Hundreds of variants clustered in genomic loci and biological pathways affect human height.

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

A Neanderthal Lower Incisor from Cova del Gegant (Sitges, Barcelona, Spain)

Cova del Gegant is located near the city of Sitges (Barcelona, Spain). The cave is a small karst system which contains Upper Pleistocene archaeological and paleontological material (DauRa et al., 2005). The site was first excavated in 1954 and then in 1972 and 1974- (Viñas, 1972; Viñas & Villalta, 1975) and in 1985 and 1989 (maRtínez et al., 1985; moRa, 1988; maRtínez et al., 1990). Finally, in 2007, Grup de Recerca del Quaternari has restarted the archaeological research at Cova del Gegant (DauRa, 2008; DauRa et al., 2010). A human mandible was recovered during the first field season in 1954 and was recently published by DauRa et al. (2005). In the present study, we describe a new human tooth (left I2) that appeared, like the mandible, in a revision of the faunal material recovered from the site in 1974-1975. The specimen preserves the entire crown and the cervical two thirds of the root (Figure 1). The lack of the root apex makes it difficult to determine if the tooth was fully developed at the time of death. However, CT analysis reveals a pulp cavity that could be still open, suggesting root formation was incomplete. The specimen shows only slight dental wear corresponding to stage 2 of Molnar (1971 en Hillson, 1996). Morphologically, the crown shows slight shovelling and a lingual tubercle and appears similar to Neandertal incisors. Standard crown measurements (buccolingual diameter=7.7 mm; mesiodistal diameter= 7.3 mm) (Figure 2) suggest a fairly large tooth, particularly in the BL dimension, again resembling Neandertals in this regard. Discriminant analysis classified the Gegant incisor as Neandertal with a 99.8% posterior probability (Table 2). Association of this tooth with the previously described mandible is considered unlikely given the different ages at death estimated for each. Thus, there appear to be two individuals preserved in the sediments of the Gegant cave, one adult and one subadult (around 8-10 years old).

Le principe de transparence dans le canton de Vaud : évaluation des chapitres I, III, IV et VI de la Loi du 24 septembre 2002 sur l'information

La Loi vaudoise sur l'information (LInfo), en vigueur depuis le 1er septembre 2003, contient les bases légales relatives à l'information communiquée par l'Etat aux médias et au public. A l'image de plus en plus de législations en la matière, elle consacre le principe de l'information sur demande, selon lequel tout individu a désormais le droit de consulter des documents officiels et d'obtenir de l'information de la part des autorités sans devoir motiver sa demande. La présente évaluation s'intéresse à comprendre comment ce principe de transparence est défini dans cette loi, quelle est son application par l'administration, dans quelle mesure il est utilisé par les citoyens et enfin quels sont ses effets six ans après son entrée en vigueur. Das waadtländische Informationsgesetz (LInfo), in Kraft seit dem 1. September 2003, liefert die rechtliche Grundlage betreffend Informationen die durch den Kanton an die Medien und die Öffentlichkeit kommuniziert werden. Als Grundlage dient dazu das Prinzip um Erhalt von Informationen, nach welchem jede Person das Recht hat offizielle Dokumente einzusehen und Informationen von den Behörden zu erhalten ohne die Anfrage begründen zu müssen. Der vorliegende Beitrag hinterfragt wie dieses Transparenzprinzip im Gesetz definiert ist und wie es durch die Verwaltung angewendet wird. Weiter wird untersucht in welchem Ausmass es durch die Bürger und Bürgerinnen angewendet wird und was das Gesetz sechs Jahre nach seinem Inkrafttreten bewirkt hat.

Common variants near MC4R are associated with fat mass, weight and risk of obesity.

To identify common variants influencing body mass index (BMI), we analyzed genome-wide association data from 16,876 individuals of European descent. After previously reported variants in FTO, the strongest association signal (rs17782313, P = 2.9 x 10(-6)) mapped 188 kb downstream of MC4R (melanocortin-4 receptor), mutations of which are the leading cause of monogenic severe childhood-onset obesity. We confirmed the BMI association in 60,352 adults (per-allele effect = 0.05 Z-score units; P = 2.8 x 10(-15)) and 5,988 children aged 7-11 (0.13 Z-score units; P = 1.5 x 10(-8)). In case-control analyses (n = 10,583), the odds for severe childhood obesity reached 1.30 (P = 8.0 x 10(-11)). Furthermore, we observed overtransmission of the risk allele to obese offspring in 660 families (P (pedigree disequilibrium test average; PDT-avg) = 2.4 x 10(-4)). The SNP location and patterns of phenotypic associations are consistent with effects mediated through altered MC4R function. Our findings establish that common variants near MC4R influence fat mass, weight and obesity risk at the population level and reinforce the need for large-scale data integration to identify variants influencing continuous biomedical traits.

Histopathological evaluation of root canal filling materials for primary teeth

This study aimed to assess the response of apical and periapical tissues of dogs¿ teeth after root canal filling with different materials. Forty roots from dogs¿ premolars were prepared biomechanically and assigned to 4 groups filled with: Group I: commercial calcium hydroxide and polyethylene glycol-based paste (Calen®) thickened with zinc oxide; Group II: paste composed of iodoform, Rifocort® and camphorated amonochlorophenol; Group III: zinc oxide-eugenol cement; Group IV: sterile saline. After 30 days, the samples were subjected to histological processing. The histopathological findings revealed that in Groups I and IV the apical and periapical regions exhibited normal appearance, with large number of fibers and cells and no resorption of mineralized tissues. In Group II, mild inflammatory infiltrate and mild edema were observed, with discrete fibrogenesis and bone resorption. Group III showed altered periapical region and thickened periodontal ligament with presence of inflammatory cells and edema. It may be concluded that the Calen paste thickened with zinc oxide yielded the best tissue response, being the most indicated material for root canal filling of primary teeth with pulp vitality.

Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations.

Chronic kidney disease (CKD), impairment of kidney function, is a serious public health problem, and the assessment of genetic factors influencing kidney function has substantial clinical relevance. Here, we report a meta-analysis of genome-wide association studies for kidney function-related traits, including 71,149 east Asian individuals from 18 studies in 11 population-, hospital- or family-based cohorts, conducted as part of the Asian Genetic Epidemiology Network (AGEN). Our meta-analysis identified 17 loci newly associated with kidney function-related traits, including the concentrations of blood urea nitrogen, uric acid and serum creatinine and estimated glomerular filtration rate based on serum creatinine levels (eGFRcrea) (P < 5.0 × 10(-8)). We further examined these loci with in silico replication in individuals of European ancestry from the KidneyGen, CKDGen and GUGC consortia, including a combined total of ∼110,347 individuals. We identify pleiotropic associations among these loci with kidney function-related traits and risk of CKD. These findings provide new insights into the genetics of kidney function.

08021-012 Sands Timber Final Report

Sands Timber Lake is a 60 acre man made impoundment near Blockton, Iowa. The lake is the centerpiece of a 235 acre park, which is owned and managed by the Taylor County Conservation Board. The park is equipped with modern campsites, hiking trails, picnic areas, and a playground. Bordering the western shoreline of the lake is a beautiful hardwood timber which inspired the parks name. Sands Timber Lake has a 4,100 acre drainage area comprised of timber, grassland, and row crop. The lake is fed by four large classic gullies which branch off into many smaller gullies dissecting the drainage area. Since construction in 1993, Sands Timber Lake has been an extremely poor fishery. In 2006 Sands Timber Lake was added to the EPA’s 303d list of impaired water bodies. Turbid water was identified as the primary stressor. In 2007 a bathometric map was made which depicts lake-bottom contours and elevations which, when compared to the original survey of the area, revealed an alarming amount of siltation. What was once a twenty-three foot deep lake in 1994 has now been reduced to a mere fourteen feet. In addition to depth being lost, the lake’s surface has been reduced by nearly ten acres, destroying vital fish habitats. Local interest in preserving and enhancing the lake has led to the completion of a thorough watershed assessment and treatment plan. Included in the plan are several elements, the first being upland treatment. Locals are insistent that if conservation is not implemented in the watershed the lake will continue to degrade and park usage will continue to decline.

Evaluation of clinician-operated sonography and fine-needle aspiration in the assessment of salivary gland tumours.

OBJECTIVES: To evaluate the combination of ultrasound (US) + fine-needle aspiration (FNA) in the assessment of salivary gland tumours in the hands of the otolaryngologist. DESIGN: A retrospective review of case notes was performed. SETTING: Two university teaching hospitals in Switzerland. PARTICIPANTS: One hundred and three patients with a total of 106 focal masses of the salivary glands were included. Clinician-operated US + FNA were the first line of investigation for these lesions. All patients underwent surgical excision of the lesion, which allowed for confirmation of diagnosis by histopathology in 104 lesions and by laboratory testing in two lesions. MAIN OUTCOME MEASURES: Primary--diagnostic accuracy in identifying true salivary gland neoplasms and detecting malignancy. Secondary--predicting an approximate and specific diagnosis in these tumours. RESULTS: The combination of US + FNA achieved a diagnostic accuracy of 99% in identifying and differentiating true salivary gland neoplasms from tumour-like lesions. In detecting malignancy, this combination permitted an accuracy of 98%. An approximate diagnosis was possible in 89%, and a specific diagnosis in 69% of our patients. CONCLUSIONS: Due to economic factors and a high diagnostic accuracy, the combination of US + FNA represents the investigation method of choice for most salivary gland tumours. We suggest that the otolaryngologist be employed in carrying out these procedures, as is already the rule in other medical specialties, while computed tomography and magnetic resonance imaging should be reserved to those few lesions, which cannot be delineated completely by sonography.

Study and modeling of the desintegration kinetics of coated paper

The disintegration of recovered paper is the first operation in the preparation of recycled pulp. It is known that the defibering process follows a first order kinetics from which it is possible to obtain the disintegration kinetic constant (KD) by means of different ways. The disintegration constant can be obtained from the Somerville index results (%lsv and from the dissipated energy per volume unit (Ss). The %slv is related to the quantity of non-defibrated paper, as a measure of the non-disintegrated fiber residual (percentage of flakes), which is expressed in disintegration time units. In this work, disintegration kinetics from recycled coated paper has been evaluated, working at 20 revise rotor speed and for different fiber consistency (6, 8, 10, 12 and 14%). The results showed that the values of experimental disintegration kinetic constant, Ko, through the analysis of Somerville index, as function of time. Increased, the disintegration time was drastically reduced. The calculation of the disintegration kinetic constant (modelled Ko), extracted from the Rayleigh’s dissipation function, showed a good correlation with the experimental values using the evolution of the Somerville index or with the dissipated energy

Study and modeling of the desintegration kinetics of coated paper

The disintegration of recovered paper is the first operation in the preparation of recycled pulp. It is known that the defibering process follows a first order kinetics from which it is possible to obtain the disintegration kinetic constant (KD) by means of different ways. The disintegration constant can be obtained from the Somerville index results (%lsv and from the dissipated energy per volume unit (Ss). The %slv is related to the quantity of non-defibrated paper, as a measure of the non-disintegrated fiber residual (percentage of flakes), which is expressed in disintegration time units. In this work, disintegration kinetics from recycled coated paper has been evaluated, working at 20 revise rotor speed and for different fiber consistency (6, 8, 10, 12 and 14%). The results showed that the values of experimental disintegration kinetic constant, Ko, through the analysis of Somerville index, as function of time. Increased, the disintegration time was drastically reduced. The calculation of the disintegration kinetic constant (modelled Ko), extracted from the Rayleigh’s dissipation function, showed a good correlation with the experimental values using the evolution of the Somerville index or with the dissipated energy

Potassium permanganate effects in postharvest conservation of the papaya cultivar Sunrise Golden

The objective of this work was to evaluate the effects of KMnO4 on the extension of postharvest life of 'Sunrise Golden' papaya, stored under modified atmosphere and refrigeration. Fruit with up to 10% yellow peel were harvested in a commercial orchard in Linhares, state of Espírito Santo, Brazil. Sets of three fruit (unit mass of 289.9±18.5 g) were wrapped in low-density polyethylene films (28 ¼m thick) containing sachets of KMnO4 at 0, 0.5, 1, 1.5, and 2 g per bag. The bags were sealed and stored at 10.4±0.9°C and 90±5% relative humidity for 25 days. After this period, the fruit were removed from the bags and maintained at 21±0.8°C and 90±5% relative humidity until complete ripening. Four days after bag sealing, CO2 concentration stabilized in all treatments, and was higher in bags without KMnO4. In all treatments, fruit reached the climacteric respiratory peak on the third day after bag removal, coinciding with peel color index of 3.5. Increasing the KMnO4 dose reduced the losses in fruit fresh matter, consistency and pulp electrolyte leakage. Potassium permanganate was effective in maintaining the fruit at the pre-climacteric stage during the 25-day storage, and did not interfere with normal ripening after bag removal.

Responses and adaptations of collembolan communities (Hexapoda: Collembola) to flooding and hypoxic conditions

Standard ecological methods (pitfall traps, trunk eclectors and soil cores) were used to evaluate collembolan community responses to different flooding intensities. Three sites of a floodplain habitat near Mainz, Germany, with different flooding regimes were investigated. The structures of collembolan communities are markedly different depending on flooding intensity. Sites more affected by flooding are dominated by hygrophilic and hygrotolerant species, whereas the hardwood floodplain is dominated by mesophilic species. The survival strategies of the hygrophilic and hygrotolerant species include egg diapause and passive drifting. The physiological adaptations to hypoxic conditions of several collembolan species were analyzed using a microcalorimeter. The activities were tested under normoxic and hypoxic/anoxic conditions as well as during post-hypoxic recovery. Lactate was increased after hypoxic intervals in the species studied, suggesting that, in addition to a massive decrease in metabolic rate, a modest glycolytic activity may be involved in the tolerance to hypoxia.

Common genetic loci influencing plasma homocysteine concentrations and their effect on risk of coronary artery disease.

BACKGROUND: The strong observational association between total homocysteine (tHcy) concentrations and risk of coronary artery disease (CAD) and the null associations in the homocysteine-lowering trials have prompted the need to identify genetic variants associated with homocysteine concentrations and risk of CAD. OBJECTIVE: We tested whether common genetic polymorphisms associated with variation in tHcy are also associated with CAD. DESIGN: We conducted a meta-analysis of genome-wide association studies (GWAS) on tHcy concentrations in 44,147 individuals of European descent. Polymorphisms associated with tHcy (P < 10(-8)) were tested for association with CAD in 31,400 cases and 92,927 controls. RESULTS: Common variants at 13 loci, explaining 5.9% of the variation in tHcy, were associated with tHcy concentrations, including 6 novel loci in or near MMACHC (2.1 Ã- 10(-9)), SLC17A3 (1.0 Ã- 10(-8)), GTPB10 (1.7 Ã- 10(-8)), CUBN (7.5 Ã- 10(-10)), HNF1A (1.2 Ã- 10(-12)), and FUT2 (6.6 Ã- 10(-9)), and variants previously reported at or near the MTHFR, MTR, CPS1, MUT, NOX4, DPEP1, and CBS genes. Individuals within the highest 10% of the genotype risk score (GRS) had 3-μmol/L higher mean tHcy concentrations than did those within the lowest 10% of the GRS (P = 1 Ã- 10(-36)). The GRS was not associated with risk of CAD (OR: 1.01; 95% CI: 0.98, 1.04; P = 0.49). CONCLUSIONS: We identified several novel loci that influence plasma tHcy concentrations. Overall, common genetic variants that influence plasma tHcy concentrations are not associated with risk of CAD in white populations, which further refutes the causal relevance of moderately elevated tHcy concentrations and tHcy-related pathways for CAD.

Sensitivity of Spring Phenology to Warming Across Temporal and Spatial Climate Gradients in Two Independent Databases

Disparate ecological datasets are often organized into databases post hoc and then analyzed and interpreted in ways that may diverge from the purposes of the original data collections. Few studies, however, have attempted to quantify how biases inherent in these data (for example, species richness, replication, climate) affect their suitability for addressing broad scientific questions, especially in under-represented systems (for example, deserts, tropical forests) and wild communities. Here, we quantitatively compare the sensitivity of species first flowering and leafing dates to spring warmth in two phenological databases from the Northern Hemisphere. One-PEP725-has high replication within and across sites, but has low species diversity and spans a limited climate gradient. The other-NECTAR-includes many more species and a wider range of climates, but has fewer sites and low replication of species across sites. PEP725, despite low species diversity and relatively low seasonality, accurately captures the magnitude and seasonality of warming responses at climatically similar NECTAR sites, with most species showing earlier phenological events in response to warming. In NECTAR, the prevalence of temperature responders significantly declines with increasing mean annual temperature, a pattern that cannot be detected across the limited climate gradient spanned by the PEP725 flowering and leafing data. Our results showcase broad areas of agreement between the two databases, despite significant differences in species richness and geographic coverage, while also noting areas where including data across broader climate gradients may provide added value. Such comparisons help to identify gaps in our observations and knowledge base that can be addressed by ongoing monitoring and research efforts. Resolving these issues will be critical for improving predictions in understudied and under-sampled systems outside of the temperature seasonal mid-latitudes.