Global variation in copy number in the human genome

Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.     

A new gamma-ray burst classification scheme from GRB 060614

Gamma-ray bursts (GRBs) are known to come in two duration classes, separated at approximately 2 s. Long-duration bursts originate from star-forming regions in galaxies, have accompanying supernovae when these are near enough to observe and are probably caused by massive-star collapsars. Recent observations show that short-duration bursts originate in regions within their host galaxies that have lower star-formation rates, consistent with binary neutron star or neutron star-black hole mergers. Moreover, although their hosts are predominantly nearby galaxies, no supernovae have been so far associated with short-duration GRBs. Here we report that the bright, nearby GRB 060614 does not fit into either class. Its approximately 102-s duration groups it with long-duration GRBs, while its temporal lag and peak luminosity fall entirely within the short-duration GRB subclass. Moreover, very deep optical observations exclude an accompanying supernova, similar to short-duration GRBs. This combination of a long-duration event without an accompanying supernova poses a challenge to both the collapsar and the merging-neutron-star interpretations and opens the door to a new GRB classification scheme that straddles both long- and short-duration bursts.     

Disruption of extended defects in solid oxide fuel cell anodes for methane oxidation

Point defects largely govern the electrochemical properties of oxides: at low defect concentrations, conductivity increases with concentration; however, at higher concentrations, defect-defect interactions start to dominate. Thus, in searching for electrochemically active materials for fuel cell anodes, high defect concentration is generally avoided. Here we describe an oxide anode formed from lanthanum-substituted strontium titanate (La-SrTiO3) in which we control the oxygen stoichiometry in order to break down the extended defect intergrowth regions and create phases with considerable disordered oxygen defects. We substitute Ti in these phases with Ga and Mn to induce redox activity and allow more flexible coordination. The material demonstrates impressive fuel cell performance using wet hydrogen at 950 degrees C. It is also important for fuel cell technology to achieve efficient electrode operation with different hydrocarbon fuels, although such fuels are more demanding than pure hydrogen. The best anode materials to date--Ni-YSZ (yttria-stabilized zirconia) cermets--suffer some disadvantages related to low tolerance to sulphur, carbon build-up when using hydrocarbon fuels (though device modifications and lower temperature operation can avoid this) and volume instability on redox cycling. Our anode material is very active for methane oxidation at high temperatures, with open circuit voltages in excess of 1.2 V. The materials design concept that we use here could lead to devices that enable more-efficient energy extraction from fossil fuels and carbon-neutral fuels.     

Detection of magnetic circular dichroism using a transmission electron microscope

A material is said to exhibit dichroism if its photon absorption spectrum depends on the polarization of the incident radiation. In the case of X-ray magnetic circular dichroism (XMCD), the absorption cross-section of a ferromagnet or a paramagnet in a magnetic field changes when the helicity of a circularly polarized photon is reversed relative to the magnetization direction. Although similarities between X-ray absorption and electron energy-loss spectroscopy in a transmission electron microscope (TEM) have long been recognized, it has been assumed that extending such equivalence to circular dichroism would require the electron beam in the TEM to be spin-polarized. Recently, it was argued on theoretical grounds that this assumption is probably wrong. Here we report the direct experimental detection of magnetic circular dichroism in a TEM. We compare our measurements of electron energy-loss magnetic chiral dichroism (EMCD) with XMCD spectra obtained from the same specimen that, together with theoretical calculations, show that chiral atomic transitions in a specimen are accessible with inelastic electron scattering under particular scattering conditions. This finding could have important consequences for the study of magnetism on the nanometre and subnanometre scales, as EMCD offers the potential for such spatial resolution down to the nanometre scale while providing depth information--in contrast to X-ray methods, which are mainly surface-sensitive.     

The ABC protein turned chloride channel whose failure causes cystic fibrosis

CFTR chloride channels are encoded by the gene mutated in patients with cystic fibrosis. These channels belong to the superfamily of ABC transporter ATPases. ATP-driven conformational changes, which in other ABC proteins fuel uphill substrate transport across cellular membranes, in CFTR open and close a gate to allow transmembrane flow of anions down their electrochemical gradient. New structural and biochemical information from prokaryotic ABC proteins and functional information from CFTR channels has led to a unifying mechanism explaining those ATP-driven conformational changes.     

Scale invariance and universality of force networks in static granular matter

Force networks form the skeleton of static granular matter. They are the key factor that determines mechanical properties such as stability, elasticity and sound transmission, which are important for civil engineering and industrial processing. Previous studies have focused on investigations of the global structure of external forces (the boundary condition) and on the probability distribution of individual contact forces. So far, however, precise knowledge of the disordered spatial structure of the force network has remained elusive. Here we report that molecular dynamics simulations of realistic granular packings reveal scale invariance of clusters of particles interacting by means of relatively strong forces. Despite visual variation, force networks for various values of the confining pressure and other parameters have identical scaling exponents and scaling function, thereby determining a universality class. Unexpectedly, the flat ensemble of force configurations (a simple generalization of equilibrium statistical mechanics) belongs to this universality class, whereas some widely studied simplified models do not. This implies that the elasticity of the grains and their geometrical disorder do not affect the universal mechanical properties.     

Parasite community of the golden cownose ray Rhinoptera steindachneri Evermann and Jenkins 1891 (Chondrichthyes: Myliobatidae), in Acapulco Bay,Guerrero, Mexico

The parasite community of the ray Rhinoptera steindachneri from Acapulco Bay was examined and quantified; analyses were based on the sex of the host and the date of sampling. A total of 171 specimens of R. steindachneri were examined during July–August of 2010, and May and July of 2012. Twenty-one species of parasites were found: three species of Monogenea; eight adult and one larval species of Cestoda; one larval species of Nematoda; five species of Copepoda; two species of Isopoda; and one species of Hirudinea. Cestodes had the greatest species richness (43% of the total species), followed by the copepods (24%). Two species of cestode, Glyphobothrium sp. and Rhinebothrium sp., were collected only from adult rays. At the component community level, species richness showed statistically significant variation between 13 and 16 species, which is similar to previous reports for other species of rays. The parasite component communities and infracommunities of R. steindachneri exhibited similar patterns: high species number and low numerical dominance by a particular species of parasite. The differences of body size of male vs. female rays, and a change in diet and feeding behaviour with the age of R. steindachneri, are likely important factors in the structuring of their parasite communities.     

Redescription of Retilaskeya horrida (di Monterosato, 1874) comb. nov. and a re-evaluation of the taxonomic affinity of the genus Retilaskeya (Caenogastropoda: Triphoroidea)

The family Cerithiopsidae H. Adams and A. Adams, 1853 is distributed worldwide, and comprises around 800 extant species divided into ~40 genera. The most speciose genus within the family is Cerithiopsis Forbes and Hanley, 1850, a taxon currently used as a general receptacle rather than as a proper phylogenetic lineage. We hereby redescribe the rare species Cerithiopsis horrida di Monterosato, 1874, review its nomenclature, known material, and distribution as well as figure the entire protoconch, operculum, and radula for the first time. Our results highlight extreme differences between ‘Cerithiopsis’ horrida and the Cerithiopsis type species Cerithiopsis tubercularis (Montagu, 1803) and strong morphological and radular similarities with species belonging to the genus Retilaskeya Marshall, 1978. A wide discussion lists several taxa that might be ascribed to the same group of species, which presumably constitute a different worldwide lineage. Pending relevant molecular phylogenetic studies of the Triphoroidea Gray, 1847, for morphological conformity we suggest transferring ‘Cerithiopsis’ horrida to the genus Retilaskeya, and the same action is presumably appropriate for its possible sister species ‘Cerithiopsis’ leopardus Rolán and Gori, 2013. Finally, Retilaskeya better conforms to Newtoniellidae Korobkov, 1955 than Cerithiopsidae.