Week 9: University of Maryland Biotechnology Institute

August 8th, 2012

Gibbs Nasir ’13: Kao Fellow in Medical Biotechnology

It seems fitting that my post for my final week in Baltimore should almost be as lengthy as the one for my first week here. However, summing things up always seems more difficult than merely recounting experiences and events – for in the former, one must also introspect and understand the significance of the experience in relation to one’s long-term goals. I will humbly try to convey as much of it as I can in this post.

The weekend after Week 8 was quite fun. Joe and the rest of us went to McLeans, Virginia for sushi. This is apparently a sort of tradition – you will find that both Megan and Elise also had this experience. Now I’ve had sushi before, but I must say that the quality of the fish here was fantastic. Also, it was a treat to go with Joe because he is a food connoisseur, and there is a lot one can learn from him. One of my regrets, certainly, is that I couldn’t pick Joe’s brain more often in all matters food. I personally have always loved food, and usually go out of my way to try new things, so hearing Joe speak about it with zeal was always fun.

The following Monday was a short day in the lab. We set up our reaction and left it overnight. However, I wanted to make the most of my time in the lab, so I convinced Eric to let me help him in some of his Ph.D work. I therefore helped Eric run a Polymerase Chain Reaction (PCR) on a plasmid vector. Since I had primarily been doing organic chemistry all summer, being in a Biology lab was exciting. On Tuesday, after thoroughly extracting my product, I did some more tasks for Eric. In the process I got an opportunity to practice my pipetting technique (Picture 1).

Picture 1. Helping Eric with a PCR

Wednesday was a pretty long day, but also the most productive. I had to give a brief presentation regarding my summer project and what we had achieved thus far. By this time, we were actually only one short step away from our final molecule. My presentation was smooth and, as always, I enjoyed being up there. Joe was actually pretty pleased with my presentation – I could see him smiling happily at the back of the room. This actually made me even more confident in front of a room full of senior scientists. Part of the reason I did well was because Joe had explained everything so well to me, that I thoroughly knew my project. The other part is probably that I ask a lot of very annoying questions. As a student, you might want to start doing this as well – leave no room for misunderstanding. I was able to answer almost all the questions that were directed toward me. Later, around 4 p.m., we started running a column to purify our compound. This must have been the slowest column ever – even at high pressure (Picture 2). I left the lab at 1:30 a.m. (Yes, 1 in the morning) and all the product still hadn’t come through. The next morning, Joe collected all the fractions before I got to the lab around 9:30 a.m, and then I worked up the rest of it.

Picture 2. Adding additional solvent to the column.

By Friday, we were successful in obtaining our final molecule. We prepared a sample for electron paramagnetic resonance (EPR) analysis. The EPR machine in the basement (Picture 3.) was made in the 70′s and the computer software that converts the analog signal into a digital one is from the 90′s. Long story short, it took us 4 hours to get the digital spectra for 4 samples.  The best part? Our molecule did exactly what we were hoping it would. In the presence of calcium, the EPR spectra significantly changed. It was an amazing moment, watching 9 weeks of work culminate in glorious success. Joe and I were both thrilled.

Picture 3. EPR Machine from the 70′s

I used the weekend following the end of my ninth and final week to visit D.C. with Eric and Meagan (Picture 4). Needless to say, my summer would have been pretty boring without these two. It was made fun also by working with two other interns at Joe’s lab – Nate and Duncan – both of whom were intelligent and witty. I learned a ton from each of these people, and I am very grateful to all of them.

Picture 4. At the Smithsonian Air & Space Museum in D.C. with Meagan and Eric.

Week 8: University of Maryland Biotechnology Institute

July 30th, 2012

Gibbs Nasir ’13: Kao Fellow in Medical Biotechnology

This last week was probably the most interesting, in terms of all that was going on. Over the weekend, I visited the National Museum of Dentistry downtown. I hadn’t been to a “dental” museum before, so I was somewhat curious as to what I would find. The museum itself was rather small, but very educational. Did you know that George Washington did NOT have wooden dentures? Yes, the wooden dentures are a myth. Apparently, this museum has all of his dentures. Also, did you know that the affluent in the Mayan Civilization would have their front teeth embedding with a gem to display their status? (Check out Picture 1. below)

Picture 1. Mayan Civilization; Gems embedded in the front teeth of the wealthy.

Anyway, on Monday, Joe and I decided not to separate our product using a column, so we discarded all the TLC results. Instead, over the course of the week, we decided to recrystallize the original product combined with the product we obtained from the filtrate. One of the many things you will hear in the lab are, “Oh, that’s common sense.” However, never be dejected by this, because unless you make mistakes, you will not learn. This is how people get extremely good at something – it’s common sense because they have done something so many times, that it has become second nature to them. They have already made the mistakes and learned from them. Chemistry is like that. You work with different chemicals, but the technique essentially remains the same. Over time, repetition helps you refine your adroitness. Also, it would be folly to assume that you can learn anything completely by merely watching. To really learn, you must do it yourself. I had almost little or no experience in research work (particularly chemistry) when I came to Kao Lab. However, now I can do all these procedures without having to think too much about them.

By the way, we finally got the Mass Spec results. After a week! Our NMR Spectra show that we are on track. Hopefully, by the time I leave, we would have created the molecule – which is actually only the first step. On a different note, on Wednesday, I noted a lot of young people downtown, dressed in anime-related costumes. I managed to find out that Baltimore was hosting some Otakon Convention for 2012, which is basically a very large halloween party that lasts several days, where most people dress up like anime (with bright wigs and all). I’m not quite sure what there is to do at the convention, but I saw this character from a video game (Assassins Creed) covertly going into the mall. So I snapped a picture. (Picture 2.)

Picture 2. An assassin (video game character) going into the mall.

Week 7: University of Maryland Biotechnology Institute

July 22nd, 2012

Gibbs Nasir ’13: Kao Fellow in Medical Biotechnology

More than seven weeks have passed, and with every week, I feel I have grown in experience, ability, and confidence. I realize, for the wary reader, that my posts may not necessarily convey everything that I have learned and observed these past few weeks, which may perhaps err on the border of redundancy. The simple truth is that in a chemistry lab, there is a set array of basic tools that are used for the purification and analysis of a product – which is almost always 80% of the overall process. The enthusiastic spark itself,  as everything becomes more familiar, naturally begins to diminish. One’s focus gradually shifts from learning about things unseen to mastering them. For example, even for a technique as simple as thin layer chromatography, there are certain techniques which one finds improve the analysis. There are subtleties that one realizes after hours of running TLCs, one after another. How to spot, how much to spot, where to spot, drying the spot, and so on. One must also be consistent with one’s technique, in order to produce reproducible results. Picture 1. shows a few of the TLCs that I ran, which, being quite OCD as I can be, I keep arranged (in increasing order of the percentage of ethyl acetate used) for Joe’s convenience.

Picture 1. Set of Thin Layer Chromatography (TLC) plates.

When I was reading my predecessors’ blogs (Meagan’s and Elise’s), the one thing I felt they did not seem to talk much about was Baltimore itself. I understand that this blog is supposed to be concerned with, for the most part, the research itself, but I feel that it behooves me to describe briefly my impression of this city – for the benefit of my successors. If you decide to ride the bus, as you very well should, you will get to experience the essence of Baltimore, that pervading energy that runs through the veins of all those who have made this city their home. Through the many streets with historic and unbelievably interesting architecture, by the many sculptures around the city (See Picture 2), and by the amazing diversity of people that use the bus to go to work and back, I’ve found that Baltimore has character; it has life. Although this city trifles in comparison with New York, where all are too busy to care, and night life is all but a cacophony of glitter and glamour, it is quite the norm for strangers to engage in friendly conversations about books, movies, or an Orioles game on the bus. Most of the time, your smiles will be returned with gusto. (*cough* Can’t say the same about New York or Nashville *cough*). I have been utterly amazed at how many people I see on the bus everyday who are engrossed in some book. Anyhow, moving on…

Picture 2. Statue of George Peabody in front of the Peabody Institute (Johns Hopkins)

Last weekend, Joe treated me and several others to dinner at Buck’s Hunting and Fishing Restaurant. I thoroughly enjoyed the food, and the conversation itself was delightful. Joe’s knowledge in all matters food is quite impressive – actually, on second thought, his breadth of knowledge in general is. There is so much that I would like to learn from Joe, but alas the internship is almost at an end. The following Monday was an excellent day, with satisfying results and good progress. I also went to the gym with Eric afterward, and we had a good workout on the basketball court. On Tuesday, we ran a column to purify our compound, and looked at the next procedure. I was happy that I was able to figure out, using my knowledge from Orgo lectures, the mechanism for the reaction that we were going to be running. We also sent in samples for Mass Spectrometry – the results of which we have not yet received. We also recrystallized the recrystallized product (Picture 3) to further remove impurities – based on the NMR spectra. On Friday, I ran a bunch of TLCs and by Friday night, we were unable to figure out the correct solvent composition for separating our new product.

Picture 3. Re-Recrystallized product.

Week 6: University of Maryland Biotechnology Institute

July 15th, 2012

Gibbs Nasir ’13: Kao Fellow in Medical Biotechnology

You know, I can’t believe I’ve been here around 6 weeks already but haven’t found time to visit D.C.! There’s so much to see in Baltimore itself that when I do get time, I end up going to some museum or something – which is exactly what I ended up doing last weekend. I visited the Baltimore Museum of Art (BMA) and spent close to two hours there. There was simply too much to absorb. (See Picture 1 below for a work of art)

Picture 1. Man Pointing by Alberto Giacometti at the Baltimore Museum of Art.

As I mentioned in my previous post, Joe had to come in on Saturday to set up our 5-day reaction because we were unable to do it by Friday night. So on Monday, we started working on creating a molecule that will eventually be placed on the larger molecule. A simple Hoffmann rearrangement on the starting molecule was required, and the reaction itself was pretty straightforward. On Tuesday, we ran a column on the product mixture because it contained both the product and the starting material and started around 4 maybe. But this column was running so SLOW that we were there till around 8 p.m. (Picture 2). Part of the product that we got had starting material still present in it. For this reason, we had to run another column to further purify our product.

Picture 2. Purifying our product using Flash column chromatography

However, because we still had starting material in part of our product, I spent the entire day Thursday testing different solvent compositions to determine which composition would give the best separation between the product and the starting material. This happened on Friday as well, and we ended up leaving the lab at 9 p.m. We thought we had found a relatively good composition based on the TLC, but when we ran that composition in a column, there was no separation. Oh and our product from Saturday, after five days of heating, had solidified just as we were expecting (Picture 3). But we haven’t been able to work it up because we’ve had our hands full trying to purify this other compound.

Picture 3. Product from the 5-day reaction.

Week 5: University of Maryland Biotechnology Institute

July 9th, 2012

Gibbs Nasir ’13: Kao Fellow in Medical Biotechnology

Needless to say, I felt pretty good going into the weekend. Running a column always takes so much longer than one thinks it will, and Joe and I ended up leaving the lab around 8 p.m. I had a productive time over the weekend exploring the nightlife of Baltimore with friends from the lab.

On Monday & Tuesday, I worked on the next step of our synthetic scheme, which included taking the two hydrolyzed products from last week and converting the molecule in each into a dimer (Picture 1). This dimer is to function as the nucleus of our final molecule (BAPTA) and is essential. The first small scale reaction we ran was successful, but the temperature in the flask was actually higher during the reaction than our personalized thermocouple showed. This is because we were using toluene with the thermocouple, which begins to boils at 130 degrees. We totally forgot about this, and had the thermocouple giving us a range of temperatures. We addressed this issue by replacing toluene with a higher boiling liquid. An NMR spectrum of the product showed us that we had gotten the desired molecule.

 

Picture 1. Forming the BAPTA backbone.

Since on Monday & Tuesday we had established that the procedure we used for creating the dimer was pretty effective, on Thursday I went ahead and ran the same reaction on a larger scale. I monitored this reaction very closely, and it all went well. Joe seemed quite happy with my work and the yield was good once again. On Friday, we hydrogenated the dimer (Picture 2), and I realized that there is still so much that I don’t know, it’s almost sad. I don’t know how Joe puts up with my five thousand questions, but he does. There is much that I am discovering about myself in the process of becoming independent in the lab. I also wish there was a scale which measured one’s ability in the lab – for e.g., after one month, you are better/worse than 80% of people who also took this test. That would at least set a standard from which one could set goals to improve. Just a thought.

Picture 2. Catalytic Hydrogenation apparatus

So after we had hydrogenated our product, both Joe and I were like two happy campers….. until we looked at the next procedure. It turned out that the next reaction needed to be heated for 5 days. FIVE DAYS. This was just shocking. We couldn’t believe we hadn’t seen it before. So we started working on setting up the reaction at 6 p.m. and by 8 p.m. we were half-way through. The problem was, the proton sponge needed to be recrystallized, and that took like 2 hours. So Joe told me he would come on Saturday and set it up. To be honest, my personality is such that I would rather have set up the reaction – even if it took till 10 p.m. – than have left it for the next day. Anyhow, in my next post, I will describe my visit to a museum as well as the outcome of this 5-day reaction (among other things of course).

Picture 3. Completely unrelated to everything in this post. This is actually someone else's column in the lab. I just thought it looked pretty cool.

 

Week 4: University of Maryland Biotechnology Institute

July 1st, 2012

Gibbs Nasir ’13: Kao Fellow in Medical Biotechnology

Time is going way too fast on this side of the east coast. Over the weekend, I had lunch with Morali, a research associate who works at Joe’s lab. On Sunday, I also got to try my hand frying Tilapia with slight modifications. You see, when I fried it the first time, even though I seasoned it well, it lacked flavor and was quite bland on the inside. I can’t say I enjoyed it very much. However, this time I fried the fish and coated both sides of the fish with butter and it turned out to be excellent. I was not expecting this. Butter does have a way of making everything taste better. Butter, therefore, might become the secret ingredient in the Tilapia recipe that I am trying to perfect over this summer. Moving on.

On Monday, we started the same reaction that we had been testing in small batches throughout last week, on a larger scale. Since I have been working with Joe for about a month now, I can easily anticipate questions that he is likely to ask. His way of progressing through something follows conventional logic, so if you can logically connect two steps, you won’t have too much difficulty. Therefore, I can usually answer most of his questions – probably because I have them figured out before he asks them. Sometimes, even though my answer is correct, it is not necessarily the way to go. This is because experience matters more than mere theory. Joe may have found, through experience, that something else works better – and that is how we go about doing it then. Also, I have to throw this out there for any future Kao Fellows. Joe has some sort of a finely tuned sixth sense. He will come into the lab JUST when you are hoping he doesn’t. But don’t worry about it, Joe won’t say anything to you. I am a perfectionist, so I don’t want Joe to see anything other than the way everything should be. Anyhow, we got done sooner on Monday because our reaction had to run overnight.

The following day, we began purifying our product from Monday. There is a lot of purification involved at the end of every reaction – this is generally true for organic synthesis. Something innovative that we did on Tuesday was this clever modification to our filtration (Picture 1). We used a tiny silica column to remove the insoluble impurities from our product mixture. This allowed us to avoid running an entire column and saved us a lot of time. I am also learning which details are important to be written down in the notebook and which aren’t.

Picture 1. Filtration with a slight modification - use of silica in a tiny column.

Wednesday was not really my day. I had definitely woken up on the wrong side of bed. I was feeling tired and sickly for some reason and since I talk quite a bit, everyone noticed it. We recrystallized the product, but decided to do the next reaction (hydrolysis) the following day. I wondered if my exhaustion had anything to do with being dehydrated, or not maintaining a balanced diet. Therefore, I started eating more consciously and targeting all the nutritional requirements.

By Thursday, I felt much better. We ran the hydrolysis reaction on our product, but because Joe wanted to go home early, decided to do the column the next day. Similarly, Friday turned out to be a pretty good day, even though it didn’t start off that way. I had woken up prepared to run the column from scratch, but I came in to find the column almost already set up. This column, though, was huge. I think Joe does this to save time. On many occasions, I have heard him say to the other intern, “Since you know how to run this, let me do it for you.” I was slightly disappointed about not being able to set up the column – which is really not a big deal, because I know i’ll get to set one up again very soon. The good thing is that since I had already run columns in the first few weeks, I knew exactly what I was doing and what work up needed to be done. So I was able to do each step independently and to give Joe my assessment of the results – which he agreed with – instead of asking him what each next step should be. Once we had the fractions, we ran another hydrolysis for the large scale reactant (Picture 2), filtered it, and left it to air dry until Monday (Picture 3). Also got an NMR spectrum for the product from Thursday – it was clean – and the yield for that was 99%. I was pretty happy with this result.

Picture 2. Hydrolysis reaction.

 

Picture 3. Product from hydrolysis.

 

Week 3: University of Maryland Biotechnology Institute

June 25th, 2012

Gibbs Nasir ’13: Kao Fellow in Medical Biotechnology

Looking back at this week, things seem to be picking up pace – but at the same time, it’s not a challenge per se because I’m getting quite good at using the equipment and I feel at home in the lab. In essence, the project which at first seemed ‘some’ project is now ‘my’ project. Anyway, I found that the weekend before this third week was a good time for me to relax, check out more of the city, and read. Over the weekend, I ended up going to the Washington monument (See Picture 1) – located in a historic and beautiful great part of the city. You look around and you can almost envision horse-carts moving about in a crowded and busy area (Picture 2). In general, I have found that the architecture in Baltimore is a sight for sore eyes, and is amazingly diverse.

Picture 1. The Washington Monument in Baltimore. A tribute to George Washington in the 18th century.

When I returned to lab on Monday, Joe and I thoroughly analyzed the NMR spectrum for our product from last week. This was somewhat like working on a puzzle – you have only some of the parts, and you try to use reason, logic, and knowledge to figure things out. In this case, we had to determine any potential side products – and sometimes, really, you just have no clue. I ran a series of TLCs to determine the correct solvent for flash column chromatography (See Picture 3); this was all basically trial and error. Since we are literally pioneering reactions, one of our tasks is to optimize the reaction conditions. The first test yielded a low yield. Therefore, Joe and I decided to run the reaction with a greater concentration of the reagent to see if the reaction will go to completion; this is practically Le Chatlier’s principle in action.

Picture 3. Flash Column Chromatography

On Tuesday, I set up test #2 and we ran it for 4.5 hours. During this time, I periodically did TLC to check the progress of the reaction. I rotovap’ed the reaction mixture and ended up with something goop-ish. Joe and I discussed why this could be, and for the third test we’ll be running the reaction both longer and at a higher temperature. All of Wednesday was dedicated to cleaning up the product from test #2, filtering it and then drying it under vacuum. However, since setting up the column and collecting fractions takes a while, we decided to do it on Thursday instead. Therefore, the next day I column chromatographed test #2 product, rotovap’ed it (See Picture 4) and dried & weighed it. The yield this time was significantly higher, around 60% or so. I also set up test #3 on Thursday – so it was a relatively busy day – and monitored it using TLC alongside collecting fractions from the column. Based on the TLC results, we decided to let it run overnight. So basically, one needs to multitask a lot and stay on top of everything.

Picture 4. Rotovap'ing crude fractions and then purifying them later.

On Friday, I purified the product from test #3 and ran a column on it all by myself. However, something very funny happened. And since Joe had quite a laugh over this incident, and because he slyly asked me about whether or not I was going to blog about it, I thought it was amusing enough to deserve a brief mention. Basically, while filling up the column with silica gel, this pin somehow fell into the column. Because I did not want Joe to see it, I slightly panicked and grabbed the large horse shoe magnet from on top of the hood and was in the process of secretly removing the pin when Joe came into the lab to check my progress. When he saw what I was doing, he started laughing, and must’ve laughed for like 5 minutes – with short pauses in between. Of course, I was hoping that he would NOT have seen me doing that, but he is pretty cool and very encouraging. He reminded me that even he messes up now and then, and that ‘if glassware in a lab doesn’t break often, it means that not enough experiments are being conducted. Good week. Looking forward to the next one.

Week 2: University of Maryland Biotechnology Institute

June 17th, 2012

Gibbs Nasir ’13: Kao Fellow in Medical Biotechnology

Now that things have become relatively more familiar, naturally the week went by more quickly. I took initiative to get to know two of my house-mates over the weekend. Both of them are graduate students studying at Hopkins. On Saturday, I went to an Asian superstore with Selina where I was able to get really fresh fruit and vegetables as well as fresh fish. If I had been in Beijing, I wouldn’t have been as surprised as I was when I discovered that the superstore also sold live bullfrogs and soft-shell turtles (Trionychidae) (See Picture 1). The problem was that I am no professional when it comes to fish – of the 20 different types over there, I was only familiar with four or five. Hence, I texted Joe asking for his opinion; as a result, I did not end up getting fresh water fish, which usually contain very fine bones.

Picture 1. Image of Bull frogs and Soft-shell turtles at the Asian Superstore

Similarly, I tagged along with Christian to Inner Harbor and had coffee with him at Starbucks. Since his field is student counseling, we primarily discussed topics including academic success, ethnic identity and the relationship between the two. As he worked on his paper, and because I had brought my kindle with me, I was able to finish reading The Plague by Albert Camus (a 20th century French existentialist).

On Monday, when I got to the lab, I was expecting an NMR – but there was none. Joe informed me that he had come in over the weekend to work up the reaction- which he did. So note that if you are wanting a research-based career, be prepared to be flexible about the days and hours you work. Joe gave me the procedure he had done and asked me to point out why he had done those particular steps. I knew some, but I was looking up the rest – like I’ve taught myself to. But no, Joe said that he wanted me to figure out the answers by THINKING about them! It’s apparently all about the thought process. Initially, I was confused a little, but now I actually feel like I’m beginning to use my brain. You can feel it.

Sadly, the product turned out to be black and, hence, crap. The entire week’s work can be summarized in one sentence: this particular reaction pathway doesn’t work efficiently. Hence, we had to order more of the starting material on Monday, which didn’t arrive until Thursday. In the meantime, I ran two TLC plates to test for the presence of the product, but didn’t find anything. Joe has a good sense of humor; he saw me staring intently at the TLC plate and remarked, “A watched TLC plate doesn’t run!”

Joe is also a consultant for biotech companies that create fluorescence indicators. On both Monday and Tuesday, I observed Joe load the indicator for calcium ions into four cell samples. He also showed me, under a microscope, the different stages of cell division during mitosis. He took one of the four samples, and tested the immediate effectiveness of the indicator – which turned out to be quite poor. On Tuesday, however, the indicator showed good results. Joe also explained to me the theory of flash column chromatography (I picked this up easily because I had already read up on it on wikipedia). When I was helping Joe collect fractions during the column chromatography, I almost felt like Joe’s colleague. Actually, I think that is the whole idea, especially once you are in graduate school.

Joe texted me on Wednesday morning, saying that I could take the day off if I wanted to, since our starting materials hadn’t arrived yet. I had heard something about ‘Tall Ships’ coming to the inner harbor for bicentennial anniversary of the writing of Anglo-American war of 1812, and the writing of the star spangled banner. So I took a bus down to inner harbor to investigate (See Picture 2). I thought it was neat to walk around on-board. On my bus-ride back, I also became friends with a professor from RIT working on microfluidics – I wasn’t very familiar with the field, so I used this opportunity to learn about it.

Picture 2. One of the Tall Ships at the Inner Harbor for the bicentennial anniversary of the War of 1812 and the Star Spangled Banner

The reagent arrived on Thursday, and Joe asked me to start up the reaction sequence again. Since I had watched him set it up during the first week and made notes, I was able – for the most part – to set it up (See Picture 3).  Also, as I become more confident about the reaction itself, I was able to point out details of the procedure to Joe. For example, he would say, “and then you can set it up for reflux,” to which I could say, “No, that’s the next reaction – we don’t reflux this one.” Joe: “Oh is that right? Very good,” etc.

 

Picture 3. Setting up the reaction again.

On Friday, we used the product we had gotten on Thursday and tested the efficiency of the reaction procedure with only 1g of it to make sure that the solvent that we were thinking about using would work. The resulting product, at this small scale, looked good! So we dried it over the vacuum rack (Picture) and stored in the freezer; we are going to work it up this Monday. Lastly, on Friday, Murali, a post-doc, gave me his cookbook – as he had given it to Megan. I may try out some of the recipes in there, though I find it’s much more fun just going to an Indian lunch buffet and taking small portions of a wide variety of things.

Week 1: University of Maryland Biotechnology Institute

June 11th, 2012

Gibbs Nasir ’13: Kao Fellow in Medical Biotechnology

This has been an exciting first week in Baltimore. This post will probably be one of the longer ones, since it will cover slightly more than the first week of work.

So when I left Cornell on the morning of May 31st, it was raining quite heavily. Wary of the possibility that my flight would get delayed, I didn’t quite know what to expect. But when I got to the gates, I wasn’t too worried anymore. It’s really funny how small the place seems – I ran into several friends from Cornell, as well as Cornell’s ex-president, Les Garner – whom I recognized and initiated a conversation with. My layover was in St. Paul, Minnesota, where I had lunch with Jordan Ng, another Cornellian.

I arrived in Baltimore on Thursday night (May 31st) using Delta Airlines (which seemed more comfortable to me than American Airlines), where my site mentor, Joe picked me up. We seemed to get along right off the bat. Among other thing, we talked about life at Cornell in general, and about the pros and cons of the block plan (specifically about the difficulty of grasping certain conceptual theorems and proofs in the brief durations of the block plan). Joe drove me to the place where I was to be staying for the next two months (See Picture 1).


Picture 1 – Charles Village Rowhouse

Although I hadn’t seen any pictures of the room I rented (having taken it on good faith due to dearth of time), it turned out to be small and comfortable. To a future Kao-fellow who might be reading this, it is crucial to start look for housing sooner, and to have at least three very strong references. Anyhow, I spoke with the landlady, Evalyn, at length on numerous topics. Evalyn was going to be leaving for a week to get away from the city, and I offered to take care of her bird feeders while she was away. She also reminds me a little of Novella Carpenter (the lady who started an urban farm and wrote a book about it) with her small patch of garden (See Picture 2). One interesting thing that I experienced was smelling this yellow rose (Rosa hemisphaerica) that Evalyn showed me. What was interesting was the calming effect smelling this flower had on me. The rapidity of the effect is what really intrigued me – of course, realize that science hasn’t quite unraveled the mystery of our olfactory machinery yet. When I later looked up scientific literature on this, I couldn’t find any paper that specifically addressed this, but I did find other non-scientific sources that talked about the blood pressure-reducing effect of the smell.

Picture 2 – Evalyn’s garden patch

On Sunday, Joe invited me to have dinner with him and several other people at his place, which was fantastic. One of Joe’s primary motivations was to test the grill that he had recently got. The food was delectable, and the conversation lively, covering a broad range of topics. I have always believed in being well-read in many areas, and this dinner emphasized the importance of that quite clearly. Earlier the same day, I had walked two blocks down to Wyman Dell park to check out the Charles Village festival that Evalyn had mentioned (an annual event, aimed at supporting several nonprofits in the area; See Picture 3).

Picture 3 – Charles Village Festival

 Monday was my first day at the lab. I mapped the public transportation closest to the house using google maps, and read up on the details of the public transport system on their website. This turned out to be crucial, because apparently the bus-fare system here is somewhat strange. The bus-fare box accepts EXACT amounts, without any concept of a change card. So, for example, if it costs $1.60 to go one-way, and you have $2.00, you can forget your 40c, because the fare-box will eat it up. Also, the first bus I caught seemed to have a significant number of sketchy-looking individuals at the back, which I was quite disappointed by. However, after recounting my experiences in the lab, I will explain that there is a way around this. On both Monday and Tuesday, Joe explained to me the theory of the project I would be working on. On Monday we covered the theoretical principles behind electron paramagnetic resonance imaging (EPRI) and on Tuesday, the theory behind the role of intracellular calcium ion concentrations in heart muscle contraction. I also got Eric, a doctoral student at the lab, to show me the cells he is working with currently – which include HeLa, T-cells, and some African monkey kidney cells. Throughout the week, I observed Joe very very closely. You have to realize that every researcher has his or her own idiosyncrasies, but there are some techniques that they have refined over many years. THESE are the techniques you want to absorb as quickly as possible and begin using them – this is one reason working with such an experienced scientist is invaluable, you can pick up these techniques in a fraction of the time it took them. The first two-three days, I mainly observed Joe do almost everything. However, this was a great opportunity to see a pro-scientist in action. We (him mainly) did the first reaction for a 9-step synthesis of an organic compound, which will serve as a calcium indicator for EPRI.

However, when I came in on Wednesday, I had an H-NMR spectrum for the product waiting for me. I LOVED THIS CHALLENGE. All the knowledge I had accumulated in Organic Chemistry came back to me. In 5 minutes, I had marked up all the peaks, and confidently showed it to Joe. However, it turned out – alas – that I had marked one of the peaks wrong. During this analysis, I also realized that the small details which we ignored in OChem were important here; we identified the small peaks by educated guessing. After purifying the product more, we submitted a sample for a second NMR. One of the things I’ve found is that Joe is tough about giving up answers. I usually ask a lot of questions, so I tend to come off as a little annoying sometimes – I admit! – but not only is Joe patient, he takes a different approach to answering my questions: He tells me to look at the system and figure it out. In contrast, most of the professors at Cornell usually answer most questions right off the bat. But I am quite alright with this; I sit in Joe’s office, while he types away on his computer, and read relevant topics in his chemistry/biology books.

On Thursday, Joe, Nate (another intern), and I went to the annual neuroscience retreat of the University of Maryland. The idea is to get the post-docs and faculty members away from their labs; it’s essentially a social academic event. The main speaker was David Linden, a neuroscientist at Hopkins and the chief-editor of the Journal of Neuroscience. It was quite a privilege to be among the select group of individuals in that room. I have added both of his books to my reading list. On Friday I evaluated a second NMR, and we determined that the product was pure enough to move on. I weighed the product, determined the % yield (93%), and calculated corresponding volumes for the next reaction. That day, Joe allowed me to do much much more. I convinced the other intern (who had had more experience in lab) to demonstrate to me how to use this equipment called the Rotovapor using acetone. Joe came back from a meeting and saw this, and I would speculate that this was one of the reasons he allowed me to operate the equipment all by myself right afterward. Joe also allowed me to set up the reaction for refluxing overnight by myself. I’ll admit that I have done some really dumb things (nothing serious) this first week – which I will obviously not be talking about, but the important thing is that you quickly learn from your mistakes, refine your skills, and move on.

One of the things I wanted to mention is the public transportation here. It goes without saying that in a cosmopolitan city such as Baltimore, the public transportation network is extensive to say the least. There’s the light-rail, the Maryland MTA, the charm city circulator, the Hopkins shuttle, etc. However, note that google maps or mapquest only cover light rail and the Maryland MTA. So there are some things that you can only learn by actually being in the city and asking a lot of people. On the first day, I remember I was walking around downtown looking for the bus stop for #27, I must’ve asked 20 different people and all 20 of them told me something different. It’s not that people are clueless or ignorant about general things about the city they live in, but that life in a big city is so fast-paced that they just don’t have the time to find out/remember these things. So the first bus that I took to the lab (#27) was just not worth it. I had to walk several blocks to catch the bus, and several blocks to the lab. Considering that you have to stand in lab a lot, I was exhausted when I got back. However, now I have found that I can take Bus #3 toward downtown (one block away), and then take the Charm City Circulator, which stops less than a minute’s walk away from the lab. The quality of people on this bus also seems better than #27. All in all, good first week. Feeling more at ease, and looking forward to the second one.

  • About
  • Fellows
  • Archives
  • Meta