Recruitment Weekends!

This past weekend was the third and final recruitment weekend for the Cell and Molecular Biology (CAMB) Graduate Group . I volunteered to varying capacities for all three weekends, and had a lot of fun. It's interesting to be on the other side of the table, so to speak. A lot of the pressure is off, but then again, we are still trying to recruit them here so we have to make a good impression just as much as the recruits do. Also, it's still pretty draining talking to people, introducing yourself, asking the same, tired questions, etc, although this time when I get bored I can leave (mostly) and go on with my life.

Here's how the recruitment weekend works, for those not in the know. Generally recruits arrive sometime on Thursday since their day begins early Friday morning. We send a bunch of grad students to meet them at the hotel on Thursday evening (for those who arrive early enough) and take them out to dinner at a local restaurant...usually Cavanaugh's, a local Irish pub in West Philly.

Friday begins early, with grad students picking up the recruits at the hotel (about 30 recruits per weekend) and busing them to campus, where they get some breakfast (continental) and sit through forty five minutes of introduction to Penn, the program, etc by the chair of CAMB (yawn) as well as presentations specific for two of the sub-concentrations within CAMB (Cell Biology and Physiology; Cancer Biology; Genetics and Gene Regulation; Developmental, Stem Cell and Regenerative Biology (formerly simply Developmental Biology); Microbiology,Virology and Parasitology; and Gene Therapy and Vaccines). We then escort the recruits to their first of four interviews with faculty members within their field of interest, most of which the recruits indicated prior to coming (though this isn't always possible). After two rounds of interviews (30min each) we bring them for another half hour of presentations, again getting two concentration specific presentations. Then they break for lunch with just the grad students, and they finally take somewhat of a breather. This is one of my favorite times because you get to really interact with the recruits, they get to ask you their pressing (and repetitive) questions, etc.

The afternoon is pretty much a mirror of the morning, with more presentations within the six concentrations and two more half-hour interviews. At the end of the day is "Happy Hour" with finger food and yes, booze. Students, faculty and staff are all invited, and this is a good opportunity for recruits to have a more casual conversation with some of the faculty they might have missed or wanted to follow up with. This is followed by dinner in the evening with grad students, and a trip to a local bar afterwords. Attendance is usually low for this night out largely because by the time Happy Hour rolls around most people are ready to drop (and they still have to go to dinner!).

Saturday recruits break into their concentrations and have brunch with grad students and perhaps faculty within their specific program. This year MVP took their brunches at Susan Weiss's house (a faculty member) and some of the other faculty living nearby also joined us...it was nice and low key. This was followed by apartment tours of two students -one living in center city, one in West Philly - which was then followed by a variety of optional activities. These included: a campus tour, trips to the Art Museum, the Mutter Museum (a house of medical oddities), the Constitution Center (and Liberty Bell + Independence Hall), and sometimes ice skating. One of the weekends we got dumped on with snow and, sadly, all the activities were canceled for that day, but such is life. Saturday evening the recruits have dinner with selected faculty and students back on campus, and then get another optional outing to a bar afterwords. Most recruits fly back home on Sunday.

It's pretty exhausting for everyone involved, depending on how much you volunteer. I might have overextended myself a little bit this weekend, especially since I have midterms for both my classes coming up this week, but it's a lot of fun and I look forward to doing them again next year. There were some really cool people out there and I am hoping to see some of them come the fall.

Grad Diary 2/23/10

Today I am officially a published scientist!

The cover story for February's Public Library of Science - Biology issue features the concerted efforts of The International Aphid Genomics Consortium to annotate the pea aphid genome.

Click on the picture to link to the full text article (they're cute aren't they?). One of the many great things about the Public Library of Science is that it's open access, which was one of the reasons the IAGC decided to publish here instead of Science or Nature.

If you look really, really, REALLY carefully in the acknowledgments section, way down in the "Virus transmission and transcytosis group" you will find my name, along with my lab mate Eric and my undergraduate research adviser Dr. Marina Caillaud.

While it is really cool to finally see this paper published (the actual publishing part took well over a year), my own personal contribution to the paper is minuscule, at best. Basically Marina asked me if I would be interested in helping her and Eric out with the annotation as a side project to my own research. I thought it would be a good experience and a small taste of doing bioinformatics work. I quickly learned that I had no taste for bioinformatics, but I could really appreciate not only what goes into making good databases for genomics, but the wealth of information that these databases and annotation projects can provide. The article is a testament to that fact.

As I said, my own efforts were minuscule compared to what a lot of other people provided, since I did not feel comfortable enough to critically analyze gene sequences for intron/exon splice junctions, promoters, enhancers and other regulatory sequences. My job was to simply compare the sequences I was assigned with the iconic model insect organism that is already well established - Drosophila melanogaster - and divine an idea of the sequence's importance through homology. This was not always easy, of course, but my job wasn't to critically analyze the sequence, but to annotate it such that others could easily come back to it and add their expertise. It was truly a lot of database work, and it gave me headaches every time I worked on it (probably due to eye strain). Still, it was a great experience, and it is cool now, over a year later, to see my name on a published paper in PLoS, even if I don't feel I own anything in the article.

Marina is currently working on finishing up a paper that is basically a fleshed out version of my undergraduate thesis, so I am looking forward to looking through the manuscript and seeing that hopefully published later this year (maybe as a birthday present??).

Anyway, take a look at the article and enjoy!

Grad Diary 2/19/10

For those of you not in the know, this week is Chinese New Year! Woo hoo! And on top of that, this year happens to be the year of the Tiger, which is my astrological sign in the Chinese zodiac.

Seeing that everyone in my lab is Chinese in some way (aside from Sante, but he's actually taking Chinese language classes!) I made it a point on Monday to ask Junpeng what the traditional greeting/saying is in Mandarin for the holiday. After a few botched attempts I eventually got a passable pronunciation of "Xin nian hao!" down, and proceeded to wish everyone in the lab a happy new year. This was met with surprised laughs and appreciation from all around, and I felt myself transported back to Japan when I spent a semester abroad as an undergrad (here's a link to my blog about my Japan adventures). I've also decided that if I decide to join Jian's lab, I was going to learn some basic mandarin phrases.

Today, Jenny and the rest of Una's lab was hosting a Chinese New Year get-together around lunch time, and invited a bunch of the neighboring labs. It was fun and nice to catch up again with everyone in the lab again. The food was, of course delicious, and it always feels nice eating with chopsticks and staying in practice (yes, I am a chopstick snob, ha ha).

May the Year of the Tiger bring me lots of luck this year, especially with my thesis lab decision in a month or so!

Grad Diary 2/15/10

As often happens in science, my project has taken a bit of a turn recently. Up till now, I have been characterizing the properties of a GFP-E2 fusion protein that would allow for visualization of viral episomes in vivo (since E2 directly binds to the viral episome and regulates replication and transcription). In vitro analyses of binding and gene transcriptional activation of the two GFP fusion proteins I had showed that they both, to differing degrees, did seem to bind and act upon their target sequences. However, when I tried transfecting these constructs into cell lines which already harbor HPV episomes, expression of the proteins was very low and did not exhibit the correct phenotype. I could spend a lot more time making new GFP mutants with perhaps a longer linker region or whatever, but Jian and I think that would be a lot of work for not very much payoff, so we are switching gears. The upshot is that I have become a lot more comfortable with cell culture, I learned three separate transfection techniques, and I reviewed how to western blot and fix and stain cells for fluorescent microscopy.

The new approach involves using an old friend in the molecular biology world, the lac operon. This "operon" consists of three genes and regulatory elements that feed into lactose metabolism when glucose reserves are scarce; it is present in both prokaryotes and eukaryotes.

The lac operator sequence is bound by LacI (inducer) rather tightly, so our strategy is to clone into the HPV 16 genome a certain number of repeats of the LacO sequence to create a binding site for flourescently labeled LacI protein. This has the advantage over the previous system in that neither LacO or LacI would be involved in the regulation of transcription/replication, so tagging the episome shouldn't adversely effect these processes (whereas GFP-E2 might not function as well in vivo as a regulator).

This is going to involve a whole lot of molecular biology work (restrction digests, ligations, a lot of gel electrophoresis and DNA purification) but fortunately I am already pretty comfortable with most of these techniques. It's going to take a bit of time but I feel pretty good that I will be able to get reasonable progress before the end of my rotation.

Grad Diary 2/11/10

Snow Day!!!!

As everyone else living in the NE is aware of, PA (and other areas...wow, look at DC!) got dumped on with snow. We've had two other big snow storms this winter, but they were always on the weekend. This time it started Tuesday evening and snowed all day yesterday and this morning. Fortunately (I mean...darn!), classes were canceled, but unfortunately, experiments still had to be done. I decided to take a half day and come in the afternoon when I would have normally. Thankfully I wasn't in a hurry, so trudging through a foot and a half of snow (which literally came up to my knees) wasn't terrible...just adventurous. Living in West Philly meant that sidewalk shoveling duties fell on the homeowners, which left the sidewalks a veritable obstacle course with certain stretches cleanly shoveled immediately followed by a wall of snow. For my own part, my landlord agency takes care of the snow, so I don't have to shovel, but my particular apt is later on the list, so I didn't get shoveled until this morning (a full 24hrs post snowfall) which made stepping off my front porch yesterday...interesting (kind hard when it's hard to see where the porch ends).

It was actually really fun walking around and admiring the snow-laden trees and shrubs. A lot of the side streets weren't even plowed, and the unlucky drivers who had their cars parked there won't be digging their vehicles out anytime soon. The best part so far has been at night, when the extreme reflective properties of the snow make the normally dark lamplight illuminate the street to almost daylight levels...seriously, you would have no problems reading outside at night (except for the fact that it's, you know, cold).

The snow has been a nice diversion thus far, but I can't wait till people get their act together and shovel some more snow...if it's still like this tomorrow I'm going to have to allot an extra ten minutes just to get to class on time in the morning (and it normally only takes me 20 minutes to begin with).

As it turns out, my youngest brother (a senior in high school) not only got school off today and yesterday, but already had a scheduled day off tomorrow and the following Monday, netting him a second Winter Break. Lucky bastard.

Let me share some of the pics I took on the way to and from work over the past two days. Enjoy!

Snow Days 2010!