Friday, December 22, 2006

Air out. Titanium tetrachloride in.

I've been blogging sporadically lately; sorry about that. In the department of simple but really useful ideas, a postdoc in the lab next door is using a vacuum food sealer to package up some moisture-sensitive reagents. I can understand that he probably doesn't want to bother using our glovebox to store chemicals. Happy Chrismahannukwanzaakah to you all, and thanks for reading.


Wednesday, December 13, 2006

Busting out (cells) all over

In keeping with the theme of Kyle's hilarious post, I'll throw in my own two cents. A couple of weeks ago some friends from the lab next door went to a Starbucks coffee tasting. It was one of the windiest, rainiest, nastiest nights in a while, so they apparently were the only ones there. By the way, the "Christmas Blend" is the same as the "Holiday Blend", in case you were wondering. Yes, the Starbucks people used a French press. The only nagging question I have is whether there is some cutesy urban legend about the connection between the coffee French press and the French press biologists use to gently crack open cells. Usually, when you want to recover a protein that you have manufactured in lab bacteria, you want a gentle method that won't damage your protein. You may also want to get at intact organelles, or something. In my very minimal protein purification experience, we would rapidly freeze, then thaw cells for a few cycles. For the proteomics I currently do, I use a Dounce homogenizer.
Here's a great basic reference for the ways to bust open cells.
Incidentally, I love Starbucks's eggnog lattes, but going to Starbucks in this town sometimes seems taboo, like you're getting your coffee from the man. Locals seem to prefer Small World coffee, and it's growing on me. Once Starbucks cans its seasonal beverage I might try to make the change permanent. (But yes, Jack, Halo Pub still makes the best mocha.) The Small World coffee tee shirt is one of the default gifts that grad students seem to get when they finish, regardless of whether they frequented the place or even whether they like coffee.

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Friday, December 08, 2006

Trying not to use the obvious title joke here..

I think my favorite science to read about is the type where the central idea is so elegant, you wonder why no one had thought of it already. PCR is like that, and in my mind, so is this recent JACS ASAP.

The ref: JACS 2006, DOI: 10.1021/ja0657307 (subscriber link)

The background:
I was in a bioinorganic/ biophysical chemistry lab a few years back, and the topic of FRET came up a lot. If you're unfamiliar, FRET stands for Förster resonance energy transfer (you'll also see fluorescence resonance energy transfer), and it is a convenient visual tool for measuring distances. This comes in handy when you want to learn more about protein-protein interactions, receptor-ligand interactions, and conformational changes.

You need 2 fluorescent dyes for a FRET experiment. In a simple case, you attach one dye to protein A and the other one to molecule B, and watch for changes in how they interact. If you did everything right, you'll see a different-colored glow depending on whether A is close to B.
Of course, you conscientiously selected your dyes so that their energy profiles overlapped just right. If A and B are close together, when you shine a light that would otherwise make A glow, what you see instead is mostly B glowing. That's because instead of glowing, A is able to hand off its energy to B in a way. That phenomenon is what's called FRET. Read this if you're interested in more details. Also, Lakowicz's Principles of Fluorescence Spectroscopy is an excellent book that discusses the field.

The authors wanted an easy way to visualize a working enzyme in a living cell in real time. In other words, no additional prep time to wash out excess dyes, or having to bust the cells open to "see" the results.
Rather than bringing in two dyes on two separate molecules, the research team made a probe with two carefully chosen dyes built in.
When the target enzyme is catalytically active, it cleaves a protective group from a phenol to yield a quinone methide. There's a leaving group involved in generating the quinone methide. In this paper, the leaving group was one of the dyes. After the labeling event, the dyes aren't close together anymore, so no more FRET. (I can't remember where the liberated acceptor dye ends up, or whether that was mentioned.) The quinone methide that's left behind is a highly reactive alkylating agent that's known to latch onto any nearby nucleophile in a protein. Bingo, protein labeling and color change in one shot.


Wednesday, December 06, 2006

Whaddaya think's in the tacos?**

The E. coli outbreak that swept central Jersey and surrounding states now seems to have been traced to green onions distributed to local Taco Bell restaurants. So, no Jersey jokes allowed.
Cue the renaissance of this 60's hit off the American Graffiti soundtrack.
I'm just glad reporters mostly shied away from the obvious "Run for the Border" headline.
Nothing's been confirmed, but Taco Bell's parent company is pulling all green onions from its shelves. For a slightly propagandistic (is that a word?) briefing on E. coli O157:H7, the virulent strain behind the food poisoning, pick yourself up a copy of Fast Food Nation.
What I remember from college is that this particular variety of E. coli produces a toxin that inhibits protein synthesis in a way similar to ricin, and often results in substantial kidney damage.
When I was a college freshman, we had case studies in our general chemistry course, and the one in the nuclear chemistry chapter was based on the Jack-in-the-Box E. coli outbreak of the 1990's. As I recall, we discussed the background of the case and debated the merits of beef irradiation.
This link about irradiated beef is pretty thought-provoking. Show me a guy who goes to McDonald's to boost his daily intake of essential vitamins, and I'll show you a doctor running a health website who does not believe in vaccinations or mammograms.
Quite a bit of the news coverage for this Taco Bell incident refers to Jack-in-the-Box, more so than the more recent E. coli outbreak in spinach. That doesn't make sense to me unless it's eventually demonstrated that the ground beef in the tacos is to blame. Maybe newswriters just think it's better to compare/ link fast food restaurants in their coverage.
I guess this is just a wake up call to me and any other non-red-meat eaters who are smugly thinking "this won't happen to me". I haven't eaten at Taco Bell in ages, but I got really cozy with arugula earlier this year.

** Hopefully a few people remember the TV show "You Can't Do That on Television"....