This Week in Science

Science  20 Nov 2009:
Vol. 326, Issue 5956, pp. 1040
  1. Methane's Path to Captivity

      The mutual repulsion of oil and water is well known. It is thus somewhat baffling that in arctic regions and in marine sediments, enormous quantities of methane lie trapped under pressure in surrounding cages of ice. Walsh et al. (p. 1095, published online 8 October; see the Perspective by Debenedetti and Sarupria) undertook extended simulations to probe the steps that guide these two normally incompatible molecules along convergent, rather than divergent, paths. Computed 2- and 5-microsecond trajectories trace the process of methane capture as ice crystals nucleate and ultimately assemble into a cage network.

    1. Cosmic Acceleration

        Cosmic rays are thought to be accelerated in the shock waves produced by supernova explosions and can generate gamma rays when they interact with interstellar particles and radiation. Starburst galaxies, with their increased star formation rates, increased stellar explosion rates, and high densities of gas and radiation fields, are considered to be promising sources of gamma-ray emission. Using the High Energy Stereoscopic System (H.E.S.S) array of telescopes, Acero et al. (p. 1080, published online 24 September) report the detection of gamma rays from one of the closest starburst galaxies, NGC 253. NGC 253 is a spiral galaxy, similar to our own Galaxy, except that its nucleus is undergoing an episode of intense star formation. The H.E.S.S. findings confirm that cosmic-ray acceleration is indeed efficient in starburst galaxies and open up new ways to understand cosmic-ray acceleration.

      1. Acidic Ocean

          One consequence of the historically unprecedented level of CO2 in the atmosphere that fossil fuel burning has caused, in addition to a warmer climate, is higher concentrations of dissolved CO2 in the oceans. This dissolved CO2 makes the oceans more acidic, and thus less saturated with respect to calcium carbonate. This has important ramifications for organisms that have calcium carbonate skeletons, which depend for their survival on the saturation state of calcium carbonate in the waters where they live. Yamamoto-Kawai et al. (p. 1098) report that in 2008, surface waters of the Canada Basin became undersaturated with respect to aragonite, a relatively soluble form of calcium carbonate incorporated into the shells or skeletons of many types of marine plankton and invertebrate. This undersaturation occurred much sooner than had been anticipated and has important implications for the composition of the Arctic ecosystem.

        1. Light in the Slow Lane

            CREDIT: BOYD AND GAUTHIER

            The speed of light is constant, reduced by a fraction from its vacuum level as it propagates through a material with a refractive index. In most transparent materials, the refractive index is slightly above unity, making the reduction in speed rather modest. Boyd and Gauthier (p. 1074) review the techniques used to reduce the speed of light down to pedestrian speeds, and describe some of the applications that such slow light (and fast light) may find.

          1. Early Ore Formation

              Ore deposits contain most of the world's metal resources, from commonly used metals such as iron, to precious and expensive metals such as platinum. Understanding how these ancient deposits form may lead to more efficient metal extraction and give clues about early Earth. Bekker et al. (p. 1086) studied sulfur and iron isotopes in 2.7-billion-year old Fe-Ni sulfide deposits from Canada and Australia and found that most of the metal-scavenging sulfur was originally atmospheric in origin. Photochemical reactions in the ancient oxygen-free atmosphere produced sulfide that eventually circulated to the sea floor and mixed with newly erupted komatite magmas. Thus, global surface processes in the oceans, atmosphere, and on continents are geochemically linked to ore-forming processes within Earth.

            1. Periplasmic Redox Regulation

                The oxidation state of intracellular and extracellular proteins are carefully managed by cellular redox machineries. Depuydt et al. (p. 1109) discovered a reducing system that protects single cysteine residues from oxidation in the bacterial periplasm. DsbG, a thioredoxin-related protein, appears to be a key player in that system and is the first reductase identified in the periplasm of Escherichia coli. Together with DsbC, DsbG controls the global sulfenic acid content of this compartment. Sulfenic acid formation is a major posttranslational modification in the periplasm, and three homologous L,D-transpeptidases are substrates of DsbG. Sulfenic acid formation is not restricted to E. coli, but is ubiquitous. Because proteins from the thioredoxin superfamily are widespread, similar thioredoxin-related proteins may control cellular sulfenic acid more widely.

              1. Demise of the Megafauna

                  CREDIT: BARRY ROAL CARLSEN/UNIVERSITY OF WISCONSIN–MADISON

                  Approximately 10,000 years ago, the Pleistocene-Holocene deglaciation in North America produced widespread biotic and environmental change, including extinctions of megafauna, reorganization of plant communities, and increased wildfire. The causal links and sequences of these changes remain unclear. Gill et al. (p. 1100; see the Perspective by Johnson) unravel these connections in an analysis of pollen, charcoal, and the dung fungus Sporormiella from the sediments of Appleman Lake, Indiana. The decline in Pleistocene megafaunal population densities (inferred from fungal spore abundances) preceded both the formation of the late-glacial plant communities and a shift to an enhanced fire regime, thus contradicting hypotheses that invoke habitat change or extraterrestrial impact to explain the megafaunal extinction. The data suggest that population collapse and functional extinction of the megafauna preceded their final extinction by several thousand years.

                1. Anti-HIV Antibody Constraints

                    CREDIT: CHEN ET AL.

                    Despite significant efforts, an effective vaccine against the HIV-1 virus remains elusive. A site on the HIV-1 gp120 envelope glycoprotein that binds to the CD4 receptor on host cells is vulnerable to antibody, but only rarely are antibodies against this site broadly neutralizing. L. Chen et al. (p. 1123) have determined crystal structures for two weakly neutralizing antibodies in complex with gp120. The epitopes recognized by these antibodies were similar to those bound by CD4 or a broadly neutralizing antibody. However, small differences in recognition induced conformational shifts in gp120 that were incompatible with formation of a functional viral spike. Thus, the antibody-vulnerable site on HIV-1 is protected by conformational constraints.

                  1. A-Maize-ing

                      Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112; see the cover) present the results of sequencing the B73 inbred maize line. The findings elucidate how maize became diploid after an ancestral doubling of its chromosomes and reveals transposable element movement and activity and recombination. Vielle-Calzada et al. (p. 1078) have sequenced the Palomero Toluqueño (Palomero) landrace, a highland popcorn from Mexico, which, when compared to the B73 line, reveals multiple loci impacted by domestication. Swanson-Wagner et al. (p. 1118) exploit possession of the genome to analyze expression differences occurring between lines. The identification of single nucleotide polymorphisms and copy number variations among lines was used by Gore et al. (p. 1115) to generate a Haplotype map of maize. While chromosomal diversity in maize is high, it is likely that recombination is the major force affecting the levels of heterozygosity in maize. The availability of the maize genome will help to guide future agricultural and biofuel applications (see the Perspective by Feuillet and Eversole).

                    1. Gardening for Ants and Termites

                        Among the social insects, ants and termites are the most diverse and ecologically dominant. Termites are known to engage in a mutualism with nitrogen-fixing bacteria, and Pinto-Tomás et al. (p. 1120) have identified similar relationships occurring among leaf-cutter ants, which maintain specialized nitrogen-fixing bacteria in their fungus gardens. Together, these mutualisms are a major source of nitrogen in terrestrial ecosystems. How is the evolutionary stability of such mutualistic cooperation maintained? Aanen et al. (p. 1103) show that the Termitomyces fungus cultured by termites remains highly related because mycelia of the same clone fuse together and grow more efficiently to out-compete rare clones.

                      1. Dysbindin Function in Synaptic Homeostasis

                          Homeostatic signaling systems are widely believed to stabilize neural function over prolonged periods of time. However, the molecular mechanisms of homeostatic signaling in the nervous system are largely unknown, and direct links between defective homeostatic signaling and disease-causing genes remain obscure. Dickman and Davis (p. 1127) performed a large-scale, electrophysiology-based genetic screen for mutations that specifically disrupt synaptic homeostasis. DTNBP1 is one of two genes that are most strongly and consistently associated with schizophrenia susceptibility in humans. The Drosophila homolog of DTNBP1 (dysbindin) was identified in the screen and was found to function during synapse development, baseline neurotransmission, and synaptic homeostasis. Dysbindin altered the calcium-dependence of vesicle release and was essential in the presynaptic neuron for both the induction and expression of synaptic homeostasis.

                        1. Hairy Polygon Solution

                            The packing of rods on the surface of a sphere leads to packing defects at the opposite poles. It is, however, possible to flat-pack rods onto a torus. This topological problem is well known as the hairy ball theorem, and arises when you place spherical particles inside a nematic liquid crystal. Lapointe et al. (p. 1083) considered the packing of liquid crystal molecules onto lithographically fabricated polygons and found that the number of dipoles that formed depended upon whether the polygon had an odd or even number of sides. The defect structures were attracted to each other, such that the liquid crystal could pull together the particles in a form of controlled self-assembly.

                          1. Building Early Continents

                              Cratons, the roots of Earth's continents, have survived billions of years of accretion, volcanism, and plate motion. Due to this tumultuous history, existing evidence for how and when they formed is hard to find. C.-W. Chen et al. (p. 1089) use geophysical data collected below the Slave craton in Canada to show that subduction of lithospheric plates in the Archean may have been a major process that controlled its assembly. Spatially aligned seismic and conductive discontinuities over 100 kilometers below the surface are caused by minerals that formed from hot fluids generated as ancient crust melted at a subduction zone. Other old cratons on Earth show similar features, suggesting plate tectonics was operating at least 3.5 billion years ago.

                            1. Plasmonic Probing of Catalysis

                                An understanding of catalytic reactions on surfaces, such as those used in industrial processes, often requires some measure of reactant concentration on the surface. Often this is expressed as the surface coverage of metal particles that are dispersed on oxide supports. Although optical probes of surface coverage would be convenient, they usually lack sufficient sensitivity to detect the small number of molecules on the surface. Larsson et al. (p. 1091, published online 22 October) have used shifts in plasmon resonances to measure surface coverages. They grow oxide coatings, decorated with metal catalyst particles, on a nanoscale gold disk, and find that these model catalysts are within the region of plasmon sensitivity. Reactions such as CO oxidation on platinum can be followed for different ratios of reactant gases with a sensitivity of 0.1 monolayer of surface coverage.

                              1. Extinction Distinctions

                                  The distribution of affected organisms can help reveal the mechanisms of mass or background extinctions. This has often been studied by comparing effects on land versus in the ocean, or across latitudes, for example. Miller and Foote (p. 1106) now analyze extinction patterns in shallow seas around continents, versus open-ocean coastal regions from the Permian through the Cretaceous, a period spanning three major mass extinctions. The mass extinctions all affected organisms in the open coastal environment greater than those inhabiting shallow seas, but at other times the pattern was opposite. Thus, organisms in these environments may have very different evolutionary histories.