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!

Finished with the GRE!

The highlight of this week (or lowlight, depending on how you look at it) was the GRE.  As I’ve said before, the GRE is basically the SAT on steroids- the question types are similar, but the difficulty is ramped up several notches.  Over the course of the summer, I learned almost 400 vocabulary words (and was reminded of the meanings of several others that I’ve used or seen before, but didn’t quite know the definition of), reminded myself of how to do basic math problems (will I ever learn probability? The world may never know...), and re-learned how to write a halfway decent essay in half an hour.  The culmination of this studying was a four and a half hour exam this Saturday.  Finishing was rather anticlimactic, but there are very few things in my life that I’m happier about being done with than the GRE.  Given a couple more months I could possibly do better, but it wouldn’t be cost-effective, so I think that I’m done with the test from ‘H-E-double hockey sticks’, as my siblings would say.  Now I can get back to fun stuff like figuring out exactly what it is that I’m doing with the rest of my life.... yay! :P

Anyways, I did do things other than take a horribly long exam this week... not many of them, but they were rather exciting things, so I’ll tell you about those rather than continuing to complain about the GRE. (And at this point all of the people reading this let out a mental cheer... :P)

On Monday my experiment failed.  I haven’t had any major failures this summer yet, so this was a good return to the old standby of having things not work the way I wanted them to. So, with an entire day’s worth of work down the drain, I started it over on Tuesday, with some minor changes to the protocol that were aimed at resolving the issue.

Tuesday’s experiment worked out fine, luckily.  And since Tuesday’s worked out well, I got to do the same thing on Wednesday, just in triplicate.  Which is always so much fun to try to coordinate, let me tell you.  Somehow doing things in triplicate doesn’t have a linear relationship with time... it’s more of an exponential relationship.  Everything took about nine times as long as it should have, which was great fun.

Wednesday also resulted in a rather fun story that really wasn’t all that fun at the time.  In order to understand it, I’m going to remind everyone that a microcentrifuge (often just called a centrifuge because we’re lazy about names :P) is a little box that you stick your samples in and it spins them around really fast to make solids fall out of solution, or various other applications. We have them sitting on top of our work benches- they’re pretty small.  Anyway, I was doing a protocol that requires you to spin your samples down approximately every two minutes after adding different chemicals.  I’d been just sticking my samples into the centrifuge and turning back to my work on my bench, which normally works just fine.  I’ve always got half an ear turned to the centrifuge though, since it sounds different when it’s speeding up or slowing down, and that lets me know when my samples are almost done.

The centrifuge made its speeding up sounds, and I went to get things ready for the next step in the protocol.  Not 30 seconds later though, it started making slowing down sounds, and then sped back up.  This is not standard procedure for centrifuges- they’re supposed to get up to speed and stay there until the time is up.  It got back up to speed okay though, so I let it continue through the step, and decided it must have just been an aberrant spin. [Note the use of aberrant there... that’s one of the 400 words that I learned. :P]  When I was doing the next spin step though, the centrifuge got up to speed, and then it sort of began slowing down and all of the lights on top began flashing.  I couldn’t stop the rotor, and the door wouldn’t open, so my samples were stuck inside.  And since my grad student was missing (he’s been spending a ridiculous amount of time doing flow cytometry, which is in another building altogether) I was sort of freaking out.  I eventually got my head together enough to Google the problem, at which point I found the user manual and found what the problem was.  Unfortunately, the fix to the problem was in French.  And I was spending a good deal of mental energy freaking out about the fact that my samples were stuck in the centrifuge, so it didn’t immediately occur to me that the power of the Internet would be able to translate the manual for me... (I was alternating between trying to find French/Spanish cognates and trying to remember if anyone in lab spoke French... not the most logical moment in my life).

I eventually got to the point where I translated the instructions and followed them (it was literally turn off the centrifuge and turn it on again... I really should have guessed).  And supposedly that should have fixed the centrifuge.  So I got my samples out and ‘fixed’ the centrifuge, did the next step, and put my samples back into the centrifuge to do the next spin step.  And the same thing happened.  This time I knew what to do, so my freaking out was significantly more under control, but it was still annoying.  Especially since my lab has a running joke that I’m the one who breaks things... the last thing I wanted to do was prove them right. :P

I reset the centrifuge again, and then decided to just use the other centrifuge for the rest of the day.  I reset the centrifuge again afterward, and did some test spins with empty sample tubes that seemed to work fine.  So I decided that the centrifuge just hated me, and was actually okay.  Of course, I was wrong.  (Anyone surprised?)  The centrifuge threw a tantrum again on Thursday when I was trying to spin down Thursday’s set of samples.  My grad student was in lab this time though, so I was able to get his opinion on what to do.  Not that that helped much, since his advice was literally ‘turn it off and on, and we’ll fix it tomorrow’.  But it was nice to know that I wasn’t crazy.

The saga of the centrifuge was probably the most exciting thing that happened last week... I took Thursday afternoon and Friday off (on a somewhat involuntary basis... my grad student sort of sent me home to study for the GRE).  I spent a large portion of that time studying, which worked out fairly well, other than the fact that I ended up having a laughing fit on Friday evening because I over-studied a tiny bit.  My friends were, once again, slightly worried for my sanity.  Not that that’s all that unusual, to be honest.  People are worried for my sanity on a worryingly frequent basis. :P

Saturday morning went pretty well.  My friend and I went to brunch before the GRE, and I had a delicious breakfast burrito (another wonderful restaurant for anyone in Boston to try- Trident Booksellers Café. It’s a bookstore and a café, also known as heaven).  Then we spent four and a half hours sitting at a computer screen taking an exam, which was great fun, of course.  And afterwards, we went out to eat again (this time I got Mexican food at Cactus Club- another delicious meal).  And when we were done with that, we got cheesecake with a third friend who took the MCAT this week as well.  It was an episode of stress eating, but it was pretty delicious.

On Sunday I went for a run in the morning, and then my friends and I trekked out to Revere Beach to spend the afternoon.  It could have been a bit warmer, but the beach was lovely.  I went in the water for the first time all summer, and the tide was farther out than I’ve ever seen it on this coast.  We saw hermit crabs, and found lots of shells, and spent a good deal of time in the sun (no sunburns though, due to some possibly overzealous sunscreening).  It’s late in the summer to be going to the beach, but it’s definitely a better late than never situation.  And it was a great way to round out the summer... it was sort of the last weekend of the summer, since next weekend I’ll be moving back into Burton Conner, and then it’ll be Orientation for the new freshmen, and then school will be starting.  So, all in all, this was an excellent ‘end’ to the summer, even if there’s about two weeks left technically.

This time next week though, I’ll be back in Burton Conner, with my stuff back, and a full kitchen on the same floor as me, and it will be lovely.  Did I mention I’m excited to go back to Burton Conner?  I’m just a little bit excited. :P  Until then!

Ridiculous Words

I’m not going to lie... I have very little to write about this week.  And that’s making it a great deal more fun to read through my old blog posts than to write this one.  I think I’ve spent the past two hours procrastinating rather than writing this post... so you’ll have to bear with me through the boring bits, since it was a strugglefest to write them.  No, strugglefest is not an actual word.  Yes, it’s something I use on a regular basis.  No, this is not at all relevant; I just felt the need to address it.  Yes, I’m still procrastinating, even as I started to write the post.  I’m going to move on from the legitimacy of the word strugglefest now, and get to some more relevant words.

A request from last week’s post was that I keep up with the crazy GRE-level vocabulary words that I included last week.  And since the list of words I’m supposed to know is now over 250 words long, I’ve got plenty to choose from.  As a result, this week’s post is going to consist of one ridiculous word per day.  I’ll give you the word and its definition, and then explain what happened that made the word fit the day.  Yay words!

Monday

erudite – having or showing great knowledge

Monday mornings in lab are almost always spent in group meeting.  The way group meeting works in our lab is that one person presents anything they’ve been working on since the last time they gave group meeting, and the rest of the lab asks them questions or offers suggestions about other experiments they could do.  I can’t say that I contribute much to these meetings, mostly because I don’t have the level of expertise that the other members of my lab do.  (To be fair, they’re all multiple years into grad school and/or already have a Ph.D., so I’m a little bit out of my league).  But the ease with which everyone is able to ask intelligent questions, or offer actual useful suggestions astounds me every Monday (and then again every other Friday, when we have Journal Club meetings and present papers). 

Basically, people in my lab are ridiculously impressive, and if I can attain their level of knowledge at some point in my life, I’ll be very happy/proud of my accomplishments.

Tuesday

toothsome – (of food) temptingly tasty

On Tuesday, one of my friends came back from spending the weekend at home.  He’d spent the last month observing Ramadan, meaning that he wasn’t eating between sunrise and sunset.  To celebrate his return to being able to eat at normal hours, we decided to go out for food.  We ended up going to Dorado Tacos, a taco restaurant in Coolidge Corner (part of the outskirts of Boston).  I had two fish tacos and un elote, or corn on the cob with seasonings, crema (sort of like sour cream) and cheese.  It was totally delicious, and very filling.  I’d definitely recommend it to anyone who has some time to kill in Boston.  I’ve been there twice now, and both times the tacos were wonderful.

Wednesday

timorous – showing or suffering from fear, nervousness, or lack of confidence

Late last week, my PI (principle investigator- the professor who’s in charge of my lab) decided that everyone working on the project that my grad student and I are involved in should have a meeting so that we can all be brought up to date on what’s going on.  This was a totally reasonable suggestion, but I was kind of dreading it because it meant that I had to talk about my work in a knowledgeable way, in front of people who are (as previously stated) really good at what they do.  In a word, I was very timorous going into (and during) the meeting.  I managed to acquit myself in a not-horrible manner though... afterwards, my grad student told me that I had done well, even if I was rather obviously nervous.  Hopefully after doing this a few thousand more times, it will become second nature and I will be less nervous.

Thursday

soporific – causing sleep or lethargy

On Thursday, I got to do a really exciting experiment, where the italics are meant to stand in for sarcasm.  Basically, I needed to figure out how long the plasmid we’re working with needed to be incubated before it was fully formed.  In order to do that, I got to take a small sample out of the solution every 30 minutes for four and a half hours, and then run them in a gel to see where the bands for every half hour fell.  And then, once we figured out that only an hour was needed to fully incubate the plasmid, I got to do 10 minute time points between half an hour and an hour.  The whole process was rather soporific, since the 30 minute intervals weren’t long enough to really do anything else, so I basically went into lab for two minutes to grab a small sample and put the larger sample back in the incubator, and then sat on my computer studying vocabulary for 28 minutes until it was time to do it again.  So much fun.  It was good that we figured out how long the plasmid needs to be incubated though, so there was a silver lining to my boredom.

Friday

ebullient – cheerful and full of energy

tremulous – shaking or quivering slightly, timid, nervous

Friday gets two words, because it was a rather full day.  The first word, ebullient, is applicable for a number of reasons.  First, my grad student found out that he got a fellowship for next year, which is a really big deal... it’s more or less a scholarship that’s awarded based on the work you’re doing in your research, but there’s only 65 of them awarded per year for the specific fellowship he was awarded, so it’s really exciting.  I didn’t really get how big a deal it was until our PI came into the office to congratulate him (she never actually comes into our office or lab... there’s always something big happening when we see her there) and then I googled it and realized that it was a big deal.  So everyone was pretty happy about that.

Additionally, all of my experiments that I was running on Friday worked the way they were supposed to, which was exciting since it meant that we could start actual work on the project on Monday.  And since the school year is almost here (when did THAT happen??) it’s nice to know that we’re more or less on track for where we want to be.

Friday was also tremulous (the quivering was only in a metaphorical sense... I’m more referring to the timid/nervous aspect here).  At the end of the day on Friday, my grad student had to go to a meeting so I was left for about an hour and a half with nothing to do (since all I had left for the day was planning the next week’s activities, which took about 5 minutes... but then I needed to discuss them with him to make sure I wasn’t forgetting something major).  As a result, I spent the hour and a half alternately freaking out about grad school and studying vocabulary.  It was mostly freaking out about grad school if I’m being honest... the fact that it’s almost the beginning of the school year, and I’m going to have to apply to grad schools in just a few months kind of hit me all of a sudden.  On the bright side, I had a good talk with my lab for about 20 minutes about what they had done to get into grad school, and where it was reasonable to apply, and how important the GRE was, and things like that.  Since it was Friday afternoon, no one really wanted to work, and they were all willing to answer my questions, which was nice.  So my tremulousness abated a little bit.

Saturday

ennui – a feeling of listlessness and dissatisfaction arising from a lack of occupation or excitement

Don’t worry, I brought this one on myself.  Saturday morning was spent doing some completely necessary grocery shopping.  And Saturday afternoon/evening was spent studying for the beast that is the GRE.  My friends and I sat down in a cubical in the Student Center for eight hours, doing practice tests and reviewing things we need to know for the exam.  At the end of eight hours, you’d think we’d be done studying.  But instead, we went home, grabbed some food, and continued studying, although perhaps not as diligently as we had been when we were in the Student Center (at least on my part).  Studying was pretty much suspended when I had a laughing fit... you know those moments when literally everything seems funny? That was a good hour or so on Saturday night.  My friends were mildly concerned for my wellbeing, since I nearly toppled over from laughter a couple of times.  I’m going to go ahead and say that I should maybe limit myself to studying for slightly less extended periods of time in the future, if only so that everyone can retain their sanity.

Sunday

noisome – having an extremely offensive smell; unpleasant, disagreeable

felicitous – well suited to the circumstances; pleasing and fortunate

Sunday was another two-word day, as it was again spent in activities with very different levels of enjoyment.  As you may have noticed, the two words have pretty opposite definitions... I did a lot of things on Sunday.  The first word, noisome, relates to the dreaded House Cleaning.  This time, rather than cleaning the first floor again, I got to clean the bathroom.  Yay.......  It wasn’t actually all that bad though.  I was expecting a lot worse to be honest, but most of it was just not thinking about what I was doing, and letting the disinfectant do its work.  Fairly painless, as far as jobs go.  Noisome still fits though, since the idea of cleaning the bathroom was certainly disagreeable. :P

The second word, felicitous, relates to the hour I spent skyping with my friends from home.  It was a little ridiculous, as my microphone decided not to communicate with the Google+ hangout we were trying to have.  Our solution was that I would call one of my friends, she would put me on speakerphone, and I would talk through that.  It worked, but I’ll need to figure out what’s wrong with my microphone at some point.  It’s not broken, since it registers sound (I just tested it with both Skype and my internal sound register thing) so it’s the way that it’s communicating with Google that’s an issue. 

Regardless, it was wonderful to talk to my friends, no matter how difficult it was to talk to them.  They’re doing ridiculously cool things with their lives, and I don’t see them nearly enough.  Hopefully that will change at some point in the future... I miss those crazy people. 

And now it’s 11:59, so I’m going to sign off... yay for new words! Next week will include the GRE, so that should be fun...

Until then!

Alycia