Lauren Donato Week 3 Mason Lab: Vaccines, CBS News, Elispots & Cloning Project :)

Lauren Donato Week 3 Mason Lab

This week has been busy. I have become a professional multi-tasker and have squeezed in eating lunch at a personal best of 8 minutes (I usually eat when a gel is running or I am waiting for something to incubate). Nobody eats at a set time here, because everyone is on their own schedule, and I'm not sure if a PhD student here ever eats, or ever leaves the lab for that matter. When I come in first thing in the morning (around 8:30ish) I sometimes run to the animal hospital attached to my lab to meet doctor Mason and whichever dog is in that day. This is often the highlight of my day because I get to meet new people and view the clinical side of my project. When these dogs come in (some from the osteosarcoma trial and some from the lymphoma trial) they either are getting vaccinated or receiving a blood analysis. She takes two tubes of blood from each dog and gives them to me to complete a PBMC and freeze down (in my last blog). What this does is freeze lymphocyte samples from these dogs for use later on. I like this part of the morning because I get to see the side of the project that I do not get to experience solitary on my lab bench. On Monday I competed a lymphocyte proliferation assay. This assay is a test used to measure the ability of lymphocytes to proliferate in response to a certain stimuli. This assay is important for our lab because it can be used to measure improvements in immunological function following therapy and to detect the presence of immune responses against specific pathogens. This assay had to be completed in the tissue culture room under a hood and it was extremely vital to be sterile! This is my hood:

my hood :)

Something incredibly funny, yet sad happened earlier this week. I spent hours prepping a virus and was on the final step to centrifuge it. This giant centrifuge is a shared centrifuge between various labs in the building. When I went upstairs to retrieve the virus hours later, to my shock the entire centrifuge was missing. It was literally gone. So I ran to show the other lab members, and they were confused as well. Apparently the lab upstairs was moving and took the centrifuge spinning at close to 8,000 G's with them. My virus was still inside, so there is now a missing biohazard on the loose. Dr.Mason thought this was hysterical, but I had to redo the procedure the next day. Another funny occurrence happened on Thursday. I walked in to the lab and on my grad students computer I saw this cupcake sitting there. I asked her (she was working) why it was there and she had no clue what I was talking about. After asking everybody in the lab where this cupcake came from, we never found out. It was like magic.

magic appearing cupcake

 Anyways, back to research. I grew B cells from another dog this week, in addition to taking care of my old ones. Growing B cells is a lot like having a pet. You need to feed them, wash them, and check on their growth. My B cells continued to proliferate by restimulating with cytokine IL4 and cyclosporin. I did a flocytometry staining of the B cells to make sure what I saw growing really were B cells. Dr mason used the FACS machine and explained to me what the results meant. Within the next 6 days, I had enough B cells to freeze down for later use as a vaccine. When this vaccine is needed for this particular dog, the tumor RNA will be electroplorated into it. This means the membrane will become more permeable and allow the tumor RNA to enter it. 

process of electroploration

Then these B cells will go back into the dog and hopefully express and kill / prohibit the tumor. Aside from my B cell lymphoma project, I started a mini cloning project as well. I did my first PCR on Tuesday. The template I am working with is called CD21 and is 3,000 bp. Our lab had a template that was 200 bp long and the purpose of my first PCR experiment was to see if this 200 bp fragment was expressed in the larger one. For this, I had to design forward and reverse primers by looking at a plasmid map. Ordering primers is a cool thing I never had to do before, but a postdoc Josefine showed me how. This experiment had many controls, and I really learned the importance of having these controls to analyze the data from the gel. When I had 11 mini PCR tubes in front of me I also appreciated the concept of labeling, haha. I made a 5X master mix with buffer, forward and reverse primers, water, and dNTP. I then had different templates as controls: no template control, cDNA from T cells, cDNA from B cells, cDNA 8-, and cDNA 8+. I used these controls to test the CD21 gene and also a housekeeping gene gapdh to make sure I didn't get any false positives. I loaded a gel of this PCR. 

our gel station

This lab loads gels a little different than I was used to. Instead of using tubes, they use a piece of wax paper to mix the sample and dye. It was actually really fun to do it this way. After examining my gel, I found out this small gene was present in the bigger gene. The next step was to amplify this bigger gene. We weren't sure if any of the enzymes we had (taq, vent, or this green mastermix) would cut it correctly, so I set up an experiment to try. I had 3 controls for each enzyme: B cell cDNA, T cell genomic DNA, and no template control. None of these enzymes worked, so the lab had to order a better one, that will hopefully come soon! I did a few mini preps of bacterial samples, and ran a restriction digest, to help out a postdoc  on the lymphoma project.

my bacterial samples (they smelled)

 It went something like this: "have you ever done a mini prep/restriction digest" "yes" " great here's the samples." And so I completed the task *successfully* with no directions. I also got to use a very cool machine following the mini prep that measured the amount of RNA I was able to extract. It was called a nanodrop 1,000. 

this is what the nanodrop data looks like

 

this was the nanodrop

 I also got to do an Elispot assay this week, which was extremely difficult but FUN!!!! The ELISPOT assay is used for monitoring Cell-Mediated Immunity, due to its accurate detection of rare antigen-specific T cells (or B cells) and its ability to display single positive cells within a population of Peripheral Blood Mononuclear Cells (PBMC) *which I spoke about in my last blog*. In this elispot, I was testing to see if B cells were presenting a specific tumor causing antigen. These Elispot plates costs 400 $ each, and are not reusable, so it was very intimidating!!! The plate looks like this:

Elispot plate 

The assay is easy to read for results, but takes about 2-3 days. This cartoon below is the basic process of the assay. The spots in the last picture of the cartoon represent one cell responding to the antibody, thus meaning that the cell presented that specific antigen. 

Elispot Assay

In my experiment, many of the cells did present the specific antigen, so Dr. Mason was excited. My favorite part of the assay was using a multi-channel pipette. It is like a super pipette that allows you to fill mutliple wells at once. This step was essential for "washing" the cells.

using multichannel pipette to "wash" the cells

On a very very super exciting note, CNN News was at the lab this week!!! I love when they come, it is so exciting. This is the news clip from a week ago that aired: http://newyork.cbslocal.com/video/10303514-dr-max-gomez-treatment-prolongs-lives-of-dogs-with-bone-cancer/ watch it !!!

This week was great !!

Lynna Ye - Week 2.2: Ware Lab

Last week, I started doing PCRs to amplify the cytochrome c oxidase I (COI) gene found in the mitochondrial DNA that I extracted from the dragonfly legs. The COI barcode has distinct differences in its sequence between species, so I will be using it to identify which species the larvae belong to by comparing their sequences to those of the adult specimens. Melissa, a grad student from Colombia, helped walk me through the procedure on Tuesday. After adding primers, Taq polymerase, etc. to my first batch of DNA, we set the temperatures and times on the thermal cycler, which subjects the DNA to specific periods of specific temperatures to allow the DNA to unwind, the primers to latch on, the polymerase to replicate the DNA, etc. in order to amplify the region that we want. Meanwhile, as the thermal cycler ran for approximately 2 hours, I continued doing extractions.

When the PCR was complete, we used gel electrophoresis,which uses an electric current to pull down the PCR product, to determine the size of the fragments I got from the reaction. Unfortunately, after running the gel we found that no distinctive bands could be seen. Melissa said that we probably have to adjust the temperatures, so the next day, I ran another PCR with the same DNA, with a few adjustments to the thermal cycler's program. However, the gel once more revealed unsatisfactory results.

The next day, we used different primers that would amplify a slightly longer portion of the COI gene and tried the PCR again, but alas, it was still unsuccessful. Also, the spectrophotometer that I was using began to give me odd and inconsistent results, so on Friday, I ran a gel instead on the extractions that I finished. Since I ran out of spin columns and the new extractions kits have not yet arrived, I cannot continue with extractions, so I spent the rest of Friday helping to label the dragonflies that Melissa and Will (another grad student) caught in their recent trip to Wisconsin. While it was a simple task, I found it fun to finally be able to touch some whole dragonflies, since until that point I have only been interacting with legs in tubes.

I am excited to see what this week has in store for me!

Alex Hauschild - Week 3 - Shields Oncology Rotation at Wills Eye

Last week was quite eventful for me. Monday we started out in Tumor Board at 6:45 as we do every Monday, and went over some curious cases that have been seen over the years so as to teach the fellow doctors, fellows, and med students about some uncommon form of ocular cancer. We then proceeded on to clinic where we saw many different types of cancers including but not limited to retinoblastoma, various melanomas, primary acquired melanosis (PAM), hemangioblastoma, and conjunctival squamous cell carcinoma to name a few. After a few hours with the doctors, we rotated out and went back to pulling charts and entering data for the research. After work, there was a party at my apartment hosted by the residents for the retiring doctors. All of the residents from the hospital came out and we had leftovers in the fridge until, well frankly, come to think of it, we still have leftovers. That was fun though, getting to meet the residents and hearing what they had to say about advice and the like there were around 40 people in total.

                Tuesday was fairly uneventful, filled with established patients mostly who just come for a follow up exam and usually end up being just fine. I was with Doctor Jerry that day and he took some time to show us some interesting stuff of note through the slit lamp.

                Wednesday was an EUA (evaluation under anesthesia) day and we got to see something fairly rare even for the Shields to see (meaning very, very rare). It was a morning glory disc to explain, a morning glory disc is a “congenital anomaly of the optic disk in which there is a funnel shaped excavation of the posterior fundus incorporating the optic nerve”. After work there was the senior resident skit which to my surprise was kind of like a Blair Day video except in that it wasn’t a pump up video but more of a good bye video. Very funny though, it made fun of most every department. The basic plot was the hospital’s quest for #1 eye hospital in the world (because right now they are second only to Bascom Palmer Eye Institute at the University of Miami). I will post the video if and when they decide to upload it to youtube. There was a massive keg of beer, boxed wine, and LOTS of really good pizza (either that or I was really hungry because I didn’t have lunch. *note: I am only saying what was there, I am in no way implying any illegal actions were taken). My mom also came down for clinic that day and we went out for dinner with some Philly friends afterwards. We had a very nice argument with the waiters about the definition of gratuity there, it was really quite humorous.

                Thursday was surgery day as always. We got to see a massive orbital tumor surgery. It took two hours to take out the mass, but given that they used no scissors or blades, only q-tips, it was quite impressive. The tumor when they took it out was the size of the patient’s whole eye. Dr. Carol gave us a chance to use the indirect which was quite interesting. I learned that it is very hard to maneuver the window of sight into the eye because of how the optics of the piece work. Other people in my group continued their study on the feasibility of iPhone photography instead of having an expensive retcam (which costs well over $100,000). We also finished putting in the data for the project with only 32 names missing out of 1,200. We took an “extended lunch” to go to one of the med student’s apartment watch the USA vs. Germany game.

Friday was just making follow-up calls to patients who haven’t come in the past 3 years or more.
This coming week we have 3 more med students joining (on top of the 16 already here) and another 4 or 5 fellows joining for the year. In total we will have about 50-60 people working in the clinic next week. 

Colby Saxton- Week 2, Linksvayer Lab

       Hello fellow readers, I have just completed my second week in my research in ant behavior. This week was a bit slower than my first week, and it was quite a bit repetitive. This week consisted mainly of many Nest Preference tests and a Pathfinder Assay a day (nifty little rhyme). But there was some new territory that I explored. Our collaborators at NJIT approved our test video for the Pathfinding program, so over the course of the week, I filmed the movement of various pathfinders and non pathfinders. We have yet to observe the videos and see if there are any trends.
       I also helped one of my coworkers with a project of his. His project is to determine if there is a relationship between caste ratio and colony size in Pharoah's Ant, while also looking at what determines if a female ant becomes a queen or a worker. Along with an ambitious project like this comes a HUGE amount of new colonies. two-hundred new colonies were required for this experiment, and everyone in the lab helped him prep the colonies: then we helped him remove pupae from each colony.
       Removing pupae from a colony is a tedious process which can test the patience of anyone. The number of pupae in a colony range from 400-1200, and this is done by using a small paintbrush to remove them one by one. I fortunately only had to remove pupae from one colony, which only had 400 in it. Then, I was given the responsibility to weigh the first twenty pupae from each colony. Although it was a great experience, I can be glad to say my job helping my co-worker with his project is complete.

Until next week,

Colby Saxton

Shivani Gupta- Week 2- Epigenetics- Reddy Lab

                                 This week, I started to plan for cloning using a program, pDRAW32, that lets you clone DNA fragments virtually by using restriction enzymes. We are cloning three different protein coding genes, YY1, Lap2B, and lmn A. While it took us a couple of hours to determine how we can clone these genes, it was exciting learning and becoming more comfortable with this software.  This week, I also did some tissue culturing, which I became much more comfortable doing under the hood with sterile technique.

On Wednesday, one of the students in my lab, Lauren, had to give a presentation for the internship program she is part of. At the seminar, I learned more about her project, which is closely connected to mine. At the seminar, a classmate of Lauren’s also gave a presentation about the connection between depression, platelet serotonin, and coronary heart disease. On Thursday, Jen, my mentor in the lab, did a western blot which consists of gel electrophoresis to locate the antibodies from which the proteins have been separated. On Friday, I had the chance of doing a Western blot by myself. On Friday, we also transfected cells and completed a Western on the DNA. After the gel ran through, we had to cut the gel under UV light and then had to melt the gel. We ended up waiting for an hour before we realized that our gel wasn’t melting because the heater was broken! After we finally melted the gel, we did gel extraction which consisted of a series of washes and running the samples, YY1, Lap2B, and lmnA, on the centrifuge. On Friday, I also went to Happy Hour, which was a chance to network with people in other research departments at Johns Hopkins. I got to meet one of the grad student’s former PI and a grad student who is also working in the epigenetics department under Dr. Taverna.

This week went by so quickly and I am looking forward to the coming weeks at my lab. 

Yvonne Zhou- Week 3- Lewis Lab

Greetings,

This week wasn't so eventful after all. On Monday, my mentor had an eye appointment so he was absent from the lab for the entire day. As I was changing the media for the cells, I noticed that the cells in the confluent control group were peeled off from the bottom of the wells, starting to aggregate, whereas the rest was fine. The lab ppl didn't figure out the exact cause, so we decided to continue on and see what would happen. I went to Chinatown that night and dined there. Unfortunately, the sketchy food taught me a lesson. I woke up with an intense stomachache the following day and could not travel to the lab. I was, however, mostly recovered on Wednesday. My mentor briefed me on the paper that he was trying to publish by September, which was on direct endothelization-printing the cells into the vasculature. We decided that I could do some coding and try to print the scaffold structure in two of the methods: cast coculture and print coculture. The latter one is harder regarding techniques utilised yet gives us a neater structure. I had more training on fluorescent and confocal microscopes. I was supposed to print out a structure coded by myself with Robomama on Thursday. Yet the World Cup was placed higher in the priority list, so we went to a bar to watch the game and had lunch. While everyone there was clearly a fan of the US team, I had supported Germany for eight years and held my belief steadfast. I attended my first lab group meeting after we returned - the lab was huge so ppl held meetings every other week. Three people presented and passed around the structures that they had been playing with. I was amazed by how the members at the meeting raised questions and suggested ideas to the presenters! They all seemed very intelligent. On Friday, I spent most of the day coding.

Peace.

Colette Gazonas-Week 1-Shadlen Lab, Columbia University

This week I ventured into the city of New York to begin my lab at Columbia. Initially, I was planning on commuting from home to the lab each day, but shortly before my lab began I opted to stay in a hotel in the city instead. This made the commute a lot easier, taking only about 10-15 minutes by train to get to the lab. I was nervous about taking the subway by myself because I am not the best at navigating and feared that I would lose my way. However, the subway station is only one street away from where I'm staying and the lab is down the street from the stop I get off at, so it's a pretty direct and error-proof route. This eliminated a lot of the fear I had about my experience in the lab as I was relieved to find out that I would have no problem making it there and back each day by myself.

On my first day I arrived at Dr. Shadlen's lab at 10:00 a.m. The lab was on the 16th floor of a very large building, connecting to two others. The first thing I did was meet Yul, the grad student I am working with, and have a fairly long conversation with him about why I was interested in his work and what my goals were by the end of the summer. He then tested my familiarity with Matlab by giving me my first assignment which I was to complete by the end of the day in conjunction with reading another one of my P.I.'s publications. Thankfully, I was able to complete the assignment by the time we had our next meeting at 4:30 p.m. that day where he monitored my progress. During this time, he introduced me to his research assistant (RA), You-Nah, a junior at Columbia who is also in her beginning stages of learning Matlab. He suggested that we help each other out with the program and try to master it together. From that day on, I spent the rest of the week working with You-Nah to become more comfortable with the computer programming software as well as to run a set of paradigms. These paradigms were identical to those performed on the lab's subjects. Each paradigm increased in difficulty and running one after the other required great focus. Detecting eye and hand movement during a set timeframe, the tests grew tiring and tedious. As long as I stayed focused on the task ahead of me I was able to complete the paradigms successfully.

Each paradigm requires the subject to fixate on a dot in the center of the screen. A cluster of dots then appears for a short duration and directly following that stimulus the subject is asked to indicate whether or not the dots appeared to be moving right or left, and whether or not the majority of the dots were blue or yellow. Each subject is tested prior to running the paradigms to determine their individual sensitivity to color. Typically a person detects yellow at a luminance of about 160 cd/m2. Based on where a person's sensitivity lies in relation to this average, the luminance of the dots is adjusted so that one color does not appear more illuminated than the other. Because it has also been proven that when a person detects a stronger luminance of yellow they associate it with leftward movement and when they detect a stronger luminance of blue they associate it with rightward movement, the lab implements a personalized formula for each person to establish equiluminance, eliminating any bias that may affect their decision making.  

These paradigms are intended to provide evidence that will allow Yul to determine whether or not the brain is capable of integrating both color and motion at the same time. His hypothesis is that if the stimulus for color is more prominent than that of the stimulus for motion, the brain will first make a decision about the color of the moving dots shown on the screen, and vise versa.

On Thursday, the lab got together at 12:00 to watch the U.S. play Germany in the World Cup. They ordered pizza and I enjoyed having that time to decompress and regain some of my energy so that I could more efficiently run a series paradigms. This gathering was also important because this is the first time I met my P.I. Although, we only exchanged brief words, I appreciated the opportunity to introduce myself. During this time I was also able to get to know some of the other lab members better. There are about 20 people in my lab so it was difficult to get to know them all over the course of only one week, but this get-together definitely made it easier and allowed me to interact with them in a more relaxed environment.

Each Friday my lab holds a lab meeting in which each person in the lab gives an overview of the project they are working on, addresses any questions or concerns about their research, and shares any progress they have made. I really enjoyed getting to hear about each person's research because thus far I was only familiar with Yul's experiment. Because each person is already aware of what the other is studying, they did not spend much time discussing the specifics or goals of their work and rather cut right to the chase. As a result, I did not understand most of the unfamiliar terminology and was unable to fully comprehend a lot of the information that was thrown at me, but I was still able to appreciate their work, especially that of which I was able to better understand. I was fascinated by the vast range of research that is being conducted in the lab, spanning from neuroeconomics to optogenetics, and hope to solidify my understanding of each of these topics by the end of my six weeks here.

For homework, Yul gave me a Matlab assignment to complete over the weekend. I am to create a matrix of M by N, calculate the standard error of the mean for each column, and make an error bar of the data. Furthermore, I was instructed to make a logistic curve which measures the probability of choosing the color blue as opposed to yellow based on logit. I was given 7 values for the logit (-1.5, -1, -.5,...,1.5) in which I am to generate 20 data points for each and plot it as a logistic curve. Then I will plot the theoretical curve as one smooth line and compare the simulated points to that of the ideal points on the curve. Although this task is quite challenging, I hope that by using a few references and committing myself to completing this assignment, I will be able to do so successfully.

Caroline Casey - Week 2 - Complex Systems Group: p-values, lab meetings and lectures - University of Pennsylvania

This was a very exciting week! I am continuing to work on the project that I started last week in Matlab. On Monday, I completed doing a correlation of the data and began working on finding the significant edges of the network. I found the p-values of the edges in order to determine which ones are significant, however, the p-values that were found along with the amount of significant edges indicated that the significant edges could all be noise. Therefore, two more steps had to be taken in order to verify which edges are truly significant and not just noise. First, I completed a false discovery test, which is a more stringent way of obtaining significant edges. However, the false discovery rate did not work (which sometimes happens) so the next step was to determine if there are any clusters in the data. If there are clusters, the edges are most likely significant and not noise.

On Monday, I also got to experience my very first lab meeting! It was very exciting! One of the post-docs in the lab, Sarah talked about her research and we then spent an hour talking about an article. A week before the lab meeting, Sarah chose the article because it sounded interesting. However, in the lab meeting, Sarah along with the other lab members tore the article apart! Sarah explained how the research conducted in the article sounds interesting but the methodology is not correct. I thought it was so interesting how critical they were of the article because for me, any published research sounds good! I definitely learned to look at everything with a critical eye. On Tuesday I was not at the lab.

On Wednesday, I continued finding the components from the data (the clusters). I then did a Permutation test. In order to do the Permutation test, I had to randomize 1000 matrices of data and in order to do this, I wrote my very first loop! A loop repeats an order of steps and arguments a defined amount of times (a for loop does that to be exact).

Dr. Bassett is running, for the first time, a Networks Visualization Program along with Sara Hodgson from Incompra Design this summer for 6 weeks. In the program they selected art majors from local Universities to use their artistic skills to create networks, while also learning more about biological systems and complex networks. From Thursday, June 26 to Wednesday, July 2, the mornings will include lectures from various professors and post-docs from around Penn who are working with networks. Dr. Bassett invited me to come to the lectures!

On Thursday morning, I listened to two lectures given by Dr. Bassett about first, networks in general and second, about neural networks and her lab in particular. We finished at around lunch time and I went back to the lab where my lab was having a U.S.A. vs. Germany lab party with food and a big projector. After the party, I continued working on the permutation test and determining the significance levels.

On Friday morning, I listened to two more lectures. One from Ann Hermundstad, a Physics post-doc at a lab that uses networks in order to analyze the interactions between neurons in the retina. The lecture was incredibly interesting. The second lecture was from Matthew O'Donnell a researcher at the Annenberg School of Communication who is part of the Communication Neuroscience Lab. The lab focuses on how the brain of an individual can predict the actions of a population. They also examine how people's social network can determine how influenced they are by a group's opinion. That lab showed me a different aspect of networks science. On Friday afternoon, I finished collecting the significance level p-values for the different data sets.

Networks science is one of the most interesting aspects of science and it is amazing to think that I barely new it existed in the beginning of the school year. I am very excited to see what the next 7 weeks have in store for me!

Dominique Escandon - NJIT Lab Week 2

I'm finally back in my lab after a long hiatus due to forms and such. I really missed it, so it's great to be back! My first day was exciting, since the grad student I work with showed me his other project, which involves plasma to make a nitrogen polymers which can be used as catalysts. He said that he uses the same chemicals that are found in cars that, upon impact, explode and inflate the safety airbags. This is fairly dangerous, considering if he ever heats it up to much it'll either dissociate or explode, and probably the reason why he and my PI decided that I shouldn't work on this project. He actually places the chemicals inside a vacuum plasma ray (so that there's no oxygen, which produces a more red-ish light so you always know whether or not it's present) and leaks in hydrogen and/or argon gas. The light emitted from the ray is a product of the gases being ionized by radio frequency.

This system is also entirely homemade! You can see in the picture that there is a ring around the tube, just about halfway along it's length. That actually creates a magnetic field in the tube, and the light around/under it is the most purple. 

Mostafa (the grad student) cut off the hydrogen gas so that only argon gas was being emitted and it created a more purple light, as opposed to hydrogen's pink hue. 

Mostafa also told me that in the days before, a beam of orange light was being emitted from the chemicals he had placed into the ray, which was actually giving him really good results. On the day I visited he actually evaporated all the water from his chemical solution, and the orange light did not appear. Turns out, the humidity level in New Jersey actually helped out his experiment! When the chemicals are damp is when they work the best for his purposes. 

I also got to go out to lunch with a friend who is working nearby and my old french teacher, which was so fun and amazing. We took the NJ Transit to Newark Penn Station and had lunch at this delicious Brazilian burger place. 

However, today was a little bit more difficult. I worked on my carbon nanotubes in the morning, and in the afternoon another grad student came in and started to show me how to operate the biofuel cell system that I will be working with. The setup was easy, but conceptually I am a bit lost. Right now, I am only working with half of a fuel cell -- one of it's electrodes, I can chose which one -- and the data I expected to see was very different to what I actually got. I am so glad I took physics this year or else I would be even more lost than I am now. Thankfully, I was given a notebook of someone who had recently done some work with the biofuel cell. It is full of data and hopefully, assisted with Google, I will be able to use it to make sense of my project!

I look forward to tackling this new challenge and hope I can make the best of my time here!

Pieter de Buck - Week 1 - Duke University

Hi everyone, I'm Pieter and this is my first week at Duke.

I arrived in Durham on June 16th and immediately ran into some problems with my apartment. There was no one there to give me the keys like I had been promised. So after waiting for 45 minutes in the not so chilly 97 degree weather, I called a cab and checked into a hotel for the night. At least I met a really nice Venezuelan Duke student, who lives across from me.

But that was not the only problem I encountered with my apartment. When I went to the general office I learned that I am living illegally at this apartment complex, because the sublease was not properly communicated with them. They told me I had 48 hours to vacate the premises. Instead I just waited out my two days and they did not seem to care when I went back to the office. I'm still trying to sort that mess out, but at least it looks like I'm not going to be evicted any time soon, which is nice.

As for the actual lab I've had a bit of a slow start, but these past few days I have really done a lot. On June 18th I met a British postdoc, Chris, who helped me sign up for computer access and a Duke card, with which I can enter all the facilities on campus. From then on I was by myself, since neither of my PI's (I'm not sure yet who I'm going to work with the most) was in the country yet. So I basically just did some more research and reading on my own until I met Dr. Nahrgang on Monday. She and my other PI are both German, so I'm looking forward to the world cup final between Germany and the Netherlands on July 13th already (Yes I'm calling it right now). Dr. Nahrgang has set me up with my first set of assignments this week.

My lab is all about the study of Quark-Gluon Plasma, which is a (sort of) phase of matter, in which even the smallest pieces of matter (Quarks and Gluons) have no forces acting upon them. It is believed that in the first few microseconds after the big bang the entire universe was in a state of Quark Gluon Plasma. One reason why the subject Quark-Gluon Plasma is so interesting is because of the fact that it has never been observed, it only exists in theory. Apart from the requirement of a multibillion-dollar particle collider, this is the reason that my lab only creates and uses computer models to simulate particle collisions. These collisions give us data that can be used as evidence for the existence of Quark-Gluon Plasma. The phenomena that are evidence are called observeables, since we can not actually observe the plasma. Dr. Nahrgang started out by giving me a file, which contained the output of one of the computer models. In this file there were about 10 million lines of text, each containing the movement in x,y and z space of a quark, and its energy. Opening up this file containing 40 million numbers with 10 decimal places would take about two ages on my laptop, so she gave me the first 100.000 lines of data. For the first observable, we would like to be able to distinguish between particles that hardly interacted and particles that went flying all over the place. To do this we calculate the pt of each particle. This basically is the movement of the particle in the x,y plane. So when we have a beam of particles firing straight at us, we look head-on how the particle scatters after a collision with another particle. We take the x and y component of that scatter and take the hypotenuse, which is called pt. A high pt particle has interacted a lot with other particles, and therefor is more interesting than a low pt particle which might have only clipped another particle, or not even hit something at all.

This is the pt distribution of 100.000 particles in a histogram. It shows the number of events per level of pt (in GeV)

The mass of this certain kind of particle can also be found with the formula: square root(energy^2 - pt^2 - movementZ^2). For this particle (bottom quark), I found a mass of 5.0 GeV. All of these calculations have been done in a computer program that I created, and the graphing tools are built-in the programming language.

Finally, I also have a cool picture of the particles scattered after the collision in 3D space:

Kristen Silvi- Week4-NYU

I'm halfway though week 4 at the Buccella Lab at NYU. We are continuing to test our probe that we made. On Monday we took more tests using the UV Vis spectrometer. We call our probe JG-1-101. In the tests we took we filled 4 cuvettes. Cuvette 1: JG-1-101 and Acetonitrile, Cuvette 2: JG-1-101, butylurea, zinc trifluoromethanesulfonate, and acetonitrile, Cuvette 3: JG-1-101, zinc, and acetonitrile, Cuvette 4: JG-1-101, butylurea, and acetonitrile. We tested each of these cuvettes to see the pattern in absorbance v. wavelength. The wavelength at which the highest absorbency is should change if the zinc or urea binds to the compound.

This graph ^ shows that zinc did bind to the compound. You can tell that it bound to the compound because there was a shift in the wavelength.

This graph ^ shows that the butylurea did not bind to the compound because there was no shift in the wavelength at which it has its highest absorbance. 

Last week we were making more of our compound JG-1-101. When we created the reaction at a high heat thus causing crystals to crash out of the reaction when it returned to room temperature. We took an NMR of these crystals today and found that they were a very pure form of our compound! 

Winston Kung - Week 2 - (6/16 - 6/20) - Silverman Lab, Columbia University

Hi there, I'm Winston and this is my EXP Summer Lab Research Experience thus far:

The highlight of Monday of this past week was that we were joined by another summer student.  Similar to my situation, she is working at Dr. Silverman's lab for several weeks during the summer.  The main difference is that she just finished her freshman year in college.
I continued to work on analyzing the OCT slit scans in order to finish my first patient.  I also had lunch today with my PI again at a Chinese restaurant nearby.  It was a good opportunity to get to know each other better outside of the lab work environment.

On Tuesday, the doctors at my lab had some sort of a conference or lecture they all had to attend, so we were told not to come in to the lab thatt day.

On Wednesday, I analyzed more OCT slit scans.  By the end of the day, I had finished my second patient.  I now, with the completion of this second patient, had finished analyzing OCT scans of eyes that were normal and were not diagnosed with keratoconus, a conical bulging of the cornea.  This is significant due to the fact that I can now compare the OCT scans and the profile plot data (obtained through the analytic process that I was conducting) of normal eyes and eyes with keratoconus.  The analyses I had conducted, as well as this comparison between eyes without keratoconus and eyes with keratoconus, are going to be briefly included in a grant proposal that my PI and another doctor in the lab are currently composing.  I was glad that I could help out with such an important aspect of a researcher's job, especially since grants are the primary source of income for a lab.

Thurs:
On Thursday, I began to create the Microsoft Excel charts that displayed the data from the OCT slit scans and the profile plots I made.  These charts are the ones that will be included in my PI's grant proposal.  I made sure to include data from a normal eye as well as an eye with keratoconus in order to be able to compare the data.
One of the other doctors in my lab did more work with rabbits today as well.  She was working on a new process that allowed corneal cross-linking with riboflavins without having to scrape off the outermost layer of the cornea, the epithelium.  Cross-linking is to compress the cornea to reduce any warping.  The usual process with this procedure, with humans as well as rabbits, is to gently scrape off the epithelium and then use the riboflavin drops to set up the cross-linking process.  After the riboflavins have enough time to soak into the cornea, you would then expose the entire eye to UV in order to actually initiate the compression that comes with cross-linking.  The process that the doctor was working was using microbubbles to slip past the epithelium.  Then these tiny bubbles would pop, expanding the tissue, making the epithelium much more permeable.

Fri:
On the last day of my second week, I begun by continuing my work on the excel charts. At about an hour and a half into the day, the other summer student and I began to clean off some ex vivo pig eyes that we had received that very morning using surgical tools such as tweezers, surgical scissors, and a syringe to inject the slightly deflated eyeball with saline.  These eyes were then stored in small plastic jars with gauze pads soaked in saline to prevent them from drying out.  Later, three of these pig eyes were used to teach me and walk me through the process of taking an OCT scan and an ultrasound scan.  But before being able to take either type of scan, we had to come up with a way to keep the eyeball steady during the actual scanning procedure so that the scans could be as accurate as possible.  We eventually came up with a rather rudimentary structure to keep the eye still and in place.
Once that was completed, we moved on to taking an OCT slit scan of the pig cornea.  Because the pig eye is considerably thicker than the human's eye, only a picture could be taken.  In other words, the machine that we used to take the OCT scan could not run any analytic programs on the picture since the cornea was simply too thick.
After that, we moved on to taking ultrasound scans of the cornea.  With the first pig cornea, my PI did the entire process, while talking to me and showing me how to do the ultrasound scan.  After him, I attempted to take an ultrasound scan on my own.  Although I was much slower than he was, I eventually made it through the scanning procedure and took 3 individual scans of the cornea.
Additionally, today we had a pretty unique lunch.  The entire lab went out together and two other doctors from a different lab even joined us.

This is what the setup for the ultrasound probe looks like.  The ultrasound transducer is connected to the vertical blue rod coming out of the plastic tub filled with saline.  The big knob at the base of the platform is used to control the height of said platform in order to match the specimen that you're scanning to the focal length of the ultrasound transducer.


This is the entire setup for the ultrasound probe.  Above the probe and computer screen lies various other machines used to adjust the frequency, strength, and attenuation of the ultrasound waves.  The machine with the many different colored buttons in the top left hand corner sends electrical pulses through the cable that connects the machine and the ultrasound transducer.  This is what actually produces the ultrasound waves.

Vamsi Sanagavarapu-Week 2-Ramachandran's Lab: RTD!!!!!

(WOW CALCULUS IS ACTUALLY IMPORTANT)

I decided not to write about my second week here because we didn't really do much. The majority of our time was spent gathering background knowledge on RTD and preparing for the experiment we are doing this week. RTD stands for residence time distribution and it is used to find out how much time a particle spends in the muller. It is expressed in the form of a graph that looks like a bell curve. It is very important to our experiment because companies would like to know the range of time each particle is spending in the muller so they can maximize production and profits. As you can see, on the x-axis, it tells you the range of time that the particle spent in the muller. When you conduct an RTD experiment, you have to inject a tracer in the muller (a dye or something of that sort) and see how long it takes for a colored particle to come out. Because at different times, different amounts of colored particles will come out,, you can conclude how much time a specific particle spent in the muller by recording the concentration of dyed particles in each sample you take. Thus, this can be expressed using an equation (in the top left corner). This tells you the fraction of molecules that have spent between time t0 and t1. This is a very complicated and hard concept so in a nutshell, residence time distribution is used to find out how many particles were in the muller between any two times or how long each particle spent in the machine. In order to complete the RTD process, we have to build a calibration curve. This curve helps us identify what the concentration of each of our samples that we collect during the RTD experiment is.

So last week, we worked on creating the calibration curve. In order to do so, we had to take a sample of alumina powder (about 400 grams) and dye it. Sounds easy right? Wrong. It was the most time consuming thing I have done so far. It took us 2 full days to do it. Let me explain. When you put a tracer into a powder, the tracer can’t affect the chemical properties of the powder or else that will give a wrong calibration curve and ultimately wrong results. So we had to use a dye. Also, when you mix the powder and the dye, you can’t use a machine because that may change the physical characteristics of the powder particles. So we had to mix it manually using a spoon and some lab equipment. But you still might be thinking that it should be easy right? Wrong again. Because the powder is so fine and the particles are so small, they stick to the dye droplets very easily and form a coat around the droplet. It forms a shell like cover so the dye can’t mix with the powder. So we had to break these droplets and when they did break, it formed even smaller droplets with shells. We couldn’t have so many lumps in the powder because that would screw up the calibration so we had to break every little lump and droplet until the powder was uniform. This took us 2 full days and I couldn’t even sit down because when we were mixing, we had to put in under a vent because we can’t inhale the powder.

We finished the mixing on Friday mid-day and now we had to make our calibration samples. Each of our samples would be 60 grams and would have different concentrations. The concentrations were 0% dyed - 100% dyed with increments of 10 so 0%, 10%, 20%...100%. In order to make this, we took some plain white alumina powder and mixed it with some of the dyed powder we made. For example, if we were to make a 30% dyed sample that was 100 grams, we would take 30 grams of dyed powder and 70 grams of white powder. So we made our samples and that was the end of the week.

I didn’t only work on RTD but I also attended the Catalyst Consortium. This was held on Tuesday and it was basically a meeting with the researchers from Rutgers and some executives from companies that sponsored this research. It was a phone conference because the people were from England and other parts of the eastern side of the world. My lab partner presented the work that she did before I got here which concerned NIR characterization of samples with different variables such as particle size, agglomerate size, water content, and smooth or roughness. I also got to listen to other research that was related to ours but I did not understand anything that they were talking about. I understood the big ideas but it was very hard for me to grasp what they were doing in the experiments and what the results meant. However, I think that with more experience I should be able to understand the research better.

I also worked with 2 guys, Sarang and Ashu, to learn how to use some equipment. Although this didn't really relate to the experiments I was doing now, it was still important because it is likely that we will use them in the future. First, Sarang taught Ashu and I how to use the laser diffraction for primary particle size measurement. Primary particle size is how big one particle takes up. I thought that machine was very cool. To measure the particle size, the machine blows air into the enclosed area containing the particles. This causes them to float around and then the machine shoots a laser towards the particles. A shadow is formed behind the particle and then the machine traces the circle of the shadow and that is how it measures the primary particles size. Cool right?

I learned a bit about density too. Density is a pretty easy concept to catch but I learned that the way we measure density at school is not completely accurate. There are two kinds of density: bulk density and true density. Bulk density is calculated using the regular way of measuring the volume and mass of the sample and dividing mass by volume. However this is inaccurate because the particles consist of millions of tiny pores that are filled with air and not the actual material. So true density is the density of the actual material excluding the volume taken up by the pores. To find out what the volume of the pores is, you have to inject a gas such has helium into the particle and see how much gas goes in. That tells you the volume of the pores and then you can calculate true density.

I guess I did a lot during this week so I'll just put this under week 2. This week was more demanding than the last but I did learn a lot about a bunch of different concepts and machinery. I tended to stay at the lab 30 minutes later than usual because we have a lot of work but I don't mind too much. Overall, this was a solid week and next week we will be running the RTD stuff which will be interesting.

 This is my office desk where I do all my reading and analysis. 

Michael King - Week 2 - Loh Lab UCSF

This week has been similar to the first one, and I have been practicing most of the techniques I learned the first week. I still am not able to work with the mice yet as I do not have sufficient training, but maintaining and performing experiments on cell cultures are proving to be time consuming tasks. A recent high school graduate has also joined the lab, so that makes for a total of three volunteers in the lab, including me. San Francisco has been pretty nice this past week, and it hasn't been as foggy as everyone else said it would be.

On Monday we actually had to deal with a contamination of our cell cultures, which was not fun. As it happens I don't think it was my fault, but we did have to toss out most of the cell lines we had cultured and thaw some more cells from the cryotubes. Apart from that it was more of the same, maintaining the new cell cultures and performing more assays to test the effectiveness of the experimental drug on the cell lines. My post doc's pilot mouse experiment is almost coming to an end, with now even the treated mice dying off. I just got my ID, so I will be able to receive some training and start working with mice soon.

I attended a symposium with the rest of my lab on Thursday about mutations in Ras, and how the Ras gene mutations lead to various types of cancer including leukemia. The talks were probably a bit too scholarly for my understanding, but I did catch a few concepts I understood here and there. Lab days have been getting a bit longer, and the workload is certainly more than the first week.

Week 1 at the Deo Lab-- Zui Dighe

This week I got to explore the city of San Francisco while also establishing routine in my lab. My commute is surprisingly easy, taking only 30 minute shuttle to arrive at UCSF's Mission Bay Campus. The short bus ride takes me from a residential neighborhood to a hub resembling Downtown/ Tribeca, New York.

On the first day I arrived to the UCSF Cardiovascular Research Institute building at 10:30 in the morning. I was overwhelmed by the size of the building and had to get my picture taken to enter the offices. I met my PI in his posh office with glass windows and a great view. We discussed my project, which diverges from the research I had done during the year. I am going to be performing the rat sector of the T Cell experiments in my lab. This sector is used for further data and observation to test id Cardiac disease has an immune response. The reactions necessary to carry out the experiment include PCR, gel purification, and cloning. This is similar to biotech; however, my samples are much more fragile and are to be done on a greater and more specific scale. 

Lab Work--First I had to allocate and dilute buffers and primers to set up my own lab station. I also observed a postdoc in the lab doing the reactions to understand the many components going into it. All this prep would aid me in completing my own PCR reactions (a three hour process). I started my own PCR reactions on Friday with Human peripheral blood samples. They were successful :) 

On Friday, my lab along with a neighboring lab hosted a small party for two students going off to grad school in UCLA. It was a nice get together to meet others and get to know the people in my lab in a more social way.

                                                        The view is average in San Francisco

                                                                       PCR Machines 

                                                                   My lab bench and setup

ज़ुई दिघे 

Alex Baum- Cohen Lab Week 1 (June 16th- June 20th)

Hello, I am Alex and I am researching at the Cohen Lab at The Children's Hospital of Philadelphia (CHOP).

I began researching at the Cohen Lab last Monday. When I came at 9 am on Monday, I was really excited! I was excited about the research I read about in the lab's articles. I was also excited because I had completed a lot of animal training modules and tons of paperwork to be approved to work at this lab. Because I will be doing animal research, I had to study/ take tests on ethical training, rodent surgical procedures, how to apply anesthetics, ext. The process of obtaining a CHOP ID is extremely intricate and took months of paperwork completion, a FBI fingerprint scan, and hands on orientation on Tuesday, June 10th. After the orientation, I was SO excited to begin researching at the lab.

CHOP animal research personnel cannot start researching until they complete required training and documentation. On June 10th, I went to CHOP for orientation and had the coolest experience ever! This was not the first day of my lab- this was a precursor to the start of my lab. I found out that my lab does research in two facilities- the Colket Translational Research Center (CTRB) and the Abramson Research Center. The main office of the Cohen Lab is located in the Abramson research Center but most of the lab mice are held in SUB-LEVEL 3 of CTRB. Research is conducted in both CTRB and Abramson. I will be working with a graduate named Colin on mice behavior before brain injury in CTRB. For at least two weeks I will conduct T-test maze trials on mice with and without intervals between each test. I think that sub-level 3 is so cool because I need to swipe my card on the elevator, past doors, and on machines to access the facilities. Because sub-level 3 is also completely sterile, all researchers put on scrubs, face masks, hairnets, gloves, smocks, and foot coverings when entering the facilities. (I feel like a spy.) Unfortunately, although I picked up my CHOP ID last Monday (my first day), the ID office has not yet given me permission to enter facilities in CTRB and I have not been able to start my research. I spent my first week watching Cohen Lab members do research in Abramson. Although it is not where or what I will be researching, I enjoyed learning about all of the research going on in the Cohen Lab.

The Cohen lab is relatively small. The lab consists of my PI, Dr. Cohen, two graduate students, Colin and Chris, Shanti (I am not sure if she is an undergrad, grad student, or postdoc), Sean, and Brian. The first two days I watched over Shanti's research. Shanti took injured (Sham) mice and non-injured mice, applied anesthesia, cut off their heads using scissors, quickly extracted the brain put it in a carbonated sucrose solution to keep the brain slices alive. Then, she cut slices of the brain using A MACHINE THAT COSTS MORE THAN $20,000! The small metal blade that cuts the brain into slices is supposedly $20,000. Then Shanti would put live slices of the hippocampus under a microscope and stimulate field potential reaction with electrodes. The field potential of the brain cell was analyzed on a computer next to the microscope. After the initial graphs, Shanti injected a GABA drug into the brain cell that inhibited field potentials.  I watched Sean take slices and make solutions on Thursday, as well. A lot of solution and machine preparations are needed before the experiments take place. In math this year we learned how to graph 3D objects, which is how Shanti and Sean controlled the electrodes on the microscope! Time is really important to all of the research at the Cohen Lab because the brain cells need to be kept alive. Each dissection takes only 90 seconds! On Wednesday, I came to the lab and sorted through a bunch of chemicals (lab cleaning). Although it was not research, I was glad for something to do. Some of the chemicals dated back to 1988! On Fridays, the Cohen Lab has lab meetings. We listened to one of Dr. Cohen's students talk about her research in the Cohen Lab. She was studying female mice and brain injury because the Cohen Lab had previously only researched male mice and they were not getting approved for grants. I personally thought that this presentation was extremely helpful to my understanding of the lab as a whole. It gave me a better understanding of the overall goal of the lab. Basically, they are determining whether or not certain GABA drugs can help fix brain impairments after TBI. I lot of the people in the lab have different projects. Most of the research relates to brain injury in the hippocampus but Chris is researching the impact of brain injury on the Amygdala. Brian works on technical and chemical research. I think my PI is awesome! He was reviewing a lot of grants last week but he was emailing back and forth all last week with the CHOP ID office to get my ID approved. We also have a strange amount of things in common! He likes New Zealand, skiing, and his son is a coxswain! Dr. Cohen told me that he is waiting for security to email him with the access corrections and that I should be able to start researching soon.  

I commute to the lab by train and like it a lot! I have to wake up around 6:45 to be at the lab by 9. I My ID is supposed to be approved by this afternoon so hopefully I will be able to do research today! 

These are the chemicals I sorted!

THIS IS THE REALLY EXPENSIVE BRAIN SLICE MACHINE! It has to be calibrated before each use. 

This is the counter where they do brain dissections. The tubes are used to oxygenate sucrose solutions because the brain needs oxygen to stay alive. The heat tray heats the sucrose solutions. The top draw to the far left is where they cut off the heads of the mice.   

Alex Hauschild - Week 2 – Shields Ocular Oncology Rotation at Wills Eye Hospital

Over the past two weeks, I have been waking up at the crack of dawn to walk four blocks up 9^th street and get to the fourteenth floor of the hospital for clinic and/or time in the OR. Their clinic takes up an entire floor of the hospital and has 17 regular exam rooms, a photography room, an ultrasound room,  multiple vision lanes... etc, basically they have a room for every exam you could possibly think of. Doctors Carol and Jerry Shields (the co-directors of the Ocular Oncology Service) are the only ones in the hospital to have an entourage following them everywhere. The entourage currently consists of 14 med students and myself soon to grow to 18 total (excluding visiting doctors, fellows, residents, and normal clinic staff). Mondays and Tuesdays are clinic days; Wednesdays are for EUAs (evaluations under anesthesia); Thursdays are for surgeries; and Fridays are research days. The doctors don’t want more than 6 students in clinic at a time (3 with Dr. Jerry and 3 with Dr. Carol) and there can only be 3 students in any given OR, so there are always times when we are sitting around not in clinic or OR. What we do in this time is research that currently consists of pulling charts and entering data into a huge spreadsheet that is compiling data for the Shields next big publication. For legal reasons, I am not allowed to say much about the research since it involves people and since the paper has not been published yet. What I can say is that all the students that have worked on this project will get their name on the paper when it gets published, which means that I will have my name on it as well!!

                Other than the fact that we need to stand for about five hours on end without even leaning on a wall (or else risk getting a death stare from the doctors), clinic and OR can be very interesting and fun. Since I first stepped foot into the hospital, I have learned how various surgeries are performed, learned countless medical terms, learned to read charts; to use a slit lamp; an indirect; an iPhone in lieu of an indirect; to perfectly time the turning of the lights on and off, and how to properly hand the doctors their colored pencils to draw a diagram of the cancer (because god forbid you hand the pencil to the doctors the wrong way). Something I have picked up on is the unwritten rule of pencils, which dictates simply that the more pencils you carry around with you, the more important you are (the minimum amount of pencils is 10 and it only goes up from there).

OR can be very interesting. One patient decided to start singing for us in the middle of their surgery. One thing that I realize with surgeries is that if a patient wakes up in the middle of it and gets told not to do something, it is exactly that something that they will do. The surgeons could be in the middle of a patient’s eye, the patient wakes up, gets told not to move, guess what the first thing they do is? – That’s right start thrashing in a panic. Cases like this will be put under general anesthesia for the remainder of the surgery. This past week I saw one of the saddest things ever: a double enucleation. (For those that don’t know, an enucleation is the surgical removal of the eye.) He did not deserve to have this happen to him; he was one of the nicest persons that I have ever met. In the post-surgical consultation, I was tearing up at the things being said about him. It was so sad and yet so inspiring. I will never forget this patient.

Outside of work I live on the corner of 9^th and South across from the Whole Foods, which is very convenient for when I need to go grocery shopping. I run every other day on the Schuylkill (because most days I will come back home with my back and legs being sore from standing all day long). I have taken a few trips to Franklin Field (big name in track) and quite a few trips up the Rocky Steps of the Philadelphia Art Museum. I stay with a family, they have a little 5 year old named Liam, and he’s really cute.  All in all I have already learned so much with my work but I haven’t even begun to scrape the surface. I look forward to the many weeks to come!

Shivani Gupta - Week 1 - Epigenetics - Reddy Lab at Johns Hopkins Hospital

I could not have asked for a better first week at Dr. Reddy’s lab at the Johns Hopkins Hospital. I moved into my apartment on Sunday, and found out that there is a shuttle that goes from my apartment directly to the Johns Hopkins Hospital, which is really convenient, especially during rush-hour in the mornings. On my first day, I met everyone in the lab including my PI, Dr. Reddy, who was so nice and welcoming and further explained to me the goals of her research. I learned that I would be working directly with Jennifer, a Phd student at Hopkins, who was equally as welcoming and encouraging as Dr. Reddy. In Dr. Reddy’s lab, there are four other Phd students and a junior in college at UNC who is also interning for the summer. Jennifer said we are getting two more graduate students Monday, so I am really excited to meet them. On my first day, my mentor in the lab, Jennifer, had a lab meeting with Dr. Reddy. During the lab meeting, both Jennifer and Dr. Reddy explained to me more about their research and told me about the project that I will be starting next week. While I was so nervous walking into the lab on the first day, I felt instantly welcomed and learned so much by the end of the day. 

                During my first week, I shadowed Jennifer around the lab as she explained all the techniques and lab equipment used in the Reddy Lab.  On my second day, I did tissue culturing on mammalian cells. While it seemed simple, it ended up taking me five minutes longer than when Jennifer did the tissue culturing. Because tissue culturing has to be done in a sterile environment, we had to work in a hood that is only slightly open, so only our hands can reach inside the hood. When using the pipettes, you had to be absolutely certain the pipette does not touch anything else. I ended up going through four pipettes because I ended up touching the table with my pipette! To begin the tissue culture, I first had to make the medium for the cells. Each day, I also had to look at the cells under the microscope to check that the cells were confluent enough. When the cells were around 70-80% confluent, we had to split the cells. On my third day in the lab, we started BioID which screens for protein interactions in a living cell. On Thursday, we did gel electrophoreses which uses electricity to separate DNA fragments and on Friday we started a Western blot. A western blot identifies the antibodies which proteins have been separated from by their size from the gel electrophoresis. On Friday, I also learned how to count cells and we did a Chromatin IP which determines whether a protein and DNA interaction is present at a given location. Jennifer told me that on Monday, we will start cloning protein coding genes such as YY1, so I am really excited to learn that!

                One of my favorite experiences so far working in the Reddy lab are the seminars. Almost every other day, we go to a seminar that is hosted by visiting PI’s from around the country. This week, a PI at the St. Jude’s hospital talked about her research with metabolism and another professor gave a talk about neuroscience. On Friday, a senior editor at Nature (one of the top three science journals) gave a talk about how to get your research published at Nature magazine and the application process and what to do if your proposal is rejected. I was surprised and shocked when she said that they get more than 200 research papers every month, and they only accept 5% to be published in their magazine!

                I am so glad that I chose to do my research at the Reddy lab, and I am looking forward for the weeks ahead!