Monday, December 31, 2012

さようなら (sayounara) 2012!

I used to be able to hold a very basic conversation in Japanese, as well as read a fair amount of it,  but now I'm reduced to looking up how to spell "goodbye" in romaji (roman letters). I was actually only a class or two away from being able to minor in Japanese at Eastern. Bah. I also took 3 or 4 years of French in high school and at least 1 full year of it in college. Can't remember much of that now, either. Maybe I'll try to re-learn some of that stuff in the coming year. I was always very good at quickly picking up foreign languages.

Although it's New Year's Eve, we're pretty much treating it like any other weekend night. I don't think we've ever procured a babysitter so we can go to NYE parties or anything - the last time we went to such a party was, I think, in 2002 when we were newly married. I'd probably feel more deprived if I hadn't spent the night at my friend Mary's house the other night. A few of us watched several episodes of Girls, we drank lots of wine and generally had a good time. When I woke up in the morning, however, I wasn't sure if I was still drunk or just really really hungover. After I managed to get stuck in the snow - for a good 30 minutes or so - trying to leave Mary's, I decided that I was just really hungover. If I had still been drunk, the whole stuck car ordeal probably would have been far more amusing than it was. Stupid German car with no snow tires. Grrr. Thankfully, Mary and a friend of her brother managed to push me free of the snow drift I was sort of wedged in. I thought that since I bought Elliot all new snow gear from L.L. Bean super early this year, we were sure to have a dry winter. I thought wrong.

As far as Phudland goes, I've survived the first six months in my chosen thesis lab. Yay! Now, I need to define the goals of my project, in consultation with the PI, in order to come up with a decent proposal over the course of the coming semester. One of the new students will be rotating in our lab starting in January. I think the PI mentioned that he will have her working on some aspect of the fish project, but no one knows exactly what just yet. I'm a little excited at the prospect of quasi-mentoring one of the first-years. For eight weeks, at least, I won't be the newbie and maybe I'll get to feel smart again, like I did when I taught at Eastern and Washtenaw. I can hope anyway.

In 2013, I hope to continue settling in and really start to think of Wayne State as my home away from home. I'm looking forward to going to the national ASM conference in Denver, as well as the Cold Spring Harbor conference in the coming year. I'm also going to try to incorporate more activity into my life and maybe get to the point where I can run a little bit - for exercise and not for my life, as in running from muggers in Detroit or bears up north. That might be nice. I'll have to get my bum knee looked at to make sure I don't injure it further (I have a probable torn meniscus), but it'll be okay. Everything will work out the way it's supposed to. More patience, less twitchy-ness, good health, safety, and happiness; those are a few of my major hopes for 2013 and beyond. I wish the same for everyone reading this, and even those who don't. Be safe and have a Happy New Year!!

Friday, December 28, 2012

The worst is finally over!

Christmas is done, bitches! And I couldn't be happier. Ok, I could always stand to be happier, but whatever. I really dislike the stresses of shopping and increased social interaction that come with the holidays. This year, I just couldn't make myself do any shopping until nearly the last minute - after the last "guaranteed delivery for Christmas" shipping deadline for any online retailer had passed. I finally decided to start, yes - start - my Christmas shopping at about 6:00 pm on the 23rd. I took with me a short list of stuff to get, a box of Kleenex (and I'm still sick, even now. This is fucking ridiculous.), hand sanitizer, and I stuffed my driver's license and credit card into my back pocket. I hate wrangling a purse - plus it makes me more of a target for thieves and other ruffians. I think I've actually thwarted one would-be purse snatcher at Meijer by not carrying a purse to be snatched, but I digress...

I started at The Rocket in Ypsi and worked my way over to Target in Canton, then I took a break for dinner around 8:00. Around 9:30 or 10:00, I went to the Westland Mall to check out Kohl's and Macy's, which both totally sucked. I tell you, Macy's is certainly no Hudson's or even Marshall Fields. After the mall, I went to the Toys R Us across Wayne Rd., which is where I probably spent most of my shopping gusto. I love, love, love that Toys R Us is open 24 hrs during the several days preceding Christmas, only finally closing at 10:00 pm on Christmas Eve. I really enjoy shopping late at night, a time when mostly only frantic dads are doing their shopping. Fewer whiny kids with their bitchy overworked mothers. I like it. Anyhow, the moral of the story is that I finished my shopping and was home by 2:00 am. Boom. Done.

Traditionally, we spend Christmas Eve with Chris's dad's side of the family; then on Christmas Day, we open presents at our house before heading off to Chris's mom's house for dinner and gifts. Finally, we go to my mom's house and visit with her and my brother before calling it a very looong day and going back home. I won't bore you with details, but here is a very short pictorial chronology of Christmas celebrations.
My very first Christmas Eve with the Visels. My (then) future father-in-law took this picture of me. I was 16 - note the pink hair.
Elliot at my mom's late on Christmas Day this year. This may have been the last smile we got out of him that night before the "tired tantrums" set in.

There was a very cute picture of Chris at his mom's in a paper crown holding up a Lego set he just built, but he forbade me from posting it online. Although I'm not happy about it, I suppose that I should abide by his wishes. Such is life.

There is nothing worth watching on TV right now. Perhaps I will pop in the first DVD from my Golden Girls box set that Chris gave me for Christmas. If that gift isn't a sign of a man's true love, then I don't know what is.

Thursday, December 20, 2012

Ms. Crabbypants

Cranky is not really the emotional state I expected to be in after the big department holiday party, but cranky/grumpy/pissy/grouchy, etc. is what I most certainly am right now. I'm guessing there are actually several reasons for this, now that I'm sitting and thinking about the day. A caveat - my reasons are likely not great reasons, but they are mine nonetheless.

I am an introvert and social situations/people in general really stress me out. Unfortunately for me, I am half of the social committee and was responsible for putting this holiday party together. This included food (was up until 2:00 am making the cookies I had stupidly promised to make), drinks, decorations, and all the time-consuming minutiae that goes along with that - standing in line at Meijer longer than it took me to shop, loading the car, unloading the car, hoping I didn't get ticketed, towed - or worse - while parked in front of a "Fire Lane - No Parking or Standing" sign. To be fair, I was the last and least obtrusive of 7 or 8 vehicles that were clogging this fire lane.

Once the party got underway and I got a hold of some social lubricant, the day was mostly enjoyable. Oddly though, as the last handful of us wrapped things up and started leaving to go home, I neither felt happy that I'd had a good time, nor was I even relieved to finally be alone with my thoughts again. I simply felt empty and unconnected to anyone or anything. All I could think was that there really is nothing new under the sun. This is the way my life is going to be until I die - a parade of new faces that come into my life and that I become very fond of and attached to, until it's time to leave and I have to tear myself away to go start the painful process over again somewhere else. Over and over again ad infinitum. And this is the way it's supposed to be, so I'm told. I don't like it.

So that was a vague and rambling diatribe. The seed for it was planted earlier today when an even more cantankerous friend of mine advised me to be careful what I write in my blog posts, lest it come back to bite me in the ass later on. I'm accustomed to being told what to do by this person, who I know only has my best interests at heart, but for some reason today the message really grated on me. Aside from that, there were stupid little things that didn't work out the way I had hoped today. I really wanted to talk science with my PI for a bit, but he had to leave earlier than I expected. I stupidly texted him while I was on my second or third gin/juice/pop concoction, asking if he'd be around tomorrow to discuss my project. No typical "drunk" texting - just science. Now I'm thinking that I'd really rather sleep in and stay home during the day tomorrow, especially if we are supposed to be getting snow. Driving to and from Detroit is enough of a challenge with the usual crazies zooming, drifting, and swerving all around me - I don't feel the need to up the ante with some weather event.

I thought there were more reasons for my shitty mood than what I've just outlined and maybe there are. It could simply be that I'm cranky because I'm old. And old people get tired and cranky late in the day. That must be it. I hope this blog post doesn't come back to bite me in the ass someday, but it probably will, and likely sooner than I think it should.

Wednesday, December 19, 2012

Holiday lab madness

Today my PI is treating our lab to lunch at The London Chop House somewhere in downtown Detroit. Apparently, it's a yearly lab tradition to go somewhere kind of fancy for lunch before Christmas. I'm not sure how long we'll be out - lunches here tend to run really really long. As in 2-5 hours long. Should be fun once I toss back a drink or two.

Tomorrow is the annual department holiday party. Since I am head of the social committee (I'm really only a puppet for the more socially-minded grad students), I am at least partly responsible for pulling this thing off. Ha! Essentially, people tell me what to do and I (eventually) go do it. We are getting pulled pork and chicken from Slow's BBQ, as well as their macaroni and cheese. The most controversial part of the party plan this year is that we are hiring a bartender. The deal is that unless we hire a bartender ($125 flat fee, 4 hour minimum), our department can be fined $4000 for unauthorized alcohol consumption. The problem with the bartender is that everyone has to supply the alcohol they want served AND each person gets only 2 drink tickets before being cut off. So that means if I bring in a six-pack of beer, this douchebag bartender will only let me have two of my own beers. WTF??! Excessive regulation tends to drive people underground, so in the spirit of fighting unjust oppression my lab mates are planning to hoard liquor in the lab and run our own speakeasy (at the opposite end of the corridor from the party). Bartender or no, there will be drunk grad students. Anyway, I said that I would make cookies (that was a dumb move) and pick up some other supplies, so I have to go to the store after lunch today.

We are also having a white elephant gift exchange, which should be fun. I have a box of rejected Christmas gifts in the basement (any gift that we haven't so much as looked at in at least the last year or longer) that I can choose from. I think I'm going to go with a giant mace gun I got for Christmas last year. When I say gun, I'm not kidding. This thing looks like a starter pistol (it's all black and doesn't say "mace" or anything on the grip, unlike the picture in the link) and it comes with a giant cartridge of mace. Working in Detroit, it sounds potentially useful. However, where the fuck am I going to keep a starter pistol full of mace and still be able to get to it if I need to use it?? Although now that I see how much the damn thing cost, maybe I'll hang on to it. It just looks ridiculous and thus perfect for a white elephant gift exchange.

Ugh. I still have two hours until lunch. I guess I should start catching up my lab notebook. I know that I've threatened to do this before, but I mean it for real this time. I think I've located all of my note scraps and put them in relative order. That's huge. Now let's hope that it all makes some kind of sense when I write everything down where it was supposed to go in the first place.

Monday, December 17, 2012

Recovery and stuff

Nursing a man cold is hard work. It's also extremely boring. I've spent pretty much the entire weekend in bed, with occasional breaks to strap on my feed bag. Never one to settle for mediocrity, I likely took the adage "starve a fever, feed a cold" way too far. Today I felt well enough to get dressed at least. Unfortunately though, I missed Elliot's field trip. His class was going to the Discovery Center in Garden City to conduct a "CSI"-type investigation. When he got home, Elliot told me that it was kind of like Law & Order: Criminal Intent. Hmm. I didn't catch what part of the field trip he was referring to, but I think maybe I should limit his exposure to the police procedural shows.

I think I'll be well enough to go to school tomorrow, but I am really not looking forward to going. I have an IMSD (Initiative for Maximizing Student Development) meeting tomorrow morning at 8:00 am, which is essentially an hour and a half of listening to other students present their research. I need to leave the house between 7:00 and 7:15 to make sure I get there on time, which means that I need to set my alarm for 5:30 and out of bed no later than 6:00. Waaaahhh!! Once I get there, I expect to receive a dressing down for not having registered for the obligatory 10 credits already. I'm supposed to do this 6-8 weeks before the start of the semester, but I always put it off. Then my PI was in Japan for two weeks, and yada, yada, yada...

I need to sit down with my PI and talk about defining the boundaries of my project. One of the classes I have to sign up for is basically the same thing as Proposal Development at Eastern. During the course, I am supposed to write up my actual research project proposal. In June or July of 2013, I am supposed to defend my proposal to the committee I will have chosen. If my proposal is accepted by my committee, then I'll be promoted to doctoral candidate from doctoral student. This promotion is supposed to come with a $1000/year raise. That comes out to roughly $35 a paycheck. I guess that will pay for my parking permit, so I shouldn't complain.

The rest of this week is going to be busy and I don't expect to get much, if any, actual lab work done. I'll write more on that tomorrow or Wednesday, but right now the boys have just come back from the store and my concentration is shot.

Sunday, December 16, 2012

Man Colds

I think I have come down with my first official man cold. A man cold is just a regular cold with a lot of unnecessary whining, complaining, and languishing. I can't breathe through my nose, but mouth breathing makes the phlegm rattle in my chest. Sleeping is a thing of the past and I wish I could die and be reanimated when this cold is done with. I don't have the energy to keep typing, so here's a picture of the demon cat under our new Christmas tree.

Tuesday, December 11, 2012

I should have known...

I should have known by the way the other grad students chuckled when they volunteered to help me load returnables into my car that the job was gonna suck big sweaty donkey balls. Let me back up a little. Our department is having its holiday party next Thursday, and tradition dictates that the new second year student (just me, in this case) is responsible for returning a year's worth of bottles and cans in order to have extra money for food and whatever. My initial thought was to just give the bags of returnables to a bum (never in short supply in Detroit) and give the secretary a wad of cash that I thought would cover the money I would've gotten had I done it the right way. A hot wave of lapsed Catholic guilt washed over me and pushed that really good idea out of my head in favor of actually taking the goddamned bottles to the store like a good girl. First of all, the returnables hardly all fit in my car. My trunk was full, as was the back seat. I just hoped to God that they didn't leak before I got to Meijers. More problems: a full grocery cart only half-emptied my car and I apparently hadn't noticed that the bottle return had been moved from the back of the store to its own separate entrance in the front facade several years prior (runonsentence,anyone??). Chris always takes the mountains of our empty beer bottles back, so I don't even remember the last time I got within 20 feet of a bottle return machine. I think I'll go thank him profusely for taking that one for the team as soon as I'm done with my rant here.

Anyway, after I'd finished storming through the whole store muttering about how upper management must think it's damn funny to hide the fucking bottle return - I had to call Chris to ask where the hell it was - I quickly figured out the reason for the earlier chuckling. Mold. If you've known me for more than 30 seconds, you'll know that my two biggest phobias are mold and parasitic worms - not necessarily in that order (the order tends to flip-flop from day to day). I could (barely) deal with the relatively light coating of mold on the cans in the two single-ply bags. I did have to work really hard to hide the look of horror on my face as I gingerly picked up each disgusting can and tried to throw it into the machine. The machine actually told me to stop throwing cans into it! What?!?! I almost punched it at that point because it just seemed like it was trying to mock me. Then I got to the last bag in my cart. Inside, I found year-old multicolored, dry, sometimes fluffy, and now airborne, mold inside nasty fermenty beer cans, and on the outside of the cans. On the potato chips someone had dumped in, thinking it was trash, as well as in the styrofoam coffee cup. I should have known something wasn't right from the way this bunch of returnables was quad-fucking-ruple bagged!! I almost thought I was trying to rip through a set of Russian nesting dolls. Okay, I thought to myself - this is far beyond my mold-tolerance capacity. I must have stood there for a good two or three minutes deciding what I should do with this bag full of nasty because I was damn sure not touching anything in it. I ultimately decided that I would grudgingly load the bag back in my car (there were no dumpsters around), drive it home, and put it in the trash toter. Sorry Mother Earth, but I think the thick coating of filamentous saprophytes will have to do the recycling here because it ain't gonna be me. I decided that the biohazardous waste I disposed of was worth about $10, which I gladly took from my wallet and put in the envelope with the money from the things I could actually stomach returning. Shhhhh!! No one (except for you, lucky readers) has to know about this little indiscretion. That is, until the holiday party when I will inevitably get wasted and want to tell a funny story. Ugh.

Sunday, December 9, 2012

Back Again

Hey, what do you know? I'm not dead! I know I haven't written in a very long time. I guess I felt kind of burned out on all the introspection I had to do in order to write. I just didn't want to think about anything substantive and I got wrapped up in doing mundane lab stuff. I've discovered that I really enjoy stuffing pipette tip boxes. It's monotonous, I don't have to engage my brain at all, and I manage to get something accomplished for the lab. It's win-win for everyone. Two things I really don't care for, however, are taking care of the biohazard waste and filling the water carboys. Biohazardous waste is gross, the bag is heavy, and it usually leaks so it really isn't a surprise that I don't like it. Because the fancy Milli-Q water machine is in the fish lab (one floor up from me), we have to schlepp the carboys upstairs, fill them, then try to get them back downstairs somehow. The first time, I used a cart. That took too long because I had to call the elevator and wait. The second time, I carried the full 50 pound carboys downstairs, hoping that my messed-up knee wouldn't give out and I wouldn't fall down the stairs and die. Fortunately, I didn't fall down and die, but my arms and hands felt like spaghetti for quite a while and were sore through the following day. 

I don't know what to say about my research or how to say it so that it makes sense to anyone, including myself. I need some time to think about what the hell I'm doing before I commit anything to "paper" (blog post). My PI said that we need to sit down and clarify the bounds of my project, but he's in Japan until next week, so...I need to figure out what I should do this week. One thing I'm doing that I'm really excited about is learning how to do histology on zebrafish. That includes all of the fixing, embedding, slicing, staining, and imaging. I asked the tech in the fish lab to show me how to do it. I think tomorrow I learn how to slice the fish I fixed last week into sections. I really like the fact that I get to do stuff that goes beyond culturing bacteria and doing molecular genetics. I feel like I'm learning some valuable skills that will make me a more well-rounded scientist. And a more marketable one to boot.

One thing writing apparently does NOT do is deter Chris from trying to talk to me about Christmas gifts for my mom and my brother. I don't want to think about Christmas and I wish it would just go away. I am ready to just buy a Festivus pole and get ready for the Airing of Grievances and Feats of Strength. Ugh. I go through this every year and I wish I didn't have to. I wish I was happy and easy-going like other people seem to be. But I'm not. I suppose that the grass always seems greener on the other side of the fence - until you jump the fence and see that the grass there is just as brown as your own.

I've had enough and I suspect that you have too. Here's an idea for you to ponder. If there's something that you want me to write about, tell me. The topic could be anything, but even I'm up for a challenge now and again.

Monday, July 16, 2012

Effing up

I knew that in the course of attempting to do some actual science I would fuck something up. Once again, ladies and gentlemen, Kristie does not disappoint. First mistake I made was to forget just how weird cholera bacteria are. They live in the environment, which is normally quite a bit cooler than body temperature (except for the last week or two), so you'd think that you could toss a Vibrio culture in the fridge and everything should be just fine. Not so. Vibrio cholerae is not only a genomic hoarder, with two chromosomes, but it's more thermopersnickety than a woman with a malfunctioning thyroid gland- it really doesn't like to be cold. So, I grew overnight Vibrio cultures for my fish infections last week and, not thinking, took them out of the incubator and popped them in the fridge while I finished up some other stuff and went to lunch. They were in the fridge for two hours at the most. When I got back, I took them out of the fridge and was spotted doing so by two of my fellow cholera cult (lab) mates:

"That wasn't Vibrio you just pulled out of the fridge, was it?"
"Uh...yeah." Uh oh...
"You know you might have just killed your cultures, right? Vibrio dies if you put it in the fridge."
Shit! "Oh, right. I totally forgot. Well, I guess we'll see if two hours is enough to kill them!"

Even though I  felt like a complete moron, I did still have the presence of mind to plate a couple of dilutions of each of my cultures, just to make sure I really didn't kill them. When I infected my fish later that day, I had no idea if I was adding live cholera or just polluting their water with dead useless cells. Dumb, dumb, dumb. At the very least, I figured out how to set up the fish infections on my own - which tank to take fish from, to make sure that they hadn't been fed first, which water/beakers to put them in, how to mix up the tricaine solution to euthanize the fish, etc. Plus all the other stupid little details that get forgotten by people who've been doing this stuff for a while - like where they keep the ethanol, how do I clean up the fish shit when I'm done, where the dissecting kits's getting a little bit easier every day. Oh, and it turns out that I hadn't killed my cholera after all! Sometimes I think a lot of research is figuring out just how much you can fuck things up without ruining the entire experiment. That sounds smart-ass-ish, but I think it's absolutely true. You need to know how much wiggle room you have in your protocols - then you try to figure out why, which sometimes leads you to new side projects. It has been strongly and repeatedly suggested to me (by a favorite cantankerous former professor of mine) that a good student should be working on at least three projects simultaneously (at the time of my scolding, I think I was only juggling two things. And rather lamely, at that).

Tomorrow, I'm going to attempt my first ELISA assay (ever!), looking for cholera toxin in last week's fish water. If it doesn't work, then there's a good possibility I fucked up precipitating protein from the fish water. I really have no idea what the hell I'm doing! I'm also still stuck in cloning hell, but so is everyone else in the lab. We think that the UV transilluminator is frying all of the DNA we try to gel purify - even though I limit the gel exposure to 15 seconds or less, plus we add guanosine to the gel to act as "sunscreen". We're supposed to be getting a blue LED transilluminator soon, I think. Maybe that will help.

I still need to get some work done tonight, but to hold you over until my next post, here are some crappy iPad pictures of the lab.

The fabulous view from my desk.

My bench, replete with impressive-looking bottles of stuff I made, new pipettors, a brand new ear-piercingly loud timer, and ice! Woot!

Thursday, July 12, 2012

How many new posts constitutes a habit?

I'm trying to get back in the blogging saddle and write more frequently, since my hellish first year is all but over. I won't promise to write every single day - a minimum of twice a week sounds more reasonable. Writing is still cathartic for me, even though I am finally getting a healthy daily dose of social interaction with the other grad students. I'm starting to feel less awkward and clueless all the time, but I still think that I cling to my seat a little too much because I'm afraid of my lab mates being aware of my presence. That thought/sentence hardly makes any sense, but I can't really clarify it. I guess the social phobia is still hanging on for dear life, despite my shrink throwing some Lexapro at me two months before turning me over to yet another new resident. That reminds me - I need to set up a fucking appointment with the newbie shrink before my Adderall runs out. I don't like having to be seen at all, but I have to play by health insurance rules if I want to remain somewhat functional. The initial appointment is the worst. All I want to have to say is, "I'm depressed, afraid of people, and I can't fucking concentrate. Give me some good drugs and I'll get out of your hair". Instead, they ask me to rehash my entire psychiatric history, even though I can see that they've already printed out the relevant information from my online chart. Blah.

I was gonna write about what I did in lab today, but now I'm too tired and cranky. I guess I lied when I said this was still cathartic. Better luck tomorrow, maybe. On Friday the 13th, no less.

Wednesday, July 11, 2012

And we're off to the races

I'm firmly establishing my own well-worn ass-groove in the leather chair that goes with my desk in the cholera lab. One thing that annoys me about my desk set-up is that the chair is fairly wide and it has armrests. The armrests are so wide that every time I scoot in toward my desk, one armrest or the other hits the side of the desk. Every. Single. Time. I've got half a mind to take a damn screwdriver to school and remove the fucking armrests. If it's annoying me now, imagine how I'll feel after five years of it. Maybe I'll wait until the PI has agreed to accept me as a full-time lab member and gives me a key to the lab before I start disassembling his furniture. Since I didn't put in as many hours during my rotation as I should have (to avoid failing my classes, not making it to prelims, and subsequently being kicked out of the program), the PI is letting me work in the lab over the summer on a "trial basis" to make sure that I will actually show up to work and generate some decent data. So I'm technically not a full member of the lab. However, I have no intention of being kicked out, asked to leave, or whatever. In my mind, I'm a permanent lab member - it's just not official yet. Unfortunately, I'm reminded of my provisional status whenever the PI sends an email to the lab, but only carbon copies me on it. I don't really understand why that arbitrary distinction has to be made in stupid two-sentence emails stating that we're having lab meeting this week at 2:00 pm - like we do just about every week. That bothers me. Alright, that's enough of the complaint department - I'm starting to feel really pissed off about my stupid provisional status, which will get me nowhere fast.

I had a good productive day in the lab today. It almost felt like it did when I worked in Jim's lab at Eastern, when the science determined what time I went home for the day- not sheer boredom. My PI is off this week, so I don't have to worry about him keeping a surreptitious eye on me. Yay! I feel like I made a butt load of media, but I don't think I actually did. Let's see, I made a liter of 5X M9 salts, 100 ml of 10X PBS, a couple of 90 ml dilution blanks, 100 ml of 20% (w/v) glucose, 100 ml of 1M MgSO4, and finally a liter of complete M9 minimal medium. The shelves atop my bench are becoming beautifully lined with bottles of stuff. Most of the bottles are identical, each containing exactly 100 ml of whatever potion I whipped up - just like everyone else's benchtop shelves. I'm telling you - I really feel like I've joined a cult. Thankfully, no one is sporting any forehead swastika tattoos and wild eyes or wearing all black outfits with gleaming new white Nike shoes.  All the perfectly filled and arranged bottles make me feel like I'm doing real science. M9 is a royal pain in the ass. I think that alone took up half my day - just autoclaving and cooling to room temperature. Fucking ridiculous. But, I had to make it because that's what I'm growing my WT cholera and ToxT deletion mutant cholera in overnight for tomorrow's zebrafish infections. I'm just trying out a very basic experiment to see if it works and to see how long the whole ordeal takes. I'll have two groups of four fish each in separate beakers of 200 ml sterile saltwater. I'm going to add my overnight cultures: WT (cholera toxin-producing) to group 1 and ToxT mutant (no cholera toxin production) to group 2 and incubate the fish at 28 degrees for 24 hours. Then, I'll euthanize the fish and collect the beaker water. The plan is to concentrate whatever protein is in the 200 ml of fish water by trichloroacetic acid precipitation - which I've never done before, so will probably screw it up. The multitude of proteins precipitated from the fish water will be used in a cholera toxin ELISA, which I will also likely screw up in some way. The idea is to see if cholera toxin is present in the fish water. In previous experiments, when naive fish were placed into water conditioned by other cholera-infected fish, the naive fish died. It was assumed that the naive fish were killed by cholera toxin that had been secreted into the water, but no assays were done to confirm this.

Oh, shit. It's almost 12:30 and I haven't had my nightly Ben and Jerry's Coffee Toffee Heath Bar Crunch ice cream gorge session yet. And I haven't finished the paper I'm supposed to read for my virology discussion tomorrow during lunch. And I'm still Jonesing for more of my second read of "Fifty Shades Darker" before I fall asleep. I just love trashy sex and romance novels (with a smattering of BDSM thrown in, as the case may be) - I am certainly NOT a fine literature critic, but I like what I like and, embarrassing as it may be, that's good enough for me. And Chris :)

Monday, July 9, 2012

I'm supposed to do what now?

I've been working in the cholera lab since the end of June now. When the PI said that he expects me to be independent, he wasn't fucking around! My research project is centered around developing a zebrafish model of cholera colonization and infection, so I'm continuing the failed cloning that I feebly worked on during my rotation. Also, now that I've passed prelims and thus should know what I'm doing (ha!), I've been charged with developing a protocol to test for the presence of cholera toxin in water that held cholera-infected zebrafish. The PI didn't tell me what strains to use (and what medium to grow them in) to infect the fish, if I should use log phase or overnight cultures, if I should do a time course, or anything. It's been surprisingly stressful trying to come up with a reasonable experimental plan. I'm sure the point of the "sink or swim" approach is that you learn better what not to do by falling on your face a few times, but this is pretty brutal for me at the moment. However, I don't have to run any ideas by him before I try something new, unless I need really expensive equipment or reagents (I don't even know what dollar amount he considers "really expensive"), so at least that's kinda nice.

 I have to rely pretty heavily on the other grad students in my lab - as well as the grad student, PI, and tech in the fish lab upstairs - for help. I hate being dependent on other people for anything. I'd rather kill myself trying to do something independently than to make my life easier by asking for help. I'm working on getting over this. Slowly. It's really strange working in a lab with other people. It almost feels like I've joined a cult. Seriously. Everyone shares all the reagents (down to the same tubes of Taq and homemade PCR buffer), and whoever uses the last of something has to make more. Sharing tubes of reagents is a little weird (why not just give everyone their own aliquots?), but replacing what you use up is not weird - I don't want to make it seem like I think it is. That is a very good thing! Everyone is assigned a certain chore like making bottles of autoclaved water, LB, autoclaving tubes, etc. The one group activity is stuffing tip boxes - which really sounded cult-like to me. I just picture us all standing at a bench in a row, stuffing tip boxes like synchronized automatons. Makes me shudder a little. As strange as all of this is to me, everyone has made it clear that I can do things the way I want to - if I want my own aliquots of PCR buffer, I can do that. But, I don't want to break away from the way the rest of the lab does things - at least not this early on. Everyone has been very accommodating and helpful though.

I apologize for such a boring blog post - I'm even boring myself right now. Hopefully I'll be back to my normal smart-mouthed self before long and I promise that I will write accordingly.

Wednesday, June 13, 2012

Prelims: conquered. Now what?

Everything should be downhill from this point. And I mean downhill as in coasting, not the crash and burn or decrepit old git kind of way. I passed all three of my prelims - bacteriology, immunology, and virology. I'm honestly shocked that I passed all three. I was pretty sure that I'd have to retake the immunology prelim, but I guess my committee members decided that they had better things to do in August than to roast me over the coals again. I am so relieved and happy that I don't have to worry about prelims anymore. I've been officially vetted and shouldn't feel the need to keep proving myself to everyone ad infinitum. The operative word there is "shouldn't", because I probably will anyway.

This afternoon, Chris, Elliot, and I went to the Immuno & Micro department picnic held on Belle Isle. Poor Elliot was the only kid, so I guess I should be grateful that he only drove me a little nuts. Chris got to put names with faces and I got congratulated by faculty and other grad students on passing prelims. I got roped into playing volleyball (!), something I haven't done since 8th grade gym class. I even managed to hit the ball a couple of times, so I considered that a total success and quit before I could fuck up my sterling record. I also managed to get a splinter in my foot and a nice sunburn on my chest and arms. That's a first for me - the sunburn, that is. We didn't get lost getting there or coming back; it was a pretty good time.

I've chosen to do my dissertation research in the cholera lab, but the only catch is that the whole lab is going to the national ASM conference in San Francisco next week. I guess I get to relax a little bit longer and catch up on vibrio literature. My actual start date is tentatively June 25. I'm kind of excited. We'll see how long this lasts...

Monday, May 7, 2012

Coming up for air

It's been two months since I last wrote anything that I actually wanted to write. I slightly modified the blog description and added a cutesy old picture of me at Lake Huron. I'm being a bit cheeky in declaring that I'm a 2nd year already, as I still have to pass prelims, but I'm trying on optimism for once just to see how it feels. I've been mired in papers, papers, and still one more paper (extra credit for Neuro - due Friday) - mostly trying to appease Dr. Dick. My prelims are the first week in June: Bacteriology on the 4th, Immunology on the 6th, and Virology on the 8th. Each is a one-hour oral exam, so I have to sit in the department library trying to field questions lobbed at me from three committee members (a different set of three faculty for each oral exam). Unfortunately, Dr. Dick is one of these committee members. I'm not sure how to study for this, while not neglecting my classes or research. I will have to figure this out - and soon. I'm a little afraid my efforts to study will look something like this:
Cock blocked (or should it be pussy blocked??)

Much has happened since I wrote last - I had a birthday in March (meh), my 10th wedding anniversary (and 20th (!!) dating anniversary) in April, and went to lunch at Mercury Burger Bar with the other grad students last month as well. This place is literally in the shadow of the old Michigan Central Depot in Corktown. MCD is really quite an eerie, imposing, yet hauntingly beautiful sight - the picture doesn't do it justice:
Mercury Burger Bar and Michigan Central Depot
Oddly enough, we went to lunch here two days after some kid climbed into an open window on the first floor and fell straight down 30 or 40 feet to the basement. Having seen it in person, I can absolutely see why it attracts "urban explorers". The place is so massive and it was so opulent in its heyday; my dad was around two years old when it opened in 1913. I really can't help but imagine a time when Detroit was young and held so much promise; this area would've been humming with the activity of so many people passing through this train depot - to visit family and see the big city, or maybe to go off to war.
Anyway, about Mercury Bar: they have good burgers, a very busy lunch hour (and correspondingly slow service), and the best garlic french fries I have ever had. I have dreamt about these fries, they were so good.
Enough for now. More in less than two months. Maybe.

Tuesday, March 6, 2012

Not dead...yet

The final rotational frontier.

It's been a while since I last posted anything and, as usual, I feel guilty about this (I knew those years of Catholic school would come in handy someday!). I just finished my rotation in the virology lab. I really learned a lot in the last few weeks: how to run SDS-PAGE, how to do a Western blot, how to do co-immunoprecipitation, beta galactosidase assays, luciferase assays...and how to screw up most of the aforementioned items. I met Henrietta Lacks for the first time last Wednesday. It was a little eerie thinking about the history of her cells as I transfected construct after construct into them. I only made her acquaintance for a short time though - on Friday I told HeLa goodbye and thank you. It was a slightly religious experience for me.

Onwards and upwards! I technically started my third and final rotation in the cholera lab yesterday, although I didn't do anything then. Or today either. In fact, I'm not entirely sure what I should be doing in the immediate future. Something about cloning GFP into something and then getting it into zebrafish?? I will be working on developing a zebrafish model of colonization/disease. This is a newish (funded!) project, which actually sounds pretty exciting. I'm fairly sure that I'll be working with the tech in my first rotation lab to figure out the best way to get the cholera bugs into the zebrafish. The GFP construct is to make it easier to track the specific location of the bacteria within the gut of the fish. I think. We'll see how this goes.

In other news, I did reasonably well on my first immunology and virology tests, and I'm trying to get caught up with reading and writing for bacterial pathogenesis. I have to present a journal club-type paper to the department at the end of the month and prelims are looming large in the not-so-distant future (first week of June). The thought of prelims really terrifies me. Especially the thought of Dr. Dick lobbing questions about secretion systems and quorum sensing - assignment #2 - at me. I'm not getting paid nearly enough for the kind of anxiety I'm experiencing. That's no joke - I think UM and MSU students get several thousand dollars more per year than I do. I feel like I should get a bonus for managing not to get mugged, carjacked, or shot at in Detroit. That should seriously count for something.

Tuesday, February 14, 2012

Death of a car & rebirth of a car payment

How sad is it that I feel guilty for not having had time to write anything in several weeks? I'm just piling that on top of my landfill of anxiety - you know, because landfills are tall and full of garbage.

On Thursday, January 26th, my 12-year-old Piece of Shit (POS) car died and left me stranded on I-94, making me late getting to the bar (obviously, the last straw for me). Chris and Elliot had to come rescue me and if I'd had a baseball bat handy, I totally would've gone Office Space on it before leaving it at the side of the road. It was the second time in two days it had left me stranded because it overheated for no obvious (translation: inexpensive) reason. We came back to get the car on Friday, hoping that I could get it home without having to have it towed. We didn't have to have it towed, but it took two days for me to get it back home. Saturday morning, I parked it in front of the house in the spot where our old VWs apparently go to die and then we drove to Perrysburg, OH to look at a used car. I drove back that night, in hock up to my eyeballs, in this:

Stock photo from the internet because I'm lame and didn't take proper pictures.

Isn't it just like me to only take a picture of the ass-end of my new car?! Still pretty awesome though!

I bought a 2007 VW GTI Fahrenheit with less than 25K miles on it! It's beauteous. I think it sends one of two possible messages: I've hit my midlife crisis early or I'm clearly not having more children. Or both. The funny thing is that I bought it from the same dealer I bought my 2000 Jetta from, brand new. VW only made 1200 Fahrenheit edition GTIs in the US and 150 in Canada, and they are all numbered (there's even a registry). As you can see, it's BRIGHT orange. It's an automatic, but it has a Direct-Shift Gearbox (DSG) with paddle shifters. Essentially, it has a dual clutch that allows for almost seamless automatic shifting as well as "manual shifting" using up/downshift paddles located on the steering wheel. I've only tried the manual mode once in an empty parking lot, as I'm a little afraid that I will break my new car. It's fast and even the exhaust burble is sweet. The downside to having a fast orange car is that it's ORANGE!!!! I've been driving it like a grandma because I'm afraid of getting pulled over. I've only ever been pulled over once and I've never had a ticket, and I don't want to start with all that now. Aside from salt trucks and road patching crews, I'm pretty much the only bright orange vehicle on the road. If the registry is reasonably accurate (I haven't updated it yet), my #722 is joining only 8 other Fahrenheits in Michigan. As far as I can tell, mine is the only one in Metro Detroit/SE Michigan, so if you see one driving around or cutting you off in traffic, it's probably me. Sorry in advance.

Tuesday, January 24, 2012

State of the confusion

The title of this post is supposed to be a play on "State of the Union", which I guess is tonight. Not a very good play on words if I have to explain it though. Yeah...

A picture is worth a thousand words, and I think this one is a fairly accurate representation of my current state. Click on the picture to make it bigger. Until next time, folks.

Saturday, January 21, 2012

Sunshine, rainbows, puppies, and snot

I'm sick. And it's my own fault, too. My first assignment for Bacterial Pathogenesis was due on Wednesday, so as I am prone to do, I started working on it Tuesday afternoon, even though I'd been given a full week to work on it. Naturally, I quickly realized that the assignment was harder and taking longer than I had anticipated. I wound up working on the stupid thing all Tuesday afternoon straight through to Wednesday at 4:30 am. I still wasn't finished and I had class early, so I took a nap and got back up at 6:00 am. Ultimately, I didn't get it done until Thursday night. Just those two days of stress and no sleep was enough for me to come down with a cold on Friday. I literally spent most of the day today in bed, miserable. I feel a little better now, but I have a splitting headache that even 800 mg of Advil won't get rid of.

Aside from all that, things are really good.  Every month, the grad students and a couple of faculty try to get together and go somewhere for lunch. Last Friday, I went with them to a hole-in-the-wall bar called Northern Lights in the New Center area. I had a great time, but I learned that on the Fridays that everyone goes to lunch, no one really plans to come back to work. I kinda figured this out after the third round of Stroh's had been ordered for everyone at the table (there were four rounds altogether). Before we left for the bar, I told Dr. R, the PI of my rotation lab, that I was going to lunch with the grad students and that I'd be back probably in a couple of hours. I was inducing protein expression in E. coli, and it had to grow for another 2-3 hours, so I figured that I had plenty of time. Ha. I was at lunch for almost four hours!! I started wondering how I was going to finish my lab work, drunk. How was I going to explain why I was drunk?! It all turned out okay - the PI was cool, I spun down my cultures and froze the pellets for the weekend, and I later discovered that my protein was expressed, so it was all good. Next time, however, I will just plan to cut out early and go eat, drink, and be merry.

I had taken pictures of my rotation lab and of stuff I can see out the window with my piece of shit cell phone, but was unable to get the damn pictures off the phone. I'm gonna have to upgrade to something less stupid soon. Elliot still calls it an "idiot phone". Grrr. So, I retook the pictures with my iPad and took the liberty of annotating a couple of them.

The current rotation lab - a view from my desk.
There are actually two labs. The above picture is in the main lab, where Dr. R's office and my desk are. The other lab is halfway across the floor, and that is where his wife, S, does tissue culture. Yes, Dr. R works with his wife, who is a research scientist. I am the only student in the lab, so it makes for an interesting dynamic sometimes. They're both very attentive and helpful though. Yesterday or the day before, they both told me (independently, no less!) how happy they are with me and that I'm catching on quickly and experiments are working. It's amazing how much good a little ego stroking can do! I think just that alone nearly made up for all the fail that swirled around me throughout my first rotation.

A view to the north from the 7th floor of Scott Hall.
 I used to drive past Fisher Body 21 every day on one of the connectors to get from the Chrysler Service Drive to I-94. Seeing it out the window (in much better resolution than is shown here) is really kind of eerie and sad.

Looking northwest. The Fisher Building is about a block north of where the Northern Lights bar is. Brush St. is my new, less congested, less anxiety-provoking, more direct route to I-94. Clean living.
Well, that's enough for today. I keep meaning to describe what I'm doing in the lab in some detail, but just thinking about it exhausts me. Maybe later. Now off to watch Ghost Adventures. Those guys are the biggest drama queens - I love it!

Monday, January 16, 2012

Like night and day

Much to my surprise and delight (at least to the extent that I can be "delighted" about anything), this semester has been as good as last semester was bad. I'm really not sure what has made the difference. The master's student decided to switch to non-thesis, so he's no longer in the IM department. This means that I'm still alone in my classes - particularly in my Microbial Pathogenesis class, where I am the only student. Once a week, I meet the professor in his or her office for a two-hour lecture. There's no book and no exams, but I have weekly assignments to complete. This week, I have to describe (in detail) the process of type III secretion, the in vitro experiments I would use to demonstrate the presence of one, as well as the molecular methods I would employ to do so. I'm taking a break from sifting through decades of primary literature on secretion systems to write this blog post.

I am excited about my new lab rotation. Now that I think about it, maybe that's the difference that makes this semester better. Even Chris says that it's nice not to see me so depressed and threatening to quit school and get a job at McDonald's. I'm working in a virology lab, where the focus is on proteins involved in HIV replication in host cells. So far, in the three days I've been there, I've done a successful transformation, induced protein expression using IPTG (thank you, TargeTron!), seen how a Western blot is done, observed some cell culture work, and I even got my very own 293-T cells to take care of! The PI would like me to do some gel shifts to see if a protein, NKLAM, binds RNA. There are only 5 papers in the PubMed database on this particular protein, so if I get some results on the gel shifts, it could be publishable. SO AWESOME!!

I need to get back to work, but I just felt compelled to write something - especially since things are going well right now. Hopefully, I'll get a chance to write some more later this week.

Sunday, January 8, 2012

Back to the grind

On the eve of my second semester of PhD school, I'm feeling quite depressed. I don't want to go back. And to make matters worse, I think the master's student has dropped out. I'm not absolutely sure about this, but he isn't showing up on the class rosters I'm able to access. We were supposed to take the same classes this semester, but it looks as though I have to go it alone again. Literally. I'm the only student enrolled for one of my classes, which should make for two very awkward hours of instruction in the professor's office every week. My second rotation is supposed to start tomorrow as well, but I've heard not a peep from the PI who will be the boss of me for the next eight weeks. I thought about emailing him all day today, but decided that I was too depressed to do it. Now it's 11:00 at night and it might be too late to message him. Oh well. Depression wins again. I hope I start to feel better about things tomorrow; right now I'm just filled with dread and anxiety and I'm not sure how I'm going to get any sleep tonight.