Alternative methods for H1 simulations in genome-wide association studies.

OBJECTIVE: Assessing the statistical power to detect susceptibility variants plays a critical role in genome-wide association (GWA) studies both from the prospective and retrospective point of view. Power is empirically estimated by simulating phenotypes under a disease model H1. For this purpose, the gold standard consists in simulating genotypes given the phenotypes (e.g. Hapgen). We introduce here an alternative approach for simulating phenotypes under H1 that does not require generating new genotypes for each simulation. METHODS: In order to simulate phenotypes with a fixed total number of cases and under a given disease model, we suggest 3 algorithms: (1) a simple rejection algorithm; (2) a numerical Markov chain Monte-Carlo (MCMC) approach, and (3) an exact and efficient backward sampling algorithm. In our study, we validated the 3 algorithms both on a simulated dataset and by comparing them with Hapgen on a more realistic dataset. For an application, we then conducted a simulation study on a 1000 Genomes Project dataset consisting of 629 individuals (314 cases) and 8,048 SNPs from chromosome X. We arbitrarily defined an additive disease model with two susceptibility SNPs and an epistatic effect. RESULTS: The 3 algorithms are consistent, but backward sampling is dramatically faster than the other two. Our approach also gives consistent results with Hapgen. Using our application data, we showed that our limited design requires a biological a priori to limit the investigated region. We also proved that epistatic effects can play a significant role even when simple marker statistics (e.g. trend) are used. We finally showed that the overall performance of a GWA study strongly depends on the prevalence of the disease: the larger the prevalence, the better the power. CONCLUSIONS: Our approach is a valid alternative to Hapgen-type methods; it is not only dramatically faster but has 2 main advantages: (1) there is no need for sophisticated genotype models (e.g. haplotype frequencies, or recombination rates), and (2) the choice of the disease model is completely unconstrained (number of SNPs involved, gene-environment interactions, hybrid genetic models, etc.). Our 3 algorithms are available in an R package called 'waffect' ('double-u affect', for weighted affectations).

A POLD3/BLM dependent pathway handles DSBs in transcribed chromatin upon excessive RNA:DNA hybrid accumulation.

Transcriptionally active loci are particularly prone to breakage and mounting evidence suggests that DNA Double-Strand Breaks arising in active genes are handled by a dedicated repair pathway, Transcription-Coupled DSB Repair (TC-DSBR), that entails R-loop accumulation and dissolution. Here, we uncover a function for the Bloom RecQ DNA helicase (BLM) in TC-DSBR in human cells. BLM is recruited in a transcription dependent-manner at DSBs where it fosters resection, RAD51 binding and accurate Homologous Recombination repair. However, in an R-loop dissolution-deficient background, we find that BLM promotes cell death. We report that upon excessive RNA:DNA hybrid accumulation, DNA synthesis is enhanced at DSBs, in a manner that depends on BLM and POLD3. Altogether our work unveils a role for BLM at DSBs in active chromatin, and highlights the toxic potential of RNA:DNA hybrids that accumulate at transcription-associated DSBs.

Enhancing physico-mechanical and antibacterial properties of natural rubber using synthesized Ag-SiO2 nanoparticles.

The incorporation of the prepared Ag-SiO2 core-shell particles in natural rubber matrix was investigated on antibacterial and mechanical properties of resulting composites. Significant antibacterial effect against S. aureus (Gram positive) and P. aeruginosa (Gram negative) was observed and achieved inhibition growth up to 85 and 90%, respectively, after 24 h depending on the amount of Ag-SiO2 core-shell. It was found that SiO2 acted as crosslinking agent and controlling the amount of silver release. UV-vis spectra and TEM, XRD showed Ag-SiO2 core-shell particles formation. SEM, FTIR, XRD and mechanical analysis showed uniform distribution of Ag-SiO2 core-shell into rubber matrix with enhanced tensile strength.

Synthesis and characterization of nanosilver-silicone hydrogel composites for inhibition of bacteria growth.

PURPOSE: Nanosilver-silicone hydrogel (NAgSiH) composites for contact lenses were synthesized to asses the antimicrobial effects. METHODS: Silicone hydrogel (SiH) films were synthesized followed by impregnation in silver nitrate solutions (10, 20, 30, 40, 60, 80ppm) and in-situ chemical reduction of silver ions using sodium borohydride (NaBH4). The silver nano particles (AgNPS) were identified by UV-vis absorption spectroscopy, Energy-dispersive X-ray spectroscopy (EDX) mapping and EDX spectrum. Physico-mechanical and chemical properties of NAgSIH films were studied. The antimicrobial effect of the hydrogels against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus aureus was evaluated. The numbers of viable bacterial cells on NAgSiH surface or in solution compared to control SiH were examined. RESULTS: The NAgSiH films were successfully synthesized. FTIR results indicated that AgNPS had no effect on the bulk structure of the prepared SiH films. From TGA analysis, NAgSiH(R80) and SiH(R0) films had the same maximum decomposition temperature (404°C). UV-vis absorption spectroscopy and EDX mapping and spectrum emphasized that AgNPS were in spherical shape. The maximum absorption wavelength of NAgSiH films were around 400nm. The light transmittance decreased as the concentration of AgNPS increased, but still greater than 90% at wavelength around 555nm. The Young's modulus increased gradually from 1.06MPa of SiH(R0) to highest value 1.38MPa of NAgSiH(R80). AgNPS incorporated into SiH films reduced the bacterial cell growth and prevented colonization. Groups NAgSiH(R60,R80) demonstrated an excellent reduction in bacterial viability in solution and on the SiH surface. CONCLUSIONS: NAgSiH composites were successfully synthesized and possessed an excellent antimicrobial effects.

Diversity of O-linked glycosylation patterns between species. Characterization of 25 carbohydrate chains from oviducal mucins of Rana ridibunda.

Amphibia egg jelly coats are formed by components secreted along the oviduct. These secretion products overlay the oocytes as they pass along the different oviducal portions. Mucin type glycoproteins are the major constituents of the egg jelly coats. In this study, the O-linked carbohydrate chains of the jelly coats surrounding the eggs of Rana ridibunda were released by alkaline borohydride treatment. Fractionation of the mixture of O-linked oligosaccharide-alditols was achieved by a combination of chromatographic techniques including gel-permeation chromatography, ion-exchange chromatography and high-performance liquid chromatography using an amino-bonded silica column. The primary structures of these O-glycans were determined by one-dimensional and two-dimensional 1H-NMR spectroscopy and matrix-assisted laser-desorption-ionization-time-of flight mass spectrometry. 25 oligosaccharide structures, possessing a core consisting of Gal(beta1-3)GalNAc-ol with or without branching through a GlcNAc residue linked (beta1-6) to the GalNAc residue (core type 2 or core type 1, respectively) are described. The most representative antennae are: HSO3(6)[Fuc(alpha1-3)]GlcNAc; Gal(beta1-2)Gal; Gal(beta1-2)Gal(alpha1-3)[Fuc(alpha1-2)]Gal; GlcA(beta1-3)-Gal(beta1-3)[Fuc(alpha1-2)]Gal; GalNAc(alpha1-4)Gal(beta1-4)Gal; Gal(beta1-3)GalNAc(alpha1-4)Gal(beta1-4)Gal and GlcA(beta1-3)Gal(beta1-3)GalNAc. These results confirm the species-specific O-glycosylation of Amphibia oviducal mucins. The significance of this observation should be linked to a symbiotic role of carbohydrates involved in host-parasite interactions.