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)
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.
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)
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)
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)
This afternoon at the ACS meeting I attended the Analytical Awardees Presentations featuring the four winners of the ACS analytical awards.
The winner of the Award for Outstanding Achievement in Mass Spectrometry was Richard Caprioli of Vanderbilt University. First reported in Nature Medicine in 2001, Professor Caprioli has been developing and applying a technique called MALDI MS Imaging. This is a fascinating technique where a tissue slice is placed directly on a sample plate, prepped with a MALDI matrix, pixilated into discrete spots, and analyzed by MALDI-TOF. The proteins present in each spot can be identified and mapped back to the location in the tissue from where it came. This results in the construction of a protein map of the tissue where different colors can be assigned to various proteins of interest and intensities reflect protein concentrations.
What’s really intriguing about this technique is the potential for a paradigm shift in the way that clinical pathologists and histologists do their jobs. For example, a histologist traditionally would use a stain to define a tumor margin in a biopsy, but the molecular profile revealed by the MALDI MS image can expose oncogenic proteins found out-of-bounds of the tumor. This can help guide surgeons in the removal of all cancerous tissue, reducing the chance of relapse.
Apparently, when Professor Caprioli first told colleagues about his idea of sticking tissue slices into a mass spectrometer, they all thought he was a little nuts. His work is a fine example of how what first seems like a zany idea in analytical chemistry can turn out to have a very practical application in the clinic!
Allison Doerr (Assistant Editor, Nature Methods)
It always takes me awhile to get my bearings at an ACS meeting…figuring out how to catch the shuttle bus to the convention center…finding where to pick up registration materials…searching for that ubiquitous Starbucks for some much-needed caffeine…deciding which one of five interesting symposia to attend… navigating the massive convention center…going back and forth between symposia that seem about a mile apart, only to find the order of the talks have been switched …and so on!
Today was no exception, but I did manage to drop in on one quite interesting symposium given by the Division of Chemical Information. Kicked off by the very entertaining George Whitesides from the chemistry department at Harvard, the symposium was entitled “The nuts and bolts of scholarly publishing”.
As an editor, I would have to say that Professor Whitesides has the writing process down pat (you might even say, down to a science), as he described his views on how to successfully write a research paper. He began by reminding the audience of the mantra that all good journalists know: if you fail to capture the readers’ attention in the first 2-3 sentences, you might as well forget about them reading the rest of your paper. The Introduction should state the principle result, the motivation, importance, and context in reference to prior work (which as Professor Whitesides astutely pointed out, is not only the ethical thing to do, but also a really good idea since the previous work was probably done by the referees reading the paper!). In the Results and Discussion, the principle result should be described first and in as brief of terms as possible (this is not the place to recount the long history of personal struggles in the lab!). Finally, the Conclusion should not be a reiteration of the abstract, but the place to compare the work to previous results, describe the significance of the new work, the benefits and limitations, as well as an opportunity to inject personal opinions. In addition, a good title and interesting and informative figures are absolutely crucial.
Overall, it was an engaging and instructive talk, reminding scientists of the integral role writing plays in research. After all, if you never write up your research and no one ever reads it, it might as well have never been done!
Allison Doerr (Assistant Editor, Nature Methods)
Some call chemistry the “central science” and it’s not hard to see why. The huge range of projects in which chemistry researchers are involved cross paths with engineering, physics, earth sciences, medicine, and biology. We at Nature Methods are particularly interested in publishing new applications of chemical compounds, tools, or analytical methods that demonstrate potential to provide valuable novel and practical contributions to biology. We’ve got a few very nice papers in our April issue that illustrate this goal well.
From the Department of Chemistry at MIT, Alice Ting and her colleagues have successfully designed a streptavidin tetramer with only one high affinity biotin binding site. While protein chemists will appreciate the design and engineering process, cell biologists will certainly find the mutant streptavidin useful for applications such as cell surface protein labeling. (Listen to Professor Ting speak about this work on Nature’s special Chemistry Podcast.)
We also have a solid contribution from Peter Schultz at the Skaggs Institute for Chemical Biology at Scripps. The Schultz lab has long been a leader in developing and refining a genetic method for incorporating functional unnatural amino acids into proteins; however, the method was somewhat technically challenging for biologists. Now they report a streamlined procedure for using the system in bacteria.
Sometimes, existing chemical tools or methods can find new life in biological applications. Helen Blau and her colleagues at Stanford University discovered that the small organic molecule “Lugal” available in the Promega Beta-Glo Assay System (to quantify β-galactosidase activity in cell culture), could also be used as a bioluminescent reagent to image β-galactosidase activity in living cells.
I welcome comments on these papers and hope to meet with some of you chemists at the ACS meeting with other interesting biological stories to tell!
Allison Doerr, Assistant Editor, Nature Methods
Welcome to “The Sceptical Chymist,” a new blog from the editors of Nature and the Research journals.
We hope that you will help us fill this blog with stimulating discussions of all things chemical… This isn’t the first blog at Nature: there’s also the “Nature Newsblog,” “Free Association” (a blog from the editors of Nature Genetics), and “Action Potential” (a blog from the editors of Nature Neuroscience). But this is our first blog in the chemical sciences and we hope that you’ll help us make it a successful one!
So, what will you find in this blog? Here’s a (partial) list of what we plan on discussing:
- Meetings we’re attending, including the upcoming 2006 Spring meeting of the American Chemical Society
- Chemistry and biochemistry papers published in Nature journals and elsewhere
- Chemistry and chemists in the news, including scientific and popular press coverage, important policy developments, new initiatives in chemistry, etc.
- Upcoming conferences, newly published books about chemistry, and interesting websites we’ve found
- And anything else you’d like to talk about...
Now if you made it this far, you’re probably wondering why we named our blog “The Sceptical Chymist.” Well, it all has to do with a book written in 1661 by Robert Boyle, who is best known for Boyle’s law, and for co-founding the Royal Society on November 28th, 1660.
In 1661, Boyle published “The Sceptical Chymist,” in which he “argued against Aristotle's view of the four elements of earth, air, fire and water” and instead “argued that matter was composed of corpuscles which themselves were differently built up of different configurations of primary particles.”
Boyle criticized alchemists, calling them ”vulgar” and “inferior," and “appealed to chemists to experiment and … pleaded that chemistry cease being subservient to medicine or to alchemy, but rise to the status of a science.” Furthermore, he “advocated a rigorous approach to scientific experiment [and] believed all theories must be proved experimentally before being regarded as true.”
So it’s not surprising that Boyle has been called the “founder of modern chemistry” as well as the “father of chemistry.” We named this blog “The Sceptical Chymist” to pay homage to Boyle and the dramatic metamorphosis that took place after the publication of this book. By no means do we think that this blog will be a 21st century equivalent of this seminal text, but we hope that – like the original book – this blog will engage the chemical community, ask important questions, and make a positive impact on the field.
We will be adding entries regularly, so please check back frequently to see what we’re writing about… And please feel free to leave comments responding to this (and/or any other) entry – if you would like to contact us via email, please email us at thescepticalchymist at boston.nature.com
Chat with you soon!
Joshua Finkelstein (Associate Editor, Nature)
Terry Sheppard (Chief Editor, Nature Chemical Biology)
Stuart Cantrill (Associate Editor, Nature Nanotechnology)
Allison Doerr (Assistant Editor, Nature Methods)
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