Science Monkey

As of last Friday, I’ve switched projects. Well, refocused my aim. No…it’s a project switch. I’ve spent approximately the last three years examining the long-range interactions along the entire domain in both human cells and in mouse tissues and have finally accepted that it might take another three to do the job completely and thoroughly. My thesis committee (and I) is dismayed about my apparent lack of concrete progress (ie, no papers) and feel I should be at a point now where there’s a clear end in sight. So, at their urging, I’ve switched to a “safe” project, one which will still be scientifically interesting but is not going to have the technical roadblocks that the whole-domain project does.

The plan now is to characterize the promoter and imprinting status of one gene within the domain, including DNase I hypersensitivity, ChIP, in vivo footprinting, methylation, etc. I’ll have the 3C data as well, but it will be focused on the one gene, rather than the entire domain.

I’m rather bummed about this, naturally. However, I think it’s the wise decision. Switching projects is my choice and I’m committed to the new project, but that doesn’t mean I have to be overly thrilled about having to do it.

The switch does give me a nice end goal, though, which is a pleasant thing to see after so many years in the mire.

Dolores Heggestad
5/3/1915 - 1/25/2007

I’ve finally finished my presentation for Chromatin. I’ve uploaded it here in case any of you want the slides. The parts of this work that are mine I am releasing under the CreativeCommons-attribution-sharealike-2.5 license. The other parts are copyright their respective owners.

The paper can be found at http://dx.doi.org/10.1038/ng1929.

The presentation can be found at http://www.sciencemonkey.net/work/070125 chromatin jc.ppt.

In celebration of getting two eggs from our chickens today, I did a little math. So far, we’ve spent $30 on the chickens themselves, $13 on the first bag of feed and a bale of hay, and $10.40 on the 50-pound bag of feed today. We’ve gotten a total of 7 eggs. That comes to a total of $7.63 per egg. Not exactly economical, but they sure are tasty. Plus, the chickens are awfully cute.

After getting dressed in the mornings, I typically forget the specifics of what I’m wearing. That is, I may know I’m wearing a blue t-shirt and jeans, but the writing/printing on the shirt is lost to the recesses of my mind. I bring this up because today I kept getting strange, half-smiling looks around the hospital. I, of course, am wearing my geek. t-shirt and have completely forgotten. *sigh*

Oh! Speaking of geek, the second-place finisher in tonight’s Jeopardy ended up with $42. Heh.

Today’s journal club was…not great. The poor guy…he was just over his head. He’s a master’s student, this was his first presentation, his English isn’t great, and this was the first meeting of the term. Even worse, the paper was pretty poor, so he didn’t have a lot to work with. I totally need to decide what I’m going to present next week. I really want to do something other than 3C and chromatin loops.

The rest of the day today was pretty good. I went in to work early — I was in the lab by 7 — and worked until a little after 5. I could’ve stayed for hours more, but decided I had done enough. I have 40 minipreps waiting for me in the freezer to do tomorrow morning. Prep, digest, gel, spec, sequence. Fun.

My first-ever self-designed Southern probe looks good! I’m pleased. Okay, so I had good instructions, but I’m still tickled about the results. I’ll develop my next three tomorrow, so we’ll see how my streak goes. I’ve also been working with radioactivity for two days now and still haven’t contaminated myself or the lab. Yes, it’s only 32P, but so what? It’s still radioactive. It might, if you swallowed a lot of it, cause a mutation or two. Seriously, it’s only dangerous to your eyes, and I found Mayur’s old yellow goggles yesterday. They’re hella-cool, man. Everything is so…crisp and vivid with them on.

I got my first set of bisulfite sequences back today, too, and they look pretty good. One set of my results was about 80 bases shorter than I expected, so I need to go make sure that I’m not amplifying Frat1 by mistake. Frat3 is a duplication of Frat1, so the sequences are awfully damned similar, and after conversion will probably be more similar. I get some Magel2 sequences tomorrow…

Blah, blah, blah. Enough about work. Life outside of work is pretty good right now. I could whine about my sleep problems, but I think I’ll skip that for now. Emma and I were supposed to have our first piano lessons yesterday, but our friend had to cancel. We’re scheduled for Sunday now. I’m excited. I even broke out my French horn the other day, got the valves unstuck, and played a little bit. I’ve forgotten a lot, but I’m hoping it will come back with some practice. I think I mentioned the other day that I bought Phil Farkas’ book (The Art of French Horn Playing) and it came in yesterday. It’s pretty good so far and it has Farkas’ own warm-up exercises, too. Of course, his warm-up would probably take all of my practice time…

Enough for now. I’m going to watch some CSI and try to crash. Maybe I’ll whine about my sleeping tomorrow night. Happy Thursday evening! Buenas noches!

I worked a half day today, because of the holiday. Well, maybe slightly more than half a day…I was at the lab from about 8 until 3, instead of 6. There was almost nobody around. The only other person in the lab was one of our undergrads (how dedicated is that?). I don’t know whether or not Tom came in…I never saw him in the lab. And since our grant is due to DSR by Wednesday, I hope he came in…I did manage to get a pretty good amount of work done, though, despite knocking off early. Fewer distractions, I suppose. Tomorrow threatens to be a busy day, particularly if we’re going to be buttoning up the grant.

In music news, Emma bought an adult beginner method book for the piano. I remember more than I thought I would, but I wouldn’t want to start at any more advanced of a level than I am. Two hands at once? Really?

In other music news, I broke out my French horn this morning and tooted around a little. The keys were only slightly stuck, and I managed to get them working nicely with just a little oil. I didn’t sound horrific, but I certainly didn’t sound good. I ordered Phil Farkas’ book this morning and am looking forward to screwing around with that in addition to the piano.

The chickens are doing quite nicely. We got another egg today, for a total of five. We gave the first to our neighbors who were so helpful when our runaway got out. We missed one when all of the chickens were running around in the backyard, but have three in the fridge. Well, two. I used one to bake brownies tonight. What a lovely yellow yolk that egg had. And a remarkably thick shell. Good chickens.
Speaking of chickens, I think I’m going to build a live webcam for them. I read the plans from Make’s weekend project today and think it’d be fun. I’m going to set one up inside the house first, so I can avoid all the weather-related issues involved in putting one outside, then I’ll get one set up in the chicken coop. I’ll put it on the lower level, so we can watch them playing around downstairs during the day. For any of you at Make reading this, my birdfeeder won’t have the greatest species diversity but sightings will occur regularly.

Time for a little God of War, then off to bed. Happy Monday, chickadees.

It wasn’t too bad this morning. I survived, which always beats the alternative. My arms were pretty sore all afternoon and my legs are starting to tighten up now, but it was a good workout. I wish I could go every day, but their times are pretty incompatible with getting any work done during the week. I could go at either 8:30 and lose the morning — class until 10:30, home and shower by 11 or 11:30, and I’m not to work until almost noon — or rush home after work to catch the 6 PM class. Maybe once a week (or so) I can plan to leave work earlier in the afternoon and go to the 6 PM class. Wednesdays might work.

Speaking of Wednesdays, Emma and I have our first piano lessons on Wednesday! We bought an electric piano (a Yamaha PX-700, I think) over the weekend and had previously found a friend who is willing to try and teach us. He’s getting his master’s in music (possibly music education), so he *should* be able to do it. Maybe I’ll break out my French horn, too, instead of letting it collect dust on the floor of my office. Well, the case is collecting dust. The horn is in beautiful condition.

I’m fairly pleased with the development of these hobbies. I’m riding my bike more, learning to play the piano, and getting more regular exercise. If only I could throw in a martial art, I’d feel all badass. Oh, and get sailing again. Damn, I miss sailing. I was looking into building a boat this past weekend, but I don’t think I have any convenient space to build it. Our shed is full of stuff, naturally. I could use the converted garage room, but I don’t know how I’d get the boat out once I was finished. I need to think about it some more…

Happy day off, for those of you playing hookey tomorrow. I’ll be at work for the morning, at least, and am hoping to just treat it like a regular day. I’ve got plenty of work, but feel free to come distract me if you’re at the building and bored.

I’m off to hot yoga, for the first time this calendar year. I haven’t been in about four weeks, so this is going to be most unpleasant, I fear. I’ll feel good afterwards…maybe if I keep telling myself that, I’ll believe it.

Forgot one project last night: analysis of mRNA levels in multiple mouse tissues of our genes, as well as determination of an appropriate control to use. Hey! Any suggestions? I’m currently trying 18S rRNA, beta-actin, and TBP. I’ve used the 18S and beta-actin before but the level of expression of our genes is so low that I’m at least 10 Ct values away. I just read about TBP as a control, so I’ve got primers to try that. We’re looking at brain, liver, heart, spleen, and lung tissue right now, but will want to include any tissue we can cleanly isolate.