Wednesday, November 29, 2006

Pimp My Instrumentation

With the arrival of the MacMillan group, change is sweeping our lil' department. We are getting three new NMR spectrometers to complement what we currently have. They won't be ready to use for a little while, but I'm really looking forward to the day when I will no longer have to wait in line to use the instrument and get the data I need to move forward.

NMR is short for Nuclear Magnetic Resonance. An NMR spectrometer is a machine that operates on the same principles as an MRI (magnetic resonance imaging). Don't get worried when you see the word "nuclear"; this instrument's no more dangerous than an MRI (unless you wear a pacemaker). We organic chemists use NMR several times a day to help figure out the chemical structure of the stuff we make.

Non-chemists, all you need to know is that compared to what we had before, this is frickin' sweet.

Now, for specifics:
Our old NMR's are Varian's and the new ones are Bruker's. Having only used Bruker as a biochemistry undergrad taking phosphorus NMR's, I can't really compare the experience. It seems like most organic chemists feel strongly that one is better than the other, and that Jeol is a distant third.
We get a couple of cryoprobes, specifically Bruker's TCI probe and QNP probe. The latter apparently allows users to switch by computer between 4 different nuclei without changing the probe tuning.
Also, we will have probes with heightened carbon sensitivity, meaning you can take a carbon NMR in the same time it would take for a proton (a couple minutes).
These instruments are actually located pretty close together and it's going to take some extra effort on Bruker's part to make sure everything works normally. Bruker may use our department to showcase their Ultrashield NMR's and the compact setup.
Each system is fully automated. We will just drop off our NMR tubes into the autosampler and the instrument will print out a spectrum and email the raw data and pdf of the spectrum to us.
There's a Bruker rep on campus every day setting up this instrument and its software, as well as the 2 other NMR's, which'll be in the next room. More as it develops.

And here's one of our babies as it stands now. (A big thank you to Istvan Pelczer for this photo.)
If you haven't seen one of these instruments before, the magnet in the instrument needs to be kept cold, so it's encased in an insulating metal container that's filled with liquid nitrogen and liquid helium. That's really cold, far below zero.


Wednesday, November 22, 2006

The big brother I never had

Early yesterday morning, a few people came by the lab to install temporary mats by some of the hoods. The general idea is to monitor how much time we spend working at the hood each day. The mats sense our weight and record a length of time in a networked "box" just outside the lab. The compiled data get downloaded later.
No, it's not some passive-aggressive move on the part of my funding agency. Princeton Chemistry is breaking ground for a new building soon (our first new home since the Coolidge administration!) and an estimate of our time spent at the hood goes into choosing the best system of new hoods for the new building.
So let me back up a bit here and tell you what a hood is and why I use one.
Fume hoods are a mainstay of the organic chemistry lab. A hood is an enclosed workspace designed so that we can perform our experiments in a space that's fairly isolated from the air we breathe. Air flows up into the hood and away from the lab, sparing us from a lot of noxious fumes and small, potentially lung-coating particles. I work at the hood standing up, though I sometimes sit at a bar-stool height seat. The hoods in our lab are about 6 or 8 feet wide and pretty deep, longer than arm's length for me. They're outfitted with places to secure our flasks, vials, test tubes, whatever. Also in my hood are magnetic plates for stirring and heating, a couple of water taps, and a line for putting reactions under a vacuum or under an inert gas (see my entry on gloveboxes for a reminder about why that's important.)
You can imagine that several hundred of these hoods constantly sucking away air makes it costly to heat and cool a building. There have been improvements in hoods' energy efficiency with new designs, and we will be getting these "improved" hoods in the new building. The MacMillan labs are already equipped with new, energy efficient hoods. I guess they just want to get an idea of the volume of airflow that the we use in a given day, hence the mats.
One problem I see is that I'm not sure whether they are assuming that everyone closes their hood to save energy when they aren't working at them. Wishful thinking in this building. I know I'm not always very good about that.
The mats are about the size of a welcome mat and nondescript gray in color. Not nearly as nice as what I currently have attached to my XBox at home for playing Dance Dance Revolution. (You laugh, but try playing the advanced level. Tell me that's not a good workout.) This is kind of similar to what we got.
Needless to say, the mats spawned a couple of creative strategies in the group for "enhancing" the hour count, from moving our argon tanks on top of the mats to offering extra credit to undergrads to stand there for you.
So basically, it looks like I might soon be able to construct a bar graph like the one Kyle made here.

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Friday, November 17, 2006

A Shot in the Arm

I got my flu vaccine for free last week through Princeton Health Services. To encourage us to get vaccinated, there was an ad blitz campuswide for "FluFest", a two-day event at the student center which featured performances by our a cappella groups and free food.
I won't bother blogging about why you should get your flu vaccine, or complaining about misguided rants, because that's been done to death. Search if you don't believe me.
For up-to-date information on the vaccine and the flu, click here to go to the Center for Disease Control's Website.
See here for more details about what's in the vaccine.
The two types of vaccine:
1) The trivalent inactivated influenza vaccine.--> I got this one.
"Trivalent" in this case means that the vaccine provides immunity to three different strains of the flu. The three strains in the vaccine change from year to year, depending on what health professionals have determined to be the most likely ones to be going around that particular flu season.
"Inactivated" means that the virus isn't infectious. You just get the parts of the virus that trick your immune system into doing its job. Mostly, that's the outer coating. It's like the story in the bible about how Jacob fooled his blind father Isaac into giving him the blessing intended for his hairier brother Esau, by wearing hairy goatskins.
2) The live, attenuated influenza vaccine.
"Attenuated" means weakened.
This vaccine is a nasal spray, not an injection.
The modified viruses for both types of the vaccine are grown in chicken eggs. This technology has been around since at least as far back as the 1950's, and it's why people with egg allergies shouldn't be given this kind of flu vaccine.
I searched PubMed for "embryonated hen's egg" and it looks like plenty of things can be grown in chicken eggs, like herpes simplex virus and hepatitis. I wonder why we still use this system. Seems to me like we should be able to make a synthetic, hypoallergenic cocoon for these things to grow by now.


Friday, November 10, 2006

I'll own up to it

I shattered a dewar for a 500 mL round-bottomed flask today. I was wearing gloves and goggles, the dewar was in my hood at arm's length, and no one was hurt, but the BANG! was so loud that I was trembling for the next five minutes.
Here's a link to Princeton's lab safety website and its recommendations on dewars.
A dewar is an insulated container that I use for my cold baths in the lab. The most common cold bath I use is a mixture of dry ice and acetone, which has a temperature of 78 degrees below zero (Celsius). It's important to run some reactions in the cold to prevent uncontrolled reactivity.
Anyway, this particular dewar is made of glass that is lined with silver. The whole thing is surrounded by aluminum metal. The reason a dewar insulates so well is that it's a double layer flask with a space for a vacuum between the walls.
Dewars implode when they are broken, meaning that they collapse in on themselves instead of exploding outward. However, there's still a risk of small glass particles flying around and injuring someone.
The most famous dewar out there is the humble Thermos that you took to lunch every day in grade school.
In homage to the Tenderbutton style of blogging, I've posted pictures of the dewar so you can see the damage for yourself. I think I needed a better camera for this. The aluminum/ glass reflects light really well and is hard to photograph.
Here's a regular dewar.

Here's my shattered one.

Kids, don't try this at home. We're trained professionals.


Blogger Beta

I finally made the switch to the beta version of the blogging website. There may be some bugs in the coming weeks (ie, in past weeks, other bloggers have not been able to see or post comments.)
So bear with me.

Wednesday, November 08, 2006

I Wish I Swore by Something with a Nice Fragrance

Late fall is upon us, and the inevitable cold weather chapping and cracking of the skin on my hands has begun. The situation is exacerbated by having to wear gloves and wash my hands repeatedly at work. Proguard is a moisturizer that's available from the Fisher catalog, which is a one-stop shopping depot for general lab supplies, as well as direct from the Princeton Chem. stockroom. It is THE ONLY THING that ever keeps my skin from cracking. I use a little every time I wash my hands and it's fantastic; I even bought one for home (Jason wears gloves, too.) I hate to waste money on one of the cute little travel size packages of scented lotion for my purse because I know it'd be purely ornamental. I just throw some Proguard in a travel size case. Ideally, I'd like to be able to take my Proguard to something like The Body Shop and just blend it with any fragrance oil to use outside of lab. Come to think of it, that's something I'll have to try, but I doubt they'd help me out unless I was buying their brand of lotion. Proguard will definitely be one of the things I miss when I graduate. Maybe someone on the inside will be able to hook me up.
Just for fun, I thought I'd do a quick comparison of the main ingredients in Proguard ("P") versus my favorite scented moisturizer (we'll call it "WVS" for short, but those of you who know me should know what I'm talking about). I don't really have any sense of the percent composition of either lotion, because the ingredients are listed in descending order of percentage with no concrete numbers, as they'd be on food. I never stopped to think about moisturizer formulation before. Moisturizers have to multitask on the outermost layers of the skin, repairing damage and sealing in water, without triggering allergies or any other adverse reaction.

emollient (skin softener):
P = cetyl alcohol
WVS = cetyl alcohol, stearyl alcohol, petroleum jelly

silicone oils: (they form a protective layer)
P = dimethicone
WVS = same

humectant (hygroscopic substance, something that absorbs water):
P = sorbitol, propylene glycol
WVS = glycerin, propylene glycol

P = diazolidinyl urea (formaldehyde-releasing goodness!), methyl and propyl paraben, tetrasodium EDTA
WVS = basically the same

the ref: Characterization and chemistry of imidazolidinyl urea and diazolidinyl urea. Contact Dermatitis 2006 54, 50-58.
So all the key ingredients are nearly indistinguishable, but the scented stuff also contains vitamins, which I'm not sure would penetrate deep enough into my skin to do me any good anyway. (Anybody know about those properties for specific vitamins offhand?) The difference in cost is negligible when you factor in the size of the package and assume a little discount for buying in bulk.
With all this newfound knowledge of moisturizers, I'm not sure I buy into the Creme de la Mer craze, what with all their "miracle formula" sales pitch. "Even now, it is not entirely clear how Creme de la Mer works," they say. To me, it seems like the ingredients that work best in moisturizers are pretty cheap (dimethicone can be found in Silly Putty!). Anyhow, for some sciencey-looking stuff (fermentors!), I recommend you click the link labeled "The Miracle" and enjoy the movie.


Monday, November 06, 2006

Belated Halloween Edition

Porphyrias are a family of relatively rare diseases that present symptoms reminiscent of the characters immortalized by Lon Chaney, Jr. and Bela Lugosi. There's ample discussion in the literature about whether these diseases spawned the myths we recognize today. Porphyria sufferers may have anemia, light sensitivity, and reddish colored urine, or excessive hair growth. The underlying problem has to do with how the body makes and utilizes porphyrin, part of an oxygen-carrying complex in our blood. The molecular underpinnings of the disease are largely unknown, but a recent Nature letter presents evidence that some porphyrias may be due to a defect in a specific protein.
the ref: Nature 2006, 443, 586-589.
This protein, called ABCB6, transports porphyrins to a place where they can bind to iron. This iron-porphyrin combo eventually ends up in hemoglobin. This work points out that it isn't necessarily just the production of porphyrins that's the problem, that getting porphyrins where they need to be so that they can do their job is equally important.
This idea reminds me a little of the distinction between Type I and Type II diabetes. The underlying theme that diseases with the same symptoms could come from "manufacturing" or "distribution" issues must be more common than I realize.
Type I diabetes: decreased or no insulin production
Type II diabetes: insulin's around, but the body isn't responding to it properly
There was supposed to be a chemistry grad student with porphyria beginning in my year, 2002. The department spent a sizable chunk of change renovating an entryway so that she could turn off all lights when she needed to, and they built her a private office and everything. (I think she would've been a computational chemist). She deferred enrollment for a year and then never arrived. Not sure where she is today.