A quantile-based method for association mapping of quantitative phenotypes: an application to rheumatoid arthritis phenotypes
Genetic association of population-based quantitative trait data has traditionally been analyzed using analysis of variance (ANOVA). However, violations of certain statistical assumptions may lead to false-positive association results. In this study, we have explored model-free alternatives to ANOVA using correlations between allele frequencies in the different quantile intervals of the quantitative trait and the quantile values. We performed genome-wide association scans on anti-cyclic citrullinated peptide and rheumatoid factor-immunoglobulin M, two quantitative traits correlated with rheumatoid arthritis, using the data provided in Genetic Analysis Workshop 16. Both the quantitative traits exhibited significant evidence of association on Chromosome 6, although not in the human leukocyte antigen region which is known to harbor a major gene predisposing to rheumatoid arthritis. We found that while a majority of the significant findings using the asymptotic thresholds of ANOVA was not validated using permutations, a relatively higher proportion of the significant findings using the asymptotic cut-offs of the correlation statistic were validated using permutations.

title: Linkage mapping of a complex trait in the New York population of the GAW14 simulated dataset: a multivariate phenotype approach
abstract: Multivariate phenotypes underlie complex traits. Thus, instead of using the end-point trait, it may be statistically more powerful to use a multivariate phenotype correlated to the end-point trait for detecting linkage. In this study, we develop a reverse regression method to analyze linkage of Kofendrerd Personality Disorder affection status in the New York population of the Genetic Analysis Workshop 14 (GAW14) simulated dataset. When we used the multivariate phenotype, we obtained significant evidence of linkage near four of the six putative loci in at least 25% of the replicates. On the other hand, the linkage analysis based on Kofendrerd Personality Disorder status as a phenotype produced significant findings only near two of the loci and in a smaller proportion of replicates.

title: Integrating sibship data for mapping quantitative trait loci.
abstract: Sibship methods have been shown to be more powerful than traditional sib-pair methods in mapping quantative trait loci. We propose a statistical procedure which integrates data on sibships into a so-called 'contrast function', a natural extension of the classical squared sib-pair trait difference proposed by Haseman & Elston (1972). We also develop a combined mean and contrast function which provides more information on linkage compared to the contrast function. Our method is extended to multiple, epistatically interacting trait loci. Monte-Carlo simulations are included to compare the efficiencies of the proposed procedures with some currently used methods. An application of our proposed method is presented using data on alcohol dependence.

title: A two-stage variable-stringency semiparametric method for mapping quantitative-trait loci with the use of genomewide-scan data on sib pairs.
abstract: Genomewide scans for mapping loci have proved to be extremely powerful and popular. We present a semiparametric method of mapping a quantitative-trait locus (QTL) or QTLs with the use of sib-pair data generated from a two-stage genomic scan. In a two-stage genomic scan, either the entire genome or a large portion of the genome is saturated with low-density markers at the first stage. At the second stage, the intervals that are identified as probable locations of the trait loci, by means of analysis of data from the first stage, are then saturated with higher-density markers. These data are then analyzed for fine mapping of the loci. Our statistical strategy for analysis of data from the first stage is a low-stringency method based on the rank correlation of squared trait-difference values of the sib pairs and the estimated identity-by-descent scores at the marker loci. We suggest the use of a low-stringency method at the first stage, to save on computational time and to avoid missing any marker interval that may contain the trait loci. For analysis of data from the second stage, we have developed a high-stringency nonparametric-regression approach, using the kernel-smoothing technique. Through extensive simulations, we show that this approach is more powerful than is a currently used method for mapping QTLs by use of sib pairs, particularly in the presence of dominance and epistatic effects at the trait loci.

title: Deciphering the genetic architecture of a multivariate phenotype.
abstract: A heritable multivariate quantitative phenotype comprises several correlated component phenotypes that are usually pleiotropically controlled by a set of major loci and environmental factors. One approach to decipher the genetic architecture of a multivariate phenotype, in particular to map the underlying loci, is to reduce the dimensionality of the data by means of a data reduction technique, such as principal component analysis. The extracted principal components are then analyzed in conjunction with marker data to map the underlying loci. We have examined the efficiency of this approach with and without taking into account the correlation structure of the multivariate phenotype when extracting principal components. We have assumed that genome-wide scan data on sibpairs are available for low-density (widely spaced) and high-density markers. Using extensive simulations, based on three models of the multivariate phenotype, we have shown that although ignoring the correlation structure of the multivariate phenotype does not have any serious impact on the efficiency of mapping the underlying trait loci in wide marker intervals, there is a significant adverse effect of this practice for fine-mapping. We, therefore, recommend that the correlation structure of the multivariate phenotype be carefully examined to decide on the strategy of extracting principal components for deciphering the genetic architecture of the multivariate phenotype.

title: A novel non-parametric regression reveals linkage on chromosome 4 for the number of externalizing symptoms in sib-pairs.
abstract: In this report, we present results of a genome-wide linkage scan using as a phenotype the number of externalizing symptoms associated with alcohol use disorders. Subjects were collected by the Collaborative Study on the Genetics of Alcoholism project from families in which at least three first degree relatives were affected by alcohol dependence. We use a novel non-parametric regression method based on kernel smoothing for our analysis. We report a statistically significant linkage close to the ADH gene cluster on Chromosome 4. We also obtain evidence for epistatic interaction between a region on Chromosome 1 and one on Chromosome 15. Although alcoholism as a covariate does not have any effect on the linkage scan, it has an effect on the epistatic interaction.

title: The Papworth BiVent tube: a new device for lung isolation.
abstract: Provision of one lung ventilation can be technically challenging, particularly for anaesthetists who are only occasionally required to isolate one lung from the other. A new double lumen endotracheal tube, the Papworth BiVent Tube, has been designed to enable rapid and reliable lung isolation using any bronchus blocker without the need for fibreoptic endoscopic guidance. In this study, an airway-training manikin was used to assess ease of tracheal intubation and lung isolation using the Papworth BiVent tube. Ease of intubation was compared to a single lumen endotracheal tube and a conventional double lumen endobronchial tube. Ease of lung isolation when using a bronchus blocker was compared to a single lumen tube combined with a bronchial blocker. Tracheal intubation using the Papworth BiVent tube was found to be easier than when using a conventional double lumen endobronchial tube. Lung isolation using the Papworth BiVent tube used in combination with a bronchus blocker was achieved more reliably and rapidly than when using a single lumen tube and bronchus blocker.

title: Thermodynamic equilibrium between blue and green copper sites and the role of the protein in controlling function
abstract: A combination of spectroscopies and density functional theory calculations indicate that there are large temperature-dependent absorption spectral changes present in green nitrite reductases (NiRs) due to a thermodynamic equilibrium between a green and a blue type 1 (T1) copper site. The axial methionine (Met) ligand is unconstrained in the oxidized NiRs, which results in an enthalpically favored (ΔH ≈4.6 kcal/mol) Met-bound green copper site at low temperatures, and an entropically favored (TΔS ≈4.5 kcal/mol, at room temperature) Met-elongated blue copper site at elevated temperatures. In contrast to the NiRs, the classic blue copper sites in plastocyanin and azurin show no temperature-dependent behavior, indicating that a single species is present at all temperatures. For these blue copper proteins, the polypeptide matrix opposes the gain in entropy that would be associated with the loss of the weak axial Met ligand at physiological temperatures by constraining its coordination to copper. The potential energy surfaces of Met binding indicate that it stabilizes the oxidized state more than the reduced state. This provides a mechanism to tune down the reduction potential of blue copper sites by >200 mV.

title: The role of sodium dodecyl sulfate (SDS) micelles in inducing skin barrier perturbation in the presence of glycerol.
abstract: The stratum corneum (SC) serves as the skin barrier between the body and the environment. When the skin is contacted with an aqueous solution of the surfactant sodium dodecyl sulfate (SDS), a well-known model skin irritant, SDS penetrates into the skin and disrupts this barrier. It is well established, both in vitro and in vivo, that the SDS skin penetration is dose-dependent, and that it increases with an increase in the total SDS concentration above the critical micelle concentration (CMC) of SDS. However, when we added the humectant glycerol at a concentration of 10 wt% to the aqueous SDS contacting solution, we observed, through in vitro quantitative skin radioactivity assays using (14)C-radiolabeled SDS, that the dose dependence in SDS skin penetration is almost completely eliminated. To rationalize this important observation, which may also be related to the well-known beneficial effects of glycerol on skin barrier perturbation in vivo, we hypothesize that the addition of 10 wt% glycerol may hinder the ability of the SDS micelles to penetrate into the skin barrier through aqueous pores that exist in the SC. To test this hypothesis, we conducted mannitol skin permeability as well as average skin electrical resistivity measurements in vitro upon exposure of the skin to an aqueous SDS contacting solution and to an aqueous SDS + 10 wt% glycerol contacting solution in the context of a hindered-transport aqueous porous pathway model of the SC. Our in vitro studies demonstrated that the addition of 10 wt% glycerol: (i) reduces the average aqueous pore radius resulting from exposure of the skin to the aqueous SDS contacting solution from 33 +/- 5 Angstrom to 20 +/- 5 Angstrom, such that a SDS micelle of radius 18.5 +/- 1 Angstrom (as determined using dynamic light-scattering measurements) experiences significant steric hindrance and cannot penetrate into the SC, and (ii) reduces the number density of aqueous pores in the SC by more than 50%, thereby further reducing the ability of the SDS micelles to penetrate into the SC and perturb the skin barrier.

title: Fluorescent probing of urea-induced chemical unfolding of bovine serum albumin by intramolecular charge transfer fluorescence probe E-3-(4-dimethylamino-naphthalen-1-yl)-acrylic acid.
abstract: Changes in polarity at the immediate binding site in protein bovine serum albumin (BSA) produces distinct changes in the solvent polarity-dependent emission band of fluorescence probe E-3-(4-dimethylamino-naphthalen-1-yl)-acrylic acid. Steady-state spectroscopy and time-resolved spectroscopy have been used to investigate this binding process. Attaching the probe to BSA and then monitoring its spectral changes with increasing urea concentration and raising temperature has also tracked the denaturation of BSA chemically and thermally. The polarity of the microenvironment was investigated employing the Reichardt E(T)(30) scale. Fluorescence anisotropy, red edge excitation shifts and acrylamide-induced quenching of fluorescence have been exploited to gain better insight into this binding process.

title: Molecular characterization of full-length genomic segment 2 of a bovine picobirnavirus (PBV) strain: evidence for high genetic diversity with genogroup I PBVs.
abstract: We report here the molecular characterization of a bovine genogroup I picobirnavirus strain RUBV-P detected from a 1-month-old diarrhoeic calf in eastern India. Sequence comparisons and phylogenetic analysis of a short stretch of gene segment 2 of RUBV-P revealed low nucleotide identities (51.2-64.9%) with and distant genetic relatedness to other genogroup I picobirnaviruses. The complete gene segment 2 sequence of RUBV-P was obtained by the single primer amplification method with modifications. Gene segment 2 of RUBV-P was 1758 bp long, encoded a predicted protein of 554 aa and exhibited low nucleotide (58.1-58.8%) and amino acid (51.3-55.4%) identities with genogroup I human strains Hy005102 and 1-CHN-97. The 5'- and 3'-end nucleotide sequences, and the three motifs of RNA-dependent RNA polymerases of double-stranded RNA viruses, were conserved among these strains. Our findings suggested that bovine strain RUBV-P might be distinct from genogroup I picobirnaviruses of humans and other animals.