Measuring departures from Hardy-Weinberg: a Markov chain Monte Carlo method for estimating the inbreeding coefficient

Many well-established statistical methods in genetics were developed in a climate of severe constraints on computational power. Recent advances in simulation methodology now bring modern, flexible statistical methods within the reach of scientists having access to a desktop workstation. We illustrate the potential advantages now available by considering the problem of assessing departures from Hardy-Weinberg (HW) equilibrium. Several hypothesis tests of HW have been established, as well as a variety of point estimation methods for the parameter which measures departures from HW under the inbreeding model. We propose a computational, Bayesian method for assessing departures from HW, which has a number of important advantages over existing approaches. The method incorporates the effects-of uncertainty about the nuisance parameters--the allele frequencies--as well as the boundary constraints on f (which are functions of the nuisance parameters). Results are naturally presented visually, exploiting the graphics capabilities of modern computer environments to allow straightforward interpretation. Perhaps most importantly, the method is founded on a flexible, likelihood-based modelling framework, which can incorporate the inbreeding model if appropriate, but also allows the assumptions of the model to he investigated and, if necessary, relaxed. Under appropriate conditions, information can be shared across loci and, possibly, across populations, leading to more precise estimation. The advantages of the method are illustrated by application both to simulated data and to data analysed by alternative methods in the recent literature.

A unique example of structural and magnetic diversity in four interconvertible copper(II)−azide complexes with the same Schiff base ligand: a monomer, a dimer, a chain, and a layer

Four new Cu(II)-azido complexes of formula [CuL(N-3)] (1), [CuL(N-3)](2) (2), [Cu7L2(N-3)(12)](n) (3), and [Cu2L(dmen)-(N-3)(3)](n) (4) (dmen = N,N-dimethylethylenediamine) have been synthesized using the same tridentate Schiff base ligand HL (2-[1-(2-dimethylaminoethylimino)ethyl]phenol, the condensation product of dmen and 2-hydroxyacetophenone). The four compounds have been characterized by X-ray structural analyses and variable-temperature magnetic susceptibility measurements. Complex 1 is mononuclear, whereas 2 is a single mu-1,1 azido-bridged dinuclear compound. The polymeric compound 3 possesses a 2D structure in which the Cu(II) ions are linked by phenoxo oxygen atoms and two different azide bridges (mu-1,1 and mu-1,1,3). The structure of complex 4 is a double helix in which two mu-1,3-azido-bridged alternating one-dimensional helical chains of CuL(N-3) and Cu(dmen)(N-3)(2) are joined together by weak mu-1,1 azido bridges and H-bonds. The complexes interconvert in solution and can be obtained in pure form by carefully controlling the conditions. The magnetic properties of compounds 1 and 2 show the presence of very weak antiferromagnetic exchange interactions mediated by a ligand pi overlap (J = -1.77) and by an asymmetric 1,1-N-3 bridge (J = -1.97 cm(-1)), respectively. Compound 3 presents, from the magnetic point of view, a decorated chain structure with both ferro- and antiferromagnetic interactions. Compound 4 is an alternating helicoidal chain with two weak antiferromagnetic exchange interactions (J -1.35 and -2.64 cm(-1)).

Dietary long-chain n-3 PUFAs increase LPL gene expression in adipose tissue of subjects with an atherogenic lipoprotein phenotype

We sought to test the hypothesis that dietary long-chain n-3 PUFA (LC n-3 PUFA) in fish oil stimulate the gene expression of lipoprotein lipase (LPL) in human adipose tissue (AT). In a randomized, double blind, placebo-controlled, cross-over study, 51 male subjects expressing an atherogenic lipoprotein phenotype (ALP) had their diets supplemented with fish oil for 6 weeks. As we previously reported for this group, supplementation with LC n-3 PUFA produced a decrease in fasting plasma triglyceride (TG) (−35%, P < 0.05), attenuation of the postprandial TG response (area and incremental area under the curve; AUC and IAUC, P < 0.05), and a decrease in small, dense LDL. The present study extended these observations by showing that these changes were accompanied by a marked increase in the concentration of LPL mRNA in adipose tissue (AT-LPL mRNA, +55%, P = 0.003) and post-heparin LPL activity (PH-LPL, +31%, P = 0.036). There was also evidence of an association between LPL gene expression and polymorphism in the apolipoprotein E gene. We conclude that the favorable influence of dietary n-3 PUFA on the ALP may be mediated, in part, through an increase in the plasma activity and gene expression of lipoprotein lipase in human adipose tissue.

The quantitation of lipoprotein lipase mRNA in biopsies of human adipose tissue, using the polymerase chain reaction, and the effect of increased consumption of n-3 polyunsaturated fatty acids

Objective: To examine the effects of the consumption of fish oils on the gene expression of lipoprotein lipase (LPL, EC 3.1.1.34) in human adipose tissue. In order to measure LPL mRNA in adipose tissue samples obtained by needle biopsy from human volunteers a competitive, reverse transcriptase PCR (RT-PCR) protocol was developed. Design: A randomised controlled, single blind cross over dietary study which compared the effects of a low level n-3 polyunsaturated fatty acids (PUFA) using normal foods enriched with eicosapentaenoic (EPA) and docosahexaenoic (DHA) (test diet), with non-enriched but otherwise identical foods (control). The diets were consumed for a period of 22 d with a wash out period of 5 months between the diets. Setting: Free-living individuals associated with the University of Surrey. Subjects: Six male subjects with a mean (±sd) age of 51.2±3.6 y were recruited. Major Outcome Measures: Pre-and postprandial blood samples were taken for the measurement of triacylglycerol (TAG), postheparin LPL activity and adipose tissue samples for the measurement of LPL mRNA levels. Results: Mean LPL expression values were 4.12´105 molecules of LPL mRNA per ng total RNA on the control diet and 4.60´105 molecules of LPL mRNA per ng total RNA on the n-3 PUFA enriched (test) diet. There was no significant difference between the levels of LPL expression following each diet, consistent with the lack of change in TAG levels in response to increased dietary n-3 PUFA intake. However, the change in LPL expression (Test-Control diet) correlated significantly with the change in fasting TAG levels (P=0.03, R=-0.87 and R2=0.75) and with the total area under the TAG-time response curve (P=0.003, R=-0.96 and R2=0.92) in individuals. Conclusions: These findings, although based on a small number of subjects, suggest that LPL expression may be a determinant of plasma TAG levels. The development of this methodology should allow further elucidation of the effects of dietary manipulation and disease processes on lipid clearance and regulation in human subjects.

Dairy products in the food chain: their impact on health

Milk is a complex and complete food containing an array of essential nutrients that contribute toward a healthy, balanced diet. Numerous epidemiological studies have revealed that high consumption of milk and dairy products may have protective effects against coronary heart disease (CHD), stroke, diabetes, certain cancers (such as colorectal and bladder cancers), and dementia, although the mechanisms of action are unclear. Despite this epidemiological evidence, milk fatty acid profiles often lead to a negative perception of milk and dairy products. However, altering the fatty acid profile of milk by changing the dairy cow diet is a successful strategy, and intervention studies have shown that this approach may lead to further benefits of milk/dairy consumption. Overall, evidence suggests individuals who consume a greater amount of milk and dairy products have a slightly better health advantage than those who do not consume milk and dairy products.

Chain extension in electrospun polystyrene fibres: a SANS study

Small angle neutron scattering techniques were used to quantify the size and shape of the chain conformation in electrospun fibres of atactic polystyrene prepared from solutions in methyl ethyl ketone. Aligned arrays of fibres were collected onto a rotating collector with tangential velocity varying between 0 ms-1 and approximately 15 ms-1. The measured radii of gyration of the polystyrene chains were found to be slightly higher than that expected for samples prepared from solutions in the concentrated regime. The ratio of the radius of gyration parallel and perpendicular to the chain axis was found to be approximately 1.05 in contrast to the substantial macroscopic shape transformation intrinsic to electrospinning. When the tangential velocity of the rotating collector was greater than the flight velocity of the fibres (ca. 4 ms-1), a further extension of the polymer chains was observed with a ratio of the radii of gyration increasing to 1.20 at the highest collector speeds. It is proposed that the heterogeneous processes involved, particularly solvent evaporation and the formation of a polymer skin during electrospinning play a significant role in determining the level of molecular anisotropy in the fibres.

A value chain approach to animal diseases risk management: technical foundations and practical framework for field application

Classical risk assessment approaches for animal diseases are influenced by the probability of release, exposure and consequences of a hazard affecting a livestock population. Once a pathogen enters into domestic livestock, potential risks of exposure and infection both to animals and people extend through a chain of economic activities related to producing, buying and selling of animals and products. Therefore, in order to understand economic drivers of animal diseases in different ecosystems and to come up with effective and efficient measures to manage disease risks from a country or region, the entire value chain and related markets for animal and product needs to be analysed to come out with practical and cost effective risk management options agreed by actors and players on those value chains. Value chain analysis enriches disease risk assessment providing a framework for interdisciplinary collaboration, which seems to be in increasing demand for problems concerning infectious livestock diseases. The best way to achieve this is to ensure that veterinary epidemiologists and social scientists work together throughout the process at all levels.