Pittsburgh Post-Gazette from Pittsburgh, Pennsylvania on November 21, 2005 · Page 8
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Pittsburgh Post-Gazette from Pittsburgh, Pennsylvania · Page 8

Pittsburgh, Pennsylvania
Issue Date:
Monday, November 21, 2005
Page 8
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C M K Y P G C M K Y P G C M K Y P G C M K Y P G Nov 21 2005 7:26:44:116AM PITTSBURGH POST-GAZETTE ■ MONDAY, NOVEMBER 21, 2005 ■ WWW.POST-GAZETTE.COM A-8 the small stuff Archaeologists have found that a 1,000-year-old ceremonial brewery located in the Andes was operated by women of high social class. The researchers have recovered from the ruins of the brewery floor 10 elegant metal shawl pins, a luxury afforded only noblewomen of the Wari Empire, a militaristic people who conquered most of what is modern Peru starting about 1,400 years ago. That suggests that the women who made a spicy brew using a combination of maize and berries from a pepper tree were part of an elite guild of brewmistresses. The brew, called chicha, was similar to beer still made in the region today, although with perhaps a bit more kick. And the brewery was no bathtub operation, either. It utilized 28 ceramic vessels that could turn out about 475 gallons a week. “Our analyses indicate that this specialty brew was a high- class affair,” said Ryan Williams, curator of anthropology at the Field Museum in Chicago and leader of research at the site, known as Cerro Baul. The beer “was drunk from elaborate beakers up to a half a gallon in volume.” A report detailing the role of the high-status women was published online last week by the Proceedings of the National Academy of Sciences. Specter, Urban honored Scientific American’s annual tally of the top 50 contributions to science and technology by individuals or groups includes nods to both Sen. Arlen Specter, R-Pa., and Nathan N. Urban, a Carnegie Mellon University neuroscientist. The SA 50 are featured in the magazine’s December issue, out tomorrow. Mr. Specter was cited, along with Sen. Patrick Leahy, D- Vermont, for introducing the Personal Data Privacy and Security Act to give people greater control over their personal information. Dr. Urban, an assistant professor of biological sciences, was recognized for developing a method for predicting how neurons synchronize their activity, the basis for coding and storing information in the brain. Restoring Muddy Creek The Friends of the Cheat River will receive $835,000 from the U.S. Environmental Protection Agency to restore Muddy Creek, the largest contributor of acid mine drainage to the lower Cheat River Basin in West Virginia. The Cheat is a large tributary to the Monongahela River. The grant, to be awarded early next year, will be used to treat and contain mine drainage and support public planning efforts for further restoration of the Cheat basin. Search engine updated The federal government last week launched the latest version of its Science.gov search engine for federal science databases. The site, www.science.gov , now features “MetaRank,” a sophisticated method for ranking science queries and other upgrades. A query on the search engine accesses 30 databases and 1,800 Web sites in 12 federal science agencies, including the departments of defense, energy, agriculture, interior and health and human services, as well as NASA, the Environmental Protection Agency and the National Science Foundation. A ‘T. Rex’ from Texas A prehistoric lizard, whose remains were unearthed at a Dallas construction site 16 years ago, lived 92 million years ago and evolved into what some call the “T. Rex of the ocean.” Known as Dallasaurus turn- eri , it is the first well-preserved early mosasaur found in North America. The lizard is an important link in the evolution of mosa- saurs, which lived in the age of dinosaurs and evolved fin-like limbs, said Michael Polcyn of Southern Methodist University, co-author of an article about the creature in a special issue of the Netherlands Journal of Geosciences this month. It is unusual because it had tiny feet and hands, which only later developed into paddles. A model unveiled last week at the Dallas Museum of Natural History showed it looked similar to a Komodo Dragon. Ancient brewery was run by women SCIENCE ENVIRONMENT science notebook E-mail: science@post-gazette.com ■ Phone: 412-263-1578 ■ Web: www.post-gazette.com/healthscience ■ Editor: Byron Spice Questions about delivery or service? Call 1-800-228-NEWS (6397). Sweating By Byron Spice Pittsburgh Post-Gazette Nanotechnology is a buzzword that often brings to mind images of microscopic gears and springs etched into silicon wafers. But if you really want to build nanomachines, ones measured in billionths of meters, or nanometers, it makes sense to consider the nanomachines of nature — proteins. That’s what Christian Schaf- meister did. “We’ve got 40,000 of these machines in our bodies that make us what we are,” explained the University of Pittsburgh chemist. Proteins digest our food, move our arms and transport materials. And the beauty of it is that all are made from about 20 different types of building blocks, called amino acids. Taking this cue from nature, Dr. Schafmeister and his students have spent the last five years concocting their own set of 14 building blocks — the molecular equivalent of Lego pieces. By his estimation, that’s enough to make roughly 140 trillion structures. So creating different shapes is no longer the challenge; rather, “it’s finding those sequences that do interesting things,” he said. New types of pharmaceuticals, chemical catalysts and sensors are all among the possibilities. “We haven’t made a big splash with this yet,” acknowledged Dr. Schafmeister, an assistant professor of chemistry and a researcher at Pitt’s Institute of NanoScience and Engineering. But that should change once applications are identified, something he hopes will occur within the next year. Even so, the work already has drawn attention within the nano- tech community. Last month, the Foresight Nanotech Institute, a nanotechnology think tank, awarded its Feynman Prize for experimental work to Dr. Schaf- meister and its Distinguished Student Award to one of his graduate students, Christopher Levins, who developed one of the building blocks. “It’s the most impressive work we’ve seen on the pathway to building useful three-dimensional structures with atomic precision,” said Christine Peterson, Foresight’s founder and vice president for public policy. “The biggest payoffs across the board in nano- technology . . . are from reaching the ultimate goal of atomic precision.” Controlling the position of each atom within a molecule would be difficult to achieve simply by trying to build molecules out of the same amino acids used so skillfully by nature. Trouble is, as good as humans may be with their hands, they still lack the intellectual dexterity needed to build machines with amino acids. Arrange a set of amino acids one way and you’ve made an enzyme; rearrange the same amino acids and you’ve got a muscle component. The reason for these dramatically different functions lies in what’s called the protein folding problem. Proteins are more than just long, floppy chains of amino acids; their function depends in large part on their shape, how they fold themselves up. And the rules that govern that folding procedure are only dimly understood. During four years of graduate school at the University of California, San Francisco, Dr. Schafmeister designed his own protein, called 4HB1, with 180 amino acids. “It’s a molecular doorstop,” he said wistfully, gazing at its structure on his computer monitor. “It doesn’t do anything. But it is well-folded.” So he reasoned that to control the shape of his molecules — and thus increase the chances of designing a molecule that does something — he would need to eliminate the folding problem. And that meant developing molecular building blocks with rigid connections between them. Rigid connections Amino acids connect to each other with single bonds, creating chains with all of the rigidity of a string of plastic beads. He and his students devised blocks with a pair of bonds, creating rigid connections between the molecules much like those between Lego blocks. Most of the blocks have been processed from 4-hydroxypro- line, a form of the amino acid proline obtained commercially from chicken feathers; two are processed from the amino acid tyrosine. Making the building blocks “is boring chemistry, pedestrian chemistry,” he said, and intentionally so. Though he and his students now make their own building blocks, he hopes that someday they will be churned out in large quantities by industry. The building blocks each have a different shape, though they are not as simple as pieces of an Erector set — no straight sections, or right angles. All twist a bit in three dimensions, but can be assembled to form a number of shapes. Simply repeating the same building block will form something roughly rod-shaped. Alternating a block with a mirror-image block will form a horseshoe- or ring-shaped molecule. Dr. Schafmeister has devised a software program that can show a designer the options available for shaping a molecule with each of the available building blocks. “You can sculpt almost anything,” said William A. Goddard III, director of the Materials and Process Simulation Center at the California Institute of Technology. “Proteins are like a piece of string, but his structure is like having a wide ribbon” that can be used to build all sorts of three- dimensional objects. This “bottom-up” approach to building nanotech devices still must be further developed, but eventually will be essentially for building nanomachines, he suggested. The “top-down” approach, particularly that used by the semiconductor industry, may soon reach its limits, Dr. Goddard explained. Computer chip makers, who etch transistors and wires into silicon wafers, now are preparing to build devices measuring 130 nanometers and have begun to struggle with 90 nanometer devices. Increasingly smaller component sizes have been the key to “Moore’s Law,” the concept that chip capabilities roughly double every year or so. On the horizon are 45- and 32-nanometer components. But within 10 years, he said, continued progress may depend on switching over from a top-down to a bottom-up strategy. “There’s a good chance that Pitt nanotech researcher devises his own versions of building blocks on a molecular scale Tony Tye/Post-Gazette Christian Schafmeister of the University of Pittsburgh has developed a system for building nanodevices using molecular building blocks. A twist on the double helix The double helix is not only the famous shape of DNA, the stuff of which genes are made, but also could someday be the basis of molecular-scale electronic circuitry, including wires, diodes and transistors. Catalina Achim, assistant professor of chemistry at Carnegie Mellon University, said that double helix shape can be used to make sturdy three-dimensional structures. And work out of her lab, published last month in the Journal of the American Chemical Society, suggests a way that circuit designers may someday be able to make connections between these twisted ladders. Her work does not involve DNA, but peptide nucleic acids, or PNAs. DNA consists of two sugar- phosphate backbones connected, like rungs of a ladder, by pairs of nucleobases. The PNAs produced by Dr. Achim substitute two peptide backbones for DNA’s sugar-phosphate backbones. PNA has better electronic properties, she noted, and while DNA twists in one preferred direction, PNA can be twisted in whichever direction a designer prefers. But both DNA and PNA rely on those base pair links. An adenine base attached to one backbone always attaches to a thymine base on the other backbone; likewise, guanine always attaches to cytosine. In this way, the backbones are considered complementary and, in DNA, the sequence of these base pairs carries the genetic code. But Dr. Achim, graduate student Richard M. Watson and colleagues discovered that their PNAs can form even if the two backbones are not totally complementary. They found that the helixes can form even if there’s a significant level of mismatch between the A-T and G-C base pairs — as much as a 40 percent mismatch. Those mismatched, unpaired bases provide opportunities for the PNA molecules to make interconnections with other PNA molecules, she explained. “We have to test the actual properties,” she cautioned, “but the building blocks are there to suggest we should be able to construct these electronic devices.” Incorporating metal ions into the PNAs gives the molecules new magnetic and electrical properties. — Byron Spice Proteins are more than just long, fl oppy chains of amino acids; their function depends in large part on their shape. by 2015, this might be the only solution to maintaining Moore’s Law,” he added. Dr. Schafmeister envisions using his building blocks, each measuring about half a nanometer, to build little boxes with lids that could serve as sensors; when a molecule of interest enters the box, the lid would shut and send a signal. The blocks might also be used as scaffolding to construct customized catalysts, which promote certain chemical reactions, or to build artificial antibodies. He also is exploring the use of his building blocks for devising multivalent drugs — drugs that bind to multiple receptors on the surface of cells, thus blocking toxins, such as cholera. Unlike the floppy molecules that now carry sugars designed to bind with these receptors, Dr. Schaf- meister’s rigid molecules could hold the sugars at the same precise distance as the spacing of the receptors on the cell. “I have so many applications I want to try,” he said. Though it’s not clear which one is likely to prove itself first, he has encountered few limitations to the underlying building blocks themselves. “If there are walls,” he said, “we haven’t hit them yet.” Post-Gazette science editor Byron Spice can be reached at bspice@post-gazette.com or 412263-1578. (very) UniversityofPittsburghchemistChristianSchafmeisterhasdeveloped14moleculesof varyingshapesthatcanbeusedtobuildawidevarietyofnanoscalestructuresanddevices. Thepathtaken HOWIT’SDONE Source:UniversityofPittsburghResearch:ByronSpice,Graphic:EdYozwick/Post-Gazette Repeatingthesamebuildingblockresultsinarod-shapedstructure.Specialsoftware displaysoverlays(darklines)showingshapechangesthatarepossiblebysubstituting anotherbuildingblock.Byselectingoneofthesealternatives,,adesignercouldputa sharpbendintothemolecule,and. 1234 A 1 3 4 2 A

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