Fine-scale structural variation of the human genome

Inversions, deletions and insertions are important mediators of disease and disease susceptibility. We systematically compared the human genome reference sequence with a second genome (represented by fosmid paired-end sequences) to detect intermediate-sized structural variants >8 kb in length. We identified 297 sites of structural variation: 139 insertions, 102 deletions and 56 inversion breakpoints. Using combined literature, sequence and experimental analyses, we validated 112 of the structural variants, including several that are of biomedical relevance. These data provide a fine-scale structural variation map of the human genome and the requisite sequence precision for subsequent genetic studies of human disease.     

Antarctic seal serum proteins, glycoproteins and lipoproteins

Résumé On a étudié les variations qualitatives et quantitatives des protéines sériques, lipoprotéines et glycoprotéines des phoques antarctiques, et on a trouvé que seulement les lipoprotéines et les lipides totales sont augmentées par rapport à celles des autres mammifères.     

Association of the ADAM33 gene with asthma and bronchial hyperresponsiveness

Asthma is a common respiratory disorder characterized by recurrent episodes of coughing, wheezing and breathlessness. Although environmental factors such as allergen exposure are risk factors in the development of asthma, both twin and family studies point to a strong genetic component. To date, linkage studies have identified more than a dozen genomic regions linked to asthma. In this study, we performed a genome-wide scan on 460 Caucasian families and identified a locus on chromosome 20p13 that was linked to asthma (log(10) of the likelihood ratio (LOD), 2.94) and bronchial hyperresponsiveness (LOD, 3.93). A survey of 135 polymorphisms in 23 genes identified the ADAM33 gene as being significantly associated with asthma using case-control, transmission disequilibrium and haplotype analyses (P = 0.04 0.000003). ADAM proteins are membrane-anchored metalloproteases with diverse functions, which include the shedding of cell-surface proteins such as cytokines and cytokine receptors. The identification and characterization of ADAM33, a putative asthma susceptibility gene identified by positional cloning in an outbred population, should provide insights into the pathogenesis and natural history of this common disease.     

Small molecule inhibitors reveal Niemann-Pick C1 is essential for Ebola virus infection

Ebola virus (EboV) is a highly pathogenic enveloped virus that causes outbreaks of zoonotic infection in Africa. The clinical symptoms are manifestations of the massive production of pro-inflammatory cytokines in response to infection and in many outbreaks, mortality exceeds 75%. The unpredictable onset, ease of transmission, rapid progression of disease, high mortality and lack of effective vaccine or therapy have created a high level of public concern about EboV. Here we report the identification of a novel benzylpiperazine adamantane diamide-derived compound that inhibits EboV infection. Using mutant cell lines and informative derivatives of the lead compound, we show that the target of the inhibitor is the endosomal membrane protein Niemann-Pick C1 (NPC1). We find that NPC1 is essential for infection, that it binds to the virus glycoprotein (GP), and that antiviral compounds interfere with GP binding to NPC1. Combined with the results of previous studies of GP structure and function, our findings support a model of EboV infection in which cleavage of the GP1 subunit by endosomal cathepsin proteases removes heavily glycosylated domains to expose the amino-terminal domain, which is a ligand for NPC1 and regulates membrane fusion by the GP2 subunit. Thus, NPC1 is essential for EboV entry and a target for antiviral therapy.     

On the role of the Agulhas system in ocean circulation and climate

The Atlantic Ocean receives warm, saline water from the Indo-Pacific Ocean through Agulhas leakage around the southern tip of Africa. Recent findings suggest that Agulhas leakage is a crucial component of the climate system and that ongoing increases in leakage under anthropogenic warming could strengthen the Atlantic overturning circulation at a time when warming and accelerated meltwater input in the North Atlantic is predicted to weaken it. Yet in comparison with processes in the North Atlantic, the overall Agulhas system is largely overlooked as a potential climate trigger or feedback mechanism. Detailed modelling experiments--backed by palaeoceanographic and sustained modern observations--are required to establish firmly the role of the Agulhas system in a warming climate.     

RIP3 mediates the embryonic lethality of caspase-8-deficient mice

Apoptosis and necroptosis are complementary pathways controlled by common signalling adaptors, kinases and proteases; among these, caspase-8 (Casp8) is critical for death receptor-induced apoptosis. This caspase has also been implicated in non-apoptotic pathways that regulate Fas-associated via death domain (FADD)-dependent signalling and other less defined biological processes as diverse as innate immune signalling and myeloid or lymphoid differentiation patterns. Casp8 suppresses RIP3-RIP1 (also known as RIPK3-RIPK1) kinase complex-dependent necroptosis that follows death receptor activation as well as a RIP3-dependent, RIP1-independent necrotic pathway that has emerged as a host defence mechanism against murine cytomegalovirus. Disruption of Casp8 expression leads to embryonic lethality in mice between embryonic days 10.5 and 11.5 (ref. 7). Thus, Casp8 may naturally hold alternative RIP3-dependent death pathways in check in addition to promoting apoptosis. We find that RIP3 is responsible for the mid-gestational death of Casp8-deficient embryos. Remarkably, Casp8(-/-)Rip3(-/-) double mutant mice are viable and mature into fertile adults with a full immune complement of myeloid and lymphoid cell types. These mice seem immunocompetent but develop lymphadenopathy by four months of age marked by accumulation of abnormal T cells in the periphery, a phenotype reminiscent of mice with Fas-deficiency (lpr/lpr; also known as Fas). Thus, Casp8 contributes to homeostatic control in the adult immune system; however, RIP3 and Casp8 are together completely dispensable for mammalian development.     

Interannual variability in the oxygen isotopes of atmospheric CO2 driven by El Niño

The stable isotope ratios of atmospheric CO(2) ((18)O/(16)O and (13)C/(12)C) have been monitored since 1977 to improve our understanding of the global carbon cycle, because biosphere-atmosphere exchange fluxes affect the different atomic masses in a measurable way. Interpreting the (18)O/(16)O variability has proved difficult, however, because oxygen isotopes in CO(2) are influenced by both the carbon cycle and the water cycle. Previous attention focused on the decreasing (18)O/(16)O ratio in the 1990s, observed by the global Cooperative Air Sampling Network of the US National Oceanic and Atmospheric Administration Earth System Research Laboratory. This decrease was attributed variously to a number of processes including an increase in Northern Hemisphere soil respiration; a global increase in C(4) crops at the expense of C(3) forests; and environmental conditions, such as atmospheric turbulence and solar radiation, that affect CO(2) exchange between leaves and the atmosphere. Here we present 30 years' worth of data on (18)O/(16)O in CO(2) from the Scripps Institution of Oceanography global flask network and show that the interannual variability is strongly related to the El Ni?o/Southern Oscillation. We suggest that the redistribution of moisture and rainfall in the tropics during an El Ni?o increases the (18)O/(16)O ratio of precipitation and plant water, and that this signal is then passed on to atmospheric CO(2) by biosphere-atmosphere gas exchange. We show how the decay time of the El Ni?o anomaly in this data set can be useful in constraining global gross primary production. Our analysis shows a rapid recovery from El Ni?o events, implying a shorter cycling time of CO(2) with respect to the terrestrial biosphere and oceans than previously estimated. Our analysis suggests that current estimates of global gross primary production, of 120 petagrams of carbon per year, may be too low, and that a best guess of 150-175 petagrams of carbon per year better reflects the observed rapid cycling of CO(2). Although still tentative, such a revision would present a new benchmark by which to evaluate global biospheric carbon cycling models.