Week 2 at the Gab Lab

Hi everyone. This is Michelle, and I will be writing about my second week at the Gabrieli Lab, a brain and cognitive sciences lab at MIT. The beginning of this week was rather similar to my first week here. I continued organizing subject folders, updated subject test spreadsheets, and created an 'Assistant Production' and 'S9' (2 month retention test) tab, along with scoring guidelines for the database I had been working on earlier. 

Screenshot of the LAP Database

I finished all this pretty quickly, so I was asked to help out with CASL, LAP's sister project. Similar to LAP, CASL is trying to find predictors of good language acquisition skills in adults  by training subjects in a new language. The only difference is, LAP uses 'Miniature Artificial Language' (MAL), which is taught by animations and games, whereas CASL focuses on Mandarin, taught by a professor in a traditional classroom setting. I was given the task of grading homework and quizzes, taking attendance, and entering this data into the CASL database. 

On Thursday, I went to the weekly LAP/CASL meeting, where we went over administrative stuff and presented new data. I was asked by Amy to explain the database that I had made, and was happy to find that everyone was super pumped, as it is safer and more efficient than Excel in terms of storing data. Then, Amy said that since I finish stuff so fast, I could  help to write parts of the lab's paper if I wanted to. That night, I was also able to sit in and observe a fMRI scan, which needless to say, was really cool. It was nice to see how people prepared for a scan (NO METAL IN THE ROOM!), what subjects actually did in the scan (play animated games, take quizzes, and watch Arrested Development), and see amazing real-time images of the brain. 

fMRI machine

Today was part 2 of the 'Data Blitz' lab meetings, where around 20 people give quick 5 minute presentations on their work. Like last week, there was a huge variety of presenters, ranging from undergrads and TA's, to our PI John, and his wife Sue, who gave a compelling presentation about using cannabis to help schizophrenic patients. The meeting was 2 hours long, but the information was really interesting, plus there was pizza and bingo! 

Bingo, Half of the Data Blitz's Program, Presentation Room

Afterwards, Lilla (high school intern) and I met with Amy, who began explaining the different parts of the brain, and different methods such as fMRI and EEG. I noticed that my preparation in the spring really helped me, as I shockingly understood everything Amy talked about. Then, Amy suggested that the 3 of us meet every week to learn more about the brain, something I am definitely looking forward to. Next, I showed her my progress on the database, which she was very impressed by and grateful for. She then mentioned that before I left, the lab was thinking of getting all the high school students to do a mini data blitz, something that has me excited, but extremely nervous. I finished the week by playing around with the database, changing the format, and adding extra calculations and formulas to improve the experience.

I have definitely enjoyed this week more than my first week. While the database was tedious, I find that I am becoming more interested in using FileMaker to create a more user-friendly layout for everyone. I think this change in attitude came after I realized how genuinely grateful everyone was for the database, and how happy they were with my work. Next week, I will be testing subjects during training, and sitting in on an EEG. Oh, and I couldn't resist posting the pictures below.

Farmers market in the building & Tri-weekly ice cream bars..what?

More Carbon Capture Experiments & Responsibilities - Week 3

Hi, I'm Alyssa. Just as a reminder, I'm working on Fluidized Bed and Carbon Capture at Columbia University.

The third week, Dr. Park, my PHD student and a few other members of the Park Group went on a science forum in Delaware on carbon sequestration, so I worked for a Post-Doc candidate, Camille, on her carbon capture experiments.

Besides myself and Camille, a few more people were in "The crew": two graduate student interns Flora and Sarah, and Post-Doc June who just arrived at our lab on Monday. We performed 3 main experiments this week. I didn't take pictures of the machines, but I did find some detailed diagrams explaining the experiments.

1. Synthesis of Solvent for CO2 Capture: we made a nano-material solvent to capture CO2 from air. This went on for the whole week, so we did it step-by-step. The final solution came out on Friday, and all of us finally felt relaxed, since we'd be back to square one if we messed up a part of the process.

2. Differential Scanning Calorimetry: we carried out experiments to measure the melting points and glass transition temperatures of about 8 elements/compounds ranging from Boron to CsCl; We also observed the entropy of melting. This experiment was not too hard to operate, because all we had to do was to put the sample in and enter a few commands. It was a very time consuming experiment. We spent on average 2 hours on testing each sample and squeezed time in between testings to carry out experiment 1. We finished it on Wednesday.

Differential Scanning Calorimetry

3. FTIR Spectroscope: The objective of this experiment was to determine characterization of molecular bonds. We put a drop of aqueous solution onto a plate that has a diamond on it (not for decoration purpose, of course =P. Because the diamond is a very reflective material, it enables good reflection and enhances signals). And then, we connected the machine with an oxygen channel. Even though Camille did the first setup herself, she gave us opportunities to connect, disconnect, and operate the system. It's quite a complicated system, but it was fun learning how to link the spectroscope with different tubes. This was the shortest experiment out of all three - a one-day process.

The first experiment was performed at my main laboratory on 10th floor, belonging to Environmental Engineering Department; the last two were done at our other lab on 3rd floor, at Engineering Terrace. So you can imagine us running up and down in the Columbia Mudd Building, allocating time slots to fit all three experiments into our schedule. It's been a fulfilling week, and it was a great chance for me to learn more about carbon capture as well as get to know more people.

And lastly, a GOOD NEWS: ICP machine is back!! My PHD student Helios, undergraduate intern Naimun and I will be using it next week. This is something I've always been looking forward to, and I'm very excited for week 4!

Week 2 @ Microdynamic Systems Lab

In the second week I finished studying Robot Operating Systems(ROS) and received my first assignment on controlling the patterns of a string of LEDs based on the state of a robot.

Although I think otherwise now, studying ROS was a very challenging process.

Different from Java, Python, and C++, ROS is not about writing individual functions or programs but organizing messages from separate programs, which in my case are a combination of C++ and Python, and produce a feature of the robot. One of the most important concepts, for example, is "publishers and subscribers". There are many "topics" in a huge robot operating program, to which publishers give information and subscribers receive information. One of my jobs is to organize the relationships and abstract the right information for the right programs.

On thursday I began my first project. I need to design patterns of the LEDs on a robot that can tell people whether the robot is asleep, ready-to-move, unbalanced, or moving in a certain direction.

Beside the robotics, I understood more the relationship between management and technology. As I was studying ROS, I tried to make good plans and time myself in every section. However, all my plans failed because I simply didn't have enough knowledge to predict the my work and solutions to problems. I realized how knowledge in science is necessary and essential for business: if one cannot understand the science oneself, one could not organize a group to research and to invent. I shared my ideas with a graduate student who came new to CMU five months ago from India, and he suggested that management should also consider creativity: if the management is too strong, the engineering will not be able to produce surprises.

Tissue Morphodynamics Labratory: Weeks 2-3

Day 5 Chicken Embryo

My second week of the lab was a little chaotic due to the Princeton bomb scare, which set back  my laboratory safety training which in turn set back my general laboratory training in microdissections. Due to the Princeton bomb scare, I was unable to start microdissections because the chicken eggs had grown past a viable embryonic stage for tissue culture. My laboratory manager told me it would be another week before I would able to start dissections for tissue culture. The second week therefore consisted of more reading and more articles about different topics, such as RhoA pathways and e-cadherins. Through these articles I learned about how pathways regulate tissue in the epithelium as well as the importance of e-cadherins in developmental biology. At the end of the second week I was also given a host of data and images to organize, analyze, and graph.

Lungs of Day 5 Chicken Embryo

At the start of the third week I finally started to learn the multiple techniques and solutions I would need to use in order to analyze chicken lungs under a confocal microscope; however the embryos were still unable to be used for tissue culture. I started by dissecting the lungs out of a day seven chicken lung under a dissecting microscope using two 5mm forceps. In order to extract the embryo from the egg, I took a syringe and poked a hole at the bottom of the chicken egg and removed some fluid in order to lower the yolk height in the egg. Then using a scissor, I cut a semicircle at the top of the egg, removed the shell and scooped the chicken embryo out of the egg and on to a petri dish filled with saline PBS solution. After successfully dissecting four lungs out of chicken embryos I learned how to fix the lungs in preparation of staining. Fixing the lungs is essentially using a solution in order to preserve the tissue of the organ and allow for storing overnight. After fixing, I stained the lungs using LCAM antibodies, which are antibodies that bind to e-cadherins on the epithelium and creates 
contrast between the epithelium and the mesenchymal tissue.  

 

Fixing and Staining of 4 Day 7 Chicken Lungs

Towards the end of the third week I was given more data to analyze, which was mainly measuring the lengths and area of the epithelium using Adobe Photoshop and ImageJ as well as counting the number of terminal end buds of previously stained chicken lungs. I also attended a microfabrications seminar with others in my lab in order to better understand how to amplify signals using biosensors on a plate. 

Making Isosteres - Week 1

The first week at the lab was really interesting and fun except for the fact that I almost broke a finger (which had nothing to do with the lab but I had to take a day off for it). Overall I was happy that I wasn't burdened with piles of articles but instead got to do a lot of hands-on work. The lab is pretty messy, my PI said that they don't do a very good job making things neat and orderly unless there's an inspection. There are only two other people besides my PI and me in the room, a grad student and an undergrad. They were pretty busy with their own projects (which were similar to what I'm doing) so I mainly worked with my PI directly and a post-doc who's working next door. Unlike some of the other labs, I didn't have to go through hours of training sessions. On the first day, basically as soon as I arrived, my PI started writing chemical structures on a blackboard  and told me that this is the reaction that I'm doing. Then I followed the instructions to weigh out the solids and get the correct volume of liquids and put them in a round-bottom flask. Although I've used all the instruments before (analytical balance, weighing paper, syringes, pipettes) and the task wasn't particularly hard, I was still a little scared because I was handling all these glassware and chemicals on my first day. The reaction I set up was a reflux reaction in which the flask is placed in a hot wax bath with a condenser on top so any solvent that evaporates will go into the condenser instead of falling back into the reaction solution.The purpose of the reaction was to replace a proton with an isobutane, the first step in a three-step process that would result in an isostere of 1,3-cyclopentanedione, the chemical I'm currently working with.

On the second day, I worked with the post-doc the whole time. He demonstrated some of the more complicated (but actually really basic) processes like thin layer chromatography (determines the solvent condition suitable for the compound and checks if there are products made), column chromatography (a tedious process that may take over an hour, separates the product solution into fractions, the fractions are then tested using TLC to see which ones contain the desired product), and purification methods including using water to quench the reaction, using ethyl acetate to separate the organic and inorganic layers, and using sodium sulfate to eliminate any left-over water. These are the standard procedures for almost every reaction that I will do.

Next day morning I got a black fingernail and went to the lab in pain. My PI showed me the Liquid Chromatography-Mass Spectrocoply (LC-MS) machine and tested the solution I collected the day before. The LC-MS basically runs a mini-column and presents a graph on the computer that contains peaks. These peaks represent the compounds in the product solution; the machine gives the molecular weight of every compound and we are trying to find the peak with the molecular weight that corresponds to the product we want. If it is a big peak then that means the reaction is successful and we got the right product. There are other peaks on the graph that corresponds to the left-over reactants and some side-products. Unfortunately we could not find the right peak and even my PI couldn't figure out what happened. After lunch I went to the ER because the finger was starting to bother me a lot. Since I couldn't use my right hand, I stayed in the dorm the next day.

After the weekend, I still couldn't use the bruised finger but my PI said it's fine and he'll help me do anything that required my right hand index finger. I still got to set up the next reaction, this time in a cold bath made of dry ice and acetone. Meanwhile we did more LC-MS tests on the product of the previous reaction and found that our desired product exists but in a very small amount compared to the main peak that had a different molecular weight. So the week ended with an unknown product.

Cognitive Development Lab

I have been at the lab for almost three weeks so far and I have really come to like it considering how the first week and a half went. I arrived on the first day and met my lab manager, Alex, and another RA, Kafu, who is a junior at Rutgers. The first week and a half of the lab is dedicated to training, and since most RAs only come in once a week and I come in every day, I received the same training every day for a week, which was frustrating, especially considering that the first training was on cold calling, or dialing up strangers and hoping they would want to bring their children into a lab. As time went on though, the work got more interesting. Several of the more senior RAs have asked me to help them with the details of some of their work, and I got to go with two PhD students to a preschool to do testing, which was fun.

At the lab there are 14 or so RAs, 11 of whom are new, two who have been there for one semester, and one who has been there for three years. There are also 3 graduate students, one post doc., and a lab manager. The grad students, post doc, manager and senior RA are all doing original research in child cognition, morality, false belief and other topics related  to Theory of Mind. Most of these studies involve either an eye tracker, for studies on children who cannot talk, and stories with question on the intentions of the characters at the end for kids who can talk. Most subjects are I may have been wrong about the fact that children develop a theory of mind at four, as a paper (Onishi and Baillargeon 2005) has provided proof, using an eye tracker to understand the mental state of the subect, that kids may have a theory of mind as young as 15 months, raising the question: Why do 3 year olds fail a verbal test (explicit test) for theory of mind but pass a test using an eye tracker(implicit test)? Anyway, here's a picture of some of the people in my lab

The person on the left is lu, a grad student. The guy in the sombrero is the lab manager, Alex. The girl in the white strippy t-shirt is Cami, an RA, and to her left is Michelle, another grad student. Behind Michelle is Katya, the post doc, and the woman next to her is Sydney, a grad student. Next to Sydney is Alan Leslie, the PI, who I've never met. 

This is Talia, the senior RA whose asked me for some help as she prepares for a research trip to Peru to study universal moral grammar 

Buffer, Learning and More Buffer- Week 2

I was awoken at 5 am by my alarm and by 5:30 my journey back to NYC began. I arrived to the lab a bit early and waited for Brismar to arrive so we could start analyzing data from the previous week. I found out we had to gather some more data since analytical chemistry requires multiple trials of the same experiment. This way the compiled data is the most accurate.

We thought we were finished making the buffer last week, but as it turns, in making another batch, that we may have added to much KOH. So to test our assumption we checked the pH and found that the buffer we made last week had a pH of 7.09 not 7. Even though it may seem like this is not a big difference, the pH that the solution is buffered at is really important. Especially when using it for our experiments, where a small change in pH could completely upset the fluorescence of a compound or its binding ability. In the ended we ended up having to spend two days making new buffer, but this time we carefully added KOH so that the pH was exactly 7.

This week NYU had a guest speaker in the chemistry department discussing bio-imaging, similar to what our lab does. With our professors suggestion, we all went to the seminar. I found the presentation extremely interesting. Him and his group are developing fluorescent probes that are able to detect different types of cells in the human body. The fluorescent sensors choose certain cells based on unique proteins and other characteristics unique to a type of cell. For example, his one probe detects stem cells, so when injected into an organism only stem cells would fluoresce. This able to show where concentrations of a type of cell exist. The goal is to be able this with all different types of cells.

In addition to this presentation, our professor gave us a presentation on presenting science, whether it be presenting research within our group or at a conference. Some of the major points I took from the presentation were 1) thinking about who your audience is, 2) what do you want them to know, and 3) make sure it's professional, not only so your audience takes you seriously but also takes your science seriously. She made it clear, multiple times, if you don't seem serious, then why is your science serious, or if you appear sloppy and your presentation is sloppy, then who knows if your science is sloppy.

The week ended with planning and preparing for an experiment Sarina and I will start Monday. We will be studying the fluorescence of three compounds in different solvents. I'm so excited to start another week because the learning never seems to end!  

Week 1 at the Donohue Lab

My first day in the lab, I was the first to arrive. I had somehow overestimated my total travel time by about 30 minutes, even though it was a simple 10 minute bike ride. As a result, I showed up at 9:30 and waited in the hallway until someone showed up at 10, when I was supposed to arrive. Finally an undergraduate student, Lien, arrived and unlocked the door to let me in. She told me that she was a rising sophomore at Duke and that we would be working on the same project together. Since the lab manager who will be helping me this summer was running late due to a doctor’s appointment, Lien began to introduce me to the project. She gave me a paper that Bri, the lab manager, had given to her to read that was a good introduction to our project since it outlined the procedure. Basically in my project, we will be keeping seeds from five different genotypes, some of which were matured in hot conditions and others in cold conditions in different water potentials for 4 days. After 4 days, they will be moved to water and the amount of seeds germinated will be counted. However we aren’t starting this project until another couple of days, so until then, I am busy helping with another experiment. After I finished the paper about my project, I met with Bri, and she told me I could start censusing seeds. This basically means counting how many seeds on a dish have germinated under a microscope. It actually is harder than it sounds because the seeds are really small and often the root that breaks from the seed is clear. As a result it took me a while to get a hang of it, but by lunch I was doing alright.

Plates with dishes that needed to be censused

When I returned from lunch, Bri had to go to a lab meeting, so I continued to census, which gave me an awful headache after a while. Then at 3, Bri came out and told me that me, her, Lien, Tarek (the postdoc), and Dr. Donohue were going to meet to discuss our project. I headed into Dr. Donohue’s office and waited for the meeting to start. Basically we talked about what the point of the project is and what Dr. Donohue wants us to focus on in the next couple of days to prepare for the project. Then we planned what papers we should read and what days we would discuss them. The meeting ended around 3:45. When we came out, we discovered that one plate had yet to be censused. As a result, Bri asked me to finish it. I finished around 4 and then looked around and everyone was beginning to leave. I turned to Lien to ask if we were allowed to leave and she told me we could so I packed up my stuff and headed home for the day.

On my second day, I showed up too early again, but luckily this time Bri was already here so the lab was unlocked. I asked her if I should begin censusing again. She told me that I should and then showed me to the room with all the plates of seeds. She explained to me the system that they used to know which plates had been censused, and which still needed to be done that day. I started by grabbing one plate and initialing that I had done it. By 1, I had censused about 6 or 7 plates, which meant around 180 dishes, each with around 12 seeds on them. But luckily, between me and Lien, we were able to finish all the censusing for that day by lunchtime. As a result, when I returned from lunch, Bri told me and Lien to review some papers since we will be discussing them on Friday. I spent the rest of the day reading and taking notes.

On Wednesday, another group needed help preparing their project, so rather than census seeds, my group helped them. We had to seed, meaning that we had to put 20 seeds on Petri dishes filled with agar in a 5 by 4 grid. The seeds were extremely small, making the work quite tedious. However, it gave me the opportunity to talk and get to know people from the lab who I normally don’t work with.

Then after lunch, we finished seeding, so I began to set up for my project. This meant cutting and counting 1200 strips of filter paper that the seeds were going to rest on in the dish.

On Thursday in the morning we did more censusing and then I finished cutting and counting the strips of filter paper. After this, I reviewed a paper that we were going to discuss together on Friday. When I returned from lunch, I cut and poked holes in weigh boats for my experiment so that they would fit in dishes where the seeds were going to grow.

Censusing in the field

On Friday, I had to come to the lab an hour early because we were going to go look at the field experiments which are about a 15 minute drive from the campus. There were three different experiments that were taking place. However 2 of them were finished for the summer because seeds were no longer germinating due to the heat; they had entered secondary dormancy. One of the experiments was still going on though so we censused the seeds that had begun to bolt and marked them down on a sheet of paper. It was surprisingly tiring and by the end of the morning my knees were sore from crouching to count seeds. However, it was cool to be able to see the lab’s field experiments, even if they were all overgrown. After lunch I censused some seeds in the lab and then discussed a really confusing paper that pertains to my project. Walking into the discussion, I was nervous that I wouldn’t know anything. However, once it started, I soon realized that I actually did understand most of the paper, and that it was ok if I didn’t understand everything. This reassured me, and by the end of the meeting, I was active in the discussion and actually enjoying myself. 

Overgrown field with weather station in middle
that records weather conditions of the field

This first week has been long, and sometimes tedious with all the censusing and seeding. However, the people in the lab that I work with have been really welcoming and have so far made this experience really fun, even though I was nervous and apprehensive walking in. I’m now excited to get to know everyone better and working on my project in the upcoming weeks.  

Staining and Running Gels - Week 2

Week 2 at my lab started off with just reading at my desk. I would always
get there around 9 but Neha would usually get there at 10:30 so for an
hour and a half I just read papers, checked my emails, and did any
unfinished work from the previous day. The Matsunami lab has a journal
club where all the grad students present a paper they read on Monday and
Hiro buys us lunch. It's like when we presented the scientific papers we
read in fall term only much longer, more sophisticated and of course with a
more in-depth understanding of the topic itself. All these papers are
related to olfaction in one way or another. This week Neha presented a
paper on "Sexually Dimorphic Neurons in the Ventromedial Hypothalamus"
that govern mating in both sexes and aggression in males. I tried reading
the paper in advance to prevent any "getting lost" but eventually she lost
me in the middle of discussing the different techniques. The parts that I
understood were really interesting. Next week, Jianghai is going to present
on Ectopic Olfactory Receptors and I have yet to read the paper!
After the meeting, we did Phospho S6 staining on four slides (2 control and
2 test), Caspase-3 staining on another four slides (2 control and 2 test)
and 2 negative controls. Phospho S6 and Caspase-3 are both antibodies
that will bind to the respective proteins in the cell. The S6 protein is
phosphorylated only when mRNA is being translated so the test mice
(which were put in the two paper buckets with acetophenone) slide should
have more staining than the control mice because acetophenone is
activated. Then we added a secondary antibody that would bind to the
primary antibody (Phospho S6 and Caspase-3). We also washed the slides
with blocking solution (which is actually skim milk!) because it prevents
any non-specific binding of the antibodies. We want our secondary
antibody to bind to our specific primary antibody. With the Caspase-3
staining, the KO mice without the RTP1 and RTP2 proteins would have more
staining because casp-3 is an indicator of cell death. Neha told me that the
smell cells of the mutants die quicker so there would be more staining in
the KO mice than in the WT mice. The 2 negative controls just had the
blocking solution and no antibodies.

After the staining we put the slides in the cold room (-4 degrees). We then
took pictures of the slides on the microscope with different light filters. We
took all the photos in black and white so they're not as pretty as you would
see on the microscope. Yesterday I started counting the positive cells for
the staining, and the number of cells with nuclear staining (bisBenzimie).
Crider came to visit at around 4! and I introduced her to Neha. Neha
showed her around the lab, microscope room, and the dissection lab. She
also got to meet Hiro!
Then Crider took me and Meg out for dinner! The food was good, but I'm
not going to comment on the restaurant itself! Thanks Crider for a nice
evening! You made me think of the bike trip and, oh, how I miss it dearly!
YOBTO '12

The next day, Neha went to the animal house and clipped the mice pups'
toes to collect DNA. Thankfully I didn't have to do any of that. She came
back with 15 tubes each containing little toes - which freaked me out at
first but then we mixed tail buffer and proteinase K to each tube to degrade
the proteins. We put these tubes into the PCR machine. Then we made a
master mix that contained water, 10x buffer, 2mM dNTP, Taq polymerase,
and the forward and reverse primers of the sequence. We centrifuged the
tubes and ran gels to determine the genotypes of the pups.

On Friday, Neha transferred the pictures we took from the microscope to
her computer and I spent 4-5 hours counting the number of cells in the
neuronal layer, the number of positive cells from staining and recorded the
area of the neuronal layer. Although I don't like the computer work very
much, my work in the lab has been very balanced between hands on
experiments and data analysis on the computer.

Hope everyone else is having a good time!

The Gab Lab: Week 1

My first week here was relatively uneventful. The first day, I met with Jenni, a research affiliate with whom I will be working with. She gave me a quick tour of the building, introducing me to several post docs, grad students, as well as showing me the fMRI and EEG rooms. I have to admit, all the winding hallways were rather confusing at first (the McGovern Institute for Brain Research is the largest neuroscience center in the world!), but I am glad to report that I have learnt to navigate them. Perhaps what surprised me the most was that the workplace isn't a typical 'lab' setting. Instead, it resembles an office, with most of the work being done in little computer-filled rooms. Here are some pictures of the building, including the very cool 'Jungle room', which has a ping pong table!

I came into the lab with no idea on what I would be working on, but I assumed that it would be on dyslexia, as that was the most current news on the lab website. However, Jenni explained that I would primarily be working on the Language Acquisition Project (LAP), a project funded by the Department of Defense to see if there are certain brain markers that indicate which adults will be better at learning new languages. To do this, subjects first take many IQ and memory tests in order to establish a neural baseline. Then, they learn the artificial language 'MAL' (known in the lab as Silly Speak) in several training sessions. They also take take an fMRI and EEG before and after these sessions, and we track their progress throughout this time via assessments. Finally, they come back after 2 months, and we test how much of the language they have retained. Jenni is also working on a 'Soldier Study', a joint project with the US Army to investigate the effects of caloric deprivation and stress on a soldier's cognitive functions. If I have time, I'll probably help out with that project as well.

Before all this cool research, I first had to take a long and tedious online training course. After I had passed, I spent the remainder of the day creating new subject folders, which entailed printing and copying a ridiculous amount of papers, and then organizing them. The second and third day, I had to go through all the completed subject folders and score the KBIT (IQ test), the MLAT (Modern Language Aptitude Test), as well as a syntactic word puzzle. Grading these and entering them into the database was incredibly tiring (and rather boring...), but I finished quickly and was able to leave the lab before 2! I also briefly met with Amy, a post doc who I will be working with starting next week (Jenni is leaving to Switzerland). She gave me the project's grant, as well as a review to read for more background info. The fourth day, I continued with more mundane administrative stuff, as Jenni gave me the task of creating a spreadsheet that detailed the lab's payment to all its subjects for each session. Here is a quick pic of my working area:

Today, things began to look more interesting. First, I attended the LAP & CASL (Chinese language test) meeting. After an hour of going over what we would do next week, the ten of us went to the lab meeting for the entire lab. The Gab Lab is huge. There are around 40 people, all working on different things. Here, I was introduced to a whole bunch of people, including my PI John Gabrieli, who is super funny, nice, and laid back (like everyone else in the lab), and Cirkine, a fellow high school intern who I share a room with. I was lucky to start this week, as this meeting involved around 15 people presenting on what they were working on, so I got to hear about topics ranging from autism and dyslexia, to marshmallows! Moreover, everyone got a bingo sheet with words the presenters talked about, so I was paying especially close attention. Afterwards, I met with Amy again, who has scheduled me for more hands on research in the coming week. Not only will I assess video recordings of subjects speaking MAL, but I will also sit in on an fMRI scan, and learn to edit brains! However, before I can assess these recordings, Amy had Michelle (a recent Brown grad who just started working here) teach me how to use FileMaker in order to create a database for the LAP Study. 

Although all this computer work has been pretty uninteresting, I am starting to see that most of a neuroscience lab's work is completed through collecting and organizing data. Yes, this is the not so glamorous side of research, but I am starting to appreciate how significant this data is, as well as how useful computer skills can be. Nevertheless, I am definitely looking forward to more practical work in the coming month, and have enjoyed my first week here. Next week 2 more high school students start (there are 10 of us!), and the three-times-a-week ice cream bars continue! What's not to like?

Week 1 (and a half): The Art of Crushing Ants

This summer I'm working at Penn in the Linksvayer Lab, which is focused on evolutionary biology through animal behavior and genetics in ants. At first my work was set back a week by a full safety class. But on June 10th I took the safety class, and after long commute by car, then train, then walking, (about 100 minutes in total, half train, and split evenly between car and walking) I started Tuesday June 11th. Although the lab focuses on animal behavior, because of my past experience in performing PCR (thank you Dr. Peretz and BioTech class!), I am starting off by comparing micro-satellites (points on the genome which we expect to change) in the different colonies of Monomorium pharaonis, called Pharaoh Ants. To do this, we (Me and Riley, the grad-student working with me), are taking 15 ants per colony, for about 15 total colonies, and going through the process of separating each ant, crushing them using a pestle and liquid nitrogen, applying many buffers and Elution, and going through tons of centrifuging. This is what I have been doing for the past week. Starting this afternoon I will begin applying 4 different marker sets to identify the ants, performing PCR, and getting each ant sequenced. For those of you doing the math: its 15 ants x 15 colonies x 4 marker sets = about 900 ants micro-satellite sequences!!!

The most amazing thing about the my experience so far is that this project is MY project! Riley has some of his own stuff, and works with me often, but the project is mine to do and complete, and the info is going to be used for future projects. I should be done this by the end of next week, and then I really start working with everyone on a BIG animal behavior project (which I'll keep a secret for now!). But once that project is finished, I'll be able to compare my results from the micro-satellite to make a final determination about the results from that project, tying in most of the work I'll be doing during my 8 weeks.

There is one more EXTREMELY awesome thing about my experience here. While Dr. Linksvayer's lab is amazing, and I'm becoming friends with the other 8 or so people working here, I have the added bonus of working with another lab! Riley has until the end of the summer to decide between Dr. Linksvayer's and Dr. Berger's lab, so in the mean time we work in both. Dr. Shelley Berger focuses still on ants, but specifically epigenetics. Dr. Berger has a lab of about 35 people, and works in the very high tech Smilow research center, still at Penn. Riley is working on completely different projects at Dr. Berger's lab, and I've gotten to help him over there when we have some time in the afternoon. There I've been able to use really high tech machines, like a Sonic Crusher, which they use to crush ant samples WITH SOUND instead of using a pestle. I've also been able to attend lab meetings, talks by visiting experts, and hopefully next week I'll be doing an ant brain dissection, which has absolutely nothing to do with my work, but everything to do with Riley's.

Not only am I getting great lab experience through my work, but I'm getting to see the work of dozens of other researchers, who are glad to tell me (and brag) about their research. I also get to compare the feeling of a huge and older high tech with a small and newer lab. I can't wait to continue my work and eventually move onto animal behavior, and I'll keep everyone posted with how it goes!

NLP week 1: visualizing social networks

This summer I work at Center for Computational Learning Systems at Columbia University.  It's great to work at a computer "lab," because we basically go to work whenever we want, and leave whenever we want.  Why?  Because computer science people are typically pretty motivated and self-disciplined, and they probably work even more at home (at night) than at work during the day.

The focus of my mentor, Apoorv, is to have computers extract a social network from text--that's right, it means computers will have to "read and understand" English text!

My job this first week is to simply build a web interface to the system that accepts arbitrary text input from anyone on the Internet, passes it on to the program that Apoorv and his team have built, collects the output of their program, parses it and visualizes it in user's browser.  Sounds too abstract?  See the following example.

In the screenshot above, the circles (vertices) are "occurrences"--each time a name appears in the text, it is an occurrence.  The arrows (arcs) between vertices denote observations (as in "I see you in the restaurant," where "I" am aware of your existence, but "you" are not aware of "my" existence).  Another type of connection is called interaction, where both parties are aware of each other.  If you are interested in this notation, read Apoorv's paper.

In the next step, I will post-process the result from Apoorv's system, and merge occurrences--as you can see, Charlie appeared three times in the generated graph above, and in the next version it will be merged into one.

In another word, I am just building a demo system to allow more users to try our system.  You may have noticed that the arrows are completely in wrong directions, and some of the connections should have arrows in both directions.  Yes--it's a known bug, and we are still trying to figure out why.

Let me show you the stack.  Bottom-up, there is Apoorv's Java program, and then a TCP socket server that I wrote in Java that listens locally for requests, parses the results in .net format and generates JSON results.  A Node.js program that I wrote with the Express framework is on top of my socket server, and it simply serves this webpage above, passes English sentences down to the Java program and transfers JSON results back to the browser.  Visualization happens mostly in your browser, in which I used D3.js library to help me to calculate the locations for the circles and lines according to physics laws, and SVG to actually represent them.

Bonus: a graph for you to play around with (a modern browser that supports SVG is required).   You can drag anyone to move them around!

Hope you liked it!

The real research hasn't started yet.  Hopefully I will actually get to the natural language processing part as early as next Monday, after I finish working on this web interface.  So, see you next week!

Added Responsibility - Week 2

Finally, a little more responsibility.  The end of my first week in lab finished with a bang as I was invited to take the validation of a new assay to completion.  Because this lab processes active patient samples, each test and modality used needs to be validated before hand.  This involves running the new and old test side by side and comparing results, specificity, and sensitivity.  Because all samples used in a validation are from previous patients, not current ones, I was able to run some of the tests.  The new assay we were testing was for HepB, both the initial antibody testing and the confirmatory assay.  In total we ran about 500 samples (at least 3 times each) and ended up with a 14 page excel sheet to prove it.  This project was a major improvement over the beginning of my week and offered some hope for the future.

My expectations were met toward the beginning of my second week.  Having observed most of the benches and tests in the lab, my PI Dr. Hodinka decided that I should get more hands on experience.  One of the tests he wanted me to run was a Western Blot HIV confirmatory assay.  This test detects proteins in a sample (HIV antibody in this case) by binding them to a strip.  Each band on the strip represents a different protein and the intensity of each band can indicate the severity of the virus present.  The blot that I ran compared two lots of controls; a high positive, low positive, and negative control.  Because this test is slightly outdated, it is preformed over night and is very labor intensive.  I had to mix my reagents and manually add them to my plate.  

HIV Western Blot      

The most exciting part of the week in my opinion was the indication that my project would begin sometime next week.  Because most advances made in the field of clinical virology in the future will be in the molecular testing area, Dr. Hodinka will most likely give me a project involving PCR of some kind.  After months of having no clue what I would be doing in the lab, this little inkling has me pretty excited.  Being the "gold standard" of molecular testing, RT-PCR (real time polymerase chain reaction) is highly specific and is a relatively efficient way of identifying and diagnosing viruses present in sample.  Differently from traditional end point PCR, real time PCR can detect amplification as it is happening and accurately report how severe an infection is based on the number of cycles it took a positive sample to pass a threshold.  This is a very useful piece of information for clinicians when making a diagnosis.

Overall I am very excited about the remainder of my time in the lab.  The people who work here are very friendly and always willing to explain something or offer insight when I need it.

Week 1 at Ware Lab of Rutgers Newark

Day 1
On the Thursday 2 weeks ago, my first day began with Dr. Ware, my PI, introducing me to all the equipments in the laboratory, showing me pretty much where everything is around Rutgers, introducing me to other students, both graduate and undergraduate, and giving me the first assignment of the day. I also received my first project - I will sequence erythemis, a genus of dragonfly which many of its species have not been studied in the past, and are ambiguously placed in the phylogenetic tree. Aside from placing known species into the tree correctly, I will also determine if some samples are actually new species.

Crosslinker in action - a convenient device used to
sterilize equipment with x-ray

There are about 10 members in the lab, most of them on the first day were away either in vacation or field studies.My first assignment is to learn about some basic safety precautions, and how to extract DNA from sample insects. Dr. Ware told we to always sterilize every piece of equipment with a Crosslinker (see picture on the right) and wipe surface with ethanol. On the other hand, DNA extraction is a bit similar to plasmid transformation experiments during Biotechnology classes, except I have to first soak tissues into chemicals. On my first day, I used 2 legs, each from a dead cockroach, as an example. We preferably pick the legs of insects, since legs have the most amount of muscles to extract DNA from, and the least amount of exoskeleton to deal with.

After I soak the legs into 2 chemicals that lysed all the cells and left only DNA behind (see the picture on Day 6), I incubate it for further extraction (the rest of the procedures is pretty much the same as plasmid DNA extraction, with all those spin columns). After extractions, we run PCR with the extthermocycleracted DNA in a thermocycler. Again, this is really similar to what we did before, except there are different thermalcycle and primer you can choose to target a specific gene to amplify. Instead of Tacq, I used a different primer and chose a different thermocycle to amplify 16s gene, an rRNA gene.

Day2
This day I met one of the graduate students of the Lab- Melissa. She's working on a different project aside from mine, but she understands and can guide me through experiments.

Today I received my results from PCR, and run a gel electrophoresis with the amplified DNA. I also repeated the experiments yesterday with 6 dragonfly legs, marking the start of my project.

Day 3

Gene alignment - matching and aligning the genome of
differen species into a comparable form.
Usually you can shift a sequence by 1-4 cells to
fix a frameshift mutation, and the sequence will align
itself automatically, much like what I got above. But eventually,
 however, sequences will go haywire like the picture below,
and become difficult to fix.

Coming back from weekend, today my professor was away in the morning, and I was told to read some papers and articles. After lunch, I spent the rest of the day learning how to align gene sequences (see pictures on the left).

Day 4 and 5

On day 4 I met another graduate student - Will. He is a very outgoing person, and aside from lab works, I asked him about student live and culture around Rutgers. For my assignments today and tomorrow, I continued to align sequences, and run another PCR with different primer and thermocycle to target another gene to amplify, then I ran another gel electrophoresis.

Day 6

The piece of leg form collector,
soacked in chemicals, after
incubation.

Today, I received a leg of erythemis fro ma collector, and I performed DNA extraction, PCR and gel electrophoresis again, just this time I will try to preserve the leg as much as possible, returning it to the collector later on without deforming it. 

After today, my professor and most graduate students would go to Germany for a conference, so over the next week, I will attend a safety training course required to work in labs at Rutgers, and spent time reading articles and papers, and aligning sequences.

An Opportunity to Learn about Carbon Capture - Week 2

This is Alyssa, I've just finished up my second week of research on fluidized bed at Columbia University.

The beginning of week 2, I finished up looking at my assigned reading from the book Fluidization Engineering. At first, I thought I was going to carry out the fluidization experiments this week, but it turned out that the computer still needed a compatible program. So most of the week a master student at my lab was working on MATLAB and I helped out at another project- carbon capture.

One thing I'm glad I did was reaching out to another intern to learn about his carbon capture work. It seemed to be very interesting when I watched him do his experiments, but I did hesitate a bit before asking if he needed help because he was quite busy. Nevertheless, I approached him with questions regarding his work and offered help. He explained to me what carbon capture is and gave me a few things to do - mixing solutions, testing pH values, acquiring data... It is indeed my area of interest and I enjoyed studying carbon capture very much. I learned from my experience that helping out at another project is always a good way to know more about other areas of study. Dr. Peretz's advice was very useful - we should always look for things to do when we are free and learn about what others in our lab are doing.

Another great experience this week was joining the other members of the Park Group to attend a meeting about the future of carbon capture. The lecturer talked about the present situation of the project and pointed out a few problems about it. At first, the researchers saw it a promising project because according to the experts, the price of building carbon pipes would be quite cheap. Yet, from what the lecturer said, the old age of power plants and the unexpectedly high cost of building carbon pipes (20-30 Million USD per 50 miles) are problems researchers face. Then, Dr. Park led us to discuss whether this project would have a future, since the current economic situation does not provide researchers with sufficient capital (the marginal profit for carbon capture is low) and people are not really aware of the environmental benefits it would bring in the long run. Through the discussion, I realized that there are a lot of factors influencing the popularity and plausibility of one research, and scientists need to be critical of the information given because it often changes.

To elaborate on carbon capture, it is basically a way of storing carbon and lowering greenhouse gas emission. Here are some pictures of the carbon capture experiments I did.

pH value measuring instrument

Pump used for water dripping experiment. Typically we put it up on a shelf, insert syringe containing DI water and mineral,  then get samples in time intervals of 5s, 10s, 30s, and 60s

Test tubes containing liquid samples obtained in 4 attempts

I had a fun and educational time in my lab this past week. I hope everyone else's research is going well too!

Finding the Link between Phenotype and Genotype. Week 1

This past week at Princeton University was an eye opener for me. My first thoughts when coming to a lab like this was based on the stereotype of research scientists by profession; brilliant, polite but not warm, and seemingly in another world.

I was proved wrong within an hour. My Principal Investigator, Joshua Shaevitz, walked towards me and greeted me with a warm smile and engaged me in a short conversation about my sporting ambitions. Who would have thought? When we walked into the lab, I met with the other members of the lab, one of which asked me if I wanted anything specific to eat for lab meeting that day.

Lab meeting was a fun experience, the Shaevitz Lab and another lab have a joint gathering in a conference room where graduate students as well as undergraduate students present their work to the post-docs. Now that's a tough crowd. Though I was lost within 10 minutes of each presentation, and even more so when questions were asked, I enjoyed it; I felt somewhat smarter, maybe just by diffusion.

Over the next couple days I was shown the data analysis equipment that I would use in a few weeks, because right now we are in the data collection phase of the experiment. Also, there was a bomb threat, to add some drama.

To end the week, I had to sit through a 3 hour safety training lecture, which I can't say was exhilarating, but it was definitely necessary. In week 2 I will begin working with the moth samples.

Week 1 @ Microdynamic Systems Lab

My research started on the morning of June 3rd. Since then I have forgotten myself and been living with agents in the Matrix, and was just now "unplugged" by Jiehan. (many thanks!!)

Researching at a robotics lab is different from my previous experimental experiences (dissecting a pig, analyze an integrated circuit with oscilloscope, titrating, etc),. By looking at the same screen for half of the time of a day, I learned new information every moment. In the first week I self-studied Robot Operating System (ROS) and understood concepts related to the research being conducted at the lab. In the other half of the time of a day, I helped mechanical engineers modeling protective skins (e.g. heat shaping) and electrical engineers fixing circuits (e.g. soldering, heat sinking), learned about integrated electromagnetics analysis, and observed the balancing of the ballbot.

One of the several lessons I learned was to balance between communicating immediately after encountering a problem and spending as much time as possible trying to figure it out before asking. Solutions depend on how much time is allowed and how effective time is used in figuring things out by self.

Best luck to best scientists!

Rehabilitating My Relationship With Chemistry -Week 1

After completing AP Chem this school year, Chemistry was one of the last things I wanted to talk about. However, after a couple hours of being in the Buccella Laboratory at NYU, I began to fall in love with the subject again.

I made my way to the 8th floor of the Brown building and rang the doorbell. I was greeted by Professor Buccella who walked me through some safety information and gave me goggles and my lab book. Then the fun began. After only being in the lab for about an hour, I began working with Sarina (a graduate student) and Brismar (a visiting undergraduate student) to make PIPES buffer.  It seemed easy enough, we weighed the necessary amount of PIPES and KCL, and quantitatively transferred them into a beaker, filled it to 750mL of water and began stirred the solution. It turned out there’s a lot more to making this buffer than just mixing two compounds in water and the buffer magically appears. Not only did we have to add KOH until the solution was clear and at a pH of 7, we had to che-lex it too. To “che-lex” is basically purifying the buffer, since it was going to be used for spectroscopy. Particularly, we wanted to filter out any metals, since we would use it to test metal sensors, and near exact concentrations of metals would be needed, so any unknown metals would affect the data. Hours later we finally finished making our buffer. The buffer was sacred that when we had to sacrifice a little during the process of making it, at particular sadness filled our hearts.

Making PIPES Buffer

The second day was much different than the first. Everyone got together and it was time for some lab clean-up! I’m a bit of a neat freak, so I was pretty excited. We had to clean tons of glassware, which involves a lot more than soap, water and a sponge. We re-organized cabinets and draws and at the end, and then labeled all of them (my favorite part). Some people would hate this but for me it was a learning experience, now I know where everything is!

The third day we were back to research. BB (Brismar) and I began our first titration experiment using her compound (sensor) she had made a weak prior. Before starting, we had to prepare a solution of the compound. It was pretty cool, because the we got to make aliquots of the solution then use liquid nitrogen to flash freeze them, in order to preserve the sensors in the -20o C freezer. Next we had to make a solution of MgCl2 mixed with some of the sensor, which was also fun, but we didn't get to use liquid nitrogen again. Finally we began our titrations using the fluorimeter to measure fluorescence as the concentration of magnesium was increased in the cuvette containing the solution of sensor. After collecting the data, we had to analyze it which took another day. Part of analytical chemistry is repeating the same experiment with no changes, and seeing if your results match, so we did the same titration again.

The last day of the week ended with some data analysis and a presentation from a prospective post-doc on about her doctoral work in an organic chemistry lab dealing with another type of sensor. Everyone in the lab has been so welcoming! They're always teaching me about chemistry, even if it doesn't apply to what were doing. I haven't met a group of people more passionate about what they're doing than this group. To sum the week up, not only have chemistry and I been reunited, but I’m learning chemistry has many forms besides AP Chem!

My New Worm Pets! -Week 1

My first day at CHOP started out soggy and gloomy, but once I reached the tenth floor of the Abramson building and entered Dr. Falk's lab, I met two other friendly students working in Dr. Falk's lab for the summer (just to remind you I'm working in Dr. Falk's lab who works with Mitochondrial Disease at CHOP). Anyway, where was I? ...oh yeah so Fred, an undergrad at Penn, had been working in the lab during the school year as well and has a lot of experience with techniques and material in the lab. Rebecca, an undergrad at Notre Dame, very recently arrived at the lab and was in my shoes exactly a week ago. Before I could get my hands dirty in the lab, I had to learn the basics about mitochondria and about the subject of our experimentation, C. elegans. Essentially C. elegans is a 1 millimeter long, transparent worm which feeds on bacteria, typically E. coli. Fred told me that I will be working with two strains of C. elegans, N2 and Gas-1. The N2 strain is the wild type meaning it is the normal, healthy strain which has nothing wrong with it. The Gas-1 strain has a malfunctioning Complex 1 (a part of the electron transport chain in the inner membrane of the mitochondria). He also taught me how to pour agar plates (on which the worms and bacteria grow) and how to spread bacteria on the plates (the food for the worms) as I watched Rebecca do both. Fred also taught me how to use the dishwasher and the autoclave in case I ever ran out of clean glassware during my experiment. Then Julian, with whom I will doing my project since he is the life-span expert (the focus of my project), gave me my own worms to play with. He asked me to try to transfer them from plate to plate using his pick, which is essentially a rod with an extremely thin platinum wire at the end. From experience Julian told me that beginners usually kill their worms within a few days and tear holes in their agar plates but after a few hours of practicing I got the hang of it.

Here's a picture of my first ever plate:

The little lines you see are actually the ridges I made with the pick by accident when I tried to pick up and put down the worms, don't get too excited! The worms are much smaller and are very difficult to see with the naked eye...especially in this picture... sorry! Maybe if you zoom in?

My third plate:

You can see this one is much clearer and less damaged in comparison to my first plate. Woo hoo!! I made progress! I'm not a worm-killer anymore! The big blob in the middle is bacteria which the worms eat.

By the fourth day in, I have my own bench space, my own box of worms in the incubator with my name on it (yay!!), a lot more knowledge about C. elegans and the Philadelphia mass-transit system (phew!) and some awesome "colleagues" as Zsoka calls us :)

I hope everyone else at their lab is having fun and learning a lot too!

-Rhea