Tanvi Dange, Entry #1, The Beginning

As many people end their EXP experience this week, I begin mine! The week of July 11- July 15, 2016 was my first week at the Franz Lab at Duke University in Durham, North Carolina. Specifically, the lab is located in the French Family Science Center on West Campus. Not everyone in the lab was in the lab this week, but I believe the lab has around 12 members, including the PI, all the graduate students, and all the undergraduates. 

View from the lab: The Duke Greenhouse

 I honestly could not have had a better first week. On my first day, I met Lizzie White, the graduate student I'll be working with, at her house near Duke, and we drove to the lab together. The reason we carpooled was because I hadn't bought a parking pass yet because I needed my Duke Card first. So in the morning on that first day, Lizzie and I drove all over campus to get my Duke Card and Parking Pass. In the time between getting the Duke Card and getting the Parking Pass I had a chance to finally meet my PI, Dr. Katherine Franz, who welcomed me to the lab with open arms. By the time we finished running these errands, it was already lunch time, so some of the undergraduate students in my lab, Emma and Mike, invited me to eat lunch with them and a couple other undergraduate students also working at Duke labs for the summer.

After lunch, Lizzie and I sat down, and she talked me through her work in the lab, and she talked to me about my project specifically, which I ended up starting that same week! Lizzie's work mostly involves Anti-Fungal Susceptibility Testing (AFST) for Fungal Cells, especially the fungus Candida albicans. Since I'm a minor, I am not allowed to work with Candida, so instead she said I would be doing AFST for Saccharomyces cerevisiae (also more commonly known as baker's yeast). 

So for some of Monday and Tuesday I mostly helped Lizzie with her projects by testing the absorbance of her compounds with copper on the UV-vis instrument and helped her make an overnight culture (ON culture) and assays for her Candida (with the assays, I just did the setup of the plates because again I'm not allowed to touch Candida). 

Lizzie taking C. albicans cells from her agar plates for her ON culture

Finally on Wednesday, it was my turn for AFST. First I made my ON culture by preparing a 1:1000 dilution of S. cerevisiae in yeast extract peptone dextrose (YPD) media. Then I incubated the ON culture for 21 hours at 30 degrees Celsius and shaking at 200 revolutions per minute. 

my ON culture in the orange falcon tube holder

Then on Thursday it was time for me to create my assays. I made three plates: one with Saccharomyces, Fluconazole in DMSO, and Copper, one with Saccharomyces, Fluconazole in DMSO and BCS; and one with Saccharomyces, Copper, BCS, and DMSO. For the first two plates, I divided the wells in half and only added the supplement of each respective plate in half of the wells. And for the last plate, the control plate, the first three wells had copper, the next three had BCS and the last row had DMSO in YPD media.

my three plates 

Once I finished the plates, I had to put them in the incubator for 48 hours. On Friday, I took a couple time points for the plates by placing them in the plate reader so that I could see how effective my concentrations of Fluconazole +/- supplement were on the strains of Saccharomyces. Since the 48 hours will be up on Saturday, Lizzie agreed to take that time point for me, so I should know the final results of the trays when I come back to the lab Monday morning for another exciting week. :)

placing my plates in the plate reading (and yes, I'm aware of how great I look in this lab coat ;)  )

  

Megan Gabruk, Entry #6, Another Great Week

            My experience in the lab continues to be great. On Monday, I had my weekly meeting with Kate. Since I finished a lot of my projects, I got even more which was nice because they were different from what I had been doing. They include identifying literature sources and coding for experimental design. Also, I continue to work on recruitment for the BABIES study. In order to do this, the other high school student and I came up with a plan for places to contact, put up flyers, and hand out brochures. We emailed many mother groups in the Bay Area as well. Along with recruitment, I also continue to identify potential funding sources. For two of the potential grants, I helped fill out the application and drafted the scientific summary/essay for them.

            On Tuesday, one of the faculty members in the lab presented on her work about suicide ideation. It was an intense topic, but the information presented continued to demonstrate how important the work in our lab is. On Wednesday, we went over how to use a statistics program which is really important knowledge. Also, before the meeting, the other high school student and I had to go pay for a participant’s parking, so they gave us a roll of quarters. When we got there, we were one quarter short, so we started looking around on the ground for quarters. Then, this really nice child came up to us and gave us a quarter, so that made our day.

            On Thursday, we had our weekly lab meeting and continued to discuss the Google project. This time, we had someone involved with the project come and talk to us about our ideas and what Google wanted from the project. That was really helpful and made us more directed in our approach.

On Friday, we had a lab happy hour to say goodbye to two full time members of the lab at a restaurant in downtown Palo Alto. Kate was very nice and invited the other high school student and me, but the other high student had to leave catch a flight. So, for the majority of the time, I was the only summer RA there/only one who had not graduated college. I sat near Kate and three other Ph.D. students who were all very nice people. They were interested in what I had to say which made the experience even better. It was really fun and great to get to know more of the members of the lab. Outside of the lab, I continue to explore the Stanford campus and Palo Alto.

Entry #4, Cait Barrett Demon Fish

This week Ben and I worked with Life Act fish, and attempted to cross and identify mutant fish in the tanks that were existing. In order to cross the fish we set up a male and female in mating boxes, which are small tanks designed to hold 1 or 2 fish. Since zebrafish will eat their eggs when they are laid, the fish are placed into a holding basin that has a net in the bottom. This net allows the eggs to fall to the bottom of the tank through the net, while the fish remain in the white holding piece. The tanks also have to be given a fake grass, as some female zebrafish will beat up the males and the grass provides a hiding spot for them. Finally we have to lid the tanks, because zebrafish are extremely jumpy and will flop out of the tank and onto the counter if not lidded.

After we collected all the eggs, we placed them into Petri dishes based on the pair they came from. To identify if they were carrying the Life Act mutation we had to look under a fluorescent microscope to see if the fish had red eyes. I was unsure if this would actually work, but after we heated up the fluorescent scope we placed the color of the bulb on the red light wave. We began to see fish with the red eye mutation marker, and counted the fish on each plate to see the ratio of mutants to wild type. The fish with red eyes looked almost like little demon fish from a sci-fi movie. From these ratios we could tell if the parents were homozygous for the mutation or heterozygous. There was a trend toward homozygous mutant fish, which was good because those were the fish Ben and I were interested in. We also ended up finding a three eyed fish that we named Triclops (original, I know).  We separated him from all the other fish in an attempt he would survive, but sadly he did not. This a fish with a red eye mutation alongside a wild type. 

In this picture it may be hard to tell but if you look at the clear region above the yolk sac and below the eyes you can see a pink dot on one side and then in the other picture the pink appears on the opposite side. This is because the pink is the blood of the fish beating through the translucent heart. 

Tiffany Budiman, Entry #1, TBI Mice

The first week at the Cahill lab at UCI has been great. The lab is located in the Gillespie Neuroscience Research Facility and the space is shared between several labs. My PI will not be around until August so Sarah, her assistant has taken me under her wing. The lab is pretty small and consists of 8 people, but on a usual day there are only 4-5 present depending on their work days and hours.

The entrance/lobby of the building

The first day I learned that the lab had a new protocol and now they are working on a project that will span about 3 years on TBI mice. At first I thought it was something completely different that what I wrote on my proposal but the research I read about provided me with the basic information that I needed to understand this new protocol. I spent all day reading that and got to help Sarah run some CPP tests on the mice that I read about. On the following days I learned and started doing some Western Blot tests and prepared some solutions that the lab needed on a daily basis. I also had to go to a compulsory animal training and vivarium tour before I was allowed to handle and transport the animals.  I also talked to Sarah and the plan for the rest of my stay here is to work alongside Sarah and Reem, a volunteer from UCLA, on a project that involves CPP and Von Frey tests on TBI mice. So far I have learned a lot about what my lab is currently doing and everyone I met has been encouraging and kind. Now that I understand the protocol and have a much clearer idea on what we are doing, I''m hoping I get results by the end of my stay. 

This is what it looks like walking into the lab and my lab's work station is the furthest back

William Ma, Entry #5, Last day at the lab :(((((((((((((((

Hey guys. It's 5:19 pm. My EXP summer experience has come to an end, and I will leave in a couple of minutes. I feel a lot right now. Six weeks I've spent here; I worked, and I laughed; But most importantly, I learned. I have just finished my own literature review a couple of minutes ago. In the past six weeks, I've gone through about 100 papers for meta-analysis, learned to do data cleaning on SPSS, created a manual for CSRP assessors and the children, helped in writing letters to the children's families, and in the last two and a half weeks, wrote a 3090 word paper by myself (Dr. Sulik provided feedback, but I did all the researching and writing alone). Now, I'm done with everything. In fact, I did more than I planned to do. I came here expecting to only work on CSRP, but ended up doing two more difficult tasks besides CSRP. I feel lucky to be able to undertake the trio of projects, because thinking back, I have learnt much more than I could have learnt by working on only one project. I've attended three presentations in my six weeks. Some were more serious than others, but all of them are very interesting and enlightening.

This is before Dr. Sulik's presentation on applying to graduate school in psychology

These two are both Meriah, one of the lab manager's presentation on how mindfulness can benefit us.

This is pretty much all I've got for you guys. It's 5:35, time to go. I will miss here, but who knows, I might come back here next summer, as an undergrad :)

David Alvarez Entry #2: Weeks 2-3

Things have definitely picked up in the last two weeks. The biggest development to occur was definitely the changing of my project. I was switched from Adaptive Multicast Services to an analysis of WebRTC-based Video Communication, where I've been able to fully dedicate my time to the experiments that Varun has been asking me to do. The project does not involve as much hard-core coding as AMuSe did, but there was still a lot that I had to learn. For example, in this new round of experiments that we are doing, I had to learn how to use this software called Wireshark, which captures TCP and UDP packets being transmitted between two machines. Also, I've had to learn how to use the Linux shell on the Ubuntu computers in the lab, which has allowed me to gain a deeper appreciation for how much better Linux machines are for development than the Windows one that I have been using since I started to learn how to code. The experiments are still in very preliminary stages, and we've just been testing different scenarios and plotting the data that we've gotten both from Wireshark and a separate website designed by one of the other people working on the WebRTC project.

Server being run from one of the Ubuntu machines during an experiment where we sent UDP packets across the LinkSys router.

The commute has gotten significantly easier. I've found a better use of my time on the train than Candy Crush, both in my school work and reading for pleasure, something I normally really enjoy but can't do because of school. A lot of the stereotypes of New Yorkers have proven to be false, and I've come enjoy the vibe of the city a lot. People here are actually pretty helpful and friendly for the most part, unless you cut in front of them in the bagel line. I've gotten to visit a couple of places in the city, my favorite being the Forbidden Planet, a comic shop in Union Square I'd been meaning to see for a long time. Also, I got to have lunch last week with Will, Sharanya, Masa, and Dr. Peretz and it was nice to catch up with everyone and see what they were doing. 

CESPR, the building I work in every day.

Overall, I am really starting to appreciate more and more the work being done in my lab. The first few days were very intimidating, but even when I don't fully understand something after having it explained, the people here have been very understanding and helpful. Another high school student, Rodda, joined us last week and he's had a lot more experience with networking than me and has helped a lot with the recent round of experiments. Yesterday, we went out to dinner as a good-bye to Bohan, a graduate student from Duke who was here for the first half of the summer, and who will be working with Deutsche Bank in London until classes start for him. I'm looking forward to Dr. Venanzi's visit on Monday, and to my remaining 4 weeks here! It's so hard to believe that I'm already pretty much halfway through my time here.

Ian Loeb, Entry #4, Nearing the End

As the end of my time in the lab draws near, the work load continues to increase. Dr. Kutch has gauged my work and determined that he can begin to unload more onto my plate. The model has come a long way, as we've implemented past trial data to model a future experiment. By using MatLab to generate the individual brain connection images from a matrix of data, we have been able to load 20 views of each connection, in addition to a base image holding all of the connections.

The base image was its own entity, and therefore not embedded within the code of the chord chart, making it a particular challenge to code the fade-in fade-out functions, and making the code for the rotation of the diagram more complex than any code I had dealt with thus far. However, through assigning the image an ID, and by numerous trials, I finally was able to use the .on("click" and .on("mouseout functions to make it happen. I've also been continuing to come up with more ideas for future additions that would hopefully make this diagram more user-friendly and efficient for viewers.

It's quite amazing how in such a long time has passed so quickly. It seems as if just yesterday we arrived in California, nervous EXP students, anxious for their first day working in a lab. The transformation has been drastic yet rapid. My remaining time will be thoroughly savored, and I honestly hope I have plenty of experiences like this to come in the future.