A genome-wide association study identifies susceptibility loci for Wilms tumor

Wilms tumor is the most common renal malignancy of childhood. To identify common variants that confer susceptibility to Wilms tumor, we conducted a genome-wide association study in 757 individuals with Wilms tumor (cases) and 1,879 controls. We evaluated ten SNPs in regions significantly associated at P < 5 × 10(-5) in two independent replication series from the UK (769 cases and 2,814 controls) and the United States (719 cases and 1,037 controls). We identified clear significant associations at 2p24 (rs3755132, P = 1.03 × 10(-14); rs807624, P = 1.32 × 10(-14)) and 11q14 (rs790356, P = 4.25 × 10(-15)). Both regions contain genes that are plausibly related to Wilms tumorigenesis. We also identified candidate association signals at 5q14, 22q12 and Xp22.     

Alhazen,Leonardo, and late-medieval speculation on the inversion of images in the eye

No one before Platter and Kepler proposed retinal reception of an inverted visual image. The dominant tradition in visual theory, especially that of Alhazen and his Western followers, subordinated the intra-ocular geometry of visual rays to the requirement for an upright image and to preconceptions about the precise nature of the visual spirit and its part in vision. Henry of Langenstein and an anonymous glossator in the late Middle Ages proposed alternatives to Alhazen, including the suggestion of double inversion of the image. Leonardo da Vinci was aware of both Alhazen's theory and Henry's contradiction, but perhaps not of the anonymous hypothesis of double inversion. Leonardo's visual ‘theory’ has more the character of a critique than of a theoretical alternative, and he did not transcend the medieval concept of visual spirit.     

Genome-wide association study identifies three new melanoma susceptibility loci

We report a genome-wide association study for melanoma that was conducted by the GenoMEL Consortium. Our discovery phase included 2,981 individuals with melanoma and 1,982 study-specific control individuals of European ancestry, as well as an additional 6,426 control subjects from French or British populations, all of whom were genotyped for 317,000 or 610,000 single-nucleotide polymorphisms (SNPs). Our analysis replicated previously known melanoma susceptibility loci. Seven new regions with at least one SNP with P < 10(-5) and further local imputed or genotyped support were selected for replication using two other genome-wide studies (from Australia and Texas, USA). Additional replication came from case-control series from the UK and The Netherlands. Variants at three of the seven loci replicated at P < 10(-3): an SNP in ATM (rs1801516, overall P = 3.4 × 10(-9)), an SNP in MX2 (rs45430, P = 2.9 × 10(-9)) and an SNP adjacent to CASP8 (rs13016963, P = 8.6 × 10(-10)). A fourth locus near CCND1 remains of potential interest, showing suggestive but inconclusive evidence of replication (rs1485993, overall P = 4.6 × 10(-7) under a fixed-effects model and P = 1.2 × 10(-3) under a random-effects model). These newly associated variants showed no association with nevus or pigmentation phenotypes in a large British case-control series.     

Density and biomass of redband trout relative to stream shading and temperature in southwestern Idaho

Density and biomass of redband trout ( Oncorhynchus mykiss gairdneri ) relative to stream temperature were examined in headwater reaches of Big Jacks and Little Jacks Creeks in southwestern Idaho. Stream shading was greater (mean of 80% versus 46%) and solar insolation was lower (mean of 7.9 versus 15.1 mJ · m -2 · day -1 ) in Little Jacks Creek ( P P ≤ 0.07) but increased more rapidly and to higher levels (24° - 26° C) in Big Jacks Creek. Daily maximum water temperatures (23 km downstream of headwater springs) during July 1996 were lower in Little Jacks Creek (ranged from 18° to 22° C) than in Big Jacks Creek (20.2° to 26° C, P P -2 and 25.0 g · m -2 ) compared to Big Jacks Creek (0.3 fish · m -2 and 8.9 g · m -2 , P = 0.01). Trout density was negatively correlated with increases in water temperature ( P = 0.03) and solar insolation ( P = 0.09) in both streams. Trout biomass increased with stream shading and was negatively correlated with solar insolation ( P < 0.1). Warmer water temperatures in Big Jacks Creek were likely due to historical summerlong livestock grazing, which drastically reduced riparian shading.     

Genome partitioning of genetic variation for complex traits using common SNPs

We estimate and partition genetic variation for height, body mass index (BMI), von Willebrand factor and QT interval (QTi) using 586,898 SNPs genotyped on 11,586 unrelated individuals. We estimate that ～45%, ～17%, ～25% and ～21% of the variance in height, BMI, von Willebrand factor and QTi, respectively, can be explained by all autosomal SNPs and a further ～0.5-1% can be explained by X chromosome SNPs. We show that the variance explained by each chromosome is proportional to its length, and that SNPs in or near genes explain more variation than SNPs between genes. We propose a new approach to estimate variation due to cryptic relatedness and population stratification. Our results provide further evidence that a substantial proportion of heritability is captured by common SNPs, that height, BMI and QTi are highly polygenic traits, and that the additive variation explained by a part of the genome is approximately proportional to the total length of DNA contained within genes therein.     

The value of data

Data citation and the derivation of semantic constructs directly from datasets have now both found their place in scientific communication. The social challenge facing us is to maintain the value of traditional narrative publications and their relationship to the datasets they report upon while at the same time developing appropriate metrics for citation of data and data constructs.     

Respiration characteristics differ among cheatgrass ( Bromus tectorum L.) populations

Cheatgrass ( Bromus tectorum L.) is a dominant weed that has increased the frequency of wildfire in the Great Basin since its introduction about 100 yr ago. This study examines characteristics of respiratory metabolism in several different populations. Seeds from 6 populations were germinated and metabolic heat rates (q) and dark respiration rates (R co2 ) of all seedlings were measured calorimetrically at 15° and 25° C or (for 3 populations) at 5° intervals from 5° to 35° C. Growth rates, substrate carbon conversion efficiencies, and Arrhenius temperature coefficients were calculated from the data. Results show that cheatgrass metabolism is most efficient at temperatures near 0° C; at temperatures above 20-25° C, efficiency goes to zero. Cheatgrass populations differ in their temperature dependencies of substrate carbon conversion efficiency and predicted growth rate. Measurements of respiratory heat and CO 2 rates as functions of temperature can be made relatively quickly and used to aid understanding of metabolic adaptation by invasive and native species to the environment.     

Winter nutritive content of black sagebrush ( Artemisia nova ) grown in a uniform garden

Winter crude protein content, in vitro digestibility, and productivity were determined for seven accessions of black sagebrush ( Artemisia nova ) grown in a uniform garden. No significant differences were detected among the accessions for any of these attributes. Mean crude protein was 6.8% of dry matter. Accessional range was from 5.8% to 7.3%. Mean in vitro digestion was 54.8% of dry matter; accessional range, 51.9% to 57.2%. Mean current year's growth (a measurement of productivity) was 4.3 cm; accessional range, from 3.7 to 5.1 cm. In comparison to other winter forages, black sagebrush ranks high for winter levels of crude protein and very high in winter digestible dry matter but low in productivity.