Welcome to Abe's Journal

So I do my work in the NIH Clinical Center. By my calculation, this is the smartest place on the planet. Why they let me in there, I will never know.

On my way out today, I happened to accidentally stroll (and in the Clinical Center, "accidentally strolling" takes on a whole new meaning) into a poster session for a Circulating Tumor Cell conference/symposium thing. The fifth poster in on the right? Roswell Park Cancer Institute. For the life of me, I cannot remember who it was or what sort of work they were doing (mainly because I'm terrible with names and don't know any science out of my narrow little understanding), but I saw that familiar blue logo and smiled a little.

You see, Roswell accidentally strolled into my life two years ago this summer and just happened to change it. Because of RPCI, I decided to head into bioinformatics and, accordingly, into graduate school. So, seeing the logo that matched the one on my badge holder made me smile just a bit.

Since my last post, I've been doing mostly research with a little bit of class and a fair amount of fun/exploring the DC Metro area. I took one of the big steps in grad school-- joining a thesis lab-- in July. My thesis work will be in my rotation advisor's (Dr. Keji Zhao) Lab of Molecular Immunology at the National Heart, Lung, and Blood Institute. (Holy shift key, Batman.)

My work will be on studying chromatin structure using the aforementioned ChIP-Seq, a modification of it called RNA-Seq (a method of determining how many copies of genes' mRNA are in a cell), and NA-Seq (short for Nucleosome Accessibility). At this moment, my day-to-day work is on the latter. NA-Seq is a cool little assay that puts multiple copies of a cell's DNA into a tube, cuts it up with restriction enzymes, and sequences the resulting fragments. After a fair bit of analysis-- where I come in-- we can figure out which sections of DNA are balled up in chromatin and which are freely accessible to the restriction enzymes, transcription factors and other elements.

In other news, I *heart* DC. We've had a near constant stream of weekend visitors and I'm getting pretty gd at the layout of the District. I've found a group of guys that play roller hockey in front of the White House on the weekends which is a great time. I may still be a Sabres fan but the likeliest first-RIT-Tiger-in-the-NHL is Steve Pinizzotto and he's in the Capitals' system. He'll be vying for a spot on the roster in training camp the next week.

I'm keeping my fingers crossed and my nose to the grindstone. It's a bit awkward but no less effective.

So I have been consistently terrible when it comes to staying updated here. I'm from Buffalo, did undergrad in Rochester, went to DC for a summer rotation, lived in Boston for a year of grad school, and am now living in Maryland, just up the street from the National Institutes of Health where I am currently rotating and looking for my thesis lab.

Boston was definitely an experience. I already mentioned the Fall semester's issues, but Spring semester also had its own. Our class continued with the challenge project which ended up with us making some interesting predictions that will be validated by the next class. My rotation with Dr. Segre' got some interesting results but nothing substantial enough for a paper. I learned tremendous amounts about metabolism and modeling procedures for rates of reactions.

In addition to research, my classes were Bioethics, Physical Chemistry, and Biological Database Systems. The Bioethics class was very enjoyable and spawned many interesting discussions about the uses of biotechnology. Physical Chemistry was an intense reminder of how long it had been since I took a physics course and just how little statistics experience I had. I really enjoyed the Database course considering my IT experience and multiple previous database courses. The final project (K-PeAD) for that class is turning into a publication as soon as we actually write it and find a place to submit it.

Speaking of publications, I am working on preparing another manuscript for my rotation last summer with Dr. Ovcharenko, as soon as the predictions are validated at the bench. I'm still in touch with Dr. Liang, formerly of RPCI and currently at Brock University, with whom I expect to produce another paper.

My current work is with Dr. Keji Zhao at the National Heart Lung and Blood Institute. I get to work at NIH's Clinical Center which is probably the single most confusing building to navigate. My work is on the differentiation of pluripotent stem cells to determine the difference in chromatin structure between T cells and B cells which are important immune cells. My rotation advisor is the credited with a technique known as ChIP-Seq (Chromatin Immunoprecipitation Sequencing) which allows me to determine which parts of the DNA are available to be transcribed in particular cells.

Besides the science, I've also moved. Moving is always somewhat of a chore and I haven't lived in any domicile for more than 9 months since I was in high school. I've signed an 18-month lease at a wonderful two-bedroom apartment within walking distance of the Metro. NIH has its own Metro stop and it's 3 stops down from mine so my commute is about half an hour. I've got one official roommate and one boarder who's waiting for his place to be finished-- both are students at Johns Hopkins who, like me, get to do their thesis research at NIH.

So things are pretty okay with me. The climate is taking some getting used to, and I'm looking forward to laughing condescendingly when the city shuts down for a few inches of snow. The work is good and very interesting, I've got a nice place to crash, and the Sabres had a pretty solid draft. I'm looking forward to crashing the Verizon center wearing my Blue & Gold.

Good work, good digs, good company-- what more can a guy ask for?

So I'm back in Buffalo for my first extended winter break. RIT only gave us two weeks so that I could be jealous of all my semester-based friends who had nearly a month. This is my repayment: now that all my friends no longer get any break at all, I get a month off.

The last I wrote, I was heading from Buffalo to Washington D.C. for my summer research rotation at the National Institutes of Health. So that means I've got a bit to catch up on.

Dr. Ivan Ovcharenko and I worked on a connection between evolutionary conservation and disease causality at NIH. In short, we believe that if you get a mutation in the genome in a sequence that is common through all mammals, it is more likely to cause a big problem. We are currently (as in right now) working on tying the results up into what could be my first publication (as in Big Deal).

I had the occasion to come back from D.C. for a weekend to help my friends get married. It's kind of interesting that, at 22, I am seeing more and more of my friends get married.

I spent a short week in Buffalo to round up things to take to Boston and then departed. Driving a UHaul over any distance is something of an adventure. I managed to make it with myself and all my stuff in one piece. My current satellite office is in Mission Hill in Boston.

Boston University has been great to us so far. There are 11 people in the Bioinformatics Ph.D. program and a few others in the Masters program. They've given us a cube farm we can work in which allows us to bounce ideas off each other and muddle our way through homework. It's been kind of a whirlwind semester, hence my absence.

In addition to a handful of courses and seminars, we participate in research rotations as well as being the guinea pigs for a "challenge project." My rotation is with Dr. Daniel Segre' at BU. Together, we are looking at a peculiar habit of cancer cells. For those of you familiar with cellular respiration, you know that it has three primary steps: glycolysis, the citric acid cycle, and oxidative phosphorylization. Cancer cells rely way more heavily on glycolysis than the other two and we're not quite sure why or how. This is called the Warburg effect.

The challenge project is sort of a group rotation. Two of my classmates and myself are working together on liver gene . It turns out that genes in the liver are expressed in different patterns in males and females according to each gender's pattern of growth hormone production. We're trying to figure out the order in which these are expressed and what causes the time-dependent levels working with Dr. David Waxman at BU.

Roswell has not been far from my thoughts though. I have been told that my old PI from Roswell, Dr. Ping Liang, has accepted a position at a college near his hometown of St. Catherine's. We have continued to work on tying the work we did at Roswell into a publication (or two). It is now a race between this paper and the aforementioned paper with Dr. Ovcharenko to determine which will be my first.

It's been quite a busy and somewhat disorienting first semester, which is to say it's been tough. I got a lot more experience with both molecular biology and computer science. Next semester is more in my area of expertise when we take courses in databases, physical chemistry, and ethics.

In the immediate future, however, the house smells like vanilla and cinnamon and the tree is lit up bright. So a happy winter solstice to you all and to all a good night (or however long until I take the train back to Boston).