Wednesday, May 18, 2011

A bit of an update and a new blog :)

It's been a long time since I did any blogging. Life's been pretty hectic in the last few months. I'll pick up where I left off.

I took my oral exam on November 9th, 2010 and I passed with no reservations. All of my classmates did well. It was definitely the most difficult thing I've ever done. Basically the 5 exam committee members ate me alive for 2 hours. But in the end, I "passed with flying colors" according to my chair. My P.I. (boss) told me it was one of the best exams he's ever been in. We had a little shindig in the lobby outside of our lab and I shot a champagne bottle cork into the ceiling, leaving a dent and initialing it, as is our lab custom when a student passes their orals. I am now no longer a Ph.D. student, I am a Ph.D. candidate!!

The rest of 2010 was pretty normal.

Flash forward until now, May 2011. Whoa boy. My experiments have been in a state of constant failure for the last 3 months, leaving me to question my abilities as a scientist. I'm simply trying to remove the chromosomal DNA from a few different strains of bacteria and use them in a method called polymerase chain reaction (PCR) which amplifies the DNA to high numbers. The basic premise is that you put the template DNA (DNA from the bacteria), DNA primers (that anneal to the template DNA), DNA polymerase (which synthesizes the new DNA), and the NTPs (the individual pieces of DNA that are being attached to the template strands). This, in theory, amplifies your DNA from 2 single strands to 2^40 single strands in about 3 hours. What I'm doing is using primers that recognize certain genes so that when I run a PCR with my bacterial DNA, only the DNA from those specific genes will be amplified. This allows me to see if the genes are present. Basically - if the gene is present, I'll see a band on a gel from my reaction. If there is no gene present, there won't be a reaction and I won't see a band. Make sense? Well for some reason, nothing is working. We think it's in my chromosomal prep. My problem is that the prep of the DNA is all done using a kit. It's supposed to be really straight forward. And it is. But it's not working for me and I don't know why. It's been a miserable few months. A lot of hanging my head; a lot of beating myself up. I can't move on with this project until it's done (if you want to know more about the specifics of my project, ask me - it's too complicated and long for this summary blog).

On a related note - I am moving to Iowa City, Iowa. My boss, after a lot of drama and stupid nonsense with the University of Minnesota, took a job as the Department Head of Microbiology at the University of Iowa. He's moving there in July and I am going with him. On one hand, it's great because the micro program at Iowa is amazing, this new job for him is incredible, I'll be the senior person in the lab, we get new lab space and I get to see a new place. The bad thing is that there are no jobs in Iowa for my fiancee so she's moving to Austin, TX to teach at a Montessori school. So after 3 years of living together, 7 years as a couple, we're going to have to do long distance. We've done it before, but never this far. I'm set to be in Iowa for 2 more years... We're doing well as far as being engaged goes, and I love her. I just don't want to have to live apart from her now. Totally lame. On another bright note, however, I get to leave a lot of the stupid drama here with some people behind and move forward with my life and hers.

On to some happy things. I finally finished my project pump marker. I ended up getting a gift card for $225 at a paintball tournament and I used it to purchase a karnivor 86* black dust pump kit from CCM. For those who don't know, CCM makes some of the nicest paintball pump markers and pump kits around. A pump kit changes an autococker marker, like my karnivor, from an electric semi-automatic marker into a marker that must be pumped before every shot. Here are some pictures of the marker:


I gave her a try at a recent event and she shoots like a dream. I love it. It needs a bit of tinkering to get it sweet-spotted, but it's a great marker. I'm very happy with it. CCM is a stellar company, so for anyone who's interested check out and get in touch with Mel there. She's fantastic.

Another great addition to my life - my new bike. My Granddad bought me a commuter bike for passing my orals/christmas gift. I could never have hoped to get a bike like this. It's the Surly Crosscheck ( ), black. I've been commuting for most of the time since January. Some of the days have been bad - I've almost been hit a few times. We just had 3 cyclists/pedestrians killed by car drivers in 1 week. Wow. I'm going to have to be careful out there. I'll post some pictures of the bike soon. I'm saving for a Brooks leather saddle (seat)... So nice, but so expensive. My legs are starting to look good ;)

A final couple of updates. Some friends of mine, some great ladies, have started a new site called Fat, Ugly, or Slutty? It's a website in which people, usually women, submit screenshots of guys being just downright rude, degenerate, chauvinistic and all-around not nice while playing online games (PC, PS3, XboxLive, etc.) The language is pretty offensive so I'd say NSFW, but if you are willing to read some crazy stuff and aren't at work, check it out. Great site. These ladies are some of the greatest. Check out follow them on twitter at @fatuglyorslutty, @likeOMGitsFEDAY @jaspirella and @_gtz_. Note: Feday has a great blog, too. Her blog is Game On! ( ) and her youtube channel is . She has some great stuff - it has been a while since she updated because of her job, but check her out peoples!!

My final update is that I will be creating a new blog soon, on top of this one. I find that science is often portrayed poorly in the media and, well, damnit, it pisses me off. Too often the media screws up or makes an incorrect assumption, or sometimes even makes a big deal out of nothing, and it hurts us scientists. We depend on public funding from the government to get our research done, and if the public doesn't trust us or understand us we won't be getting anymore funding. Right now we need all the help we can get. So! At some point in the future, when I have some time, I'm going to be making a blog in which I write article reviews on current research papers and topics and discuss them so that they make sense and are easily understood. Won't happen for a bit, but I'll link it here for those who are interested when it happens.

Pip pip, cheerio!

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