Bayesian analysis of the linear reaction norm model with unknown covariate

The reaction norm model is becoming a popular approach for the analysis of G x E interactions. In a classical reaction norm model, the expression of a genotype in different environments is described as a linear function (a reaction norm) of an environmental gradient or value. A common environmental value is defined as the mean performance of all genotypes in the environment, which is typically unknown. One approximation is to estimate the mean phenotypic performance in each environment, and then treat these estimates as known covariates in the model. However, a more satisfactory alternative is to infer environmental values simultaneously with the other parameters of the model. This study describes a method and its Bayesian MCMC implementation that makes this possible. Frequentist properties of the proposed method are tested in a simulation study. Estimates of parameters of interest agree well with the true values. Further, inferences about genetic parameters from the proposed method are similar to those derived from a reaction norm model using true environmental values. On the other hand, using phenotypic means as proxies for environmental values results in poor inferences

Development of body mass and sexual size dimorphism in Danish red foxes (Vulpes vulpes)

<span class="fontstyle0">In this study, we examine the development of body mass and sexual size dimorphism (SSD) in 178 juvenile wild Danish red </span><span class="fontstyle0">foxes </span><span class="fontstyle0">from 99 litters </span><span class="fontstyle0">using </span><span class="fontstyle0">piecewise analyses of regression lines for age </span><span class="fontstyle2">versus</span><span class="fontstyle0"> weight</span><span class="fontstyle0">. When fox cubs are younger than 100 days, only slight (SSD=1.7%) and no significant difference</span><span class="fontstyle0"> (t-test: t=1.2, p=0.24) </span><span class="fontstyle0">was found in the mean weight of </span><span class="fontstyle0">males (2.03± kg) and females (1.93± kg), and</span><span class="fontstyle0"> no significant difference was found in the slope of regression lines </span><span class="fontstyle0">for </span><span class="fontstyle0">males and females </span><span class="fontstyle0">(F=0.97E-5, p = 0.99). In the growth period between 100 days of age and mating around 275 days of age, the regression line in males steepens more than that of females (difference in slopes, F=5.9, p&lt;0.02) and the difference in mean weight of the sexes become highly significant (SSD=7.4%, difference in mean t=4.6, p=2.2E-5). After mating the growth curve levels off i.e. the slope of the regression lines for age </span><span class="fontstyle2">versus</span><span class="fontstyle0"> weight is not significantly different from zero. Yearly variation was revealed in the growth rate of juvenile foxes (difference in slope for males; F=3.9, p&lt;0.01 and females; F=8.6, p&lt;0.001). Conclusion: SSD in red foxes mainly develop </span><span class="fontstyle0">as a result of a faster grow rate in males </span><span class="fontstyle0">between indepency and maturity. Ontogony of red foxes may genetically be disposed to prevent males outcompeting females in the early stages of life (&lt;100 days), when cubs are still fed by adults and the increase in SSD before mating, may be an adaption to selective forces benefitting larger males. </span><span class="fontstyle0">The growth rate of juvenile foxes of both sexes is influenced by environmental variation in different years.</span> <br /

BioConcens: Biomass and bioenergy production agriculture – consequences for soil fertility, environment, spread of animal parasites and socio-economy

The research programme called “international research cooperation and organic integrity” was commenced for a period 2006-2010. It is coordinated by DARCOF (The Danish Research Centre for Organic Farming). The whole programme, with acronym DARCOF III, consists of 15 projects (http://www.darcof.dk/research/darcofiii/index.html). One of them is BIOCONCENS - Biomass and bioenergy production in organic farming – consequences for soil fertility, environment, spread of animal parasites and socio-economy (http://www.bioconcens.elr.dk/uk/). The production of bioenergy in organic agriculture (OA) can reduce its dependency of fossil fuels and decrease green house gasses emission; consequently it will increase sustainability of organic farms. Biorefinery concept based on co-production of biogas, bioethanol and protein fodder in organic farming will be developed within the BIOCONCENS project and the background for the project and the different work packages will be presented in this paper

Diffusion of gold nanoclusters on graphite

We present a detailed molecular-dynamics study of the diffusion and coalescence of large (249-atom) gold clusters on graphite surfaces. The diffusivity of monoclusters is found to be comparable to that for single adatoms. Likewise, and even more important, cluster dimers are also found to diffuse at a rate which is comparable to that for adatoms and monoclusters. As a consequence, large islands formed by cluster aggregation are also expected to be mobile. Using kinetic Monte Carlo simulations, and assuming a proper scaling law for the dependence on size of the diffusivity of large clusters, we find that islands consisting of as many as 100 monoclusters should exhibit significant mobility. This result has profound implications for the morphology of cluster-assembled materials

A semisynthetic strategy to generate phosphorylated and acetylated histone H2B

Proteins are subject to numerous post-translational modifications (PTMs) that can alter the chemical structure, and hence function, of the molecule. The astonishing diversity of PTMs possible on proteins is exemplified by histones, nuclear proteins that form the protein core of the nucleosome particle. Histones can be modified in a variety of ways including acetylation, phosphorylation, methylation, ADP-ribosylation and ubiquitylation. Moreover, many, if not all, of these modifications can occur in combination. Indeed, there is growing evidence that functional cross-talk between histone PTMs is essential for the regulation of gene expression and ultimately cell fate and identity. Biochemical studies into the role of histone PTMs are often confounded by the difficulty associated with obtaining large quantities of homogeneously modified proteins. For this reason chemical approaches to obtaining post-translationally modified histones have received considerable attention in recent years. Among the available strategies, the protein ligation approach, expressed protein ligation (EPL), offers the most flexibility in terms of the number and type of PTMs that can be incorporated. To date, EPL has been used to generate phosphorylated, acetylated, and methylated forms of histone H3, acetylated H4, and ubiquitylated H2B. Nonetheless, many modified histones have yet to be accessed using semi-synthesis. A notable case in point is the N-terminal region of H2B, which has been described to possess several PTMs, including (poly)lysine acetylation and serine 14 phosphorylation, which have been implicated in transcription and apoptotic chromatin compaction, respectively. Differentially modified semi-synthetic H2B analogs would be useful to assess the affect of acetylation on both antibody recognition as well as on the efficiency of phosphorylation. In this report, we describe a general semi-synthetic route to H2B that allows the installation of PTMs into an otherwise native polypeptide background