A mixed-model approach for genome-wide association studies of correlated traits in structured populations

Genome-wide association studies (GWAS) are a standard approach for studying the genetics of natural variation. A major concern in GWAS is the need to account for the complicated dependence structure of the data, both between loci as well as between individuals. Mixed models have emerged as a general and flexible approach for correcting for population structure in GWAS. Here, we extend this linear mixed-model approach to carry out GWAS of correlated phenotypes, deriving a fully parameterized multi-trait mixed model (MTMM) that considers both the within-trait and between-trait variance components simultaneously for multiple traits. We apply this to data from a human cohort for correlated blood lipid traits from the Northern Finland Birth Cohort 1966 and show greatly increased power to detect pleiotropic loci that affect more than one blood lipid trait. We also apply this approach to an Arabidopsis thaliana data set for flowering measurements in two different locations, identifying loci whose effect depends on the environment.     

Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite

From the standpoints of both basic research and biotechnology, there is considerable interest in reaching a clearer understanding of the diversity of biological mechanisms employed during lignocellulose degradation. Globally, termites are an extremely successful group of wood-degrading organisms and are therefore important both for their roles in carbon turnover in the environment and as potential sources of biochemical catalysts for efforts aimed at converting wood into biofuels. Only recently have data supported any direct role for the symbiotic bacteria in the gut of the termite in cellulose and xylan hydrolysis. Here we use a metagenomic analysis of the bacterial community resident in the hindgut paunch of a wood-feeding 'higher' Nasutitermes species (which do not contain cellulose-fermenting protozoa) to show the presence of a large, diverse set of bacterial genes for cellulose and xylan hydrolysis. Many of these genes were expressed in vivo or had cellulase activity in vitro, and further analyses implicate spirochete and fibrobacter species in gut lignocellulose degradation. New insights into other important symbiotic functions including H2 metabolism, CO2-reductive acetogenesis and N2 fixation are also provided by this first system-wide gene analysis of a microbial community specialized towards plant lignocellulose degradation. Our results underscore how complex even a 1-microl environment can be.     

Distribution records and comments on fleas in southwestern South Dakota

From October 2003 through April 2006, we collected 565 fleas incidental to a distribution survey of mammals in southwestern South Dakota. Sixty-one specimens, representing 18 species of mammals, possessed 20 species of fleas. The geographic distributions of these flea species revealed 8 new records for the Black Hills and its adjacent grasslands. Four species— Megarthroglossus divisus, Stenoponia americana, Odontopsyllus dentatus, and Amaradix euphorbi —constitute new records for South Dakota, thus increasing the state’s known flea fauna to 42 species. Hunters, trappers, and field biologists should be aware that serosurveillance during the 1990s revealed the presence of sylvatic plague and tularemia in the Black Hills area. Desde octubre de 2003 hasta abril de 2006, colectamos 565 pulgas de manera incidental durante un estudio de la distribución de mamíferos en el suroeste del estado de Dakota del Sur. Los 61 especímenes, que representaban 18 especies de mamíferos, albergaban 20 especies de pulgas. Sus distribuciones geográficas revelaron 8 nuevos registros para las Colinas Negras (Black Hills) y las praderas adyacentes. Cuatro de estas especies ( Megarthroglossus divisus, Stenoponia americana, Odontopsyllus dentatus y Amaradix euphorbi ) constituyen nuevos registros para Dakota del Sur. Esto aumenta el número de especies de pulgas conocidas del estado a 42 especies. Los cazadores, tramperos y biólogos de campo deben estar conscientes de que la vigilancia serológica durante la década de los 1990 reveló la presencia de la plaga silvática y la tularemia en el área de las Colinas Negras.     

Liquid crystal phase transitions in suspensions of polydisperse plate-like particles

Colloidal suspensions that form periodic self-assembling structures on sub-micrometre scales are of potential technological interest; for example, three-dimensional arrangements of spheres in colloidal crystals might serve as photonic materials, intended to manipulate light. Colloidal particles with non-spherical shapes (such as rods and plates) are of particular interest because of their ability to form liquid crystals. Nematic liquid crystals possess orientational order; smectic and columnar liquid crystals additionally exhibit positional order (in one or two dimensions respectively). However, such positional ordering may be inhibited in polydisperse colloidal suspensions. Here we describe a suspension of plate-like colloids that shows isotropic, nematic and columnar phases on increasing the particle concentration. We find that the columnar two-dimensional crystal persists for a polydispersity of up to 25%, with a cross-over to smectic-like ordering at very high particle concentrations. Our results imply that liquid crystalline order in synthetic mesoscopic materials may be easier to achieve than previously thought.     

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

Population structure causes genome-wide linkage disequilibrium between unlinked loci, leading to statistical confounding in genome-wide association studies. Mixed models have been shown to handle the confounding effects of a diffuse background of large numbers of loci of small effect well, but they do not always account for loci of larger effect. Here we propose a multi-locus mixed model as a general method for mapping complex traits in structured populations. Simulations suggest that our method outperforms existing methods in terms of power as well as false discovery rate. We apply our method to human and Arabidopsis thaliana data, identifying new associations and evidence for allelic heterogeneity. We also show how a priori knowledge from an A. thaliana linkage mapping study can be integrated into our method using a Bayesian approach. Our implementation is computationally efficient, making the analysis of large data sets (n > 10,000) practicable.     

Biochemical dysfunction and memory loss: the case of Alzheimer's dementia

Among the different types of cognitive impairment that appear with increasing age, Alzheimer's disease (AD) is rated as the most frequent. Despite intensive research, key questions concerning AD aetiology remain elusive, but it appears that many biochemical events crucial for neuronal communication and synaptic plasticity fail during the course of the disease. The aim of this review is therefore to provide an overview of intracellular cascades involved in AD pathology. For almost all factors. it is a matter of controversy whether their contribution should be considered to be cause or effect. However, intracellular signalling may be crucial as it is in learning and memory mechanisms and malfunction of biochemical pathways may be a common denominator in neurodegenerative processes, thus providing new venues for treatment and therapeutic strategies.     

Social evolution: kin preference in a social microbe

Kin recognition helps cooperation to evolve in many animals, but it is uncertain whether microorganisms can also use it to focus altruistic behaviour on relatives. Here we show that the social amoeba Dictyostelium purpureum prefers to form groups with its own kin in situations where some individuals die to assist others. By directing altruism towards kin, D. purpureum should generally avoid the costs of chimaerism experienced by the related D. discoideum.