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.

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.

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.

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.

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!

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.

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.