Iris pigmentation as a quantitative trait: variation in populations of European, East Asian and South Asian ancestry and association with candidate gene polymorphisms

In this study, we present a new quantitative method to measure iris colour based on high‐resolution photographs. We applied this method to analyse iris colour variation in a sample of individuals of East Asian, European and South Asian ancestry. We show that measuring iris colour using the coordinates of the CIELAB colour space uncovers a significant amount of variation that is not captured using conventional categorical classifications, such as ‘brown’, ‘blue’ or ‘green’. We tested the association of a selected panel of polymorphisms with iris colour in each population group. Six markers showed significant associations with iris colour in the European sample, three in the South Asian sample and two in the East Asian sample. We also observed that the marker HERC 2 rs12913832, which is the main determinant of ‘blue’ versus ‘brown’ iris colour in European populations, is also significantly associated with central heterochromia in the European sample

Vitamin D Status of Older Adults of Diverse Ancestry Living in the Greater Toronto Area

Background: Physiological and lifestyle factors put older adults at an increased risk of vitamin D insufficiency and resulting negative health outcomes. Here we explore the vitamin D status in a sample of community dwelling older adults of diverse ancestry living in the Greater Toronto area (GTA). Methods: Two hundred and twenty-four (224) adults over 60 years of age were recruited from the Square One Older Adult Centre, in Mississauga, Ontario. Circulating 25-hydroxyvitamin D (25(OH)D) concentrations were measured from dried blood spot cards. Dietary and supplemental intakes of vitamin D were assessed via questionnaires. Skin pigmentation was assessed quantitatively by measuring melanin levels using a reflectometer. Results: The mean 25(OH)D concentration in the total sample was 82.4 nmol/L. There were no statistically significant differences in serum 25(OH)D concentrations, supplemental or dietary vitamin D intakes between the three major ancestral groups (East Asians, Europeans and South Asians). Females had significantly higher 25(OH)D concentrations than males (84.5 nmol/L vs. 72.2 nmol/L, p = 0.012). The proportion of participants with 25(OH)D concentrations below 50 nmol/L and 75 nmol/L were 12.1%, and 38.8%, respectively. The mean daily supplemental intake of vitamin D was 917 IU/day. Vitamin D intake from supplements was the major factor determining 25(OH)D concentrations (p \u3c 0.001). Conclusions: Mean concentration of 25(OH)D in a sample of older adults of diverse ancestry living in the GTA exceeded 80 nmol/L, and there were no significant differences in 25(OH)D levels between ancestral groups. These results sharply contrast with our recent study focused on young adults of diverse ancestry living in the same geographic area, in which we found substantially lower 25(OH)D concentrations (mean 39.5 nmol/L), low supplemental vitamin D intake (114 IU/day), and significant differences in 25(OH)D levels between ancestral groups. High daily intake of supplemental vitamin D in this sample of older adults likely accounts for such disparate findings with respect to the young adult sample

Tropical Pacific SST influence on seasonal streamflow variability in Ecuador

This study presents a basin wide assessment about the spatio-temporal variability of streamflows in Ecuador for the period 1979-2015. The influence of the tropical Pacific sea surface temperature (SST) on stremaflow variariability from February to April (FMA) period, as the months showing maximum stramflow for the wet season in Ecuador, and from the June to August (JJA), correspondign to the dry season, was analysed. First, a long-term trend analysis was carried out by applying the Sen's slope estimator and the Mann-Kendall test to monthly streamflow data from 45 gaging stations located in different basins across Ecuador. While the coastal region showed the highest generalized positive trends from July to January, the results for the Pacific Andean area suggested a strengthening of the seasonality, presenting an overall increase in the streamflow for all months except August, September and October, which showed negative trends. Second, a singular-value decomposition (SVD) was applied in order to find the main coupled variability patterns between the FMA streamflow and the quasi-coetaneous SST (December-February, DJF) and between the JJA streamflow and the coetaneous SST. The results revealed two main coupled modes for DJF SST/FMA streamflow, the first associated with the canonical El Ni\~no and the second with El Ni\~no Modoki. The latter exerted a major influence on FMA streamflow over most of Ecuador. For JJA streamflow, however, the pattern associated with the traditional El Ni\~no was even more relevant. These results establish the foundations for streamflow modelling in Ecuador based on the Pacific SST, showing the strong response of the streamflows to different types of El Ni\~no event

Projected changes in the Iberian Peninsula drought characteristics

High spatial resolution drought projections for the Iberian Peninsula (IP) have been examined in terms of duration, frequency, and severity of drought events. For this end, a set of regional climate simulations was completed using the Weather Research and Forecasting (WRF) model driven by two global climate models (GCMs), the CCSM4 and the MPI-ESM-LR, for a near (2021-2050) and a far (2071-2100) future, and under two representative concentration pathway (RCP) scenarios (RCP4.5 and RCP8.5). Projected changes for these simulations were analyzed using two drought indices, the Standardized Precipitation Evapotranspiration Index (SPEI) and the Standardized Precipitation Index (SPI), considering different timescales (3- and 12-months). The results showed that the IP is very likely to undergo longer and more severe drought events. Substantial changes in drought parameters (i.e., frequency, duration, and severity) were projected by both indices and at both time scales in most of the IP. These changes are particularly strong by the end of the century under RCP8.5. Meanwhile, the intensification of drought conditions is expected to be more moderate for the near future. However, the results also indicated key differences between indices. Projected drought conditions by using the SPEI showed more severe increases in drought events than those from SPI by the end of the century and, especially, for the high-emission scenario. The most extreme conditions were projected in terms of the duration of the events. Specifically, results from the 12-month SPEI analysis suggested a significant risk of megadrought events (drought events longer than 15 years) in many areas of IP by the end of the century under RCP8.5

JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis

Motivation: Rapid advances in genotyping and genome-wide association studies have enabled the discovery of many new genotype–phenotype associations at the resolution of individual markers. However, these associations explain only a small proportion of theoretically estimated heritability of most diseases. In this work, we propose an integrative mixture model called JBASE: joint Bayesian analysis of subphenotypes and epistasis. JBASE explores two major reasons of missing heritability: interactions between genetic variants, a phenomenon known as epistasis and phenotypic heterogeneity, addressed via subphenotyping. Results: Our extensive simulations in a wide range of scenarios repeatedly demonstrate that JBASE can identify true underlying subphenotypes, including their associated variants and their interactions, with high precision. In the presence of phenotypic heterogeneity, JBASE has higher Power and lower Type 1 Error than five state-of-the-art approaches. We applied our method to a sample of individuals from Mexico with Type 2 diabetes and discovered two novel epistatic modules, including two loci each, that define two subphenotypes characterized by differences in body mass index and waist-to-hip ratio. We successfully replicated these subphenotypes and epistatic modules in an independent dataset from Mexico genotyped with a different platform. Availability and implementation: JBASE is implemented in Cþþ, supported on Linux and is available at http://www.cs.toronto.edu/goldenberg/JBASE/jbase.tar.gz. The genotype data underlying this study are available upon approval by the ethics review board of the Medical Centre Siglo XXI.No sponso

Fertilización con macronutrientes en manzano: producción y contenido foliar de micronutrientes

El manzano se cultiva en 23 estados de la república mexicana en una superficie de 61,292 ha con un potencial de producción de 630 mil 500 toneladas, las principales entidades de producción de manzana en orden de importancia: Chihuahua 73.3%, Durango 10.2%, Coahuila 5.9% y Puebla 4.4% (SAGARPA, 2011). Para conocer las necesidades de la planta y evitar la contaminación ambiental, el manejo de la fertilización requiere que la demanda de la planta sea entendida y que los métodos de aportación sean eficientes. El objetivo fue obtener la superficie de respuesta para macronutrientes sobre producción y contenido óptimo de micronutrientes. El estudio se realizó en arboles de manzano ‘Golden Delicious’/ MM111 plantados en 1990, se utilizó una estructura Taguchi L25, con cinco factores (N, P, K, Ca y Mg) y cuatro niveles por cada factor con 5 repeticiones, distribuidos en seis aplicaciones desde pre-brotación hasta pre cosecha. Se determinó contenido foliar de Fe, Mn, Zn, Cu y Ni, y producción. Se logró obtener una producción media estimada de 52 T ha-1 con 73N-49P-20K-138Ca-18Mg. Los macronutrientes que requieren incremento en su dosis para ubicar a los micronutrientes en el rango suficiente son N, K y Mg; mientras que se deben disminuir P y Ca. El orden en que se deben atender los micronutrientes son Cu, Mn, Zn, Fe y Ni, respectivamente. Ni fue el único micronutriente que mostró tendencias en su respuesta en función de los niveles de macronutrientes utilizados

Influence of climatic variables on crown condition in pine forests of Northern Spain

Producción CientíficaThe aim of this study was to find relationships between crown condition and some climatic parameters to identify which are those having a main influence on crown condition, and how this influence is shown in the tree (crown transparency), and to contribute to the understanding of how these parameters will affect under future climate change scenarios

Candida albicans Pma1p Contributes to Growth, pH Homeostasis, and Hyphal Formation

Candida albicans occupies diverse ecological niches within the host and must tolerate a wide range of environmental pH. The plasma membrane H+-ATPase Pma1p is the major regulator of cytosolic pH in fungi. Pma1p extrudes protons from the cytosol to maintain neutral-to-alkaline pH and is a potential drug target due to its essentiality and fungal specificity. We characterized mutants in which one allele of PMA1 has been deleted and the other truncated by 18–38 amino acids. Increasing C-terminal truncation caused corresponding decreases in plasma membrane ATPase-specific activity and cytosolic pH. Pma1p is regulated by glucose: glucose rapidly activates the ATPase, causing a sharp increase in cytosolic pH. Increasing Pma1p truncation severely impaired this glucose response. Pma1p truncation also altered cation responses, disrupted vacuolar morphology and pH, and reduced filamentation competence. Early studies of cytosolic pH and filamentation have described a rapid, transient alkalinization of the cytosol preceding germ tube formation; Pma1p has been proposed as a regulator of this process. We find Pma1p plays a role in the establishment of cell polarity, and distribution of Pma1p is non-homogenous in emerging hyphae. These findings suggest a role of PMA1 in cytosolic alkalinization and in the specialized form of polarized growth that is filamentation

The use of multiple displacement amplification to amplify complex DNA libraries

Complex libraries for genomic DNA and cDNA sequencing analyses are typically amplified using bacterial propagation. To reduce biases, large numbers of colonies are plated and scraped from solid-surface agar. This process is time consuming, tedious and limits scaling up. At the same time, multiple displacement amplification (MDA) has been recently developed as a method for in vitro amplification of DNA. However, MDA has no selection function for the removal of ligation multimers. We developed a novel method of briefly introducing ligation reactions into bacteria to select single insert DNA clones followed by MDA to amplify. We applied these methods to a Gene Identification Signatures with Paired-End diTags (GIS-PET) library, which is a complex transcriptome library created by pairing short tags from the 5′ and 3′ ends of cDNA fragments together, and demonstrated that this selection and amplification strategy is unbiased and efficient