This Week in Science

Science  04 Oct 2013:
Vol. 342, Issue 6154, pp. 11
  1. Sponge Pump


    “Darwin's Paradox” asks how productive and diverse ecosystems like coral reefs thrive in the marine equivalent of a desert. De Goeij et al. (p. 108) now show that coral reef sponges are part of a highly efficient recycling pathway for dissolved organic matter (DOM), converting it, via rapid sponge-cell turnover, into cellular detritus that becomes food for reef consumers. DOM transfer through the sponge loop approaches the gross primary production rates required for the entire coral reef ecosystem.

  2. Gas Separations

    When gas separation membranes are made thinner, they usually allow permeating gases to pass through faster. However, a thinner membrane may be poorer at separating between gas species. Kim et al. (p. 91) examined the permeability and selectivity of layered graphene and graphene oxide membranes. Gas molecules diffuse through defective pores and channels that form between the layers. Controlling these structures tuned the properties of the membranes to allow the extraction of carbon dioxide from other gases. Li et al. (p. 95) describe membranes as thin as 1.8 nanometers made from only two to three layers of graphene oxide. Small defects within the layers allowed hydrogen to pass through, separating it from carbon dioxide and nitrogen.

  3. Resetting the Circadian Clock

    Fatigue and other symptoms of jet lag arise when the body's internal circadian clock is out of sync with environmental light-dark cycles. Studying genetically modified mice lacking two receptors for the peptide hormone vasopressin under experimental conditions simulating jet lag, Yamaguchi et al. (p. 85; see the Perspective by Hastings) concluded that vasopressin signaling in the suprachiasmatic nucleus (SCN)—a region of the brain known to control circadian rhythms—impedes adjustment to the environmental clock. Infusion of vasopressin receptor antagonists directly into the SCN of wild-type mice accelerated their recovery from jet lag, suggesting that this pathway may merit further investigation as a pharmacological target for treating jet lag.

  4. Same As It Ever Was

    Nitrogen constitutes approximately 78% by volume of Earth's atmosphere and is a key component in its chemical and physical characteristics. It is not clear whether N2 has been so abundant throughout Earth's geological history. Marty et al. (p. 101, published online 19 September) analyzed the isotopic compositions of nitrogen and argon from fluid inclusions trapped in hydrothermal quartz formed 3 to 3.5 billion years ago. The partial pressure and isotopic composition of atmospheric N2 were similar to today's. Thus, other factors are needed to explain why liquid water existed on Earth's surface despite the Sun being 30% less luminous.

  5. Silencing a Silent Killer

    Hypertrophic cardiomyopathy (HCM) is a leading cause of sudden death in young athletes. HCM is caused by dominant mutations in genes encoding constituents of the cardiac sarcomere, the contractile unit that keeps the heart pumping. Studying a mouse model that recapitulates a severe form of HCM caused by a mutation in a β myosin heavy chain gene, Jiang et al. (p. 111) investigated whether sarcomere dysfunction could be corrected by selectively silencing expression of the mutant allele. Mice treated shortly after birth with a viral vector encoding an appropriately designed RNA interference cassette did not develop cardiac hypertrophy or myocardial fibrosis—the pathologic manifestations of HCM—for at least 6 months.

  6. RNA on the Attack

    Plant microbial pathogens often work through protein effectors that are delivered into the plant cells to disrupt critical cellular functions. Weiberg et al. (p. 118; see the Perspective by Baulcombe) have now found that small RNAs (sRNAs) of the fungus Botrytis cinerea can play a similar role. After fungal infection of tomato or Arabidopsis leaves, the plant cells contained a suite of fungal-derived sRNAs. Three sRNAs were found to bind to the plant's own Argonaute protein, thereby silencing the plant's fungal defense genes.

  7. Reactive Conformations


    Most molecules manifest a fair amount of flexibility at room temperature, in particular through interconversion of rotational conformers—structures that differ by the relative orientation of groups on either side of a single covalent bond. Chang et al. (98; see the Perspective by Heaven) devised a method to explore the comparative reactivities of different conformers. A mixture of the conformers was prepared in a molecular beam cold enough to preclude interconversion; then an electric field was used to push the different conformers apart, spatially resolving subsequent collisional interactions with a target of trapped ions.

  8. Citation Grabbers

    Is there quantifiable regularity and predictability in citation patterns? It is clear that papers that have been cited frequently tend to accumulate more citations. It is also clear that, with time, even the most novel paper loses its currency. Some papers, however, seem to have an inherent “fitness” that can be interpreted as a community's response to the research. Wang et al. (p. 127; see the Perspective by Evans) developed a mechanistic model to predict citation history. The model links a paper's ultimate impact, represented by the total number of citations the paper will ever receive, to a single measurable parameter inferred from its early citation history. The model was used to identify factors that influence a journal's impact factor.

  9. Identifying Important Identifiers

    Each of us has millions of sequence variations in our genomes. Signatures of purifying or negative selection should help identify which of those variations is functionally important. Khurana et al. (1235587) used sequence polymorphisms from 1092 humans across 14 populations to identify patterns of selection, especially in noncoding regulatory regions. Noncoding regions under very strong negative selection included binding sites of some chromatin and general transcription factors (TFs) and core motifs of some important TF families. Positive selection in TF binding sites tended to occur in network hub promoters. Many recurrent somatic cancer variants occurred in noncoding regulatory regions and thus might indicate mutations that drive cancer.

  10. Two Are Not Necessarily Better Than One

    Gene duplication is one of the major drivers of the evolution of gene and protein networks. However, specific examples of how genes change to maintain two paralogous gene copies within an organism are relatively rare. Baker et al. (p. 104) examined the functional divergence of the paralogs Mcm1 and Arg80, MADS-box transcription factors in the yeast Saccharomyces cerevisiae. The partitioning of ancestral functions in a fungal transcription factor appeared to be affected by competitive interference between the newly formed gene duplicates. Thus, in yeast, gene duplication has created a selective conflict between the paralogs, which appear to have driven the evolution of a novel protein function.

  11. pH Gradient in Light of Electroneutrality


    Photosynthesis in plant chloroplasts depends on a proton gradient to convert light energy into adenosine triphosphate. Studying Arabidopsis, Carraretto et al. (114, published online 5 September; see the Perspective by Rochaix) identified the potassium channel TPK3 in the stacked membranes of the chloroplast's thylakoids as key to sustaining the proton gradient. As the thylakoid lumen acidifies on exposure to light, electroneutrality derives from TPK3 activity. TPK3 was able to optimize chloroplast responses to light across a wide range of intensities. Plants lacking functional TPK3 appeared normal when grown at modest light levels, but at higher light levels, the plants showed disruptions in overall growth and in thylakoid organization.

  12. Pumping Out Sodium

    Mammalian cells contain relatively high concentrations of potassium but low concentrations of sodium. This balance is maintained by an ion pump, the Na+, K+–adenosine triphosphatase, in an adenosine triphosphate–driven transport cycle that results in the export of three sodium ions and the import of two potassium ions. Structures of potassium-bound conformations of the pump have been determined. Now, Nyblom et al. (p. 123, published online 19 September) report on the high-resolution crystal structure of a Na+-bound conformation, which reveals conformational changes associated with Na+ binding.