Editors' Choice

Science  08 Feb 2008:
Vol. 319, Issue 5864, pp. 699

    The Ups and Downs of Stress

    The Hawaiian Islands have formed sequentially as the Pacific Ocean crust has moved over a locus of melting in the mantle. As each island grows, the huge weight of cooled magma, a pile extending many kilometers above the ocean floor, bends the ocean crust downward. Two related large (Mw = 6.0 and 6.7) earthquakes struck the island of Hawaii on 15 October 2006 and have helped reveal important aspects of this process. Both earthquakes occurred in the mantle. One was particularly deep, 39 km below the surface, and implied local extension; the other was shallower, at a depth of about 19 km, and suggested lateral compression. Through finite-element modeling, McGovern shows that the different mechanisms reflect modification of the broad bending process by the different strengths of the lower crust and mantle, producing compression at depths shallower than about 32 km and extension below, with strain focused near the depth of the deeper quake. In addition, compression at a depth of 19 km would tend to restrict the ascent of magmas, consistent with the notion that the crust is being underplated by cooled magmas at this depth. — BH

    Geophys. Res. Lett. 34, L23305 (2007).


    Pared to the Essentials

    The RNA world is alive and well—deeply embedded in plants. Plant viruses, traveling messenger RNAs, gene-silencing RNAs, these and more are the various guises of RNA in plants. For infectious RNAs, structural motifs—sequences that form hairpins and loops and bulges—are necessary both for RNA replication and for RNA trafficking between cells. Using a genome-wide mutational analysis of potato spindle tuber viroid (PSTVd), which replicates in the host cell's nucleus, Zhong et al. have investigated what these two processes share in terms of structural motifs. Potatoes produced by plants infected by this viroid are smaller and lumpier than usual, and the viroids move through the leaf cells, into the phloem, and then on to distant parts. The PSTVd RNA adopts a rod-shaped structure, and all of the loops were essential for fully successful replication and trafficking. Loops toward one end of the rod and in the middle were critical for replication; damage to loop 11 produced viroids able to travel well but not so apt to replicate; finally, one loop in its native state actually seemed to repress replication. Comparisons with other types of viroid RNAs hint at a conservation of structure-function relationships for some loops. — PJH

    Plant Cell 20, 10.1105/tpc.107.056606 (2008).


    Light amid Disorder

    In semiconductors, the concept of an energy gap that separates conducting electrons from localized valence states is fundamental to understanding the materials' optical and electronic properties. Researchers discovered in the 1980s that photons can behave in a similar way: Optical materials fabricated with just the right periodic structures exhibit energy (or frequency) regions where light passes through and other energy zones where transmission of light is blocked. Just as semiconductor band gaps lead to a wide range of useful technological properties, photonic band gaps can do the same for optical materials. Researchers have assumed that in order to produce the photonic band gaps, high-quality crystalline materials are required. Edagawa et al. present computational results showing that amorphous diamond without lattice periodicity can also exhibit strong photonic band gaps. The results challenge the traditional view that photonic band gaps are strictly a consequence of Bragg reflection and interference in which electromagnetic waves are scattered from various planes formed by a periodic atomic lattice. Thus, a range of photonic band gap systems could potentially be synthesized from materials such as polymers, proteins, and colloids that lend themselves naturally to amorphous structures. — DV

    Phys. Rev. Lett. 100, 13901 (2008).


    Profiles in Charge

    The availability of high-power lasers emitting intense pulses over femtosecond and picosecond time scales enables the study of high-field processes such as photo-dissociation and photo-excition of atoms and molecules in the laboratory. Such processes are relevant across a range of disciplines, from the study of photoinduced chemical reactions in the atmosphere to the more fundamental probing of the electronic excitations in atoms. When an intense laser pulse hits a cloud of atoms or molecules, the intensity profile of the laser pulse will produce a specific distribution of ions. After exciting a cloud of Xe atoms with intense laser pulses, Strohaber and Uiterwaal implement a time-of-flight technique that samples the pulse focal region with micrometer resolution, allowing the distribution of ions to be mapped out in three dimensions. On the flip side, the profile of the ion distributions can be used as an intensity sensor to aid the characterization and optimization of intense laser pulses. — ISO

    Phys. Rev. Lett. 100, 23002 (2008).


    A High-Salt Lifestyle

    Bonneau et al. describe progress in an effort to link systems-level analysis to events at the molecular and organismal levels. Using experiments and computation, they have pooled transcriptome, protein-protein interaction, structural, and evolution-related data to generate a dynamic model of the halophilic organism Halobacterium salinarum. This model was trained on data sets that included more than 200 microarray experiments measuring responses to genetic perturbations and environmental factors (oxygen, sunlight, transition metals, ultraviolet radiation, and desiccation and rehydration). The model, known as EGRIN (environment and gene regulatory influence network) represents transcriptional regulation for 1929 of the 2400 genes in H. salinarum, and it was used to predict transcriptional changes after environmental or genetic perturbations (or combinations thereof) that had been held out of the training data sets. As an example, the gene nhaC3 encodes a Na+ extrusion pump that allows this organism to grow under high-salt conditions. Analyses of a map of protein-DNA interactions generated from ChIP-chip data could not dissect which of five possible transcriptional regulators governed expression of the gene, yet one of these was predicted by EGRIN to have the strongest effect, which was confirmed in laboratory experiments. — BJ

    Cell 131, 1354 (2007).


    The Debt of Nations

    Tracking the worldwide depletion of ecosystem resources is a complex international problem. Srinivasan et al. have used a simplified accounting framework to link populations who experience ecological damage to those who cause it. The largest and most blatant imbalance is the debt we (high-income countries) owe to low-income countries because of climate change. On a per capita basis, people in high-income countries are responsible for almost six times more greenhouse gas emissions than their low-income counterparts. Included in the tally is, for instance, the luxury debt accrued by high-income consumers of farmed shrimp; this demand encourages the destruction of coastal mangrove trees to clear the way for shrimp ponds. The resulting loss of storm protection is increasing the risk to adjacent cities as sea levels rise and coral reefs collapse (see also Grimm et al., Review, p. 756). Similarly, middle-and high-income countries consume most of the world's fish; nevertheless, several food-deficient African countries charge only modest access fees for the mining of their rich offshore fisheries. Despite the difficulties of measurement and the need to simplify, this analysis raises provocative questions about the division of responsibilities for environmental harm. — CA

    Proc. Natl. Acad. Sci. U.S.A. 105, 10.1073/pnas.0709562104 (2008).


    Hearing Essentials About Glutamate Transporters

    Although three vesicular glutamate transporters (VGLUTs) have been identified, only two are found in identified glutamatergic neurons. In contrast, VGLUT3 is expressed in several populations of neurons that release other classical neurotransmitters, including inhibitory GABAergic interneurons in the hippocampus and cortex. Seal et al. found that mice lacking VGLUT3 were profoundly deaf: They failed to show a startle response to loud noises and did not exhibit auditory evoked potentials. Electrophysiological analysis revealed a defect in signaling from the inner hair cells (IHCs) of the cochlea to the auditory nerve, and morphological analysis showed abnormalities of IHC synapses. Immunofluorescence revealed that VGLUT3 was present in synaptic regions of the IHCs of wild-type mice. Whereas the conductances in the IHCs of the mice lacking VGLUT3 resembled those in wild-type mice, electrophysiological analysis indicated that these neurons failed to release glutamate. The authors conclude that VGLUT3 is essential for hearing and plays an important role in the regulation of cortical excitability. — EMA

    Neuron 57, 263 (2008).