The gut microbiome: Relationships with disease and opportunities for therapy.

Over the past decade, our view of human-associated microbes has expanded beyond that of a few species toward an appreciation of the diverse and niche-specialized microbial communities that develop in the human host with chronological age. The largest reservoir of microbes exists in the distal gastrointestinal tract, both in the lumen, where microbes facilitate primary and secondary metabolism, and on mucosal surfaces, where they interact with host immune cell populations. While local microbial-driven immunomodulation in the gut is well described, more recent studies have demonstrated a role for the gut microbiome in influencing remote organs and mucosal and hematopoietic immune function. Unsurprisingly, therefore, perturbation to the composition and function of the gut microbiota has been associated with chronic diseases ranging from gastrointestinal inflammatory and metabolic conditions to neurological, cardiovascular, and respiratory illnesses. Considerable effort is currently focused on understanding the natural history of microbiome development in humans in the context of health outcomes, in parallel with improving our knowledge of microbiome-host molecular interactions. These efforts ultimately aim to develop effective approaches to rehabilitate perturbed human microbial ecosystems as a means to restore health or prevent disease. This review details the role of the gut microbiome in modulating host health with a focus on immunomodulation and discusses strategies for manipulating the gut microbiome for the management or prevention of chronic inflammatory conditions

Three-photon resonant four-photon ionization of H_2 via the C^1 ∏_u state

Ab initio calculations are presented for the vibrational branching ratios in three-photon resonant four-photon ionization of H_2 via the C^1Π_u state. Energy and internuclear distance dependences of the boundfree electronic transition matrix element are explicitly included to estimate deviations from the Franck-Condon approximation. While our calculated branching ratios confirm certain important trends seen experimentally, some differences remain

Photoionization cross sections of rovibrational levels of the B^1Σ^+_u state of H_2

We report theoretical cross sections for direct photoionization of specific rovibrational levels of the B ^1Σ^+_u electronic state of H_2. The calculated cross sections differ considerably from values recently determined by resonant enhanced multiphoton ionization (REMPI) studies. In an attempt to understand the disagreement, we analyze in detail the REMPI dynamics and find that the multiphoton ionization probability is extremely sensitive to the spatial and temporal profiles of the laser pulses. Accurate characterization of laser profiles and their jitter is therefore necessary for a comparison between theory and experiment

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

(2+1) resonant enhanced multiphoton ionization of H_2 via the E, F^(1)Σ^+_g state

In this paper, we report the results of ab initio calculations of photoelectron angular distributions and vibrational branching ratios for the (2+1) REMPI of H_2 via the E, F^(1)Σ^+_g state, and compare these with the experimental data of Anderson et al. [Chem. Phys. Lett. 105, 22 (1984)]. These results show that the observed non‐Franck–Condon behavior is predominantly due to the R dependence of the transition matrix elements, and to a lesser degree to the energy dependence. This work presents the first molecular REMPI study employing a correlated wave function to describe the Rydberg–valence mixing in the resonant intermediate state

Statistical multifragmentation model with discretized energy and the generalized Fermi breakup. I. Formulation of the model

The Generalized Fermi Breakup recently demonstrated to be formally equivalent to the Statistical Multifragmentation Model, if the contribution of excited states are included in the state densities of the former, is implemented. Since this treatment requires the application of the Statistical Multifragmentation Model repeatedly on the hot fragments until they have decayed to their ground states, it becomes extremely computational demanding, making its application to the systems of interest extremely difficult. Based on exact recursion formulae previously developed by Chase and Mekjian to calculate the statistical weights very efficiently, we present an implementation which is efficient enough to allow it to be applied to large systems at high excitation energies. Comparison with the GEMINI++ sequential decay code shows that the predictions obtained with our treatment are fairly similar to those obtained with this more traditional model.Comment: 8 pages, 6 figure

Light transmission assisted by Brewster-Zennek modes in chromium films carrying a subwavelength hole array

This work confirms that not only surface plasmons but many other kinds of electromagnetic eigenmodes should be considered in explaining the values of the transmittivity through a slab bearing a two-dimensional periodic corrugation. Specifically, the role of Brewster-Zennek modes appearing in metallic films exhibiting regions of weak positive dielectric constant. It is proposed that these modes play a significant role in the light transmission in a thin chromium film perforated with normal cylindrical holes, for appropriate lattice parameters.Comment: 5 pages, 4 figures. Published versio

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