The Week in Numbers

What? Blog post? No, I totally didn’t forget, I don’t know what you’re talking about.... Okay, maybe I forgot. But just a little. Sorry guys, this one might be a tiny bit late.

Alrighty, where to begin? Last week seems like it somehow took a much longer time than all the other weeks... I’m not quite sure how that happened, but it did. It probably has something to do with the fact that I did more things in the last week than I can actually remember... I’m going to go back and try to count some of the things I did, just to give you some perspective.

48

Hours, that is. I ran a 48 hour time course at the beginning of the week- basically this means that I set up some samples on Monday afternoon and let them incubate until Wednesday afternoon, taking small samples at various intervals in between. Although the experiment wasn’t very taxing at all, it was a relief to take the last sample at the 48 hour mark. I think it was just very satisfying to be done. Unfortunately for me, the experiment didn’t quite go as planned (I’ll explain below, in the next section) so I get to do another set of 48 hours this week.

11

Gels, this time. Over the course of the last week, I ran at least 11 gels, five of them on one day. If you remember, this means that I loaded my DNA into wells at the top of the gel, and then connected leads to the gel box so that there was a current running through the gel. The DNA has a slight negative charge, so it runs away from the negatively charged end of the box (like charges repel). Since the DNA is running through an agarose gel, it ends up getting separated by size, as the larger pieces of DNA get ‘stuck’ in the gel and don’t run as far as the smaller pieces of DNA. Eleven gels might not seem like a lot of work, but considering that for every two gels there are at least six hours of work that go into getting the DNA that needs to be run on the gel, I’d say that eleven is a lot for one week.

This is also the section where I’m going to explain the failed experiment, since it has to do with two of the gels that I ended up running last week. The samples that I was taking at various intervals during my time course were run out on a gel. We were trying to see how long it takes a certain enzyme to fully digest our plasmid that contains a thymine dimer (a specific DNA mutation- it’s the kind of DNA mutation you get when you get a sunburn or other UV damage). In theory, incubating the plasmid with the enzyme should result in full digestion after 16 hours, but we’d previously seen that that wasn’t the case, so we were trying to see how long it actually took. So, after 48 hours, I ran the samples out on a gel, and then imaged the gel to see where the bands were, and if the plasmid had been fully digested or not.

As it turned out, all of the bands of my plasmid of interest were at a height that didn’t make sense. They weren’t the same height as our negative control (plasmid that definitely wasn’t digested) or our positive control (plasmid that was definitely digested). We were flummoxed. So we ran an untreated sample on a gel that my grad student was running anyway, and found that the DNA used for the 48 hour time course wasn’t plasmid DNA at all, but linear DNA. How it got to be linear DNA, we still don’t know, since it was definitely plasmid DNA when I extracted it from the gel. But anyway, the experiment was unsuccessful since it’s impossible to tell if linear DNA has been digested with this specific plasmid, and it was too late in the week to start another 48 hour time course (the perks of being an undergrad... you don’t work weekends. In grad school I would have just immediately started the experiment over). As a result, that’s one of the things I’m doing this week.

4 (9)

This one has two numbers, which is confusing, but I’ll explain. The four refers to the number of new cell lines I thawed last week so that we can start using them in experiments. Thawing cells is relatively simple, but these are a new type of cell that I haven’t worked with before, so it’s taking some getting used to. Previously, all the cells I’ve worked with have been adherent, meaning that they grow attached to the side of the flask they’re in. The new cells are suspended, meaning that they just sort of float in the media. It’s both easier and harder to take care of them, since you don’t have to remove them from the side of the flask every time you want to use them, but you also have to keep them at very specific densities or they won’t grow well. I’m reserving judgment on which cell type I like better until I’ve had a bit more time to work with these new cells.

The nine refers to the total number of cell lines I’m now ‘in charge of’. In charge of is in quotes mostly because I’m technically the one taking care of them, but my grad student keeps using my original five cell lines for his experiments, which means that I don’t need to do anything to keep those cells healthy, which is nice.

14

Fourteen is for the number of times I walked across the bridge into Cambridge or back into Boston this week. In a normal week, I walk across the bridge ten times- two for each work day. Where do the extra four crossings come from, you ask? I moved back into Burton Conner this weekend, and moving my stuff out of Sig Ep and into BC required four trips across the bridge (two into Boston and two into Cambridge). It was a good workout- my muscles are protesting the walk today. As it turns out, I’m something of a packing god (I learned from the best, of course), which is both a good and a bad thing. On the plus side, it means that I only had to take two trips back into Cambridge. On the minus side, it means that my suitcase was probably well over 75 pounds and dragging it across the bridge was not fun, by any means.

My packing god status also means that I have an utterly ridiculous amount of things. Every time I have to pack or unpack my stuff, I’m amazed at how many things I’ve managed to acquire over the past three years. I was unpacking yesterday and felt like I was pulling things out of Mary Poppins’ purse, the way stuff just kept coming out of the box. It was really rather incredible. As a result of my crazy amounts of stuff though, my room is still a mess and not quite organized yet, so I’m going to hold off on pictures until a later post (I also haven’t charged my camera yet... although I do have the charger now, so that’s a thing that will be happening).

3

This is the number of times I ate out last week (not including lunch, which I had to buy because I ran out of lunch food). On Monday my friends and I went to the Boston Burger Company, which was quite yummy. On Wednesday, we ordered in Asian food, because I had a coupon for 20% off, and it was rainy and gross out, and just a generally miserable day, so no one felt like cooking. I got pad thai, which was delicious. And on Thursday, we went into Brookline to celebrate a friend’s birthday and we ended up going out to eat at Rami’s, which is an Israeli/Middle Eastern restaurant in the Coolidge Corner area. It was also delicious, although extremely busy for a Thursday evening. I think we managed to walk in right at the peak of the dinner rush, so that’s probably why it was so crazy. The food was definitely worth it though.

I think that about sums up my week in numbers- for my last number I’ll tell you that it’s 11:44 and I’m sleepy, so I’m going to sign off now. Until next week!