Grad Diary 12/22/09

I am now officially home for winter break.

Holy Cow, what an end to the semester.

I mentioned in my last post that my project was shifting gears. Add onto this the fact that my data looked promising enough to be added to the grant proposal Una needed to submit by January 3rd, and suddenly my workload tripled overnight (that was two weeks ago). And of course, I was excited about what was going as well and really wanted to complete things before the end of the semester, so I was totally complicit in the increased workload.

This past week was my last week of experiments, and the earliest I left the lab was somewhere around 7:30pm. I actually distinctly remember one night the only reason I left (around 9:15pm) was because I needed to eat something and perhaps sleep before classes the next morning. It was so crazy that on Monday, during lab meeting, I basically diagrammed on the white board everything that needed to happen on a day to day basis and started delegating certain experiments/tasks to people so they would all get done. It was like my own little project with Jenny suddenly expanded into a rather ridiculously large lab endeavor, and I somehow got the task of overseeing it all. Did I mention that I was supposed to be studying for my Cell Biology final during this time?

Somehow, things got done and I was able to organize things in a way that would let Una and the lab move forward, but last week was easily the most stressful week of my entire grad school experience thus far.

This experience proved to be very instructive, though, in that I got a ton of support and encouragement from the entire lab, and everyone was ready and willing to chip in to get things done, especially since we were going to try to include my stuff in the grant proposal. Last week summarized pretty nicely how my overall lab experience has been in the O'Doherty lab; I have gotten along extremely well with everyone in the lab, I have felt completely supported and encouraged, I have been pushed scientifically and technically, and I learned a lot. It has been a truly fantastic experience in Una's lab this semester, but I am still really happy to have some vacation time...I've earned it.

Oh, and yesterday I had my final exam for Cell Biology. It was pretty much the same as the previous two, and compared to what happened in lab last week, it seems almost inconsequential, ha ha. Hopefully I will get my grades back around New Year's?

I'll be taking a break from blogging for a while. Look for my return once classes start up again in January! Have a happy holiday season and a great 2010!

Grad Diary 12/2/09

Up till now I've been attempting to isolate HIV linear DNA through a TOPO-cloning technique. I think I mentioned previously that after coming back from a conference, Una was very excited about moving on to an alternative technique which we had been considering, called the Hirt extraction, which is a method of isolating small nucleic acids within a background of high-weight chromosomal DNA. Theoretically this technique could be applied to HIV as a method of isolating non-integrated species of HIV DNA.

I am now shifting gears to trouble shoot the method, and in addition, we will now start looking at 2 LTR circles, a non-productive non-integrated HIV DNA species that may or may not be indicative of productive/latent infections. There's a lot to work out and I am a little concerned that I won't get as far as I would like before the end of the semester (just a few weeks!). Fortunately I am getting a lot of help from Jenny so hopefully things will go well.

Oh, and there's always the final exam for Cell Biology coming up...

Grad Diary 11/25/09

I'll be heading home for Thanksgiving soon. I've been spoiled at Ithaca, where we got the entire week of Thanksgiving off. This week I had my second cell biology exam on Monday evening, which went pretty much the same as the first one (clocking in at about 1hr 10min). I probably would have gone home yesterday but things in lab have been going pretty crazy, largely because we have moved in a new direction technique wise and there is a lot to be done before the end of the semester.

Surprisingly, they STILL had a lecture this morning for cell biology! Not only is it right after we took our exam on Monday, it's the day before Thanksgiving! I only came this morning because I wasn't able to go home till today anyway. Not surprisingly, instead of 40-50 students there were not more than 20 students in class today.

Anyway, I'm glad that's all over and can't wait to be home. I could really use the break.

Grad Diary 11/19/09

I just took a trip up to Ithaca this week to talk about graduate school, and it was a great trip. I had made a trip back to Ithaca at the beginning of the fall to visit some friends and old professors. While there the director of the Honors Program, Bob Sullivan, asked me if I was interested in making a return to trip to talk to the first year honors students about applying to graduate school. I thought about it and over the next few weeks we worked out the details. Since I was already going to be on campus I e-mailed the department chairs for biology and chemistry to see if they wanted me to do the same for them, and they were thrilled. So, Tuesday night I found myself driving up to Ithaca and checking into a hotel room already paid for by the honors program and enjoying the irony of being invited back as a "guest" when I haven't been out of school for more than six months. It was very surreal...and kind of cool.

My talks were at noon (for the honors kids) and at 4:00pm (for the science kids). I spent the morning and afternoon between those times running all over campus stopping into professor's offices and catching up. It was very hectic. The talks themselves went well, though I will be honest and say that I was more excited and gave a better overall presentation to the science kids, because I could focus exclusively on my own experiences (which were still pretty fresh). The turn out was small, but I wasn't expecting much (having recently graduated). Still, the students who did come seemed to have gotten a lot out of my presentation, and actually one of the professors asked if i would send him a copy of my presentation for him to use with his own students, which I thought was pretty awesome.

It was a great trip all in all, and I am looking forward to making more in the future, especially once I've gotten some research under my belt and can actually present some science!

The HMGS Certificate Program

In addition to my regular course work in the Cell and Molecular Biology program, I opted into a special "certificate" program at Penn sponsored by the Howard Hughes Medical Institute. This program (or similar variants) exist in a few other schools around the country (I think there are a dozen of us in total). The program, currently called the HHMI Med into Grad Scholars Program, of HMGS. Basically the program is offered to interested graduate students in the biomedical sciences who want to get more exposure/get involved in more "translational research."

"Translational research" is one of those phrases currently in the biomedical community that means different things to different people, and is such a buzzword in the NIH that you can't find a single grant proposal without this phrase in it. Because of that, it's almost become a bad word, but generally speaking translational research expresses the linking together basic science research with clinical/medical practices. In my mind, translational research is supposed to be a close collaboration of the two, and a perfect example is a clinician who works on breast cancer in the hospital, and who also does basic research on the underlying mechanisms of breast cancer as a means of developing new therapeutics (this is actually a real example, I will talk more about him in a moment).

Anyway, what the heck does that mean for me, a lowly grad student? Basically the program functions similar to a minor in undergrad, in that you take some specialized courses that complement your training and which encompass this "translational research" motif. You also spend two or three weeks shadowing a clinician in a field of your interest during a summer to get real life exposure to the field, and there are a few talks and symposia associated with the program as well.

There are four classes involved, one each for the four semesters leading up to your Prelims. I am currently taking the first one, which is a journal club type class where we read two papers each week, a student presents one of the papers during the class and we discuss it. Specifically, each week has a unique clinical topic, and we are assigned a "basic science" and a "clinical" paper about it, and a resident expert in the field comes in as well. For example, my first paper was on large diffuse B cell lymphoma (a cancer of white blood cells in very watered down terms). My paper was a clinical paper that looked at using a proteasome inhibitor as a way to treat a particular subset of these patients with a unique molecular profile (I will spare you the details, although it was quite interesting). The other student that day presented a basic research paper that described the signaling pathways involved in this subset of cancer patients, which also explained why targeting the proteasome (normally a ridiculous idea as a therapy since you would screw up all sorts of stuff) actually made sense (in principle anyway). Other topics included obesity, HIV, color blindness, etc. It's been pretty cool.

The other classes include a cellular immunology course (I can't wait!), a basic physiology course, and finally a more advanced class that will look at the cellular/physiological pathology of certain diseases. They are all meant to be ways to expose us to more clinically relevant topics and help us apply our backgrounds towards the clinic.

In addition there are speakers from Penn who come in and talk to us about their research. The first speaker was a clinician who was a breast cancer specialist (as I alluded to above). In addition to his normal clinical practice, his lab was working on eliciting immune responses against breast tumors, and he already had some clinical trials in the works for some of the therapies that had come out of his lab and collaborators'. It was a really cool presentation and got me even more interested in doing basic science that would be more directly involved in human health.

I think it's a pretty cool program and so far I am really enjoying the exposure. Programs like these are not very common in most universities and it's an opportunity I am glad to take advantage of.

Volunteering - Saturday Science Education Academy

Last month I signed up to be a volunteer in a program called "Saturday Science Education Academy," or SSEA. I heard about the program through a biomedical graduate student listserv. After learning more about the program I decided I wanted to get involved.

The SSEA started up a year or two ago, and is organized by Jay Gardner, the lab coordinator for one of the virology faculty at Penn. The program functions as a special, outside of school opportunity for kids in the 2nd, 3rd and starting this year 4th grade to get extra, hands on experience in science. It is specifically open to kids in the West Philadelphia school systems, which I will note is a public school with predominantly black students from a variety of backgrounds. The program runs for three six-to-seven week sessions, meeting every Saturday during the session for about two hours. Kids come based on interest in the program and are separated by grade for the activities. The SSEA works with the kids by providing numerous hands-on activities and directed learning as a way to expose kids to the scientific method and to teach them basic scientific principles. Jay meets with teachers to develop the curriculum to complement what the kids are learning in class.

I got really interested in the program for a couple of reasons. Primarily, I like to teach and tutor, and I want to get as much opportunity as I can to develop my teaching skills. Getting exposed to a younger group of students will help expand my skills and my ideas about teaching. I also saw this as a way to help out in the community. I don't have a good history of volunteering and I think it's time for me to get out there and do something.

I also want to mention that the listserv that tipped this off to me functions through the EE Just Biomedical Graduate Student Society. The society is named after Ernest E Just, a black scientist at Penn, and is a group made up of graduate students in the biomedical sciences from historically under-represented minorities (African Americans, Hispanics/Latino(a)s, Native Americans). I don't normally get involved in these kinds of groups because I don't have a strong association with my Hispanic roots. But, it is a well known fact that for whatever reasons, it is around the fourth and fifth grade when African American kids start to diverge in academics and social skills and you can track those students who will finish school and those who will drop out. While the factors involved in this can be debated, the statistical truth is very hard to refute. I saw this as an opportunity to not only help out in the community, but to get involved at a critical juncture in students' lives where their interest in science and learning might get tossed to the side in the face of other social pressures at home and at school.

So far I've had two sessions with the students, and it's been a great experience (and challenging!). We generally put two grad students per grade level, and this session I will be involved with the second graders (we don't come every week, so each grade will see up to four or five different teachers throughout the session, but we generally get one grade to help facilitate teaching). This session the second graders are learning about balances. Over the course of the session they will explore the concept of balance (what is a fulcrum?), weight, and measuring. We also introduce them to parts of the scientific method like observation and hypothesis.

The first session I had with students was relatively easy; I had another grad student helping me, and we only had two students, a boy and a girl. I tried my best to guide the kids through the lesson by asking questions instead of just teaching them, which was kind of difficult at times. They stayed on task for the most part but we did have to sometimes get them back on track or make concessions (like shorten the amount of reading and have more hands-on activity). All in all it wasn't so bad, and I even had fun.

The second session was a little more...exciting, ha ha. I was the only student teaching the second graders, and I had not two, not three, but six students. I tried to suppress the mini heart attack I had as I guided the tiny tykes up to the classroom. Fortunately, I was granted an angel in human flesh (i.e. a parent volunteer) who sat in my class and helped me manage all the personalities (and once she got an idea of what the activity was she also helped with that, although that wasn't her primary role).

It was a very different experience, partly because I was the only teacher and felt more in command of how the activities were going to be presented, and also because I had to deal with a greater variety of...personalities. One boy in particular, Mohammad, just LOVED to talk. He would stay on task for maybe two minutes and then as his attention moved elsewhere he would start talking about other things (like recent events at school, at home, a movie he saw, etc). I had to repeatedly bring him back on task, especially because he would then get other students distracted as well. I tried my best to be as flexible as possible and not authoritarian. Eventually, though, I knew I needed to convey to Mohammad that I needed him to stay focused and stop interrupting the class. I was reviewing what they had learned about balances and Mohammad started going off again. So in order to diffuse the situation I stopped what I was doing and said, "So Mohammad, you seem to like to talk about all sorts of things. Can you help remind the class what you learned about fulcrums?" Some of his classmates started giggling and Mohammad grinned sheepishly for a moment. He did finally offer one or two ideas that were more or less correct and I took it from there. This little moment awarded me about...five minutes of interrupted control before I lost it again. I realized later that this particular method of discipline might not necessarily work for all students (especially very sensitive ones) and that there probably wasn't any one method that works well all the time. It made me think even more about how teachers learn to deal with their students' behaviors, and I am beginning to develop an even stronger respect for the hard work they put into their jobs.

Even with an adult's help it was much more difficult to get through the activities just because there were so many more students. But they all seemed to have fun and hopefully learned something, which is the whole point anyway, so I felt it was a successful lesson, if more draining for me. And I've been learning a lot as well. It's harder with a larger group of students because you get a broader range of aptitudes and interest levels, but trying to manage this can be rewarding. I've noticed that a large proportion of the students are Muslim, which has been a great experience for me; many of the girls come in with head scarves (I'm pretty sure they were hijab, but I am completely illiterate in Muslim practices I couldn't tell you for sure). I've had the great pleasure of learning pronounce such colorful names as Sukainah, Ahmed (pronounced Ak-med), and Jermirr. It's been a great learning experience for me.

So far I like it a lot and am planning on continuing to do it for the next two sessions after the winter break. It provides a nice break from the serious business of studying, ha ha.

Grad Diary 11/2/09

Una has been asking me all last week whether I got my exam back...she wanted to make sure that, if I didn't do so well, I start taking more time to study and spend less time in lab. And, needless to say, many of my classmates informed me they noticed how early I finished my exam. To say I've been dying to know how I did would be to put it mildly.

Well, today after class they finally returned the exams.

They showed us a histogram of the scores. The average was very high: 78% or so. I took note of the trends towards the top of the distribution, where I hoped to be, and saw that there was a good amount in the >90 range. This of course didn't mean anything to me, but at least if I did really well I wasn't the only one, ha ha.

I picked mine up and, with a great deal of self-control, managed not to look at it as I walked back to the lab. The entire way I became more and more anxious, wondering if I did as well as I thought I did, and whether my record-breaking timing hurt me in the end.

I finally made it to my lab, put all my stuff down, and tried to calm my breathing as I turned over the cover page. In thirty seconds that passed by like an eternity, I scanned through the exam, reading the comments and the points deducted.

To put it mildly, I did very well. Very, very well.

I was very excited and announced to everyone that I had totally Aced my exam, and there was general celebration. I even made the mistake of actually showing Una what my score was. Her response was, "Well done sir. Looks like I can give you a lot more work to do!"

We got a second round of good news when Luis came back from his committee meeting later this afternoon and told us he was given permission to write his thesis. All in all, it was a very good day for the O'Doherty lab.

Grad Diary 10/22/09

It's nice to be back in the swing of things. It was kinda strange on Tuesday to put gloves back on...it felt like forever ago when I last used a pipette and did an experiment. Things are starting to move forward with my project, which is nice, and we are starting a new section in Cell Bio. I also gave my last presentation in my journal club class last night, and it went really well. Now I just have to make sure to read (or at least skim) the articles for class for the rest of the semester and I will be good to go.

The director of the Microbiology department, who is very interactive with the grad students in his program, likes to send the first year micro students with a few upperclassmen out to dinner during the week after the exam. I went last week with three other first years and two upper classmen to Buddakan, an asian fusion restaurant in center city. We all got $50 to "play with" which we used to its fullest (did not cover alcohol though...fortunately, since I'm not a drinker that wasn't a big deal for me). The food was very good, and I was excited to have "real" sashimi again! (I haven't had good sashimi/sushi since going to Japan a year ago). It was a really nice dinner, and the restaurant wasn't too pricey; I could definitly see myself going there again once in a while.

All in all, it's been a good week, with two major accomplishments out of the way. I suddenly find I have a lot more free time now that my presentations are done and my first exam is out of the way. I still can't wait to see how I did though!

Grad Diary 10/19/09

So......I just took my exam.

Actually, that wasn't so bad.

The exam time was 6:00pm to 9:00pm. Class this morning and last Friday was solely review sessions given by the TA's, and they were marginally useful. They were useful in that I felt I could explain the topics as well or maybe even better (or at least clearer) than they did, which made me feel I knew what I was talking about.

Anyway, as I said, they gave us three hours, but they designed it so that a "well prepared" student should only take an hour and a half.

I was done on my first run through in an hour.

I went through the exam one more time and spent some time thinking carefully about one or two questions that were a little trickier. Even then, I was sitting at an hour and ten minutes of test-taking time. I sat for maybe another five minutes trying to decide if I should wait any longer or just hand it in...I mean, I was done REALLY early, and I knew people would notice. Fortunately another student walked down and dropper off her exam at that point, so I took this as a cue to do to the same (at least I wasn't first). And yes, I'm sure some of my friends noticed.

I'm not that surprised, to be honest; I normally take tests really fast (I was definitely that guy in college), and I was already pretty familiar with the material. Still, I can't wait to get the results back just to see.

Anyway, all in all, the exam wasn't too bad (although the last question was quite strange), and now it's time to work on my presentation for Wednesday...

Grad Diary 10/14/09

I haven't been doing any experiments this week for two reasons. First of all, my results were kind of...interesting. Una suggested I take a day or two to think about it, come up with some hypotheses and some simple experiments to get a handle on what's going on. More importantly, though, next Monday evening is the first exam for my Cell Biology class. The first exam is especially notorious for tripping people up because many people are still trying to figure out how prepare and how to approach the problems. Fortunately they have posted the exam from the previous two years, which has been a really great help in giving me an idea of the kinds of questions and answers they are looking for.

It's been really weird coming to lab and not actually doing any experiments. On the other hand, it's been nice to spend the time to prepare and practice; I'm feeling pretty confident. One big difference with the exam is that the questions are all experimentally based. Therefore, the fact that the exam is open note/book actually doesn't help you that much. What we have to do is apply our knowledge of a system (say, vesicular trafficking) and interpret experimental results that are thrown at us. This interpretation requires a knowledge of the techniques (and what they do and don't tell you) as well as a basic understanding of the subject (which can be supplemented by notes). But coming up with the interpretation, and then designing new experiments to answer new questions, are all coming from you, not from your notes. Fortunately, I did get some of that with my last cell bio class, though I would say it made up between 30 and 50% of any given test.

I'm not terribly concerned about the exam - the material is all pretty familiar to me anyway, and the practice exams have been very useful - but Monday will be the day of truth. We'll see. Needless to say, this weekend will be wholly devoted to it.

Fall Rotation Profiles

I've been working in my fall rotation lab for a few weeks now, as you already know, and I thought now would be good time to give you all an introduction to the lab in a manner similar to my last lab intro.

The O'Doherty Lab
Una O'Doherty is an MD/PhD at Penn who is currently studying mechanisms of HIV latency. HIV latency is the primary reason HIV infection remains a treatable but non-curable disease. Latency - it's establishment, maintenance, and reactivation - is the next big frontier for HIV research. The O'Doherty lab is investigating whether a low-level of viral replication and infection continues despite therapy, and whether naive/resting cells are able to be infected by HIV.

Una's lab was actually one that caught my eye when I was looking at Penn, and during my interviews she was one of my interviewers. Even during interviews we hit it off great and I knew that if I went to Penn I wanted to do a rotation with her.

Una runs her lab differently than Dr. Fraser. For one, it is a lot smaller (more on that in a minute), and she likes to keep it that way so that she can spend a lot of time with her grad students. The lab atmosphere in general is super-collaborative; a major lab philosophy is that we talk a lot about our experiments with each other, give a lot of thought and feedback, and thereby do the experiments much better in the long run. Lab members regularly talk to each other not just to get feedback on their own experiments, but to also see what other people are doing. This is greatly facilitated by the fact that the lab is so small, and the net effect is a very strong community feel, and everyone is very willing to help you out or give advice.

Finally, while the atmosphere is very congenial and collaborative, Una has from the get-go pushed me to start thinking independently about my project and to take my researching skills to the next level; while I certainly started that in my last rotation, it was more self-motivated than now.

The lab just finished applying for a new grant not too long ago, so things have been pretty crazy, but now that things are settling down I am getting more time to talk with Una on an individual basis, which has been really fantastic.

Overall, the lab dynamic and level of involvement is exactly what I am looking for.

Technician
The lab has one tech, Jenny Yu. Jenny has a master's and is closer to my mom's age (actually, her kids are close in age to me and my siblings, which is kinda funny). She is an extremely skilled and knowledgeable researcher who has experience in a lot of different biological fields. She is also technically excellent, and is definitely a major asset to the lab. She does a lot of experimental work with other people in the lab and has a few projects of her own as well. In fact, the project I am working on came directly from Jenny and therefore I am working under her wing this semester, which is great because my technique will hopefully increase due to her instruction.

As the lab tech, she also handles all of the vendors and lab supplies. In this area, I am constantly astounded by Jenny's talent for getting a lot of stuff for pretty a great price. Jenny is a master haggler, something I have enjoyed watching frequently in the lab. Even more impressive, she does it in a way that usually ends up with both parties in a win-win situation, and for that reason she is well known among the vendors as a great customer. (Indeed, when a new sales representative for Invitrogen stopped by our lab to introduce herself, we mentioned that Jenny was our lab tech and the sales rep immediately recognized her name and was excited to be working with her).

She is really great to work with and has been a great mentor and guide these past few weeks. I am looking forward to continuing my project with her over the next few months.

Postdoctoral Fellow
The lab has one postdoc; a veterinarian by training, Angela Mexas is currently studying HIV infection of naive and memory T cells. I didn't interact with her a whole lot in the first few weeks but over time we have had more interaction and she is very friendly and helpful. She works a lot with Erin, another grad student, and a bit with Jenny, so we don't collaborate very much, but I enjoy chatting with her at lunch and around the lab.

Graduate Students
There are three full-time grad students who are in various stages of their theses. Luis Agosto is a fifth-year grad student who is planning on defending his thesis in May. He has been investigating whether HIV-1 can actively infect resting T-cells, and then moved on to test various HIV-1 mutants/constructs to develop possible gene therapy vectors using HIV machinery. He's super friendly and helpful, and lends a lot of energy to the lab. He is originally from Puerto Rico, and came to the states for his undergrad education (at Penn State Univeristy) before coming here for Grad School. Between Luis, Angela and myself, half the O'Doherty lab is fully Hispanic, which is actually kind of fun, although growing up in predominantly white communities my whole life has dulled my sense of Hispanic identity. Anyway, Luis is really smart and capable, and similar to everyone else in the lab, goes out of his way to help you out or give you advice.

Matthew Pace is a third year grad student who finished his preliminary exams (also called qualifying exams) earlier this year with flying colors. While Luis will soon be asking his committee for permission to begin writing his thesis, Matt is just getting started on his thesis, and is just now enjoying the fine pleasure of trying to get five people's schedules to line up for a first committee meeting. Similar to Luis, Matt is currently investigating different viral constructs, but with the goal of elucidating possible entry restrictions in resting T cells. Matt is the resident "organizer" of the lab, meaning that Una usually leaves it to him to handle administrative things like reserving rooms for lab meetings and sending papers out for our weekly journal club. Outside of Jenny, Matt has taken made it a point to introduce me to as many aspects of the lab as possible, including where to go to pick up cells or reagents, how to use different equipment, the ins and outs of the biosafety cabinet, etc.

Erin Graf is the final graduate student in the lab, and she just started her second year. Because she is only a year ahead of me, and because she is in the same certificate program I am, she is another great resource for me when it comes to questions about classes, rotations, etc. Her preliminary exams are in May, so until then she isn't working on a formal thesis project per se, but is rather doing some research and putting her ideas together to come up with her project. I am not as informed about her project. She is working a lot with clinical samples from HIV+ patients on retrovirals, measuring viral DNA levels to get a handle on whether there is active viral replication in resting T cells (a major question in the lab). Actually, my project is more related to hers in the respect, which I will talk about in a minute. She is also looking at elite suppressors, patients who are HIV+ but who control their virus so well that they don't need treatment and don't progress to AIDS. Our benches are close to each other, and we both make heavy use of the Real Time PCR machine so we interact a lot with each other.

My Project
My project is relatively simple to describe but very hard to do in practice. HIV is an RNA virus (meaning its genome is RNA not DNA), and as such after initial infection it needs to "reverse transcribe" it's DNA back into RNA (which is "backwards" from how most living things do it). After making DNA from RNA, this DNA is then integrated into the host cell DNA where new viruses are then made. When people are on retroviral drugs, the capacity for viral replication is greatly reduced. Una's lab proposes that, in at least some patients, viral replication still occurs, but at low levels. One way of examining this question is to look at viral DNA levels; we already have a good grasp of how to do this with viral DNA that has already been integrated, but it's been hard to directly look at viral DNA that is not integrated (episomal). My project is, in a nutshell, to develop a method to measure "linear" HIV DNA.

I won't go into the details, but suffice to say that it is pretty tricky, although I have a few methods to try out. The assay is PCR based, which is great because I already have a lot of experience with PCR. If I can get an assay that works then it will be a huge boon to the lab, but if I can't, then at least I tried (and will have learned a lot in the process).

Anyway, that, in a nutshell, is everyone in the lab. All in all, everyone has been extremely helpful and interactive, and it is full of energy. So far it is exactly the kind of lab atmosphere I am looking for and I am enjoying it immensely. All that remains is to make some progress on my project and keep up with classwork!

Grad Diary 10/2/09

This week, lab was hell.

For whatever reason(s), nothing seemed to work. My experiments gave weird results and I couldn't even do the most mundane of things like a gel extraction. I think there is some type of karmic law that states that the first two weeks in a new lab, everything goes beautifully and you develop a sense that you can make real progress in your project. Then...WHAM. Equipment fails, experiments go wrong, calculations never produce the same answer twice, and you feel completely incompetent.

Fortunately, I know from my research at Ithaca and from my summer rotation that this is a common occurrence in research. Still, I wish it wasn't happening so early in my rotation! I feel like the only thing I'm proving at this point is that I have poor lab technique...Which is, of course, an exaggeration. No one else in the lab, my PI included, is too concerned about it...they know I will figure it out and they don't think my technique is bad, I'm just having "one of those weeks."

And mercifully, today I have begun dissecting what has been going wrong and starting to move out of my rut, with a lot of help from Jenny, the lab technician that is taking me under her wing. Still, it's been an incredibly stressful week. Thank God for the weekend.

Classes, Seminars, Lab Work - The Life of a Grad Student

So things are CRAZILY busy right now! I knew things would be intense but I didn't think it would pick up so quickly!

I'm going to give you an idea of what my schedule is like, which revolves around three major things: classes, seminars, and the lab.

Classes

This semester I only have two classes - Cell Biology and Physiology, and Topics in Molecular Medicine. Cell Bio meets MWF for an hour and a half, and Topics is a seminar/journal club class that meets every Wednesday for two hours.

Cell Bio uses the same text I used when I took Cell as an undergrad at Ithaca, and since it was the newest edition at the time, I didn't have to buy a new one (woot!). So far, I am pleased to say that my undergrad cell bio class has prepared me pretty well for the grad level...while we are definitely going into more detail on all the topics, I have enough background knowledge to follow everything pretty easily (thanks Professor Cluett). The readings in the text are review since I've already done them before last year. All in all I am pretty confident I am going to do well in the course, although we are definitely going at a somewhat accelerated pace.

The course is taught by a variety of professors, with one of them acting as class coordinator. Basically they bring in the resident expert on the topic and have them give a lecture about it. This is both a blessing and a curse; on the one hand, you are getting very expert explanations of the material, but on the other hand you sometimes run the risk of dissecting the topic to a level of detail that is not really useful for our purposes. Since there are so many professors giving lectures, you also see a the gamut of presentation/teaching skills; some professors are definitely better than others when it comes to giving presentations. Again, the advantage here is that we aren't stuck with one particular teaching style but that also means we are constantly adapting to new presentation patterns. So far it hasn't been terribly difficult but it can sometimes be a challenge (or just annoying). Another drawback is that professors often don't know what has already been taught in the course, and may explain a process that we've already gone over in a lot of detail, or breeze over something we haven't seen yet. This was highlighted in the lecture on the nucleus where, to my surprise, the lecturer spent about five minutes at the end of the lecture talking very rapidly about the RanGTP cycle and its contribution to nuclear import/export; up to this point, no one had gone over the Ras-like GTPases and their regulators like GEF's, GAP's and GPI's, so while I understood what he was saying, I know many of my peers had a hard time following him. Fortunately, this was covered in more detail in a later lecture but it was still pretty disconected.

The professors also often give us "assigned reading" from primary sources. Initially I would try do all of these readings, but it very quickly became way too much (especially when the mitochondria lecturer posted five articles, two of which were twenty page reviews). I decided that, while some of the primary articles were interesting, they were really only useful as references for a more detailed look at the system or as a review to complement the textbook. I decided I would look at them only if I found a topic to be interesting or confusing, and I wanted some more reading about it.

Since I've already taken a Cell bio class, I have an idea of what works for me in learning the material, so I feel like I'm good to go.

My other class is a journal club type class which looks at the molecular basis of certian diseases and their treatments. We read two papers a week, a "clinical" and "basic science" article relating to a specific disease or condition - say, Diffuse Large B-Cell Lymphoma. Two students present the papers and we have discussions. It's in pretty much the same style as my capstone Biochem course. This class isn't so bad, it's just a lot of reading. One plus side is that, after my senior year and into this year, I am finding that my proficiency at reading and interpreting scientific papers has really improved, and I can spend more time thinking about the experiments and interpretations rather than figuring out what the nomenclature means.

Seminars
So, in addition to classes, there are various seminars hosted by different departments on campus. They are usually once a week and for the most part invite faculty outside of Penn to come and give a one hour talk, though sometimes in-house faculty or even upper classmen grad students give talks...and sometimes its an actual thesis presentation.

Just within my concentration, there are four seminars that are directly applicable: Virology, Prokaryotes, Parasitology, and Microbiology (ostensibly a mix of the three, though it usually is light on parasites). In addition, there is the occasional immunology seminar that might be applicable/interesting. And since Penn is a Center for AIDS Research (CFAR), there is also a seminar series hosted by them. Put them all together, and that's a lot of seminars. In practice, I go to Virology and Microbiology seminars regularly, the former because it is directly related to my interests, and the latter because, even when it's not a virology talk, the speakers are excellent. Every now and then I'll pop into an Immnunology or CFAR talk, but it's hard to go to all of them. While this doesn't seem like a whole lot, if you add these seminars to the time I spend in class, you will find they very quickly eat up your day. And these are just the seminars that are directly related to my major.

I find that the seminars are very useful because you will always learn something new. They can be good sources of new ideas, techniques or approaches. The departments also host lunches with the speakers and invite grad students to join, so they can be excellent networking opportunities, especially for grad students starting to look at life after graduation. And if nothing else, they can often be a very cool story about an organism or system you didn't know about.

Lab
Basically any time not spent in class and seminar should be spent in lab. The specific schedule you develop in the lab really depends on your commitments and the inclinations of the PI and your lab mates. I generally work till sometime between 5pm and 6pm, and on the days I don't have a morning class I try to get in around 9:30. It has been somewhat of an adjustment for me because I am coming out of a summer rotation where the entire day was devoted to lab; now some days have more lab time than others, and I have to make sure to budget enough time to do my readings and study.

In addition, most labs have a weekly lab meeting, and ours is no exception. In addition, our lab does a somewhat informal journal club where once a week (usually Friday over lunch) we read and discuss an article that is related to someone's project or that is a hot new finding in the HIV field.

Fortunately, most labs are pretty flexible about when you do your work; people are more concerned that you are making progress than when you are doing it. Because I live relatively close, I could do lab work in the evenings or come in on the weekends to do an experiment or two; this flexibility makes trying to get everything done much easier, but it has so far still been rather challenging. Now that I'm a few weeks into things I am starting to develop a rhythm; my online calendar has been invaluable in keeping my commitments straight.

The take-home message is that time-management skills are a must!

Grad Diary 9/12/09

This past week was orientation, which was both exciting and really, really boring.

Some of the sessions were kind of useless, especially because a lot of the initial advice was about how to select your rotation labs and make the most of them, or basic safety guidelines, all of which I already have plenty of experience with after my time in the summer. Some were more useful, like the various panels of different resources there are on campus, which as and undergrad didn't seem as pertinent (I always had someone to point me in the right direction), but as a more independent grad student felt more useful. We also had various speakers from faculty at the university, which were on the whole not so bad.

On the plus side, there were plenty of receptions and lunches to keep us well fed for this first week, which was pretty sweet. Not to mention that because most grad students are of age, all of these events included free booze. I'm not a drinker myself, but I could appreciate the novelty.

The receptions were also great opportunities to meet people within and outside your programs. Some of them also included upper classmen, so these were great networking/socializing events. It was really nice to have spent the summer early because I already knew a couple of students, which helped me navigate these sometimes awkward events. I will admit that often people would clump with their program, especially by the fourth and fifth day, but on the whole it was a nice opportunity to see who was out there.

I'm glad that orientation is over...on the whole it was a little boring but there were some good parts as well. I'm excited for classes to begin on Monday. I'll also be starting my next rotation with Una O'Doherty on Tuesday, so I'm pretty excited.

Grad Diary 9/7/09

It's Labor Day, and I was on my way up to campus from my apartment to run some errands. My apartment is in West Philadelphia, about 10 blocks west of the main campus. It's a nice area with lots of trees and Victorian style houses. On my way to campus I walk past two blocks or so of Penn fraternities and sororities before entering the campus proper. Up until now I hadn't really taken notice of them.

As I was walking to campus on this fine September morning, I started noticing the debris of what had to be quite the block party. As I walked closer and closer to campus, the volume of beer cans, red cups, glossy party announcement, and the pungent aroma of stale beer increased with every step. On one porch I could see a couch that was clearly no longer serviceable after the previous night's debauchery. In fact, you could use the cups and beer cans to track the very epicenter of this veritable explosion of undergrads celebrating their return to campus.

Ithaca doesn't have any fraternities on campus aside from a few music/honors frats. So most of this kind of action would have taken place on the Cornell campus. As I reached the opposite end of the two blocks of frats, a bemused expression on my face, I realized that I had fully entered the world of the grad student; the undergraduate population, which I had not too long ago been a part of, now felt so far removed from me that the site of such mayhem provoked a sense of detached hilarity.

The campus had been quite beautiful and relatively quiet all summer. It's going to be interesting to see how the return of the undergrads would change the dynamics.

Grad Diary 9/3/09

Today was my last day in the Fraser lab. I gave a presentation summarizing my project and what I've learned during this past week's lab meeting. I'm also wrapping up a mini-paper to submit to Dr. Fraser by the end of the week.

The summer really flew by and I didn't fee like I got as much done as I would have liked, but that's what happens when you work in a lab for only 11 weeks or so. I learned a lot of things, and not just technique wise (though that was obviously a major component). I learned to navigate the lab and it's various personalities and how to begin working more independently on my projects and research questions.

I also learned that I really like writing papers and putting presentations together, which totally ups my nerd factor. And though I was still nervous at the beginning of my talk (which was totally silly) I felt pretty confident talking about my work, answering questions and being honest about what I didn't know or the weaknesses in certain experiments, etc. I have to give a lot of credit to the training I got at Ithaca, which gave me lots of practice putting together and giving presentations.

I am pretty sure I won't return to this lab for thesis work. I would want a lab with more interaction with the PI, and a lab environment where there is more interaction among the people in the lab. This is not to say that I didn't enjoy my time in the Fraser lab. My primary objective for this rotation was to learn a lot of basic techniques, get a feel for doing research at the next level, and begin acclimating myself to UPenn, and I feel I met all those goals very well.

I'll be looking forward to my next rotation with Una O'Doherty, but I will definitely be coming back to visit the Fraser lab to say hello. All in all, it was a successful summer; I'm really excited for classes to start!

Grad Diary 7/15/2009

So, today I had a lab meeting with Dr. Fraser. It was my first formal meeting with him since I've started in his lab almost a month ago. Iryna was with me too. It went pretty well, although in the beginning I had my doubts. His opening question was, "pretend I'm one of your classmates and explain to me what you're doing." This took me completely by surprise because I was expecting to give him a status update, not a mini talk. While I knew the basics of what I was doing, I didn't feel prepared to talk about all of the biology involved in my project - I would need to review some material before that, so I was a little flummoxed. It was also weird trying to give this little talk to the mastermind behind the whole project to begin with.

After stammering my way over some of the introductory stuff I caught my groove once I started talking about my projects, and things went smoothly after that. Predictably, Dr. Fraser said I should give more details on the background, but he was impressed with my explanation. He had specifically given me no warning before hand to see how I would do...apparently he does this a lot, especially to newbies.

He probed me a bit during my explanations to make sure I understood not only what I was doing but why. This wasn't a big problem because I generally make a commitment to knowing why things are done the way they are done. It's very easy, especially in microbiology, to get sucked into running protocols and not understanding why each step is needed or what the underlying scientific principles are.

I did run into one small crisis when I was talking about bacterial transformation. This is a process where you introduce novel genes into bacteria, which are very good at picking up foreign DNA and incorporating them into their genomes. While this can be a pain when bacteria share antibiotic resistance, it also makes it easy for us to engineer them to make things we want, like human insulin. Anyway, I was explaining how I was constructing my target plasmid by isolating my desired insert using restriction endonucleases and ligating them into a vector plasmid. One important step is dephosphorylating the vector plasmid after you've cut it open. I kind of brushed over this and Dr. Fraser asked me why we would dephosphorylate the vector and not the insert. It had been a while since I had reviewed the actual science behind restriction endonucleases and plasmid construction, and I was stumped for a moment.

Before letting myself panic, I calmly started to reason out loud why this would be the case. "Well, let's see. You need a phosphorylated 3' end if you're going to add a nucleotide since the polymerase doesn't add one, and you also need one if you're going to do ligation..." and as I said this in my mind I saw an endonuclease cut up my vector, making a nice open space for my insert. On the opposing 3' ends were bright yellow phosphate groups (phosphates are always yellow in biochem texts). I then pictured a DNA ligase coming in and before my insert was able to move in place, it neatly sealed up my vector back to its initial state. This all took probably a second and suddenly I knew the answer.

"Oh, of course. It's to keep the vector from re-ligating and excluding my insert."

"Very good!"

I felt a mixture of pride (for thinking quickly on my feet and being able to reason it out) and stupidity (for not knowing this sooner). All in all, Dr. Fraser was happy with my progress and impressed with my level of understanding, which made me feel pretty good.

Lessons of the day: 1) Make sure you understand the science behind everything you do. 2) If posed a question you don't know the answer to immediately, calmly reason it out using what you already know.

Who's Who - Fraser Lab

So it's been a bit longer than I initially wanted before another update, but now things are starting to slow down a bit. Today I'm going to introduce you to everyone in my lab and in the process explain the "hierarchy" of lab personnel that you may or may not be familiar with.

The set up for my lab is pretty typical for most labs, with the exception that there aren't any grad students in it except for me.

Some Background
For those without undergraduate backgrounds in biology/biochemistry skip this section unless you want to be bored to tears. This is just to give some context for what everyone in the lab is doing.

As I mentioned in my previous post, the Fraser lab studies mechanisms of latency in Herpes simplex 1 (HSV-1, currently there is no vaccine or cure). I also mentioned that Herpes simplex, when infecting epithelial cells (like skin) produces an acute infection with active replication and virion production. When these virions infect neuronal cells, however, they become latent (dormant) and do not actively transcribe most of their genes. No matter the cell type, HSV-1 DNA immediately becomes associated with histones in the host nucleus, which is thought to be a host defense mechanism to silence viral genomic material. For whatever reason (this is still being hotly investigated), in epithelial cells the histones are modified to look like "euchromatin," i.e. active replication still occurs (this is how your own genes are transcribed - they often still have histone proteins associated but in a modified state to allow for transcription). In neurons, however, these crucial histone modifications do not happen. Instead, the HSV-1 DNA becomes tightly associated with histones to form "heterochromatin" (i.e. the transcriptionally silent form of chromatin), though it does produce one transcript in high quantity. This transcript is an RNA species termed the Latency Associated Transcript (LAT), which exists as an extremely stable 1.5kb intron-like structure. It is thought that the LAT facilitates in keeping HSV-1 DNA transcriptionally silent. The exact mechanisms by which latency is relaxed in response to neuronal stress (to give rise to recurrent outbreaks characteristic of herpes infection) is not yet well understood.

With all that said you will now be able to understand what most of us are doing in the lab. I will now go down the "command line" of the lab starting with the PI going down to undergrads.

The Primary Investigator (PI)
My PI's name is Dr. Nigel Fraser, and he is a well known expert on Herpes simplex. His lab has been investigating mechanisms of HSV-1 latency for some time now. He has a one year sabbatical coming up this fall, and this summer he is busy attending conferences and setting up his sabbatical work. I don't see him much; when he's here I usually run into him once or twice a day, say hello, and maybe tell him what I am up to for the day. This is how a lot of labs function, as the PI's primary role is to manage his/her research group, and more importantly apply for funding and present at conferences. At this point I don't meet with him regularly for an update on what I'm doing, most likely because he's been out of the office half of the time thus far. Still, I know he is keeping an eye on me in other ways, and every now and then we will chat for fifteen or twenty minutes or so about what's going on in the lab and how my rotation is going.

Senior Research Assistant

A senior researcher is someone who has a PhD and a lot of experience but instead of heading their own lab, are working for another PI. This might be because of a long time as a collaborator or a really good post doc experience, etc. The senior researcher is often the second highest up person in the lab as far as experience and direction is considered, as s/he is directly below the PI. Our senior researcher is Jaewook Oh. Jaewook is Korean, and he is working on mapping the regions of the HSV-1 DNA that are commonly associated with histone proteins (nucelosomes). Right now this is being investigated using microarray technology which will allow him to probe the entire HSV-1 genome using DNA probes derived from HSV nucelosomes (this is done by purifying HSV DNA and then treating with Micrococcal nuclease, an enzyme which degrades DNA not associated with Histones). He also does a lot of ChIP (Chromosome ImmunoPrecipitation) and is investigating the histone modfications common in latent HSV DNA. I don't talk with him very much. His English is good but sometimes communicating about science kind of difficult at times (he gave a lab meeting presentation last week which at times was kind of hard to follow for this reason). He seems like an overall nice guy but when he needs to do something you better get out of his way because he can be pretty direct at times.

The Post-Doc's
A "postdoc" is a "post-doctoral fellow" which, as the name implies, is someone who has completed their PhD training and is now working in a lab as a fellowship. These fellowships are generally for two years, and are a way to get very intensive training in a technique the lab is famous for, or for exploring a very specific model or question. When full professors go on sabbatical, they sometimes do something similar (usually for a year) where they spend time in a lab to hone their skills or get a new perspective. It is expected that researchers will have at least one postdoc experience before going into industry, and two or more if you want to go into academia. In research labs, the post docs are often the "lieutenants" of the lab, in charge of very specific projects, and they often have a grad student working with them. They are considered full time employees of the PI. Our lab has a rather large number of postdocs (4). They are:

Kerry - Kerry is investigating the stability and properties of the LAT intron species. The LAT transcript can be alternatively spliced into different forms with varying structures (the major species is a lariot common to spliced-out introns but is not degraded). Her work is more genetically oriented, which is pretty cool. I don't talk with her very much either, and like Jaewook she seems nice overall but can be a little rough around the edges when she's working or needs to get something done.

Gerald - Gerald just started in the Fraser lab a month before I came. He is actually investigating the uses of HSV as a possible gene vector for neuronal-related diseases (since HSV targets neurons so efficiently). His work is more neuroscience releated and he will be working a lot with mice. He is really easy to talk to and quick to laugh, and is really approachable if you have a question about something. His wife just gave birth to their second child (a girl) last Wednesday, so we are all pretty excited for him.

Ketna - Ketna just joined our lab last Wednesday. I have no idea what she will be working on, though she's been working with Gerald a lot these past few days. She seems nice, though I haven't had a chance to talk with her past my introduction. I'm hoping to catch lunch with her this week to have a longer chat. At this point her work is pretty boring as she will be doing a LOT of background reading (I'm still doing that now!).

Iryna - Iryna is originally from the Ukraine. She earned her PhD at the University of Oklahoma doing lots of genetics work, which means she has a similar background as I do (in that she has more experience with genetics and is learning virology). I have been assigned to Iryna for the summer, which thus far has worked out really well, as she also commutes into the city every day, and our schedules match up well. At first I thought she was kind of distant and direct, but then learned it was more of a function of English being her second language. She is actually fun to talk and joke with and has been a good match for me thus far in that she expects good work from me but let's me make mistakes too. Right now she is working on two projects; she is collaborating with Jaewook (above) to prepare the DNA probes for the microarray. Her major project is developing an HSV-1 strain that, when latenlty infected, can be visualized in an easy way (i.e. latently infected cells can be spotted under the microscope). Since latenly infected cells produce only LAT transcript (at high levels) this transcript is a great candidate as a molecular marker. Iryna is trying to introduce a construct with GFP (green fluorescent protein) sequence dowstream of the LAT promoter, which will create a GFP-LAT fusion protein. If this works, the virus will produce fluorescently labeled LAT's that can be visualized in a microscope (and sorted). She is currently tyring to do this via homologous recombination using HSV DNA and a plasmid with her LAT-GFP construct, which has a very low success rate (1%). If she can do it, though, it will be an extremely useful tool for studying latenly infected neurons.

Lab Technicians
The lab techs are sometimes the most neglected people in the lab, which is a shame because they are the people keeping the labs running smoothly, and they often have the most expertise with the lab's research questions (often more than the post docs). Lab techs are often people just out of undergrad or who have their master's. They do a lot of the grunt work for the lab like preparing solutions, ordering reagents, maintaining cell lines and growing virus. They often have side projects that they work on as well. They are an indispensable part of the team. Our lab tech's name is Jared. I thought he was not much older than me, and was surprised to learn he was 28. He's been working in the Fraser lab for almost seven years now, and he has a lot of expertise. He's also really fun and approachable. He went out of his way to make sure I was all set up and had everything I needed, and he has been very patient telling me how things are run in the lab (how do I dispose of this? where can I get more pipette tips? Where do you store ethanol?) He's very good at what he does, is very efficient and organized, but also the main source of lab hilarity. He's somewhat of a joker and keeps the lab environment light. He also commutes into the city and sometimes we walk back to 30th street station together after work. I feel really comfortable going to him for help (often!) and it's great having someone in the lab that you can turn to without worrying about stepping on someone's toes.

We also have a lab tech in training, Sindura, who is from India. If I remember correctly she got her Masters in biomedical engineering and is currently working with Jaewook on his project and with Jared to learn how to be a technician. She's nice to talk to, and someone else I can turn to if I have a question about where something is in the lab, though when it comes to questions regarding viral preps or protocols I still turn to Jared.

Grad Student(s)
Generally there will be a grad student or two working on their thesis project(s). Dr. Fraser doesn't currently have any grad students doing thesis work, just me doing my summer rotation which is a temporary affair anyway. You already know about me, but as far as what I'm actually doing: I am mainly learning as many techniques as possible in the lab, including growing and maintaining cells in culture, growing up virus, titering virus (purifying and quantifying virus), producing recombinant virus, etc. As far as my project is concerned, I will basically be following Iryna's work in parallel, except instead of using GFP I will be making a fusion protein with a related fluorescent protein called "mCherry." The disadvantage with using GFP is that when cells die they sometimes autofluoresce in a wavelength similar to GFP, so you can get false positives. Using mCherry (which is, predictably, red) eliminates this. We'll see how far I can get.

Undergrad(s)
Sometimes you have undergrads in the lab working on little projects to get their feet wet. At a large research university like Penn, it is usually not nearly as intensive as my experience was at Ithaca because the labs are so much bigger. Right now there are two undergrads doing a work study. There is Prioty, who was born in Bangladesh but lived most of her life in Canada. She's an undergrad at Penn, and she's studying for the MCAT's right now (God bless her) and is pretty smart. Prioty is working with Kerry on the LAT transcript. There is also Jenny, who is doing a workstudy through Drexel (which is famous for their co-ops) and is working closely with Jared. Jenny is from Vietnam originally. She's really nice and a little timid around the lab, probably because she feels everyone around her is much more experienced than her. I try to keep her at ease as much as possible. It's kind of strange to already be seeing undergrads and not count myself one of them, but I can honestly say the transition has been pretty rapid. Anyway, Prioty and Jenny are good workers and fun to talk with, and it's nice to know I'm not the only one who is trying to figure out what the hell is going on.

And that is pretty much everyone! It's quite a group! I feel fortunate that there aren't any ridiculous personality issues within the lab, which can be a real pain. Everyone pretty much keeps to themselves, though there is some soicializing every now and then (usually with the undergrads, Jared and/or Gerald). I really like the people I'm working with and feel that, while I have a lot to learn, I have the resources and the environment I need to do well and enjoy myself.

Looking forward to sharing more in the coming days. Hope you all had a great fourth of July and I hope to hear from you soon!

Grad Diary 6/24/09

This afternoon I found myself in a rather delicate when Prioty, an undergrad who is doing a workstudy in our lab this summer, asked me a seemingly innocuous question: what voltage do I normally run my agarose gels?

True, it seems like a simple enough question (unless you have no idea what electrophoresis is), unless you knew why she was asking me. You see, Prioty is an undergrad and is working under one of the post-docs in the lab, Kerry. A post doc is someone who already has their PhD but is getting specialized training in a lab, usually for two or three years. Anyway, Prioty has been working with Kerry for the past few months, and recently she's been running agarose gels of radiolabeled DNA. Things had been going smoothly, but recently her gels were showing poor results - there was streaking, the bands were bowed like smiley faces, or sometimes she wouldn't get bands at all. For the fifteen minutes before Prioty asked me for my input, I could easily overhear the two of them discussing her latest gel, and Kerry was trying to diagnose where the problem step was (the buffer? the voltage? pouring the gel?). Kerry is pretty good at what she does, but she is not a very good teacher, and she isn't very patient...she knows how she does it but doesn't do a good job of explaining why she does it that way.

So after having this conversation with Kerry, Prioty was told that she should run the gel at a lower voltage.

I could easily overhear all of this going on (they are right behind my bench) so I knew exactly why Prioty asked me what voltage I normally run my gels. On the one hand she wanted to get help, but really she wanted to get back at Kerry by getting my approval for how she was running the gel.

I found this position to be kind of amusing - I mean, she obviously thought I was smart enough to be a credible source of advice - but at the other hand I didn't appreciate the passive aggressive route she was taking in her relationship with Kerry. So I tried to be as helpful as I could without giving Prioty any ammo to shoot at Kerry (the last thing I needed was to get on anyone's bad side, I've only been here a few weeks!).

Fortunately, when it comes to doing electrophoresis, the voltage depends on a lot of factors: the size of the fragments you're interested in, the concentration of the gel you've poured, the buffer you're using, how well you need to separate bands of differing sizes. So I was able to tell Prioty quite truthfully that, though she should take all these things into account, the best person to ask would be someone who actually has experience with her particular experiment - i.e. Kerry.

While I obviously didn't give her what she really wanted, she seemed satisfied with this answer and went on her way. All in all, I found the entire thing quite amusing, though I also learned a valuable lesson; it's sometimes important to take note of the dynamics of the lab and not always be caught up with what you are doing.

One word to those just getting into research; if you disagree with someone about how best to do an experiment, be open about it. It's much better to find out why someone does an experiment a particular way and to talk about the relative merits of doing it differently rather than try to prove you're smarter than the other person.

Cheers!

First Week of Summer Rotation

And so it begins!

My years as an undergraduate are now over (as of May 17), and graduation was followed by about four weeks of relaxation, visiting friends, having a fantastic graduation party, and gearing up for my summer rotation, which started this past week (Monday June 15).

Most everyone I spoke to had advised me to take the summer off to relax and enjoy myself before I entered the "real world." Granted, some people may not think that graduate school is the "real world" (and to an extent they are right), but it very much is the real world in the sense that I am entering into a lifestyle that will demand 50+ hours a week of work, odd work hours, little vacation time, and for the summer at least, a long commute. Anyway, I don't have a lot of money to be traveling this summer and most of my friends are getting jobs now, so the prospect of sitting at home all summer and working a part time job did not seem appealing. Since my efforts to secure a summer internship didn't pan out, I decided I would do an early rotation during the summer.

During the first year of grad school we will rotate through three different labs in an effort to find a lab/research advisor/project that we want to continue for our thesis. These are ten week appointments where we learn the techniques being used in the lab, get a feel for the project(s) going on there and the way the people in that lab work together (or don't) and even get a small project of our own. Because these rotations generally happen while we also have classes, we aren't expected to produce results or get a lot of great data; rather we are expected to get a feel as to whether this lab works well for us or not.

We have the option to do one of these rotations during the summer. I decided to take advantage of this for a variety of reasons: a) I will be paid for it (as I will be in general as a grad student), b) I will get a rotation out of the way, leaving me with more flexible time during the upcoming academic year, c) this rotation will not be burdneded with class time, giving me the whole day to learn techniques and work on projects, and d) my transition to Philadelphia and Penn will be earlier and smoother once classes start in the fall.

Since I live close enough to Philly to commute, I decided to hold off on getting an apartment until sometime during the summer. I am currently looking at apartments and am looking at moving in early August. This means that for the time being I am commuting to Penn, which thus far has been manageable, if exhausting. I take the R5 train into Philadelphia, which takes about 45 minutes from Ambler Station (a twenty five minute drive from home), and then walk from 30th St Station to my lab, a fifteen minute walk mostly through Penn's beautiful campus, making my total commute from my house to my lab approximately an hour and a half. Half of that is riding the train though, which is a great break and an opportunity to read, listen to music/podcasts, and just prepare myself for the day or begin unwinding. I'll be honest though, it's a LONG day, about twelve ours including commute time, but I'm slowly adjusting. Needless to say, I am looking forward to moving into the city soon, though living at home does have its perks ;)

I am working this summer in Dr. Nigel Fraser's lab. He is a molecular virologist (exactly what I want to do) and he works with Herpes simplex-1 (Herpes simplex-2 is the sexually transmitted one very similar to HSV-1). In layman's terms, one of the things he is looking into is the underlying mechanisms by which HSV becomes latent (dormant) in certain host cells. This latency strategy is what makes Herpes simplex a chronic disease that periodically "comes back."

For the more scientifically inclined:

HSV-1 establishes an acute infection when it encounters epithelial cells, producing blistering/cold sores commonly assoicated with the disease. During this acute infection, the active production of new virions eventually causes the infection of nearby neurons. When infecting neurons, a latent infection is established where lytic phase genes are repressed. This latent infection can be reactivated by means that are still under investigation. What makes Herpes very interesting is that when it's genomic material enters the host cell nucelus (Herpes is a DNA virus), the host cell will wrap up the HSV DNA in histones and chromatin in an effort to silence the foreign DNA. The Herpes virus carries with it proteins that then modify this chromatin formation to either relax histone binding for an acute infection in epithelial cells, or which supplement histone association to form a latent infection in neurons. We are still trying to figure out all the proteins involved in the decision to go into lytic or latent mode, and to maintain these decisions. Additionally, in latently infected cells there exists a Latency Associated Transcript (LAT), an RNA species that helps to maintain latency by mechanisms still under investigation. It's pretty amazing how HSV has developed a response to histone association, which would normally completely shut off HSV DNA and inhibit viral propagation. I love it.

Anyway, the lab uses a lot of basic virology (growing up host cells in tissue culture, infecting with virus, manipulating viral DNA, growing up and titering virus, etc) which will give me a good foundation in viral methodology. And it also does a lot of DNA manipulation that I am already pretty familiar with after working for so long in a genetics lab. I am working closely with a post-doc in the lab, Dr. Iryna Sanders, who is working on two projects: mapping the regions of HSV DNA that are closely associated with histones, and generating a genetically engineered virus that will express a GFP-tagged LAT, an RNA transcript associated with the maintenance of latency in neurons (see above). I will be helping her with these projects, and my own project will be a parallel of the GFP tagging project, but using a different fluorescent tag (m-Cherry).

So, this past week was my introduction into the Fraser lab. I technically started on Tuesday because on Monday everyone was at a huge Herpes virus conference held on the Penn campus while I went to summer orientation and took care of other errands. I am working very little with Dr. Fraser directly; rather I have been assigned to Dr. Iryna Sanders, one of three post-docs in the Fraser lab. She earned her PhD last spring and just started her virology training with Dr. Fraser last year, and so she's still learning too (though obviously quite a few steps ahead of me). She also has a relatively long commute, so our schedules will mesh quite well.

This week has been kind of crazy. I have a desk to myself, though I don't really have my own bench quite yet (I will probably get my space cleared next week). This whole week I've been shadowing Iryna in her virology work, trying to strike a balance of asking questions and observing, and then furiously taking notes. Fortunately I have enough lab experience to have a sense of what I should just watch and internalize (for example, certain tricks in tissue culture) and what to write down (protocol steps, centrifugation conditions, where things are stored, etc). I've also been given plenty of background reading material to get me up to speed, which has been a bear to get through, but very interesting. It's also kind of hard to keep track of everything since Iryna is working on two different projects simultaneously, but by the end of the week I've come up with a system to organize all my notes and my notebook. I'm also getting a hold of as many protocols as I can, and typing up my own (especially after editing the written protocol with what Iryna actually does). It's been a little overwhelming at times but all so exciting.

This week was also a test of whether my education at Ithaca has adequately prepared me for "the real deal," and I can honestly say that I am more than prepared for my work here, even though my experience with virology is limited. When Iryna was explaining the background and her projects, I was pleasantly suprised to find that I was able to follow all of the basic science and the rationale for the experiments quite easily, while small particulars (like the names of cell lines, certain viral proteins and other more specialized terms) were still unfamiliar but easily picked up after some background reading. It was very empowering to hear things like "we are currently working up DNA for MNase digestion so we can use a microarray to map the histone association sites" and not need an explanation of what MNase or microarrays are or why one would use those techniques (even though I've never personally done those experiments). Even the papers I've been reading as background haven't been too bad to get through, though they are mostly reviews and not too experimentally heavy.

There are two other post-docs in the lab with their own students, but they pretty much keep to themselves working on their own projects. I've introduced myself to all of them briefly but haven't really gotten to know them well yet. The lab technician, Jared, has been very helpful and friendly thus far, checking in daily to make sure I have everything I need. He and Iryna are the two people I talk to the most. For the most part everyone does their own thing, though they are also relatively approachable. I will probably talk more about their personalities in a few weeks when I have a better idea of who they are. All in all, it's pretty comfortable in the lab, if also a bit individualistic. I see Dr. Fraser in passing most days. I will be sitting in my first lab meeting next Tuesday, which should prove to be interesting.

I think that should do it for today. In the coming days I'll talk more about some of the social events I've attended so far, getting to know the other grad students in my program(s) and stuff about Penn and Philly. I'm looking forward to what the summer will bring both in the lab and out. Hope you all are enjoying your summer!

Grad Diary 6/15/09

So, today was Orientation for those students opting to do a summer rotation. I chose to do one of my three lab rotations in the summer for a variety of reasons: a) I live relatively close to Philly, and so I can commute (for the summer at least), b) I would get my stipend sooner (and since I'll be commuting, save some major $), and c) I had nothing better to do for the summer, ha ha.

Anyway, as I mentioned, I'm planning on commuting to Philly for my lab work, at least for the summer. Once classes start, there is no way that commuting will be feasible, so I'll be moving into the city in August (almost done picking my apartment at the moment).

So I had today pretty well planned out; I had my map of campus, my train schedule, and a ton of nervous excitement to get me going.

I arrived in Philly at 30th St station a half hour before orientation started; plenty of time to catch the trolly (green line) to campus and find the meeting room. While I hadn't actually used the trollys (they go above and below ground in the West Philly area in addition to the traditional subway), I figured it would be fine, and I knew that the ride should only take about 5 minutes to go from 30th Street to 37th and Spruce, my destination.

I should note that, from 30th street to about 40th street the trolly runs underground like the subway system before returning to street level. My route would be entirely subterranean.

Boy was I in for an adventure.

As luck would have it (or rather, by Murphey's Law), the day I decide to take the trolly is the day that there are major technical difficulties as we make our way to the next station. The trolly in front of us was having mechanical difficulty, and to top it off, the driver was a newbie who didn't know what he was doing. As the minutes ticked away I tried to remain calm and refrain from constantly checking my cell phone for the time. I went over again and again in my mind where I needed to go so that, when I finally got off this god-forsaken contraption I could make my way quickly to my destination.

Eventually (30 minutes) we (literally) pushed our way to the next station...at 33rd street (yes, that's three blocks). At this point it was 9:00am, which was when orientation was scheduled to begin, and I quickly madem y way to the street level. No way I was going to continue on that nightmare. It took me a minute or two to figure out where I was exactly (I was smack dab in the middle of Drexel University) but I quickly figured it out and made my way to my orientation. I arrived there fifteen minutes late (that's right, it took half as long to walk the remaining six or seven blocks than it took to go three blocks on the trolley), and of course had to enter the door at the FRONT of the room, where everyone saw me rush in and find an empty chair way in the back.

In short, I was "that guy."

Great way to start my grad school experience.

A neat little twist to this story is that, since I came in late I wasn't able to grab my folder of orientation information, so I had to wait until there was a break to pick it up (at which point I apologized profusely). Before this, while the meeting was going on, another fellow arrived late and made his way to the back, sitting at the table next to mine. One of the administrative assistants walked over and asked for his name, then went ahead and retrieved his folder for him, while I remained folderless. The fact that this particular young man happened to be in a wheel chair probably had a lot to do with the differential treatment, which I thought was...interesting. Granted, I don't begrudge him for having different treatment because of his being differently abled - I am glad she gave him a hand, but it's not like I had any control over whether the trolly decided to malfunction that morning. This didn't bother me too much, but it did make me wonder about how we judge each other based on our outward conditions.

Anyway, the rest of orientation went fine, and I ran a few errands around campus for the rest of the afternoon (picked up my ID card, dropped some forms off, etc). I'll be starting my lab rotation tomorrow and I'm really excited, to say the least.

In the meantime, I have determined that I will be walking to work for the rest of the summer...

Take care!

Welcome to Jason's Grad School Blog!

Hi All, and Welcome to my Grad School Blog!

I had been intending to keep a blog of my experiences at grad school as a means to keep in touch with all of my friends and professors. While visiting Ithaca at the end of August, Susan Swensen, current chair of Biology Dept, mentioned that my blog might be a cool resource for undergrads who are considering grad school in the sciences. While this wasn't my original plan for the blog, I really liked the idea, so I am going to focus my blog towards an audience that has some background in science and might be interested in grad school.

To that end, I'm going be writing up two different types of posts. The pieces with titles on them (like this one) are going to be longer, essay style entries where I will talk in depth about a particular topic. For example, today's topic is going to be how the graduate school education is structured, how it's different/similar to the undergrad set-up, etc.

In addition, there will be diary/journal style entries titled "Grad Diary" followed by the date; here I might make a little comment about something funny or interesting that happened during the day, a "progress report" update, a cool show I went to, whatever. These will generally be shorter and are meant to offer a glimpse into the day to day.

Still, since this is going at a rather PUBLIC audience, I will probably not be giving a whole lot about my personal life. On the one hand, I want to give you an idea of what life is like as a grad student, but on the other hand I don't think I need to burden you all with every little detail about my life.

As a word of caution, I can't promise that this won't be science heavy - there's just no way for me to talk about my experiences without being somewhat technical. I'm going to try to keep my language so that an undergrad who has some experience in biology and chemistry can follow along (ex: I will not explain what transcription or translation are, or what an agarose gel is used for, etc). However, I also realize that even people with a scientific background may be a bit fuzzy on what homologous recombination entails, what nucleosomes are, etc, so I'm going to hyperlink terms you should know but I'm not going to explain. They will be linking to a wikipedia page describing the phenomenon, technique, etc. While wikipedia is not the greatest resource out there, most of the science articles aren't too bad, so you should be just fine. Nothing replaces a good refresher in a reference text or, better yet, consulting the resident expert on the topic.

Finally, I want any and all readers out there who are thinking about grad school, or even about undergrad, to feel free to contact me with questions. I will be happy to offer my thoughts, advice, and opinions, and direct you to people who can help you more than I can.

With all that being said, let me explain what my grad school experience is going to entail. While this is going to be focused on how the Biomedical Graduate group at Penn works, most of this is widely applicable to pursuing a PhD in general in the basic sciences.

Research Structure
I think that it might be helpful to understand how research is done at universities like Penn, because it will help to explain the whole education and financing process. Each lab is headed by a faculty member, who is called the "Primary Investigator," or PI. The PI directs the research projects in his/her lab, and spends a very large amount of time writing proposals for new grants or presenting results. Research is funded largely through grants from outside institutions (more on that below) so grant writing is a very important part of a PI's job. Depending on the size of the lab, the PI may or may not spend a lot of time at the bench actually doing research. Generally, the larger the lab, the more likely that grant writing and publications will take up the PI's time. In smaller labs, the PI is doing more of the research at the bench - this is especially true for staff seeking tenure (where publications are directly tied to tenure decisions).

Under the PI are technical staff (lab techs), who are full-time employees who work directly for the PI. They are often people who have a bachelor's or master's degree, and are comfortable just being at the bench. Lab tech's generally do the grunt work of the lab, liking making up reagents, ordering equipment/supplies, perhaps cleaning dishware. They are often the most knowledgeable person in the lab as far how to actually do science.

In addition to lab techs there are post-doctoral researchers, or postdocs. A postdoc is a two year position (generally) granted to someone who has finished his/her PhD. A postdoc experience is generally to help hone a researcher's skills more rigorously and on a particularly specific system - say HIV viral entry specifically instead of virology generally. It is often the case that your postdoc experience defines your future research much more than your PhD experience. People who stay in research generally do one or two postdoc experiences before finding a position in academia, industry, or other research organizations like the Centers for Disease Control or the National Institutes of Health. The PostDoc(s) are often seen as the PI's "lieutenants," and are generally focused on a specific project within the lab. In large labs, it is often the case that a PhD student will get assigned to a Postdoc and refer to them for their research and not have a lot of contact with the PI.

There may also be a senior research assistant, who is like a post doc except that s/he is staying with the PI for a long-time engagement. A senior researcher is often the PI's right hand (wo)man, though this is not always the case. A senior researcer is often very knowledgeable about the questions being pursued in the lab, and like lab techs, are a great resource.

Finally, under the lab techs and postdocs are the PhD thesis students, who are working full time towards their theses. You generally begin working in your advisor's lab during year two, and begin your thesis in year three, and work until you finish.

Publications are the lifeblood of research. Papers always go to a peer-reviewed journal where they are reviewed by other experts in your field before being put into publication. If you look closely at the list of authors, generally the first author is the person who actually did most of the research, followed by other students or lab techs and collaborators who worked on various aspects of the project in descending order of contribution, and finally the primary investigator's name is always last, which indicates whose lab the research came from. A lab that is not producing publications is a lab that is not doing well.

Generally, the PI can be seen as the CEO of the lab, and his/her name is attributed to every publication that comes out of his/her lab, regardless of whether s/he actually did any of the research. They generally focus on securing funding for their projects, presenting the results and findings, and overseeing the overall direction of the research. It is the postdocs, lab techs and grad students who actually do the work (mostly).

Finances
Pursuing a PhD in the sciences is, generally speaking, a very economical choice. In basically all PhD programs, the institution will pay for your tuition, and in addition pay you a yearly stipend with some health benefits. In Penn's case, my stipend will be $28,500 plus basic health insurance. This means that pursuing a PhD does not represent any cost to you outside of living expenses (which is definitely a concern in areas like Boston and NYC). In addition, I am able to freeze my payments on my undergraduate student loans while in grad school, which is immensely helpful.

This seems too good to be true, right? Let me explain how it works. Generally, for masters programs and for other advanced schooling it is an added expense, but most of these fields are "professional," i.e. corporate related fields where an advanced degree isn't necessarily needed to succeed(though it certainly helps). If you want to do research, however, an advanced degree is essential, because these degress entail what are basically apprenticeships in doing science - they are experiential. With an undergraduate degree, the best you can be is working at the bench for someone else. Especially now, if you don't have a PhD in science, you are not seen as a fully trained researcher. For this reason, most people who go into research don't get their masters - that's only if you want to do something outside of research, like consulting, marketing, etc, though that is not always the case.

The real reason that it is so economical, though, is that funding for research is largely from public money. Depending on what your field is, you may apply for funding from a different agency, but it's pretty much the same. Since my field is direclty related to health (i.e. "biomedical science") most of my funding comes from the National Institutes of Health (NIH), a research and funding agency set up by the federal government. All of the research that goes on at Penn is funded from outside the university. These grants usually apply for about 5 years, which means that investigators are constantly writing new grants to keep their projects funded.

So how does this work for the student? Well, the specifics vary by instiution. Generally, for the first year students are supported by the university. By the second year, the student should have already selected his/her thesis advisor, and have begun working in their lab. For most programs, the student's stipends and tuition are paid for by the thesis advisor out of the PI's grant money. After the second year, in most institutions the student is supported solely by the thesis advisor. In return, the thesis advisor gets another researcher in his/her lab to actually do the work and produce results that will guarantee more funding in the future.

Often the university will employ you as a teaching assistant for undergraduate classes and labs, or possibly graduate classes when you are older. In many schools, these TA jobs are the direct source of your income, so you may have to teach more than you would like. None of the programs I applied to required you to teach, mainly because there is so much money in the health sector that you don't really need to TA to supplement your stipend. Other programs may require you to teach more.

At Penn it's a bit modified to the advantage of the thesis advisor (and no real disadvantage to the student). As far as the student is concerned, the tution and stipend are guarenteed up to six years. For those interested in the details: Penn covers the tution for up to six years. The stipend is paid for by the university for the first year. For the second and third years, the students apply for an NIH Training grant, which is a grant specifically designed for student researchers that covers two years of income; if the student is not awarded a training grant, Penn will still pay for your 2nd and third year. At this time I will have chosen a thesis advisor, and s/he will have to pay almost nothing to cover my stipend, though I will have begun working in his/her lab already. Then, beginning year 4 or so, my adviser will take full responsibility of my stipend until I successfully graduate. In addition, Penn does not require you to TA any classes, and actually only lets you TA two or three times (probably because they want you to focus on research and don't want to pay you more than they have to). This money will be a small addition to my yearly stipend.

I want to emphasize here that while much of this is true for most programs, it is by no means true for all of them. A lot of factors play into how funding is handled, and it is not necessarily done the same within an institution. What I've described is true only for the Biomedical graduate group at Penn. The Chemistry Department, as an example, requires a lot more teaching assistantships to support their students. If you are looking at different schools, be sure to thoroughly reseaerch your funding situation.

Taxes are a complicated topic which I still don't fully understand yet. Look back here during tax season for a run down.

Grad Student Education
Now we get to the good stuff. This is my projected academic timeline for the next few years. Based on this and what I've written above, it should be clear that pursuing a PhD is a full time job, and then some; we definitely earn our stipend (in dividends).

During the first year I will have the heaviest class load, designed to bring everyone up to speed on the current knowledge in the field. My program is divided into three tiers of organization. Generally, I am within the Biomedical Graduate Studies group, which is distinct from other graduate programs like physics, chemistry, engineering, etc. Anything related to health and biology is lumped here. The BGS is housed within the School of Medicine. Within this extremely large group of 700 grad students are 7 interdisciplinary groups - I am within the Cell and Molecular Biology Group (CAMB), distinct from other groups within BGS like Biochemistry and Molecular Biophysics, Immunology, Epidemiology and Biostatistics, Genomics and Computation Biology, etc. CAMB is the major group that I will be associated with.

Within CAMB there are six divisions: Cell Biology and Physiology, Cancer Biology, Developmental Biology, Genetics and Gene Regulation, Gene Therapy and Vaccines, and finally Microbiology, Virology, and Parasitology (MVP). This last group is the division I will be working under. I will generally be referring to CAMB as the umbrella group, and MVP as my specific area of study.

My first year I will be taking a general Cell Biology which all CAMB students have to take, a gene regulation course, and an immunology course designed for the CAMB department. In addition, I am to complete three 10-12 week lab rotations during my first year. These lab rotations are to help locate a thesis advisor, and a lab that you are interested in working in. If you can't decide on an advisor based on these three, you are allowed a fourth rotation. During the rotations, students are not generally expected to produce incredible results; rather, they are expected to learn the techniques used in the lab, get to know the projects, and get a feel for the personalities and style of the lab. During the first year, it is expected that when you are not in class you are in lab working. Students often come in on the weekends to finish experiments off or whatever for a couple of hours. And when you aren't in class or in lab, you are studying (or trying to maintain your sanity).

During the first summer, you might take one class or two and maybe another rotation. During the summer you are to have chosen your thesis advisor, who will basically be your mentor and lifeline for the rest of your educational experience. At this point I will be paid through a combination of my PI's grants and NIH training grant which I will have to apply for. During the second year, I am expected to work in my advisor's lab full time, as well as attend one or two MVP specific and elective courses each semester (Virology, Bacteriology, etc). The second year is very similar to the first, except that there is more time in the lab, and you are working specifically in the lab that you will be doing your thesis research in (and hopefully getting some preliminary data). At the end of the second year, you take qualifying exams which include an oral and written component; the exams will test us on anything and everything that has been covered in our classes. Upon successfully passing the examination, I am allowed to begin my thesis research. The proposal for the thesis is due sometime before qualifying exams. After your proposal has been accepted, you spend the rest of your time in the lab working on your project, and maybe taking one or two electives every year. In addition, you will meet at least once a year with your thesis committee to have a progress report.

Once you are in your third year onward, you can basically focus exclusively on your own research, hopefully get a few papers out and attend some conferences, etc. Most people take about three years to finish their research, at which point they give their thesis defense and write up a report. For MVP, the average length of time from start to finish is 5.3 years.

Throughout the entire process, we do get a few holidays off (a few days for Thanksgiving, Christmas/New Years, memorial day, etc) and in addition we are entitled to two weeks of vacation, which you generally will have to negotiate with your thesis advisor.

It's a full time job.

In addition to what I've mentioned above, I will be doing a "certificate program" in translational research (HHMI Med Into Grad Scholars Program). This program is designed to provide PhD students in the biomedical sciences a background in clinical research, disease pathology, and how basic research and clinical research intersect. I am drawn to doing things that blend different specialities and backgrounds, and as someone interested in viruses I am also interested in disease and health, so this program seemed perfect for me. The requirements include a couple of other classes that cover the topics I've already mentioned as well as a clinical clerkship, where I spend a summer in a clinical lab, and shadowing an MD.

Research Interest
As a brief conclusion, if you want to know what it is I am actually studying, I want to study how viruses infect cells and use cellular machinery to "reproduce" and infect other cells. I'm especially interested in viral gene regulation and latency strategies. This invloves a combination of cell biology, molecular biology, and virology, or "molecular virology" as I like to call it. Penn has one of the largest number of dedicated virologists on the East Coast, if not the US, so I should be pretty set to go in that department.

If you want to learn more about the program(s) I'm in follow these links:

Biomedical Graduate Studies at Penn
Cell and Molecular Biology
Microbiology, Virology, and Parasitology
HHMI Med Into Grad Scholars Certificate Program