A novel non-parametric regression reveals linkage on chromosome 4 for the number of externalizing symptoms in sib-pairs.
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: 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: 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: How Do Homozygous Parents Affect TDT as a Test for Association?
abstract: The traditional transmission disequilibrium test (TDT) (Spielman et al., 1993) is a powerful test for association only in the presence of linkage. Since allele transmissions from homozygous parents do not carry any information on linkage, the TDT statistic uses data only on heterozygous parents. However, homozygous parents carry information on association between alleles at a marker locus and a disease locus. In this article, we explore whether inclusion of homozygous parents increases the power to detect association. The resultant test statistic follows a χ2 distribution with 2 degrees of freedom. Monte-Carlo simulations are included to compare the performance of this test with the traditional TDT under different disease models.

title: A nonparametric regression-based linkage scan of rheumatoid factor-IgM using sib-pair squared sums and differences
abstract: Parametric linkage methods for quantitative trait locus mapping require explicit specification of the probability model of the quantitative trait and hence can lead to misleading linkage inferences when the model assumptions are not valid. Ghosh and Majumder developed a nonparametric regression method based on kernel-smoothing for linkage mapping of quantitative trait locus using squared differences in trait values of independent sib pairs, which is relatively more robust than parametric methods with respect to violations in distributional assumptions. In this study, we modify the above mentioned nonparametric regression method by considering local linear polynomials instead of the Nadaraya-Watson estimator and squared sums of sib-pair trait values in addition to squared differences to perform a genome-wide scan of rheumatoid factor-IgM levels on sib pairs in the Genetic Analysis Workshop 15 simulated data set. We obtain significant evidence of linkage very close to the quantitative trait locus controlling for RF-IgM. We find that the simultaneous use of squared differences and squared sums increases the power to detect linkage compared to using only squared differences. However, because of all the sib pairs are selected for rheumatoid arthritis, there is reduced variance of RF-IgM values, and empirical power to detect linkage is not very high. We also compare the performance of our method with two linear regression approaches: the classical Haseman-Elston method using squared sib-pair trait differences and its extension proposed by Elston et al. using mean-corrected sib-pair cross-products. We find that the proposed nonparametric method yields more power than the linear regression approaches.

title: Bioactive natural compounds for the treatment of gastrointestinal disorders.
abstract: Many healthy subjects and patients are taking natural bioactive products for the prevention and treatment of multiple conditions, including gastrointestinal disorders. Based on current evidence, the scientific validity of the use of many of these commercial compounds by the general public is severely limited, with quality control and regulatory issues continuing to be a concern. Nevertheless, there is sufficient preliminary data to warrant further research of these products in order to identify novel compounds for potential clinical use in addition to performing formal randomized controlled clinical trials of the commercial preparations.

title: Evidence for interstate transmission and increase in prevalence of bovine group B rotavirus strains with a novel VP7 genotype among diarrhoeic calves in Eastern and Northern states of India.
abstract: During a surveillance study (2003-2005) in a cattle market in Kolkata city, state of West Bengal, Eastern India, 34 (13.0%) of 260 calves with diarrhoea were positive for group B rotaviruses (GBR) by RNA electrophoresis in polyacrylamide gels. Analysis of the partial VP7 gene sequence of 28 of the 34 GBR strains revealed maximum identities (97.7-99.5% at nucleotide level and 97.8-100% at amino-acid level) with the novel bovine GBR 'Kolkata strains' reported in an earlier surveillance study (1.5%, n=192, 2001-2002) from the same cattle market, and shared low identities of 73.7-78.9% and 80.8-89.6%; 62.6-66.2% and 59.8-65.4%; 58.9-62.2% and 48.6-54.9% at nucleotide and amino-acid level with other bovine, human, and murine GBR. The GBR-infected calves were traced to districts in neighbouring states of West Bengal. Therefore, the present study reports a rapid increase in prevalence (13.0% in 2003-2005 against 1.5% in 2001-2002) of novel GBR strains among calves with diarrhoea, and provides evidence for interstate transmission of GBR.

title: Correlation of macular thickness and posterior hyaloid change following bevacizumab and triamcinolone in diffuse diabetic macular edema in middle-aged patients
abstract: To compare changes in posterior vitreous detachment (PVD) following intravitreal injection of bevacizumab and triamcinolone in diffuse diabetic macular edema in middle-aged type 2 diabetes patients and to correlate this change with change in central macular thickness (CMT).  Fifteen consecutive patients treated by intravitreal bevacizumab (group A) and ten patients treated by intravitreal triamcinolone (group B). Institutional study carried out by retrospective analysis of patient registers including serial optical coherence tomography (OCT) images at baseline, and after 1 and 4 months. A central macular thickness (CMT) and vitreomacular relationship was noted on OCT. PVD was graded on a linear scale (0–4). Change in grade of PVD was correlated with change in CMT at each follow-up. At month 4, the decrease in mean CMT from baseline was 51.2 μ (P = 0.000) and 45 μ (P = 0.022) in group A and group B, respectively, with no significant difference between the two groups (P = 0.874). A change in grades of PVD from baseline to month 4 was significant in both group A (P = 0.001) and group B (P = 0.004) with no significant difference between the two groups (P = 0.906). A significant correlation between change in PVD and reduction of CMT was observed in group A (P = 0.011) but not in group B (P = 0.315). Both bevacizumab and triamcinolone caused a significant reduction in macular thickness and a significant change in grade of PVD. Change in PVD played an influential role in the reduction of macular thickness following bevacizumab.

title: Interaction between Caveolin-1 and the Reductase Domain of Endothelial Nitric-oxide Synthase
abstract: Endothelial nitric-oxide synthase (eNOS) is targeted to caveoli through interaction with caveolin-1 (cav-1). cav-1 binding to a consensus site in the eNOS oxygenase domain is proposed to antagonize calmodulin (CaM) binding and thereby inhibit eNOS nitric oxide (NO) synthesis. To study the mechanism, we examined how cav-1 scaffolding domain peptide (amino acids 82–101; cav-1P) would affect NO synthesis, NADPH oxidation, cytochrome c reduction, and ferricyanide reduction by full-length eNOS or its isolated oxygenase and reductase domains. Cav-1P equivalently inhibited NO synthesis and NADPH oxidation by full-length eNOS in a manner reversible by CaM but did not affect NADPH-independent NO synthesis by full-length eNOS or its oxygenase domain, indicating inhibition required the reductase domain. Similar concentrations of cav-1P inhibited cytochromec reduction by full-length eNOS or the reductase domain (amino acids 492–1205) in a CaM-reversible manner, indicating cav-1P interaction with reductase or full-length eNOS are equivalent. Ferricyanide reduction was unaffected by cav-1P in all cases. Immunoblotting showed that full-length eNOS, eNOS oxygenase, and eNOS reductase all bound to an immobilized glutathioneS-transferase-cav-1 fusion protein. Thus, cav-1 interacts independently with both oxygenase and reductase domains of eNOS. The reductase interaction occurs independent of a cav-1 binding motif, is CaM-reversible, and is of sufficient affinity to match cav-1P inhibition of NO synthesis by full-length eNOS. We propose that cav-1 binding to eNOS reductase compromises its ability to bind CaM and to donate electrons to the eNOS heme, thereby inhibiting NO synthesis.

title: Application of rbcL based molecular diversity analysis to algae in wastewater treatment plants.
abstract: The molecular diversity of algae in the final clarifier or denitrification filter outfall from three wastewater treatment plants (WWTPs) with activated sludge based treatment was analyzed using the rbcL gene as a phylogenetic marker. The rbcL gene encodes the large subunit of the CO(2) fixing enzyme RuBisCO. Among algae identified at the WWTPs were diatoms, green algae, cyanobacteria, Eustigmatophyceae, and unknown heterokonts. A high level of diversity was observed within WWTPs with 19-24 unique rbcL sequences detected at each plant. Algae composition also varied between treatment plants. Our results show that the rbcL gene can be used as a phylogenetic marker for algae diversity analysis in a wastewater treatment context.