Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia

Sickle cell anemia (SCA) is a paradigmatic single gene disorder caused by homozygosity with respect to a unique mutation at the beta-globin locus. SCA is phenotypically complex, with different clinical courses ranging from early childhood mortality to a virtually unrecognized condition. Overt stroke is a severe complication affecting 6-8% of individuals with SCA. Modifier genes might interact to determine the susceptibility to stroke, but such genes have not yet been identified. Using Bayesian networks, we analyzed 108 SNPs in 39 candidate genes in 1,398 individuals with SCA. We found that 31 SNPs in 12 genes interact with fetal hemoglobin to modulate the risk of stroke. This network of interactions includes three genes in the TGF-beta pathway and SELP, which is associated with stroke in the general population. We validated this model in a different population by predicting the occurrence of stroke in 114 individuals with 98.2% accuracy.     

Population structure, differential bias and genomic control in a large-scale, case-control association study

The main problems in drawing causal inferences from epidemiological case-control studies are confounding by unmeasured extraneous factors, selection bias and differential misclassification of exposure. In genetics the first of these, in the form of population structure, has dominated recent debate. Population structure explained part of the significant +11.2% inflation of test statistics we observed in an analysis of 6,322 nonsynonymous SNPs in 816 cases of type 1 diabetes and 877 population-based controls from Great Britain. The remainder of the inflation resulted from differential bias in genotype scoring between case and control DNA samples, which originated from two laboratories, causing false-positive associations. To avoid excluding SNPs and losing valuable information, we extended the genomic control method by applying a variable downweighting to each SNP.     

Detection and imaging of atmospheric radio flashes from cosmic ray air showers

The nature of ultrahigh-energy cosmic rays (UHECRs) at energies >10(20) eV remains a mystery. They are likely to be of extragalactic origin, but should be absorbed within approximately 50 Mpc through interactions with the cosmic microwave background. As there are no sufficiently powerful accelerators within this distance from the Galaxy, explanations for UHECRs range from unusual astrophysical sources to exotic string physics. Also unclear is whether UHECRs consist of protons, heavy nuclei, neutrinos or gamma-rays. To resolve these questions, larger detectors with higher duty cycles and which combine multiple detection techniques are needed. Radio emission from UHECRs, on the other hand, is unaffected by attenuation, has a high duty cycle, gives calorimetric measurements and provides high directional accuracy. Here we report the detection of radio flashes from cosmic-ray air showers using low-cost digital radio receivers. We show that the radiation can be understood in terms of the geosynchrotron effect. Our results show that it should be possible to determine the nature and composition of UHECRs with combined radio and particle detectors, and to detect the ultrahigh-energy neutrinos expected from flavour mixing.     

Prion protein remodelling confers an immediate phenotypic switch

In a variety of systems, proteins have been linked to processes historically limited to nucleic acids, such as infectivity and inheritance. These atypical proteins, termed prions, lack sequence homology but are collectively defined by their capacity to adopt multiple physical and therefore functional states in vivo. Newly synthesized prion protein generally adopts the form already present in the cell, and this in vivo folding bias directs the near faithful transmission of the corresponding phenotypic state. Switches between the prion and non-prion phenotypes can occur in vivo; however, the fate of existing protein during these transitions and its effects on the emergence of new traits remain major unanswered questions. Here, we determine the changes in protein-state that induce phenotypic switching for the yeast prion Sup35/[PSI(+)]. We show that the prion form does not need to be specified by an alternate misfolding pathway initiated during Sup35 synthesis but instead can be accessed by mature protein. This remodelling of protein from one stable form to another is accompanied by the loss of Sup35 activity, evoking a rapid change in cellular phenotype within a single cell cycle.     

Orbital forcing of Cretaceous river discharge in tropical Africa and ocean response

The tropics have been suggested as the drivers of global ocean and atmosphere circulation and biogeochemical cycling during the extreme warmth of the Cretaceous period; but the links between orbital forcing, freshwater runoff and the biogeochemistry of continental margins in extreme greenhouse conditions are not fully understood. Here we present Cretaceous records of geochemical tracers for freshwater runoff obtained from a sediment core off the Ivory Coast that indicate that alternating periods of arid and humid African climate were driven by orbital precession. Our simulations of the precession-driven patterns of river discharge with a global climate model suggest that ocean anoxia and black shale sedimentation were directly caused by high river discharge, and occurred specifically when the northern equinox coincided with perihelion (the minimum distance between the Sun and the Earth). We conclude that, in a warm climate, the oceans off tropical continental margins respond rapidly and sensitively to even modest changes in river discharge.     

Genetic effects on sperm design in the zebra finch

Sperm design and function are important determinants of male reproductive success and are expected to be under strong selection. The way that spermatozoa phenotypes evolve is poorly understood, because there have been few studies of the quantitative genetics of sperm. Here we show, in the zebra finch Taeniopygia guttata, an extraordinary degree of inter-male variation in sperm design that is independent of sperm swimming velocity. A quantitative genetics study using data from over 900 zebra finches in a complex breeding experiment showed that sperm head, mid-piece and flagellum length are heritable, that negative genetic correlations exist between sperm traits, and that significant indirect (maternal) genetic effects exist. Selection on the zebra finch sperm phenotype may be low because sperm competition is infrequent in this species, and this, in combination with negative genetic correlations and maternal genetic effects, may account for the variation in sperm phenotype between males. These results have important implications for the evolution of sperm in other taxa.     

Discovery of a flank caldera and very young glacial activity at Hecates Tholus, Mars

The majority of volcanic products on Mars are thought to be mafic and effusive. Explosive eruptions of basic to ultrabasic chemistry are expected to be common, but evidence for them is rare and mostly confined to very old surface features. Here we present new image and topographic data from the High Resolution Stereo Camera that reveal previously unknown traces of an explosive eruption at 30 degrees N and 149 degrees E on the northwestern flank of the shield volcano Hecates Tholus. The eruption created a large, 10-km-diameter caldera approximately 350 million years ago. We interpret these observations to mean that large-scale explosive volcanism on Mars was not confined to the planet's early evolution. We also show that glacial deposits partly fill the caldera and an adjacent depression. Their age, derived from crater counts, is about 5 to 24 million years. Climate models predict that near-surface ice is not stable at mid-latitudes today, assuming a thermo-dynamic steady state. Therefore, the discovery of very young glacial features at Hecates Tholus suggests recent climate changes. We show that the absolute ages of these very recent glacial deposits correspond very well to a period of increased obliquity of the planet's rotational axis.