Showing papers by "San Diego State University published in 2012"

Structure, function and diversity of the healthy human microbiome

Abstract: The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.

Guidelines for the use and interpretation of assays for monitoring autophagy

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

A framework for human microbiome research

Abstract: A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 to 18 body sites up to three times, which to date, have generated 5,177 microbial taxonomic profiles from 16S rRNA genes and over 3.5 Tb of metagenomic sequence. In parallel, approximately 800 human-associated reference genomes have been sequenced. Collectively, these data represent the largest resource to date describing the abundance and variety of the human microbiome, while providing a platform for current and future studies.

Planetary Candidates Observed by Kepler, III: Analysis of the First 16 Months of Data

Abstract: New transiting planet candidates are identified in sixteen months (May 2009 - September 2010) of data from the Kepler spacecraft. Nearly five thousand periodic transit-like signals are vetted against astrophysical and instrumental false positives yielding 1,091 viable new planet candidates, bringing the total count up to over 2,300. Improved vetting metrics are employed, contributing to higher catalog reliability. Most notable is the noise-weighted robust averaging of multi-quarter photo-center offsets derived from difference image analysis which identifies likely background eclipsing binaries. Twenty-two months of photometry are used for the purpose of characterizing each of the new candidates. Ephemerides (transit epoch, T_0, and orbital period, P) are tabulated as well as the products of light curve modeling: reduced radius (Rp/R*), reduced semi-major axis (d/R*), and impact parameter (b). The largest fractional increases are seen for the smallest planet candidates (197% for candidates smaller than 2Re compared to 52% for candidates larger than 2Re) and those at longer orbital periods (123% for candidates outside of 50-day orbits versus 85% for candidates inside of 50-day orbits). The gains are larger than expected from increasing the observing window from thirteen months (Quarter 1-- Quarter 5) to sixteen months (Quarter 1 -- Quarter 6). This demonstrates the benefit of continued development of pipeline analysis software. The fraction of all host stars with multiple candidates has grown from 17% to 20%, and the paucity of short-period giant planets in multiple systems is still evident. The progression toward smaller planets at longer orbital periods with each new catalog release suggests that Earth-size planets in the Habitable Zone are forthcoming if, indeed, such planets are abundant.

Planet Occurrence within 0.25 AU of Solar-Type Stars from Kepler

Abstract: We report the distribution of planets as a function of planet radius, orbital period, and stellar effective temperature for orbital periods less than 50 days around solar-type (GK) stars. These results are based on the 1235 planets (formally "planet candidates") from the Kepler mission that include a nearly complete set of detected planets as small as 2 R_⊕. For each of the 156,000 target stars, we assess the detectability of planets as a function of planet radius, R_p, and orbital period, P, using a measure of the detection efficiency for each star. We also correct for the geometric probability of transit, R_*/a. We consider first Kepler target stars within the "solar subset" having T_eff = 4100-6100 K, log g = 4.0-4.9, and Kepler magnitude K_p 2 R_⊕ we measure an occurrence of less than 0.001 planets per star. For all planets with orbital periods less than 50 days, we measure occurrence of 0.130 ± 0.008, 0.023 ± 0.003, and 0.013 ± 0.002 planets per star for planets with radii 2-4, 4-8, and 8-32 R_⊕, in agreement with Doppler surveys. We fit occurrence as a function of P to a power-law model with an exponential cutoff below a critical period P_0. For smaller planets, P_0 has larger values, suggesting that the "parking distance" for migrating planets moves outward with decreasing planet size. We also measured planet occurrence over a broader stellar T_eff range of 3600-7100 K, spanning M0 to F2 dwarfs. Over this range, the occurrence of 2-4 R_⊕ planets in the Kepler field increases with decreasing T_eff, with these small planets being seven times more abundant around cool stars (3600-4100 K) than the hottest stars in our sample (6600-7100 K).

Averting biodiversity collapse in tropical forest protected areas

Abstract: The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon(1-3). With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses(4-9). As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world's major tropical regions. Our analysis reveals great variation in reserve 'health': about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Abstract: Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/humann. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies.

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Abstract: Microbial communities carry out the majority of the biochemical activity on the planet, and they play integral roles in processes including metabolism and immune homeostasis in the human microbiome. Shotgun sequencing of such communities' metagenomes provides information complementary to organismal abundances from taxonomic markers, but the resulting data typically comprise short reads from hundreds of different organisms and are at best challenging to assemble comparably to single-organism genomes. Here, we describe an alternative approach to infer the functional and metabolic potential of a microbial community metagenome. We determined the gene families and pathways present or absent within a community, as well as their relative abundances, directly from short sequence reads. We validated this methodology using a collection of synthetic metagenomes, recovering the presence and abundance both of large pathways and of small functional modules with high accuracy. We subsequently applied this method, HUMAnN, to the microbial communities of 649 metagenomes drawn from seven primary body sites on 102 individuals as part of the Human Microbiome Project (HMP). This provided a means to compare functional diversity and organismal ecology in the human microbiome, and we determined a core of 24 ubiquitously present modules. Core pathways were often implemented by different enzyme families within different body sites, and 168 functional modules and 196 metabolic pathways varied in metagenomic abundance specifically to one or more niches within the microbiome. These included glycosaminoglycan degradation in the gut, as well as phosphate and amino acid transport linked to host phenotype (vaginal pH) in the posterior fornix. An implementation of our methodology is available at http://huttenhower.sph.harvard.edu/humann. This provides a means to accurately and efficiently characterize microbial metabolic pathways and functional modules directly from high-throughput sequencing reads, enabling the determination of community roles in the HMP cohort and in future metagenomic studies.

Prevalence of major cardiovascular risk factors and cardiovascular diseases among Hispanic/Latino individuals of diverse backgrounds in the United States.

Abstract: Results Age-standardized prevalence of CVD risk factors varied by Hispanic/Latino background; obesity and current smoking rates were highest among Puerto Rican participants (for men, 40.9% and 34.7%; for women, 51.4% and 31.7%, respectively); hypercholesterolemia prevalence was highest among Central American men (54.9%) and Puerto Rican women (41.0%). Large proportions of participants (80% of men, 71% of women) had at least 1 risk factor. Age- and sex-adjusted prevalence of 3 or more risk factors was highest in Puerto Rican participants (25.0%) and significantly higher (P.001) among participants with less education (16.1%), those who were US-born (18.5%), those who had lived in the United States 10 years or longer (15.7%), and those who preferred English (17.9%). Overall, self-reported CHD and stroke prevalence were low (4.2% and 2.0% in men; 2.4% and 1.2% in women, respectively). In multivariate-adjusted models, hypertension and smoking were directly associated with CHD in both sexes as were hypercholesterolemia and obesity in women and diabetes in men (odds ratios [ORs], 1.5-2.2). For stroke, associations were positive with hypertension in both sexes, diabetes in men, and smoking in women (ORs, 1.7-2.6). Conclusion Among US Hispanic/Latino adults of diverse backgrounds, a sizeable proportion of men and women had adverse major risk factors; prevalence of adverse CVD risk profiles was higher among participants with Puerto Rican background, lower SES, and higher levels of acculturation.

A bacterial driver-passenger model for colorectal cancer: beyond the usual suspects.

Abstract: Cancer has long been considered a genetic disease. However, accumulating evidence supports the involvement of infectious agents in the development of cancer, especially in those organs that are continuously exposed to microorganisms, such as the large intestine. Recent next-generation sequencing studies of the intestinal microbiota now offer an unprecedented view of the aetiology of sporadic colorectal cancer and have revealed that the microbiota associated with colorectal cancer contains bacterial species that differ in their temporal associations with developing tumours. Here, we propose a bacterial driver–passenger model for microbial involvement in the development of colorectal cancer and suggest that this model be incorporated into the genetic paradigm of cancer progression.

Generational differences in young adults' life goals, concern for others, and civic orientation, 1966-2009.

Abstract: Three studies examined generational differences in life goals, concern for others, and civic orientation among American high school seniors (Monitoring the Future; N 463,753, 1976–2008) and entering college students (The American Freshman; N 8.7 million, 1966–2009). Compared to Baby Boomers (born 1946–1961) at the same age, GenX’ers (born 1962–1981) and Millennials (born after 1982) considered goals related to extrinsic values (money, image, fame) more important and those related to intrinsic values (self-acceptance, affiliation, community) less important. Concern for others (e.g., empathy for outgroups, charity donations, the importance of having a job worthwhile to society) declined slightly. Community service rose but was also increasingly required for high school graduation over the same time period. Civic orientation (e.g., interest in social problems, political participation, trust in government, taking action to help the environment and save energy) declined an average of d .34, with about half the decline occurring between GenX and the Millennials. Some of the largest declines appeared in taking action to help the environment. In most cases, Millennials slowed, though did not reverse, trends toward reduced community feeling begun by GenX. The results generally support the “Generation Me” view of generational differences rather than the “Generation We” or no change views.

Transiting circumbinary planets Kepler-34 b and Kepler-35 b

Abstract: Most Sun-like stars in the Galaxy reside in gravitationally bound pairs of stars (binaries). Although long anticipated the existence of a ‘circumbinary planet’ orbiting such a pair of normal stars was not definitively established until the discovery of the planet transiting (that is, passing in front of) Kepler-16. Questions remained, however, about the prevalence of circumbinary planets and their range of orbital and physical properties. Here we report two additional transiting circumbinary planets: Kepler-34 (AB)b and Kepler-35 (AB)b, referred to here as Kepler-34 b and Kepler-35 b, respectively. Each is a low-density gas-giant planet on an orbit closely aligned with that of its parent stars. Kepler-34 b orbits two Sun-like stars every 289 days, whereas Kepler-35 b orbits a pair of smaller stars (89% and 81% of the Sun’s mass) every 131 days. The planets experience large multi-periodic variations in incident stellar radiation arising from the orbital motion of the stars. The observed rate of circumbinary planets in our sample implies that more than ~1% of close binary stars have giant planets in nearly coplanar orbits, yielding a Galactic population of at least several million.

Physical Education's Role in Public Health: Steps Forward and Backward over 20 Years and HOPE for the Future.

Abstract: The 1991 paper, “Physical Education's Role in Public Health” described the importance of physical education in addressing public health problems. On its 20th anniversary, this article reviews accomplishments in improving the health impact of physical education and identifies areas lacking progress. Major accomplishments include development of evidence-based programs, documentation of health and academic benefits of physical education, and acceptance of physical education as a public health resource. Additional work is needed to evaluate the uptake of evidence-based programs, improve national surveillance of physical education quantity and quality, establish stronger policies supporting active physical education, and achieve wide acceptance of public health goals within the physical education field. These opportunities constitute an agenda for actualizing the promise of Health-Optimizing Physical Education before the next 20-year anniversary.

Incidence of Contralateral and Ipsilateral Anterior Cruciate Ligament (ACL) Injury After Primary ACL Reconstruction and Return to Sport

Abstract: Objective Incidence rate (IR) of an ipsilateral or contralateral injury after anterior cruciate ligament reconstruction (ACLR) is unknown. The hypotheses were that the IR of anterior cruciate ligament (ACL) injury after ACLR would be greater than the IR in an uninjured cohort of athletes and would be greater in female athletes after ACLR than male athletes.

Kepler-47: A Transiting Circumbinary Multiplanet System

Abstract: We report the detection of Kepler-47, a system consisting of two planets orbiting around an eclipsing pair of stars. The inner and outer planets have radii 3.0 and 4.6 times that of Earth, respectively. The binary star consists of a Sun-like star and a companion roughly one-third its size, orbiting each other every 7.45 days. With an orbital period of 49.5 days, 18 transits of the inner planet have been observed, allowing a detailed characterization of its orbit and those of the stars. The outer planet’s orbital period is 303.2 days, and although the planet is not Earth-like, it resides within the classical "habitable zone," where liquid water could exist on an Earth-like planet. With its two known planets, Kepler-47 establishes that close binary stars can host complete planetary systems.

Going viral: next-generation sequencing applied to phage populations in the human gut.

Abstract: Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods. These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere. Here, we briefly review the incipient rise of a phage biology renaissance, which has been catalysed by advances in next-generation sequencing. We explore how work characterizing phage diversity and lifestyles in the human gut is changing our view of ourselves as supra-organisms. Finally, we discuss how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of our gut microbiomes.

Home environment relationships with children’s physical activity, sedentary time, and screen time by socioeconomic status

Abstract: Background: Children in households of lower socioeconomic status (SES) are more likely to be overweight/obese. We aimed to determine if home physical activity (PA) environments differed by SES and to explore home environment mediators of the relation of family SES to children’s PA and sedentary behavior. Methods: Participants were 715 children aged 6 to 11 from the Neighborhood Impact on Kids (NIK) Study. Household SES was examined using highest educational attainment and income. Home environment was measured by parent report on a survey. Outcomes were child’s accelerometer-measured PA and parent-reported screen time. Mediation analyses were conducted for home environment factors that varied by SES. Results: Children from lower income households had greater media access in their bedrooms (TV 52% vs. 14%, DVD player 39% vs. 14%, video games 21% vs. 9%) but lower access to portable play equipment (bikes 85% vs. 98%, jump ropes 69% vs. 83%) compared to higher income children. Lower SES families had more restrictive rules about PA (2.5 vs. 2.0). Across SES, children watched TV/DVDs with parents/siblings more often than they engaged in PA with them. Parents of lower SES watched TV/DVDs with their children more often (3.1 vs. 2.5 days/week). Neither total daily and home-based MVPA nor sedentary time differed by SES. Children’s daily screen time varied from 1.7 hours/day in high SES to 2.4 in low SES families. Media in the bedroom was related to screen time, and screen time with parents was a mediator of the SES--screen time relationship. Conclusions: Lower SES home environments provided more opportunities for sedentary behavior and fewer for PA. Removing electronic media from children’s bedrooms has the potential to reduce disparities in chronic disease risk.

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

Abstract: Prophages are phages in lysogeny that are integrated into, and replicated as part of, the host bacterial genome. These mobile elements can have tremendous impact on their bacterial hosts’ genomes and phenotypes, which may lead to strain emergence and diversification, increased virulence or antibiotic resistance. However, finding prophages in microbial genomes remains a problem with no definitive solution. The majority of existing tools rely on detecting genomic regions enriched in protein-coding genes with known phage homologs, which hinders the de novo discovery of phage regions. In this study, a weighted phage detection algorithm, PhiSpy was developed based on seven distinctive characteristics of prophages, i.e. protein length, transcription strand directionality, customized AT and GC skew, the abundance of unique phage words, phage insertion points and the similarity of phage proteins. The first five characteristics are capable of identifying prophages without any sequence similarity with known phage genes. PhiSpy locates prophages by ranking genomic regions enriched in distinctive phage traits, which leads to the successful prediction of 94% of prophages in 50 complete bacterial genomes with a 6% false-negative rate and a 0.66% false-positive rate.

Is Fat a Feminist Issue? Exploring the Gendered Nature of Weight Bias

Abstract: Although research and scholarship on weight-based stigma have increased substantially in recent years, the disproportionate degree of bias experienced by fat women has received considerably less attention. This paper reviews the literature on the weight-based stigma experienced by women in North America in multiple domains, including employment, education settings, romantic relationships, health care and mental health treatment, and portrayals in the media. We also explore the research examining the intersection of gender and ethnicity related to weight stigma. Across numerous settings, fat women fare worse than thinner women and worse than men, whether the men are fat or thin. Women experience multiple deleterious outcomes as a result of weight bias that have a significant impact on health, quality of life, and socioeconomic outcomes. Because of this gender disparity, we argue that feminist scholars need to devote as much attention to the lived experiences of fat women as they have to the “fear of fat” experienced by thin women.

Berkeley Supernova Ia Program – I. Observations, data reduction and spectroscopic sample of 582 low-redshift Type Ia supernovae

Abstract: In this first paper in a series, we present 1298 low-redshift (z ≲ 0.2) optical spectra of 582 Type Ia supernovae (SNe Ia) observed from 1989 to 2008 as part of the Berkeley Supernova Ia Program (BSNIP). 584 spectra of 199 SNe Ia have well-calibrated light curves with measured distance moduli, and many of the spectra have been corrected for host-galaxy contamination. Most of the data were obtained using the Kast double spectrograph mounted on the Shane 3 m telescope at Lick Observatory and have a typical wavelength range of 3300–10 400 A, roughly twice as wide as spectra from most previously published data sets. We present our observing and reduction procedures, and we describe the resulting SN Database, which will be an online, public, searchable data base containing all of our fully reduced spectra and companion photometry. In addition, we discuss our spectral classification scheme (using the SuperNova IDentification code, snid; Blondin & Tonry), utilizing our newly constructed set of snid spectral templates. These templates allow us to accurately classify our entire data set, and by doing so we are able to reclassify a handful of objects as bona fide SNe Ia and a few other objects as members of some of the peculiar SN Ia subtypes. In fact, our data set includes spectra of nearly 90 spectroscopically peculiar SNe Ia. We also present spectroscopic host-galaxy redshifts of some SNe Ia where these values were previously unknown. The sheer size of the BSNIP data set and the consistency of our observation and reduction methods make this sample unique among all other published SN Ia data sets and complementary in many ways to the large, low-redshift SN Ia spectra presented by Matheson et al. and Blondin et al. In other BSNIP papers in this series, we use these data to examine the relationships between spectroscopic characteristics and various observables such as photometric and host-galaxy properties.

A model-data comparison of gross primary productivity: Results from the North American Carbon Program site synthesis

Abstract: [1] Accurately simulating gross primary productivity (GPP) in terrestrial ecosystem models is critical because errors in simulated GPP propagate through the model to introduce additional errors in simulated biomass and other fluxes. We evaluated simulated, daily average GPP from 26 models against estimated GPP at 39 eddy covariance flux tower sites across the United States and Canada. None of the models in this study match estimated GPP within observed uncertainty. On average, models overestimate GPP in winter, spring, and fall, and underestimate GPP in summer. Models overpredicted GPP under dry conditions and for temperatures below 0°C. Improvements in simulated soil moisture and ecosystem response to drought or humidity stress will improve simulated GPP under dry conditions. Adding a low-temperature response to shut down GPP for temperatures below 0°C will reduce the positive bias in winter, spring, and fall and improve simulated phenology. The negative bias in summer and poor overall performance resulted from mismatches between simulated and observed light use efficiency (LUE). Improving simulated GPP requires better leaf-to-canopy scaling and better values of model parameters that control the maximum potential GPP, such asemax (LUE), Vcmax (unstressed Rubisco catalytic capacity) or Jmax (the maximum electron transport rate).

CALTECH CORE-COLLAPSE PROJECT (CCCP) OBSERVATIONS OF TYPE IIn SUPERNOVAE: TYPICAL PROPERTIES AND IMPLICATIONS FOR THEIR PROGENITOR STARS

Abstract: Type IIn supernovae (SNe IIn) are rare events, constituting only a few percent of all core-collapse SNe, and the current sample of well-observed SNe IIn is small. Here, we study the four SNe IIn observed by the Caltech Core-Collapse Project (CCCP). The CCCP SN sample is unbiased to the extent that object selection was not influenced by target SN properties. Therefore, these events are representative of the observed population of SNe IIn. We find that a narrow P-Cygni profile in the hydrogen Balmer lines appears to be a ubiquitous feature of SNe IIn. Our light curves show a relatively long rise time (>20 days) followed by a slow decline stage (0.01-0.15 mag day–1), and a typical V-band peak magnitude of MV = –18.4 ± 1.0 mag. We measure the progenitor star wind velocities (600-1400 km s–1) for the SNe in our sample and derive pre-explosion mass-loss rates (0.026-0.12 M ☉ yr–1). We compile similar data for SNe IIn from the literature and discuss our results in the context of this larger sample. Our results indicate that typical SNe IIn arise from progenitor stars that undergo luminous-blue-variable-like mass loss shortly before they explode.

Kepler-22b: a 2.4 Earth-radius Planet in the Habitable Zone of a Sun-like Star

Abstract: A search of the time-series photometry from NASA's Kepler spacecraft reveals a transiting planet candidate orbiting the 11th magnitude G5 dwarf KIC 10593626 with a period of 290 days. The characteristics of the host star are well constrained by high-resolution spectroscopy combined with an asteroseismic analysis of the Kepler photometry, leading to an estimated mass and radius of 0.970 ± 0.060 M ☉ and 0.979 ± 0.020 R ☉. The depth of 492 ± 10 ppm for the three observed transits yields a radius of 2.38 ± 0.13 Re for the planet. The system passes a battery of tests for false positives, including reconnaissance spectroscopy, high-resolution imaging, and centroid motion. A full BLENDER analysis provides further validation of the planet interpretation by showing that contamination of the target by an eclipsing system would rarely mimic the observed shape of the transits. The final validation of the planet is provided by 16 radial velocities (RVs) obtained with the High Resolution Echelle Spectrometer on Keck I over a one-year span. Although the velocities do not lead to a reliable orbit and mass determination, they are able to constrain the mass to a 3σ upper limit of 124 M ⊕, safely in the regime of planetary masses, thus earning the designation Kepler-22b. The radiative equilibrium temperature is 262 K for a planet in Kepler-22b's orbit. Although there is no evidence that Kepler-22b is a rocky planet, it is the first confirmed planet with a measured radius to orbit in the habitable zone of any star other than the Sun.

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

Abstract: Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.

Reduction in carbon uptake during turn of the century drought in western North America

Abstract: The severity and incidence of climatic extremes, including drought, have increased as a result of climate warming. Analyses of observational and reanalysis data suggest that the strength of the western North American carbon sink declined by 30–298 Tg carbon per year during the drought at the turn of the century. Fossil fuel emissions aside, temperate North America is a net sink of carbon dioxide at present1,2,3. Year-to-year variations in this carbon sink are linked to variations in hydroclimate that affect net ecosystem productivity3,4. The severity and incidence of climatic extremes, including drought, have increased as a result of climate warming5,6,7,8. Here, we examine the effect of the turn of the century drought in western North America on carbon uptake in the region, using reanalysis data, remote sensing observations and data from global monitoring networks. We show that the area-integrated strength of the western North American carbon sink declined by 30–298 Tg C yr−1 during the 2000–2004 drought. We further document a pronounced drying of the terrestrial biosphere during this period, together with a reduction in river discharge and a loss of cropland productivity. We compare our findings with previous palaeoclimate reconstructions7 and show that the last drought of this magnitude occurred more than 800 years ago. Based on projected changes in precipitation and drought severity, we estimate that the present mid-latitude carbon sink of 177–623 Tg C yr−1 in western North America could disappear by the end of the century.

An assessment of the carbon balance of Arctic tundra: comparisons among observations, process models, and atmospheric inversions

Abstract: Although Arctic tundra has been estimated to cover only 8 % of the global land surface, the large and po- tentially labile carbon pools currently stored in tundra soils have the potential for large emissions of carbon (C) under a warming climate. These emissions as radiatively active greenhouse gases in the form of both CO2 and CH4 could amplify global warming. Given the potential sensitivity of these ecosystems to climate change and the expectation that the Arctic will experience appreciable warming over the next century, it is important to assess whether responses of C ex- change in tundra regions are likely to enhance or mitigate warming. In this study we compared analyses of C exchange of Arctic tundra between 1990 and 2006 among observa- tions, regional and global applications of process-based ter- restrial biosphere models, and atmospheric inversion mod- els. Syntheses of flux observations and inversion models in- dicate that the annual exchange of CO2 between Arctic tun- dra and the atmosphere has large uncertainties that cannot be distinguished from neutral balance. The mean estimate from an ensemble of process-based model simulations sug- gests that Arctic tundra has acted as a sink for atmospheric CO2 in recent decades, but based on the uncertainty esti- mates it cannot be determined with confidence whether these ecosystems represent a weak or a strong sink. Tundra was 0.6 C warmer in the 2000s compared to the 1990s. The cen- tral estimates of the observations, process-based models, and inversion models each identify stronger sinks in the 2000s compared with the 1990s. Some of the process models in- dicate that this occurred because net primary production in- creased more in response to warming than heterotrophic res- piration. Similarly, the observations and the applications of regional process-based models suggest that CH4 emissions from Arctic tundra have increased from the 1990s to 2000s because of the sensitivity of CH4 emissions to warmer tem- peratures. Based on our analyses of the estimates from ob- servations, process-based models, and inversion models, we estimate that Arctic tundra was a sink for atmospheric CO2 of 110 Tg C yr 1 (uncertainty between a sink of 291 Tg C yr 1 and a source of 80 Tg C yr 1 ) and a source of CH4 to the atmosphere of 19 Tg C yr 1 (uncertainty between sources of 8 and 29 Tg C yr 1 ). The suite of analyses conducted in this study indicate that it is important to reduce uncertainties in