Estimating coverage and power for genetic association studies using near-complete variation data

Although studies suggest that SNPs derived from HapMap provide promising coverage and power for association studies, the lack of alternative variation datasets limits independent analysis. Using near-complete variation data for 76 genes resequenced in HapMap samples, we find that coverage of common variation by commercial genotyping arrays is substantially lower compared to the HapMap-based estimates. We quantify the power offered by these arrays for a range of disease models.     

Mutations in the cyclin family member FAM58A cause an X-linked dominant disorder characterized by syndactyly, telecanthus and anogenital and renal malformations

We identified four girls with a consistent constellation of facial dysmorphism and malformations previously reported in a single mother-daughter pair. Toe syndactyly, telecanthus and anogenital and renal malformations were present in all affected individuals; thus, we propose the name 'STAR syndrome' for this disorder. Using array CGH, qPCR and sequence analysis, we found causative mutations in FAM58A on Xq28 in all affected individuals, suggesting an X-linked dominant inheritance pattern for this recognizable syndrome.     

Ultra-broadband semiconductor laser

The fundamental mechanism behind laser action leads in general only to narrowband, single-wavelength emission. Several approaches for achieving spectrally broadband laser action have been put forward, such as enhancing the optical feedback in the wings of the gain spectrum, multi-peaked gain spectra, and the most favoured technique at present, ultrashort pulse excitation. Each of these approaches has drawbacks, such as a complex external laser cavity configuration, a non-flat optical gain envelope function, or an inability to operate in continuous mode, respectively. Here we present a monolithic, mid-infrared 'supercontinuum' semiconductor laser that has none of these drawbacks. We adopt a quantum cascade configuration, where a number of dissimilar intersubband optical transitions are made to cooperate in order to provide broadband optical gain from 5 to 8 microm wavelength. Laser action with a Fabry-Pérot spectrum covering all wavelengths from 6 to 8 microm simultaneously is demonstrated with this approach. Lasers that emit light over such an extremely wide wavelength range are of interest for applications as varied as terabit optical data communications or ultra-precision metrology and spectroscopy.     

Evidence for deep-water production in the North Pacific Ocean during the early Cenozoic warm interval

The deep-ocean circulation is responsible for a significant component of global heat transport. In the present mode of circulation, deep waters form in the North Atlantic and Southern oceans where surface water becomes sufficiently cold and dense to sink. Polar temperatures during the warmest climatic interval of the Cenozoic era (approximately 65 to 40 million years (Myr) ago) were significantly warmer than today, and this may have been a consequence of enhanced oceanic heat transport. However, understanding the relationship between deep-ocean circulation and ancient climate is complicated by differences in oceanic gateways, which affect where deep waters form and how they circulate. Here I report records of neodymium isotopes from two cores in the Pacific Ocean that indicate a shift in deep-water production from the Southern Ocean to the North Pacific approximately 65 Myr ago. The source of deep waters reverted back to the Southern Ocean 40 Myr ago. The relative timing of changes in the neodymium and oxygen isotope records indicates that changes in Cenozoic deep-water circulation patterns were the consequence, not the cause, of extreme Cenozoic warmth.     

Predator diversity dampens trophic cascades

Food web complexity is thought to weaken the strength of terrestrial trophic cascades in which strong impacts of natural enemies on herbivores cascade to influence primary production indirectly. Predator diversity can enhance food web complexity because predators may feed on each other and on shared prey. In such cases, theory suggests that the impact of predation on herbivores relaxes and cascading effects on basal resources are dampened. Despite this view, no empirical studies have explicitly investigated the role of predator diversity in mediating primary productivity in a natural terrestrial system. Here we compare, in a coastal marsh community, impacts of arthropod predators on herbivores and plant productivity between a simple food web with a single predator species and a complex food web with a diverse predator assemblage. We show that enhancing predator diversity dampens enemy effects on herbivores and weakens trophic cascades. Consequently, changes in diversity at higher trophic levels can significantly alter ecosystem function in natural systems.     

Mapping complex disease loci in whole-genome association studies

Identification of the genetic polymorphisms that contribute to susceptibility for common diseases such as type 2 diabetes and schizophrenia will aid in the development of diagnostics and therapeutics. Previous studies have focused on the technique of genetic linkage, but new technologies and experimental resources make whole-genome association studies more feasible. Association studies of this type have good prospects for dissecting the genetics of common disease, but they currently face a number of challenges, including problems with multiple testing and study design, definition of intermediate phenotypes and interaction between polymorphisms.     

Evidence for substantial fine-scale variation in recombination rates across the human genome

Characterizing fine-scale variation in human recombination rates is important, both to deepen understanding of the recombination process and to aid the design of disease association studies. Current genetic maps show that rates vary on a megabase scale, but studying finer-scale variation using pedigrees is difficult. Sperm-typing experiments have characterized regions where crossovers cluster into 1-2-kb hot spots, but technical difficulties limit the number of studies. An alternative is to use population variation to infer fine-scale characteristics of the recombination process. Several surveys reported 'block-like' patterns of diversity, which may reflect fine-scale recombination rate variation, but limitations of available methods made this impossible to assess. Here, we applied a new statistical method, which overcomes these limitations, to infer patterns of fine-scale recombination rate variation in 74 genes. We found extensive rate variation both within and among genes. In particular, recombination hot spots are a common feature of the human genome: 47% (35 of 74) of genes showed substantive evidence for a hot spot, and many more showed evidence for some rate variation. No primary sequence characteristics are consistently associated with precise hot-spot location, although G+C content and nucleotide diversity are correlated with local recombination rate.     

Creation of ultracold molecules from a Fermi gas of atoms

Following the realization of Bose-Einstein condensates in atomic gases, an experimental challenge is the production of molecular gases in the quantum regime. A promising approach is to create the molecular gas directly from an ultracold atomic gas; for example, bosonic atoms in a Bose-Einstein condensate have been coupled to electronic ground-state molecules through photoassociation or a magnetic field Feshbach resonance. The availability of atomic Fermi gases offers the prospect of coupling fermionic atoms to bosonic molecules, thus altering the quantum statistics of the system. Such a coupling would be closely related to the pairing mechanism in a fermionic superfluid, predicted to occur near a Feshbach resonance. Here we report the creation and quantitative characterization of ultracold 40K2 molecules. Starting with a quantum degenerate Fermi gas of atoms at a temperature of less than 150 nK, we scan the system over a Feshbach resonance to create adiabatically more than 250,000 trapped molecules; these can be converted back to atoms by reversing the scan. The small binding energy of the molecules is controlled by detuning the magnetic field away from the Feshbach resonance, and can be varied over a wide range. We directly detect these weakly bound molecules through their radio-frequency photodissociation spectra; these probe the molecular wavefunction, and yield binding energies that are consistent with theory.     

Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease

Genes and mechanisms involved in common complex diseases, such as the autoimmune disorders that affect approximately 5% of the population, remain obscure. Here we identify polymorphisms of the cytotoxic T lymphocyte antigen 4 gene (CTLA4)--which encodes a vital negative regulatory molecule of the immune system--as candidates for primary determinants of risk of the common autoimmune disorders Graves' disease, autoimmune hypothyroidism and type 1 diabetes. In humans, disease susceptibility was mapped to a non-coding 6.1 kb 3' region of CTLA4, the common allelic variation of which was correlated with lower messenger RNA levels of the soluble alternative splice form of CTLA4. In the mouse model of type 1 diabetes, susceptibility was also associated with variation in CTLA-4 gene splicing with reduced production of a splice form encoding a molecule lacking the CD80/CD86 ligand-binding domain. Genetic mapping of variants conferring a small disease risk can identify pathways in complex disorders, as exemplified by our discovery of inherited, quantitative alterations of CTLA4 contributing to autoimmune tissue destruction.