The signature of hot hydrogen in the atmosphere of the extrasolar planet HD 209458b

About ten per cent of the known extrasolar planets are gas giants that orbit very close to their parent stars. The atmospheres of these 'hot Jupiters' are heated by the immense stellar irradiation. In the case of the planet HD 209458b, this energy deposition results in a hydrodynamic state in the upper atmosphere, allowing for sizeable expansion and escape of neutral hydrogen gas. HD 209458b was the first extrasolar planet discovered that transits in front of its parent star. The size of the planet can be measured using the total optical obscuration of the stellar disk during an observed transit, and the structure and composition of the planetary atmosphere can be studied using additional planetary absorption signatures in the stellar spectrum. Here we report the detection of absorption by hot hydrogen in the atmosphere of HD 209458b. Previously, the lower atmosphere and the full extended upper atmosphere of HD 209458b have been observed, whereas here we probe a layer where the escaping gas forms in the upper atmosphere of HD 209458b.     

Importance of rain evaporation and continental convection in the tropical water cycle

Atmospheric moisture cycling is an important aspect of the Earth's climate system, yet the processes determining atmospheric humidity are poorly understood. For example, direct evaporation of rain contributes significantly to the heat and moisture budgets of clouds, but few observations of these processes are available. Similarly, the relative contributions to atmospheric moisture over land from local evaporation and humidity from oceanic sources are uncertain. Lighter isotopes of water vapour preferentially evaporate whereas heavier isotopes preferentially condense and the isotopic composition of ocean water is known. Here we use this information combined with global measurements of the isotopic composition of tropospheric water vapour from the Tropospheric Emission Spectrometer (TES) aboard the Aura spacecraft, to investigate aspects of the atmospheric hydrological cycle that are not well constrained by observations of precipitation or atmospheric vapour content. Our measurements of the isotopic composition of water vapour near tropical clouds suggest that rainfall evaporation contributes significantly to lower troposphere humidity, with typically 20% and up to 50% of rainfall evaporating near convective clouds. Over the tropical continents the isotopic signature of tropospheric water vapour differs significantly from that of precipitation, suggesting that convection of vapour from both oceanic sources and evapotranspiration are the dominant moisture sources. Our measurements allow an assessment of the intensity of the present hydrological cycle and will help identify any future changes as they occur.     

Epithelial-cell-intrinsic IKK-beta expression regulates intestinal immune homeostasis

Intestinal epithelial cells (IECs) provide a primary physical barrier against commensal and pathogenic microorganisms in the gastrointestinal (GI) tract, but the influence of IECs on the development and regulation of immunity to infection is unknown. Here we show that IEC-intrinsic IkappaB kinase (IKK)-beta-dependent gene expression is a critical regulator of responses of dendritic cells and CD4+ T cells in the GI tract. Mice with an IEC-specific deletion of IKK-beta show a reduced expression of the epithelial-cell-restricted cytokine thymic stromal lymphopoietin in the intestine and, after infection with the gut-dwelling parasite Trichuris, fail to develop a pathogen-specific CD4+ T helper type 2 (T(H)2) response and are unable to eradicate infection. Further, these animals show exacerbated production of dendritic-cell-derived interleukin-12/23p40 and tumour necrosis factor-alpha, increased levels of CD4+ T-cell-derived interferon-gamma and interleukin-17, and develop severe intestinal inflammation. Blockade of proinflammatory cytokines during Trichuris infection ablates the requirement for IKK-beta in IECs to promote CD4+ T(H)2 cell-dependent immunity, identifying an essential function for IECs in tissue-specific conditioning of dendritic cells and limiting type 1 cytokine production in the GI tract. These results indicate that the balance of IKK-beta-dependent gene expression in the intestinal epithelium is crucial in intestinal immune homeostasis by promoting mucosal immunity and limiting chronic inflammation.     

Why endophenotype development requires families

Endophenotypes are heritable quantitative traits that are associated with disease liability, can be measured in both affected and unaffected individuals, and provide much greater power to localize and identify risk genes for mental illness than does affection status alone. Traditionally, endophenotypic markers for psychiatric illnesses include in vivo neuroanatomic and functional magnetic resonance imaging measurements and indices of neurocognitive abilities. However, neurocognitive and neuroimaging measures are by no means the only classes of endophenotypes that could be useful for identifying genes for mental illness. Given the advantages of endophenotype-based strategies for elucidating the genetic underpinnings of psychiatric disorders, it would seem prudent to develop a wide range of putative endophenotypes. In order for a measure to be considered a valid endophenotype, it must meet a number of criteria. Specifically, the trait must (1) have moderate to high heritability, (2) be associated with the illness, (3) be independent of clinical state, and (4) impairment must co-segregate with the illness within a family, with non-affected family members showing impairment relative to the general population. While each of these criteria is critical, the heritability and co-segregation requirements are really what differentiate an endophenotype from a simple biomarker. At this time, one requires an experimental design that includes families to demonstrate both heritability and co-segregation. The assertion that novel endophenotypes can not be fully established without family data does not preclude work in unrelated individuals, rather that unrelated samples will only be able to nominate potential candidate endophenotypes that subsequently need to be confirmed in family-based experiments.     

Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy

Latency and ongoing replication have both been proposed to explain the drug-insensitive human immunodeficiency virus (HIV) reservoir maintained during antiretroviral therapy. Here we explore a novel mechanism for ongoing HIV replication in the face of antiretroviral drugs. We propose a model whereby multiple infections per cell lead to reduced sensitivity to drugs without requiring drug-resistant mutations, and experimentally validate the model using multiple infections per cell by cell-free HIV in the presence of the drug tenofovir. We then examine the drug sensitivity of cell-to-cell spread of HIV, a mode of HIV transmission that can lead to multiple infection events per target cell. Infections originating from cell-free virus decrease strongly in the presence of antiretrovirals tenofovir and efavirenz whereas infections involving cell-to-cell spread are markedly less sensitive to the drugs. The reduction in sensitivity is sufficient to keep multiple rounds of infection from terminating in the presence of drugs. We examine replication from cell-to-cell spread in the presence of clinical drug concentrations using a stochastic infection model and find that replication is intermittent, without substantial accumulation of mutations. If cell-to-cell spread has the same properties in vivo, it may have adverse consequences for the immune system, lead to therapy failure in individuals with risk factors, and potentially contribute to viral persistence and hence be a barrier to curing HIV infection.     

Genome sequence and analysis of the tuber crop potato

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.     

A dynamic early East Antarctic Ice Sheet suggested by ice-covered fjord landscapes

The first Cenozoic ice sheets initiated in Antarctica from the Gamburtsev Subglacial Mountains and other highlands as a result of rapid global cooling ～34 million years ago. In the subsequent 20 million years, at a time of declining atmospheric carbon dioxide concentrations and an evolving Antarctic circumpolar current, sedimentary sequence interpretation and numerical modelling suggest that cyclical periods of ice-sheet expansion to the continental margin, followed by retreat to the subglacial highlands, occurred up to thirty times. These fluctuations were paced by orbital changes and were a major influence on global sea levels. Ice-sheet models show that the nature of such oscillations is critically dependent on the pattern and extent of Antarctic topographic lowlands. Here we show that the basal topography of the Aurora Subglacial Basin of East Antarctica, at present overlain by 2-4.5?km of ice, is characterized by a series of well-defined topographic channels within a mountain block landscape. The identification of this fjord landscape, based on new data from ice-penetrating radar, provides an improved understanding of the topography of the Aurora Subglacial Basin and its surroundings, and reveals a complex surface sculpted by a succession of ice-sheet configurations substantially different from today's. At different stages during its fluctuations, the edge of the East Antarctic Ice Sheet lay pinned along the margins of the Aurora Subglacial Basin, the upland boundaries of which are currently above sea level and the deepest parts of which are more than 1?km below sea level. Although the timing of the channel incision remains uncertain, our results suggest that the fjord landscape was carved by at least two iceflow regimes of different scales and directions, each of which would have over-deepened existing topographic depressions, reversing valley floor slopes.