This Week in Science

Science  31 Oct 2008:
Vol. 322, Issue 5902, pp. 645
  1. Transporter in Action


    Secondary active transporters couple transport of substrate to an ion gradient. Transport is proposed to occur through an alternating access mechanism in which a substrate binding site located toward the center of the protein has alternating access to either side of the membrane. Structures of two secondary transporters, the leucine transport protein LeuT and the galactose transport protein vSGLT, are available, but in both structures the substrate is occluded from both sides of the membrane. Now Weyand et al. (p. 709, published online 16 October) report outward facing open and substrate-bound occluded conformations for a nucleobase transporter. Comparison of the outward facing conformations with the inward facing substrate occluded conformation of vSGLT suggests a structural model for how alternate opening and closing of inward and outward facing cavities is achieved.

  2. Clocking Clock Components

    Like most cells and organisms, cyanobacteria contain a circadian clock that helps to optimize its metabolism for the daily cycles of light, dark, and temperature. This clock can be reconstituted in vitro with just three protein components—KaiA, KaiB, and KaiC. Johnson et al. (p. 697) review how the high-resolution structures of these proteins show that their interactions result in conformational changes and phosphorylation events over a 24-hour period. Sequential phosphorylation of two amino acids in KaiC may be enforced by the structure of the protein, causing a built-in ratcheting mechanism that drives the oscillator unidirectionally. Thus, the structural features of the three essential clock components, combined with biochemical and biophysical data, reveal molecular mechanisms of biological timekeeping.

  3. Getting Angrite

    Angrites are a type of primitive meteorite from some of the earliest formed planetesimals in our solar system. Weiss et al. (p. 713) show that angrites preserve a remnant magnetic field that was probably generated internally. These fields were perhaps as large as 20% of that of Earth. Thus it seems that, even in these small primitive bodies, a molten iron core formed rapidly after the formation of the solar system.

  4. Sediments in Motion

    Many models of Earth surface dynamics employ some criteria for determining the conditions that lead to particle entrainment, when oscillating or flowing objects move in step together. An example of this is the dislodging of particles from a sedentary bed into a mildly turbulent flowing stream. In general this has been modeled by considering the time-average boundary shear, which is connected to the maximum force impacts on the particles. Diplas et al. (p. 717) show that this criterion is not sufficient, and that instead one should consider the impulse, which is a combination of the force and duration, in determining sediment motion.

  5. Lithographic Liquids

    The ability to use polymers for nanometer-scaled imprint lithography depends on being able to control their flow and final dimensions as they are squeezed into shape. One might expect that longer polymers would always show the highest viscosities, because they can form the greatest number of entanglements, and that increasing the applied strain should act on all molecular sizes in a similar way. Rowland et al. (p. 720, published online 2 October; see the Perspective by Soles and Ding) studied a series of polystyrene polymers compressed by a flat rigid die and observed unusual, nonlinear behavior for the thinnest films, where the dimensions of the film approach the unconstrained dimensions of the polymer chains. Thus, at the smallest dimensions, it may be easiest to process very long polymers, which may provide the best lithographic resolution.

  6. NOX


    Atmospheric nitrogen oxides (NO2 + NO, collectively referred to as NOX) are important in the environment, where NO2 is a precursor for nitrate, an essential macronutrient for plants, as well as in the atmosphere, where they are important components of the ozone cycle and particle formation. Although much attention has been paid to regulating the emission of NOX, its atmospheric concentration is increasing globally, even in very remote regions, due to continued and increasing emissions in some parts of the world and long-range transport. Morin et al. (p. 730) present results of isotopic measurement of N and O in atmospheric nitrate from the High Arctic, which reveal how a combination of transport and springtime photochemical emissions of reactive nitrogen from the snowpack produce an overwhelming flux of NOX. This is important in the process of evaluating pollution threats to the air quality and ecosystems of that region and for understanding the potential impact on climate and biodiversity.

  7. Emergence of Modern Human Behavior

    The time and rate at which modern humans colonized the planet, and the interactions that they had with the indigenous biota, remains a source of continuing debate. Jacobs et al. (p. 733) report new and precise ages for two short-lived bursts of technological innovation associated with the emergence of modern human behavior during the southern African Middle Stone Age. These key archaeological events cannot be explained by environmental factors alone, but were contemporaneous with—and may have catalyzed—the prehistoric expansion of human populations within Africa and the first successful exodus of people 80 to 60 thousand years ago.

  8. Tuna Mix

    Bluefin Tuna are split into two populations. The western population spawns in the Gulf of Mexico and the eastern population spawns in the Mediterranean Sea. The western population is in a particularly vulnerable state, and conservation management zones that are currently arbitrarily demarked by 45°W longitude do not seem to be alleviating the population decline. In an attempt to find out why tuna management is ineffective, Rooker et al. (p. 742, published online 2 October) have taken cores from otoliths in the fishes' ears and measured carbon and oxygen isotope ratios to obtain a chemical signature characteristic of the fishes' birthplace. Adolescent fish from both populations, oblivious to the 45°W management boundary, mix on their extensive migrations to feed in the Atlantic Ocean. As the tuna mature they exhibit a strong tendency to return, like salmon, to their birthplace to spawn. Unexpectedly, the waters around the Gulf of Maine and St. Lawrence were refugia for mature adults from the western population, which may have implications for revising tuna management across international boundaries.

  9. Mussels and Self-Organization

    The concept of spatial self-organization, where small-scale interactions between individual organisms drive large-scale spatial patterns, is the main explanation for coherent spatial patterns in a wide range of terrestrial and aquatic ecosystems. Van de Koppel et al. (p. 739) present an experimental test of the mechanisms underlying spatial self-organization in an ecosystem—mussels on the seabed. Regular spatial patterns emerge in a mussel bed under experimentally controlled conditions, which modeling suggests arise from interactions between individual mussels. A subsequent field study showed the positive effects of self-organization on ecosystem-level processes, in particular, secondary production and resistance to wave disturbance, pointing to the need for conservation of spatial structure within ecosystems.

  10. Of Glia and Senses


    Sensory organs are the main conduit by which an animal perceives its environment, and these organs have been remarkably conserved in anatomy, morphology, and molecular biology from Caenorhabditis elegans to humans. To explore the role of glial cells in sensory perception Bacaj et al. (p. 744; see the Perspective by Reichenbach and Pannicke) examined their functions in the amphid, the largest C. elegans sense organ, and revealed essential functions for glia in regulating neuronal morphology and activity. The sheath glial cell of the amphid is required for several functional aspects of the ensheathed sensory neurons.

  11. HARPing On

    The complementarity of DNA and RNA is of great utility for the conveyance of genetic information, as well as (mainly in the case of RNA) the formation of secondary and tertiary structure critical for function. Still, for the information to be read, or the structures to be assembled or disassembled, the base-paired strands of nucleic acid need to be pulled asunder. This feat is carried about by a ubiquitous class of enzymes known as helicases. Yusufzai and Kadonaga (p. 748) have now characterized precisely the opposite activity, a human enzyme, HARP (HepA-related protein), a distant member of the SNF2 family of ATP-driven molecular motor proteins, that uses ATP to zip up stably separated strands of DNA. Mutations in HARP result in Schimke immuno-osseous dysplasia, a fatal autosomal recessive disorder. In patients, the severity of the disease correlates with the loss of reverse helicase activity of the enzyme.

  12. TRPM7 and T Cell Development


  13. Aneuploidy and Proliferation

    Many cancer cells are aneuploid and have an incorrect number of chromosomes, but whether aneuploidy actually contributes to or inhibits a tumorigenic phenotype is not clear. Williams et al. (p. 703; see the Perspective by Hernando) constructed mouse embryonic fibroblast cell lines that contained an extra copy of one of four different chromosomes. Aneuploidy increased expression of genes present in an extra copy by about 1.5-fold and caused inhibition of cell proliferation that was independent of the particular chromosome overrepresented, but was dependent on chromosome size. Aneuploidy had variable effects on immortalization of the cells in culture. The findings open the way for further understanding of a process that also leads to miscarriages and mental retardation in humans.

  14. Impure

    The ratio of Mg/Ca of calcite in calcifying marine organisms can be used as a proxy for the temperature in which the organism grew. However, a strict correspondence of Mg/Ca and temperature is compromised by what are known as “vital effects,” which are poorly understood and difficult to quantify, and which can make reconstructions of past ocean temperatures problematic. Stephenson et al. (p. 724) conduct laboratory experiments to show that the presence of a simple hydrophilic peptide similar to macromolecules found at sites of calcification can increase the Mg content of the calcite by as much as 3 mol%—enough to introduce an artifact of 7° to 14°C into the reconstructed temperature. Thus, organic molecules can affect the synthesis of carbonates, and impurities can be regulated during material production.

  15. Bounce Bounce

    Buildings in seismic zones need to be designed to maintain integrity during strong shakings. Recent instrumentation is now revealing unexpected dynamics close to earthquake epicenters. Aoi et al. (p. 727; see the Perspective by O'Connell) show that ground acceleration exceeded 4 times gravity in a recent magnitude 6.9 quake in Japan. Interestingly, the upward acceleration was greater than the downward one. The authors explain the signal with a model of a shallow soil layer bouncing on a trampoline formed by the underlying crust. This high of an acceleration and dynamics poses challenges in earthquake design.

  16. Universal Truths?

    General theoretical frameworks accounting for how a developing organism allocates energy for growth and the maintenance of existing biomass have traditionally been based on rates of either food consumption or metabolic energy expenditure. Hou et al. (p. 736) present a model for energy uptake and allocation over an organism's growth and development that reconciles rates of food assimilation with rates of allocation to maintenance, biosynthesis, activity, and storage. This model predicts that growth and assimilation rates for all organisms should cluster closely around two universal curves. Data for mammals and birds of diverse body sizes and taxa support these predictions.

  17. A Question of Balance

    To balance the gene dosage experienced by XX female cells and XY male cells, mammals evolved a system in which one of the female X chromosomes is shut down, a process known as X inactivation. The noncoding RNA Xist, which is expressed from and coats the inactive X chromosome, is central to the whole-chromosome inactivation process, although the details of how it does this remain unclear. Zhao et al. (p. 750) identify a small internal transcript from within Xist, RepA, that includes the Repeat A sequence, known to be required for silencing. The RepA RNA binds to the Ezh2 subunit of the Polycomb complex, PRC2, independently of Xist, and is able to recruit PCR2 to the X chromosome to initiate X inactivation. The Xist antisense RNA Tsix, also encoded on the X chromosome, competitively inhibits this interaction and in this way may regulate X inactivation.

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