DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

Chromosome 17 is unusual among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second highest gene density in the genome. It is also enriched in segmental duplications, ranking third in density among the autosomes. Here we report a finished sequence for human chromosome 17, as well as a structural comparison with the finished sequence for mouse chromosome 11, the first finished mouse chromosome. Comparison of the orthologous regions reveals striking differences. In contrast to the typical pattern seen in mammalian evolution, the human sequence has undergone extensive intrachromosomal rearrangement, whereas the mouse sequence has been remarkably stable. Moreover, although the human sequence has a high density of segmental duplication, the mouse sequence has a very low density. Notably, these segmental duplications correspond closely to the sites of structural rearrangement, demonstrating a link between duplication and rearrangement. Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome.     

Modelling conservation in the Amazon basin

Expansion of the cattle and soy industries in the Amazon basin has increased deforestation rates and will soon push all-weather highways into the region's core. In the face of this growing pressure, a comprehensive conservation strategy for the Amazon basin should protect its watersheds, the full range of species and ecosystem diversity, and the stability of regional climates. Here we report that protected areas in the Amazon basin--the central feature of prevailing conservation approaches--are an important but insufficient component of this strategy, based on policy-sensitive simulations of future deforestation. By 2050, current trends in agricultural expansion will eliminate a total of 40% of Amazon forests, including at least two-thirds of the forest cover of six major watersheds and 12 ecoregions, releasing 32 +/- 8 Pg of carbon to the atmosphere. One-quarter of the 382 mammalian species examined will lose more than 40% of the forest within their Amazon ranges. Although an expanded and enforced network of protected areas could avoid as much as one-third of this projected forest loss, conservation on private lands is also essential. Expanding market pressures for sound land management and prevention of forest clearing on lands unsuitable for agriculture are critical ingredients of a strategy for comprehensive conservation.     

Land-atmosphere coupling and climate change in Europe

Increasing greenhouse gas concentrations are expected to enhance the interannual variability of summer climate in Europe and other mid-latitude regions, potentially causing more frequent heatwaves. Climate models consistently predict an increase in the variability of summer temperatures in these areas, but the underlying mechanisms responsible for this increase remain uncertain. Here we explore these mechanisms using regional simulations of recent and future climatic conditions with and without land-atmosphere interactions. Our results indicate that the increase in summer temperature variability predicted in central and eastern Europe is mainly due to feedbacks between the land surface and the atmosphere. Furthermore, they suggest that land-atmosphere interactions increase climate variability in this region because climatic regimes in Europe shift northwards in response to increasing greenhouse gas concentrations, creating a new transitional climate zone with strong land-atmosphere coupling in central and eastern Europe. These findings emphasize the importance of soil-moisture-temperature feedbacks (in addition to soil-moisture-precipitation feedbacks) in influencing summer climate variability and the potential migration of climate zones with strong land-atmosphere coupling as a consequence of global warming. This highlights the crucial role of land-atmosphere interactions in future climate change.     

Proteorhodopsin phototrophy in the ocean.

Proteorhodopsin, a retinal-containing integral membrane protein that functions as a light-driven proton pump, was discovered in the genome of an uncultivated marine bacterium; however, the prevalence, expression and genetic variability of this protein in native marine microbial populations remain unknown. Here we report that photoactive proteorhodopsin is present in oceanic surface waters. We also provide evidence of an extensive family of globally distributed proteorhodopsin variants. The protein pigments comprising this rhodopsin family seem to be spectrally tuned to different habitats--absorbing light at different wavelengths in accordance with light available in the environment. Together, our data suggest that proteorhodopsin-based phototrophy is a globally significant oceanic microbial process.     

Pre‐recession pattern of six economic indicators in the USA

This paper applies a tightly parameterized pattern recognition algorithm, previously applied to earthquake prediction, to the problem of predicting recessions. Monthly data from 1962 to 1996 on six leading and coincident economic indicators for the USA are used. In the full sample, the model performs better than benchmark linear and non‐linear models with the same number of parameters. Subsample and recursive analysis indicates that the algorithm is stable and produces reasonably accurate forecasts even when estimated using a small number of recessions. Copyright © 2000 John Wiley & Sons, Ltd.     

Caveolar targeting links Kv1.3 with the insulin-dependent adipocyte physiology

The voltage-dependent potassium channel Kv1.3 participates in peripheral insulin sensitivity. Genetic ablation of Kv1.3 triggers resistance to diet-induced weight gain, thereby pointing to this protein as a pharmacological target for obesity and associated type II diabetes. However, this role is under intense debate because Kv1.3 expression in adipose tissue raises controversy. We demonstrated that Kv1.3 is expressed in white adipose tissue from humans and rodents. Moreover, other channels, such as Kv1.1, Kv1.2, Kv1.4 and especially Kv1.5, from the same Shaker family are also present. Although elevated insulin levels and adipogenesis remodel the Kv phenotype, which could lead to multiple heteromeric complexes, Kv1.3 markedly participates in the insulin-dependent regulation of glucose uptake in mature adipocytes. Adipocyte differentiation increased the expression of Kv1.3, which is targeted to caveolae by molecular interactions with caveolin 1. Using a caveolin 1-deficient 3T3-L1 adipocyte cell line, we demonstrated that the localization of Kv1.3 in caveolar raft structures is important for proper insulin signaling. Insulin-dependent phosphorylation of the channel occurs at the onset of insulin-mediated signaling. However, when Kv1.3 was spatially outside of these lipid microdomains, impaired phosphorylation was exhibited. Our data shed light on the putative role of Kv1.3 in weight gain and insulin-dependent responses contributing to knowledge about adipocyte physiology.     

Robust estimation of conditional variance of time series using density power divergences

Suppose Z _t is the square of a time series Y _t whose conditional mean is zero. We do not specify a model for Y _t , but assume that there exists a p ×1 parameter vector Φ such that the conditional distribution of Z _t | Z _{t ?1} is the same as that of , where Z _{t ?1}=(Z _{t ?1},…,Z _{t ?p} )^T for some lag p ?1. Consequently, the conditional variance of Y _t is some function of . To estimate Φ , we propose a robust estimation methodology based on density power divergences (DPD) indexed by a tuning parameter α ∈[0,1], which yields a continuum of estimators, , where α controls the trade‐off between robustness and efficiency of the DPD estimators. For each α , is shown to be strongly consistent. We develop data‐dependent criteria for the selection of optimal α and lag p in practice. We illustrate the usefulness of our DPD methodology via simulation studies for ARCH‐type models, where the errors are drawn from a gross‐error contamination model and the conditional variance is a linear and/or nonlinear function of . Furthermore, we analyze the Chicago Board Options Exchange Dow Jones volatility index data and show that our DPD approach yields viable models for the conditional variance, which are as good as, or superior to, ARCH/GARCH models and two other divergence‐based models in terms of in‐sample and out‐of‐sample forecasts.     

What's nu? A re-examination of Maxwell's ‘ratio-of-units’ argument,from the mechanical theory of the electromagnetic field to ‘On the elementary relations between electrical measurements’

This re-examination of the earliest version of Maxwell's most important argument for the electromagnetic theory of light—the equality between the speed of wave propagation in the electromagnetic ether and the ratio of electrostatic to electromagnetic measures of electrical quantity—establishes unforeseen connections between Maxwell's theoretical electrical metrology and his mechanical theory of the electromagnetic field. Electrical metrology was not neutral with respect to field-theoretic versus action-at-a-distance conceptions of electro-magnetic interaction. Mutual accommodation between these conceptions was reached by Maxwell on the British Association for the Advancement of Science (BAAS) Committee on Electrical Standards by exploiting the measurement of the medium parameters—electric inductive capacity and magnetic permeability—on an arbitrary scale. While he always worked within this constraint in developing the ‘ratio-of-units’ argument mathematically, I maintain that Maxwell came to conceive of the ratio ‘as a velocity’ by treating the medium parameters as physical quantities that could be measured absolutely, which was only possible via the correspondences between electrical and mechanical quantities established in the mechanical theory. I thereby correct two closely-related misconceptions of the ratio-of-units argument—the counterintuitive but widespread notion that the ratio is naturally a speed, and the supposition that Maxwell either inferred or proved this from its dimensional formula.