July 2010 Archives

Genetic information is transcribed from DNA to RNA and translated from RNA to make proteins. Because each step entails a modest number of molecules, gene expression, as the DNA-to-protein conversion is termed, is inevitably noisy: Identical genes in identical cells don't yield identical numbers of proteins. But how noisy? Sunney Xie of Harvard University and his collaborators have used single-molecule fluorescence microscopy and microfluidics to find out. They started by modifying the DNA of Escherichia coli to create 1018 different strains of the single-celled bacterium. In each strain, the code for a yellow fluorescent protein (YFP) was inserted after the gene for a different protein. To see the rate at which one gene is expressed in one cell of one strain, you’d illuminate the cell with a laser and measure the YFP emission through a microscope. To gather gene-expression statistics for a sample of cells from all 1018 strains, the Harvard team sent streams of cells through channels cut in a microfluidic chip and imaged them. The figure shows sample images for three proteins, YjiE, AtpD, and Adk. Ninety-six strains could be processed at once at a total throughput of 160 cells per second. The team found that the least abundant proteins appear at 10⁻¹ molecules per cell; the most abundant, at 10⁴ per cell. Gene expression is indeed noisy, but with a twist. As you’d expect, the least abundant proteins have the largest cell-to-cell fluctuations. But for proteins whose mean abundance is 10 per cell or higher, the expression noise saturates, presumably because the various molecules that mediate gene expression inside a cell are in limited supply. (Y. Taniguchi et al., Science 329, 533, 2010.)—Charles Day

The field of nanotechnology is in part rooted in the 1985 Nobel Prize–winning laboratory synthesis of buckyballs—the soccer-ball-shaped carbon molecule, C₆₀—by Rice University chemists Richard Smalley and Robert Curl and their collaborator, University of Sussex chemist Harold Kroto. The synthesis was guided by Kroto’s hypothesis that complex carbon chains could naturally form in the interstellar medium of aging carbon-rich, hydrogen-poor giant branch stars. Now, 25 years later, Jan Cami at the University of Western Ontario and his colleagues have reported the clearest evidence yet of such complex carbon structures in space. The research team analyzed IR spectroscopic data—collected by the Spitzer Space Telescope—of the circumstellar region of a planetary nebula known as Tc 1. As the image shows, the spectrum contains several prominent peaks of C₆₀ (red arrows) and peaks of the rugby-ball-shaped C₇₀ (blue arrows); both molecules were uncharged and in the solid phase. Previous spectra of other carbon-rich planetary nebulae indicated strong emission peaks of volatile polycyclic hydrocarbons, which were completely absent in the monitored region of Tc 1. Cami and his colleagues suggest that the planetary nebula may have ejected its hydrogen envelope a few thousand years ago and that a recent thermal pulse prompted the ejection of the pure carbon dust they’re now observing. (J. Cami et al., Science, in press, doi:10.1126/science.1192035.)—Jermey N. A. Matthews

For thousands of years, children have delighted in hoop rolling. Certainly, most of them have not considered that the rings are subject to gravitational and inertial forces; in any case, the hoops are stiff enough that they maintain their circular form despite those forces. But what happens to a rolling hoop that’s not so stiff? John Bush of the MIT mathematics department, along with visiting student Pascal Raux and colleagues, has answered that question in a recent study of more general systems—rolling bands that may be wider than they are high. Bush and company’s work was both experimental and theoretical. In their experimental investigations they took pictures of a vinyl polysiloxane loop placed on the inner surface of a rotating drum. The figure shows how the form of a representative loop changes as the drum speed is increased; blue corresponds to low speeds; red, high. In their theoretical work, the investigators confirmed the intuitive idea that the rolling band deforms as the inertial or gravitational force overwhelms the internal stiffness force. Indeed, if either gravity or inertial effects are strong enough, the top of the band can make contact with the bottom; new forces then come into play and the team’s analysis is no longer valid. Rolling droplets, tumbling blood cells, and carbon nanotubes deformed by van der Waals forces, the authors note, all display similar shapes to the rolling ribbons; the dynamics of those varied systems may be elucidated by the relatively simple ribbon study. (P. S. Raux et al., Phys. Rev. Lett., in press.)—Steven K. Blau

At the heart of the Balinese percussive orchestra known as a gamelan is the large gong called the gong ageng wadon. It features a large, protruding dome or boss in the middle; when the boss is struck with a padded mallet, the gong produces a pronounced acoustic beating or ombak (meaning "wave"), as can be heard in this sound file. Using acoustical and vibrometric analyses, David Krueger and his colleagues at Brigham Young University have studied the sources of the ombak. Although some beating was found to come from asymmetric vibration modes with closely spaced frequencies, those appear to contribute mostly to the gong's timbre. The more significant contribution arises from the gong ageng wadon's nonlinear structural response. The gong's two dominant vibration modes, both axially symmetric, have nearly a 2:1 frequency ratio. That relationship gives the gong its perceived pitch, but the ratio isn't exact. So when the gong is struck, causing displacements large enough to produce overtones, the fundamental generates harmonics and interacts with the second axisymmetric mode to yield sum and difference frequencies. The resulting sound spectrum features strong peaks of similar amplitudes that are spaced only a few hertz apart and give rise to the distinctive sound of ombak. (D. W. Krueger, K. L. Gee, J. Grimshaw, J. Acoust. Soc. Am. 128, EL8, 2010.)—Richard J. Fitzgerald

Two years ago, astronomers in Canada directly imaged what seemed to be a gas giant planet in a very distant orbit—more than 300 times the Earth–Sun distance of one astronomical unit (AU)—around a star much like our Sun. (For comparison, Jupiter's orbit is 5.2 AU, Neptune's is 30 AU.) Such a scenario poses difficulties for all the major planet-formation models in current use: core accretion, gravitational instability, and fragmentation of a pre-stellar core. The main difficulty is that either much larger objects, like another star, or much smaller ones are expected at such a great distance. Now, with further observations in hand from the Gemini North telescope and its adaptive optics, University of Toronto astronomers Ray Jayawardhana, Marten van Kerkwijk, and David Lafrenière (now at the University of Montreal) have confirmed the puzzle: The planet, with about eight times the mass of Jupiter, is moving through space gravitationally bound to the parent star, known by its nickname 1RXS 1609. Besides astrometric observations, the direct imaging (shown here) along with spectroscopic and photometric data allowed the researchers to further characterize the planet and confirm that no other large planets are farther out in the system. A mere toddler at only 5 million years old, 1RXS 1609 is about 500 light-years away. Hundreds of other exoplanets have been discovered in recent years, but this one is expected to keep theorists busy for some time. (D. Lafrenière, R. Jayawardhana, M. H. van Kerkwijk, Astrophys. J., in press.)—Stephen G. Benka

Light is a useful carrier of quantum information, but no method yet exists for storing and retrieving it without significantly corrupting its quantum state. Now, Matthew Sellars (Australian National University, Canberra) and colleagues have taken a step closer to a useful quantum memory by mapping a light pulse’s state onto an ensemble of praseodymium ions doped into a transparent crystal. Capitalizing on the Stark effect, the researchers used an electric-field gradient, as shown in the figure, to shift the ions’ transition energies. Absorption of an input light pulse created a coherent superposition of ground and excited states, whose phase in each ion evolved at a rate proportional to the transition energy. Flipping the electric field’s sign reversed the transition-energy distribution and brought the ions back into phase, at which point the pulse was re-emitted. The innovation was in how the researchers countered the spectral line’s natural broadening due to inhomogeneities in the crystal lattice: Applying a frequency-stabilized laser beam to the side of the long, thin crystal, they pumped atoms whose transition energies lay outside a narrow range into an out-of-the-way hyperfine state. Using the sharpened spectral line, which Sellars says may be “the sharpest optical filter ever demonstrated,” the researchers stored pulses of up to 500 photons more faithfully than could be done classically. When pulses were stored for 1.3 µs, the retrieved ones were 69% as intense—the previous record was 15%. (M. P. Hedges et al., Nature 465, 1052, 2010.)—Johanna Miller

A single plane of carbon atoms, graphene can be isolated using an exceedingly simple method: In 2004, the University of Manchester’s Andrey Geim and colleagues used common, clear cellophane tape to peel off weakly bound layers from bulk graphite. That process can produce millimeter-sized graphene flakes and is still common, particularly among researchers exploring graphene’s astonishing electronic properties. Many applications, though, require a large, continuous sheet of graphene. One promising approach is to grow graphene epitaxially atop some other crystal that can be etched away afterward. Recently, two groups—one led by MIT’s Jing Kong, the other by Byung Hee Hong of Sungkyunkwan University (SKKU) in South Korea—used chemical vapor deposition of methane to grow graphene on thin nickel films. The graphene was then either patterned lithographically or transferred onto silicon or plastic. The SKKU team has now adapted that approach to a scalable industrial manufacturing process that uses copper rather than Ni. In roll-to-roll production, as outlined in the figure, graphene-laden Cu was pressed against a polymer support, bathed in an etchant that removed the Cu, and then dry-transferred to another flexible polymer. To increase the film’s conductivity, multiple layers of graphene were stacked together and chemically doped in a bath similar to that used for etching. As proof of concept, the SKKU group produced a 76-cm-diameter flexible electrode, whose conductivity and transparency make it comparable to the commercial state of the art in touch-screen displays, indium tin oxide. (S. Bae et al., Nat. Nanotech., in press, doi:10.1038/nnano.2010.132.)—R. Mark Wilson

The shell model of nuclear structure predicts that nuclei with certain magic numbers of neutrons or protons—indicative of closed shells much like the closed electron shells of atomic physics—will be much more stable than their neighbors on the chart of nuclides. In particular, the elite subset of “doubly magic” nuclei, with closed shells of both neutrons and protons, should be rigidly spherical and strongly resistant to deforming excitations. But the validity of such predictions for short-lived nuclei with large neutron excesses has been an open question. A particular challenge for experimenters has been doubly magic tin-132, which has 8 more neutrons than the heaviest stable Sn isotope and a half-life of only 40 seconds. Astrophysicists share the nuclear theorists’ keen interest in ¹³²Sn because it sits very close to nuclides that are presumed to be way stations in the creation of the heaviest nuclei in supernova explosions but cannot be studied in laboratories. Now Kate Jones and coworkers at Oak Ridge National Laboratory’s Holifield Radioactive Ion Beam Facility have demonstrated that ¹³²Sn does indeed have the doubly magic properties predicted by the shell model. They did so by running a beam of energetic ¹³²Sn ions into a deuterium-rich target and showing that single neutrons stolen from the deuterons landed precisely in the ¹³³Sn valence orbits one expects to form around a rigidly spherical nuclear core. The picture shows the Holifield facility’s enormous tandem Van de Graaff accelerator, in which the beam was accelerated. (K. L. Jones et al., Nature 465, 454, 2010.)—Bertram Schwarzschild