coming to the end of the semester

its been awhile since i've blogged. so, yes, i must admit, i don't have as much free time in Pullman as i thought. things this semester have been busy.

my two rotations after Pat Hunt were John Nilson and Mike Griswold... both respected people in the reproductive biology.

John Nilson is the current president of the Society for the Study of Reproduction as well as the director of the School of Molecular Biosciences. Obviously, a busy person. His research lies mostly in the pituitary hormone, LH and its effect in the ovary. However, the project I worked on with Travis, his postdoc, was much more at the gonad level. Estrogen at high levels has been shown to cause DNA damage, specifically double stranded breaks. Since follicles in the ovary produce estrogen, they hypothesize that it must have some way of repairing its DNA efficiently and rapidly. At the bench, I learned cell culture and was doing Western blot after Western blot.
Figure 1. My western blot probing for the DNA repair protein, ATM. I did TONS of these.

Mike Griswold is also very respected for being the forerunner in spermatogenesis research. He currently has a couple huge grants on basic mechanisms of spermatogenesis as well as a grant for male contraception. Yes, I never thought I'd take such a liking to male reproductive studies i already realize how funny that sounds but this lab really charmed me. They have an incredibly organized lab manager, a SUPER knowledgeable postdoc from Australia, a senior grad student, Beth, who is super friendly and helpful, and 2 techs that are also very friendly and easy-going. 2 weeks ago, it really was a toss up whether I was going to join the Hunt lab or unexpectedly go Griswold. The fact that Griswold is also researching BPA, but in the male was also a big attention-getter to me. During my rotation I worked on the EGR4 knockout mouse, which is infertile in the male, but not in the female, with no extensive work so far on why this occurs. Check out these slides of testes I cross sectioned. These knockout EGR4 male mice have many more regressed seminiferous tubules (where sperm develop) compared to normal mice, causing their infertility. But what role EGR4 actually plays in the seminiferous tubule hasn't been determined... and won't be by me at least since my rotation ended friday.
Figure 2. Cross section of day 150 male mouse testes from a normal mouse (has EGR4). Orange arrow indicates normal tubule with developing sperm in the middle.

Figure 3. Cross section of day 150 male mouse testes from a knockout mouse (lacks EGR4). Orange arrow indicates normal tubul with developing sperm in the middle. Pink arrows indicate regressed tubules, lacking the cells that develop into mature sperm. These knockouts had up to 30% regression compared to normal mice. I know. I counted.

In the end I chose Pat Hunt. She and her husband Terry have huge resources as well as notoriety in the genetics world. Their work on meiosis, and Pat's work on BPA's effect on meiosis is really what draws me to the lab. I've done the, if you will, 'gonadal' level of research in my undergrad, and felt that studying meiosis leaves me a bit more flexible in choosing what to do after my PhD. It's better to learn different things, more than what you already know. Pat is also known for her attention in forming presentation and writing skill, and overall I think I will be most challenged in her lab--equaling the best possible training. I can't say I don't have some apprehensions-- she's tough. If she doesn't like you, it's bad news. REAL bad. But I hope to use this as extra motivation to do well, and do it quickly. If I want to be out quickly, which is definitely a high priority, I need to produce.

Finals are Tuesday (molecular biology) and Thursday (biochemistry). There's a departmental party Monday night, which is supposedly drunken faculty bonanza so I can't miss it for the world. Friday night us first years are having a little soiree of our own.

Then home!

Oh and yeah, it snowed a TON today. Well, not a ton, but more than 6 in. for sure.

Pieces of Pullman (part II): the drive to Moscow

Pieces of Pullman (part I) : winco

So my first real blog about nothing associated with school, but about life in Pullman in general. Or in this case, Moscow, ID, which is where my supermarket, Winco, is located. It's definitely a far cry from the Trader Joe's and Whole Foods that I've left behind, and more of a cross between Costco (price-wise) and Super A (atmosphere-wise). ...I know. you can't believe I'm shopping here.

<--But check this out! ALL THAT FOOD!!! FOR $44.09!!! 2 fillets of snapper, buttersquash soup, tomato soup, milk, wheat bread, udon, yogurt, veggies, the list goes on. It blows my mind. Another idea I'm completely drawn to is their cereal aisle. They have the normal boxes too, but this way, I can have a different bowl of cereal everyday for 30 days! How amazing! Theoretically I could just buy 7 different boxes of cereal and alternate between boxes, but I'm one of those people who feels guilty about opening a new box before the old one is finished. Then there are those little tiny-individual-bowl boxes of cereal, but that option consists of way too much packaging and is consumerism to the max. This way, I have my cereal variety and my mind is at ease. The barrels on the floor are different baking mixes-- muffin mix, cornbread mix, chocolate cake mix, etc. so you don't need to buy the boxes and you can buy as much or as little as you want.


And, as my mom pointed out when she was here, they have some of the asian stuff I wouldn't have expected them to. i.e wonton skins, BOTH types of tofu, and more than one kind of soy sauce. The Japanese student in my lab, So, told me the quality of fish here is not very good, but considering I can't go 6 months without fish, I've made do. So far I've tried the sockeye salmon, red snapper, and dover sole. The dover sole has been the best was the best so far. I've got a catfish fillet still in the fridge, but my hopes aren't high. They are all however, wild-caught and pretty fresh by the packaging date. I'll lay off the red snapper since I realized its an eco-worst fish. Sad, since my recipe was really delicious.

egg sucking

It is no longer the hot summer it once was. The days so far have been beautiful. The campus is speckled with these trees--half orange and red, the other half still green and yellow, that show a rainbow of autumn colors. Again, its just been gorgeous. The fields, however, are a little bare since the harvest has come and gone. Soon though there will be new crop.

School has been fine; 2 weeks til first exams. Rotation has been going well, concentrating on improving my egg sucking skills. Getting better at identifying them, but still moving slower than I should. A brief explanation into the technical work of egg sucking:

What you are looking for is the germinal vesicle oocytes (Figure 1). This is a clean picture. In reality, you must hunt for these in a brownish pink solution amongst bad oocytes and secondary (larger) oocytes you don't want, and all other cell types out of the ovary that you just mascerated.

Figure 1. Notice that clear circle in the middle of the egg. Within that, is the nucleus. We refer to these eggs as the ones with the 'winkies'.

A good micropipette can make or break you.
1) Pipette is too big-- this will just suck up everything.
2) Pipette is too small--can dent your oocytes and also becomes easily clogged with other unwanted cells.
It will take you longer if you encounter these issues, and oocytes are very fickle, they start degenerating if you don't move quickly. They start looking like this (Figure 2) and even this (Figure 3).

Figure 2. The sides of the oocytes become dented and the nucleus is no longer visible.

Figure 3. The zona pellucida surrounding the oocyte has become thick and dark granules appear inside the oocyte.

The oocytes should not really sit for more than 15 minutes. After collection, you culture them in an incubator overnight, then check how many of them have produced a polar body (Figure 4). Collecting them and putting them in culture inspires the oocytes to undergo meiosis I, to produce the polar body.

Figure 4. Oocyte and its 1st polar body.

Recombination has occurred, but each cell is still diploid and will need one more division to become haploid. Since most of the lab is interested in the recombination events during meiosis I, this is where most people fix their oocytes onto slides. The percentage of ones that did produce a polar body must be 85%, or else you cannot use any of the oocytes. I have yet to fulfill that, but according the Ailene, the lab tech/'egg queen' it can take people weeks-months to get this perfected to get 85%.

On Friday I practiced collecting some 2 cell embryos from pregnant females (Figure 5).

Figure 5. Mouse 2-cell embryos. Have undergone 1 round of mitotic division, polar body still visible.

The embryos are much more stable than the oocytes, and definitely more forgiving when it comes to time. They are also quicker to collect because instead of looking for unfertilized oocytes still in the yucky brownish slurry mess of an ovary, oocytes have already been ovulated out of the ovary, become fertilized and continue their travel down the oviduct/fallopian tube, where you find them. The oviduct which is a much tougher and whiter piece of connective tissue, making it much easier to see and collect the embryos. This is encouraging since my project involves working with embryos (8-cell).

My animals began getting their BPA dosages and I'll be collecting their embryos on Tuesday and Thursday. I may not be able to FISH them because our lab ran out of the X chromosome probe I would need. I may wait for it to come in, or use another probe to look at something else entirely. I'll have to caucus with Pat and the lab on Tuesday to determine the best plan of action. Only 2 more weeks of my lab rotation!

Come Together

It's the end of the first week of classes and Labor Day Weekend. Well deserved. Classes so far have been mostly review. DNA replication in Molecular Cell Biology and the first 3 chapters of Lehninger in Biochem. We don't have an exam until the last week of September, so it will be ton of information, and our exams for both classes are in the same week, for every exam, which is pretty lame.

Rotation has been the complete opposite as far as requiring my brain power. After a brief pow-wow with Pat on Tuesday, she felt that she already knew what I was capable of, especially after seeing my poster at SSR, and that she was comfortable with me finding my own project. She didn't feel like the end point was necessarily that important, since it's only 5 weeks, but that I get to get a feel for the lab and the people. So of course, I had no idea what to do, given all that freedom. After talking with almost everyone in the lab and freaking out a little, Ailene, one of the research associates, brought up a project that one of the recently graduating students was planning to undertake, but never got around to. Long story short, I pitched it to Pat, and she gave me the green light. In the meantime, I have learned:
1) their kill/collection process
2) how to collect tiny TINY mouse oocytes (eggs) (becoming a master of micropipette making in the process)
3) how to fix embryos on slides
4) #2 and #3 require the odd and ancient skill of mouthpipetting.

Simply put, my rotation project will be exposing pregnant female mice to a short-low-dose regimen of BPA (3 day exposure). I will then collect their embryos which should be in their 8-cell blastocyst stage. I will then use fluorescence in situ hybridization (FISH) to look for aneuploidy where the cells have an abnormal number of chromosomes. The trick to this project is really just getting it done in the 5 weeks I have. I also have to rely on other people to expose the animals since I haven't been trained to that, and the person who does that training just had back surgery--so that won't happen anytime soon. Im excited to work on this, if it works, and there is aneuploidy in the embryos, it will mean that BPA, even at low doses given only for a short period of time, can cause extreme defects if it is during a critical point in pregnancy. It will be a good chance to impress Pat and the rest of the lab. Hopefully I can pull it off.

Last night was a fun get together at a house some second years and a first year live in. I thought it was adorable that it was painted pink. It was a beautiful house, nice front and backyard, granite countertops, and pretty large bedrooms. There was an abundance of food, alcohol, and fun conversation. And Rock Band. Which I am now a fan of. :)

It's also been a whole week with my new little kitten, Mochi. Which no one in Pullman knows how to pronounce, let alone what it is. sigh. Too ethnic I suppose. It's been delightful. She's adorable, extremely entertaining, and very smart as most cats are. She's been handling her time alone surprisingly well. She had a problem with trying to sleep on my face in the middle of the night, and has learned to cozy up just above my head. She also can become overactive between 3-5am, but hasn't done it for awhile, so hopefully she is settling in.


PS-As you can see, the camera made it.

anticipation

So today is the first day of classes.

I spent last week in Spokane on a retreat where everyone (grad students, faculty, post docs and lab techs) from the School of Molecular Biosciences got together to listen to speakers, from the school and not, and to get to know each other a little better. Overall, it was good times: nice hotel, wine, good speakers. The first night ended with the 1st and some 2nd years checking out some of the Spokane nightlife. I know a chuckle is in order, but don't laugh because we actually ended up at a cute bar which was actually to my liking, called Zolas. Stylish, with its lantern lights and cozy corners where people could sit and talk, or play cards, as some did. Dancing also ensued. Of the people I've met-- I like them. There are definitely some characters, which I can only hope will keep things interesting--in a good way.

One thing that was quite worrisome, is that of the 15 or so 2nd years that started out last year, only 8 remain. When I inquired about the situation, one of the surviving 2nd year said gravely, 'PASS YOUR CLASSES...'. Not that I thought the classes would be easy by any means, I didn't think they would have the same odds of passing as the Black Death.

Also, a student mentioned that Pat Hunt:
a) the amazing scientist who put together that Bisphenol A, a chemical known to be in plastic, can result in infertility (that you hear all about in the news stories-->see b)
b) who, because of the news stories, received a call from Nicole Richie (of all people) because she was concerned about her baby--seriously, like Bisphenol A was the first thing she was worried about?
c) who, because of the impact of her study, was awarded with Scientific American's Top 50 Researchers of 2007 (http://www.sciam.com/article.cfm?id=sciam-50-2007),
d) who I really REALLY wanted to work with when I originally applied to WSU,
e) and thus, who I am starting my first rotation with,
has a 'sink or swim' mentoring style. It's a little intimidating, coming from a lab where my PI was a little more of a 'coach' mentor style. So there really is only one option-- swim. Mary Hunzicker-Dunn, another really prominent reproductive biologist reminds me a lot of Dr. Young, so I may try her lab for my second rotation. Her work revolves around cell signaling in ovarian cells. It's always a good thing to learn signal transduction techniques.

So here I am, sitting outside the classroom before it starts with all this going through my head. Sort of one of those 'first days of the rest of your life' kind of moments. I would be lying if I said I wasn't excited, or scared. But I'm ready for it. I think.

ps- my camera is on its way.

Los Angeles, CA to Pullman, WA (1,216 mi)

So, I've been in Pullman for a solid week. I don't really have that much to report. But for those that are wondering, here's a very quick recap:

Wednesday, August 6th
Left LA. Got to Pullman, with family in tow. It's about 2 minutes from the airport to my apartment. Which isn't surprising because in Pullman, anywhere is about 2 minutes from anywhere else. Got my keys to my place. Checked it out thoroughly. I have to say... it's pretty sweet. I was also particularly psyched about my old fridge and stove. And I actually don't mean that sarcastically. I really liked that they were olive green and from the 1970s. My soft spot for old things is probably going to be detrimental and some point. Keep that in mind.
First thing was first after getting my keys-- find a bed that could be delivered today. When that was done, went shopping for essentials i.e. food and miscellaneous stuff like ziploc bags and dish washing soap. Of course the only places to go are ShopKo and Walmart. Of which we went to the latter. Don't tell my dad.

Thursday, August 7th
Went through the myriad of tasks when one moves into a new place. Went shopping for all the miscellaneous items you don't think you need until you need them. Started unpacking the majority of my stuff. Lined all my closets with contact paper. I also successfully assembled a floor lamp. Went to Costco in nearby Clarkston. Which is side by side its neighboring city, Lewiston. Clarkston, is in Washington, while Lewiston is in Idaho. Why Lewis and Clark didn't want to be in the same state is beyond me. But they are separated by the very pretty Snake River. Maybe they both wanted a piece of it, without one being upstream of the other. I know. I analyze a bit. Bought 2 important things from Costco. A fan, it was so hot when we first moved in and more food.

Friday, August 8th
Yard sales early in the morning. Found my first piece of furniture besides my bed, a skinny side table with nesting bench and little stool. Also bought an iron and an ironing board. Which I needed. Badly. All of my clothes are completely crunched and wrinkled from the journey. My aunt came in from Seattle in the afternoon, it was nice to see her. She also bought me a bunch of goodies from IKEA. Desk lamp, table lamp, comforter and cover, clothes hanger, candles according to my aunt, 'for when your electricity goes out', kitchen stuff, knives, cutting board, glasses which I thought were a LOT bigger when I asked for them, they're more like large shot glasses, dishes, utensils, etc. Spent Friday night at the hotel my aunt was staying at, right across the street from my apartment, watching the opening ceremony of the olympics. I still can't get over the fact there were people in those moving square pegs, for people who saw it.

Saturday, August 9th
More yard sales, about 7 in total. Down the road from me was a farm having a yard sale. They let me pet their pig. ended all arguements about Pullman being, well, one big farm, that has a really good school dropped in the middle. Bought a computer chair for $1. Yes, $1. And its an awesome chair. Also bought a white board for $2. At the 3rd house I fell in love with this great trunk that the person there sold to me for $50. I couldn't haul it myself so they were willing to drop it off for me. Long story short, schmuck calls me back and said they changed their mind about selling it. I was pretty heartbroken to say the least. It was an amazing piece. I now have a vendetta to find something even more cool.
Also got my internet situation under control. I now have unlimited access. Anytime. Anywhere. Thanks Aunt Judy. It's changed my life. :) Also, my car got delivered! YAY! Unpacked everything I had in there, an ottoman, more clothes, dishes, towels, books, some of my art supplies and pictures from home.

Sunday, August 10th
Went to a church in the morning. Lots of white people, just short of 200 people, which is a change from my not-so-many, Chinese church back home. Pullman's not short on churches, so we'll see if I end up going back there. Overall I did like it, the people were very friendly, and it had a mix of old, in between, and really young which is nice to see. Said goodbye to my aunt, who left back to Seattle. We spent the night putting together a kitchen table and four chairs. THEN... the refridgerator incident. We took an ice cream break to realize that the ice cream was completely melted! My fridge was not working. So, quick thinking, my apartment manager helps us move all our food into the apartment next door that hadn't been moved into yet.

Monday, August 11th
7am. My fridge is pronounced dead. The maintanance guy tried fixing the breaker in the wall, as well as the fuse, and it still didn't work. He popped in a new fridge, and wah la. It works. I was sad, which you can understand if you can recall my adoration for it. Now the stove is lonely. I hope it will be kind to the new fridge. He can't help being new. For those who are reading, this is sort of what being alone in Pullman has done to me. Stoves talking to fridges... but then again. It's not really something I would have never said either.

Said goodbye to mom, Kev, and Aunt Sara. I don't know what I would have done if I had gotten here by myself. Much scarier probably. I was glad to have had the time with them that I did.

Tuesday, August 12th
Went to the DMV to get my WA State Driver's license. Which was a bust. Apparently you need to prove you live here to get one. Which I couldn't really do, since a lease didn't cover it, and I didn't have any other documents that were on their list. A concealed weapons permit would have done it. Darn. I didn't think of bringing my .45. Went furniture shopping, fell in love with this adorable store in Moscow, ID (8 miles from Pullman). It was called Now and Then, and had a bunch of cool vintage furniture, most of it I couldn't afford, but it was great fun looking around at old vanity tables, glass milk bottles, and old 1920s love letters they were selling for a dollar each. On the way home found this really sweet chair for $8 at the Goodwill store.

So if you are keeping score of the furniture I have-- a bed, a table, a bench, a stool, an ottoman, a chair, a kitchen table and four chairs, and 3 lamps.

Wednesday, August 13th
Didn't do very much of anything that day. Cleaned up mostly. Did laundry. Watched a bunch of tv online. Started setting up this blog. Emailed people about furniture they listed on craigslist. That's about it. Turned in early so I could wake up early for the auction they were having. See below.

Thursday, August 14th
Went to an auction the school was having for old school property. It was way cooler than I thought it'd be. They had so much stuff. The normal stuff you would think of when you think of school i.e. desks, tables, chairs, computers, etc. But they had tons of other stuff like cars, kitchen equipment, even animals. What intrigued me were just the random wierd things you want for the sake of having them. For example, they had a light box you use to view x-rays, a popcorn machine, and a polygraph machine (it sold for $15) and I totally regretted not bidding on it right after. How fun would that be at a dinner party? ;) It's going on tomorrow too, and I may go back for a couch I liked and an old lab desk I'm thinking of using as an art/work table. Since they won't deliver it, I'm not sure how I'll get either into my apartment, but I'm working on a solution.
Went back to the DMV and got my drivers license. I was lucky enough to have gotten a piece of mail from my electric company that made the cut. They hole-punched my Cali ID. I'm sorta sad about that, but it doesn't really matter. I will always be Californian. That'll definitely hold up whenever winter comes around. I also registered to vote. Today was rather productive.

Writing this has made me realize I need a camera. Bad. It's on the list.