La aplicación de nanoparticulas de SiO2 como pretratamiento disminuye el impacto de la sequía en la performance fisiológica de Prunus mahaleb (Rosaceae)

La aplicación de nanoparticulas de SiO2 como pretratamiento disminuye el impacto de la sequía en la performance fisiológica de Prunus mahaleb (Rosaceae). En este trabajo se estudiaron respuestas fisiológicas de Prunus mahaleb (Mahaleb) a la sequía luego de la aplicación de diferentes concentraciones de nanoparticulas de SiO2 (SNPs) por irrigación como pretratamientos. Se aplicaron 4 concentraciones de SNPs (0, 10, 50 and 100 mg L-1) durante 45 días y, a posteriori, las plantas fueron sujetas a tres regímenes hídricos que incluyeron control (300 mL cada 3 días), estrés hídrico moderado (150 mL cada 3 días) y estrés hídrico severo (sin riego) por 19 días. El intercambio de gases – fotosíntesis, conductancia estomática y transpiración –se redujo menos frente a la sequía en las plantas que recibieron pretratamientos con SNPs. El estado nutricional de las plantas tratadas con SNPs visto por la concentración de N, P y K se mantuvo bajo sequía moderada. Las plantas pretratadas con SNPs mantuvieron el largo de sus raíces y sufrieron menor impacto en su biomasa radical ante sequía. Se concluye que la aplicación de SNPs como pretratamiento podría ser una práctica agronómica para sitios propensos a déficit hídricos en épocas cercanas a la plantación.We studied the physiological responses of Prunus mahaleb (Mahaleb) seedlings to drought stress when previously irrigated (or not) with different concentrations of SiO2 nanoparticles (SNPs). SNPs were applied at four concentrations (0, 10, 50 and 100 mg L-1) for 45 days, and then seedlings were subjected to three watering treatments including low (300 mL water every 3 d), moderate (150 mL water every 3 d) and severe drought stress (no irrigation) for 19 days. Results showed that gas exchange ? photosynthesis, stomatal conductance, and transpiration rate ? were signifcantly less impacted by severe drought stress when seedlings were pretreated with SNPs at high concentrations. Benefcial effects of SNPs pretreatment were evident in the nutritional status of the plants as the concentration of N, P and K, were maintained at similar levels than in well-watered seedlings. Pretreated seedlings were able to maintain the root length and to reduce the impact of severe drought on root dry mass accumulation. Therefore, application of SNPs as pretreatment should be considered as a promising agronomic practice in sites prone to suffer from water defcitFil: Ashkavand, Peyman. Tarbiat Modares University; IránFil: Zarafshar, Mehrdad. Agricultural Research, Education and Extension Organization; IránFil: Tabari, Masoud. Tarbiat Modares University; IránFil: Mirzaie, Javad. University of Ilam; IránFil: Nikpour, Amirreza. Gorgan University; IránFil: Bordbar, Seyed Kazem. Ohio State University; Estados UnidosFil: Struve, Daniel. Department Of Horticulture And Crop Science; Estados UnidosFil: Striker, Gustavo Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentin

Review of the initial validation and characterization of a chicken 3K SNP array.

In 2004 the chicken genome sequence and more than 2.8 million single nucleotide polymorphisms (SNPs) were reported. This information greatly enhanced the ability of poultry scientists to understand chicken biology, especially with respect to identification of quantitative trait loci (QTL) and genes that control simple and complex traits. To validate and address the quality of the reported SNPs, assays for 3072 SNPS were developed and used to genotype 2576 DNAs isolated from commercial and experimental birds. Over 90% of the SNPs were valid based on the criterion used for segregating, and over 88% had a minor allele frequency of 2% or greater. As the East Lansing (EL) and Wageningen University (WAU) reference panels were genotyped, 1933 SNPs were added to the chicken genetic map, which was used in the second chicken genome sequence assembly. It was also discovered that linkage disequilibrium varied considerably between commercial layers and broilers; with the latter having haplotype blocks averaging 10 to 50 kb in size. Finally, it was estimated that commercial lines have lost 70% or more of their genetic diversity, with the majority of allele loss attributable to the limited number of chicken breeds used

Biological networks and epistasis in genome-wide association studies

Over the last few years, technological improvements have made possible the genotyping of hundreds of thousands of SNPs, enabling whole-genome association studies. The first genome-wide association studies have recently been completed to detect causal variant for complex traits. Although increasing evidence suggests that interaction between loci, such as epistasis between two loci, should be considered, most of these studies proceed by considering each SNP independently. One reason for this choice is that looking at all pairs of SNPs increases dramatically the number of tests (approximatively 50 billions of tests for a 300,000 SNPs data set) that faces with computational limitation and strong multiple testing correction.
We proposed to reduce the number of tests by focusing on pairs of SNPs that belong to genes known to interact in some metabolic network. Although some interactions might be missed, these pairs of genes are good candidates for epistasis. Furthermore the use of protein interaction databases (such as the STRING database) may reduce the number of tests by a factor of 5,000.
Results using this approach will be presented on simulated data sets and on public data sets.
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Variant of TYR and Autoimmunity Susceptibility Loci in Generalized Vitiligo.

BACKGROUND Generalized vitiligo is an autoimmune disease characterized by melanocyte loss, which results in patchy depigmentation of skin and hair, and is associated with an elevated risk of other autoimmune diseases. METHODS To identify generalized vitiligo susceptibility loci, we conducted a genomewide association study. We genotyped 579,146 single-nucleotide polymorphisms (SNPs) in 1514 patients with generalized vitiligo who were of European-derived white (CEU) ancestry and compared the genotypes with publicly available control genotypes from 2813 CEU persons. We then tested 50 SNPs in two replication sets, one comprising 677 independent CEU patients and 1106 CEU controls and the other comprising 183 CEU simplex trios with generalized vitiligo and 332 CEU multiplex families. RESULTS We detected significant associations between generalized vitiligo and SNPs at several loci previously associated with other autoimmune diseases. These included genes encoding major-histocompatibility-complex class I molecules (P=9.05×10−23) and class II molecules (P=4.50×10−34), PTPN22 (P=1.31×10−7), LPP (P=1.01×10−11), IL2RA (P=2.78×10−9), UBASH3A (P=1.26×10−9), and C1QTNF6 (P=2.21×10−16). We also detected associations between generalized vitiligo and SNPs in two additional immune-related loci, RERE (P=7.07×10−15) and GZMB (P=3.44×10−8), and in a locus containing TYR (P=1.60×10−18), encoding tyrosinase. CONCLUSIONS We observed associations between generalized vitiligo and markers implicating multiple genes, some associated with other autoimmune diseases and one (TYR) that may mediate target-cell specificity and indicate a mutually exclusive relationship between susceptibility to vitiligo and susceptibility to melanoma

Methodological Issues in Multistage Genome-Wide Association Studies

Because of the high cost of commercial genotyping chip technologies, many investigations have used a two-stage design for genome-wide association studies, using part of the sample for an initial discovery of ``promising'' SNPs at a less stringent significance level and the remainder in a joint analysis of just these SNPs using custom genotyping. Typical cost savings of about 50% are possible with this design to obtain comparable levels of overall type I error and power by using about half the sample for stage I and carrying about 0.1% of SNPs forward to the second stage, the optimal design depending primarily upon the ratio of costs per genotype for stages I and II. However, with the rapidly declining costs of the commercial panels, the generally low observed ORs of current studies, and many studies aiming to test multiple hypotheses and multiple endpoints, many investigators are abandoning the two-stage design in favor of simply genotyping all available subjects using a standard high-density panel. Concern is sometimes raised about the absence of a ``replication'' panel in this approach, as required by some high-profile journals, but it must be appreciated that the two-stage design is not a discovery/replication design but simply a more efficient design for discovery using a joint analysis of the data from both stages. Once a subset of highly-significant associations has been discovered, a truly independent ``exact replication'' study is needed in a similar population of the same promising SNPs using similar methods.Comment: Published in at http://dx.doi.org/10.1214/09-STS288 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

Detecting epistasis via Markov bases

Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specific phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher's exact test. To perform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of SNPs