Memorial Day...

We went to Buffalo to visit the family over the weekend (well, not Memorial Day, since Jenny worked that day). Good times and great weather all around. We grilled burgers, brats, and kabobs (and bananas), and had dessert and wine out on the dock.

Chris and I took the canoe down the Crow River, opened some beers, and floated Huck Finn-style down the way. We saw some deer, muskrats, and a beaver (which caused me to spill my beer, as they tend to do). Fantastic.

The next day Jenny and I took the canoe to a spot farther upstream and did the same thing -- this time with Larry lounging in the middle with a fishing rod in hand. We're such bums.







Flickr set here.

Now I can hear "Celes' Theme" live...

Operation 88 Keys was a success!

For those who don't know, for our one-year anniversary I surprised Jenny with a piano. The whole clandestine enterprise was hampered by her current night float schedule, meaning that if I wanted to keep it a secret, all the pieces had to fall into place after 5:30 pm. At the last minute I managed to recruit some hale coworkers (mainly with the promise of beer) to assist with moving the corpulent klavier and, excepting a bit of rain while driving the piano home, it all went off without a hitch.

Well, technically there was a hitch, as that's what I had to attach the rented trailer to. That's a story of its own, really, because I borrowed Larry's Vandura for the job and the alternator crapped out just after I returned it...

Anyway, the tuneless, soulless piano was in the living room in time to surprise Jenny the next morning (along with a collection of Tchaikovsky sheet music), so -- all the subterfuge aside -- I'm a hero. I didn't have the foresight to have the video camera ready when she saw it, but I fished it out just in time to catch her playing one song. I'll post the video when I get around to uploading it.

e-i-e-i-o...

We just put in our garden for this year. And when I say "we" I mean "Jenny." I was doing other yard work at the time, but I did help construct that bicycle wheel contraption. Last year we were all about odd varieties, but this year we just went for staples: sugar snap and snow peas, yellow beans, yellow peppers, and red cabbage. We also got free seeds from the Living Green Expo for a few beets and one carrot, and Michelle got some lettuce (but Jenny spilled the pot... twice).



The tepee-looking thing at the back will eventually have gourds and mini-pumpkins when we get around to planting those, but you can see the little red cabbage plants interspersed in the plot. The big plant is the perennial rhubarb. Snow peas are buried in rows in the front and the sugar snaps and beans will (hopefully) climb that maypole.

We also put in some gladioli in front of the house, and have ambitious plans for sunflowers and Indian corn along the fence.

I've always enjoyed the idea of gardening, but I have no horticultural knowledge whatsoever, and the only real experience I had growing up was weeding -- not really the funnest part of the whole ordeal, if I'm honest. It's also difficult to hone one's skills when your garden is smaller than your car (and I have a small car).

I sat through a (not very good) workshop on building cold frames while at the expo, and I'm considering putting one together for next year to help extend the growing season (and expand plantable real estate).

That, of course, will never happen. Maybe I'll just ask Cindy Lueth if she has an old one I can have. I can't believe there are none listed on Craigslist. Lame.

Biology 202...

In an earlier post, I complained about trying to schedule a long experiment when sick. Now that I have a bit more time, I can explain what that experiment was all about.

This is a continuation of the leukemia studies I'm currently doing. I've been analyzing tumors to determine how certain genes promote leukemia, and I've gathered a fair amount of data about what the cancer cells look like and how they develop.

To understand the reason for my experiment, one must understand how cancers grow. Unfortunately, cancer is a widely variable disease, so there are a lot of characteristics that determine what sort of tumor you have and how it behaves. Fortunately, cancer has a set of identified "hallmark" characteristics that are absolutely critical for tumors to grow. Some of these include the ability to promote blood vessel growth within the tumor (angiogenesis) and the ability to prevent immune responses.

Two other characteristics are the ability of cells to divide forever (limitless replication) and ability to avoid death signals (evading apoptosis). The difference between these two is subtle but important. Normally, a cell has checkpoints that control when it divides and how long it can divided for. Similarily, if something goes wrong in a cell, there are checkpoints to prevent that cell from dividing and basically tell it to commit suicide. That means there are two ways for a cell to proliferate into a cancer: either divide at an alarming rate, or fail to die when they should.

To illustrate this idea, think of the number of people living in a town. You could get a population boom because people are zealously procreating with no second thought to contraception or family planning. In conrast, another town could reproduce at a normal rate, but due to longer lifespans, the old buggers don't die off. After a bit of time, both towns would be overpopulated. Essentially, the Baby Boomers represent both these scenarios...

That's right, I just called the Baby Boom generation a cancer...

So the question I have about my tumors is how they're growing: are they dividing too much, or just outliving their potential?

To answer that, you just have to look at how quickly cells are dividing. There are a number of ways to do this, but one common technique involves treating cells (in vitro or in vivo) with a green dye called CFSE. The dye gets taken up by cells, and each time a cell divides, the amount of green color inside that cell is reduced by half. Essentially, the green is diluted out. You can then tell how many times cells divide in a given amount of time based on how green (or not green) they are.

Another common technique is one I'm using called BrdU staining. Understanding this technique requires an understanding of what happens during cell division. For a dividing cell to ensure the right amount of genetic material ends up in the daughter cells, it makes a copy of all its DNA. When this DNA is replicated, it gets opened up and synthesized from molecules you may have heard of: A, T, C, and G. Bromodeoxyuridine (BrdU) is a an analog of thymadine (the "T" of A, T, C, and G), and can take its place during DNA synthesis. Thus, if you treat an organism with BrdU, dividing cells will incorporate it into its DNA in place of T, while non-dividing cells will not.

To detect the cells that have BrdU, you follow up with flow cytometry (which I described in my previous lesson). This lets you detect the BrdU with a fluorescent anti-BrdU antibody, so you can just look to see which cells are fluorescent to know which are in the process of dividing.

"But wait!" you say. "How can you detect DNA with an antibody? DNA is inside the cell! Antibodies can't get there!"
Yeah, well, that's an easy solution. Treating the cells with a permeabilizing reagent (often the detergent saponin) pokes holes in the cell membrane and lets antibodies in. Done.

So anyway, it looks like my cells are indeed rapidly dividing, because they have copious amounts of BrdU in them. Importantly, this doesn't rule out the possibility that the cells are also avoiding apoptosis. It's likely that both unchecked division and death avoidance is going on in these leukemias.

That's like having the baby boomers discover immortality. Scary.


Currently listening to: NPR - Science Friday