Sophie Kennedy B.I.O.S. week 4

 This week I got to live in one of the dorm rooms at BIOS which was an awesome experience because I finally had the chance to bond with the interns outside of the lab. Monday and Tuesday we made dinner at another intern’s apartment and then Dr. Peretz came to Bermuda on Wednesday!!! Dr. Peretz and I went to the town of Hamilton for dinner. I had hoped to take her to harbor nights (a Wednesday night event in town similar to a street fair) but it turned out to be a stormy night. I really enjoyed showing her our lab and the BIOS facility as both of us dreamed of bringing a group of Peddie kids here. (I’m thinking an EXP field trip?)

 On Tuesday we went out to collect and put back the corals from the patch reef. The corals are put back on the reef by using underwater cement that Lea and I made a few days before. We were supposed to collect the rim reef corals and put some back however the weather was not quite working in our favor this week. On Wednesday the wind was so strong that it snapped the roof of our wet lab in half. So I spent most of the week helping Kevin take pictures and map the growth of the spat (settled planula).  The process of mapping spat growth starts with cleaning each tile: ensuring that each spat is growing on a flat surface, can be photographed, and is circled. In order to obtain the reasonable data, we sometimes need to kill a spat that is growing into another. Then by attaching a lens that extends into the microscope to the camera, I can take pictures of each circled spat. We had a worm infestation one day and found that many spat had been eaten but with thorough washing our tanks are nice and worm free now!

The past few weeks have consisted more of collecting data versus settling the planula or looking for spat. I spent most days taking pictures for the 10 day, 20 day, and 4 week checks for the porites and favia. As tiles are lost and spat are accidently touched our data is messed up. I was shocked at how much human error is present in scientific experiments. In school labs I always mentioned human error as a possible source of error however it wasn’t until my time in Sam’s lab that I truly saw how often it occurs.

I finally made it out on Friday for my two last open water dives. I am now a certified open water SCUBA diver! We dove a shipwreck a couple miles off shore (a rim reef). I was amazed at all the brain coral and sea fans.  I also had the chance to meet a few other interns- one goes to Princeton!

I could not be happier with my choice to work at B.I.O.S. this summer. I never just have to concentrate on my lab work but, with my P.I.'s encouragment, I was able to get my open water certification, help teach a class with her, and get my lionfish spearfishing permit. I do wish that I had my own project that I worked on all summer however I have learned so much with the 5 of us working as a team. Overall it has been an amazing experience and I am torn that I only have a little over a week left here.

Corals at the rim reef dive site. (notice the clarity)

Showing Dr. Peretz our coral lab!

 20 day Favia growth picture from the Y tank. (Low light, high temperature)

Alex Hauschild - Shields Oncology Research Rotation - Week 8 (the final week)

           Back two weeks ago when ABC news came in to interview Dr. Carol, we got to do a couple shots of us in the clinic. I managed to make it into the final cut: http://www.wsoctv.com/news/news/special-reports/9-investigates-cancer-mystery-huntersville/ngpwT/?__federated=1 (at 2:27)

As my great experience learning with the inspiring people of the 14^th floor clinic of Wills Eye Hospital winds to a close, I am at a loss for words. Oddly enough, this is the first time I have ever worked doing anything where I only wish that I could stay longer and do more work. As I look back at all the experiences I had this summer and all the people that I met, I believe I made some powerful connections and managed to find not only one but two welcoming homes in the process: one at Wills and another at the apartment of the Kleinbergs whom I stayed with all summer. I only want to thank all who made this possible including my wonderful mother and astute teachers Drs. Peretz and Crider whose keen guidance helped me find a place with the Shields, the Shields and associates who put up with all the students for two months while we learned all that they had to offer, Teri who opened her home to me and taught me the basics of cooking gourmet food, and of course the med-students who helped me understand everything when I was first starting and helped me write my poster and article. The list goes on as to all the people that I could thank, but one thing is for sure: I will never forget the summer of 2014.

                My final week in review: Monday – nothing new, just the usual retinoblastoma, uveal melanoma, nevi in various shapes and forms, and another sad case of melanoma that required enucleation. Of course research was also done on all days.

Tuesday – other than the typical scarring and loss of vision because of radioactive plaque treatment and other secondary problems associated with treatment, we managed to see some paving stone retinal degeneration which was very cool.

Wednesday – In the morning, I went around with Dr. Jerry Shields seeing patients and saw some pretty interesting stuff. One patient we saw had a multifocal melanocytosis of the uveal tract with multiple melanocytomas very interesting but luckily completely benign. Another was a highly unusual variant of hyperplastic limbal epithelium which presented as a small white elevated mass on the edge of the cornea. The final case that was of interest was one of only four patients in the entire system of patients that the Shields treat whose cancer is unclassifiable. “This tumor just defies diagnosis” said Dr. Jerry Shields. Needless to say that it is beyond rare to have the Shields come up empty handed, period. I went down for some time in the OR after that to watch some EUAs. Just the normal stuff really, typical retinoblastoma cases that are either new or are coming in for a follow up to be sure that everything is fine.

Thursday I started the day by bringing in some donuts from the best donut shop in Philadelphia – Federal donuts all of the students pitched in to get some stuff for the clinic staff and doctors. We even brought some down to the break room in the OR so that the doctors could snack on them as well. In Dr. Jerry’s OR (which I started in) I saw a removal of a conjunctival lesion and a very long removal of a lacrimal gland cyst. After watching a plaque with Dr. Carol, she decided that she would introduce us to some of the other surgeons and lend a few of us out. I had the opportunity to watch Dr. Maguire of the Wills retina service perform some surgeries in his OR. The first was to fix a macular hole. The surgery went something like this: first a vitrectomy was done to remove all the vitreous from the posterior chamber and replace it with balanced solution (similar in molecular composition to the vitreous). Kenelog is then injected into the posterior chamber to help visualize the hyaloid membrane adhering to the macula. This membrane is then carefully removed and suctioned up. Indocyanine green (ICG) is then injected to stain the internal limiting membrane (ILM) which is then carefully removed. After removal of the ILM, the solution in the posterior camber is replaced with high pressure air forcing the macula back together. The air is then replaced with SF₆ gas to preserve the anatomy of the eye and help it heal. While the gas is in the eye, the patient will not be able to see, but this will resolve in 2 weeks time when the vitreous starts to return. I then went back to Dr. Carol’s OR to see an aspiration of an iris cyst – kind of self-explanatory. I left just as the enucleation was beginning and returned to Dr. Maguire’s OR to watch another macular hole surgery.  Once the surgery was completed I thanked him for letting me observe and went back to Dr. Carol’s enucleation and made it just as they were pulling out the eye. We all crowded around a small prep-table as the doctors opened up the eye to harvest tissue samples from the tumor. It was quite a sight: 17 people crowded around one table with nothing on it but a very out of place looking eye. It should be noted that the table was no bigger than a common student’s desk. Shortly after that, I counted 21 people in that room. To say that this was an exciting day would be an understatement.

Friday was my final day. I spent the morning helping the fellows with research (mostly pulling charts and entering data). I left to have lunch with Teri, the nice graduated-resident-of-Wills that I was staying with for the summer. I came back to do some more work before a few of the remaining students suggested that we all get our eyes dilated and have a full workup by the photography department. Just a few of the photos taken:

Apparently I have a spot of pigment on my right iris...

The back of my right eye

The retina (as shown by the cake like layering), the fovea (the little dip in the middle), the Choroid (the bulging sponge like mass under it), the orbit under that, and the optic nerve to the far right. This is the macula of my right eye.

 We took our last photos as a group with the Drs. Shields and said our goodbyes. Dr. Carol gave me some great advice on applying to her alma mater: The University of Notre Dame. Exciting things including the strongly implied fact that all of the students who worked on the massive project would be given author status on the publication once it goes to print in about a year or so. She also said that any EXP-ers would be welcome to spend the summer doing something similar and I would be welcome back anytime… She actually said that she expects me to come back for another summer sometime again. Something tells me that my experiences in medicine are only just beginning…

Dr. Carol (center) and the students, 5 not pictured.

                As I finished writing this, I was actually offered another research job by Dr. Levin in the pediatrics department working on redefining convergence insufficiency. For reference, the study that I was working on for most of the summer had 1200 patients in it, and with 20 people working on it for 4 hours per day, it got done in about 2 months. In truth, it still has more work to be done on it. Comparatively, my the pediatric study is fairly large, encompassing some 800+ patients and with only 3 people working on it, something tells me that it will take a very long time to complete... 

Michael King - Week 8 - Loh Lab UCSF

Last week was a great week, as we were able to produce some very good results that were consistent with my postdoc's hypothesis. My postdoc will be on vacation for my last week, so we focused a lot this week on making sure I could do western blots on my own for the last week. Western blots are an important experiment in determining protein expression, and it really isn't too hard as my postdoc has already optimized his protocol. We conducted our final experiments on the cell cultures, and froze them down on Friday, as they will not be needed for this next week. Everything else has been going smoothly, and our lab also went out for lunch together on Monday. Next week a lot of people will not be in lab, though. When things are going well sometimes there is not always much to write about. I finally got a few more pictures of the equipment in my lab.

 An example of the results from the experiments we conducted. Above is a graph representing a cell titer glo assay, measuring proliferation of different cell samples treated with drugs. The bottom is the western blot of the cells treated with drugs to identify induction of certain protein expression.

One of the three hoods in my lab, where cell culturing is conducted to ensure sterility. The large centrifuge is in the background, and this is where I spent most of my mornings in lab.

 The setup for preparing the Vicell samples to measure cell viability. The flasks contain the various cell lines, and the small tubes in the front hold the samples. On the side are boxes of pipette tips, which we often run out of.

 Something new we got at our lab, the metal beads replaced the water normally in our heater. It is used to warm up cell media and various things used in cell culturing. The metal beads will help prevent contamination that might have resulted from dirty water continuously being heated, but they do not heat up as quickly.

 An important piece of equipment in lab, a microscope is especially important in checking for contamination in cell cultures.

 My flasks among some others in the incubator, which regulates the temperature and CO2 content. Incubators should not have any smell, and a strange odor usually indicates some sort of contamination, which was an issue in one of our two incubators.

This is the lab bench I work at with my postdoc. Lots of pipettes and multichannels along with various chemicals needed to process cells for the various experiments he conducts. Although it might look a bit cluttered, we utilize pretty much everything in this picture on a fairly regular basis.

My postdoc is in Alaska right now, and I will have to perform two full western blots by myself this week, but I am definitely ready for it. My time here is almost coming to an end, but I have definitely learned a lot about working in a lab.

Colette Gazonas-Week 6-Shadlen Lab, Columbia University

This week was my last week in Dr. Shadlen's lab. Because we had already finished all of the paradigms by the end of my fifth week, I dedicated the entire week to creating my poster. Yul asked me to create a new set of visuals and to create a rough draft of the entire poster on the template. Each day I sent him a revised copy and he would respond with feedback each night.

On Tuesday Yul, You-Nah, and I met to discuss how the poster was coming along. You-Nah read it over and gave me suggestions on how to make it better. I generated a diffusion-to-bound model and a more intricate illustration of the experimental procedure. I also fixed the problems I had encountered when graphing the logistic predictions.

Because my poster was near completion by the end of Tuesday night, Yul assigned me another matlab exercise. I was to simulate drift-diffusion using the software. To do this I repeated adding some random Gaussian random value until the absolute value of the accumulated evidence reached or exceeded beta. I utilized a for loop and scaled the mean in terms of delta t(time).

I ran this simulation for various coherences, both positive and negative. I simulated up to 3 seconds and ran 1000 trials per coherence level. Then, I plotted a histogram of the decision times.

On Friday I attended my last lab meeting. Afterwards my PI asked me to meet with him for a brief discussion about my experience in the lab. He asked me about what I felt I had learned, accomplished, and asked what he could do in the future to better prepare students in my position coming into the lab. He admitted that at first he was skeptical about whether or not I would be able to contribute anything to the lab, but said that he was pleasantly surprised and would consider taking on another high school student in the future. At the end of the meeting he offered to write me a letter of recommendation and told me that the lab should feel like a second home to me, so if I was ever in the area again I should stop by.

Overall, working in the lab this summer was a great experience. I learned much more than anticipated and am overly satisfied with the fashion in which I was both welcomed and mentored in the lab. I will definitely miss working with Yul, You-Nah, and Dr. Shadlen and hope that we will stay in touch in the future.

Chris Oh Week 3 - Gabrieli Lab, MIT

My third week at the Gabrieli Lab was tough but productive.
On Monday, I continued searching for tutorials that would teach me how to use Python to manipulate Excel spreadsheets.  Finding only few materials online helpful, I struggled for most of the day to figure out the basics.  By the end of the day, I was able to create and format a new spreadsheet.
On Tuesday, I was learning how to read exisiting Excel spreadsheets.  Because creating and reading Excel files require different libraries, I had to get used to the slightly different commands.  As Zhenghan asked me to do, I wanted to add a column for the Subject ID to each spreadsheet.  But again, editting existing Excel files require a different library, I was not sure how to convert to xlwt(editting) from xlrd(reading).
On Wednesday, Zhenghan was the speaker for our undergraduate/high school students weekly reading group.  Her presentation focused mainly on ASD, Autism Spectrum Disorder, and why it is important to learn more about the disorder.  She discussed the ongoing experiments regarding the language deficiency among ASD patients.  Most of the studies done on Autism are still inconclusive, which made the topic more interesting.  After much struggle that afternoon, I was able to come up with a script, but strange error kept occurring so I decided to seek Michelle's help.  Michelle and I wrestled with Python for almost an hour, and we were finally able to fix the problem.  When we opened the spreadsheet with xlrd and then copied the file with xlrt, we were able to write on the existing spreadsheet.
Finally on Thursday, I was able to write a script for overall average response time for each subject and add those numbers to the mastersheet.  I was even able to write another script to find the overall average duration for each syllable group, which yielded quite strange results.  In contrary to my previous assumption, the data showed that the longer the word lesser time it took for the subjects to respond.  The difference between the average duration for two syllables and five syllables was about 0.08 seconds.  After much thought as to why this was the case, I hypothesized that it must be because when subjects are presented with a longer word, knowing that they have limited time to respond, they rush not to get their responses cut off by the next scanner noise.  Now the only task left was to find the average response time for each syllable group in each subjects.
On Friday, by noon, I was able to complete my task by adding numerous if statements to get average response time for each syllable group in individual subjects.  I sent Zhenghan the finished products for her to look at.  Impressed by my work, Zhenghan asked me to meet with her on Monday to go over plotting the data.
What my script looks like:

Basic overview of my project (from Anna's PowerPoint):

Caroline Casey - Week 7 - Complex Systems Group: Edge Strengths, First Presentation, and Interference Distributions - University of Pennsylvania

This week was busy and exciting; I completed a lot of work and had my first presentation about my project, where I presented the PowerPoint that I was working on for the past few weeks! Dr. Bassett also invited me to present my project at the lab meeting on August 18, I am very excited and grateful for that opportunity.

Dr. Bassett was away on Monday and Tuesday. So, Monday I continued working on my paper; adding information and editing what I have so far. I also emailed Dr. Bassett a PowerPoint of what I completed the previous week when she was away.

On Tuesday, Dr. Bassett emailed me that she was intrigued by the community structure I got from the consensus partitions and suggested I look further into it. So, first, I completed community detection and consensus partitions on the brain coherence matrices (from the original fMRI adjacency (coherence) matrices in order to see if the community partitions were significantly different from the partitions from the networks where the edges of the correlation between interference and the scans (coherence matrices). I completed that and observed that the community partitions were significantly different than the consensus partitions indicating that interference plays a role in creating and changing the community structure. Dr. Bassett also wanted me to look at the edge strength of the networks. Since up until now I have been working with binary matrices, (containing only 0s and 1s) I went back and re-did everything using edge weights.

I continued working on re-doing everything with edge weights on Wednesday.

Thursday, Dr. Bassett and I met and decided that using binary matrices produced better results than using the matrices with edge weights, so we decided to stick to using binary matrices. Dr. Bassett and I also went over the PowerPoint that I would present to two other researchers on Friday. The rest of Thursday, I spent making changes to the PowerPoint.

Friday was a very exciting day. I prepared for the conference in the morning and at noon, I met with Dr. Bassett and we had a conference call with two researchers, Nicholas and Scott. I sent my PowerPoint to them and talked about each slide over the phone. Scott and Nicholas than gave us suggestions on what I could do with the results and data we have. It was really helpful to hear their thoughts and ideas! They suggested that I look at the distribution of the interference values for the different sessions in order to see if they follow a normal distribution, or if there are out-liars. I spent Friday completing the distributions for the sessions using interference values from the ANOVA and also using the difference between pre and post movement times for the sessions as interference values. After creating those plots, I went on to combining the interference values of the 20 subjects for both scanning sessions and splitting the now 40 subject group into 2 groups based on if the subject had interference or didn't have interference. I did that twice for the interference values from the ANOVA and the difference between pre and post movement times for the 2 sessions. For the ANOVA, if the p-value was significant, than the subject had interference. For the difference between pre and post movement times, if the difference was negative, than the subject had interference. I then completed a t-test between the two groups, for the two different ways I found the interference values.

I feel like I am learning so much at this lab, I am excited to see what else I learn and complete during my remaining 3 weeks at the lab!

Shivani Gupta-Week 6- Reddy Lab

Shivani Gupta-Week 6-Reddy Lab

                Unfortunately, our colonies for the BirA-YY1 fusion did not grow. We determined that the reason must be that we didn’t add enough DNA in our ligation reaction. We did the ligation over, and grew the colonies on amp plates. Luckily, about 25 colonies grew on the BirA-YY1 plates. I then did the mini-preps over using these colonies and then digested the BirA-YY1 with Xmal. After doing the restriction digest verification, we found out that only one of our 10 samples had the correct band length and we could send to sequencing.

                We then picked 10 more colonies from our plates and repeated the cloning procedure by first doing mini-preps and then the restriction digest verification. Unfortunately, I didn’t have enough DNA in my samples and had too much RNA, so I couldn’t see the bands when I imaged my gel for the digest verification. We think that it was because we may have lost some of our DNA during the mini-preps. Next week we are going to grow new BirA-YY1 colonies on our plates, and hopefully we will be successful.

                Thankfully, one of the sequences for the BirA-L2B matched the original construct, so I have successfully made a fusion protein!

                On Thursday, Dr. Crider came to visit my lab. Jen and Dr. Reddy came to lunch with Dr. Crider and I, and we ended up eating lunch in the newer part of the hospital. The cafe was so crowded, we ended up sitting at a kids table, but it was still a great experience!