Detecting recent positive selection in the human genome from haplotype structure

The ability to detect recent natural selection in the human population would have profound implications for the study of human history and for medicine. Here, we introduce a framework for detecting the genetic imprint of recent positive selection by analysing long-range haplotypes in human populations. We first identify haplotypes at a locus of interest (core haplotypes). We then assess the age of each core haplotype by the decay of its association to alleles at various distances from the locus, as measured by extended haplotype homozygosity (EHH). Core haplotypes that have unusually high EHH and a high population frequency indicate the presence of a mutation that rose to prominence in the human gene pool faster than expected under neutral evolution. We applied this approach to investigate selection at two genes carrying common variants implicated in resistance to malaria: G6PD and CD40 ligand. At both loci, the core haplotypes carrying the proposed protective mutation stand out and show significant evidence of selection. More generally, the method could be used to scan the entire genome for evidence of recent positive selection.     

Warm tropical ocean surface and global anoxia during the mid-Cretaceous period

The middle of the Cretaceous period (about 120 to 80 Myr ago) was a time of unusually warm polar temperatures, repeated reef-drowning in the tropics and a series of oceanic anoxic events (OAEs) that promoted both the widespread deposition of organic-carbon-rich marine sediments and high biological turnover. The cause of the warm temperatures is unproven but widely attributed to high levels of atmospheric greenhouse gases such as carbon dioxide. In contrast, there is no consensus on the climatic causes and effects of the OAEs, with both high biological productivity and ocean 'stagnation' being invoked as the cause of ocean anoxia. Here we show, using stable isotope records from multiple species of well-preserved foraminifera, that the thermal structure of surface waters in the western tropical Atlantic Ocean underwent pronounced variability about 100 Myr ago, with maximum sea surface temperatures 3-5 degrees C warmer than today. This variability culminated in a collapse of upper-ocean stratification during OAE-1d (the 'Breistroffer' event), a globally significant period of organic-carbon burial that we show to have fundamental, stratigraphically valuable, geochemical similarities to the main OAEs of the Mesozoic era. Our records are consistent with greenhouse forcing being responsible for the warm temperatures, but are inconsistent both with explanations for OAEs based on ocean stagnation, and with the traditional view (reviewed in ref. 12) that past warm periods were more stable than today's climate.     

Nucleosynthetic signatures of the first stars

The chemically most primitive stars provide constraints on the nature of the first stellar objects that formed in the Universe; elements other than hydrogen, helium and traces of lithium present within these objects were generated by nucleosynthesis in the very first stars. The relative abundances of elements in the surviving primitive stars reflect the masses of the first stars, because the pathways of nucleosynthesis are quite sensitive to stellar masses. Several models have been suggested to explain the origin of the abundance pattern of the giant star HE0107-5240, which hitherto exhibited the highest deficiency of heavy elements known. Here we report the discovery of HE1327-2326, a subgiant or main-sequence star with an iron abundance about a factor of two lower than that of HE0107-5240. Both stars show extreme overabundances of carbon and nitrogen with respect to iron, suggesting a similar origin of the abundance patterns. The unexpectedly low Li and high Sr abundances of HE1327-2326, however, challenge existing theoretical understanding: no model predicts the high Sr abundance or provides a Li depletion mechanism consistent with data available for the most metal-poor stars.     

Doping semiconductor nanocrystals

Doping--the intentional introduction of impurities into a material--is fundamental to controlling the properties of bulk semiconductors. This has stimulated similar efforts to dope semiconductor nanocrystals. Despite some successes, many of these efforts have failed, for reasons that remain unclear. For example, Mn can be incorporated into nanocrystals of CdS and ZnSe (refs 7-9), but not into CdSe (ref. 12)--despite comparable bulk solubilities of near 50 per cent. These difficulties, which have hindered development of new nanocrystalline materials, are often attributed to 'self-purification', an allegedly intrinsic mechanism whereby impurities are expelled. Here we show instead that the underlying mechanism that controls doping is the initial adsorption of impurities on the nanocrystal surface during growth. We find that adsorption--and therefore doping efficiency--is determined by three main factors: surface morphology, nanocrystal shape, and surfactants in the growth solution. Calculated Mn adsorption energies and equilibrium shapes for several nanocrystals lead to specific doping predictions. These are confirmed by measuring how the Mn concentration in ZnSe varies with nanocrystal size and shape. Finally, we use our predictions to incorporate Mn into previously undopable CdSe nanocrystals. This success establishes that earlier difficulties with doping are not intrinsic, and suggests that a variety of doped nanocrystals--for applications from solar cells to spintronics--can be anticipated.     

FOXA1 is a key determinant of estrogen receptor function and endocrine response

Estrogen receptor-α (ER) is the key feature of most breast cancers and binding of ER to the genome correlates with expression of the Forkhead protein FOXA1 (also called HNF3α). Here we show that FOXA1 is a key determinant that can influence differential interactions between ER and chromatin. Almost all ER-chromatin interactions and gene expression changes depended on the presence of FOXA1 and FOXA1 influenced genome-wide chromatin accessibility. Furthermore, we found that CTCF was an upstream negative regulator of FOXA1-chromatin interactions. In estrogen-responsive breast cancer cells, the dependency on FOXA1 for tamoxifen-ER activity was absolute; in tamoxifen-resistant cells, ER binding was independent of ligand but depended on FOXA1. Expression of FOXA1 in non-breast cancer cells can alter ER binding and function. As such, FOXA1 is a major determinant of estrogen-ER activity and endocrine response in breast cancer cells.     

Mutations in voltage-gated potassium channel KCNC3 cause degenerative and developmental central nervous system phenotypes

Potassium channel mutations have been described in episodic neurological diseases. We report that K+ channel mutations cause disease phenotypes with neurodevelopmental and neurodegenerative features. In a Filipino adult-onset ataxia pedigree, the causative gene maps to 19q13, overlapping the SCA13 disease locus described in a French pedigree with childhood-onset ataxia and cognitive delay. This region contains KCNC3 (also known as Kv3.3), encoding a voltage-gated Shaw channel with enriched cerebellar expression. Sequencing revealed two missense mutations, both of which alter KCNC3 function in Xenopus laevis expression systems. KCNC3(R420H), located in the voltage-sensing domain, had no channel activity when expressed alone and had a dominant-negative effect when co-expressed with the wild-type channel. KCNC3(F448L) shifted the activation curve in the negative direction and slowed channel closing. Thus, KCNC3(R420H) and KCNC3(F448L) are expected to change the output characteristics of fast-spiking cerebellar neurons, in which KCNC channels confer capacity for high-frequency firing. Our results establish a role for KCNC3 in phenotypes ranging from developmental disorders to adult-onset neurodegeneration and suggest voltage-gated K+ channels as candidates for additional neurodegenerative diseases.     

A Mal functional variant is associated with protection against invasive pneumococcal disease, bacteremia, malaria and tuberculosis

Toll-like receptors (TLRs) and members of their signaling pathway are important in the initiation of the innate immune response to a wide variety of pathogens. The adaptor protein Mal (also known as TIRAP), encoded by TIRAP (MIM 606252), mediates downstream signaling of TLR2 and TLR4 (refs. 4-6). We report a case-control study of 6,106 individuals from the UK, Vietnam and several African countries with invasive pneumococcal disease, bacteremia, malaria and tuberculosis. We genotyped 33 SNPs, including rs8177374, which encodes a leucine substitution at Ser180 of Mal. We found that heterozygous carriage of this variant associated independently with all four infectious diseases in the different study populations. Combining the study groups, we found substantial support for a protective effect of S180L heterozygosity against these infectious diseases (N = 6,106; overall P = 9.6 x 10(-8)). We found that the Mal S180L variant attenuated TLR2 signal transduction.     

A close halo of large transparent grains around extreme red giant stars

An intermediate-mass star ends its life by ejecting the bulk of its envelope in a slow, dense wind. Stellar pulsations are thought to elevate gas to an altitude cool enough for the condensation of dust, which is then accelerated by radiation pressure, entraining the gas and driving the wind. Explaining the amount of mass loss, however, has been a problem because of the difficulty of observing tenuous gas and dust only tens of milliarcseconds from the star. For this reason, there is no consensus on the way sufficient momentum is transferred from the light from the star to the outflow. Here we report spatially resolved, multiwavelength observations of circumstellar dust shells of three stars on the asymptotic giant branch of the Hertzsprung-Russell diagram. When imaged in scattered light, dust shells were found at remarkably small radii (less than about two stellar radii) and with unexpectedly large grains (about 300 nanometres in radius). This proximity to the photosphere argues for dust species that are transparent to the light from the star and, therefore, resistant to sublimation by the intense radiation field. Although transparency usually implies insufficient radiative pressure to drive a wind, the radiation field can accelerate these large grains through photon scattering rather than absorption--a plausible mass loss mechanism for lower-amplitude pulsating stars.