Binary Trait Mapping in Experimental Crosses With Selective Genotyping

Selective genotyping is an efficient strategy for mapping quantitative trait loci. For binary traits, where there are only two distinct phenotypic values (e.g., affected/unaffected or present/absent), one may consider selective genotyping of affected individuals, while genotyping none or only some of the unaffecteds. If selective genotyping of this sort is employed, the usual method for binary trait mapping, which considers phenotypes conditional on genotypes, cannot be used. We present an alternative approach, instead considering genotypes conditional on phenotypes, and compare this to the more standard method of analysis, both analytically and by example. For studies of rare binary phenotypes, we recommend performing an initial genome scan with all affected individuals and an equal number of unaffecteds, followed by genotyping the full cross in genomic regions of interest to confirm results from the initial screen.WE consider the problem of mapping genetic loci contributing to a binary trait in an experimental cross with selective genotyping. There are two clear approaches for linkage analysis with a binary trait. Typically, we compare the proportion of affected individuals across genotype groups (Xu and Atchley 1996). Alternatively, we can compare genotype frequencies between affected and unaffected individuals, similar to Henshall and Goddard (1999). Beyond these two basic approaches, binary trait mapping has seen fundamental advances in regression models (McIntyre et al. 2001; Deng et al. 2006), extensions to multiple-QTL mapping (Coffman et al. 2005; Chen and Liu 2009), and the development of Bayesian algorithms (Yi and Xu 2000; Huang et al. 2007). However, the original data structure and approach have remained intact. Existing methods for binary trait mapping largely require the availability of genotype and phenotype data for a representative sample of both affected and unaffected individuals, and we have not yet seen a well-developed framework for binary trait mapping in the presence of selective genotyping.It is not uncommon to see genotype data on affected individuals only, in which case the above methods cannot be used. Instead, we can compare observed genotype frequencies to the expected segregation ratios given the cross type, in a test for segregation distortion (see Faris et al. 1998; Lambrides et al. 2004). For example, the expected segregation proportions for an intercross are 1:2:1. The observed genotypes can then be described by a multinomial model, and statistically significant deviation from the expected segregation ratios among the genotyped affected individuals would suggest genotype–phenotype association. Gene mapping approaches that model genotypes rather than phenotypes have been developed extensively in the analysis of affected human relative pairs (see, for example, Risch 1990; Holmans 1993; Hauser and Boehnke 1998). In the analysis of experimental crosses, however, this type of approach has been developed primarily for the identification of monogenic mutants (Moran et al. 2006).Once all affected individuals are genotyped, an investigator may go on to genotype unaffected individuals. With this genotyping strategy in mind, we present several potential methods of analysis that might be applied in this context. First, we consider a standard analysis of the genotyped individuals, with disease proportions compared across genotype groups (Xu and Atchley 1996). Having omitted ungenotyped individuals, this method of analysis appears invalid because the estimated disease proportions are biased upward, reflecting an overrepresentation of affecteds in the set of genotyped individuals under consideration. As an alternative, we develop a reverse approach with genotype frequencies compared across phenotype groups. Because selective genotyping does provide a representative sample of genotypes for each phenotype group, this reverse approach does not face the bias in parameter estimation seen with the standard approach. We further extend the reverse approach to incorporate a segregation assumption, as is necessary for an affecteds only analysis. Finally, we present a full-likelihood analysis accounting for selective genotyping, similar to that suggested by Lander and Botstein (1989) for quantitative traits. We develop the full-likelihood approach both with and without incorporating an assumption on the genotype segregation proportions.Having put forth each of these methods, we derive analytic relationships among them. These relationships provide important insight regarding application of the presented methods under selective genotyping. Most notably, we find that making a segregation assumption can lead to spurious evidence of a QTL, but is necessary to treat the case of affecteds only genotyping. We demonstrate properties of the methods in an analysis of recovery from infection by Listeria monocytogenes in intercross mice and further compare power of the methods through computer simulations. Finally, we synthesize our analytical and simulation results to offer more general suggestions for the analysis of binary trait data with selective genotyping.     

The complex mutual connection between stroke and bone health

Both stroke and osteoporosis are prevalent conditions among the elderly. With increasing life expectancy across the world, despite better preventative measures, the incidence of both conditions is set to rise in the ageing populations. Alongside with sharing several common risk factors, the current evidence suggests that these conditions are risk factors for each other albeit more clear support for the effects of stroke on bone health. In this article, we present aetiopathophysiology of these two conditions and the current evidence of impact on each other particularly the impact of stroke on bone health. We also provide suggestions for improving bone health in people living with stroke based on the currently available evidence.     

Distribution of Cereal Luteoviruses and Molecular Diversity of BYDV‐PAV Isolates in Central and Southern Iran: Proposal of a New Species in the Genus Luteovirus

During a survey , 148 wheat, 70 barley and 24 wild grass samples of plants showing symptoms of yellowing or reddening of leaves and general stunting were collected in central and southern provinces of Iran and tested for Barley yellow dwarf virus (BYDV) and Cereal yellow dwarf virus (CYDV) infection by enzyme‐linked immunosorbent assay (ELISA) and tissue print immunoassay (TPIA). The results showed the presence of the viruses in most regions. Positive reactions to BYDV‐PAV, BYDV‐MAV, CYDV‐RPV and BYDV‐SGV antisera were recorded. BYDV‐PAV was the most prevalent virus. The genetic diversity of BYDV‐PAV isolates in central and southern provinces was studied by analysing ORF1 (903 nt) and read through domain (RTD) (575 nt) of 13 and nine isolates respectively. Sequence analysis of RTD at nucleotide and amino acid levels revealed a high identity (91.8–97.2% and 91.4–100% respectively) between Iranian and other available isolates in the GenBank. However, in regards to ORF1, a high genetic diversity among Iranian and other known PAV isolates at both amino acid (2–16.9%) and nucleotide (4.1–16.5%) levels were detected. Based on phylogenetic analysis of ORF1, two major groups of BYDV‐PAV isolates were distinguished. The Iranian isolates were divided between the two clusters. Our results suggest that the occurrence of two genetically distinct groups of PAV isolates in central and southern Iran, from which according to the ICTV criteria for species demarcation in the family Luteoviridae, four isolates from central parts of the country, qualify for designation as new species.     

Antifungal activity of some essential oils against toxigenic Aspergillus species

Increasing attentions have been paid on the application of essential oils and plant extracts for control of postharvest pathogens due to their natural origin and less appearance of resistance in fungi pathogens. Some Aspergillus species are toxigenic and responsible for many cases of food and feed contamination. Some Toxins that produce with some Aspergillus species are known to be potent hepatocarcinogens in animals and humans. The present work evaluated the parameters of antifungal activity of the essential oils of Zataria multiflora, Thymus migricus, Satureja hortensis, Foeniculum vulgare, Carum capticum and thiabendazol fungicide on survival and growth of different species of Aspergillus. Aerial part and seeds of plant species were collected then dried and its essential oils isolated by means of hydrodistillation. Antifungal activity was evaluated in vitro by poisonous medium technique with PDA medium at six concentrations. Results showed that all essential oils could inhibit the growth of Aspergillus species. The essential oil with the best effect and lowest EC50 and MIC (Minimum Inhibitory Concentration) was Z. multiflora (223 microl/l and 650 microl/l, respectively). The chemical composition of the Z. multiflora essential oil was analyzed by GC-MS.     

Concentration dependent dual effect of thrombin in endothelial cells via Par‐1 and Pi3 Kinase

Disruption of endothelial barrier is a critical pathophysiological factor in inflammation. Thrombin exerts a variety of cellular effects including inflammation and apoptosis through activation of the protease activated receptors (PARs). The activation of PAR‐1 by thrombin is known to have a bimodal effect in endothelial cell permeability with a low concentration (pM levels) eliciting a barrier protective and a high concentration (nM levels) eliciting a barrier disruptive response. It is not known whether this PAR‐1‐dependent activity of thrombin is a unique phenomenon specific for the in vitro assay or it is part of a general anti‐inflammatory effect of low concentrations of thrombin that may have a physiological relevance. Here, we report that low concentrations of thrombin or of PAR‐1 agonist peptide induced significant anti‐inflammatory activities. However, relatively high concentration of thrombin or of PAR‐1 agonist peptide showed pro‐inflammatory activities. By using function‐blocking anti‐PAR‐1 antibodies and PI3 kinase inhibitor, we show that the direct anti‐inflammatory effects of low concentrations of thrombin are dependent on the activation of PAR‐1 and PI3 kinase. These results suggest a role for cross communication between PAR‐1 activation and PI3 kinase pathway in mediating the cytoprotective effects of low concentrations of thrombin in the cytokine‐stimulated endothelial cells. J. Cell. Physiol. 219: 744–751, 2009. © 2009 Wiley‐Liss, Inc.     

Liquid chromatography tandem mass spectrometry identification of proanthocyanidins in rat plasma after oral administration of grape seed extract

Proanthocyanidin rich plant extracts derived from grape seed extract (GSE), hawthorn and cranberry are on markets for their preventive effects against cardiovascular diseases and uroinfections in woman. However, the importance of these health beneficial effects of these botanicals remains elusive due to incomplete understanding of uptake, metabolism and bioavailability of proanthocyanidins in vivo. In the present study rats were given GSE orally (300 mg/kg, twice a day) and blood and urine were collected over a 24 h period. Monomeric catechins and their methylated metabolites, and proanthocyanidins up to trimers were detected in blood samples treated with GSE using LC-MS/MS operating in the multiple reaction monitoring (MRM) mode. A new tetramethylated metabolite of dimeric proanthocyanidin (m/z 633) in GSE-treated urine was tentatively identified. Using LC-MS/MS, (+)-catechin and (?)-epicatechin were identified in the brain conclusively. These data suggested that GSE catechins cross the blood brain barrier and may be responsible for the neuroprotective effects of GSE.