Basefree

Burma Road

I recently had another spectacular weekend at Smith Rock.

I spent most of my time mountain biking since I was the only beginner climber in the group and have been needing to get on my bike for a while now. I watched Lisa and our friends climb quite a bit too. One of them almost redpointed a 5-14 route! Mountain biking in the desert is quite different than riding in rainforests of western Washington/Oregon. I kept feeling like I was going to fly off the side of the trail and perhaps over a cliff because there were no trees lining the path.

The ride was basically up and then down. The "up" part consisted of a horrific three-mile climb of pain up the aptly named Burma Road.

I wasn't too upset about the climb since a couple other molecular biology grad students and I are in the process of training for a half-marathon, so I need every workout I can get. After climbing the Burma Road, I decided to climb even more in order to get to the top of the tallest geographical feature in the area. The trail to the top of the peak was horrendously steep however, as well as covered in large loose rocks so I ended up pushing the bike to the top of the hill.

The view at the top of the hill was pretty damn nice. It was even better the next day I climbed it, but I didn't take a picture on that day (oops).

Since I was riding alone, I attempted to use the timer on my cheap digital camera to take a self portrait on the top of the peak, but the results were a bit questionable.

The ride back down was pretty intense. It involved a lot of fishtailing and praying that my front tire wouldn't wash out. At the bottom of the hill when I had come all the way down, my disk brakes smelled kind of funny. They are definitely broken-in now. Soon, my name will be "Mr. Nose-Wheelie", or perhaps (and more likely) "Mr. Painful Endo as a Result of an Attempted Nose-Wheelie".

In other news, I have decided on a lab for my Ph.D. research. Starting this summer, I will be working in the Johnson lab. I will probably be doing all kinds of wacky genomic/proteomic experiments involving exposing fruit flies to esoteric stresses. I am also going to be a part of the first ChIP-Chip experiments done on a “real” eukaryotic organism (i.e. something other than yeast).

Gordon

Several people, well... actually only J-4, has/have been asking about what I am doing in school these days. I am in the middle of my final rotation at the moment and am in the process of trying to decide on a lab to settle in for the next few years.

I am currently working on trying to establish zebrafish as a model organism for studying the roles of intestinal microflora in gut development. In humans, the number of bacteria living in the digestive tract is at least an order of magnitude greater than the number of cells in the human body, so it isn't surprising that this "normal flora" plays many important roles, including aiding in digestion, protecting us from all sorts of nasty pathogens, and is necessary for normal development. Historically, "germ-free" mice, rats, hamsters, and even kooky animals like cows and goats have been used to study the interactions between hosts and their microflora. Zebrafish have several advantages over the traditional model organisms used for studying these interactions. Namely, fish embryos and larvae are clear, lots is known about their development, and they reproduce frequently and mature quickly making them useful for all kinds of fun genetic techniques.

So, I have been looking at conventional and germ-free fish, attempting to see differences in cell proliferation (using BrdU labeling and/or antibodies to phosphorylated histone H3) and glycoconjugate expression on the surfaces of epithelial cells that line the lumen of the gut (using fluorescently conjugated lectins). All of my stains/antibodies are working, but raising germ-free fish has been a colossal pain in the ass. I either don't kill all the bacteria, or I kill both the bacteria and the embryos. I need to find a happy medium in my killing.

Here is a picture I took last week. Red is fluorescently conjugated soybean agglutinin (SBA), green is anti-BrdU, and blue is autofluorescence.

P.S. Anyone who can figure out why "Gordon" is the title of this entry gets a gold star.

B1k3 pr0n

Here, for no particular reason, is a picture of my bike. It was originally a 96 GT Ricochet, but it has since morphed and evolved extensively, and now all that remains from the original bike is the headset. It has gained a bit of weight lately, but it is worth it. Riding scary technical terrain is much more fun on a bike that feels indestructible.

Here are the specs for anyone that cares:
2001 19" Deep Cove Stiffee FR frame
2001 Marzocchi Z1 MCR fork with 5" of travel
2000 XT derailleurs, shifters, cassette, and cranks/bottom bracket
2002 Hope M4 disk brakes (big hunks of British-made machined billet aluminum)
Sun Singletrack rims (basically disk-only Rhyno-Lites) laced to XT Disk hubs with big fat spokes
Easton EA50 riser bar and seatpost
WTB Motoraptor tires or Wierwolfs depending on trail conditions
ODI lock on grips
SRAM PC-89 chain (way better than Shimano chains)
Specialized Body Geometry Comp seat (paid like $99 for it then J to the 4-cob got one for like $20 a week later)
Cheap-o Redline BMX platform pedals

Observation #2: Community Members

While I don't feel nearly as confident about the content of my lectures as I did last term in cell biology, being a TA for ecology and evolution has been a kick in the man-pants this quarter. I am relearning all sorts of things, and get to participate in activities seldom undertaken by molecular biologists such as wandering through the forests of western Oregon and picking up salamanders.

In other science news, look for an update in a couple of days in which I will describe the research I have been doing this term.

You'll never defeat Andross

I got an email from the sperm whale the other day. Apparently he is in a rock band these days, and is working on finishing a degree in electrical engineering at WWU. Attempting to think of the kinds of stuff Anderson will create with his electrical expertise makes my head hurt. I miss that guy. Does anyone remember the fateful day when we discovered that Unix had eaten Linux? The horror...

On a lighter note, here is a kick ass recipe that I call "Tasty Ginger-Mango Lassi of Joy". I am pretty sure that it is ultra healthy, and it tastes like God. It serves 3-4 people, depending on how much you want. I like to make it for dessert at night and refrigerate the leftovers for breakfast the next day. If you try it, comment and let the world know what you think.

*In a blender, combine: 3 cups of chopped peeled ripe mango, 1/2 cup of water, 1/3 cup of sugar, 3 tablespoons of chopped peeled fresh ginger, 1 tablespoon of lemon juice, and 2 cups (16oz) of low-fat vanilla yogurt.
*blend until smooth
*drink and feel joyful with the knowledge that you are tasting God.

Uh! What is it?

I have been walking past this chalkboard just about every day for the past month. Each and every time I see it, I must stop and ponder: who the hell made this horrific creation? What in god's name does it mean? It is in a hallway with a bunch of synthetic organic chemistry labs, so perhaps ether was somehow involved in its creation. Any ideas on what the significance of this piece of art might be?