This Week in Science

Science  26 May 2006:
Vol. 312, Issue 5777, pp. 1101
  1. Making the Switch


    Riboswitches are regions of untranslated messenger RNA that switch their conformations when they bind specific metabolites to regulate the expression of proteins involved in the biosynthesis of the bound metabolites. For example, in bacteria, archaea, and eukaryotes, the production of the essential cofactor thiamine pyrophosphate (TPP) is tightly regulated by TPP-binding riboswitches. Thore et al. (p. 1208, published online 4 May) determined the structure of the eukaryotic Arabidopsis thaliana TPP riboswitch bound to TPP at 2.9 angstrom resolution. The structure shows how the bound “off” conformation, which suppresses expression of a gene involved in TPP biosynthesis, is stabilized. TPP riboswitches are attractive targets for antimicrobial drugs, and the structure rationalizes the mechanism of resistance to the antibiotic pyrithiamine.

  2. Jumping the Barrier

    The rupture of faults causing earthquakes may be complicated by local tectonic conditions, but to date these subtleties have been difficult to disentangle. Robinson et al. (p. 1203) show that the rupture of the 23 June 2001 Peru earthquake (moment magnitude 8.4), the world's third largest since 1965, jumped a seismic barrier. After traveling for 70 kilometers, the rupture detoured around a hard block with an area 6000 square kilometers before continuing on for another 200 kilometers along the original fault. After a delay of half a minute, the block itself ruptured and released most of the earthquake's energy. The barrier is identified as a fracture zone on the subducting oceanic plate.

  3. Deforming Slip by Slip

    By recording nanoscale slip events in nickel microcrystals, Dimiduk et al. (p. 1188; see the Perspective by Miguel and Zapperi) quantitatively observe the critical dynamics in the plastic deformation of crystalline metals. Under a very slow loading rate, the sample deformed intermittently and the events followed a power-law distribution over more than two orders of magnitude in event size. This deviation from smooth laminar flow confirms the predictions of a number of models and acoustic measurements made on ice samples. The results may lead to an improved theoretical understanding of microscale deformation and may also relate to the behavior of magnetic noise and avalanches.

  4. Why So Small?

    In the standard Big Bang model, the amount of dark energy in the universe is roughly the same order of magnitude as energy in the form of matter, but this need not have been the case. Dark energy, parameterized as the cosmological constant, could have been trillions of times greater or smaller. This fine tuning has been explained by the anthropic principle—we would not be here if the cosmological parameters had been much different. Steinhardt and Turok (p. 1180, published online 4 May; see the Perspective by Vilenkin) propose an alternative way to tune the cosmological constant down to a small value. They model dark energy in a cyclic universe—a repeating succession of universes growing from big bangs and collapsing into big crunches—and find that most of the time the value of the cosmological constant is small and positive.

  5. Making and Breaking a Metal Atom-Molecule Bond


    Molecular electronics tries to exploit changes in conductivity of molecules held between metal electrodes, but the nature of the metal-molecule contact is not well understood. Repp et al. (p. 1196) followed the interaction of a gold atom with a pentacene molecule, both adsorbed on a thin NaCl film grown on a metal substrate. A scanning tunneling microscope (STM) tip was used to bring the Au atom into close contact with the molecule. Resonant inelastic electron tunneling (IET) through the lowest unoccupied orbital of pentacene led to bond formation, and the resulting changes in bond hybridization could be imaged. The bond could be broken by IET through the molecular complex. The resulting changes could be understood by comparison with density functional calculations.

  6. The In and Outs of Carbon Nanotubes

    The inherent strength of carbon nanotubes has made them candidate materials for reinforcing composites. It is also possible to put a second material into the core of a nanotube for electronic applications or for use as contrast agents. Sun et al. (p. 1199; see the Perspective by Wang and Zhao) exploit both these properties and use carbon nanotubes as state-of-the-art high-pressure chambers that allow in situ observations of pressure-induced processes at atomic scale. Defects induced on the surface of the nanotubes moved and coalesced, which caused the tubes to contract and squeeze out metal particles that had been trapped inside.

  7. Pathogen Puts a Spanner in the Works

    So-called bacterial effector proteins usurp or mimic a eukaryotic activity and contribute to virulence. Many of the known virulence factors from the pathogenic bacterium Yersinia pestis, the causal agent of plague, have been assigned mechanisms, but YopJ has remained a mystery. Mukherjee et al. (p. 1211; see the Perspective by Worby and Dixon) now show that YopJ acts as an acetyltransferase that modifies serine or threonine residues in the activation loop of the MAPKK superfamily of signaling kinases. This modification prevents these residues from being phosphorylated by upstream signaling machinery and interferes with innate immune responses.

  8. How a SNP Promotes Disease

    Single-nucleotide polymorphisms (SNPs) are one-base variations in DNA sequence that can often be helpful when trying to find genes responsible for inherited diseases. De Gobbi et al. (p. 1215) have discovered a SNP in a gene regulatory region that causes a human genetic disease through an unusual mechanism. In a study of individuals with α thalassemia, a blood disease characterized by reduced production of hemoglobin, the authors identified a SNP between the upstream regulatory region and the promoter sequences of the α-globin gene cluster on human chromosome 16. The disease-associated allele creates a new promoter-like element whose activity appears to disrupt transcription of the downstream globin genes. Thus, SNPs that fall within intergenic regions, while seemingly innocuous, can occasionally have medically important functional consequences.

  9. CRACing Calcium Channels

    Calcium release-activated calcium (CRAC) channels mediate influx of calcium across the plasma membrane when intracellular stores of calcium are depleted, an important event in receptor-stimulated calcium signaling in many cells. Vig et al. (p. 1220, published online 27 April) moved the search for the molecular identity of the CRAC channel one step closer by completing a high-throughput RNA interference screen for gene products required for CRAC channel function in Drosophila. Two membrane proteins, CRAC modulators 1 and 2 (CRACM1 and CRACM2), could be part of the CRAC channel itself or part of the regulatory machinery that controls it.

  10. The Dance of Development


    The path from an egg into an adult requires a complex dance of thousands of genes. Imai et al. (p. 1183; see the Perspective by Lemaire) tracked the expression of regulatory genes on a cell-by-cell basis in the developing embryo of the sea squirt, Ciona intestinalis. The authors generated a map of the network of gene interactions from which they extract information about specific developmental pathways, such as the formation of notochord, or brain. The results give a snapshot of development in an organism that stands between invertebrates and vertebrates.

  11. Bigger Bones

    Adult bone mass is determined by the rates of bone formation by osteoblasts and bone resorption by osteoclasts. Genetic mutations that disrupt the function of these cells can lead to problems with skeletal development, including excessive postnatal bone formation. Pivotal in osteoblast differentiation is the transcriptional regulator Runx2. Jones et al. (p. 1223) reveal how this master control protein is itself regulated. Mice lacking the adapter protein Schnurri-3 accumulated bone mass because of increased osteoblast activity resulting from abnormal Runx2 turnover within the cell. Runx2 is normally regulated by ubiquitin-mediated degradation through the Schnurri-3-dependent association with the E3 ubiquitin ligase WWP1. The identification of this upstream pathway regulating postnatal bone formation might help reveal therapeutic avenues for treating bone abnormalities and deficiencies, such as osteoporosis.

  12. Fisheries' Effects on Coastal Marine Ecosystems

    Fishing removes top predators, and runoff from the land deposits large amounts of excess nutrients into coastal waters. The relative impact of these top-down and bottom-up factors on marine species and communities has been assessed by Halpern et al. (p. 1230), who used a database of species' abundances from southern California kelp forest communities spanning multiple years and a broad spatial scale. There is 7- to 10-fold greater influence of top-down control, despite wide-ranging levels of primary production, an effect that is strongest for the algae in the system. This result contradicts the idea that giant kelp are strongly regulated by nutrient levels. Instead, it seems top-down control is having a much greater impact on coastal ecosystems than bottom-up regulation, which argues that management strategies should focus on control of fisheries.

  13. Growing Graphene on Silicon Carbide

    The impressive electronic properties of carbon nanotubes arise from the two-dimensional confinement of electrons that results from graphene sheets closing tightly upon themselves. Recently, ultra-narrow graphene strips supported on substrates such as silica and prepared from exfoliated graphite have exhibited similar electronic properties. Berger et al. (p. 1191) now show that graphene layers can be prepared on SiC single crystals by hydrogen etching and vacuum graphitization and patterned by oxygen etching. Their conductivity varied with the width of the strip. Strips 250 nanometers wide showed quantum confinement effects up to ∼60 K; narrow strips (50 nanometers) would likely show such effects at room temperature.

  14. In the Dark

    The behavior of Earth's hot mantle at depth depends on many mineral phase transitions in common mantle oxides, such as ferropericlase and iron magnesium perovskite. Goncharov et al. (p. 1205) analyzed absorption changes occurring in the infrared to ultraviolet wavelength ranges of these minerals as they were subjected to increasing pressure. They suggest that a spin-pairing transition occurring around 50 gigapascals in mantle iron oxides shifts charge around the lattice and causes low-spin iron minerals to become more opaque at depth. Thus, this transition alters heat transmission in the mantle.

  15. Providing Direction for Auxin Trafficking

    The “where” of auxin signaling is critical to regulating developmental responses during plant growth. Auxin is shunted through cells from one place to the next using influx and efflux carriers. The localization of these carriers thus has a direct effect on auxin signaling. Dharmasiri et al. (p. 1218, published online 11 May) have now cloned the AXR4 gene and show that the auxin influx carrier is localized according to directions provided by the AXR4 protein.

  16. Genetics and Pituitary Tumors

    Pituitary adenomas are slow-growing, generally benign, tumors that may occur in as much as 25% of the population. These tumors can pose serious health risks through mechanical compression of adjacent tissue and/or through altered secretion of pituitary-derived hormones, such as growth hormone. Little is known about the molecular mechanisms by which these tumors arise. Taking advantage of genealogy data in Finland dating back to the 1700s, Vierimaa et al. (p. 1228) discovered that many individuals with pituitary adenomas are genetically predisposed to develop these tumors because they carry mutations in the gene encoding the aryl hydrocarbon receptor interacting protein (AIP). These results should facilitate the identification of at-risk individuals as well as stimulate research into the functional role of AIP in the pathogenesis of these tumors.