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Researcher of the Month

February 2012

Oleksandr (Alex) Gorbatsevych 

Biology major, Class of 2012

Research Mentor: Dr. Eckard Wimmer, Molecular Genetics & Microbiology


AlexGTwo of the best kept secrets for Undergraduate Biology majors at Stony Brook are the array of research opportunities available through Medical Center departments (e.g. Molecular Genetics & Microbiology,Pathology, Anesthesiology to name a few); and the opportunity to do “departmental honors” in the major by writing a research thesis. For Alex Gorbatsevych, this was an irresistible draw. But he had only one year to do it —he was entering his 5th, "super-senior" year in 2011-2012. . . Would he be welcome in a lab? After all, he'd taken lots of Biology, Pharmacology and Biochemistry coursework and done very well; but had no hands-on experience in a laboratory. 

Alex also had a very specific interest: and was becoming more and more enthralled with the topic of codon pair bias and the exciting work on synthetic virology in the laboratory of Distinguished Professor,Dr. Eckard Wimmer. Happily, Dr. Wimmer recognized Alex's strong motivation and potential for research, and offered him a position in the lab in fall 2011.   Alex was assigned to Molly Arabov, a graduate student who proceeded to train him in molecular biology before going on maternity leave. And with the benefit of her teaching, plus the certain deadline of knowing that Molly would not be available past December, Alex worked hard —packing as many hours as humanly possible in the lab so as to get up to speed in qRT-PCR, infections, transfections, transformations, in vitro translation, RNA extraction and purification—so that he could work independently. The result?: Alex will be among the few, proud half dozen or so of 300-400 Biology graduates, class of 2012, who will graduate with departmental honors this May!

Alex's project is titled "Competition between wild-type and codon pair optimized Polio virus in HeLa cells”—work which he will present at the URECA campus-wide poster symposium on April 25 (as well as to the UG Biology thesis committee). Asked why he waited until this year to pursue an independent research opportunity, Alex explained: “In part, the reason why I waited until my final 5th year was because I felt I had nothing to contribute to a lab. …Sure I might have started earlier. But I’m working independently now. If there are results I don’t understand, I have to go back, find the protocol and adjust it.  …You have to know stuff to do this. Without the background I built from 4 years of taking many biology and biochemistry classes, I wouldn’t have belonged there!” Now, Alex is at home as a member of the Wimmer lab, and attends all the Synthetic Virology meetings—avidly learning all he can about the field.

Alex previously gained clinical research experience as an assistant to Dr. Mark Gudesblatt at South Shore Neurologic (2010-present), and has contributed data analysis for an upcoming group presentation & publication(pending) at the Multiple Sclerosis Consortium (CMSC). He has also completed the EMT Basic program at the School of Health, Technology and Management. Following graduation in May, Alex plans to continue to work in research, take his MCATs next year and to pursue an MD or PhD/MD in 2014.

Alex was born in Kiev, Urkaine and moved to the US when he was 6 years old, with little knowledge of English. He attended Valley HS in Las Vegas, NV, and graduated from Smithtown HS in Long Island. He credits his parents, both of whom have medical degrees, for inspiring him in many different ways to work hard, to pursue a medical career—and his mother in particular with making him read many classic writers (and the Dictionary!), which has inspired a love of writing and literature. In his spare time, Alex is somewhat obsessed with (Ideas worth Spreading), playing chess, writing creatively, and playing guitar. Below are excerpts of his interview with Karen Kernan, URECA Director.

The Interview

Karen: Tell me about what you’re working on, what your undergraduate thesis is all about. 
Alex.  My project in the Wimmer lab centers on competition between wild-type and codon pair maximized Polio virus in HeLa*. Essentially, because there is a bias in which pairs of codons are used to code for amino acids, one can attenuate a viral genome but retain amino acid sequence. The principle behind the bias suggests that there is also a way to 'maximize' the translatability of RNA by synthesizing a nucleotide sequence with over-represented codon pairs. My thesis centers around a competition between wild-type and a codon-pair 'maximized' version of polio virus in human cells. The implications here are interesting; if Max beats out wild type it may suggest that evolution is not as optimal as we think. . . 
*These cells by the way come from an African-American women with cervical cancer cells a long time ago, Henrietta Lacks….There was a book published in 2010 about her. When Prof. Wimmer asked who read this book and nobody raised their hand, he said “ I’m buying 5 copies. Everyone must read this!”

Tell me – how did you get originally get involved with the Wimmer lab?
I was taking Cell Biology during the summer, and I asked the graduate TAs, Evelyn Prugar and Betty Lavoie, during one of the recitation sessions about research. I told them I was going into my fifth year --a “super senior””—and that I really wanted to do some research before I graduated from Stony Brook. They gave me a whole list of suggested mentors, and Dr. Eckard Wimmer was one of the names on the list. 
As I began doing the background research and reading about their papers, doing my homework to best prepare myself … I became really infatuated with the idea of working with Wimmer. Did you know he has his own Wikipedia page? That he was the first to grow a virus outside of a cell?!! Now that’s something…..! 
When I walked into Life Sciences, I didn’t expect him to be there, but he was! So I introduced myself, and told him I was interested in doing an honors undergraduate thesis. The only catch was I that had only one year to do it (which I knew from experience some PIs might not be interested in). Then I started sending him follow-up emails to show him how interested I was. At first, no response …but I kept coming back …And the second time I walk in there, and had a chance to talk with him, he introduced me to Molly Arabov, a PhD student in the lab. Eckard even remembered my name. And he told me that they had a project that I would feasibly be able to complete on time for my thesis while Molly was on maternity leave. 
I was – and am –really really interested in codon pair bias, and had read a lot about it. And that’s the project I was put on. Prof. Wimmer also gave me a bunch of papers, and gave me an office.

What a tremendous opportunity!
To have the chance do independent research in the Wimmer lab was incredible. It was an amazing opportunity. I would also add: he’s the most intelligent, most charismatic scientist I’ve ever met. He’s an amazing person… I went to Thanksgiving at his house. (He holds Thanksgiving for the lab members.)  He always has lots of stories, and there are  other great people that I get to interact with in the group,  like Dr. Stefan Mueller,…

Do you work with live viruses? Is it dangerous?
The competitions are with live virus. So I had to get a polio booster shot before I was allowed to work in there. I did safety training.. … you take precautions. You always wear gloves, you work under the hood. But it’s only BSL 2. It’s not like Plum Island...

Did you have any previous lab experience? 
The crazy thing is: I had never done bench work (e.g. working with a pipette) before.  I’d taken Bio 205. But that was my only experience with pipette and PCR. I had no idea what I was doing. For the longest time, I couldn’t get the most basic PCR to work. You make a gel and you don’t see anything. First you make the plasmid, you insert the plasmid into E. coli. You grow that out, you get the colonies, you extract the DNA with one of those mini prep kits…You translate that. You finally run it. And there’s nothing there and you just spent 8 hours doing that! That whole day was nothing. You wasted a lot of time. And you wasted money! …So this goes on for a while. One of the postdocs, Sam Shen, assured me: “Science is ~98% failure.”  And I could see what he meant because  for the longest time I could not get anything to work. I was putting in a lot of effort. I was there unreasonable hours, on the weekends, all the time… And finally, I think two months in, some things started working! I got the PCR to work! I got the qRT-PCR to work! But don't get me started about purifying out RNA. That will always be a nightmare.

Was Molly, your graduate student mentor, helping you at the start with navigating your way in the lab?
A lot! I was completely dependent in the beginning. Every three seconds I would go up to her and ask her, “How do I do this? How do I do that?” And everyone on the lab was very, very helpful. {Probably they also didn’t want me to contaminate anything!} …Molly left on maternity leave towards the end of December, right as the semester was ending. So by that time, I had to have learned everything, all the techniques I needed to know to run the experiment independently. But the fact that I’ve been given this opportunity to work independently…without any prior experience, and Molly put so much work into teaching me these things, completely anew…it made me want to put all that effort in. Hopefully I have some solid stuff to show her when she comes back to lab, in April.

And you attend regular lab meetings? 
Yes – our Synthetic Virology meetings. I think I may be the youngest there by several years. These Synthetic Virology meetings are really interesting. There are people there from other departments, including the Computer Science department. A surprising thing I’ve learned working in research is that a lot of the things that they talk about in the meetings— that everyone there knows to be common knowledge—is not even published, it’s just word of mouth. You wouldn’t be able to find out about it by reading journals, or on the internet.

What do you like most about doing research, and working in the lab?
I’ve mentioned the downside—the 98% failure rate,  that you’re frequently on no sleep, you’re getting no results. You might have just wasted a week of work and when you test your sample, it’s all botched; everything is horrible. . . But when it finally works, … it’s such a gratifying  feeling! 
But here’s the thing. I remember when I was working on reviewing an analysis of the QRT, looking at the amplification plots. They looked a little funny to me. And I remember thinking to myself: I wonder what this should look like? (You know how In chemistry lab, or physics lab, you always ask yourself: what are my results supposed to look like (even though you’re not supposed to) …Then I realize, like an epiphany, that nobody in the world knows what it’s supposed to look like!  I’m working on answering something that nobody knows. What our lab is doing is at the forefront.  And when you realize that you’re working at something that’s at the forefront of human understanding, human knowledge…it’s  a very profound, incredible feeling.

Would you say that the experience you have in your lab, doing your independent research project, is substantially different than a classroom lab research?
Everyone says this: that you learn more in the lab than anywhere else. But it’s definitely true, not even just about biology but about the way research actually works. Interestingly enough, one of my friends was taking Bio 311 at the same time while I started working in the Wimmer lab. We were doing some of the same techniques. But the difference is that you have this idea, again when you’re in a class, of what is it supposed to look like. You’re doing a little experiment that’s already been done. It’s not as interesting I think as when you have your own project where you don’t know the outcome…Last semester, in my neurophysiology lab class, Bio 335, we did some things in lab that were just recently published—something to do with dopamine binding, and different parts of the brain. Now that was pretty interesting because we were analyzing and repeating an experiment that was just done only very recently. That’s cool. But when you’re going back and repeating an experiment that was done a longer time ago….I mean, it’s still fun but it doesn’t feel your own. It doesn’t feel like your baby. When you’re working in the lab, it’s your own stuff. That’s your reagent. You’re responsible for that. You’re responsible for getting the project going. It’s a more independent kind of feeling.

What your future plans?
After I graduate in May, I am going to continue in the Wimmer lab for awhile. I plan to take my MCATs next winter.  I got my EMT certification, and I’m going to be using that to go on a medical mission perhaps in South Africa or South America…I’m still looking at possible programs. And then I hope to start medical school in 2014.

Tell me about your other research experience, in the Neurology clinic.
My other research project is with a Neurology clinic on the South Shore with Dr. Mark Gudesblatt.  Right now we are working on a better cognitive model for the clinical diagnoses of Multiple Sclerosis. Most recently our data suggests that a lot of patients are inappropriately diagnosed with benign symptoms because there is insufficient correlation using current models between cognitive impairment and more malignant forms of the disease, and this is certainly not true -simply, the models are just bad. We have a publication (pending) on this…I’ve been working on this and related projects for about two years now.

With all these very intensive research experiences is it difficult for you to balance your time?
With the Neurology project, the cool thing is I don’t have to go there physically. A lot of the data analysis I can do anywhere – here on campus. Or in the lab.  But I have had to teach myself about time management. Sometimes I have to remind myself to stop – I’ve done enough for today. Stop– I have to study for this now. Stop– I have to study for MCATs. Stop–  have to start writing … There are so many things all the time that have to get done. You learn time management because you have to! 
If you don’t put in that one hour a day, then you’re already behind, and then things accumulate and it’s a horrible disaster! The other thing you learn is efficiency. I can be extremely neurotic  – and when I first started, I would sit there too long , trying to exactly pipette one microliter and make sure there’s no bubble in the media – only to find my RNA is already dead. It was off the ice for too long. So you have to be good enough to make it work and you have to learn to be efficient with your time. 
So for example, if I’m doing infections in the hood, it takes me about two hours. I’m sitting there nonstop for two hours.  If I’ve just recorded the pharmacology lecture, I’ll put that in and listen while working in the hood. As soon as you take the cells out you’re rocking them. . . You don’t waste any time. You want to split cells as quickly as possible in the other hood. So you have two hoods working at the same time. One is doing infections. You’re listening to lecture. And you’re splitting cells for the next three days in the other hood for more infections. It gets even more micromanaged than that when you take the cells you have to put trypsin on them to make the cells come off so you can dilute them and split them up. Usually it takes two minutes to trypsinize cells in the incubator. During those two minutes, you have labeled 15 plates. You’ve already prepared the dilutions with the media…you might still have 15 seconds to spare. Then you think, what are some of other things to do with these extra 15 seconds?... All the while listening to lecture. Or NPR.

Sounds exhausting!
It requires a lot of energy which is why I realized, from past experience living on cup ramen alone, that you can’t do this on a poor diet. I’ve started reading research papers on centenarian diets. So now after I eat I always drink green tea. I try to get the diet aspect down. Still, sometimes I find I don’t have enough energy. So then other things come into play including massive amounts of coffee, energy drinks…!

Did you come to Stony Brook knowing you wanted to be premed?
I’ve known I was premed for as long as I can remember. My father is a doctor. Both of my parents got medical degrees in the Ukraine. My father took me to the hospitals on rotations in Ukraine when I was one or two years old. …It’s been built into me.

Had you learned English in the Ukraine? How old were you when you moved here to the States?
I was 6 when I came to the US. The only English class I took in Ukraine was when I was 4 years old ... …they teach you words like giraffe, and elephant. But my mother did something I appreciate. When we first moved to the US, I wanted to read Goosebumps, those RLStine novels. But she would adamantly refuse to let me read that. She gave me Jack London, Kafka, Edgar Allen Poe. She would make me read that. And she used to make me read the dictionary. A to Z. Fun! .. I think it led to an interest in writing. I’ve discovered I like to write. I have little books, little journals where I just write interesting ideas down. I’ve always wanted to compile them, and write something and submit it to a publication.

So now as you approach graduation, five years in, how would you say Stony Brook has worked out for you?
I like Stony Brook a lot! The faculty here are some of the best in the nation. …I think you  just have to approach it the right away as an undergrad. A lot of the faculty are hesitant to take someone on unless you prove that you’re going to be a good investment. But if you can do that, if you have the willpower to do that, and you have some intellect, you can get in there and you can work with some of the best.  I sometimes wish I could explore other departments too, but unfortunately, there’s no time. Definitely if it were up to me, I would be doing everything. I would have every PhD, every Master, every Bachelor’s …

Haven't you at this point taken many –if not most of  the bio classes offered?
I have the cell biology and the neurophysiology concentrations almost done. I’m missing one lab. For Biochemistry, I’m missing Pchem. For Pharm, I’m just missing the two labs. But it is my intention to learn what I can. I like learning about lots of different areas. Take the pharmacology classes. I love these classes – which are a culmination of everything. You apply physiology, immunology, microbiology – it really combines everything. That’s exciting . ….To be creative as a scientist is not this magical thing. It’s your ability to draw on other things and apply them to a different situation, to a different topic. That’s why you need to learn from all these other classes, to gain a wider network of thoughts ….

What advice would you give to an entering freshman at SB?
For one, don’t trust what other premeds have to say! But I would say is: …It’s really hard to bring your GPA back up. That’s what happens a lot. That’s the common college condition. An upward trend is all well and good, but it’s really difficult to do that because the classes will only get harder. So if you have a competence for studying and you set off a little bit of time each day, it really does help a lot. If you don’t have to worry about getting your GPA up, that will save you from a lot of stress.

How is the thesis project going currently?
The real reason I stayed here this year was to do my thesis. I took the extra time. I was adamant about that. That’s the only way to graduate with honors. You may have a good GPA but you’re not going to graduate with honors if you don’t do a thesis. And surprisingly, many don’t even know about this option. ….Getting the hands on research experience, this senior  undergraduate thesis project, has been a highlight of my education here. And when I work in the lab, I look at it not only as a learning experience but I also think of it as a job. They’re dependent on me. I work there and I have a responsibility to the lab. I don’t do things part way. If I do something, I’m going to put a lot of effort on it.

I’m glad waiting until the fifth year didn’t preclude you from having a research experience.
In part, the reason why I waited so long until my final 5th year was because I felt I had nothing to contribute to a lab. …Sure I might have started earlier. But I’m working independently now. If there are results I don’t understand, I have to go back, find the protocol and adjust it.  You have to know stuff to do this. I’m already lost in the meetings . . . .  Without the background I built from 4 years of taking many biology and biochemistry classes I wouldn’t have belonged there!

What qualities are important for being successful at research? 
You need luck. Efficiency.  You need to be a person who does not get dejected and depressed when dealing with bad results. And I’m talking about back-breaking work and no results!  If you can stand up after that – research is for you!

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