The Drosophila melanogaster Genetic Reference Panel

A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics.     

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.     

Discovery of a short-necked sauropod dinosaur from the Late Jurassic period of Patagonia

Sauropod dinosaurs are one of the most conspicuous groups of Mesozoic terrestrial vertebrates. They show general trends towards an overall increase in size and elongation of the neck, by means of considerable elongation of the length of individual vertebrae and a cervical vertebra count that, in some cases, increases to 19 (ref. 1). The long neck is a particular hallmark of sauropod dinosaurs and is usually regarded as a key feeding adaptation. Here we describe a new dicraeosaurid sauropod, from the latest Jurassic period of Patagonia, that has a particularly short neck. With a neck that is about 40% shorter than in other known dicraeosaurs, this taxon demonstrates a trend opposite to that seen in most sauropods and indicates that the ecology of dicraeosaurids might have differed considerably from that of other sauropods. The new taxon indicates that there was a rapid radiation and dispersal of dicraeosaurids in the Late Jurassic of the Southern Hemisphere, after the separation of Gondwana from the northern continents by the late Middle Jurassic.     

Life cycles and host–parasitoid relationships of five species of Leucospis wasps in Argentina (Hymenoptera: Leucospidae)

The genus Leucospis Fabricius is comprised of parasitoid wasps relatively uncommon in nature. Their immature stages develop on aculeate Hymenoptera, in particular solitary bees, but hosts are known for only around 25 Leucospis species (about 20% of 115–120 world species), so the true relationship of this family with bees is largely unknown. Here we report on individuals of five species of Leucospis wasps which emerged from nests of different bee and wasp species during distinct sampling periods during a trap-nesting programme, in two contrasting areas: agro-ecosystems and natural habitats in the Pampean region. Some of these nests were parasitised by L. cayennensis Westwood, L. coxalis Kirby, L. egaia Walker, L. pulchriceps Cameron and L. signifera Bou?ek. Our results expand the available information of host species for L. cayennensis, L. coxalis, L. egaia and L. pulchriceps and represent the first record of hosts associated with L. signifera. The hosts were only bee species of the genera Centris, Tetrapedia (family Apidae) and Megachile (Megachilidae). These species were more abundant in the natural reserve than in agro-ecosystems, suggesting that anthropogenic activities could negatively affect their populations. Most nests were attacked in one (43.7%) or two (40.7%) cells, but the remaining nests (16.5%) had more (up to seven cells). However, the position of the attacked cells was variable, suggesting that females of Leucospis species oviposit in recently built cells, and that the hatching of larvae is delayed, or that the first larval stage waits until the host larva reaches a sufficient size to attack.     

Shrinkage‐Based Tests of Predictability

In this paper we derive a test of predictability by exploring the possibility that forecasts from a given model, adjusted by a shrinkage factor, will display lower mean squared prediction errors than forecasts from a simple random walk. This generalizes most previous tests which compare forecast errors of a benchmark model with errors of a proposed alternative model, not allowing for shrinkage. We show that our test is a particular extension of a recently developed test of the martingale difference hypothesis. Using simulations we explore the behavior of our test in small and moderate samples. Numerical results indicate that the test has good size and power properties. Finally, we illustrate the use of our test in an empirical application within the exchange rate literature. Copyright © 2012 John Wiley & Sons, Ltd.     

IGF and FGF cooperatively establish the regulatory stem cell niche of pluripotent human cells in vitro

Distinctive properties of stem cells are not autonomously achieved, and recent evidence points to a level of external control from the microenvironment. Here, we demonstrate that self-renewal and pluripotent properties of human embryonic stem (ES) cells depend on a dynamic interplay between human ES cells and autologously derived human ES cell fibroblast-like cells (hdFs). Human ES cells and hdFs are uniquely defined by insulin-like growth factor (IGF)- and fibroblast growth factor (FGF)-dependence. IGF 1 receptor (IGF1R) expression was exclusive to the human ES cells, whereas FGF receptor 1 (FGFR1) expression was restricted to surrounding hdFs. Blocking the IGF-II/IGF1R pathway reduced survival and clonogenicity of human ES cells, whereas inhibition of the FGF pathway indirectly caused differentiation. IGF-II is expressed by hdFs in response to FGF, and alone was sufficient in maintaining human ES cell cultures. Our study demonstrates a direct role of the IGF-II/IGF1R axis on human ES cell physiology and establishes that hdFs produced by human ES cells themselves define the stem cell niche of pluripotent human stem cells.     

Epitaxial self-assembly of block copolymers on lithographically defined nanopatterned substrates

Parallel processes for patterning densely packed nanometre-scale structures are critical for many diverse areas of nanotechnology. Thin films of diblock copolymers can self-assemble into ordered periodic structures at the molecular scale (approximately 5 to 50 nm), and have been used as templates to fabricate quantum dots, nanowires, magnetic storage media, nanopores and silicon capacitors. Unfortunately, perfect periodic domain ordering can only be achieved over micrometre-scale areas at best and defects exist at the edges of grain boundaries. These limitations preclude the use of block-copolymer lithography for many advanced applications. Graphoepitaxy, in-plane electric fields, temperature gradients, and directional solidification have also been demonstrated to induce orientation or long-range order with varying degrees of success. Here we demonstrate the integration of thin films of block copolymer with advanced lithographic techniques to induce epitaxial self-assembly of domains. The resulting patterns are defect-free, are oriented and registered with the underlying substrate and can be created over arbitrarily large areas. These structures are determined by the size and quality of the lithographically defined surface pattern rather than by the inherent limitations of the self-assembly process. Our results illustrate how hybrid strategies to nanofabrication allow for molecular level control in existing manufacturing processes.     

Interpretation of tomography and spectroscopy as dual forms of quantum computation

It is important to be able to determine the state of a quantum system and to measure properties of its evolution. State determination can be achieved using tomography, in which the system is subjected to a series of experiments, whereas spectroscopy can be used to probe the energy spectrum associated with the system's evolution. Here we show that, for a quantum system whose state or evolution can be modelled on a quantum computer, tomography and spectroscopy can be interpreted as dual forms of quantum computation. Specifically, we find that the phase estimation algorithm (which underlies a quantum computer's ability to perform efficient simulations and to factorize large numbers) can be adapted for tomography or spectroscopy. This is analogous to the situation encountered in scattering experiments, in which it is possible to obtain information about both the state of the scatterer and its interactions. We provide an experimental demonstration of the tomographic application by performing a measurement of the Wigner function (a phase space distribution) of a quantum system. For this purpose, we use three qubits formed from spin-1/2 nuclei in a quantum computation involving liquid-state nuclear magnetic resonance.