Showing papers by "University of California, Santa Cruz published in 2011"

Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

Abstract: Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high-quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high-quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.

Integrated genomic analyses of ovarian carcinoma

Abstract: A catalogue of molecular aberrations that cause ovarian cancer is critical for developing and deploying therapies that will improve patients' lives. The Cancer Genome Atlas project has analysed messenger RNA expression, microRNA expression, promoter methylation and DNA copy number in 489 high-grade serous ovarian adenocarcinomas and the DNA sequences of exons from coding genes in 316 of these tumours. Here we report that high-grade serous ovarian cancer is characterized by TP53 mutations in almost all tumours (96%); low prevalence but statistically recurrent somatic mutations in nine further genes including NF1, BRCA1, BRCA2, RB1 and CDK12; 113 significant focal DNA copy number aberrations; and promoter methylation events involving 168 genes. Analyses delineated four ovarian cancer transcriptional subtypes, three microRNA subtypes, four promoter methylation subtypes and a transcriptional signature associated with survival duration, and shed new light on the impact that tumours with BRCA1/2 (BRCA1 or BRCA2) and CCNE1 aberrations have on survival. Pathway analyses suggested that homologous recombination is defective in about half of the tumours analysed, and that NOTCH and FOXM1 signalling are involved in serous ovarian cancer pathophysiology.

Trophic Downgrading of Planet Earth

Abstract: Until recently, large apex consumers were ubiquitous across the globe and had been for millions of years. The loss of these animals may be humankind's most pervasive influence on nature. Although such losses are widely viewed as an ethical and aesthetic problem, recent research reveals extensive cascading effects of their disappearance in marine, terrestrial, and freshwater ecosystems worldwide. This empirical work supports long-standing theory about the role of top-down forcing in ecosystems but also highlights the unanticipated impacts of trophic cascades on processes as diverse as the dynamics of disease, wildfire, carbon sequestration, invasive species, and biogeochemical cycles. These findings emphasize the urgent need for interdisciplinary research to forecast the effects of trophic downgrading on process, function, and resilience in global ecosystems.

Hydrogen-Treated TiO2 Nanowire Arrays for Photoelectrochemical Water Splitting

Abstract: We report the first demonstration of hydrogen treatment as a simple and effective strategy to fundamentally improve the performance of TiO2 nanowires for photoelectrochemical (PEC) water splitting. Hydrogen-treated rutile TiO2 (H:TiO2) nanowires were prepared by annealing the pristine TiO2 nanowires in hydrogen atmosphere at various temperatures in a range of 200–550 °C. In comparison to pristine TiO2 nanowires, H:TiO2 samples show substantially enhanced photocurrent in the entire potential window. More importantly, H:TiO2 samples have exceptionally low photocurrent saturation potentials of −0.6 V vs Ag/AgCl (0.4 V vs RHE), indicating very efficient charge separation and transportation. The optimized H:TiO2 nanowire sample yields a photocurrent density of ∼1.97 mA/cm2 at −0.6 V vs Ag/AgCl, in 1 M NaOH solution under the illumination of simulated solar light (100 mW/cm2 from 150 W xenon lamp coupled with an AM 1.5G filter). This photocurrent density corresponds to a solar-to-hydrogen (STH) efficiency of ∼1...

Sdss-iii: massive spectroscopic surveys of the distant universe, the milky way, and extra-solar planetary systems

Abstract: Building on the legacy of the Sloan Digital Sky Survey (SDSS-I and II), SDSS-III is a program of four spectroscopic surveys on three scientific themes: dark energy and cosmological parameters, the history and structure of the Milky Way, and the population of giant planets around other stars. In keeping with SDSS tradition, SDSS-III will provide regular public releases of all its data, beginning with SDSS DR8 (which occurred in Jan 2011). This paper presents an overview of the four SDSS-III surveys. BOSS will measure redshifts of 1.5 million massive galaxies and Lya forest spectra of 150,000 quasars, using the BAO feature of large scale structure to obtain percent-level determinations of the distance scale and Hubble expansion rate at z 100 per resolution element), H-band (1.51-1.70 micron) spectra of 10^5 evolved, late-type stars, measuring separate abundances for ~15 elements per star and creating the first high-precision spectroscopic survey of all Galactic stellar populations (bulge, bar, disks, halo) with a uniform set of stellar tracers and spectral diagnostics. MARVELS will monitor radial velocities of more than 8000 FGK stars with the sensitivity and cadence (10-40 m/s, ~24 visits per star) needed to detect giant planets with periods up to two years, providing an unprecedented data set for understanding the formation and dynamical evolution of giant planet systems. (Abridged)

CANDELS: The Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey

Abstract: The Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey (CANDELS) is designed to document the first third of galactic evolution, from z approx. 8 - 1.5. It will image > 250,000 distant galaxies using three separate cameras on the Hubble Space Tele8cope, from the mid-UV to near-IR, and will find and measure Type Ia supernovae beyond z > 1.5 to test their accuracy as standard candles for cosmology. Five premier multi-wavelength sky regions are selected, each with extensive ancillary data. The use of five widely separated fields mitigates cosmic variance and yields statistically robust and complete samples of galaxies down to a stellar mass of 10(exp 9) solar mass to z approx. 2, reaching the knee of the UV luminosity function of galaxies to z approx. 8. The survey covers approximately 800 square arc minutes and is divided into two parts. The CANDELS/Deep survey (5(sigma) point-source limit H =27.7mag) covers approx. 125 square arcminutes within GOODS-N and GOODS-S. The CANDELS/Wide survey includes GOODS and three additional fields (EGS, COSMOS, and UDS) and covers the full area to a 50(sigma) point-source limit of H ? or approx. = 27.0 mag. Together with the Hubble Ultradeep Fields, the strategy creates a three-tiered "wedding cake" approach that has proven efficient for extragalactic surveys. Data from the survey are non-proprietary and are useful for a wide variety of science investigations. In this paper, we describe the basic motivations for the survey, the CANDELS team science goals and the resulting observational requirements, the field selection and geometry, and the observing design.

Candels: The cosmic assembly near-infrared deep extragalactic legacy survey - The hubble space telescope observations, imaging data products, and mosaics

Abstract: This paper describes the Hubble Space Telescope imaging data products and data reduction procedures for the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS). This survey is designed to document the evolution of galaxies and black holes at z 1.5-8, and to study Type Ia supernovae at z > 1.5. Five premier multi-wavelength sky regions are selected, each with extensive multi-wavelength observations. The primary CANDELS data consist of imaging obtained in the Wide Field Camera 3 infrared channel (WFC3/IR) and the WFC3 ultraviolet/optical channel, along with the Advanced Camera for Surveys (ACS). The CANDELS/Deep survey covers ~125 arcmin2 within GOODS-N and GOODS-S, while the remainder consists of the CANDELS/Wide survey, achieving a total of ~800 arcmin2 across GOODS and three additional fields (Extended Groth Strip, COSMOS, and Ultra-Deep Survey). We summarize the observational aspects of the survey as motivated by the scientific goals and present a detailed description of the data reduction procedures and products from the survey. Our data reduction methods utilize the most up-to-date calibration files and image combination procedures. We have paid special attention to correcting a range of instrumental effects, including charge transfer efficiency degradation for ACS, removal of electronic bias-striping present in ACS data after Servicing Mission 4, and persistence effects and other artifacts in WFC3/IR. For each field, we release mosaics for individual epochs and eventual mosaics containing data from all epochs combined, to facilitate photometric variability studies and the deepest possible photometry. A more detailed overview of the science goals and observational design of the survey are presented in a companion paper.

Why intraspecific trait variation matters in community ecology

Abstract: Natural populations consist of phenotypically diverse individuals that exhibit variation in their demographic parameters and intra- and inter-specific interactions. Recent experimental work indicates that such variation can have significant ecological effects. However, ecological models typically disregard this variation and focus instead on trait means and total population density. Under what situations is this simplification appropriate? Why might intraspecific variation alter ecological dynamics? In this review we synthesize recent theory and identify six general mechanisms by which trait variation changes the outcome of ecological interactions. These mechanisms include several direct effects of trait variation per se and indirect effects arising from the role of genetic variation in trait evolution.

The UCSC Genome Browser database: update 2011

Abstract: The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a ‘mean+whiskers’ windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.

The Eighth Data Release of the Sloan Digital Sky Survey: First Data from SDSS-III

Abstract: The Sloan Digital Sky Survey (SDSS) started a new phase in 2008 August, with new instrumentation and new surveys focused on Galactic structure and chemical evolution, measurements of the baryon oscillation feature in the clustering of galaxies and the quasar Lyα forest, and a radial velocity search for planets around ~8000 stars. This paper describes the first data release of SDSS-III (and the eighth counting from the beginning of the SDSS). The release includes five-band imaging of roughly 5200 deg2 in the southern Galactic cap, bringing the total footprint of the SDSS imaging to 14,555 deg2, or over a third of the Celestial Sphere. All the imaging data have been reprocessed with an improved sky-subtraction algorithm and a final, self-consistent photometric recalibration and flat-field determination. This release also includes all data from the second phase of the Sloan Extension for Galactic Understanding and Exploration (SEGUE-2), consisting of spectroscopy of approximately 118,000 stars at both high and low Galactic latitudes. All the more than half a million stellar spectra obtained with the SDSS spectrograph have been reprocessed through an improved stellar parameter pipeline, which has better determination of metallicity for high-metallicity stars.

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Abstract: The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

The developmental transcriptome of Drosophila melanogaster

Abstract: Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.

High plant diversity is needed to maintain ecosystem services

Abstract: Biodiversity is rapidly declining worldwide, and there is consensus that this can decrease ecosystem functioning and services. It remains unclear, though, whether few or many of the species in an ecosystem are needed to sustain the provisioning of ecosystem services. It has been hypothesized that most species would promote ecosystem services if many times, places, functions and environmental changes were considered; however, no previous study has considered all of these factors together. Here we show that 84% of the 147 grassland plant species studied in 17 biodiversity experiments promoted ecosystem functioning at least once. Different species promoted ecosystem functioning during different years, at different places, for different functions and under different environmental change scenarios. Furthermore, the species needed to provide one function during multiple years were not the same as those needed to provide multiple functions within one year. Our results indicate that even more species will be needed to maintain ecosystem functioning and services than previously suggested by studies that have either (1) considered only the number of species needed to promote one function under one set of environmental conditions, or (2) separately considered the importance of biodiversity for providing ecosystem functioning across multiple years, places, functions or environmental change scenarios. Therefore, although species may appear functionally redundant when one function is considered under one set of environmental conditions, many species are needed to maintain multiple functions at multiple times and places in a changing world.

Characteristics of planetary candidates observed by Kepler. II. Analysis of the first four months of data

Abstract: On 2011 February 1 the Kepler mission released data for 156,453 stars observed from the beginning of the science observations on 2009 May 2 through September 16. There are 1235 planetary candidates with transit-like signatures detected in this period. These are associated with 997 host stars. Distributions of the characteristics of the planetary candidates are separated into five class sizes: 68 candidates of approximately Earth-size (R_p < 1.25 R_⊕), 288 super-Earth-size (1.25 R_⊕ ≤ R_p < 2 R_⊕), 662 Neptune-size (2 R_⊕ ≤ R_p < 6 R_⊕), 165 Jupiter-size (6 R_⊕ ≤ R_p < 15 R_⊕), and 19 up to twice the size of Jupiter (15 R_⊕ ≤ R_p < 22 R_⊕). In the temperature range appropriate for the habitable zone, 54 candidates are found with sizes ranging from Earth-size to larger than that of Jupiter. Six are less than twice the size of the Earth. Over 74% of the planetary candidates are smaller than Neptune. The observed number versus size distribution of planetary candidates increases to a peak at two to three times the Earth-size and then declines inversely proportional to the area of the candidate. Our current best estimates of the intrinsic frequencies of planetary candidates, after correcting for geometric and sensitivity biases, are 5% for Earth-size candidates, 8% for super-Earth-size candidates, 18% for Neptune-size candidates, 2% for Jupiter-size candidates, and 0.1% for very large candidates; a total of 0.34 candidates per star. Multi-candidate, transiting systems are frequent; 17% of the host stars have multi-candidate systems, and 34% of all the candidates are part of multi-candidate systems.

The ecoresponsive genome of Daphnia pulex

Abstract: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.

Tracking apex marine predator movements in a dynamic ocean

Abstract: Pelagic marine predators face unprecedented challenges and uncertain futures. Overexploitation and climate variability impact the abundance and distribution of top predators in ocean ecosystems. Improved understanding of ecological patterns, evolutionary constraints and ecosystem function is critical for preventing extinctions, loss of biodiversity and disruption of ecosystem services. Recent advances in electronic tagging techniques have provided the capacity to observe the movements and long-distance migrations of animals in relation to ocean processes across a range of ecological scales. Tagging of Pacific Predators, a field programme of the Census of Marine Life, deployed 4,306 tags on 23 species in the North Pacific Ocean, resulting in a tracking data set of unprecedented scale and species diversity that covers 265,386 tracking days from 2000 to 2009. Here we report migration pathways, link ocean features to multispecies hotspots and illustrate niche partitioning within and among congener guilds. Our results indicate that the California Current large marine ecosystem and the North Pacific transition zone attract and retain a diverse assemblage of marine vertebrates. Within the California Current large marine ecosystem, several predator guilds seasonally undertake north-south migrations that may be driven by oceanic processes, species-specific thermal tolerances and shifts in prey distributions. We identify critical habitats across multinational boundaries and show that top predators exploit their environment in predictable ways, providing the foundation for spatial management of large marine ecosystems.

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43

Abstract: We used cross-linking and immunoprecipitation coupled with high-throughput sequencing to identify binding sites in 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein that, when mutated, causes amyotrophic lateral sclerosis. Massively parallel sequencing and splicing-sensitive junction arrays revealed that levels of 601 mRNAs were changed (including Fus (Tls), progranulin and other transcripts encoding neurodegenerative disease-associated proteins) and 965 altered splicing events were detected (including in sortilin, the receptor for progranulin) following depletion of TDP-43 from mouse adult brain with antisense oligonucleotides. RNAs whose levels were most depleted by reduction in TDP-43 were derived from genes with very long introns and that encode proteins involved in synaptic activity. Lastly, we found that TDP-43 autoregulates its synthesis, in part by directly binding and enhancing splicing of an intron in the 3' untranslated region of its own transcript, thereby triggering nonsense-mediated RNA degradation.

A high-resolution map of human evolutionary constraint using 29 mammals.

Abstract: The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.

Dark matter halos in the standard cosmological model: results from the bolshoi simulation

Abstract: Lambda Cold Dark Matter (?CDM) is now the standard theory of structure formation in the universe. We present the first results from the new Bolshoi dissipationless cosmological ?CDM simulation that uses cosmological parameters favored by current observations. The Bolshoi simulation was run in a volume 250 h ?1?Mpc on a side using ~8 billion particles with mass and force resolution adequate to follow subhalos down to the completeness limit of V circ = 50?km?s?1 maximum circular velocity. Using merger trees derived from analysis of 180 stored time steps we find the circular velocities of satellites before they fall into their host halos. Using excellent statistics of halos and subhalos (~10 million at every moment and ~50 million over the whole history) we present accurate approximations for statistics such as the halo mass function, the concentrations for distinct halos and subhalos, the abundance of halos as a function of their circular velocity, and the abundance and the spatial distribution of subhalos. We find that at high redshifts the concentration falls to a minimum value of about 4.0 and then rises for higher values of halo mass?a new result. We present approximations for the velocity and mass functions of distinct halos as a function of redshift. We find that while the Sheth-Tormen (ST) approximation for the mass function of halos found by spherical overdensity is quite accurate at low redshifts, the ST formula overpredicts the abundance of halos by nearly an order of magnitude by z = 10. We find that the number of subhalos scales with the circular velocity of the host halo as V 1/2 host, and that subhalos have nearly the same radial distribution as dark matter particles at radii 0.3-2 times the host halo virial radius. The subhalo velocity function N(> V sub) scales as V ?3 circ. Combining the results of Bolshoi and Via Lactea-II simulations, we find that inside the virial radius of halos with the number of satellites is N(> V sub) = (V sub/58 km s?1)?3 for satellite circular velocities in the range 4 km s?1 < V sub < 150 km s?1.

Sn-Doped Hematite Nanostructures for Photoelectrochemical Water Splitting

Abstract: We report on the synthesis and characterization of Sn-doped hematite nanowires and nanocorals as well as their implementation as photoanodes for photoelectrochemical water splitting. The hematite nanowires were prepared on a fluorine-doped tin oxide (FTO) substrate by a hydrothermal method, followed by high temperature sintering in air to incorporate Sn, diffused from the FTO substrate, as a dopant. Sn-doped hematite nanocorals were prepared by the same method, by adding tin(IV) chloride as the Sn precursor. X-ray photoelectron spectroscopy analysis confirms Sn4+ substitution at Fe3+ sites in hematite, and Sn-dopant levels increase with sintering temperature. Sn dopant serves as an electron donor and increases the carrier density of hematite nanostructures. The hematite nanowires sintered at 800 °C yielded a pronounced photocurrent density of 1.24 mA/cm2 at 1.23 V vs RHE, which is the highest value observed for hematite nanowires. In comparison to nanowires, Sn-doped hematite nanocorals exhibit smaller fe...

Architecture and Dynamics of Kepler's Candidate Multiple Transiting Planet Systems

Abstract: About one-third of the ~1200 transiting planet candidates detected in the first four months of Kepler data are members of multiple candidate systems. There are 115 target stars with two candidate transiting planets, 45 with three, 8 with four, and 1 each with five and six. We characterize the dynamical properties of these candidate multi-planet systems. The distribution of observed period ratios shows that the vast majority of candidate pairs are neither in nor near low-order mean-motion resonances. Nonetheless, there are small but statistically significant excesses of candidate pairs both in resonance and spaced slightly too far apart to be in resonance, particularly near the 2:1 resonance. We find that virtually all candidate systems are stable, as tested by numerical integrations that assume a nominal mass-radius relationship. Several considerations strongly suggest that the vast majority of these multi-candidate systems are true planetary systems. Using the observed multiplicity frequencies, we find that a single population of planetary systems that matches the higher multiplicities underpredicts the number of singly transiting systems. We provide constraints on the true multiplicity and mutual inclination distribution of the multi-candidate systems, revealing a population of systems with multiple super-Earth-size and Neptune-size planets with low to moderate mutual inclinations.

High-Frequency Dynamics of Ocean pH: A Multi- Ecosystem Comparison

Abstract: The effect of Ocean Acidification (OA) on marine biota is quasi-predictable at best. While perturbation studies, in the form of incubations under elevated pCO2, reveal sensitivities and responses of individual species, one missing link in the OA story results from a chronic lack of pH data specific to a given species’ natural habitat. Here, we present a compilation of continuous, high-resolution time series of upper ocean pH, collected using autonomous sensors, over a variety of ecosystems ranging from polar to tropical, open-ocean to coastal, kelp forest to coral reef. These observations reveal a continuum of month-long pH variability with standard deviations from 0.004 to 0.277 and ranges spanning 0.024 to 1.430 pH units. The nature of the observed variability was also highly site-dependent, with characteristic diel, semi-diurnal, and stochastic patterns of varying amplitudes. These biome-specific pH signatures disclose current levels of exposure to both high and low dissolved CO2, often demonstrating that resident organisms are already experiencing pH regimes that are not predicted until 2100. Our data provide a first step toward crystallizing the biophysical link between environmental history of pH exposure and physiological resilience of marine organisms to fluctuations in seawater CO2. Knowledge of this spatial and temporal variation in seawater chemistry allows us to improve the design of OA experiments: we can test organisms with a priori expectations of their tolerance guardrails, based on their natural range of exposure. Such hypothesis-testing will provide a deeper understanding of the effects of OA. Both intuitively simple to understand and powerfully informative, these and similar comparative time series can help guide management efforts to identify areas of marine habitat that can serve as refugia to acidification as well as areas that are particularly vulnerable to future ocean change.

Kepler-16: A Transiting Circumbinary Planet

Abstract: We report the detection of a planet whose orbit surrounds a pair of low-mass stars. Data from the Kepler spacecraft reveal transits of the planet across both stars, in addition to the mutual eclipses of the stars, giving precise constraints on the absolute dimensions of all three bodies. The planet is comparable to Saturn in mass and size and is on a nearly circular 229-day orbit around its two parent stars. The eclipsing stars are 20 and 69% as massive as the Sun and have an eccentric 41-day orbit. The motions of all three bodies are confined to within 0.5° of a single plane, suggesting that the planet formed within a circumbinary disk.

A closely packed system of low-mass, low-density planets transiting Kepler-11

Abstract: When an extrasolar planet passes in front of (transits) its star, its radius can be measured from the decrease in starlight and its orbital period from the time between transits. Multiple planets transiting the same star reveal much more: period ratios determine stability and dynamics, mutual gravitational interactions reflect planet masses and orbital shapes, and the fraction of transiting planets observed as multiples has implications for the planarity of planetary systems. But few stars have more than one known transiting planet, and none has more than three. Here we report Kepler spacecraft observations of a single Sun-like star, which we call Kepler-11, that reveal six transiting planets, five with orbital periods between 10 and 47 days and a sixth planet with a longer period. The five inner planets are among the smallest for which mass and size have both been measured, and these measurements imply substantial envelopes of light gases. The degree of coplanarity and proximity of the planetary orbits imply energy dissipation near the end of planet formation. NASA's Kepler mission, a space observatory designed to detect and study extrasolar planets that transit across the disk of their host star, has hit the jackpot with the discovery of a six-planet system orbiting a Sun-like star now named Kepler-11. Five of the planets have orbital periods of between 10 and 47 days, and these are among the smallest for which size and mass have both been measured. The sixth and outermost transiting planet has been less well characterized thus far. Only one other star has more than one confirmed transiting planet (Kepler-9, which has three). This newly discovered system resembles our own Solar System in being close to coplanar, but Kepler-11's planets orbit much closer to their star. Kepler is due to continue to return data on Kepler-11 and its planets for some time yet, and it should provide many valuable constraints on models of the formation and evolution of solar systems in general. When an extrasolar planet passes in front of its star (transits), its radius can be measured from the decrease in starlight and its orbital period from the time between transits. This study reports Kepler spacecraft observations of a single Sun-like star that reveal six transiting planets, five with orbital periods between 10 and 47 days plus a sixth one with a longer period. The five inner planets are among the smallest for which mass and size have both been measured, and these measurements imply substantial envelopes of light gases.

Drosophila suzukii (Diptera: Drosophilidae): Invasive Pest of Ripening Soft Fruit Expanding its Geographic Range and Damage Potential

Abstract: Spotted wing drosophila, Drosophila suzukii Matsumura, a native of eastern and southeastern Asia, is a pest of small and stone fruits. First detected in California in 2008, the insect is now found across the Pacific Coast states. Its penchant for attacking healthy, ripening fruit (as opposed to overripe and rotting fruit favored by other so-called “vinegar flies”) makes it a potential economic threat to a host of soft- and thin-skinned fruit crops including cherry, raspberry, blackberry, blueberry, strawberry, peach, plums, pluots, nectarines, juice grape, table grape, and wine grape. Coordinated research projects to determine host preference, seasonal phenology, biology, and management options are taking place among entomologists in Washington, Oregon, and California. A description of the pest and initial findings on its biology, life history, known and expected geographic range, management and monitoring techniques, and economic considerations are presented and discussed.

GALAXY STRUCTURE AND MODE OF STAR FORMATION IN THE SFR-MASS PLANE FROM z ∼ 2.5 TO z ∼ 0.1

Abstract: We analyze the dependence of galaxy structure (size and Sersic index) and mode of star formation (ΣSFR and SFRIR/SFRUV) on the position of galaxies in the star formation rate (SFR) versus mass diagram. Our sample comprises roughly 640,000 galaxies at z ~ 0.1, 130,000 galaxies at z ~ 1, and 36,000 galaxies at z ~ 2. Structural measurements for all but the z ~ 0.1 galaxies are based on Hubble Space Telescope imaging, and SFRs are derived using a Herschel-calibrated ladder of SFR indicators. We find that a correlation between the structure and stellar population of galaxies (i.e., a "Hubble sequence") is already in place since at least z ~ 2.5. At all epochs, typical star-forming galaxies on the main sequence are well approximated by exponential disks, while the profiles of quiescent galaxies are better described by de Vaucouleurs profiles. In the upper envelope of the main sequence, the relation between the SFR and Sersic index reverses, suggesting a rapid buildup of the central mass concentration in these starbursting outliers. We observe quiescent, moderately and highly star-forming systems to co-exist over an order of magnitude or more in stellar mass. At each mass and redshift, galaxies on the main sequence have the largest size. The rate of size growth correlates with specific SFR, and so does ΣSFR at each redshift. A simple model using an empirically determined star formation law and metallicity scaling, in combination with an assumed geometry for dust and stars, is able to relate the observed ΣSFR and SFRIR/SFRUV, provided a more patchy dust geometry is assumed for high-redshift galaxies.

Extragalactic background light inferred from AEGIS galaxy-SED-type fractions

Abstract: Theextragalacticbackgroundlight(EBL)isoffundamentalimportancebothforunderstanding the entire process of galaxy evolution and for"-ray astronomy, but the overall spectrum of the EBL between 0.1 and 1000µm has never been determined directly from galaxy spectral energy distribution (SED) observations over a wide redshift range. The evolving, overall spectrum of the EBL is derived here utilizing a novel method based on observations only. This is achieved from the observed evolution of the rest-frameK-band galaxy luminosity function up to redshift 4, combined with a determination of galaxy-SED-type fractions. These are based on fitting Spitzer Wide-Area Infrared Extragalactic Survey (SWIRE) templates to a multiwavelength sample of about 6000 galaxies in the redshift range from 0.2 to 1 from the All-wavelength Extended Groth Strip International Survey (AEGIS). The changing fractions of quiescent galaxies, star-forming galaxies, starburst galaxies and active galactic nucleus (AGN) galaxies in that redshift range are estimated, and two alternative extrapolations of SED types to higher redshifts are considered. This allows calculation of the evolution of the luminosity densities from the ultraviolet (UV) to the infrared (IR), the evolving star formation ratedensityoftheUniverse,theevolvingcontributiontothebolometricEBLfromthedifferent galaxy populations including AGN galaxies and the buildup of the EBL. Our EBL calculations are compared with those from a semi-analytic model, another observationally based model and observational data. The EBL uncertainties in our modelling based directly on the data are quantified, and their consequences for attenuation of very-high-energy"-rays due to pair production on the EBL are discussed. It is concluded that the EBL is well constrained from the UV to the mid-IR, but independent efforts from IR and"-ray astronomy are needed in order to reduce the uncertainties in the far-IR.

Ultraviolet Luminosity Functions from 132 z ~ 7 and z ~ 8 Lyman-break Galaxies in the Ultra-deep HUDF09 and Wide-area Early Release Science WFC3/IR Observations

Abstract: We identify 73 z ~ 7 and 59 z ~ 8 candidate galaxies in the reionization epoch, and use this large 26-29.4?AB?mag sample of galaxies to derive very deep luminosity functions to < ? 18?AB?mag and the star formation rate (SFR) density at z ~ 7 and z ~ 8 (just 800?Myr and 650?Myr after recombination, respectively). The galaxy sample is derived using a sophisticated Lyman-break technique on the full two-year Wide Field Camera 3/infrared (WFC3/IR) and Advanced Camera for Surveys (ACS) data available over the HUDF09 (~29.4?AB?mag, 5?), two nearby HUDF09 fields (~29?AB?mag, 5?, 14?arcmin2), and the wider area Early Release Science (~27.5?AB?mag, 5?, ~40?arcmin2). The application of strict optical non-detection criteria ensures the contamination fraction is kept low (just ~7% in the HUDF). This very low value includes a full assessment of the contamination from lower redshift sources, photometric scatter, active galactic nuclei, spurious sources, low-mass stars, and transients (e.g., supernovae). From careful modeling of the selection volumes for each of our search fields, we derive luminosity functions for galaxies at z ~ 7 and z ~ 8 to < ? 18?AB?mag. The faint-end slopes ? at z ~ 7 and z ~ 8 are uncertain but very steep at ? = ?2.01 ? 0.21 and ? = ?1.91 ? 0.32, respectively. Such steep slopes contrast to the local ? ?1.4 and may even be steeper than that at z ~ 4 where ? = ?1.73 ? 0.05. With such steep slopes (? ?1.7) lower luminosity galaxies dominate the galaxy luminosity density during the epoch of reionization. The SFR densities derived from these new z ~ 7 and z ~ 8 luminosity functions are consistent with the trends found at later times (lower redshifts). We find reasonable consistency with the SFR densities implied from reported stellar mass densities being only ~40% higher at z < 7. This suggests that (1) the stellar mass densities inferred from the Spitzer Infrared Array Camera (IRAC) photometry are reasonably accurate and (2) that the initial mass function at very high redshift may not be very different from that at later times.

Does plant diversity benefit agroecosystems? A synthetic review

Abstract: Predictive theory on how plant diversity promotes herbivore suppression through movement patterns, host associations, and predation promises a potential alternative to pesticide-intensive monoculture crop production We used meta-analysis on 552 experiments in 45 articles published over the last 10 years to test if plant diversification schemes reduce herbivores and/or increase the natural enemies of herbivores as predicted by associational resistance hypotheses, the enemies hypothesis, and attraction and repellency model applications in agriculture We found extensive support for these models with intercropping schemes, inclusion of flowering plants, and use of plants that repel herbivores or attract them away from the crop Overall, herbivore suppression, enemy enhancement, and crop damage suppression effects were significantly stronger on diversified crops than on crops with none or fewer associated plant species However, a relatively small, but significantly negative, mean effect size for crop yield indicated that pest-suppressive diversification schemes interfered with production, in part because of reducing densities of the main crop by replacing it with intercrops or non-crop plants This first use of meta-analysis to evaluate the effects of diversification schemes, a potentially more powerful tool than tallies of significant positive and negative outcomes (vote-counting), revealed stronger overall effects on all parameters measured compared to previous reviews Our analysis of the same articles used in a recent review facilitates comparisons of vote-counting and meta-analysis, and shows that pronounced results of the meta-analysis are not well explained by a reduction in articles that met its stricter criteria Rather, compared to outcome counts, effect sizes were rarely neutral (equal to zero), and a mean effect size value for mixed outcomes could be calculated Problematic statistical properties of vote-counting were avoided with meta-analysis, thus providing a more precise test of the hypotheses The unambiguous and encouraging results from this meta-analysis of previous research should motivate ecologists to conduct more mechanistic experiments to improve the odds of designing effective crop diversification schemes for improved pest regulation and enhanced crop yield