Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease

Integration of genome-wide expression profiling with linkage analysis is a new approach to identifying genes underlying complex traits. We applied this approach to the regulation of gene expression in the BXH/HXB panel of rat recombinant inbred strains, one of the largest available rodent recombinant inbred panels and a leading resource for genetic analysis of the highly prevalent metabolic syndrome. In two tissues important to the pathogenesis of the metabolic syndrome, we mapped cis- and trans-regulatory control elements for expression of thousands of genes across the genome. Many of the most highly linked expression quantitative trait loci are regulated in cis, are inherited essentially as monogenic traits and are good candidate genes for previously mapped physiological quantitative trait loci in the rat. By comparative mapping we generated a data set of 73 candidate genes for hypertension that merit testing in human populations. Mining of this publicly available data set is expected to lead to new insights into the genes and regulatory pathways underlying the extensive range of metabolic and cardiovascular disease phenotypes that segregate in these recombinant inbred strains.     

Seismological evidence for mosaic structure of the surface of the Earth's inner core

The transition from the Earth's solid inner core to liquid outer core is the location where the inner core grows and from which compositional convection in the outer core originates. Most seismological models of the Earth describe the inner-core boundary as sharp and simple, although experimental data requiring the presence of a thin transition layer at the bottom of the outer core have been reported. The density jump at the inner-core boundary--an important parameter determining gravitational energy release and constraining the compositional difference between the inner and outer core-is also not well known. Estimates of this density jump obtained using free-oscillation eigenfrequencies give low values of 0.25-1.0 g cm(-3), whereas a method using the amplitude ratio of core-reflected phases yielded values of 0.6-1.8 g cm(-3) (refs 14, 15, 16-17). Here we analyse properties of waves precritically reflected from the Earth's inner core (PKiKP phases) that show significant variability in amplitude, consistent high-frequency content and stable travel times with respect to a standard Earth model. We infer that the data are best explained by a mosaic structure of the inner core's surface. Such a mosaic may be composed of patches in which the transition from solid inner to liquid outer core includes a thin partially liquid layer interspersed with patches containing a sharp transition.     

In situ multi-satellite detection of coherent vortices as a manifestation of Alfvénic turbulence

Turbulence in fluids and plasmas is a ubiquitous phenomenon driven by a variety of sources-currents, sheared flows, gradients in density and temperature, and so on. Turbulence involves fluctuations of physical properties on many different scales, which interact nonlinearly to produce self-organized structures in the form of vortices. Vortex motion in fluids and magnetized plasmas is typically governed by nonlinear equations, examples of which include the Navier-Stokes equation, the Charney-Hasegawa-Mima equations and their numerous generalizations. These nonlinear equations admit solutions in the form of different types of vortices that are frequently observed in a variety of contexts: in atmospheres, in oceans and planetary systems, in the heliosphere, in the Earth's ionosphere and magnetosphere, and in laboratory plasma experiments. Here we report the discovery by the Cluster satellites of a distinct class of vortex motion-short-scale drift-kinetic Alfvén (DKA) vortices-in the Earth's magnetospheric cusp region. As is the case for the larger Kelvin-Helmholtz vortices observed previously, these dynamic structures should provide a channel for transporting plasma particles and energy through the magnetospheric boundary layers.     

Palaeoclimatology: the record for marine isotopic stage 11

The marine isotopic stage 11 (MIS 11) is an extraordinarily long interglacial period in the Earth's history that occurred some 400,000 years ago and lasted for about 30,000 years. During this period there were weak, astronomically induced changes in the distribution of solar energy reaching the Earth. The conditions of this orbital climate forcing are similar to those of today's interglacial period, and they rendered the climate susceptible to other forcing--for example, to changes in the level of atmospheric carbon dioxide. Here we use ice-core data from the Antarctic Vostok core to reconstruct a complete atmospheric carbon dioxide record for MIS 11. The record indicates that values for carbon dioxide throughout the interglacial period were close to the Earth's pre-industrial levels and that both solar energy and carbon dioxide may have helped to make MIS 11 exceptionally long. Anomalies in the oceanic carbonate system recorded in marine sediments at the time, for example while coral reefs were forming, apparently left no signature on atmospheric carbon dioxide concentrations.     

A recyclable catalyst that precipitates at the end of the reaction

Homogeneous catalysts--which exist in the same (usually liquid) phase as reactants and products--are usually more selective than heterogeneous catalysts and far less affected by limitations due to slow transport of reactants and products, but their separation from reaction products can be costly and inefficient. This has stimulated the development of strategies that facilitate the recycling of homogeneous catalysts. Some of these methods exploit the preference of a catalyst for one of two solvents with thermoregulated miscibility; others exploit a dramatic decrease in catalyst solubility as one reagent is consumed or temperature changed after completion of the reaction. Here we describe a tungsten catalyst for the solvent-free hydrosilylation of ketones that retains its activity until essentially all of the liquid substrate is converted to liquid products, which we can then simply decant to separate the catalyst that precipitates from the products of the reaction. We attribute the ability of the catalyst to retain its solubility and hence activity until completion of the reaction to the transient formation of liquid clathrate that contains a few molecules of the substrate per molecule of the otherwise solid catalyst. Insights into the fundamental processes controlling the formation of this liquid clathrate might help to tailor other catalysts and substrates, so as to develop efficient and solvent-free schemes for reactions of practical interest.     

Zero-resistance states induced by electromagnetic-wave excitation in GaAs/AlGaAs heterostructures

The observation of vanishing electrical resistance in condensed matter has led to the discovery of new phenomena such as, for example, superconductivity, where a zero-resistance state can be detected in a metal below a transition temperature T(c) (ref. 1). More recently, quantum Hall effects were discovered from investigations of zero-resistance states at low temperatures and high magnetic fields in two-dimensional electron systems (2DESs). In quantum Hall systems and superconductors, zero-resistance states often coincide with the appearance of a gap in the energy spectrum. Here we report the observation of zero-resistance states and energy gaps in a surprising setting: ultrahigh-mobility GaAs/AlGaAs heterostructures that contain a 2DES exhibit vanishing diagonal resistance without Hall resistance quantization at low temperatures and low magnetic fields when the specimen is subjected to electromagnetic wave excitation. Zero-resistance-states occur about magnetic fields B = 4/5 Bf and B = 4/9 Bf, where Bf = 2pifm*/e,m* is the electron mass, e is the electron charge, and f is the electromagnetic-wave frequency. Activated transport measurements on the resistance minima also indicate an energy gap at the Fermi level. The results suggest an unexpected radiation-induced, electronic-state-transition in the GaAs/AlGaAs 2DES.     

Selective oxidation with dioxygen by gold nanoparticle catalysts derived from 55-atom clusters

Supported gold nanoparticles have excited much interest owing to their unusual and somewhat unexpected catalytic properties, but the origin of the catalytic activity is still not fully understood. Experimental work on gold particles supported on a titanium dioxide (110) single-crystal surface has established a striking size threshold effect associated with a metal-to-insulator transition, with gold particles catalytically active only if their diameters fall below approximately 3.5 nm. However, the remarkable catalytic behaviour might also in part arise from strong electronic interaction between the gold and the titanium dioxide support. In the case of industrially important selective oxidation reactions, explanation of the effectiveness of gold nanoparticle catalysts is complicated by the need for additives to drive the reaction, and/or the presence of strong support interactions and incomplete understanding of their possible catalytic role. Here we show that very small gold entities ( approximately 1.4 nm) derived from 55-atom gold clusters and supported on inert materials are efficient and robust catalysts for the selective oxidation of styrene by dioxygen. We find a sharp size threshold in catalytic activity, in that particles with diameters of approximately 2 nm and above are completely inactive. Our observations suggest that catalytic activity arises from the altered electronic structure intrinsic to small gold nanoparticles, and that the use of 55-atom gold clusters may prove a viable route to the synthesis of robust gold catalysts suited to practical application.     

A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25

Lung cancer is the most common cause of cancer death worldwide, with over one million cases annually. To identify genetic factors that modify disease risk, we conducted a genome-wide association study by analysing 317,139 single-nucleotide polymorphisms in 1,989 lung cancer cases and 2,625 controls from six central European countries. We identified a locus in chromosome region 15q25 that was strongly associated with lung cancer (P = 9 x 10(-10)). This locus was replicated in five separate lung cancer studies comprising an additional 2,513 lung cancer cases and 4,752 controls (P = 5 x 10(-20) overall), and it was found to account for 14% (attributable risk) of lung cancer cases. Statistically similar risks were observed irrespective of smoking status or propensity to smoke tobacco. The association region contains several genes, including three that encode nicotinic acetylcholine receptor subunits (CHRNA5, CHRNA3 and CHRNB4). Such subunits are expressed in neurons and other tissues, in particular alveolar epithelial cells, pulmonary neuroendocrine cells and lung cancer cell lines, and they bind to N'-nitrosonornicotine and potential lung carcinogens. A non-synonymous variant of CHRNA5 that induces an amino acid substitution (D398N) at a highly conserved site in the second intracellular loop of the protein is among the markers with the strongest disease associations. Our results provide compelling evidence of a locus at 15q25 predisposing to lung cancer, and reinforce interest in nicotinic acetylcholine receptors as potential disease candidates and chemopreventative targets.     

Tools, Objects, and Chimeras: Connes on the Role of Hyperreals in Mathematics

We examine some of Connes’ criticisms of Robinson’s infinitesimals starting in 1995. Connes sought to exploit the Solovay model ${\mathcal{S}}$ as ammunition against non-standard analysis, but the model tends to boomerang, undercutting Connes’ own earlier work in functional analysis. Connes described the hyperreals as both a “virtual theory” and a “chimera”, yet acknowledged that his argument relies on the transfer principle. We analyze Connes’ “dart-throwing” thought experiment, but reach an opposite conclusion. In ${\mathcal{S}}$ , all definable sets of reals are Lebesgue measurable, suggesting that Connes views a theory as being “virtual” if it is not definable in a suitable model of ZFC. If so, Connes’ claim that a theory of the hyperreals is “virtual” is refuted by the existence of a definable model of the hyperreal field due to Kanovei and Shelah. Free ultrafilters aren’t definable, yet Connes exploited such ultrafilters both in his own earlier work on the classification of factors in the 1970s and 80s, and in Noncommutative Geometry, raising the question whether the latter may not be vulnerable to Connes’ criticism of virtuality. We analyze the philosophical underpinnings of Connes’ argument based on Gödel’s incompleteness theorem, and detect an apparent circularity in Connes’ logic. We document the reliance on non-constructive foundational material, and specifically on the Dixmier trace ${-\hskip-9pt\int}$ (featured on the front cover of Connes’ magnum opus) and the Hahn–Banach theorem, in Connes’ own framework. We also note an inaccuracy in Machover’s critique of infinitesimal-based pedagogy.