Week 3 with smells and further discussions

This is Jocelyn and I'm working on olfaction in mice at Duke University. This is
my third week here.

This week in general was very low key. For the first two days, I counted cells and
analyzed photos taken by the microscope on ImageJ. These photos were of the olfactory
epithelium. There were two versions of the photos we took. One was the nuclear
staining which stained nuclei in the tissue; the other was the cy3 staining which
is the antibody staining. Unfortunately I don't have any of those photos but
they're brilliant! Especially when you see the different colors under the
microscope.
For journal club on Monday, Jianghai presented his paper on Expression of Ectopic
Olfactory Receptors. I read the paper in advance so I understood most of what he
discussed during the meeting. Next monday, Yue is going to present about
earwax! Yue got held up by some bureaucratic stuff and only came back last week
from China. Anyway I'm excited to read the paper.

On Wednesday, we meet with different departments and first year grad students
present their research topic. This week Edward presented the effect of UV light on
egg-laying site preference in Drosophila. It was really cool! After that, the rest of
the day was pretty uneventful and I got to leave at 14:30! which was nice since I
had been staying until at least 6 on some nights the previous week.
Neha gave me some papers to read about RTP1 and RTP2 proteins. There were a
lot of terms I didn't know and since I didn't have my computer with me that day, I
asked Neha to explain them. She ended up taking half an hour explaining all of
the terms in full detail. It helped me understand our project even more too.

Yesterday we made a plan to make two clearing solutions (Scale and SeeDB) that
make the brain samples clearer to see. Scale contained urea, glycerol and triton X.
SeeDB contained different %s of fructose. We made all the calculations. Then we
made 4% Pfa which fixes the brain samples onto the slide.

(People sensitive to or against using animals in the lab, please don't read this
paragraph because you'll be disturbed. I was.)
After lunch - we were going to dissect. Neha didn't specify what we were
dissecting so when she brought in six mice to sacrifice then dissect, I was
shocked. The lab's method of euthanasia was a chamber full of CO2. We went into
the dissection lab and Neha showed me how to sacrifice the mice. She grabbed
one mouse by the tail then put it into the chamber. After two minutes or so, the
mouse was still and Neha basically dislocated the vertebrae from the rest of the
body. Then she decapitated the mice and started dissecting. At this point, I was
speechless. The room started getting really cold - I think that was just me. I told
Neha that I couldn't do it and she was really nice about it. I ended up sacrificing
one mouse but I couldn't dissect it. It was definitely a once-in-a-lifetime
experience.

Earlier in the week, Hiro (my PI) came to talk to me about what I'd be doing on the
days that Neha would be gone (next wednesday-friday). He is a great PI and so
hands on. He's been working with another summer student and he's always
around. I told him that we needed to present our projects at Science Night at the
end of fall term and he offered to make a time for me to present to the lab my last
day. I think it's going to be a good experience for me! to talk to grad students
about the research Neha and I did. It'll be good practice for Science Night too!

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!