Technical Difficulties

            Okay... I’m sorry this is so late. This week was rather full of technical difficulties. And unfortunately, technical difficulties occurred in pretty much all my areas of life, so everything is late. (Admittedly, there was perhaps a bit of time mis-management that occurred... but it somehow seems better if I blame everything on technical difficulties).

            On to the stuff I know you’ve been dying to hear- how the combination of construction and biology turned out. What we know is that the drill served its intended purpose, which was to shear the cells and separate the nuclei from the remainder of the cells. (For non-biology people, a very simplified explanation of how animal cells work is that there’s a little pouch encircled by a big pouch. The little pouch is the nucleus, which contains the majority of the genetic information in the cell. The big pouch (the cell) contains everything else.) We were guessing that our protein of interest was contained in the nucleus, which would explain why we hadn’t been seeing it. If the protein were only expressed in the nucleus, it wouldn’t show up in our original tests because the ‘pouch’ of the nucleus would hide it. The goal of the electric drill was basically to break the ‘pouches’ of the cell and nucleus open, respectively, allowing us to see some protein. We know that the drill worked because the pellet of cells kept getting smaller, and our supernatant got more and more viscous, indicating that there was cellular stuff in it.

            Unfortunately, in what I consider the first technical difficulty of the week, none of the protein was visible, even after the drilling. We don’t really know why this is, but we decided, like the good scientists that we are, to move on and continue our tests in new and ever more inventive ways. The good news is that I’m going to be doing fewer Western Blots until we figure out what proteins are actually present in our samples. Knowing how to run a Western Blot is a good skill to have, which is why my postdoc had me doing so many of them. Now that I’m something of a master at Western Blotting (knock on wood), we’re going to do some of the simpler, faster, down-and-dirty protocols that will get us answers quickly, rather than extremely accurately. Once we’ve gotten our quick answers, we’ll go back to the fancy stuff.

            In the second major technical difficulty of the week, I kind of screwed up big time. So I guess it’s not really a technical difficulty, since I directly caused it. But it wasted about three days worth of work... so I’m going to categorize it as a technical difficulty. Back at the beginning of the summer, my postdoc decided that I had something of a Midas touch when running PCR (a method of quickly replicating specific pieces of DNA in order to get enough to run it out in a gel so that you can tell what genotype a sample is (where a sample’s genotype is like its genetic signature)). Basically, she decided that I could run a clean PCR, which was apparently a big deal, and she more or less assigned me to run all the PCRs for the rest of the summer. Since this basically just involves mixing some things in specific proportions and sticking them in a machine to replicate the DNA, I was fine with this assignment. The problem came about when she asked me to prepare the samples for genotyping. All this requires is sticking some tissue samples in some chemicals that will dissolve the tissues, and leaving them overnight in an incubator. Sounds easy. It probably is actually one of the easiest things to do in lab. Which, of course, means that I found a way to mess it up.

            During the period when she had me start preparing the samples for genotyping, my postdoc decided to have a more ‘hands-off, let her make mistakes’ style of teaching. Which I’m all for, usually. I think it occasionally makes a lot more sense to teach through fixing mistakes than it does to teach by hovering over your student’s every move. In this case, however, I probably could have used a tiny bit more hovering. There’s a specific chemical we use when preparing DNA samples that breaks apart the tissue by essentially dissolving protein bonds, called Proteinase K. It’s kind of like a chemical version of the drill from earlier. I had no clue where to find the Proteinase K when I was first doing the DNA prep. I managed to convince myself that I remembered the Proteinase K having this other name though- ‘ACK’. Since there was a tube labeled ‘ACK’ sitting on the lab bench, I decided that that was right. And I used it to digest my tissue samples. For anyone who’s worked in a lab that lysed cells for any reason, you might recognize ACK as a lysis buffer. Regardless of whether or not you’ve worked in such a lab, I’m hereby informing you that I was not meant to be adding this lysis buffer to my samples. Although it didn’t really ruin the samples, it did mean that I didn’t get any DNA out of them. Coincidentally, after the second time this week that I tried to prep my DNA samples with ACK and nothing happened, we did the protocol that actually required the ACK buffer to lyse some blood cells. At this point I realized what I had done, and proceeded to spend the rest of the day and weekend worrying that my postdoc was going to do whatever the UROP equivalent of firing someone is to me for making stupid mistakes. Luckily for me, when I explained what had happened today, she was mildly shocked at the amount of craziness that had gone into one mistake, but she was actually very nice about the whole thing, and explained about her wanting me to make some mistakes, so I would know they could be fixed. And since we had saved the base sample that I was trying to digest, this was a fixable mistake. I don’t know if we’ll see DNA yet (I’ll find that out tomorrow, with any luck), but I did use the real Proteinase K, so I actually have a chance at getting some results.

            In the non-work-related world, there were also technical difficulties. The webcam on my computer mysteriously stopped working (I can neither confirm nor deny that I may or may not have dropped my computer prior to this occurrence). Unfortunately, this occurred immediately prior to my attempt to skype with my friends who are in various other parts of the world. Luckily, other people who I was with had computers available, so this was not totally disastrous. Unluckily, it precludes me from taking pictures with my computer or using it to video chat until I am willing to give it up for a week to get it fixed. So that’ll probably be a little while.

            Some things this week didn’t have any technical difficulties- on Friday night we got dressed up to go to the MIT Symphony Orchestra’s performance. They played some gorgeous music, and I thoroughly enjoyed listening to them. On Saturday, we went to the Commons for more free-concert-y things. There was some good music, and some not-so-good music, but the really cool thing was a performance from the Boston Ballet School. Some of their older students did some dances inspired by various world dance forms, and it was really incredible what they were able to do. We went for lunch at an Asian restaurant, and I had sushi with raw fish for the first time, which was not as gross as I was expecting. Not something I’ll necessarily be seeking out, but not disgusting.

            On Sunday, one of my friends and I went to Revere Beach to see the sand castle competition. Unfortunately, my camera died, so I was unable to take pictures. But in my opinion, the sculptures were awesome. Some of them were seven or eight feet tall, and they were made only out of sand and water. I still have no idea how the artists managed to keep sand sculptures standing for three days when they’re made only of sand and water. But it’s pretty incredible, however they do it. Also while at the beach, I was for some reason mistaken as someone who speaks Spanish. I do speak Spanish, but I’ve never been randomly pointed out as someone who speaks Spanish, probably because I look very Eastern European. I then had a short conversation in Spanish, which was interesting.

            And, since this is so late, I can tell you about what happened on Monday. Work was not overly exciting, other than figuring out what Proteinase K actually was. I took my computer into the Apple Store to see if they could fix my camera quickly, and found out that they couldn’t. The highlight of my day was after work, when I went to the North End with a group of pikans, in search of pastries. Boston’s North End is the Italian district- it’s heavily saturated with Italian restaurants, each boasting a better pizza or pasta dish than the next. We ended up at a little bakery that had pretty much everything- it reminded me of the Salvadorean bakery at home, but with Italian food. My impression was that everything was delicious, and I probably need to go back to try more of the things. On that note, I’m issuing an open invitation to anyone who’s in Boston to come with me- I’ll happily eat more pastries with you. :)

            Unfortunately, it’s now very late, and as a result I should sleep. Given that I just misspelled sleep, I think that actually sleeping is a logical next step. I hope that everyone has a wonderful week!