This Week in Science

Science  18 May 2012:
Vol. 336, Issue 6083, pp. 771
  1. Cage, Book, and Prism


    The array of hydrogen bonds governing the extended structure of liquid water is so intricate that chemists have often sought to understand it by studying simpler clusters. Even so, it has been challenging to get a handle on the preferred arrangement adopted by just six water molecules. Interdependent theoretical and spectroscopic studies have narrowed down the lowest-energy hexamer structures to three isomers—respectively designated the cage, the book, and the prism—but their relative energies remain uncertain. Now, Pérez et al. (p. 897; see the Perspective by Saykally and Wales) have observed all three isomers in a single experiment, using Fourier transform microwave spectroscopy, and were able to establish definitively their energy ordering.

  2. Water-Assisted Proton Diffusion

    Proton diffusion on metal oxide surfaces can play an important role in many catalytic processes. The presence of water is thought to accelerate proton diffusion. Merte et al. (p. 889) used high-speed, high-resolution scanning tunneling microscopy to study proton diffusion on an iron oxide. On oxygen-terminated FeO monolayer films formed on Pt, molecular water accelerated proton diffusion. Density function theory calculations implicated a H3O+ transition state in the diffusion process.

  3. Mechanisms in Methanol Catalysis

    The industrial production of methanol from hydrogen and carbon monoxide depends on the use of copper and zinc oxide nanoparticles on alumina oxide supports. This catalyst is “structure sensitive”; its activity can vary by orders of magnitude, depending on how it is prepared. Behrens et al. (p. 893, published online 19 April; see the Perspective by Greeley) used a combination of bulk and surface-sensitive analysis and imaging methods—along with insights from density functional theory calculations—to study several catalysts, including the one similar to that used industrially. High activity depended on the presence of steps on the copper nanoparticles stabilized by defects such as stacking faults. Partial coverage of the copper nanoparticles with zinc oxide was critical for stabilizing surface intermediates such as HCO and lowering energetic barriers to the methanol product.

  4. Radioactive Resonance

    Nuclear magnetic resonance (NMR) spectroscopy and its spatially sensitive cousin, magnetic resonance imaging, have found widespread application in chemical and biological characterization studies. For the most part, these studies take advantage of the energy bifurcation manifested by hydrogen nuclei with oppositely directed spins in a strong magnetic field. More generally, many heavier elements manifest the same effect—including carbon-13, fluorine, and phosphorus. In theory, researchers have known for 50 years that plutonium nuclei have a net spin conducive to NMR. Yasuoka et al. (p. 901; see the Perspective by Albrecht-Schmitt) have now at last observed the resonance of the Pu-239 isotope in a sample of plutonium dioxide.

  5. Keep Your Distance

    Conspecific negative density dependence (CNDD), whereby the abundance of a species is limited by negative interactions between individuals of the same species, is thought to have an important influence on the composition and dynamics of forest communities, but studies have generally been limited to few species and small areas. Johnson et al. (p. 904) analyzed CNDD in over 200,000 plots from a database of more than 3 million individuals of 151 species spanning 4 million square kilometers across forests in the eastern United States and found that the strength of CNDD strongly predicted the relative abundance of tree species. Because tree seedlings are unlikely to become established where conspecific adults are common, CNDD may provide a general mechanism maintaining diversity in forests.

  6. Bring In the Inspectors

    In order to assess the impact of occupational and health practices in the state of California, Levine et al. (p. 907) compared more than 400 uninspected firms with a matched set of inspected firms that were chosen at random. Employees at the inspected firms were less frequently injured and, consequently, the inspected firms suffered fewer injury-related costs. Encouragingly, there were no significant differences in other economic outcomes, such as sales and employment levels, between control and inspected firms.

  7. Ultimate Blockade


    A Rydberg atom has an electron in a highly excited energy state, close to being set free, but not quite. Ensembles of such atoms interact strongly, sometimes leading to blockade effects where the excitation of one atom prevents the excitation of another. Dudin and Kuzmich (p. 887, published online 19 April; see the Perspective by Grangier) demonstrate the generation of a many-body excitation with no more than one Rydberg atom in a mesoscopic ensemble of ultracold atoms. When the principal quantum number was increased beyond 70, the excitation was converted into a photon. The ability to control the creation of excitations provides a promising system for quantum information storage, as well as a source of correlated photons.

  8. Accounting for Lac

    When Escherichia coli expresses the lac operon, it needs to balance the potential increase in growth rate conferred through having the encoded proteins (which help it to take up and metabolize lactose) with the potential reduction in growth rate because of the resources needed to express and fold the encoded proteins. To investigate these inherent tradeoffs, Eames and Kortemme (p. 911) investigated the costs and benefits associated with the lac operon and surprisingly found that the main constraint on the system is not caused by the manufacture of the proteins themselves but by the lactose permease activity encoded by the LacY gene.

  9. The Hibernating Ribosome

    When bacteria enter stationary phase, their ribosomes are inactivated. In Escherichia coli, ribosome modulation factor (RMF) causes dimerization of the 70S ribosome and the dimer is stabilized by, hibernation promotion factor (HPF). Alternately, the stationary phase protein, YfiA, inactivates 70S ribosomes. Polikanov et al. (p. 915) present high-resolution structures of the Thermus thermophilus 70S ribosome bound to each of these three factors. The structures suggest that RMF binding inhibits protein synthesis by preventing initial messenger RNA (mRNA) binding and that HPF and YfiA have overlapping binding sites and would both interfere with binding of mRNA, transfer RNA, and initiation factors.

  10. An Aspirin a Day?

    The protein kinase AMPK (adenosine monophosphate–activated protein kinase) directly monitors cellular energy stores as reflected by changes in cellular concentrations of AMP, adenosine diphosphate (ADP), and adenosine triphosphate (ATP). Through phosphorylation of its targets, it helps to control metabolism, polarity, autophagy, and the restraint of cell proliferation. Activation of AMPK is also proposed to be beneficial for the treatment of diseases, including cancer and diabetes. Hawley et al. (p. 918, published online 19 April; see the Perspective by Shaw and Cantley) report that AMPK can be activated by high concentrations of salicylate, a compound derived from the very commonly used drug aspirin. In mice, salicylate promoted fatty acid and carbohydrate metabolism in an AMPK-dependent fashion.

  11. Suicidal B cells


    In response to an infection, immunological B cells undergo a maturation process that results in the production of immunoglobulin (Ig) that is better able to bind and clear the invading pathogen. This occurs through somatic cell hypermutation and class switch recombination of the Ig gene and requires activation-induced deaminase (AID). Péron et al. (p. 931, published online 26 April) observed that the 3' cis-regulatory region of the heavy-chain locus is transcribed and undergoes AID-mediated mutation and recombination. The resulting deletion of the Ig heavy gene cluster generates B cells that are no longer able to express Ig on the cell surface. Because cell-surface Ig expression is essential for B cell survival, this process is termed “locus suicide recombination” (LSR) and may be important in shaping the dynamics of B effector cell differentiation and homeostasis.

  12. Deep Breathing

    Living microbes have been discovered many meters into marine sediments. On a cruise in the North Pacific Gyre, Røy et al. (p. 922) discovered that oxygen occurred for tens of meters into the sediment. The bacteria living in these sediments were respiring the oxygen but at a slower rate than the supply of organic material dropping out of the water column, allowing these ancient deep marine sediments to remain oxygenated. Modeling showed that the rate of respiration of specific carbon decreased as a function of sediment depth, that is, its age. Thus aerobic metabolism can persist in deep marine sediments.

  13. Color and Movement

    From humans to insects, color and motion information are thought to be channeled through separate neural pathways for efficient visual processing, but it remains unclear if and how these pathways interact in improving perception of moving colored stimuli. By using sophisticated Drosophila genetics, intracellular electrophysiology, two-photon imaging, and behavioral experiments, Wardill et al. (p. 925) found that early in the processing stage-color photoreceptors influence the motion pathway and that this input improves the flies' optomotor performance in a flight simulator.

  14. Distinguishing Epigenetic Marks

    Methylation of the cytosine base in eukaryotic DNA (5mC) is an important epigenetic mark involved in gene silencing and genome stability. Methylated cytosine can be enzymatically oxidized to 5-hydroxymethylcytosine (5hmC), which may function as a distinct epigenetic mark—possibly involved in pluripotency—and it may also be an intermediate in active DNA demethylation. To be able to detect 5hmC genome-wide and at single-base resolution, Booth et al. (p. 934, published online 26 April) developed a 5hmC sequencing chemistry that selectively oxidizes 5hmC to 5-formylcytosine and then to uracil while leaving 5mC unchanged. Using this method, mouse embryonic stem cell genomic DNA was sequenced to reveal that 5hmC is found enriched at intragenic CpG islands and long interspersed nuclear element–1 retrotransposons.

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