Running Around Crazily

I think I finally understand what it means to be running around like a chicken with its head cut off. If the past three days are any indication, it has something to do with going from activity to activity to activity with no breaks while you’re awake, and then rolling into bed when it’s time to sleep, because you’re so tired that you physically can’t stay awake any longer. That’s pretty much how my return to MIT has felt. As a result, the past week is a little bit of a blur, so you’ll have to excuse me if I forget anything.

The first order of business to take care of is actually something from last week. While I was home, there was a mouse running around in our garage. My dad, after much effort, caught it, so my house is again mouse-free. He has also requested that I mention that he found a vole in a filter in a thing in my grandparents’ basement. I’m not doing the story justice at all... I will leave it to him to tell the real story in the comments, if he so chooses.

And now for Monday. Monday was my mom’s first day back at work from her vacation. She took a week off while my German cousin and her friend were visiting the States. So... on Monday I got to play with babies! It was pretty much an amazing day. Even though it was a little bit crazy running around after two three-year-olds and a six-month-old, it was surprisingly relaxing not to think about science for a week.

Tuesday was even crazier, since there were four small children running around. We took them on a walk to the pet store to see the animals, which was a good way of getting out of the house for a bit. That being said, I believe that I took a nap on Tuesday afternoon, so the running around after four children was still very tiring.

Wednesday and Thursday were more of the same- I played with babies until they took a nap in the afternoon, at which point I read or napped until they woke up, and then I played with them some more until they left. (I should probably mention at some point that my mom is a nanny... the majority of this post probably doesn’t make much sense without that information.) After the babies went home, my family and I would eat something delicious for dinner, and then we would hang out, or watch a movie, or do some activity together.

The one non-routine thing that I did while I was home was picking blackberries for a pie. I got a little bit scratched up (battle wounds- totally worth it) and covered in blackberry juice, but the pie was delicious, so I’m certainly not complaining.

On Thursday night I flew back to Boston. I was excited to go back, but sad to be leaving, which seems to be a theme when I’m going places these days. I arrived in Boston at 7:30 Friday morning, Boston-time, and then began my trek back to MIT, which was pretty painless. I spent some time rearranging my room and finishing up one of the murals that we had been painting on our floor.

Saturday was the semi-official beginning of REX, MIT’s Residential Exploration Period. I hosted two events: a mural painting event, at which there were no freshmen, and an event where we watched random YouTube videos that was actually pretty well attended. My roommate came back to Burton Conner that night, so we re-rearranged the room so that we could fit everything in, and lifted my bed, which was a lengthy, complicated process that only resulted in one injury, surprisingly.

On Sunday I helped out at a bunch of events and worked desk for an hour, during which I was quizzed about life at Burton Conner for about twenty minutes by some parents. It was a lot of go-go-go, and I was very tired afterward. More people came back on Sunday though, so I got to see a good number of my friends who had been gone over the summer, which was wonderful.

I am obviously missing home and cookies though, because I have recently become addicted to a game where you make virtual cookies. It’s not all that realistic though, since I’m making almost 200,000 cookies a second right now. That’s not really feasible in real life, I don’t think. :P

I have to go to another event in a few minutes, so I’m going to end it here... I hope everyone has a great week!

Hello from Seattle!

All right… this is really, really late. I have no excuse, except for the fact that I’m home and had more interesting things to do (read: play with babies and laze around all day) than write… So. My apologies for the delayed nature of this post… it’s entirely my fault this time, no technical difficulties to speak of. :P

This blog post comes to you from… Seattle! I’m home, and not writing this on my laptop, which is very sad (the sad part is that my laptop and I are separated, not that I’m home :P) (it had to get fixed… the internal camera stopped working). Anywho… it’s really awesome to be home, and get to see everyone and everything that I haven’t seen for 9+ months. Before I get into the amazingness that is being home though, I should talk about my last week of work.

            The week was kind of a blur… my postdoc was leaving the lab to move to another one the day after I went home, so we had a lot of last minute, get-everything-in-order type things to do. On Monday, I finished up last week’s Western Blot, which confirmed again that we had found our protein of interest. Unfortunately, I used the wrong color of fluorescing antibody, so I had to redo the blot. (Each blot needs to be tested for at least two proteins: the one we’re looking for, and one that should be ubiquitously present, which will allow us to quantify the amount of protein in the blot after imaging. These two proteins need to be probed for in different channels of fluorescence, so that we can make sure that stray ‘phantom bands’ aren’t counted toward the amount of protein present in the blot.)

            As a result, Tuesday and Wednesday were largely spent doing my final Western blot (which confirmed, again, that our protein is present. Yay for being sure about things!) and trying to figure out how to use my computer to analyze the amount of protein present in the blot. Luckily, this wasn’t actually all too complex… but it did involve downloading some programs and doing some research to find out what people had done in the past, so it took some time. I also spent a good deal of time genotyping the last mice that we used in the Western blots. If you’ve ever done genotyping/PCR, you know that there are times when no matter how well you set it up, you won’t get clean results. (If you’ve never done genotyping or PCR before, you’re going to have to take my word for it. :P ) The gods of PCR saw fit to frown on me on Wednesday, so despite my best efforts, I only got clean DNA bands for two of the mice I was trying to genotype. It was too late to finish all of the genotyping again on Wednesday, so I had to just set up the PCR to run overnight and hope that Thursday would be a better day for running genetic tests.

            Thursday morning rolled around, and I showed up for my last day of summer UROP bright and early. The only things left to do were organize the remaining notebooks and data, clean out the fridge for the nth time that week (somehow things kept ending up back in there…), and run out the genotyping. Luckily, this time the bands showed up as they were supposed to, and I was able to confirm the genotype of all of the necessary mice.

            Once all of the work-related things were done, my postdoc took me out to lunch, which was a lot of fun. We discussed what she’ll be doing starting in September, and what I’ll be doing starting in September, and she gave me some good advice about how to survive MIT and make the most out of my time here (she was an undergraduate at MIT, so she knows what she’s talking about). After lunch, the only things left to do were confirm that everything was wrapped up and go over some logistical details about the paper my postdoc is going to be writing. She’s not going to be in the lab while she’s writing it, so she wanted to make sure she could get me to look up details for her if she needs them. After that, I packed up my stuff, said goodbye to everyone, and headed out. And with that, my summer of working in the lab was over.

            As much as I enjoyed working in Boston this summer, I was also really excited to go home. Which is probably why I decided to go to the airport three and a half hours early. For those of you who have never flown through Logan Airport, it’s not exactly huge. I’d say that for the most part, on domestic flights, an hour before your flight is more than enough time to get through security and find your gate. As a result, I had two and a half hours to kill. Honestly, this wasn’t awful. Before I left campus, I had downloaded some ebooks, and I had a bag of Chex Mix to keep me company. All in all, it was not a bad wait at the airport. I was missing my laptop at this point, but it’s probably good for me not to have it for a while… there is certainly such a thing as having too much of a good thing, and I think I’ve probably reached that point with my laptop, several times over.

            The flight home was fairly uneventful. We left about half an hour late, because we were waiting on passengers on a connecting flight, but the flight itself was about 25 minutes shorter than it was supposed to be, so we landed in Seattle more or less on time. My parents were waiting at the gate to pick me up, and were, of course, very excited to see me.

            On Friday morning, I went with my siblings to the University of Washington bookstore to look for some of their school books. The UW bookstore is kind of a dangerous place… it has books as far as the eye can see, and lots of little trinkets that are too much fun for their own good. So basically it’s my perfect store. I managed to control myself and not buy anything, but I was definitely making a mental list of all of the fun things that I would have liked to buy.

            Most of Saturday was kind of a lazy day… I went down to my grandparents’ house with my dad, and he changed a filter/pump of some sort while I chatted with my grandma. Then, after lunch, my siblings and I walked to the library with our dog. And finally, in the evening, some of my friends from the West Coast came over to West Seattle to visit. We talked about life and ate delicious food, and generally had a wonderful time.

            On Sunday, my family and I went down to the Pike Place Market and walked around a bit. We hit most of the major landmarks of the market- the doughnut shop, Bavarian Meats, Beecher’s Cheese, and various flower shops. We bought some doughnuts (an assorted dozen… which didn’t include a maple-bacon doughnut, much to my father’s chagrin) and a large bouquet of flowers to bring down to my grandparents’ house. We headed down there for dinner, where I saw most of my Seattle-based family. We had a lot of good laughs (many at my expense :P ) and some delicious food. I ate a bit too much, but it was delicious, so it was worth it.

           

            Given that it’s now Tuesday evening on the West Coast, I could tell you about Monday and Tuesday… but then I would be left with nothing to write about next week, so I’m going to stop here. Hopefully next week’s post will be up in a more timely manner! 

Last Post of the Summer (from Boston)

            It’s weird how as time goes by, and there’s less of it left, things seem to get more and more awesome. Specifically, this past week was my last full week of work before going home for the summer, and it was pretty darn amazing.

            It started out on a high note- my postdoc was giving group meeting on Monday, so she presented all of the work she’s been doing for the past semester and a half or so. Her presentation was really good, and it seemed like everything made a decent amount of sense. She also recognized my work over the summer, and it’s level of importance to her work, which was nice to hear.

Additionally, we finally figured out why we hadn’t been seeing any protein all summer (turns out that we weren’t using a high enough concentration of antibody for it to signal that any protein was there.) So on Monday, I got back some results that had been running over the weekend, and lo and behold, there was evidence of what we had been looking for. It was pretty exciting to see any evidence at all of our protein, even if that evidence came less than two weeks before I’m leaving for the end of the summer. Of course, finding our protein meant that I needed to repeat the experiments twice over to confirm the results. So Monday’s successes lead directly into the rest of the week’s activities.

Tuesday began by starting the process of protein preparation, running everything out on a gel, and doing a Western Blot over again for the nth time this summer (In reality, it’s probably only about the tenth time... but it feels like a lot).  Actually, that was all of Tuesday. Sneak peek- it’s actually all of the entire week, with some random fun things thrown in. :P

Wednesday morning, I imaged the first of the new set of Western Blots, and confirmed that our protein was where we expected it to be. I continued to check for the loading control (the protein that should always be expressed, in even amounts in any given type of tissue), and found that it was where it was expected to be, in even amounts, which more or less confirmed that the protein samples had been loaded correctly, and I wasn’t getting totally wacky results about our protein of interest.

On Wednesday afternoon, I had a meeting with one of the grad students in my lab about what he’s working on. He’s going to be my supervisor starting in the fall, and it was really cool to hear about what he’s doing. In really basic terms, he’s trying to develop a system of markers to tell which proteins in a cell are functioning at a given time. The way this relates to cancer is that the proteins he’s looking at are proteins that repair DNA strand breaks- if the proteins aren’t working, mutations that lead to cancer are more likely to develop. By testing living cells for whether or not the proteins are functioning, he’s hoping to create a test that can screen for cancer risk before any cancerous cells actually develop. It’s a really cool concept, and it fits really well in the trend of personalized medicine that’s developing right now.

On Thursday, I took the day off to meet with one of my friends from home who was in Boston for the day. She had a day’s layover between when she finished her trip and when she needed to fly home, so we got to spend some time together, which was really awesome, especially since I hadn’t seen her in over a year. We ended up just walking around Boston, discussing life and how we had changed over the past few years. Although it wasn’t some sort of grand adventure, it was wonderful.

On Friday, it was back to work. I imaged another blot and found evidence of our protein, and got started on some new protein preparations. It was a little bizarre realizing that the protein preps on Friday were the last ones I’d be doing for the summer. At the beginning, it felt like the summer was never going to end... and now all of a sudden I’m doing ‘last’ things. Time flies, and it only seems to fly faster and faster.

On Saturday, my friends and I decided we were going to make a daytrip out of going to watch the Perseid meteor shower. We wanted to get away from the city lights, so we decided to go to the Blue Hills Reservation, which is about 15 miles outside of Boston. We decided to go to dim sum before heading out, which was a lot of fun, and very filling. We ended up wandering around downtown a bit, and we went to C-mart, which is kind of like Uwajimaya in Seattle, except a lot cheaper (non-Seattleites: C-mart and Uwajimaya are Asian food markets, and Uwajimaya is huge and a lot of fun, but fairly pricy).

After a lot of riding the T and walking, we found our way into the reservation and wandered around for a bit. It’s always a bit bizarre to find densely nature-y parts of Massachusetts so close to Boston. Boston and Seattle are very similar in many regards, but for some reason I always assume that there’s no nature anywhere around here. Luckily for me, that assumption is very wrong, and I got to enjoy some beautiful nature this weekend.

The pond we saw when we walked into the reservation

Some of the lovely trees at the reservation

We came to the decision that the reservation wasn’t really the best place for watching the meteor shower, so we ended up just going back to Boston. I really enjoyed being out of the city for a bit, but it was also really nice to come back to pika for dinner. My roommate and I ended up getting up at 4 a.m. and going up to the roofdeck to watch the meteor shower. I only saw two meteors, but it was totally worth it. I can’t remember ever seeing a meteor before, so it was a fun new experience.

Unsurprisingly, after I got up at 4 in the morning, I decided to sleep in on Sunday. I got up and had breakfast, and then did the Sunday crossword with a few friends. It was challenging- we finished the majority of it, but after spending two hours trying to finish it, we ended up just randomly filling in a couple of letters. Sunday afternoon, a group of people from the house walked to Inman square and got ice cream at Christina’s, which is a gourmet ice cream store. It was really good, and a lot cheaper than Tosci’s, which is where I usually go. It was about twice as far away as Tosci’s though, so there are pros and cons. Attached to Christina’s ice cream store, there’s also a spice shop, which was fun to browse. They sell loose teas and pretty much every spice I can think of, so it was fun to look around. We also browsed a used bookstore (very dangerous!) and a vintage store that was playing great blues music. All in all, Sunday was a pretty good day.

That more or less sums up the week... it’s weird, because this is the last blog post I’ll be writing from Boston this summer. Next Monday I’ll be home, so there’ll be a lot of Seattle stuff to talk about, I’m sure. There’ll also be the wrapup from my summer of research, and we’ll see if anything comes of my last set of Western Blots. Lots to look forward to! :D

Loooong Week

            This week was really, super busy. I somehow managed to work for more than eight hours everyday, and I did something after work for more than half the week. It was exciting, and busy, and at the end of it, I kind of just wanted to take a long nap.

            Anyway, Monday was pretty dull as far as Mondays go. I passaged the cells that we’ve been trying to immortalize, I looked for some more protein, I set up some PCR reactions. I was very efficient (read- constantly busy without any time to sit down and do things on my computer. So actually working all day. It was a long day. (At this point I’m imagining my father making a crack about me finally being a functioning member of society... Love you Dad! :D )) Unfortunately, I slightly overestimated my ability to be efficient and ended up staying about half an hour late to bring everything to a stopping point. I probably should have realized at that point that I’m not as efficient as I thought I was. Unfortunately, it’s not something I realized until pretty much right now. So yeah... it was a long week.

            Tuesday was equally busy, although it was more exciting than Monday had been. We began the process to make a new cell line- pretty much the same thing I’ve been doing since the beginning of the summer. The difference here though, is that instead of immortalizing wild-type cells, we were trying to immortalize knockout cells- cells that lack the gene that encodes our protein of interest.

The point of immortalizing knockout cells this time, rather than wild type cells, lies in the meaning of the terms ‘wild type’ and ‘knockout’. Wild type cells, or organisms, have a normal copy of the gene of interest. The gene encodes the protein of interest normally; basically, a wild type cell, or organism, or gene is one which is unchanged from what you would see in nature- hence the term wild type. In contrast, a knockout version of the same gene/cell/organism is one in which the gene of interest has been manipulated in such a way that it no longer functions- the protein normally encoded by the gene is not expressed, and the way that the cell or organism functions is often changed as a result. With knockout cell lines, researchers can examine what happens in organisms with knockout mutations without having to actually work with the organisms. Knockout cells and organisms also allow researchers to determine the function of a protein of interest. When the protein is not expressed, it can be fairly simple to look at an organism and determine, by process of elimination, what the function of that protein is. The process can obviously be complicated by extenuating factors, but in general the point of creating a knockout version of something is to determine what the function of the missing protein is.

Tuesday was mostly filled up with that. Creating a new cell line requires several hours of sitting in front of a tissue culture hood, moving things from dish to dish and test tube to test tube. Since tissue culture hoods aren’t the most ergonomically designed pieces of equipment, I gained a new understanding for exactly why my postdoc had taken up yoga. I imagine that if you were doing tissue culture work everyday, you would have lots of angry muscles.

Wednesday was a bit different- I was on a tighter schedule, since we (some friends and I) were going to a baseball game in the evening. As a result, I wanted to make sure that my experiments were finished as close to 5 o’clock as possible. One of my favorite parts of baseball games is the National Anthem, and I didn’t want to miss it. I didn’t do too badly- I was pretty efficient, and managed to finish at about five minutes after 5 o’clock. After scarfing down some dinner, I was walking to the Central Square T station with one of my friends who were going to the game when I realized that I had forgotten the tickets in my backpack. So we had to turn around and walk back to her dorm where we had left our bags. From there, it was quicker to walk over the BU bridge, rather than the Harvard bridge, so we decided that we would walk over the BU bridge, and our friends who we were meant to meet in Central Square would meet us at the game.

After various misadventures and a bit of wandering around in the general direction that we needed to go, we all made it to Fenway and sat down to watch the game. After the first few innings, I was pretty convinced that it was going to be the shortest game of my life- the teams made it through five innings in the first hour. The next few innings proved me wrong though, as each team managed to score, and they ended up tied at the bottom of the ninth. They went into overtime, but when no one had scored again by the bottom of the twelfth inning, (which was at about 10:40 pm) we decided it was time to go home and sleep. As it turns out, this was probably a good decision, as the game lasted through 15 innings, and ended at 12:40 am. I felt bad for the players- they all had another game the next night.

It was really cool to go to a baseball game at Fenway, and it was even cooler because the two teams playing were the Mariners and the Red Sox. I had a bit of trouble deciding who to cheer for... and my friend had to keep reminding me that it was probably best not to loudly cheer for the opposing team while sitting amongst a bunch of (slightly to very) drunk Red Sox fans. In the end the Red Sox won, so it didn’t really matter that I was rooting for the Mariners secretly... but I can’t say it wouldn’t have been nice to see them win a game. :)

Me sitting in the stands, before the game started.

Fenway Park!

A picture of the actual game, just so you can see I'm not lying about attending a baseball game. :P

Me with a statue of the Red Sox mascot, Wally the Green Monster (or Monstah, as they say in Boston)

Thursday was my longest day of the week- I severely overestimated my ability to do things in a timely manner and ended up at work until 7 pm. Luckily, I was planning to go to a movie/free food event at 7:30, so I got something to eat pretty soon after I got out of work. The movie we watched was ‘3 Idiots’, and it was good, but strange. First of all, it’s in Hindi and English, with English subtitles. The two languages are intermixed, so I spent a good portion of the movie trying to figure out whether or not my ears had broken. Secondly, the main plotline of the movie is set in an engineering school in India, and it was a bit bizarre to see how similar life in engineering schools on opposite sides of the world can be. Obviously the movie is fictional, and probably portrays a caricature of what life is really like in an engineering school, but there were some salient points that struck home. Most of all though, the movie was a bizarre mix of hilarious and shockingly sad. It switched between the two emotions with very little warning, so watching it was something of an emotional roller coaster. Overall, I would say that it’s a very well done movie, and I thoroughly enjoyed it, although I’m not sure that I would recommend it to people, just because it is a very bizarre film. And it’s almost three hours long. So there’s that as well.

Friday, while still a long day, was less long than Thursday was, primarily because it was broken up into more manageable pieces. The lab had a postdoc visiting who is looking into a position with the lab, so we listened to a presentation about her work and had a lab luncheon, which was delicious. These activities broke up the morning into more manageable pieces, which made Friday seem shorter than it actually was. I still spent almost nine hours at work that day, but it was easier because there were some random activities to break up the day.

Work on Friday mostly consisted of running more Western Blots and freezing down the knockout cells that we had started culturing earlier in the week. Since there’s not nearly enough time left in the summer to immortalize the knockout cells, we basically just passaged them once and then cryogenically preserved them so that whoever wants to use them will be able to bring them up and immortalize them for use. Cryogenics is a pretty cool concept, and not one that I’m very well acquainted with, so I’m excited to learn more about it.

After work on Friday, I went home and ate dinner (we had, among other things, taro fries, which were really good, surprisingly) and then went back to campus to watch a free movie. The movie was ‘Rise of the Guardians’, which is a total kids’ movie, but it was really nice not to watch something intellectual after a long week.

In keeping with that theme, I had a very lazy weekend. I spent most of Saturday and Sunday marathoning a TV show with a friend. The marathon paused for meals, and specifically for dinner each day. On Saturday, pika had a neighborhood barbecue, which turned out to be a lot of fun. We invited our neighbors to come over and we barbecued pretty much every type of food that it’s possible to grill (no, Dad, we didn’t make any cake. You’re still the grill master. :P ). It was really cool to meet the neighbors and hear about their life stories. A lot of them are doing really cool things, and it was fun to hear about life after college.

We stopped our TV marathon for dinner on Sunday because, as I mentioned last week, I cooked for pika. Cooking dinner at pika happens in pairs- a big cook and a little cook. The big cook usually plans the meal and gathers ingredients, and the little cook helps put everything together. Since it was a weekend, and I really wasn’t doing anything important, I (in my capacity as little cook) went with the girl who was big cooking to get ingredients. We bought a lot of things- including four pounds of pasta (to supplement the other 6 pounds we already had at the house) and 5 pineapples. Pineapples are surprisingly heavy for their size. That doesn’t have much to do with my week, but it’s something I realized.

We ended up making a lot of pesto pasta, a three bean salad, and a massive fruit salad. I chopped all five pineapples, which was actually quite a feat, considering I’d never cut a pineapple before. By the last one though, I was actually getting all the skin off without too many of the pokey bits left. And I didn’t hear anyone complaining about being poked in the mouth, so I’m going to go ahead and declare myself a master of cutting pineapples.

Anyway, that’s about it for this week... I know that it’s already Monday, and I could theoretically tell you about today. But this post is already pretty long (to match the long week), so I think I’m going to save it for next week.

Lots of love,

Alycia