Major Life Changes

Wow, so it's been a while. Sorry for the radio silence! This year has been quite busy for me. I spent all of the spring semester completing my master's thesis, entitled "Fermentative Production of Short-Chain Fatty Acids and Methyl Ketones in Escherichia coli." It was a huge endeavor and the longest paper I've ever written. I can't believe that I ever struggled with 4 page papers in high school. My thesis was 76 pages! I defended in April and passed, and commencement was in May. So I'm officially a Master of Science! Graduate school is probably the hardest thing I have done so far, but the payoff was worth it.
My family visited me for graduation and we went to the Botanical Gardens in Madison. I will try to post the pictures soon. It was a huge place with large outdoor gardens and I really liked it. I could have spent an entire day there. At the end of our vacation we all went to Chicago and saw The Who on their current tour.
Thankfully, after I got back from vacation I was able to get in touch with a recruiter at Aerotek Scientific and they were able to help me find a job. I've been at my new position for about a month now and I enjoy it. I'm a Pharmaceutical Quality Control technician now at a veterinary company in Des Moines. It's very different from working in a biology lab. It's essentially analytical chemistry and there is a whole load of paperwork and very specific rules about everything because it's quality control. I've adjusted pretty well so far and I like the job itself. Commuting does suck though so next year I am planning on trying to move closer.
My garden is still growing. No harvests yet so I don't have anything to show off, but I can probably harvest some basil and lemon balm soon. There are lots of green tomatoes so I'm just waiting on them to finish growing and ripen!

No pictures today

I'm way behind on uploading my garden pictures. Life has been really busy and I keep putting it off. I'll try to get some up soon, maybe tomorrow. This week is starting off busy. I have a two-day conference that I spent all day at today, and half the day tomorrow. It's a scientific conference on biorenewable chemicals. I had to give a short presentation and a poster today, which was the longest day. Tomorrow won't be so bad, and I'll be able to come home and take a little nap in the afternoon. It's just a very draining process to be on point and talking science for eleven hours today and six tomorrow.

I told myself so

So just as I totally predicted, I feel about a million times better after spending my first day in Dr. Bobik's lab. I can't be too specific about what I'm doing on the internet because people would definitely try to scoop us all over the place, but I can say that I'm engineering E. coli to produce industrially relevant chemicals to replace petroleum derived products. And that's about all I can say about the research. However, I can say that the people in the lab are pretty awesome. It's currently pretty small because several people recently graduated and got postdocs, but that is fine with me. The two guys I'm working with are both pretty chill and have that sarcastic kind of humor that I do, so already I feel comfortable around them. One of them had no experience in this kind of stuff before he started working there as well, so I don't feel totally in over my head. Dr. Bobik is in the lab actually working on experiments pretty often as well, so it's neat to see my PI more than once a week in a lab meeting. It's a nice lab too, with plenty of room and windows (oh god the windows are the best) and we don't have to share too many instruments. It probably sounds bad, but I hate having to share all my lab equipment with random people so if I'm in a lab that has all its own stuff that makes me happy. Anyway, I feel a lot better now and I think everything is going to be alright.

Omaha Zoo Desert Dome

 This is the geodesic dome that the desert exhibits at the Omaha Zoo are in. It's a gigantic dome.

 This is a desert cat. It was very sleepy and ignored me while I took its picture. It was pretty cute though.

 There were five or six of these pretty birds. I wish we had more colorful birds like this in Iowa.

 I was able to get a close up of one of the pretty birds. They were really cool!

 This is some kind of funky bird with little thin legs. I don't remember exactly what it was called though.

 This desert deer was in the same enclosure as the meerkats. All these kids were freaking out at the meerkats, and the deer just stood there chewing something. It was very calm. So I took a picture of it because I liked it better than the meerkats.

 It's a kooaburra! I really want one. They are super pretty! My dad said they were all over the place when he visited Melbourne.

 Lynxes! I was lucky to get a shot of both of them together, because the one on the left was prowling around a lot.

Desert tortoises. Their shells are more colorful in person.

Time goes by

It's October already. That happened both really fast and really slowly. I don't know, it seems like it went by kind of fast, but then it seems like I've been in Ames forever, and how is it only October? Time is being weird. I'm told this only gets weirder once you have children. Since I'm not doing that soon, I guess I will have to wait and see if that's the truth.
I'm actually feeling a lot better today than I have in a while. I'm still waking up anxious, but it goes away sooner and I don't feel quite so nauseous, so I can at least drink some milk and coffee in the morning. It's still annoying but at least it isn't horrible. My first counseling appointment is tomorrow morning so hopefully that will go well and I'll start getting some more help with this stuff.
School is going fine. Biochemistry is boring and I really could not possibly care less about it, but I have to at least make an effort so that I can get a decent grade. The professor isn't bad, it's just that I do not care about bond angles and hydrogen bonds and crap like that. It's too small scale for me. Pathogenic Microorganisms just started last week and that class is really interesting. I like pathogens though so I could have called that. After that one is done then I have Bacterial Genetics in November. I'm a little nervous about that one because genetics is not necessarily easy to learn and remember for tests. Also if the professor is who I think it is I'm not sure his teaching style or grading style will be very nice. We'll see.
Lab is actually going a little better. I have been pretty meh about it, especially since I had a small issue with the lab manager, but today she was really helpful and pleasant, so maybe things are okay. My PI and I talked and he wants to add two more experiments for me to do, which is a lot of work, but it might end up going in a paper that I could get authorship credit on, so it's worth it. I just hope that the data is good and useful, because nothing is sadder than doing a lot of work and getting crappy data out of it.
So yeah, that's what's happening at the moment. I am looking forward to November because I can finally go back home for a week, but hopefully October won't be as crappy as September was.

First Rotation!

I got my first lab rotation set up today! Sweet relief. I was getting kind of nervous there because technically all of us are supposed to start our rotations by next Tuesday. So yeah, it got cut pretty close, but I am officially rotating in Dr. Bogdanove's lab. I have meetings scheduled with two other professors, so hopefully I'll have all three rotations set soon.
Anyway, Dr. Bogdanove works on plant pathology, specifically pathogens of rice. The bacteria make these proteins called TAL effectors. When the bacteria infect a plant, they secrete the TAL effectors which go into the plant nucleus, bind specific DNA promoters, and activate transcription of those genes. Usually the genes that are transcribed help the bacteria infect the plant cells better in some way, but some plants have evolved some resistance mechanisms. The interesting part is the TAL effectors, because they're specific and they can be engineered to recognize pretty much any DNA sequence. There are several projects going on, but I picked to work on the one that requires the most plant pathology, and therefore I know the least about. I figured that I might as well learn a bunch of stuff right away rather than stay in my comfort zone with basic molecular biology. So I'm going to be taking TAL effectors from one type of this bacteria, putting them into another type of the bacteria, and then infecting the plants to see if the different TAL effectors change how the bacteria infect the plant. I'll be able to explain it better once I'm doing it, I'm sure. But I'm really looking forward to starting!

23AndMe Results!

So about a month ago I decided to do genetic testing on myself, mostly for curiosity's sake. I went with 23andme because I've had several friends use it and like it. Just last night my results came in, so instead of going to bed like a normal person I stayed up for two hours looking at everything. Obviously I can't talk about my increased risks or anything like that because even though there's a genetic non-discrimination act in place, I wouldn't count on anyone following through on it. So here's the other stuff.
mtDNA haplogroup: I'll start with this one because it really threw me for a loop. I'm Native American on my mother's side. My great-great-grandmother spoke Cherokee. This is how I was raised, this is what I am. That's important. My haplogroup is H2a1, which originated about 26,000 years ago in the Middle East, around Turkey. It slowly spread through Eastern, Northern, and parts of Western Europe. It is not one of the haplogroups that indicates Native American ancestry. My first reaction was something like WHAT. Then I poked around on the 23andme forums and found out some interesting things. First of all, the haplogroups to determine NA ancestry and the modern Asian haplogroups because they're aren't many NA people who've done genotyping to compare to. Secondly, many people, some of whom have more documentation than I do, who are related to NA tribes on the Eastern seaboard do not have a typical NA haplogroup. Weird, huh? Currently there are a couple of hypotheses floating around to explain that. There's the Solutrean Hypothesis, which no one can really prove or disprove at this time, which posits that people came from southwestern Europe to the Americas about 20,000 years ago, before the Bering Land Bridge, and they're the ancestors of lots of eastern tribes. The second is that this maternal haplogroup came from Vikings who settled in the Americas before Columbus. The third, which is possible for my family in particular, is that we picked up this haplogroup from one of the Roanoke colonists who intermarried with local Native Americans. So that was weird, and I've just joined Ancestry.com to see if I can follow a paper trail and get more information about my family that way.
Decreased Risks: I'm at decreased risk for breast cancer, Alzheimer's disease, lupus, MS, melanoma, ovarian cancer, and osteoarthritis. All of which makes me very happy.
Traits: So I obviously don't have the alcohol flush response, which it accurately predicted. It also accurately knew that I was a bitter supertaster. It also accurately predicted my eye colour (blue), my hair curl (it's wavy), and that I'm more of a sprinter than an endurance runner. One of the things I thought was fun is that I'm apparently less susceptible to contracting leprosy if I'm exposed to it. I can armadillos with impunity! It also accurately showed that I have extremely good episodic memory.
Drug Response: So apparently I would have a really good response to interferon beta if I ever took it. I guess that's good. But I'm extremely susceptible to liver toxicity from floxacillin. Luckily that drug isn't used in the US, but if I go back to Europe it's good to know. It also says that I'm a slow caffeine metabolizer, so the reason I need so much coffee to feel an effect must be because I drink too much or something like that.
Yeah, so that's my DNA!

2.14.2011

I think I'm getting sick. I went home early from work because I was so tired, and my head hurt like crazy, and after dinner I started feeling grumbly in the GI tract. I'm sucking down ginger ale, but I have a feeling that I might be working from home tomorrow.
I usually don't have the opportunity to work from home, because I work in a cancer biology lab, but on Tuesdays there's no cell culture to be done unless I'm setting up experiments. There's no experiment to set up this week, so no bench work tomorrow. Right now I'm actually working on the lab budget. My supervisor is working on a grant proposal and we need to include a budget. Since we just became our own lab, we're still trying to figure out how much everything costs. So that's what I'm doing, and I can keep working on that at home. It's interesting and enlightening because I never realized how much some of the stuff we use costs. I can definitely understand the stress of getting grants and keeping them, because without money the whole lab just falls apart. It makes me a little nervous about my future, since grant funding from the NIH is getting harder and harder to come by, but I'm sure it will work out. If all else fails there are usually jobs available at biotech or pharmaceutical companies, so I could always join the dark side and work in industry. Maybe there will be more grants available by the time I'd need to apply for them (I'm not holding my breath) which would make it a little easier. It's like a decade away so I'm not obsessing too much about it right now. But it has been good to get some experience working on a grant, because it's usually some kind of nebulous thing to a grad student in science. You know that you need them to run a lab and have a career, but you don't really know how it all works until suddenly you need a grant. Crazy, huh?

Christmas and other stuff

Last weekend we chopped down a Christmas tree and put it in our house. We do this every year because fake trees are sad. I especially enjoy it because when I move back out, I'll probably be moving into an apartment that only allows sad fake trees. So I relish having a real, pine-tree smelling white spruce in the living room. Now that we finally decorated, it feels a little more Christmassy around here, which makes me less grumpy about it getting dark at 5pm.
What still makes me grumpy is that my science is not behaving. I've been trying to do this GLUT4 blot for two months now, and Aliccia and I cannot get the cells to respond to insulin. We're trying one more time this week, and I really hope it works, because if it doesn't I'm pretty sure we've got serious problems. I hate working ten to twelve hour days when I have a two hour round trip commute so I'm tired and grumpy. So I really hope this works so I can stop working long Thursdays and Fridays.

What the heck do I do at my job anyway?

I've worked at Karmanos Cancer Institute for almost nine months now as a research assistant in one of the breast cancer research labs. I got the job in a roundabout way that involved my step-aunt's best friend, the CFO of Karmanos, passing my resume to my now-boss who called me because I was apparently well-qualified. The upshot being that I work as a research assistant now, which means I do most of the work without getting much of the glory. Oh well. It's not forever.
At the moment, I am in the midst of a rather large experiment involving a panel of genes that are candidates as either oncogenes or genes that are regulated by an oncogene. What I do with these candidate genes is make an shRNA against each one and infect my target cells with said shRNA to knock down the gene's expression. Then I wait and measure growth and viability with a luciferase assay to determine the effect of knocking down the gene. In this experiment I have 20 genes and 148 shRNA constructs. That means I spent all of last week making 148 viruses to infect my target cells with. It was unpleasant. This week I get to infect my target cells, which are MCF10A and SUM225 lines. I do the infection in triplicate, which worked out to 444 wells, or four and a half 96-well plates. It's also unpleasant, mostly because I have to add the virus one at a time and can't use a multichannel pipettor. After that, I wait and see what happens. Our constructs have a GFP tag in them so after 24-48 hours I should be able to see some of my infected cells glowing green, and that's how I know that the infection worked.
Anyway, that's what I'm doing at the moment. Previously I did some work on PHGDH knockdown and insulin independence, which was mostly growth assays, Western Blots, and qPCR. I'm not fond of Western Blots. I'll complain about them another time. I've actually learned a lot in the nine months I've been working, and I feel a lot more confident that I can do science and could have a career as a research somewhere. Although I feel my leanings are toward some part of microbiology, the time I've served in cancer research will definitely benefit me.