Last Week at The Park Group - Week 5

Hi, this is Alyssa and I'm writing about my last week working as an intern at The Lenfest Center for Sustainable Energy at Columbia University.

Dr. Peretz visited my lab on Monday! I showed her around the 2 labs I primarily worked in, and we chatted with my PI, PHD student as well as other people in the lab. Reflecting on my experience, I would highly recommend my lab to future EXPers. The people here are always willing to help, and Professor Park even includes us the interns in group activities. It's like a big family: we work hard, and at the same time have a lot of fun.

On Monday night, we had a group dinner at an Indian restaurant nearby to celebrate's Camille's new job in London and to say farewell to her. I'm grateful for her guidance over the past few weeks and I'm glad that I get opportunities to bond with the rest of the Park group.

The last week of my summer EXP, our experiments were mostly on Tuesday and Wednesday. Naimun and I were asked to repeat the dilution experiments on 2 more batches of samples (same experiment as the one in week 2). So we acquired the solutions through the pump, and the two of us headed to the third floor to carry out dilution for the two batches of samples as directed by the lab manual. The rest of the week, we also used the ICP for a few more times.

So that's about everything I did during my last week at the Park Group. I said goodbye to my lab on  Friday and took a midnight flight back home. It was really, really nice working here this summer, and I would like to thank both Peddie and Professor Park for the opportunity. I will have a chance to present my research at Peddie next fall using powerpoint and poster, so see you then :)

The Gab Lab: Week 4

Hi, this is Michelle. I've just finished my fourth week at the Gabrieli Lab, a brain and cognitive sciences lab at MIT. If I had to describe this week in one word, it would be busy. Throughout the week, I continued my usual administrative duties whenever I had time to spare. These tasks ranged from more scoring, organizing, and entering data, to creating an official MIT certificate of completion for the subjects who had taken part in the CASL study.  I also scored these subjects' final exams, known as the HSK test. The HSK is China's standardized test of Chinese language proficiency for foreigners, and amazingly, nearly everyone passed after just 2 weeks of training! 

In addition to running a Session 1 on Monday, I also touched base with Amy, who decided that it was time for me to edit brains. As a result, I met up with Nayeon, one of the lab's many undergrads here through UROP (MIT's undergraduate research opportunities program). Nayeon showed me how to edit brains using Mindhive (MIT's portal for brain research) and FreeSurfer, a program created specifically for the reconstruction of the brain's cortical surface from structural and functional MRI data. Editing brains is a 5 step process that takes around 3 days to be completed. I spent the day going through the first three steps: skullsplitting (the thinning out of the skull to create an image of good quality), control point edits (the adding of white matter that the program did not initially include), and white matter edits (the editing of white matter volume to erase gray matter that is inside the surface boundary). While this was an informative and enjoyable experience, what I found surprising was how much computer skills were required. Not only did I have to use Terminal, which is code that commands a Mac, but FreeSurfer and MindHive were also heavily based on computer coding. I forgot to take pictures of the process, but I'll be sure to upload some next week because they are really cool.

This week I also had a lot of meetings. On Tuesday, Amy organized a statistics club for the LAP & CASL members. As this was the first session, we started off relatively 'simple' (for them!) by looking at the general linear regression model. Having little stats experience, I was nervous because I had not understood the paper we had to read. However, I found that Amy and Caitlin's (undergrad) step by step explanations were incredibly helpful, and by the end of the meeting, I understood everything and was active in discussion. This week we went over the basic regression model, matrices, and rank deficiency, and next week we will be continuing this. Then, the other interns and I gathered for a lunch meeting with Satra Ghosh, a research scientist who focuses on 'finding novel computational approaches for representing data in the context of clinical disorders, and developing models for diagnosing and predicting treatment outcome'. During these lunches, which were organized by post doc Joanna, we get the chance to ask these scientists anything we want. We talked to Satra about his bee farm, his dream to build a super robot, and his profession, which he refers to as a 'social engineer', because of the opportunity to interact with a very diverse group of people. Today we met with Dr. Maiya Geddes, who spends half of her time in the lab as a post doc researching cognitive reserve in aging, and the other half in the hospital as a clinical neurologist, where she meets patients ranging from having dementia or schizophrenia, to patients who are slowly losing their memory or ability to speak. This talk was fascinating, but the best part was when she offered to let us 'shadow' her in the hospital on Wednesdays, which we are hoping to do next week! 

On Wednesday and Thursday, I ran several Session 1's again, but was not able to administer the KBIT, as Kelly, who was going to approve me for testing, unfortunately was out sick this week. Following Amy's instructions, I also taught Lilla and Louisa (interns) how to use the LAP database to score production recordings. When we all met up with Amy today, we had many questions concerning patterns and individual language components (verbs, subjects, articles, conjugations), which sounds boring, but is actually extremely fascinating. As a result, Amy decided that I should further modify the database to include all these patterns that we have been noticing. Then, we discussed a cognitive neuroscience article about the different methods to study the brain (EEG, fMRI, PET, MEG), which was also highly informative and interesting. 

Next week, I will continue running Session 1's and helping out with fMRI's. I will also meet up with Kelly to discuss the psychological background and use of the tests I am scoring, have another lunch meeting with a lab member, and observe an EEG that Amy scheduled me for. Needless to say, I am super excited for my last week here at the Gab Lab!

Linksvayer Lab: mid Week 5

Hi my name is Ben Wagner and I've been working in the Linksvayer Lab at Penn. We work on evolutionary biology and collective decision making in ants.

At the middle of week 5 I am still working on the microsatellites project, still with hope that I'll be able to get onto an animal behavior in the coming weeks. To remind you what my current project is... I have been taking 15 ants from a large number of colonies, and individually crushing, adding buffers, centrifuging, letting incubate, and finally perform PCR on these samples. There are also steps of Nano Dropping, where I use a Nano Drop machine to test light refraction at certain wave lengths, telling me how much DNA in is the sample, and running gel electrophoresis after PCR, in order to see the size of my samples. We are looking for microsatellites, also known as Short Tandem Repeats (STRs), in order to tell the difference between the genetic codes of the different colonies. Due to the caste systems Pharaoh (and other) ants use, the genetic code of a single colony is very identical, and two sister worker ants are more related than any human is to another human on average, except for identical twins. We are not trying to sequence the entire genome because that takes a long time and is very expensive. Instead we are looking fro Micro Satellites, which we expect could be different between colonies. As an example,we might be looking for a code that says to make a little extra of a certain protein in one colony when compared to another, as opposed to the code that says grow legs, or something all ants do.

Unfortunately I am currently in an awkward spot in time, as we have run out of the Taq MasterMix Polymerase needed to run PCR, as well as multiple of the markers needed to do multiplexing, which is marking the genetic sequence. So for the next few days I am starting up on new colonies, and preparing them for PCR. This means the project is likely to continue even longer, since we had not originally planned on doing more colonies (past the amount from my last post), and because we need to wait for delivery.

Hopefully things will become more exciting here in the near future, but for now its back to crushing ants!

Computer Networking Lab weeks 2-5

Hi, this is Sohan and I am working in a computer networking lab at Columbia University this summer.

Over the past few weeks, my daily work has remained very similar. It mostly consists of running our experiment remotely on the Orbit Lab. Slowly I have progressed to running the experiment on all 400 nodes, which is a bigger accomplishment that it seems. More often that not , the nodes are unresponsive, or are unable to upload the requisite operating system for us to run our experiment unto their consoles (we usually run the most basic version of Ubuntu available but other experimenters upload other various operating systems best suited to run their experiments). On a good test run, typically 100 or so are unresponsive and another 25 fail to upload the Ubuntu operating system, but obtaining data for 275 nodes is more than enough.

More recently, Varun has had be deal with other pieces of code besides shell scripts. When running the experiment, we retrieve the data and it is stored as several hundred .pcap files on the computer (.pcap files are typically used to log the traffic passing across a wireless network). In essence, the .pcap files are a collection is millions and millions of 1's and 0's which obviously mean nothing to humans, but which the computer can interpret. In order to process the .pcap files, we use a Python script (python is a programming languages) which ultimately outputs information such as the total number of bytes transmitted or the average speed at which these bytes are traveling in KBPS (kilobytes per second). Working with Python was very new to me since prior to this, I had done most of my coding in languages like Java or in C/C++, but nonetheless, learning a new language like Python can never hurt.

The last new major change in my routine has been the implementation of certain MATLAB scripts (MATLAB is also another programming language). The MATLAB scripts are designed to take the specific numbers and data outputted from the aforementioned Python scripts and create histograms based on that data. Data is usually easier to interpret when presented visually and thus we can usually analyze the histograms and see if there are any changes to be made and if the algorithm is working.

Outside of the work, the lab experience has also been helpful and entertaining. There are 4 other member of our lab in the same work area as me and we frequently have conversations as a group about things besides our research. They all give me ample advice on college and what to do/what not to do freshmen year which typically, you can only learn from someone who has experienced it themselves.

I've really enjoyed my time working here thus far and eagerly await the next few weeks of researching!

Week 3 at the Donohue Lab

Hi this is Meg again. I just finished my third week of working in the Donohue lab at Duke University. Finally after about 2 weeks of setting of for my experiment, we were able to begin on Monday. To summarize my experiment, we will be putting seeds from different genotypes and different maternal conditions (some maternal plants were grown in hot temperatures and some were grown in cold temperatures) in dishes of different water potentials. Water potential (Ψ) helps to describe where water will move due to diffusion and more specifically osmosis; the area with the more negative water potential is where the water will move to. After the plates have been seeded, we will then census the dishes every other day to count how many have germinated. Once the all the data has been collected, hopefully we will find a threshold or base water potential (Ψ_b), which is the lowest water potential at which germination will still occur, for each of the genotypes and maternal conditions.

So this week on Monday, we started to seed both my experiment and an undergraduate’s experiment. Lien, the undergrad, is also working with different water potentials but her experiment focuses on a different aspect of water potential. However, she has a very similar setup, and therefore we have been working together on both projects. Overall, on Monday, we seeded 270 plates, 120 of those with 24 seeds, and 150 with 12 seeds, which made for a pretty tiring day.

On Tuesday we ended up seeding 50 more plates than we had originally planned, which meant that we seeded 270 plates again. Then on Wednesday, luckily it was a little less with 220 plates. On Thursday, even though it was the Fourth of July, we had to come in and finish seeding for our experiment. However, because we had done extra on Tuesday, we only had to seed 170 dishes, which meant that we were all able to leave the lab by around 1.

Buchner funnel attached
to Buchner flask

Funnel and Flask attached
to vacuum

In Lien’s experiment, the seeds are kept at in dishes with varying water potentials, just as mine are. However, after 4 days, the seeds are switched from dishes with negative water potentials to dishes with distilled water (water potential of 0). The goal of this is to see if the first treatment with varying water potentials helps the seed to progress towards germination, without actually germinating. If the negative water potentials do help the seeds progress towards germination, the amount of time it takes for the seed to germinate will decrease. In order to transfer the seeds to dishes with water, we first needed to rinse the seeds to ensure that all of the solution from the original treatment is washed off. On Friday, we began this process.

Cutting filter paper
with seeds on it

 To rinse the seeds, first we cut out the filter paper that the seeds were resting on in the plate and placed it on paper that absorbs the excess solution. Next, we placed a piece of filter paper in a Buchner funnel, which fed into a Buchner flask. The funnel is made of ceramic and has many small holes. The outside of the funnel is surrounded by a rubber stopper to create a seal. The flask has a hose barb so that a hose can connect the flask to a vacuum. Then we placed the now dry filter paper with the seeds in the funnel on top of the other filter paper. 

Rinsing seeds. The soapy-
looking water in the flask is
the dirty water that is sucked
in due to the vacuum

Next we rinsed the seeds twice with 10 ml of distilled water. Because there is a vacuum in the flask, but the paper cannot pass through the funnel, only the water that the seeds are rinsed with moves into the flask, leaving the seeds clean and sitting on dry filter paper. Finally, we placed the original filter paper in weigh boats filled with 20 ml of water, which is where they are seeded from onto the new distilled water plates. This whole process is really time consuming and stressful because the water scatters the seeds everywhere so that some are lost in the process. We couldn’t lose more than 12 of 24 seeds each time in the process or else there wouldn’t be enough seeds to complete the experiment. 

Rinsed seeds in weigh
boat, ready to be seeded

Also, because the time the seeds are placed in the dish is important to the experiment’s results, we couldn’t take any breaks until we had rinsed all the seeds for that day. As a result we had to work from 9 am to 3pm with no breaks. In addition to this, because plants don’t understand the concept of weekends, we had to work through the weekend, rinsing seeds for 6 hours straight. Finally this Monday we finished rinsing, meaning that for now on we only have to census the seeds since all seeds are in the correct plates and solutions.

Although my third week felt extremely long and stressful, and I haven’t had a day off in a while, this week was actually pretty enjoyable. In the weeks prior, seeding was pretty annoying. However, this time around, because it was my own experiment and we had been preparing so much for this week, the seeding was actually pretty exciting. I thought it was interesting that the in first 2 weeks of the lab I had just been helping everyone around me, but now everyone was actually helping me. In addition to this, the busyness of this week helped the days pass by quickly. I remember my first week in the lab the days seemed to last forever because all I really did was read articles since there wasn’t much else to do. Now that I’m a lot busier, my days feel a lot quicker and are a lot more interesting, making my overall experience a lot more enjoyable.

               

Fluorescence; The Crazy World of Wavelengths Week 4

Just a reminder, my name is Colton and I’m visiting the Buccella Laboratory at New York University. The lab is part of the chemistry department. More information about the lab can be found at  http://www.nyu.edu/fas/dept/chemistry/buccellagroup/ .

Monday morning started off early as usual. As I waited for everyone to arrive, I ate my breakfast overlooking Washington Square Park. It is such a beautiful view, but It isn’t just the view that is astounding; it’s a combination of NYU, their facilities and more importantly the friendly, intelligent people I’ve been able to work with.

Finally when Sarina arrived,(the graduate student I’ve been working with), I found out that I would be continuing my mini-project. My mini-project is fluorescent tests on 3 different compounds in various solvents, that I mentioned in “Fluorescence; The Crazy World of Wavelengths Week 3”. I had to finish testing compound 1c, which took up the morning and went into the afternoon.

The next day I planned to continue the experiment, but there was a catch. I've come to found that this often happens in research and it is generally time related. I could technically start, but I couldn't collect data till the following day. The issue was a matter of equilibration. Compounds 1a and 1b that I would now be testing had to equilibrate for at least 6 hours in 2 of the solvents I was testing them in, PIPES buffer and water. I prepared these solutions and all the others, so I would not have to take the time to make them the following day. After a quick lunch we continued our ATP titrations. A brief reminder; we are testing a fluorescent compound’s fluorescence when bound to Magnesium and the effects ATP has on the system. *For a more detailed background of the experiment please see week 2 and 3 of my blogs.  10 fluorescent scans had to be taken every ½ hour which meant we were going to be in the lab a while. Combined with our late start in the afternoon and the amount of time needed between scans, we didn’t finish the experiment until 8:30pm. It was all worth it in the end, we gathered the data we needed and found out that we don’t have to wait as long between scans in future experiments. On the overhand, we were still unsure what exactly was happening within the system. We believe it could be photo bleaching or slow equilibration. Photo bleaching is the breaking down of a compound over time as it is subjected to light (excited). Photo bleaching occurs at different rates for every compound, and the goal is for a compound to slowly photo bleach, meaning it can be excited multiple times before truly breaking down.  

The next day I was able to continue my mini-experiment on the UV-Vis & fluorimeter immediately. I have figured out a fairly proficient system for running my tests, which allowed me to finish them in a few hours.

Uv-Vis

Fluorimeter 

At group meeting this week, Debbie presented techniques used in the paper “Labeling Lysine Acetyltransferase Substrates with Engineered Enzymesand Functionalized Cofactor Surrogates”. You can access the article by clicking on its' title above. Although there was some information I did not have enough biology background to understand, I found that Debbie did well presenting the information, only adding to my comprehension. The big picture for me was learning more about the ways in which biology and chemistry interact.

Next week should be just as exciting as we begin to explore the reasons behind the results of the ATP titrations!

Working with the ICP - Week 4

Hi, my name is Alyssa and I'm writing about my 4th week at the Park Group at Columbia University's Environmental Engineering Department.

My PI and PHD student finally came back from the conference, and we started using the ICP to analyze our samples. Primarily, we worked in a much larger lab on the 3rd floor, where the rest of the Park Group conducts experiments.

 ICP is the abbreviation of Inductively Coupled Plasma mass spectrometer. It is used to detect metals and several non-metals at extremely low concentrations. The machine ionizes the samples with inductively coupled plasma (a type of plasma source in which the energy is created by induction) and then separate the ions using a mass spectrometer.

The process involves high temperature heating in the upper chamber and a cooling mechanism below it.     So as I was standing in front of the ICP, it was like being in two worlds - one sweltering and one cold. 

I would say the ICP process is rather straight forward - prepare samples, position test tubes, enter commands in the computer program, and GO! But since each sample takes 6-10 minutes and I need to make sure nothing goes wrong during the process, it needs to be watched over. One night, I even had to stay until 8pm to wait till the experiment was done. But the fascinating thing about ICP and the computer program is, I got to watch the testing needle dip into each test tube accurately, knowing exactly where the samples were positioned, and all I had to do is watch this happen. 

The rest of the week, I spent time reading papers from Dr. Park and helped Camille dumping some chemicals.