Grad Diary 5/10/10

And I'm back!

Sorry for the long wait. As my last post indicated, I was spending quite some time reading the literature and developing my ideas. A month later, I clocked in about five weeks of reading or so and burned through about 50-60 papers (I wish I was exaggerating). It was intense, both boring and exciting, and totally worth it. These periods of intense canvassing through the literature are really critical at times, especially at the beginnings of projects or when things start to become ambiguous. It is a great opportunity to see what is known in the field, get ideas of how things have been done and possibly adapt approaches for new questions, etc. I knew I was coming to an end of my reading when I recognized many of the references listed in the papers I was reading (I call it coming "full circle").

Of course, the reading never really ends. There's always new findings to stay on top of, controversial claims to think critically about, etc, but now I have a good idea of what is known about HPV integration, what isn't and the questions I am interested in asking.

During that time I also got a brand new MacBook, which has completely revolutionized my life, ha ha. My old laptop has been with me since I started college, and it served me faithfully through the past five years. It was starting to show its age, though, and it was time for an upgrade. It's amazing how having access to a sleek, fast and portable computer can really change your work output. I also came to appreciate how much of my research requires or is enhanced by having a computer. Granted, my experiments are done at the bench, but my literature searches, my presentations, data management, etc are all done on the computer, and it's much more enjoyable now that I have a really efficient one at my disposable. The transition from Dell to Mac has actually been kind of fun, mainly because I enjoy learning way too much. And the trackpad is simply too awesome.

I digress. Another big thing that has happened since my last post is the end of spring classes (thank god!). I ended up doing really well. I was especially happy with my success in Immunology, a topic for which I had very little background but which I found extremely interesting and complicated. The end of classes means I can now focus my entire day on research, and when I go home in the evening, I can devote almost my entire time just relaxing and doing things for me, without having to worry about reading or studying for class. It's pretty nice!

Anotherl big thing was that Luis, the senior grad student in Una's lab, gave his thesis defense mid-April, and (of course) passed. We had a nice little reception afterwords and will have another sending-off party at the end of May when he finally moves out. He is going to be doing a post-doc at Yale. He will be greatly missed.

Finally, one of our post-docs, Sunny, finished her time with us and returned to China last week. It was very sad, but she may be returning to work with us again after two years or so (it's weird considering the fact that I will still be here, ha ha). We had a nice little lab outing to send her off and gave her various Penn souvenirs. She's got two papers in the works that we will probably finish via e-mail over the coming months, so I'm sure we'll stay in contact for a bit.

That's all the major news from me for now. I've developed some good ideas for experiments to do and questions to address regarding HPV integration and am now getting started with them. It feels good to be doing experiments again. After things develop for a bit Jian and I will probably start working on developing a secondary project as well. It's always good (especially in the beginning) to work on two or even three things at once, because you never know which one(s) will take off and which one(s) will tank. Either way, the summer looks to be a very productive and fun time.

Grad Diary 4/5/10

Wow...I feel like my head's about to explode.

My project came to an end a little over a week ago when my ligation reactions, once again, failed to produce viable colonies for me to expand. I wrapped things up in my notebook, noted things to do differently, and who knows, I might come back to it down the road.

Now that I'm an official member of the lab, I wanted to really dive into my ideas for thesis projects. I am especially interested in integration, which is necessary (but insufficient) for cancer progression. I am especially interested in the mechanisms underlying integration, which is not known. However, Jian's lab doesn't specialize or focus on these questions directly, so I wanted to take some time to read up on the relevant literature, define my questions and develop experimental approaches. Basically, come up with a thesis project.

So I've been reading non-stop for two weeks now, and sometimes I feel like my head is going to burst. It's kind of interesting to see how, over the course of a week, I have gotten to the point where I can pretty much breeze through the introduction (been there, done that) and go straight to the results and discussion. Sometimes I also spend a lot of time in the materials and methods section. It's been simultaneously super exciting and super boring. I am not doing any real lab work, which is boring, but I am learning a lot, making connections, developing ideas, and asking questions, which is very exciting.

I spent almost an hour and a half with Jian today talking about some of the papers I've been reading and refocusing my inquiries. We also started talking about experimental approaches which was useful but a little premature. I am hoping that after another week or so of reading I will be able to really home in on the questions I want to ask and then start coming up with ways of addressing them.

Additionally, I am giving lab meeting this week, which will be a summary of my rotation experience and a small taste of what's to come. This will probably mean I will get a little less reading done this week, but that's okay. I'm not exactly pressed for time or anything yet.

So far it's been a really great experience going through the literature, but I have quickly found that the paper trail never ends...almost every paper references another paper that I think is worth reading, which then references another paper. Sometimes you can pick out a few key papers in the field which are commonly referenced but I could literally spend a year reading up on everything HPV related and never get through it all. It's been hard trying to establish limits but I am getting better at it.

I will hopefully have more interesting things to share in the coming week(s) so stay tuned!

Grad Diary 3/22/10

For the past three weeks or so I have been unsuccessfully trying to insert a particular sequence into a plasmid vector containing the HPV16 genome. What makes this particular cloning experiment hard is that the vector is rather large (~10kb!) and my insert is not only small, but it is a mixture of various polymers of the same sequence (anywhere from five to over a hundred repeats). I don't know how many agar plates I went through (maybe twenty?) while I've been trying to get things to work. Jian has been helping me troubleshoot throughout the way to optimize the ligation reaction, DNA extraction methods (for example, is it better to do a gel extraction or the tried and true phenol:chloroform:isoamyl alochol extraction with ethanol precipitation?) It got to the point where I am literally running out of both vector and insert.

Finally, after working on this for weeks, I came in this morning and checked my plates and was surprised to see an explosion of growth! Unfortunately, even my ligation control plate (which is vector without insert) also showed an explosion of growth, so that means that one of the key steps that has been hampering my progress is the de-phosphorylation step with CIP. We ordered new CIP. Fortunately, this is still pretty good since, at first blush, it seems like my ligation reactions still had more growth than the controls. I re-plated my reactions at a much smaller volume, and hopefully they will have reasonably sized colonies for me tomorrow.

It was one of those moments where, after weeks of banging my head against the wall, there was suddenly an "Aha!" moment, and things looked like they are finally falling in place. There is still some work to do to see if there is anything usable, but even if I have to start over, I now have everything in place that it will only take a week to go from start to finish, instead of almost a month. Still, Jian and I have decided that I will stop after this week so I can focus more on reading and preparing my ideas for my thesis project(s). Maybe I can get one of the undergrads to finish things for me. It's kind of nice being able to say that, ha ha.

Thesis Lab Decision

As I am coming to the end of my third and final rotation in Jianxin's lab, I have come to the point where I have to decide which lab I would like to formally join as a full-time grad student.

Initially I thought this decision would be pretty easy; at the conclusion of my rotation with Una last semester, I was 99.999% sure I would join that lab, and I came into Jian's lab with the feeling that I would just enjoy myself and learn as much as I could.

As time progressed in Jian's lab, however, I became really fascinated by the HPV field and some of the unanswered questions, especially mechanisms underlying integration, a critical (and necessary) step for the onset of cervical cancer caused by the virus. And although my rotation project had nothing to do with this, I took time to read more and more and become even more excited about the possibilities. I also found that I was much more actively engaged during lab meetings, offering critical observations about the data and offering my ideas. In short, I have been much more engaged scientifically in Jian's lab than I ever was in Una's lab.

This past week I met with both PI's individually to seriously discuss potential thesis projects, expectations for me as a grad student, things I was interested in or would like to see happen in the lab if I were to join. I finished the week by meeting with Bob Doms, the chair of the microbiology department, and talking to him about my decision and listening to his advice, concerns, and suggestions. It was definitely helpful, and validated my own feelings about my choices and where I thought I wanted to be.

In the end, I decided to join Jian's lab. It feels like the best decision in pretty much every parameter I can think of - funding, research interests, support, etc - but that has not made coming to this decision or moving forward with it easier. My time with Una was fantastic, and it was, by the far, the best environment of people I could ever have hoped for - I hope I will be half as lucky finding labs that felt so much like a family to me and that worked so well together. But in the end, I am here to do research, to investigate and learn, and I think the Jian's lab offers me the best opportunities for all of that.

There are still risks and unknowns in joining Jian's lab: I will be her first graduate student (largely because she is so new here), and that brings with it some uncharted territory for both of us. But this is also an incredible opportunity for me to have a huge impact in the development of the lab, in attracting new students to the lab, in directing where the research goes, etc. There is also the risk in joining a lab with a faculty who hasn't formally received tenure yet. Normally I would stay far, far away from such a lab, because there is the risk the faculty member won't receive tenure while you are in the middle of your graduate work, and generally there is a stronger push to produce papers and get work done in the process of securing tenure. However, in this case, Jian is very well on her way towards receiving tenure and she has had a great team of post-docs who have been helping to establish the lab. Bob (the chair of Microbiology I mentioned above) has no doubt that she will receive tenure, and he probably has the largest voice in that decision out of anyone, so I trust his judgment. I think in this case, the risks involved in joining a junior faculty's lab are much less than other labs I see here at Penn.

I am extremely excited to count myself as Jian's first graduate student, and will be taking the next month or so to really develop my ideas for the questions I am interested in pursuing. Fortunately, a large component of my interest will greatly benefit from Una's expertise in HIV integration, and I have already talked to her about this collaboration. She was extremely excited about it, and I am glad to say that I foresee continuing working with her and her talented crew well into the future.

Grad Diary 3/9/10

I'm two days into my "spring break" and so far, it's been nice.

As I mentioned in my previous post, I don't have classes this week (and the undergrads are gone! no long lines at the carts for lunch!). In addition to taking the time to focus on lab stuff, I decided that I would take this week to seriously weigh my options between Una and Jian's lab, and try to come to a decision by the end of the week. To that end I've set up meeting times with both PI's (on different days) to talk seriously about potential thesis projects (both what they are interested as well as my own ideas) as well as wrapping up other concerns/expectations that come with being a full time graduate student.

Bob Doms, the chair for the Microbiology Department, has been very helpful. He works very closely with the graduate students who work in his faculties' labs (mostly MVP students) and meets with them at least once a semester (if not more) to check in, talk about upcoming decisions, etc. A few weeks ago he and I chatted about my vacillation between the two labs, and was happy with the extent and seriousness I have been considering the decision up till now. He did offer some helpful perspective and commentary, and we decided I would check in again when I thought I had made a decision. I will meet with him on Friday to talk about what I feel is the best decision for me (after having met with both PI's) and then make a "formal" announcement to both groups.

To that end I've been making lists and thinking about what the realities might be in both labs, the pros and cons, the differences in lab demeanor and philosophies, the opportunities, and the unknowns (recall that Jian doesn't have any full time grad students...I would be her first). I feel i am coming to a decision already, but I definitely want to take the time to hash it out with both PI's first.

I'll wait until next week to post again with my formal lab decision and how things are moving forward. Wish me luck!

Grad Diary 3/4/10

Man, these past two days have been tough.

Yesterday morning I had my first Immunology exam, and I think it went well. We were given eight questions and had to answer four. We had an hour and a half, which was just enough time for most people. The questions really varied in style, depth, and approach, leaving something for everyone (I guess). I was a little wary about this test if only because I have never had immunology before, so I tried to be extra careful in preparing and reviewing my notes. I felt pretty good after taking it, and I hope I did well.

This morning was a different story. It was the Gene Regulation exam, and I felt much more prepared for it, having had some background on most of the material already, and the format being similar to the Cell Biology exams I had last semester. The test included six questions, of which we had to answer four, and ideally it should have been doable in one in a half hour. The let us come in an hour early, however, because certain students had a second exam today directly following this one. I came in at the usual time (not feeling a need for a whole extra hour) and was surprised to see pretty much everyone was already there working on it (that shouldn't have surprised me, in retrospect). I picked up my exam, spent a minute or two searching for a free seat and got started. An hour and fifteen minutes later I was done, feeling very fried, and for the first time wishing I had a little more time to feel confident in my answers. I came and left before most anyone else left. Most people used the entire 2.5 hrs. I felt considerably more drained after this exam than after Immunology, and I am not as confident I did as well, but we shall see in a few weeks. Once again my "speedy" test taking was commented on later (though, to be fair, I basically used up the entire time that was supposed to be allotted us anyway).

I'm glad that's all over with and that I can take a week or so to cool off. Next week is "spring break" and I don't have classes next week, but I'll be staying to do lab work. It'll be really nice not having to worry about classes for a few days and just focus on lab stuff and taking it easy. Thank god tomorrow is Friday.

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!

Class Roster for Spring 2010

Classes for the spring semester started a few weeks ago, and like last semester, my course load is relatively light. I only have two classes, but both are very interesting (to me).

The first class is somewhat of an extension from last semester's Cell Biology class, and is focused on Genetic Regulation (of mostly eukaryotic cells). This is similar to a class I took this time last year as I finished up undergrad (Biochemistry II) which was a molecular biology course focused on nucleic acids, the Central Dogma (regarding transcription and translation), etc. This class will focus more on regulatory mechanisms at all levels, and will hopefully expand my knowledge of cell cycle checkpoints, etc. I am most excited about the content regarding chromatin modifications and epigenetics, since this is really where genetics is moving forward and is already exploding in terms of discovery.

That being said, I am actually even more excited for my other class, which is a cell biology based Immunology class. I haven't taken immunology yet, so I am anticipating this will be a bit harder for me and require more preparation, but I find the content so interesting (and complicated!) that I doubt I will have trouble drumming up the motivation to study. The "suggested" textbook (required for me!) looks to be extremely well put together, and I am already impressed with the way the figures are laid out. After doing a rotation in an HIV lab I quickly discovered that my lack of immunology background would severely cripple me if I were to be serious about doing virology, especially HIV work, so I am really excited about this class.

Both classes meet only twice a week for 1.5 hrs, and the genetics class has a weekly discussion section with TA's where we discuss weekly papers that parallel the course content. I don't have classes on Fridays, and this has proven to be a great breath of fresh air already. Both classes have a midterm in March and a final exam. All in all, not too stressful at the moment. We'll see how things go once exams roll around...

iNSPIRE

This semester I started a second volunteering experience similar to the SSEA, but a little more structured and with a different demographic.

The program is called "iNSPIRE" and is run by iPRAXIS, a non-profit whose goals include providing exposure and education within the sciences to students from K-12. The iNSPIRE program has a few components, and at this time of the academic year they partner with a number of Philadelphia Schools for the annual Science Fair. Other activities include career days and even lessons/classroom activities.

I got an e-mail about the program through a graduate student listserv (similar but different from how I learned about SSEA), and I saw this as another opportunity to interact with students and develop my teaching/mentoring skills. This program required a little more legwork from me (including submitting various background checks, etc) and recruits a wide range of volunteers including undergraduate and graduate students, teachers, professors and professionals.

Today was my second day with the program, and so far it looks like it will be a good run. I am at the Alain Lock Elementray School, which houses K-8, and is literally blocks away from my apartment (which isn't so convenient considering I'm usually at the lab before hand). We come in every Thursday for a class period (about 1hr 15min) and we guide our group (avg. 4 students) work through a science fair project.

These first two weeks have been much more educational for me than for my students, by far. The school is a public school in the heart of West Philadelphia, so in many ways it is very different from the schools I went to growing up (which were in upper-middle class, suburban, predominantly white public schools). I remember the first day I arrived at the school, the first thing I noticed was the enhanced security...it wasn't severe, but it was not as inconspicuous as it was in my high school. At least one of the guards looked like (and probably was) an actual officer. I signed into the visitor desk at the front and was directed to the office, where they cleared me to go to the classroom upstairs. On my way up I encountered a young, white woman who was probably no more than two or three years older than me, patiently dragging (literally) a small child (maybe 2nd grade?) who was clearly being sent to the office. The rest of the class followed in tow, orbiting the pair like a cloud of electrons (or perhaps a plasma membrane? ha ha, I love science). The kid was yelling and complaining but the teacher just calmly tugged him inch by inch down the hallway. As I gingerly picked my way past and started up the stairs I asked myself "what I have I gotten myself into?"

Once I got to the classroom, I discovered I was a bit early, and saw that the class was wrapping up. I introduced myself to the other "Scienteers" (as we are called) most of whom were on their way out. I met Scott, the coordinator for the program and whom I had been e-mailing to set things up.

I took a few minutes to collect myself and figure out what exactly I had thrown myself into. Ms. McGinness, another young white woman (again, probably two or three years ahead of me, if even that) was apparently taught seventh and eighth graders. I was surprised (and happy) to see the classroom outfitted with a smart board, and I later saw that she also had about twenty Mac notebooks which stayed in the classroom (locked) but which the students used every day they were with us.

These two weeks showed me the incredible juxtaposition of the difficulties inherent in teaching inner city kids (mainly behavior issues) and the lack of funds (making certain things inaccessible) buttressed by clear attempts to improve the educational potential of the classroom, evidenced by the costly smart boards and laptops.

Honestly, the kids themselves were not very different from middle school students anywhere else. The only possible exception was a more frequent disregard for authority and rules, which made running the classroom much more about controlling out-of-line behavior than about actually teaching...to a degree that was more reminiscent of elementary school.

My group of students included (initially) Amir, Jermirr, and Tyree, and they were later joined by Laneigh, a soft spoken girl who quickly proved to be very creative and the most engage of all of them in the project. I initially had my doubts about how well my group was going to work together, but by the end of the first day (where we came up with our hypothesis) all of them seemed to be on board and interested in the project. Today was the second day, and they all continued to show interest and worked well together (meaning there was no bickering our other behavior problems), which was definitely not true for some of the other groups.

I think it will be a good run with these kids, but only time will tell. So far the experience has already been richly rewarding for me, and I am looking forward to being re-immersed in the drama of middle school...and to later extricating myself from it. I have been quickly reminded why I decided that teaching anything below high school was simply not an option for me, ha ha. Still, it should be fun, and I am looking forward to the coming months.

Spring Rotation Lab Profiles

I've been in my final rotation for about two weeks now and I think I am ready to give you all a quick tour of the members of the lab and the general questions being addressed in the lab.

Primary Investigator
Dr. Jianxin You (she goes by "Jen") is an assistant professor at Penn; she joined the school two years ago and is on track for getting tenure in a couple of years. Her research is on the Human Pailloma Virus (HPV). Most strains cause benign warts, genital warts, and in a few cases, persistent infection may lead to cervical cancer in women (the second most common cancer in women).

To understand her research interests I will have to give you a really quick primer on HPV genomics; HPV is a DNA virus which maintains its genome an independent circular episome within the nucleus. The major way that HPV maintains its episome within the host cells is by physically tethering the episome to host chromosomes so that, when cells divide, the episomes are similarly segregated among the daughter cells. A major constituent of this "tether" had been previously found to be a viral protein (called "E2"), but it was not certain how this protein bound to host chromosomes. Jian published an important paper in 2005 that demonstrated that the E2 protein binds to both the HPV genome (which was already very well established) but also to a host protein called Brd4, which is a chromatin-associating protein. Ever since that paper she has been focused on elucidating all the functions and implications host Brd4 may have on HPV gene expression, viral persistence in the host, etc. Her lab uses a variety of experimental approaches including proteomics, molecular biology, and cell biology based techniques.

I got interested in Jian's research after she gave a "chalk talk" back in September (chalk talks were short presentations given by faculty where they explained their research and possible rotation projects). I was also really interested in working in a lab where I could expand my technique repertoire beyond nucleic acid work (i.e. I am getting tired of PCR!!!).

So far Jian has been giving me a lot of one-on-one time, which I really like. I've been reading a LOT of papers to get some background on HPV and on Brd4, etc, and then reviewing what I learned with Jian to make sure I am getting up to speed.

Jian has a small lab, and currently does not have any permanent graduate students (mostly because she is so new), though a couple have rotated with her.

Post Docs
There are three post docs in Jian's lab, although technically Jing has a full-time position. They are all originally from China and have spent varying amounts of time in the US:

Junpeng Yan is a relatively quiet but really nice and friendly post doc, and he shares the other half of my bench (so he's my benchmate). He is currently working on elucidating possible Histone Acetyl Transferase (HAT) activity in Brd4 and a special fusion protein Brd4Nut, which is present in a really rare but very aggressive carcinoma. After a few days of warming up to each other, he is a bit more talkative with me (I think he's just shy) and has been really helpful with finding reagents/equipment and answering basic questions.

Sunny Li is another post-doc, and though she's not as quiet as Junpeng, they are both always pretty busy so I haven't gotten to know her very well yet. She is a little more direct but just as helpful as Junpeng when I've been trying to find things in the lab. Sunny is working on a couple of projects, but one of her bigger ones is further elucidating Brd4/E2 interactions.

Jing Jiao is a full time research specialist in the lab. She has been at Penn for a couple of years now in another lab and recently moved to Jian's lab (this past December). We are both learning together where everything is in lab. She does a lot of tissue culture and bacteria work, but I'm not entirely sure what she is working on.

All three of them are super friendly and really nice, and I have enjoyed getting to know them bit by bit over the past two weeks. They are really focused and busy most of the time, so there isn't as much chit-chat during the day, but that hasn't bothered me so far.

Undergraduates
There are two undergrads in the You lab. Susan is an upperclassman (I think a senior?), and she has worked in the lab for a while now. This semester she is wrapping things up and organizing her research, so I am pretty sure she is done once this semester ends. She comes in once a week for a couple of hours so I don't interact with her very much, but she seems nice enough.

The other undergrad, Sante, is working in the lab as a technician. I think he is a second or third year. He comes in most every day in the afternoon and works for a couple of hours, but he is very, very quiet and keeps to himself so I haven't gotten to know him at all so far.

And that's basically everyone in the lab. They are all pretty quiet and keep to themselves mostly, but when engaged they are really friendly and helpful, and so far this hasn't bothered me. Unlike Dr. Fraser's lab, which was similarly quiet, there is a much stronger sense of collaboration between everyone, and I don't feel nearly as isolated as I did in Dr. Fraser's lab.

As for my own project, I am initially working on characterizing and troubleshooting a GFP-tagged E2 construct which could be used as a means of visualizing HPV episomes in cells (the construct has already been made, I am just characterizing and assaying it). I am also reading A LOT, and I may get new project ideas as my reading progresses.

So far things are going well and I think it will be a good final rotation. I'll be keeping you updated!

Grad Diary 1/19/10

Today's virology seminar aptly summed my current feelings regarding my lab rotations. I have found that, even with only a week or so into Jian's lab, I am really enjoying my time here and the interactions I've been having with everyone in the lab. I am wondering if this lab will become a strong contender against Una's lab, which I have, up to this point, been so sure I was going to join.

At virology seminar I walked in with Jian and we sat near the front. Una happened to walk in a bit late (and she almost never goes to these seminars) and since we were in the front, sat on my other side. I was literally caught between two PI who I know would love to keep me in their lab. It was really ironic, and this irony was not lost on the rest of Una's lab, who were also in attendance.

I am trying to remain honest to both PI's by indicating my interest in each lab, but I foresee my thesis lab decision to be a bit harder than I initially anticipated. We shall see...