The CCSM4 ocean component

Author Posting. © American Meteorological Society, 2012. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 25 (2012): 1361–1389, doi:10.1175/JCLI-D-11-00091.1.The ocean component of the Community Climate System Model version 4 (CCSM4) is described, and its solutions from the twentieth-century (20C) simulations are documented in comparison with observations and those of CCSM3. The improvements to the ocean model physical processes include new parameterizations to represent previously missing physics and modifications of existing parameterizations to incorporate recent new developments. In comparison with CCSM3, the new solutions show some significant improvements that can be attributed to these model changes. These include a better equatorial current structure, a sharper thermocline, and elimination of the cold bias of the equatorial cold tongue all in the Pacific Ocean; reduced sea surface temperature (SST) and salinity biases along the North Atlantic Current path; and much smaller potential temperature and salinity biases in the near-surface Pacific Ocean. Other improvements include a global-mean SST that is more consistent with the present-day observations due to a different spinup procedure from that used in CCSM3. Despite these improvements, many of the biases present in CCSM3 still exist in CCSM4. A major concern continues to be the substantial heat content loss in the ocean during the preindustrial control simulation from which the 20C cases start. This heat loss largely reflects the top of the atmospheric model heat loss rate in the coupled system, and it essentially determines the abyssal ocean potential temperature biases in the 20C simulations. There is also a deep salty bias in all basins. As a result of this latter bias in the deep North Atlantic, the parameterized overflow waters cannot penetrate much deeper than in CCSM3.NCAR is sponsored by the National Science Foundation. The CCSM is also sponsored by the Department of Energy. SGY was supported by the NOAA Climate Program Office under Climate Variability and Predictability Program Grant NA09OAR4310163.2012-09-0

In Situ Microbial Community Control of the Stability of Bio-reduced Uranium

In aerobic aquifers typical of many Department of Energy (DOE) legacy waste sites, uranium is present in the oxidized U(VI) form which is more soluble and thus more mobile. Field experiments at the Old Rifle UMTRA site have demonstrated that biostimulation by electron donor addition (acetate) promotes biological U(VI) reduction (2). However, U(VI) reduction is reversible and oxidative dissolution of precipitated U(IV) after the cessation of electron donor addition remains a critical issue for the application of biostimulation as a treatment technology. Despite the potential for oxidative dissolution, field experiments at the Old Rifle site have shown that rapid reoxidation of bio-reduced uranium does not occur and U(VI) concentrations can remain at approximately 20% of background levels for more than one year. The extent of post-amendment U(VI) removal and the maintenance of bioreduced uranium may result from many factors including U(VI) sorption to iron-containing mineral phases, generation of H2S or FeS0.9, or the preferential sorption of U(VI) by microbial cells or biopolymers, but the processes controlling the reduction and in situ reoxidation rates are not known. To investigate the role of microbial community composition in the maintenance of bioreduced uranium, in-well sediment incubators (ISIs) were developed allowing field deployment of amended and native sediments during on-going experiments at the site. Field deployment of the ISIs allows expedient interrogation of microbial community response to field environmental perturbations and varying geochemical conditions

The Rise and Fall, and the Rise (Again) of Feminist Research in Music: 'What Goes Around Comes Around'

This article reports from a two-phase study that involved an analysis of the extant literature followed by a three-part survey answered by seventy-one women composers. Through these theoretical and empirical data, the authors explore the relationship between gender and music’s symbolic and cultural capital. Bourdieu’s theory of the habitus is employed to understand the gendered experiences of the female composers who participated in the survey. The article suggests that these female composers have different investments in gender but that, overall, they reinforce the male habitus given that the female habitus occupies a subordinate position in relation to that of the male. The findings of the study also suggest a connection between contemporary feminism and the attitudes towards gender held by the participants. The article concludes that female composers classify themselves, and others, according to gendered norms and that these perpetuate the social order in music in which the male norm dominates

Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.

Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (P < 5 × 10(-8)) for 123 signals at 106 genomic loci associated with age at menarche. Many loci were associated with other pubertal traits in both sexes, and there was substantial overlap with genes implicated in body mass index and various diseases, including rare disorders of puberty. Menarche signals were enriched in imprinted regions, with three loci (DLK1-WDR25, MKRN3-MAGEL2 and KCNK9) demonstrating parent-of-origin-specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and γ-aminobutyric acid-B2 receptor signalling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition

Subsurface Biogeochemical Heterogeneity (Field-scale removal of U(VI) from groundwater in an alluvial aquifer by electron donor amendment)

Determine if biostimulation of alluvial aquifers by electron donor amendment can effectively remove U(VI) from groundwater at the field scale. Uranium contamination in groundwater is a significant problem at several DOE sites. In this project, the possibility of accelerating bioreduction of U(VI) to U(IV) as a means of decreasing U(VI) concentrations in groundwater is directly addressed by conducting a series of field-scale experiments. Scientific goals include demonstrating the quantitative linkage between microbial activity and U loss from groundwater and relating the dominant terminal electron accepting processes to the rate of U loss. The project is currently focused on understanding the mechanisms for unexpected long-term ({approx}2 years) removal of U after stopping electron donor amendment. Results obtained in the project successfully position DOE and others to apply biostimulation broadly to U contamination in alluvial aquifers

Recombinant human complement component C2 produced in a human cell line restores the classical complement pathway activity in-vitro: an alternative treatment for C2 deficiency diseases

Background: Complement C2 deficiency is the most common genetically determined complete complement deficiency and is associated with a number of diseases. Most prominent are the associations with recurrent serious infections in young children and the development of systemic lupus erythematosus (SLE) in adults. The links with these diseases reflect the important role complement C2 plays in both innate immunity and immune tolerance. Infusions with normal fresh frozen plasma for the treatment of associated disease have demonstrated therapeutic effects but so far protein replacement therapy has not been evaluated. Results: Human complement C2 was cloned and expressed in a mammalian cell line. The purity of recombinant human C2 (rhC2) was greater than 95% and it was characterized for stability and activity. It was sensitive to C1s cleavage and restored classical complement pathway activity in C2-deficient serum both in a complement activation ELISA and a hemolytic assay. Furthermore, rhC2 could increase C3 fragment deposition on the human pathogen Streptococcus pneumoniae in C2-deficient serum to levels equal to those with normal serum. Conclusions: Taken together these data suggest that recombinant human C2 can restore classical complement pathway activity and may serve as a potential therapeutic for recurring bacterial infections or SLE in C2-deficient patients

Carbon uptake by mature Amazon forests has mitigated Amazon nations' carbon emissions

Background: Several independent lines of evidence suggest that Amazon forests have provided a significant carbon sink service, and also that the Amazon carbon sink in intact, mature forests may now be threatened as a result of different processes. There has however been no work done to quantify non-land-use-change forest carbon fluxes on a national basis within Amazonia, or to place these national fluxes and their possible changes in the context of the major anthropogenic carbon fluxes in the region. Here we present a first attempt to interpret results from groundbased monitoring of mature forest carbon fluxes in a biogeographically, politically, and temporally differentiated way. Specifically, using results from a large long-term network of forest plots, we estimate the Amazon biomass carbon balance over the last three decades for the different regions and nine nations of Amazonia, and evaluate the magnitude and trajectory of these differentiated balances in relation to major national anthropogenic carbon emissions. Results: The sink of carbon into mature forests has been remarkably geographically ubiquitous across Amazonia, being substantial and persistent in each of the five biogeographic regions within Amazonia. Between 1980 and 2010, it has more than mitigated the fossil fuel emissions of every single national economy, except that of Venezuela. For most nations (Bolivia, Colombia, Ecuador, French Guiana, Guyana, Peru, Suriname) the sink has probably additionally mitigated all anthropogenic carbon emissions due to Amazon deforestation and other land use change. While the sink has weakened in some regions since 2000, our analysis suggests that Amazon nations which are able to conserve large areas of natural and semi-natural landscape still contribute globally-significant carbon sequestration. Conclusions: Mature forests across all of Amazonia have contributed significantly to mitigating climate change for decades. Yet Amazon nations have not directly benefited from providing this global scale ecosystem service. We suggest that better monitoring and reporting of the carbon fluxes within mature forests, and understanding the drivers of changes in their balance, must become national, as well as international, priorities

Hyperdominance in Amazonian Forest Carbon Cycling

While Amazonian forests are extraordinarily diverse, the abundance of trees is skewed strongly towards relatively few ‘hyperdominant’ species. In addition to their diversity, Amazonian trees are a key component of the global carbon cycle, assimilating and storing more carbon than any other ecosystem on Earth. Here we ask, using a unique data set of 530 forest plots, if the functions of storing and producing woody carbon are concentrated in a small number of tree species, whether the most abundant species also dominate carbon cycling, and whether dominant species are characterized by specific functional traits. We find that dominance of forest function is even more concentrated in a few species than is dominance of tree abundance, with only ≈1% of Amazon tree species responsible for 50% of carbon storage and productivity. Although those species that contribute most to biomass and productivity are often abundant, species maximum size is also influential, while the identity and ranking of dominant species varies by function and by region

Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels

Vitamin D is a steroid hormone precursor that is associated with a range of human traits and diseases. Previous GWAS of serum 25-hydroxyvitamin D concentrations have identified four genome-wide significant loci (GC, NADSYN1/DHCR7, CYP2R1, CYP24A1). In this study, we expand the previous SUNLIGHT Consortium GWAS discovery sample size from 16,125 to 79,366 (all European descent). This larger GWAS yields two additional loci harboring genome-wide significant variants (P = 4.7x10(-9) at rs8018720 in SEC23A, and P = 1.9x10(-14) at rs10745742 in AMDHD1). The overall estimate of heritability of 25-hydroxyvitamin D serum concentrations attributable to GWAS common SNPs is 7.5%, with statistically significant loci explaining 38% of this total. Further investigation identifies signal enrichment in immune and hematopoietic tissues, and clustering with autoimmune diseases in cell-type-specific analysis. Larger studies are required to identify additional common SNPs, and to explore the role of rare or structural variants and gene-gene interactions in the heritability of circulating 25-hydroxyvitamin D levels.Peer reviewe