.  I then had to rinse off the secondary and expose the westerns to ECL in order for the proteins to become visible in the imager.  After successfully imaging the westerns, I used the stripping buffer in order to prepare them for the next primary, in order t...

Week 2 and 3 My second week largely involved further familiarizing myself with the lab, its members, and the cellular analytic work I was tasked with. I continued my work with the image processing of brain slices to highlight the contrast between cell bodies and the “background noise” (while maintaining the original pixel data of image). This was in hopes that we could use some sort of automated way to count all the cells. Although quantifying the relative intensity of the pixels of cells was a somewhat viable method to “count” the cells, the ultimate goal was to actually count the cells. I took a stab at counting the cells in one brain slice – 1181 red cells and 381 green cells – definitely not fun and this only motivated me further to find an alternative method. After some research, I then turned my attention towards a machine-learning program called Trainable Weka Segmentation. By “training” the program to identify cells, specifically where they start/end, the program co...

The last two weeks consisted of hot-water extractions, TOC analysis, and experimental design. Initially, Dr. Plante told us to run two trials with three samples in each of our individual trials. Kyle and I would be using two different soil-to-water ratios in order to figure out which is better. I had a lot of free time in the lab when the samples were on the end-to-end shaker or were heating up for TOC analysis, so I spent the time reading some primary articles and sometimes my summer reading when I was tired. For TOC analysis of trial 1, we used mid-range kits, which allow for smaller concentrations of carbon, but it turned out that some concentrations were higher than the range of 15-150mg/L, so we decided to use high-range kits for trial 2. In trial 2, one of the sample concentrations was negative, which represented an experimental error. After discussing with Dr. Plante, we decided to add a trial 3. However, our results were not nice either. We did not use syringes for the...

The last two weeks have been slightly hectic.  My first week in the lab I became used to the easy 7 minute walk from my apartment to the Schattner building.  However, due to the need to go through some mandatory training for Penn, I was required to take a 17 minute walk past Penn and past Drexel to reach the Environmental Health and Radiation Safety (EHRS) office.  This training session covered basic, common sense rules, such as "Do not eat in the lab" and more specific guidelines for chemical safety and biohazards.  I was glad to find that I already knew much of what was explained during the training, thanks to having worked in a fume hood before for chemistry and having had some hands on experiments in my previous science classes. On Tuesday of my second week, Dr. Peretz, Ms. Cozine, and Ms. Terhaar came to take all of the EXPers in Philadelphia (except for Wendy) out to lunch at the White Dog Cafe.  It was really exciting to see some alumni and catch up with...

     I started work on June 4, just a week after spring term exams. Thankfully I didn't have much trouble finding my lab's building because I had visited it in fall term for an interview. For the duration of my lab, I start work at 9:30 AM and end at 5 PM.      "We're going to the mouse room to injure some mice," my postdoc voiced, walking me to said mouse room. It was only my first day in lab; talk about hitting the ground running. After selecting two boxes of mice in a room lined with shelves of them, my postdoc Dr. Elisia Tichy, or Elisia as we call her, explained to me that she would injure the muscles of the mice. To do so, she anesthetized them and injured their target muscles using injections of notexin, an enzyme found in snake venom. The notexin injuries would cause the muscle stem cells of the mice to activate and divide in abundance. Next week, we will collect their muscle stem cells and analyze them using telomere assays ...

I woke up early on Monday, June 11 th in preparation for any unforeseen events on my way to the Fuccillo lab for the 1 st time. Thankfully, I did – I got lost and turned a 15 minute walk into an unfortunate 40 minute walk through Philadelphia, in particular Penn Campus and CHOP. In hindsight, trying to find a shortcut on the first day may not have been the best idea. To add, Apple maps led me to wrong building, but Google maps saved the day. In the end, however, it all worked out as I arrived just in time to meet with the postdoc I would be under, Dr. Kyuhyun Choi, or Kyu for short. He led me to Dr. Fuccillo’s office (the PI) where we discussed some plans for the summer. I was then introduced to some of other the lab members, which included 2 undergraduates, 3 graduate students, a lab manager, and 1 other postdoc. Everyone was warm and welcoming. Kyu also toured me around the 3 lab spaces the Fuccillo lab uses. These include the main lab area, a separate testing area, as well a...

I happened to start on a Tuesday, so, on Monday, I was left on my own to travel around Philadelphia.  I was incredibly lucky and thankful because I have a friend in the area who did not have school and drove me around to her favorite touristy spots in the city.  First, my friend Sofia took me to Reading Terminal in order for us to have lunch because she told me I would be missing out if I spent 8 weeks in Philadelphia without visiting Reading Terminal at least once.  After, she took me to the Magic Gardens, which originally was a vacant lot, but is now an extremely large mosaic by Isaiah Zagar who is still constantly working on the museum and gallery.  Sofia, who had been to the Magic Gardens many times before, and I were thrilled to see mosaics not only in the museum, but also in the street. Last, but not least, we drove to Harbor Park in order to enjoy ice cream and swing in a hammock before she dropped me off at my apartment. I was incredibly nervous walking...

I started work this past Monday, June 11 th . On the first day, I arrived at Hayden Hall, where the lab is located, a little bit earlier than Dr. Plante (My PI) did. I got into the building when he arrived, and we started working right away. He told me about a change in my project. My project is a based on the research of Liz Coward, one of Dr. Plante’s former PhD students. We planned to extract mineralized-carbon in soil samples, and then conduct thermal analysis on the residues to figure out the soil composition. However, as Dr. Plante was emailing Liz to settle on my project, Liz told him that she kept the residue samples of her extractions in the lab so that I did not have to conduct the extractions again. Dr. Plante decided that I could conduct a different kind of extraction, hot water extraction (HWE), and yield a new set of data. After everyone arrived, he introduced me to other people in the lab. Gabe is an undergrad from the University of Minnesota, and he works with...