This Week in Science

Science  20 May 2011:
Vol. 332, Issue 6032, pp. 891
  1. Dissecting the Spikemoss Genome

    CREDIT: JING-KE WENG

    The lineage to modern lycophytes (club mosses, quilworts, and spikemosses) diverged from that of flowering plants long ago. Banks et al. (p. 960, published online 5 May) have now sequenced the genome of the lycophyte, Selaginella moellendorffii, whose genome, compared to other plants, is particularly compact at 110 megabase pairs. The gene density is similar to that of Arabidopsis, but the genome does not carry traces of polyploidization. This analysis of the genome lends insight into unique deployments of small RNA and RNA editing functions, and hints at the evolutionary transitions needed to go from nonvascular to vascular plants.

  2. Understanding Yeast

    Fission yeast, Schizosaccharomyces pombe, is a key model eukaryote that has been studied in context of its distant relationship to other organisms. Rhind et al. (p. 930, published online 21 April; see the cover) compared genome sequences of four fission yeast species, including S. pombe. Transposon structure and number differ significantly among species, and—while gene content, gene structure, and gene order are conserved—the degree of amino acid substitution is high. Antisense transcription was enriched for meiotic genes, suggesting that these transcripts may help to coordinate their expression. Furthermore, regulatory motif evolution and innovations in gene content and regulation may underlie the parallel evolution of ethanol metabolism in fission and budding yeast.

  3. Prescribing Order

    Interfaces between transition metal oxides exhibit a wide range of behavior; insulating, metallic, magnetic, and superconducting behaviors can all be induced by a gate voltage. Moving into bulk systems, Boris et al. (p. 937; see the Perspective by Hammerl and Spaldin) found that varying the thickness and number of layers of a heterostructure of thin LaNiO3 and LaAlO3 layers could control the dimensionality of the superlattice. This approach provides a route to manipulate the collective behavior of charge and spin order within metal oxide superlattice systems.

  4. Organic Devices Find a Closer Match

    Indium tin oxide (ITO) electrodes are transparent and robust and are often used as an electrode in many organic devices, such as light-emitting diodes (LEDs). Helander et al. (p. 944, published online 14 April) report a method for chlorinating ITO that increases its work function—the energy needed to emit an electron—so that the electron energy better matches that of the typical organic active layers. The need to use multiple layers of different materials to build a stepwise charge injection process is avoided, and device efficiency for green organic LEDs is high.

  5. Indecisive Magnetic Interactions

    CREDIT: FRANKE ET AL.

    A magnetic atom adsorbed on the surface of a superconductor could undergo two different types of interactions: It could be screened by free electrons that remain in the normal metal state through the Kondo effect, or it could couple with electron pairs of the superconducting state. Franke et al. (p. 940) used scanning tunneling microscopy and spectroscopy to study manganese phthalocyanine molecules adsorbed on a lead surface. Both types of magnetic ground state that could be produced through these interactions were observed. The states alternated spatially on nanometer length scales and formed a superstructure with a Moiré-like pattern.

  6. The Fingerprints of Tides

    Ocean tides result in substantial variations of the amount of stress that is applied by the ocean to the sea floor and nearby continents. This stress can influence the motion of the crust—a response that could be used to determine properties of Earth's interior. By monitoring the response of Earth's crust to the tides with a dense Global Positioning System array, Ito and Simons (p. 947, published online 14 April) determined the regional structure of the mantle below the western United States. The crustal motion data are compatible with independent seismic data and provide direct estimates of previously inaccessible properties such as density.

  7. Ozone and Rainfall

    The widespread commercial and industrial use of chlorofluorocarbons during the second half of the 20th century caused a stratospheric ozone hole over Antarctica. The resulting modification of the thermal structure of the atmosphere led to dynamic changes in atmospheric circulation both within the Antarctic atmospheric vortex and at lower latitudes. Kang et al. (p. 951, published online 21 April; see the Perspective by Feldstein) report on one of the consequences of this process—a summertime increase in precipitation in the southern subtropics. This change resulted from a poleward shift of the extratropical westerly jet in the Southern Hemisphere, illustrating the importance of the polar regions to the hydrology of the subtropics.

  8. The Better to Smell You With

    Mammals possess advanced olfactory and tactile senses. Enlargement of sensory regions in the mammalian brain reflect these specializations. Rowe et al. (p. 955; see the Perspective by Northcutt) used x-ray tomography to create endocasts of two pre-mammal species and compared these to existing data on brain shape and size in extinct and extant species within the mammalian lineage. Brain enlargement and specialization in mammals proceeded in three pulses. First, there was an increase in the ability to perceive and process sensory cues, including tactile stimuli through body hair and olfactory cues from the environment. This was followed by improved neuromuscular coordination, and finally, in the first true mammals, development of nasal architecture increased the surface area available for olfactory receptors and water balance.

  9. Black or Light

    CREDIT: ILIK SACCHERI

    The evolution and spread of industrial melanism in the peppered moth (Biston betularia) is one of the most well known examples of evolution by natural selection. However, the genetic basis of the polymorphism remains unclear, as does whether the melanic form evolved once or multiple times. Van't Hof et al. (p. 958, published online 14 April) go some way to answering these questions by mapping the carbonaria locus, which shows that all melanic individuals carry the same haplotype. This finding suggests the rapid spread of the melanic form from a single mutation event. Furthermore, the genomic region responsible for the polymorphism also explains wing pattern and color variation in other lepidopteran species.

  10. Break Down to Build Up

    At certain points during development and aging, cells appear to catabolize their own constituents in order to provide the amino acids required for new protein synthesis. Narita et al. (p. 966, published online 21 April; see the Perspective by Zoncu and Sabatini) identified a protein recycling factory that can be formed to enhance protein synthesis in order to facilitate en masse secretion. This mTOR-autophagy spatial coupling compartment allows the simultaneous activation of both mTOR and autophagy, leading to concurrent protein synthesis and degradation and significantly enhancing protein turnover.

  11. Tolerance by TLR

    Our bodies harbor over a billion bacteria, the majority of which are commensal rather than pathogenic. Why does the immune system attack only pathogenic bacteria? Round et al. (p. 974, published online 21 April) examined the underlying immune mechanisms that allow for the colonization of colonic mucosal tissue by the human commensal, Bacteroides fragilis. In germ-free mice and in mice colonized with only B. fragilis, the B. fragilis–secreted molecule, polysaccharide A, signaled through Toll-like receptor 2 (TLR2) to promote immune tolerance. This finding is rather unexpected because TLR2 signaling is typically associated with immune activation and bacterial clearance. Thus, commensal bacteria may produce factors that promote tolerance by signaling through classical innate immune response pathways.

  12. Reconstituting Nucleosome Positioning

    Nucleosomes occupy specific defined positions around the transcription start sites of many genes, and up to half of all specific nucleosome positions are defined by the underlying DNA sequence. To determine whether histones and DNA are sufficient to determine proper nucleosome positions, Zhang et al. (p. 977) reconstituted chromatin in vitro. Most nucleosome positions were not predominantly sequence-intrinsic, nor were they determined by statistical positioning, where fixed barriers act as guides, nor were they driven by transcription. Rather, reconstitution of nucleosome position and occupancy level around the 5′ ends of many yeast genes required the presence of whole-cell extract and adenosine triphosphate (ATP), implying that an ATP-driven chromatin remodeler is involved.

  13. Ribosome Times Two

    The ribosome is the molecular machine responsible for protein synthesis. During synthesis, a ratchet-like rotation of the small ribosomal subunit relative to the large subunit facilitates translocation of messenger RNA (mRNA) and transfer RNA (tRNA). A key intermediate is a hybrid state in which tRNA is bound simultaneously to the peptidyl-tRNA site (P-site) on the small subunit and to the exit site (E-site) on the small subunit. Dunkle et al. (p. 981) describe two high-resolution structures of the Escherichia coli ribosome. The first positions tRNA in the P-sites of both the small and large subunits. The second has tRNA bound in the P/E state, stabilized by the ribosome recycling factor. Together, the structures provide insight into the ratcheting mechanism of the ribosome.

  14. Chromatin in Lineage Determination

    In early mouse development, cells of the ventral foregut endoderm adopt different fates to form the liver or pancreas. Although a number of genes are known to function in ventral foregut endoderm, it is not clear whether specific histone modifiers assist in this decision process. Xu et al. (p. 963) performed a screen for diverse chromatin marks in embryonic endoderm at genes that are poised to be activated for either the liver or pancreas cell fate. Regulatory elements for the liver and pancreas genes possessed different chromatin patterns. The enzymes involved in producing these patterns played a modulatory role but did not absolutely govern the number of cells specified to the liver and pancreas lineages. Thus, a functional “pre-pattern” of chromatin states is involved in the production of different tissues from multipotent progenitors.

  15. Host Versus Diet

    The number of cells living within the lumen of a mammal's gut can exceed the number of somatic cells by an order of magnitude. How have these symbionts coevolved with their hosts and how do they respond in the shorter term, as well as on an evolutionary scale to dietary input and functional output? In a survey of mammals that included humans, Muegge et al. (p. 970) found that, although the species composition and nuances in function may differ with different diets, an overall core repertoire of microbial genes could be discerned. However, even within a single free-living species, the structure and function of the gut microbiome was significantly affected by host dietary intake.