Sunday, June 24, 2007

Summer in Boston - Week Two

I hope everyone has been well: my second week here in Boston has officially come to a close, and I love it here! The climate is similar to that of Minnesota, but seeing sailboats on the Charles River still shocks me. I have yet to see the ocean, but I'll get there soon...hopefully I can find a beach that hasn't been shut down by the public health department in Boston.

This past weekend, I spent Saturday morning at the Cambridge River Festival: weather was gorgeous, kettle corn was hot, and people were really enjoying the free samples of Burt's Bees, Luna Bars and Dunkin Donuts Iced Coffee. On Sunday, some of the members of the BE REU program went downtown to Boston Gardens and had a leisurely ride in the Swan boats before heading off to dim sum at a really crowded restaurant in Chinatown: it was fantastic! We spent about two hours wandering through Newbury Street (full of really high end clothing stores) before finally ending up back at MIT.

On Tuesday, I was also able to meet with a friend of a friend (a native Bostonian) who showed me around Fenway Park and the neighborhood surrounding Boston University. He has promised to take me to visit the Italian part of Boston, as well as his hometown: I'm so glad to have friends that connect me to others all around the country!

Yesterday, I went to the MIT Museum: there were some really great robot exhibits that were there (if you are thinking of visiting Boston). Today I'll actually be switching rooms: when I arrived, I shared a room, but they were able to find me a single room on the fourth floor. The bed is lofted and there are no stairs, so I'm going to develop some killer upper arm muscles by the time I leave here.

As far as lab goes, I'm really enjoying the work I'm doing: I work from about 9-7 weekdays, and afternoons on weekends: it is a lot of time, but I'm really enjoying what I do. Speaking of, here's a better summary:

The post-doc that I'm working for (Alexandria) did her doctoral thesis on using the liver scaffolding that the Griffith lab has worked with to develop a model of chronic infection with the hepatitis B virus: she cultured liver cells (primary cells that had been isolated from a rat) and transfected them with the receptor gene, a membrane receptor called duck carboxypeptidase D (rat livers don't have the receptor for hepatitis B infections, but ducks and people do...since ducks aren't exactly an efficient clinical model, Alexandria used rat cells transfected with this receptor gene instead). This effectively makes the rat liver cells more like human cells, and along with the bioreactor scaffolds, she created a much more human-like model for drug testing and simply improving the scientific knowledge on hepatits B infections.

So, this receptor, duck carboxypeptidase D (DCPD) is a cell receptor protein (peptide) that is an enzyme (-ase) that cleaves proteins at the carboxy-terminus (ends with COOH; carbon-oxygen-oxygen-hydro
gen). It allows for the production of free arginine (a semi-essential amino acid) and cGMP, both important intermediates preventing apoptosis (mediated cell death).

To insert DCPD into rat cells, Alexandria used adenoviruses, a type of virus that has most of the dangerous genes taken out and the genes of interest put back in...however, treatment with adenoviruses is still quite potent and although the potential for using adenoviruses as a vector for gene therapy is very high, human subjects have died during clinical trials, thus leading to a temporary stall in gene therapy research.

When Alexandria was transfecting these rat cells with DCPD, she noticed that, unlike those control cells infected with a virus with no receptor or genetic material, many more of the cells survived. So, my job this summer is to investigate how and to what extent DCPD prevents cell death in liver cells as well as flesh out applications for this novel approach in gene therapy.

So, my days in lab are spent working with cell culture of rat cells transfected with DCPD (as well as the control vectors), and attempting to optimize our measurements of apoptosis using a fluorescent detection system. As time goes on, I will most likely be testing different time points for apoptosis, as well as other variables involved with preventing cell death in culture.

Thursday, June 14, 2007

Summer in Boston - Week One

Hello all! First, I want to apologize for any lack of communication: I have not had internet access until this evening (slightly ironic considering this is the Massachusetts Institute of Technology).

Sunday was spent doing lots of traveling, as well as seeing first hand the cost of driving a car in Boston: even though the airport is about 3 miles from campus, the taxi cost over $35. I am living in a fraternity house that looks like a very old boarding house from the turn of the century. It looks nothing like the large mansions of Frat Row on the U of MN campus, or even the houses at IWU: it just blends in with the nearby brownstones and commercial buildings (mostly biotech start-ups, but there is a division of the Tootsie Roll Company a block away whose delicious smells put me into a fantastic mood in the morning).

It is not nearly as green in greater Cambridge as it is in Minnesota, but the MIT campus is beautiful. It is a mishmash of Greek academia, 1950s Catholic high school, 1970s architecture and brand new modern styles (think the new Walker Art Center Annex). There are about 12,000 students at MIT (grad students and undergraduates) as well as many more researchers and professors.

Some interesting things about MIT:
-No one calls buildings by their names…I kind of feel bad for all the trustees that gave millions to MIT to have their name on a building but it’s on a plaque in the corner someplace in the building… Instead, you call everything by its number: so I work in building 56, but walk through buildings 7, 3, 16, and 66 to get to lab in the morning. I feel sorry for anyone who is dyslexic.
-You never know what you’ll find in the hallway. Jet engines, meteorites…you name it, it’s here somewhere.
-Hacking…no, not computer hacking. It’s more like physical hacking of buildings. MIT students will do things like travel in underground tunnels, have study groups on the roofs of buildings, park police cars in lobbies, steal the Cal-Tech Cannon and drive it cross country just because, put up murals during finals week as a way to de-stress…it’s really cool.
-I will meet more people from around the world than original Bostonians: everyone is from all over: China, Norway, France, Greece, Arizona, Canada, Brazil, and many more.
-There are lots of “squares” (Kendall, Tech, College, Harvard, Center, etc…)
-There are no degrees of honor awarded at all
-Because MIT is non-profit (unlike Harvard down the street), it pays no taxes to the city of Cambridge. Instead, whenever the university wants to put up a new building, they pay the city a lot of money: it’s an interesting system.

We went out to dinner as a group on Sunday night, but we had to make it back to the house in time for chores….mine this week was cleaning the kitchen (industrial sized with five refrigerators…let’s just say it took awhile). I share a room with a lovely girl named Becky: she’s a rising junior chemistry major at Colby College in Maine, and she lives about an hour outside of Boston.

Monday was spent doing orientation: we walked around campus and saw many of the building we’d be working in as well as the surrounding community. The Charles River is gorgeous, and you can bet that I’ll be taking advantage of the free sailing lessons on Wednesday evenings. We also had presentations from the MIT police (a Bostonian-Irishman named O’Connor who said Hah-vahd just right), as well as some safety presentations.

However, before we could get started in lab, we had presentations from 14 research groups in the Biological Engineering Department: everything from analysis of different types of pectin to searching out damaged DNA nucleotides to building artificial scaffolds for liver cells to better simulate the liver in drug testing. On Tuesday, we spent most of the day running around MIT meeting the professors and graduate students to learn more about their research and specific experiments we’d be doing.

At 4:30, we dropped off our top three choices, and spent the night bumming around Cambridge: we found this amazing dollar-a-pound thrift store that basically uses a backhoe to pile clothes in a huge room. It’s amazing. We also hit up the local hardware store since it takes TechCash (as a part of our stipend, we receive $100 a week for food…or any store that takes TechCash). Everyone in the program is really great: even though we have only known each other for three days, we get along really well and are already planning several group dinners and outings throughout the summer.

This morning, we all slept in and went to campus at about 10:30 to pick up our assignments: I will be working for the lab of Dr. Linda Griffith, and more specifically, the newly graduated Alexandria Sams. Dr. Griffith won a MacArthur Genius Grant in 2006 for her work in tissue engineering. See the websites below for more details:

However, the work I will be doing is more on the biochemical side of her research with nitric oxide synthesis in liver cells and how this affects programmed cell suicide (apoptosis). I will be jumping into the deep end tomorrow with my first experiment, and I’m really excited to start work here at MIT! I will have more updates on what exactly I’m doing within the next two weeks, so I’m sure you’ll here more about the coolness surrounding carboxypeptidase D.