Almost every chemist has used mass spectrometry at some point at some point in his or her scientific life, but did you know about all of its cool applications in the study of proteomics? This field has been growing by leaps and bounds as more and more biologists discover the power of mass spectrometry. Check out Nature Methods' special Focus issue on mass spectrometry in proteomics applications.
Allison Doerr (Associate Editor, Nature Methods)
One of our featured protocols this month is for the partial reduction of electron-deficient pyrroles under both Birch (Li/NH3) and ammonia-free (Li/DBB) conditions using the formation of pyrrolines 2, 3 and 5 as examples (for reaction scheme click here). Pyrroles 2 and 5 have recently been published by Donohoe et al. as key intermediates in the of the biologically active natural products 1-epiaustraline, hyacinthacine A119and omuralide (also known as lactacystin -lactone).
Besides being an excellent protocol with beautiful photographs of reactions in progress, it is the first of our Nature Protocols to have associated with it two Network Protocols. These are for the preparation of the starting materials 1 and 4, namely the N-Boc pyrrole 2,5-methyl diester and the N-Boc pyrrole 2-ethyl ester.
Our Protocols Network has two components: protocols, such as these, that are uploaded by users (or suppliers); and comments that can be made both on the open access and the peer-reviewed content. If you would also like to participate, by uploading your favourite method or suggesting modifications to those that have already been published, you could follow the links from our homepage. A Guide to Authors for the Protocols Network also contains more information about this part of our content.
References:
1. Donohoe, T.J. et al. Utility of the ammonia-free Birch reduction of electron-deficient pyrroles: total synthesis of the 20S proteasome inhibitor, clasto-lactacystin -lactone. Chem. Eur. J. 11, 4227–4238 (2005).
2. Donohoe, T.J. & Sintim, H.O. A concise total synthesis of ( )-1-epiaustraline. Org. Lett. 6, 2003–2006 (2004).
3. Donohoe, T.J., Sintim, H.O. & Hollinshead, J. A noncarbohydrate based approach to polyhydroxylated pyrrolidizines: total syntheses of the natural products hyacinthacine A1 and 1-epiaustraline. J. Org. Chem. 70, 7297–7304 (2005).
4. Donohoe, T.J., Sintim, H.O., Sisangia, L. & Harling, J.D. An efficient synthesis of lactacystin -lactone. Angew. Chem. Int. Ed. 43, 2293–2296 (2004).
In the August issue of Nature Methods, which just came out on Monday, we have an exciting and decidedly chemistry-based paper from Werner Nau and colleagues at Jacobs University Bremen in Germany (and it even made the cover!). The authors describe a new concept for enzyme assays using a macrocycle as a receptor for a fluorescent dye and for an enzyme product. When the enzyme arrives on the scene and begins converting the substrate (which does not interact with the macrocycle) to product, the product starts displacing the fluorescent dye from the macrocycle, causing a switch-on in fluorescence. Of course, the macrocycle and dye need to be carefully chosen for each application such that the dye is out-competed by the enzyme product, but once a suitable pair is found, it provides a simple and convenient readout for enzyme activity.
Also of interest: a Review on caged compounds and their application in living cells and an Article describing a rapid method for detecting infectious scrapie prion protein.
A bit of a stretch for a chemistry blog, perhaps, but I couldn’t resist sharing this lovely find. The designer Makoto Tojiki has created some stunning light sculptures with a little bit of science thrown in. Well worth a look if you get a chance as they’re really quite beautiful. Pi is cited to a large number of decimal places along the side of the glowing twisted tapes that make up the sculptures, and he’s called the design ‘Archimedes dream’, apparently because Archimedes was renowned for being a bit of a visionary and ahead of his time.
In some places on the web people are saying that these sculptures are made from organic light-emitting diodes (which is what first attracted my attention). After a closer look, however, this doesn’t seem to be the case. The electroluminescent (EL) tapes appear to be a copper wire threaded through a layer of phosphor, covered in a protective plastic sheath. I’ve never seen them before, though, and I can’t locate more information than that – does anyone know which kind of phosphor is used for them? They tapes are available in a range of colours and I can think of a number of uses for them, though to be fair, most of them involve me doing my own Tony Hart impression and trying to create something artistic out of them.
Vicki
Vicki Cleave (Senior Editor, Nature Materials)
My fellow Cambridge-London commuters; did you work it out? Once you know that it depicts a gene, it’s annoyingly obvious. But despite travelling past it by train about three days per week, I failed to identify the thousands of brightly coloured bars painted on the cycle path next to the rail track near Cambridge’s Addenbrooke’s hospital as a nucleotide sequence. It should have been a clue that only four colours are used.
It probably comes from generally not being very biochemistry minded, as a straight-physics editor. Nevertheless, a friend of mine mentioned he had heard about the biology-inspired cycle path artwork and after some quick Googling, the rumour was confirmed; the colourful sequence stands for the BRCA2 gene, implicated in breast cancer and discovered in 1995.
What a good idea to combine scientific topics with railway scenery. After five years of commuting I would welcome more of these puzzles along the rail track to keep me entertained!
Liesbeth
Liesbeth Venema (Senior Editor, Nature)
A little while ago I read that the French firm J&M Plast, part of the European packaging group Sphere, was turning to potato starch to make a new biodegradable plastic material for bin bags (unsurprisingly called ‘Bioplast’). L’Usine Nouvelle reports on it here - the link is in French but you’ll find an English version on Matthieu Fossoux’s blog. Biodegradable polymers are now widely investigated – starch-based polymers, polylactic acids (PLA) and polyhydroxyalkanoates (PHA), naturally produced by bacteria, being among the most promising.
Meanwhile, retailers are increasingly switching to a “pay per bag” policy. This has proved to be very effective in the past, with a reduction by 90% in plastic bag consumption in the Republic of Ireland, where customers have been charged per bag since 2002. The Swedish furniture manufacturer Ikea has also adopted a similar policy in the UK, and is reporting a massive 95% drop since last June. Ikea is now extending this scheme to the US and all the profits (with a limit of $1,750,000 within 12 months) are to be donated to the non-profit organization American Forests to plant trees and offset carbon dioxide emissions.
While too many shops still routinely give out plastic bags, these reports are certainly encouraging – and the great news is: we can all contribute.
Anne
Anne Pichon (Intern, Nature Reviews Drug Discovery)
Hello, fellow readers and bloggers. I'm back from a blogging break and just wanted to share some exciting chemistry-related papers from the March issue of Nature Methods.
From Ruedi Aebersold and colleagues, we have a paper that compares the three most popular enrichment strategies for analyzing the phosphoproteome by mass spectrometry. Using an unbiased approach, they discovered that none of these strategies alone was sufficient for comprehensive analysis of all phosphorylated proteins in the proteome of cells from a fruit fly. Also in the mass spectrometry arena, we have a Perspective from Steven Gygi and Joshua Elias that provides a guide to researchers using the target-decoy database search strategy to increase confidence in peptide identification.
Peter Schultz and company now present a method to genetically incorporate unnatural amino acids into proteins in mammalian cells, which could open up a whole new range of exciting biological experiments in mammalian systems. And finally, we even have some nanotechnology! Michelle Wang and colleagues describe a method to reproducibly fabricate quartz nano-cylinders, and use them to measure DNA twisting in an angular optical trap.
Thanks for reading!
Allison Doerr (Associate Editor, Nature Methods)
For reasons that will hopefully become clear in the near future, I’ve recently been working on a list of chemistry-oriented papers that have appeared in Nature Materials, and attempting to categorise them into ‘type of chemistry’. You may think that this would be quite simple for a materials journal, and that you could simply lump them all under the ‘materials chemistry’ heading. Sadly (for my workload), not so, and as seems to be the case so often these days in research, most papers fit into several categories at once. Take our paper from last year, for instance, on photocontrolled living polymerisations – clearly of interest to materials chemists, but also relevant for the categories of synthesis and polymer chemistry. Or our paper on redox-controlled permeability of microcapsules – the materials chemistry is of interest here, but the paper has great relevance for biochemists looking at potential drug delivery, too.
All this has reminded me of a discussion meeting I went to last year hosted by the RSC, entitled “Defining materials chemistry”. The meeting brought together many materials chemists and the aim was to pin down exactly where the boundaries of this research area lie. But this seemingly simple remit turned out to be a lot more difficult than I thought it would be. Needless to say, there was plenty of debate, and we ended up questioning whether we could even come up with a perfect definition of ‘materials science’ or what precisely a ‘material’ is in this context. The OED gives quite a good definition of materials science, but doesn’t even try to define ‘materials chemistry’.
The report from the meeting makes interesting reading, although I wouldn’t say we arrived at a definitive answer, so I was wondering if anyone out there had their own definition that might fit the bill? Just putting it into words seems to get harder the more you think about it - though perhaps it's easier to come up with a personal definition than to reach a consensus amongst a group.
Despite the interesting debate, I can't help thinking that for most researchers, the most important definition lies in the research they’re doing, and not the label they are given.
Vicki
Vicki Cleave (Senior Editor, Nature Materials)
Catherine’s entry on toys (here) reminded me of clothing and accessories items I had seen earlier. Kyle at Chem Blog has been selling T-shirts, mugs, wall clocks or postal stamps – which are legal in the US and everything. I didn’t even know that was possible, but I just checked and found out that, in several (all?) countries, you can indeed customize stamps.
The folks at YellowIbis also make T-shirts featuring chemical structures. They picked molecules particularly relevant / amusing – so you can let everybody know that you’re cool as *insert menthol structure*, wear a green jumper showing the structure of a “lucky” 18-crown-6-ether for Saint Patrick’s Day, or alternatively you might want to give this T-shirt to a labmate.
In particular, I’d come across the made with molecules jewellery line, representing the actual structure of certain molecules influencing our behaviour (such as neurotransmitters or hormones). In a less obvious way – except for the DNA ones – the design of these items at Sci Wear also refers to chemical substances, each piece containing the actual microscopic picture of a molecule.
Which molecule would you like to wear? Personally – and you might say I’m biased – I can’t decide between the caffeine necklace and the chocolate (theobromine) earrings...
Anne
Anne Pichon (Intern, Nature Reviews Drug Discovery)
This is my first post...it's all very exciting...so here goes! Has anyone been listening to crusading environmental chemist Jim Lovelock recently?
Bizarrely I fell asleep to his voice on Sunday night then woke up to it again in the morning (on Radio 4 of course). Lovelock strongly believes that nuclear is the only viable energy option for the future, because climate change is ‘past the point of no return’ and renewable energy is underdeveloped. Read a Times review of his latest (and rather pessimistic) book and find out why he says wind farms aren’t green.
Five ways to save the world on BBC2 Monday night presented high tech solutions to climate change. What do people think about these ideas, or about nuclear power for that matter?
Samia
Samia Mantoura (Intern, Nature Physical Sciences)
Hi everyone, this is my first entry so I thought I’d blog about… well, blogging.
Last week I attended a talk by Tony Hey, from Microsoft. He was speaking about e-science and, among other things, talked about CombeChem, an EPSRC project based at the University of Southampton. A small part of the project (see this BBC news article last year) involves replacing the traditional notebook by a digital form. The degree of privacy of the digital lab book could be determined by the user (only themselves? their research group? their university?). Of course the ultimate openness in science is Jean-Claude Bradley’s Open Notebook Science initiative at Drexel University, where he and his group use a wiki as a lab notebook (UsefulChem) and make all their data publicly available. Bill Hooker at 3 Quarks Daily also refers to it in his trilogy about the future of open science, where his posts progress from Open Access to the research literature (here), to the “openness” of data (here), to a fully open practice of science (here).
Nobody can really predict what the future of science will look like. But for now, would you consider blogging about your unsuccessful experiments - those that will never make it into a paper or thesis - to make them available to everyone?
Anne
Anne Pichon (Intern, Nature Reviews Drug Discovery)
Well, yet another ACS has come and gone. I leave you with a rainbow of chemistry talks.
"The formation of chromium rich particles by the dissolution of red clays in groundwater monitoring wells." Mysterious chromium in Oklahoma wells found out.
"Identification and characterization of off-flavor aroma impact compounds in canned orange juice"
Canned orange juice's flavor attributes are "tropical fruit, grapefruit, cooked/caramel and medicine." Yum.
"Research on environmental fate of phenanthrene in Lanzhou Reach of Yellow River." Math says the pollutants will be stable in the river sediment in 70,000 hours.
"The Pennsylvania Green fluorophore: A hybrid of Oregon Green and Tokyo Green for the construction of hydrophobic and pH-insensitive molecular probes." The search for the next fluorescent marker. Amazingly, there doesn't seem to be a band called "Tokyo Green."
"Highly efficient fluorene-based UV-blue light-emitting polymers with controlled effective conjugation length." Ah, making things that glow.
"Purple: The dye of dyes" A history lesson with recent archeological findings thrown in. I wish I had seen it.
Polymers and biology, together in perfect harmony. This meeting has intrigued me with a number of sessions about bio-related polymers. Timothy Long's group had two: one about determining which physical properties of polymers make the best vectors for gene therapy, and one about using DNA base pairs to make a polymer with two sets of properties. Heat it to disassociate the base pairs, and you get a flowy substance, cool to clamp them together again, and you've got something strong enough to do something with. Plus, there's bio-inspired dental polymers from Temple University, enzymes in polymers for sensors from Hawaii Natural Energy Institute, and polymers derived from soybean oil, feathers, and rice. Finally, there was a presentation on making better cigarette filters from Salmon sperm, from the Ogata Research Laboratory, Ltd.
The general crush on bio-related polymers seems to stem from their ability to acquire reactive, "smart" properties from their biological components, as well as from the environmental advantages of making stuff from things that aren’t petroleum. Now, can they produce the self-drying jacket from Back to the Future II?
J.J. La Clair, the controversial chemist (for background, see http://www.nature.com/news/2006/060731/full/442492c.html) in the mutton chop sideburns, gave a talk today to a packed room. It was hot, stuffy, and young in there, as he talked us, mic-less, through what he called "an approach used in a number of labs that I've developed, optimized and made easier to use." As far as I could tell as a layman, the approach had to do with designing synthesis of natural products with florescent labeling and biological tests in mind. I'll leave an evaluation of the technical content to others more synthesis (or biology)-savvy than I. I'll just mention that his first slide talked about his Xenobe Research Institute (which is pronounced "zen-OH-bee"). His slide said that the company was working on 80 studies with academe, industry and government. He must be a pretty busy man.
He acknowledged the contretemps over his claimed synthesis of hexacyclinol—and even included on his acknowledgement page a shot of the T-shirt being sold which memorializes the controversy, saying that he salutes creativity in all forms. And yes, that was my headline on the shirt, but I didn't write it. Reporters very rarely write our own headlines—but we do get to write our own blog post titles. So I decree that the title of this post shall be: "butternut squash soup", since that is what I am eating right now.
-Our gung-ho enthusiasm for antidepressants mean that there is a certain amount of Prozac in the water these days. Freshwater mussels are less than pleased, though, since Prozac is making them release their larvae before they are viable. Freshwater mussels are sensitive creatures, and 70 percent of the species native to North America are extinct.
-In an irresistible item, a peculiar bird called the Black-Bone Silky Fowl has been found to be packed with carnosine, which has a rep for anti-aging and other positive health effects. The bird is a staple of Chinese medicine, and has soft white feathers over black flesh and bones.
-Check out the brand new Chemical Structure Lookup Service, hosted at NIH,. http://cactus.nci.nih.gov/cgi-bin/lookup/search
-Fucoxanthin, from brown seaweed, is taken up by the fat. It seems to both reduce adipose tissue and turn the fat a bright orange. Anti-obesity clinical trials are in the works.
-Adrienne Kozlowski, retired chemist, and her husband, have taken up hot air ballooning as a hobby. They say it is a perfect diversion for chemists, because manipulating the balloon is all a matter of mastering the laminar flow of the air.
-Peter Murray Rust, of Cambridge, on the future of Chemical information: "We are going to start mashing, and it is going to amaze the world."
I went to a talk on by UCSB's Robert Vestberg, on "Synthesis of hydrogels with well defined network structure using Click chemistry", because I have been hearing this buzzword floating around – "click chemistry"—and I wanted to figure out what it was.
But first, hydrogels. Hydrogels are polymers all cross-linked together and stuffed with water. They can be useful in medicine, for example, as soft contact lenses. They are biocompatible, key molecules can diffuse through them, and they are tough. Often the crosslinks are induced by a blast of radiation—like UV light, for example.
Vestberg and his colleagues are using "click chemistry" to do their linking. The click concept was described quickly as a reaction catalyzed by copper (I) that seems to be a one-size-fits-all room temp process that organizes your molecules into a regular structure. Functional groups can be knitted right in.
At least that was the impression I got. The meeting room in the Marriot was next to some sort of noisy kitchen or workroom, and it was hard to concentrate. It sounded like they were banging the lumps out of large cookie sheets on the other side of the wall. The "backing up" beep of some kind of vehicle was also intermittently heard.
Anyway, the hydrogels are made in little Teflon molds. You can make them with other fluids besides water, too. "We've done it in crappy Australian wine that I got from my boss," says Vestberg, who is pleased with his gels, which can be stretched to 1500% their original length before they break, much more than UV crosslinked hydrogels.
After the talk, I did some reading on click chemistry, which was invented by Barry Sharpless. It seems like a kind of Lego chemistry to me. You may be interested to know that searching the program of abstracts for this meeting with the term "click" yields 42 hits.
This meeting has it all. Today I caught a wonderful presentation by Frank Lee of Nanchang University about efforts to introduce “Good Agriculture Practice” or GAP (See the FAO’s page on this approach here), on the growing of herbs for traditional medicines. The idea is to make sure the medicines are what they purport to be, are not chock-full of mercury or other toxins, and are being harvested in a sustainable way.
So, field labs have been set up in Inner Mongolia to work of the harvesting of licorice there—used as a medicine to “invigorate the heart, lungs, spleen and stomach,” among other thing. The most interesting challenge they face is supervising the transition from collecting wild plants to growing them as a crop. They are watching to make sure that the domestication process does not affect expression of the active component. Awesome.
The hype-heavy world of haute cuisine has recently been rolling its tongue over the phrase “molecular gastronomy”, said to be practiced by such chefs célèbres as Pierre Gagnaire and Ferran Adrià. The trend is for innovative foods, and new ingredients. Shrimp treated with protein-knitting enzymes, so it can be coaxed into noodle shape, glass-like spheres of isomalt, filled with the smoke from roasting mushrooms, flavored foam.
But On Food and Cooking author Harold McGee, in a session this morning, opined that the term should be ditched. He noted that most chefs labeled as molecular gastronomists rejected the label and say that their experiments rarely take place on the molecular level. Apparently, the phrase came from a workshop about the science of cooking, held in Sicilly in the early 1990s—but the workshop was, according to McGee, was all about the chemical underpinnings of traditional cuisine, and has nothing to do with the Julia Child-meets-Dale Chihuly creations of the new cooking.
These chefs aren’t looking into molecules, says McGee, “they are cooking with ingredients. They are artists, not chemists.”
That said, there are some firm links between the new daring cooks and chemistry. Fat Duck chef Heston Blumenthal questioned the age-old custom of removing the jelly and seeds from tomatoes before cooking with them. To his palate, they were tastier than the flesh. He worked with Don Mottram of the University of Reading to see why, and they found that the jelly has tons more glutamic acid—the source of the famous meaty, nummy umami flavor (See http://www.nature.com/news/2003/030707/full/030707-3.html)--than the flesh.
So, special note to my boyfriend: I now have scientific proof that de-seeding tomatoes is silly.
I bet $100 that this is the first ACS meeting where a session has featured a slide of Jesus Christ with an erection.
Yes, you guessed it, it is the presidential session celebrating Carl Djerassi: chemist, novelist, and playwright. He was a top chemist for many years, specializing in synthesis of marine natural products, and collecting awards like pogs. Then, late in his career, he turned to literature. Lately, plays have been his thing, and at the end of the laudatory session, there was a reading of selections from his play "Phallacy". He played the character Prof. Rex Stolzfuss. But it was in a scene where a young art historian chats with a young chemist about the representations of Christ's genitals in art that the image, an engraving from the 1520s called “Man of Sorrows”, according to the online text of the play, appeared. Alas, no amount of googling can summon up an image, but rest easy, Jesus is clothed…but showing.
I am no theater critic, so I won’t say anything more about the play. I will say, though, as a feminist, it is fun to see the man who first synthesized progesterone—which led to the birth control pill.
Went to some sessions on hydrogen storage (you know, so that cars can run around emitting just clean, pure water vapor, and so that we can enter the "hydrogen economy") today and was introduced to ammonia borate by Bill Tumas of Los Alamos. I liked him, because he kept telling us "the hard cold facts". I've heard people talk about the "cold hard facts," but somehow, the "hard cold facts" seem even more bitterly inevitable. One of these was that no one has found a solution to storing hydrogen. The other is that his favorite candidate—ammonia borate—is not going to slot neatly into the current infrastructure.
The stuff may be good at holding onto hydrogen until you want to go vroom, and then letting it go, and it has a glimmer of a hope of getting the hydrogen compact enough so that one can drive 300 miles on a full cell—the standard measure of success—but it isn't possible to just shoot more hydrogen into it when it's gone "dry". So in this version of the hydrogen economy, one would buy a fuel cell, drive until it was used up, then return it to the fuel station for a full one. The old one would have to go back to the plant for some more complex chemical treatments. For some reason, everyone seems to think that this makes the technology completely impractical, but I don't see why. Everyone used to return their empty milk bottles when they picked up a full one. Maybe we can even take a page from the golden age of dairy and hire fuelmen, who will take the empty fuel cells from your front porch and leave full ones. They can even wear those swell hats.
Well, I suppose we ought to work out whether ammonia borate will even work before we start designing uniforms. In the meantime, I suggest Tumas get his own show on cable news called "The Hard Cold Facts with Bill Tumas."
The conference gets underway even before my plane lands. A fellow from a microscopy concern is leaning across the aisle chatting to a chemist about his latest model. In the airport shuttle to downtown, chemists wedge inside the van, their poster tubes making the whole process seems like some complex protein folding problem. And today the streets of downtown San Francisco are alive with chemists--teeming with badged hordes looking for a cup of coffee between sessions.
The ACS meeting is big. It has strong points and weak points, but most of all, it is big. This year sees the innovation of satellite registration desks in hotels throughout downtown, and a mind-boggling number of papers—almost 10,000. And I am going to "cover" the meeting. Ha ha ha.
Catherine Goodman, below, says she ends up more or less walking the poster sessions as her fancy takes her. This is perhaps the perfect way to approach a meeting of this size—both posters and talks. Why see all the talks in your own field, when half of it will be old news? Why not stab a pin into the program or just amble into any old session? I pledge to spin the wheel of fate at least once this time—stay tuned for some chemical Kismet.
As the conference winds down, I think it was, all in all, a good thing. It will be interesting to see how it develops. Will it become a mega-meeting, like the ACS meetings, or will it find some sort of niche, disciplinary or otherwise?
It was quite windy for most of the week, with the main plenary tent creaking and popping like a schooner in full sail. I thought about making some corny pun about these being the winds of change sweeping over Europe, as they find their collective identity and become a force to reckon with. This would have been just too pat though, and in any case, we will have to wait and see.
And so, Viszontlátásra from Budapest!
A big conference just isn't a big conference without a lot of handing out of medals. So here's congrats to Jonathan Nitschke of the University of Geneva, for winning the European Young Chemist's award. He got an IOU from the Italian Chemical Society for 1,800 €, and a nice gold medal. Lee Cronin promised me that if he didn't win, he would get up and shout 'It's rigged! It's rigged!', but unfortunately, he got one of the silver medals, and so we didn't get to see a temper tantrum in the tent.
Analytical chemists won't run out of work any time soon. The world is reassuringly full of unknowns. Perhaps less reassuring is the nature of some of these unknowns. Koni Grob at the Kantonales Laboratory in Zurich, which he calls 'a nano FDA', has been looking at the compounds that food packages shed into the food we eat. His most recent focus has been on the plastic gaskets found inside jar lids. He finds that when oil–like that in tomato sauce, for example-touches these gaskets, all sorts of known and unknown things leach out into the food.
'Many people want to have bio or organic food, but I think that they are not aware that by far the highest source of contamination is food packaging.' Many compounds, like epoxidized soybean oil and Bisphenol-A diglycidyl ether are present in oily jarred foods in levels far exceeding the maximums for contamination at the plant. And there are hundreds or thousands of other things in there that he has found with gas chromatography but not yet identified.
However, there is no need to ditch all your tasty oily foods in a panic. Grob is clear that this is a challenge for analysts, not a worry for consumers. In fact, he's ambivalent about getting media coverage of his project. 'Our philosophy is to inform those really involved and not the consumers, he says. 'It is the authorities that have to do a lot more about this.'
- Kosuke Yoshida of Tokai University in Shizuoka, Japan has found a marine microalga, with the handsome name Nannochloropsis oculata, that can be trained to chop the noxious chemical formaldehyde into relatively benign ethyl formate. Yoshida is interested in using the trained strain to mitigate formaldehyde used to control parasites that live on fish gills in aquaculture.
- Hungarian Chemistry celeb George Olah was here yesterday, promoting his new book, Beyond Oil and Gas: The Methanol Economy. He chatted with invitees just a few yards from where he is immortalized on a plaque listing Hungarian Nobel prize winners.
- A chat in the hotel bar with a fellow attendee reveals to ignorant old me that there is such a thing as Philosophy of Chemistry, and that it’s main journal is elegantly named Hyle, after the ancient Greek for “matter”. Further investigation reveals that Nature regular Phil Ball has a paper in the latest edition examining attitudes towards chemists in recent American fiction. The rest of the issue, all about the public image of chemistry is also very interesting. Awesome.
- Mobile phones might be bad for you, especially if your head is a vat of solution of lactoperoxidase, according to Roberta de Carolis of the University of Rome.
- Broccoli sprouts have more glucosinolates—a precursor to cancer-preventing Isothiocyanates—than full grown broccoli.
- The Seine is filled with caffeine and pain relievers.
Su Doku, the number game that is sweeping the world, has been adapted by the Royal Society of Chemistry into a puzzle where each square must have only one of nine elements listed at the bottom of the page. The play is exactly the same as the digit version, except that one contemplates the likes of lanthanum and cerium while one plays. Check it out at www.rsc.org/puzzle.
The big tent where we saw the folk dancers was packed this morning for Jean Marie Lehn's plenary on self-organizing systems. I heard lots of ebullient murmuring on the way out, so I think it went well, though some of it may have been the celebrity-induced glow of those who have just heard a Nobel laureate speak.
The general idea is that if one works hard, one can find molecules that when introduced, get along and immediately start building complex structures on their own. Lehn showed us grids and other cunning structures that had been got up by molecules that recognized each other and then bound predictably.
Much of his work was on those superstructures bound together with metal ions, so that one way to look at his grids was a field of regularly spaced metal ions, potentially useful as a computer chip. So these "supramolecules" are, he said, "a powerful alternative to nanofabrication. Don't make components, design them to make themselves."
He also showed how mixed soups of molecules will segregate themselves into structural units—so you'll have a bunch of double helixes forming alongside a bunch of triple helixes. This relies on recognition, and then selection of the appropriate molecule to fraternize with. In a challenging finale, Lehn wondered if this effect might not represent a kind of "chemical Darwinism."
His other quoteable moment: "Chemistry is the science of informed matter".
I heart food chemistry, and for more than one reason. First of all, it is easy to get into the science when you can immediately relate it to cheese or grapes or Parma ham or something nummy like that. And secondly, it demonstrates how seriously we take the pleasure of eating. Much of food chemistry is concerned with ensuring that when we decide to spend an evening eating bon bons and drinking champagne in the bath our chocolate is not adulterated with inferior cocoa butter fat equivalents and our champagne is actually from Champagne.
Elke Anklam, of the European Community Joint Research Centre in Belgium, gave a nice overview of food authentication this morning, which revealed that despite being armed with electronic noses, chromatography of various kinds, spectroscopy ditto., natural isotope fractioning, and PCR, they still can't easily tell if olive oil is being cut with hazelnut oil…"even if you can taste it."
Ha ha! So the best and least scientific means of authentication is still the human tongue. That being said, I was recently informed that most people cannot tell red wine from white with their eyes shut. Incredulous, I put it to the test. I shut my eyes and had my companions at dinner hand me glasses. I called the first red, the second white, and, taking a cue from the snickering I heard, the third a mixture of the two. Turns out it was the same glass of red wine all three times. Oh!
Today's programme is chock full of environmental chemistry, including a few sessions on pharmaceuticals in the environment. In the last few decades chemistry has given us more and better drugs, and we have not been shy about taking them. One graph of pharmaceutical consumption in France from 1970 to the present was hair-raisingly steep. All those drugs that aren't broken down by our bodies are, well, let's be scientific here, excreted and enter the waste-treatment stream. Some end up in rivers and lakes.
So it is good that chemists are busy inventing new tools to understand the scope of the problem and what it's implications might be—beyond trout blissed out on Prozac or crustaceans with the caffeine shakes.
Outside the environmental session room, a poster by Mei-Fang Chou and colleagues from Tri Service General Hospital in Taipei, Taiwan, gives me pause. They've managed to tweak the non-speedy alertness enhancer and mood brightener modafinil (sold as Provigil) so that it also is an anti-inflamatory pain reliever. Holey moley—what a blockbuster that could be. A cure for pain, sleepiness and unhappiness in one drug. Look out fish.
Mark Peplow, former Nature staffer, and current editor of the Royal Societyof Chemistry's Chemistry World is here in Buda, and he's recording his impressions on a brand new soft-launched blog, which is available here: http://prospect.rsc.org/blogs/cw.
Well, the reception was delightful. The food was excellent and the wine got good reviews. But before the eating and drinking came the speeches by chemistry worthies from across the continent. Generally, they were short and expressed pleasure in European chemistry coming together in this conference, and in the umbrella organization, EuCheMS. The MS on the end stands for "molecular science," and is part of a decided emphasis on the molecule which seems to me to be a bit of an attempt to grab more territory for the field.
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Jó napot kívánok from Budapest, where the European chemistry community has decided to get together in the first ever European Chemistry Congress. The scale of the thing is impressive for it being a first: 2,500 registrants from 65 countries and an abstracts book the size of a phone book (do they still make those?).
Before the official start, I sat down with organizer Gábor Náray-Szabó, and asked him the obvious question: is this conference a challenge to the American Chemical Society meeting, that twice-annual mass migration of chemists?
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[JF - Bronwen Dekker, an Assistant Editor for Nature Protocols has asked me to post this.]
Nature Protocols is a new online journal for the presentation of both new and old methods in a step-by-step/recipe format. Packed full of useful information in the form of CRITICAL STEPs, CAUTIONs and TROUBLESHOOTING tables, these protocols should be a valuable resource for bench researchers. There are two submission routes: protocols that have been commissioned, peer-reviewed and edited will be published in the 'Nature Protocols' section and non peer-reviewed material can be posted as 'Network Protocols.' The content of Nature Protocols will be free until the end of July, but the Network Protocols will always be freely available.
While most of the content at present is geared toward the biological sciences, we think that this will also become a useful resource for synthetic and analytical chemists as it could be a forum where labs can post their methods thus sharing valuable information on how to perform syntheses or analyses of specific classes of compounds. In the moderated commenting facility, other researchers will be able to suggest modifications to the published steps that improve results in their hands. Other functionality includes links to key information, such as articles where the procedure has been used previously and information about relevant reagents and equipment.
Current content includes methods for analyzing proteins using mass spectrometry (for example, for quantifying changes in the abundance of specific proteins by in-gel isotope labeling - Asara et al.), radiolabeling protocols (for example, labeling proteins with indium-111 and yttrium-90 - Cooper et al.), and the synthesis of reagents (for example, the preparation and use of azido ruthenium, a new photoreactive probe for investigating calcium-binding proteins - Israelson et al.).
Bronwen
Bronwen Dekker (Assistant Editor, Nature Protocols)
As if New Yorkers like myself didn’t already have enough to worry about, the local news last week helpfully informed us of another threat: the potential for a major hurricane to hit New York City.
Most scientists believe that increased emissions of greenhouse gases have contributed heavily to global warming, which has in turn been responsible for the increase in the number and strength of Atlantic hurricanes. Hurricanes do not usually hit states above North Carolina with great force because the ocean temperature must be at least 80°F (27°C) for a hurricane to maintain its destructive momentum. But with global warming causing an increase of ocean temperatures worldwide, the potential for a major hurricane to reach New York and other coastal areas in the northeast is growing.
I looked up a few facts and figures, which unfortunately seemed to confirm the news report.
After Miami and New Orleans, New York is considered the third most likely city for a major hurricane disaster (and of course we all remember what happened to Miami and New Orleans in 2005!).
The United States Landfalling Hurricane Project reports that there is an approximately 26% chance that New York City or Long Island will be hit with a Category 3+ hurricane in the next 50 years.
If a Category 3 hurricane hits NYC, the storm surge will flood the Brooklyn-Battery tunnel and cause extensive flooding of the subways.
The NYC Office of Emergency Management has posted maps of hurricane evacuation zones for all of the New York boroughs. I was somewhat dismayed to find that my apartment in Brooklyn is in the green zone, which means it is in trouble if a Category 3 ever heads my way (luckily, I live on the third floor of a four-story house). However, the NPG office is in even more danger in the yellow zone in Manhattan, meaning that it is at risk from a Category 2 storm surge!
Allison Doerr (Assistant Editor, Nature Methods)
More ACS news by me at the Nature Newsblog. I’ve got fried food and chemists being snarky about physicists and a guy whose life mission is to keep your beer cold. Sounds like a party to me.
The Ronald Breslow Award for Achievement in Biomimetic Chemistry symposium given this afternoon in the Division of Organic Chemistry recognized and honored the outstanding research accomplishments of Barbara Imperiali of MIT, in addition to featuring fantastic talks from Virginia Cornish, Ben Cravatt, and Dennis Dougherty.
Professor Dougherty of Caltech recounted a very amusing but quite helpful trick taught to him by Professor Imperiali (from her days as a professor at Caltech) for remembering the 1-letter amino acid code of tryptophan, W, which is to think of "twyptophan" (as if you were Elmer Fudd). Now I know I will never have future trouble remembering what “W” stands for!
I wish I had a trick for remembering the 1-letter codes of glutamine and glutamic acid (I’m Googling this as I write, I’m embarrassed to say, since I honestly can’t remember which is which!). Does anyone have any helpful tips for remembering these or any of the 1-letter amino acid codes? Please share!
Allison Doerr (Assistant Editor, Nature Methods)
