He proved he could talk fluent human

This is a comment made by a Guardian Unlimited commentator about Gordon Brown, future prime minister of Britain.

HANK (to Larry): Look, you seem like a nice guy, so I'm telling you this for your own good: judging by the two times I've met you, your life has been a waste so far. Forget these chorus guys and find a nice girl, or at least something productive to do like a stamp collection. Your local postmaster can help you. Here's his number.

Who knows where words come from...

So yesterday marked two milestones: I am done writing the Materials and Methods section of my thesis and I applied for my first jobs (about 10) for after graduation. I have been fretting over what statistical methods to use in my thesis but my adviser told me that there is a biostatistician that I can talk to that would help me (thank goodness). I have one more paper that I want to get and read and then I am done with all my background reading. But best of all I heard the best word today. It was on an episode of this American Life and there was a little section about pledging to NPR and Ira Glass used the allure of the rewards of various "merch" to encourage donations. I will be using this word when ever appropriate now.

BOBBY: What we need is a class full of girls who don't know us very well.
JOSEPH: Yeah! We could pretend we're from the future, and we need to experiment on 'em!... Wait, this is why girls don't like me, right?

A 45 second minute

The title comes from a description I made of the power supply I am using to run gels for the past week. Either the internal clock on the power supply is off (and running fast) or I have lost the ability to tell time. I am really close to setting a defense date for my thesis, either July 2nd or 3rd. My third committee member will be leaving town on the fourth and be gone until August so that kind of made the first few days of the July the best days. I don't really mind have my defense early in the month, that means that I can leave Iowa earlier. I am so close to being done with my research. I have already prepared about 56 of my samples to be sequenced. I also have maybe four more papers that I want to get and then I can start really writing my background (instead of just organizing it my head). I am planning on making a rough outline this weekend. So for the first time in a while, I actually feel confident that I am going to graduate in the foreseeable future (so please don't rain on my parade!). I got to expand my baking repertoire yesterday when I made a devil's food cake for a labmate's birthday. I meant to take a picture of the cake to post but I forgot.

" Oh, dang, someone's coming! Lie back and think of England. Hugh Grant. Spice Girls. Paddington!" - Bobby Hill

When life gives you the short end of the stick

make shortbread (with dried cranberries). I took a picture of my fancy shortbread but the picture didn't turn out very well, and you can't see the United Kingdom related impression (a thistle for Scotland, a dragon for Wales, and a Tudor rose for Britain). But it is really good shortbread!

ANNOUNCER: Up next: "History's Mysteries, with Nazi Hidden Gold," followed by "Building the Nazi War Machine" and "Nazis of the Desert, Nazis of the Sea."
LUANNE: Wow, the Nazis did a lot.

Satellites Lost

It has almost been two weeks since I have posted (and I sure lots of people are sitting at home wondering what has happened to me!). This is mostly due to the fact that I had to replace the hard drive on my laptop last week and I usually write my posts in the evening between reading papers and writing parts of my thesis. I've been pretty busy in the lab but I was able to make time to go home to the farm for Mother's Day which was quite nice. I got to spend lots of time with my parents and was the least stressed that I have been for a month. And my mom made me delicious ribs for dinner on Sunday. It would not be a trip home if I didn't have some car trouble driving back to school (okay this is just the third problem out of multiple trips). This time I had a leak in my radiator so after 100 miles all the antifreeze had leaked out so my dad loaded up the trailer and picked me up outside of Gridley (on the bright side I did get some papers read while waiting and thought about how I wanted to organize sections of my background in my thesis). After replacing the radiator, we also replaced the shocks and the muffler. So I drove back Tuesday morning and worked in the lab for six hours. The extra day at home hasn't affected my lab work too much. I also have my laptop back so hopefully I will better about posting.

"I know it's you Dale. You're smoking the same brand of cigarettes you did in third grade" - Rusty Shackleford (the real one!)

"I didn't die in third grade Dale, I just moved away."- Rusty Shackleford

One piece at a time

For once I have good news, I am half-way done with my research in the lab. Thank goodness, because the pace I have been going has been tough but I think that it will slow down a little to a less exhausting pace. But I have some bad news, which is that my laptop is acting up a little bit so I haven't been able to work on my thesis in evening so I have been reading lots of papers. I have made a significant dent in the materials/methods. But now time for more papers and reading!

RAY: You ever hear of a guy named Jack?
HANK: Well, I went to high school with a guy named --
RAY: No, no, this guy never went to school, he grew up in the hills. But he wrote the book on homemade bait. 'Course it's just a bunch of scribbles 'cause he never went to school.

Who ever invented rope is a total a-hole

What do you do when you been spending every day for the past two weeks in the lab (for 4-9 hours a day)? Well if you are me, you go see the movie "Blades of Glory" with Will Ferrell and Jon Heder. I knew that the movie was going to be really silly but honestly it was totally what I needed. It was nice to just relax and not really think about anything for two hours. It was pretty enjoyable and a good break (also the source of the title). And I am feeling pretty good because I figured out the NPR Sunday Morning puzzle almost right after I heard it (unlike usual where I have no idea what the answer is). There are also two episodes of "King of the Hill" tonight making today one pretty good Sunday.

"Wait a minute. Every time I leave, you call John Redcorn. I know what's going on here. Your headaches are a desperate bid for my attention. But what do I do? I pawn you off on some Indian healer so I can have my Dale time at the gun club, or breeding show turtles, or on the Internet investigating unexplained phenomenona. God, I am so selfish!" - Dale Gribble

Slowly collapse like a flan in the cupboard

Things in the lab have been going pretty well, but very busy. I went in for about 8 hours over the weekend, which actually wasn't that bad because there wasn't as many people in the lab so fewer people asking me about 30 questions each and trying to share equipment. Which was one of the problems that I had today. There is a labmate that I mentioned previously who is difficult to work with mostly because she feels that her work takes precedence over everyone else's work. Everyone else that I share lab space with tries to work together so everyone can use the equipment and space with as few problems as possible. The equipment that everyone was sharing (about 5 people) today was the centrifuge. At about 3 pm, the bitchy girl comes in and claims that everyone using the centrifuge was getting in the way because her experiment is time sensitive. It would be logically for her to tell us in the lab that she would need the centrifuge at regular intervals so we could plan around it (since we were already planning around 5 people). By the way, the girl never comes in on the weekend and leaves without fail at 5pm. So it is any wonder that working on the weekend is more enjoyable?

DALE: I have more pressures than any of you. You ever try replacing a cockroach's blood with root beer?
HANK: You know I haven't.
DALE: Then don't judge me.

Mmm... lung tissue

Today was another day of DNA isolation from lung tissue. I am teaching the Big Blue Assay to two people so they can do it after I am long gone! Today, I taught Bingxuan (a Chinese grad student that I worked on the a PCR project with and I like a great deal) how to do the isolation. Part of the process involves using a tissue grinder to break down the tissue and then lyse the cells. And today I broke the tissue grinder while I was grinding some lung tissue. So as the homogenate is spilling all over my gloves and the paper towels, I attempted to calmly open the package with the cell strainer (Bingxuan had gone to get the next tissue to grind) and then rinse the cells off my gloves with lysis buffer and scrape some of the tissue off the paper towel. As a result I can't imagine that I will get good DNA from the tissue but on the bright side the lung lobe from the rat was pretty large so I will be able to do a second isolation. And for the first time in about two weeks, I will be leaving before 4 pm (but coming in the weekend, so it really evens out) to watch some Hetty Wainthropp.

"Pittman, firing people can give you a pretty good buzz, but it's a poor substitute for killing. I realize that now." - Dale

Need some motivation?

See more Star Trek posters by clicking here

And more cat related poster by clicking here

"I don't know, Hank. Cotton working as a cop? He has a terrible human rights record." - Peggy Hill

Let's tune out by turning on the radio

After spending lots of time in the lab in the last few days, I was looking forward to unwinding a little bit tonight. I was really in the mood to watching the movie "Strictly Ballroom". Unfortunately, I sent the movie over to Rachel in Germany last July. So I did the next best thing, which was to download the soundtrack. Almost as good as watching the movie.

"To be honest, we're more into the invasion of privacy business, not the creation of privacy business." - Dale Gribble

Transpacking all day long

I am finally going to talk about the next step in the Big Blue assay which is called the Transpack reaction. The basic idea is to "package" the DNA into to a phage (a virus that infects bacteria) to infect the E. coli and insert the DNA into the E. coli DNA; the phage will kill the E. coli within a few growth cycle. Any mutation in the rat DNA is then put into to the E. coli and so I can identify the mutant. The E. coli is grown on a huge plate and creates a lawn of bacteria on the agar. Any E. coli that has been infected with the phage with die creating a clear spot on the lawn of bacteria. Mutant are identified by a clear spot with a ring a blue (basically the E. coli can breakdown the X-gal due the mutation for a few growth cycles and then dies). The basics of the Transpack reaction is this: I add the isolated DNA to a red tube (this is how what it is called in the manual, you have to buy the tubes from Stratagene) and then incubate it for 90 minutes. Then I add some of solution for a blue tube (again the official name in the manual) and then incubate it for 90 minutes. I forgot to mention that there are two different agar that I use a top agar and a bottom agar (the composition varies slightly between the two). Before I start the Transpack reaction, I make petri dishes that have bottom agar in them. After the second incubation is over I infect diluted E. coli with the Transpack reaction and incubate the mix for 15 minutes in a 5ml tube. Once the 15 minutes are up, I add 3-4 ml of cooled top agar to the mix, pour it on top on the bottom agar in the petri dishes, invert it and incubate it over night. The next day, I count the number of plaques (clear spots) and that determines the efficiency of the transpack reaction and also the number of big plates I need to pour to identify the mutants.


"Yeah, yeah, everything is one way then it's the other." -Hank Hill

Nobody puts baby in the corner

I saw an ad for Dirty Dancing and the fact that it will be shown in theaters in May (for 2 days) to celebrate the 20th anniversary. I'm not sure why it is being shown in theaters again. It's not like the viewing of the movie is enhanced by showing it on the big screen (and let's all admit the best thing about that movie is the soundtrack minus the weird Patrick Swayze song.) Maybe Patrick Swayze it trying to restart his career by reminding the American public that there was a five year period where he was on fire.

"I hear what you are saying. And I believe you believe it's important." - Hank Hill

Completion!

Here are some picture of my completed quilt top without any borders.












And here it is with the borders added:


"I have a new relaxation tape of me making ocean sounds." - Yogi Victor

I wish it was a musical number

So two of my sisters have asked for an explanation of the big blue assay that I am working on. I've decided to break it up into 3 parts. This assay is used to determine genetic changes in transgenic rats (you can also use mice or cells) following exposure to a substance. The rats have the LacI and LacZ gene incorporated on the 4th chromosomes which allows for you to determine genetic changes. The LacI is a genetic region that is control the ability of a cell to breakdown lactose, its acts as a repressor. If there is a change sequence in the area of the LacI (a region of about 1300 bp in length) it will generate beta-galactosidase. Beta-galactosidase will breakdown a substrate called X-gal which turns blue. And this is why it is called the Big Blue Assay. Although the company Stratagene has also created the same assay using a temperature sensitive based mutations but still gets called the big blue assay. The tissue that I am using is from a 28- repeat dose exposure study using PCB 3 and a PCB metabolite. I am using the lung from the male exposure for my particular experiment although last year I was helping Jim do the big blue using the liver from female exposure group. So the first thing that I do is isolate the DNA from the tissue. This involves pulverizing the tissue then adding enzymes that will digest the proteins, lipids, and RNA. Then I apply the DNA to a dialysis cup that will allow for small molecules to be separated from the DNA (the dialysis cup sits on the surface of buffer). The DNA will dialyze for about 48 hours and as a result will be very viscous. And then I use this DNA for the next step.

"How embarrassing! I thought I had removed the laces from this shoes." - Bill Dauterive

past and pending

Here are the other two blocks from my quilt:











BOBBY (shopping for a wallet): This one's pretty snazzy, and it looks like it could hold a ton of money. That way, if I wanted to impress someone, I could pull out a really big wad of cash -- bam! Dad, gimme a big wad of cash!
HANK: What are you trying to do, get us mugged?

one by one all day long ....

Here is one block (that is not completely pieced yet) of the quilt I am working on.



HANK: What kind of sick bastard runs a water-pipe through a stud without installing a nail-guard?
BOBBY: I don't know!

To the public at large, you are a regular a-hole

I have discovered another reason to love public radio. I have discovered two new musical artists that I love. The first is LCD Soundsystem which is an electronica band that I heard on Fresh Air. The other is William Elliot Whitmore who is one the other end of the musical spectrum. He sings folk music that is heavy on the banjo (which I love).
Work in the lab is going well for once. I've cleared two big hurdles, namely making sure that things that I need to run the big blue assay haven't been destroyed due freezer melting down last month, in the past week. So I can start doing the big blue assay in earnest.
In other interesting news, an recent study found that African women infected with AIDS can actually cut the rate of transmission to their children by breast-feeding. Read the whole article here . I guess this is just one more reason to breast-feed.

HANK: I'm just so frustrated with Bobby. He thinks insurance is some magic fairy who just waves her wand and makes teenage jackassery disappear.
PEGGY: "Her" wand? I always think of insurance as a boy.

You all know why you're here, you're rich and famous and you can't keep your piehole shut

I mentioned that I have been listening to podcasts at work. I have mostly been listening to science and literature based podcasts, but today I found the best podcast. There is an NPR podcast called the Unger Report that is completely hilarious (which I get from iTunes). It is a 5 minute "satire" report about different topics (like celebs going to rehab which is the source of the quote to the upcoming election). Another podcast that I recommend is EatFeed (which you can get from EatFeed.com). There are two podcasts that I listen to, EatFeed In Season which they discuss what foods are in season and then EatFeed Midwest which discusses the cuisine of the Midwest.

"You could get your arm ripped off and there is no one to sue." - Lucky

That is why God created March, so that people who have never had a hangover will know what it feels like

So for past week or so I have been in kinda of a crappy mood mostly due my ever-lasting cold and work at the lab stretching on for days with no end in sight. But now, I'm in a much better mood. My cold is finally gone (so I can stop blowing my nose every ten minutes!). And work in the lab is going much better. I was finally able to start work on the Big Blue Assay and find out if the freezer meltdown from earlier in the month has really messed eveything up. So far the tissue seems to be OK (which I found out after isolating DNA last week) and the E. coli is still viable. There is really only one more thing that I have to test tomorrow. I've also been listening to all sorts of Podcasts while I work. I'm half way through a lecture series about Medieval England (given at Oxford) as well as NPR books and various Garrison Keillor shows (the title is from a recent "News from Lake Wobegon" airing).
And I have been watching the BBC show "All Creatures Great and Small" which has made me miss home and at also relieved that I decided that I wouldn't want to be a vet (specifically when James doesn't use gloves!). My mom's post about the vets working four hours also made me happy about ruling out that career. I think I would have given up after two hours! I also love that the James and Siegfried wear nice shirts and blazer and then bring work clothes, seems that they should just wear their work clothes. I'm also excited because pledge time on PBS is finally over so I can watch FRONTLINE tonight!

"I've always wanted to see walnut in the wild."- Hank Hill