Gut Microbial Metabolism and Nonalcoholic Fatty Liver Disease.

The gut microbiome, the multispecies community of microbes that exists in the gastrointestinal tract, encodes several orders of magnitude more functional genes than the human genome. It also plays a pivotal role in human health, in part due to metabolism of environmental, dietary, and host-derived substrates, which produce bioactive metabolites. Perturbations to the composition and associated metabolic output of the gut microbiome have been associated with a number of chronic liver diseases, including nonalcoholic fatty liver disease (NAFLD). Here, we review the rapidly evolving suite of next-generation techniques used for studying gut microbiome composition, functional gene content, and bioactive products and discuss relationships with the pathogenesis of NAFLD

Adaptive evolution of molecular phenotypes

Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.Comment: Figures are not optimally displayed in Firefo

Studies on growth rates in pigs and the effect of birth weight

End of project reportThe purpose of this study was to assess some environmental and management factors that affect growth performance on commercial pig units. In experiment 1, a survey was carried out on 22 pig units of known growth performance in south-west Ireland to compare management factors between those showing poor and good growth rates. Low growth rate appears to be due to the cumulative effect of a combination of factors. Experiment 2 was conducted to determine the effects of providing an additional feeder on performance of weaned piglets. No benefits were recorded. Feed consumed from the additional feeder was a replacement for feed that otherwise would have been consumed from the control hopper feeder. Experiment 3 was designed to determine if pig performance and efficiency of growth were affected by weight at birth and at weaning. Lightweight pigs showed inferior growth performance up to the finisher period. Although they compensated some of the inferior growth towards the time of slaughter, they never reached the weights of the heavy birth-weight animals. Males were either significantly heavier or tended to be heavier than females throughout. There was no significant difference between the sexes in the number of days to slaughter. Light and heavy pigs did not differ in the levels of IGF-1 in their blood plasma; however lightweight pigs had significantly lower IgG preweaning. Experiment 4 aimed to determine whether piglet birth weight influenced growth performance, plasma IGF-1 concentrations and muscle fibre characteristics at day 42 of life. At slaughter (Day 42) light birth weight pigs were significantly (P < 0.001) lighter. Plasma IGF-1 concentration was lower by 28% (P=0.06) in light pigs. Muscle fibre cross sectional area and total fibre number were not significantly different between groups. This study should be repeated with bigger numbers

First Supramolecular Sensors for Phosphonate Anions

Fluorescent tripodal anion sensors with a 1,3,5-triethylbenzene core display a turn-on fluorescence response to phosphonate and phosphate anions and may be used as optical sensors. The properties of the receptors and sensors as well as their anion binding behavior were investigated both in solution and in solid state. The turn-on fluorescence response can be leveraged in sensing of phosphate anions and, most importantly, hydrolysis products of the nerve gas sarin, isopropyl methylphosphonate (IMP), and methylphosphonate (MP). The fluorescence signal amplification in the presence of anions allows for application of these molecules in a sensor microarray suitable for high-throughput screening.NSF CHE 0750303, EXP-LA 0731153BGSU (TIE Grant)Chemistr

Stochastic delocalization of finite populations

Heterogeneities in environmental conditions often induce corresponding heterogeneities in the distribution of species. In the extreme case of a localized patch of increased growth rates, reproducing populations can become strongly concentrated at the patch despite the entropic tendency for population to distribute evenly. Several deterministic mathematical models have been used to characterize the conditions under which localized states can form, and how they break down due to convective driving forces. Here, we study the delocalization of a finite population in the presence of number fluctuations. We find that any finite population delocalizes on sufficiently long time scales. Depending on parameters, however, populations may remain localized for a very long time. The typical waiting time to delocalization increases exponentially with both population size and distance to the critical wind speed of the deterministic approximation. We augment these simulation results by a mathematical analysis that treats the reproduction and migration of individuals as branching random walks subject to global constraints. For a particular constraint, different from a fixed population size constraint, this model yields a solvable first moment equation. We find that this solvable model approximates very well the fixed population size model for large populations, but starts to deviate as population sizes are small. The analytical approach allows us to map out a phase diagram of the order parameter as a function of the two driving parameters, inverse population size and wind speed. Our results may be used to extend the analysis of delocalization transitions to different settings, such as the viral quasi-species scenario

The collective quantization of three-flavored Skyrmions revisited

A self-consistent large $N_c$ approach is developed for the collective quantization of SU(3) flavor hedgehog solitons, such as the Skyrmion. The key to this analysis is the determination of all of the zero modes associated with small fluctuations around the hedgehog. These are used in the conventional way to construct collective coordinates. This approach differs from previous work in that it does not implicitly assume that each static zero mode is associated with a dynamical zero mode. It is demonstrated explicitly in the context of the Skyrmion that there are fewer dynamical zero modes than static ones due to the Witten-Wess-Zumino term in the action. Group-theoretic methods are employed to identify the physical states resulting from canonical quantization of the collectively rotating soliton. The collective states fall into representations of SU(3) flavor labeled by $(p,q)$ and are given by $(2J, \frac{Nc}{2} -J)$ where $J={1/2},{3/2},...$ is the spin of the collective state. States with strangeness $S > 0$ do not arise as collective states from this procedure; thus the $\theta^{+}$ (pentaquark) resonance does not arise as a collective excitation in models of this type.Comment: 12 pages; uses package "youngtab

From ultraviolet to Prussian blue: a spectral response for the cyanotype process and a safe educational activity to explain UV exposure for all ages

Engaging students and the public in understanding UV radiation and its effects is achievable using the real time experiment that incorporates blueprint paper, an 'educational toy' that is a safe and easy demonstration of the cyanotype chemical process. The cyanotype process works through the presence of UV radiation. The blueprint paper was investigated to be used as not only engagement in discussion for public outreach about UV radiation, but also as a practical way to introduce the exploration of measurement of UV radiation exposure and as a consequence, digital image analysis. Tests of print methods and experiments, dose response, spectral response and dark response were investigated. Two methods of image analysis for dose response calculation are provided using easy to access software and two methods of pixel count analysis were used to determine spectral response characteristics. Variation in manufacture of the blueprint paper product indicates some variance between measurements. Most importantly, as a result of this investigation, a preliminary spectral response range for the radiation required to produce the cyanotype reaction is presented here, which has until now been unknown

Non-diffusive transport in plasma turbulence: a fractional diffusion approach

Numerical evidence of non-diffusive transport in three-dimensional, resistive pressure-gradient-driven plasma turbulence is presented. It is shown that the probability density function (pdf) of test particles' radial displacements is strongly non-Gaussian and exhibits algebraic decaying tails. To model these results we propose a macroscopic transport model for the pdf based on the use of fractional derivatives in space and time, that incorporate in a unified way space-time non-locality (non-Fickian transport), non-Gaussianity, and non-diffusive scaling. The fractional diffusion model reproduces the shape, and space-time scaling of the non-Gaussian pdf of turbulent transport calculations. The model also reproduces the observed super-diffusive scaling