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!