Error, bias, and long-branch attraction in data for two chloroplast photosystem genes in seed plants

Sequences of two chloroplast photosystem genes, psaA and psbB, together comprising about 3,500 bp, were obtained for all five major groups of extant seed plants and several outgroups among other vascular plants. Strongly supported, but significantly conflicting, phylogenetic signals were obtained in parsimony analyses from partitions of the data into first and second codon positions versus third positions. In the former, both genes agreed on a monophyletic gymnosperms, with Gnetales closely related to certain conifers. In the latter, Gnetales are inferred to be the sister group of all other seed plants, with gymnosperms paraphyletic. None of the data supported the modern ‘‘anthophyte hypothesis,’’ which places Gnetales as the sister group of flowering plants. A series of simulation studies were undertaken to examine the error rate for parsimony inference. Three kinds of errors were examined: random error, systematic bias (both properties of finite data sets), and statistical inconsistency owing to long-branch attraction (an asymptotic property). Parsimony reconstructions were extremely biased for third-position data for psbB. Regardless of the true underlying tree, a tree in which Gnetales are sister to all other seed plants was likely to be reconstructed for these data. None of the combinations of genes or partitions permits the anthophyte tree to be reconstructed with high probability. Simulations of progressively larger data sets indicate the existence of long-branch attraction (statistical inconsistency) for third-position psbB data if either the anthophyte tree or the gymnosperm tree is correct. This is also true for the anthophyte tree using either psaA third positions or psbB first and second positions. A factor contributing to bias and inconsistency is extremely short branches at the base of the seed plant radiation, coupled with extremely high rates in Gnetales and nonseed plant outgroups. M. J. Sanderson,* M. F. Wojciechowski,*† J.-M. Hu,* T. Sher Khan,* and S. G. Brad

EFFECTS OF JOINT PRODUCT MANAGEMENT STRATEGIES ON E.COLI 0157:H7 AND FEEDLOT PROFITS

The objective of this study was to determine the effect of Escherichia coli 0157:H7 on feedlot profits. Fecal samples from 711 feedlot pens in 73 feedlots in Nebraska, Kansas, Oklahoma, and Texas were tested for E. coli 0157:H7. Average daily gain and feed-to-gain ratios were computed for each feedlot pen, and managers from each feedlot provided information on various feedlot management practices. Cattle performance and E. coli 0157:H7 prevalence are both affected by feedlot management practices. The indirect effect of E. coli 0157:H7 on potential feedlot profits was determined by measuring the effects of management practices on E. coli 0157:H7 levels and cattle performance. Management practices that affect cattle performance were identified using ordinary least squares regressions. A negative binomial regression was used to identify management practices that affect E. coli 0157:H7 prevalence. Certain feedlot management practices were identified that have a joint impact on cattle performance and E. coli 0157:H7 prevalence. Using predatory insects to control flies, controlling for stray dogs, foxes, and coyotes in feed areas, removing manure from pens during finishing, and including tallow in the ration were management strategies associated with higher feedlot profits and lower E. coli 0157:H7 prevalence. Using mobile sprinklers for dust control and including alfalfa or sorghum hay or silage in the ration were associated with lower E. coli 0157:H7 prevalence and lower feedlot profits. Increasing days between cleaning water tanks and restricting movement of horses were associated with higher feedlot profits and higher E. coli 0157:H7 levels. Controlling for stray cats in feed areas and including liquid protein in the ration were associated with lower feedlot profits and higher E. coli 0157:H7 levels. These specific management strategies, which were not robust through a sensitivity analysis, should be interpreted with caution. The general categories of management strategies, however, were robust and consistent with past researchLivestock Production/Industries,

Lift, Drag and Thrust Measurement in a Hypersonic Impulse Facility

This paper reports the extension of the stress wave force balance to the measurement of forces on models which are non-axisymmetric or which have non-axisymmetric load distributions. Recent results are presented which demonstrate the performance of the stress wave force balance for drag measurement, for three-component force measurement and preliminary results for thrust measurement on a two-dimensional scramjet nozzle. In all cases, the balances respond within a few hundred microseconds

Dissection of a composite volcanic earthquake at Santiaguito, Guatemala

Volcano earthquake sources associated with eruptions at Santiaguito volcano in Guatemala are complex. Rock fracture, fluid now, and gas expansion occur at variable time scales and induce superposed ground motions, including both static and dynamic deformation, and atmospheric pressure disturbances. Dissection of this composite event is facilitated through extra-seismic observations, such as infrasound, geodetic, and visual monitoring. Multi-parametric investigation of an eruptive event on Jan. 4th 2009 reveals increased degassing, apparent as both geodetic tilt and harmonic seismoinfrasonic tremor, preceding an explosive event. The explosive event itself entails surface dome uplift, multiple eruptive pulses, and subsequent re-equilibration of the volcanic edifice manifested in derived tilt. We report here on an integrated approach to discerning the physical processes at the actively effusing and exploding Santiaguito volcano and describe the composite earthquake that ' occurs here

Crossover between ionic/covalent and pure ionic bonding in magnesium oxyde clusters

An empirical potential with fluctuating charges is proposed for modelling (MgO)_n clusters in both the molecular (small n) and bulk (n->infty) regimes. Vectorial polarization forces are explicitely taken into account in the self-consistent determination of the charges. Our model predicts cuboid cluster structures, in agreement with previous experimental and theoretical results. The effective charge transferred between magnesium and oxygen smoothly increases from 1 to 2, with an estimated crossover size above 300 MgO molecules

Environmentally relevant iron oxide nanoparticles produce limited acute pulmonary effects in rats at realistic exposure levels

Iron is typically the dominant metal in the ultrafine fraction of airborne particulate matter. Various studies have investigated the toxicity of inhaled nano-sized iron oxide particles (FeOxNPs) but their results have been contradictory, with some indicating no or minor effects and others finding effects including oxidative stress and inflammation. Most studies, however, did not use materials reflecting the characteristics of FeOxNPs present in the environment. We, therefore, analysed the potential toxicity of FeOxNPs of different forms (Fe3O4 , α-Fe2O3 and γ-Fe2O3 ) reflecting the characteristics of high iron content nano-sized particles sampled from the environment, both individually and in a mixture (FeOx-mix). A preliminary in vitro study indicated Fe3O4 and FeOx-mix were more cytotoxic than either form of Fe2O3 in human bronchial epithelial cells (BEAS-2B). Follow-up in vitro (0.003, 0.03, 0.3 µg/mL, 24 h) and in vivo (Sprague–Dawley rats, nose-only exposure, 50 µg/m3 and 500 µg/m3 , 3 h/d × 3 d) studies therefore focused on these materials. Experiments in vitro explored responses at the molecular level via multi-omics analyses at concentrations below those at which significant cytotoxicity was evident to avoid detection of responses secondary to toxicity. Inhalation experiments used aerosol concentrations chosen to produce similar levels of particle deposition on the airway surface as were delivered in vitro. These were markedly higher than environmental concentrations. No clinical signs of toxicity were seen nor effects on BALF cell counts or LDH levels. There were also no significant changes in transcriptomic or metabolomic responses in lung or BEAS-2B cells to suggest adverse effects

The long-term fate of permafrost peatlands under rapid climate warming

Permafrost peatlands contain globally important amounts of soil organic carbon, owing to cold conditions which suppress anaerobic decomposition. However, climate warming and permafrost thaw threaten the stability of this carbon store. The ultimate fate of permafrost peatlands and their carbon stores is unclear because of complex feedbacks between peat accumulation, hydrology and vegetation. Field monitoring campaigns only span the last few decades and therefore provide an incomplete picture of permafrost peatland response to recent rapid warming. Here we use a high-resolution palaeoecological approach to understand the longer-term response of peatlands in contrasting states of permafrost degradation to recent rapid warming. At all sites we identify a drying trend until the late-twentieth century; however, two sites subsequently experienced a rapid shift to wetter conditions as permafrost thawed in response to climatic warming, culminating in collapse of the peat domes. Commonalities between study sites lead us to propose a five-phase model for permafrost peatland response to climatic warming. This model suggests a shared ecohydrological trajectory towards a common end point: inundated Arctic fen. Although carbon accumulation is rapid in such sites, saturated soil conditions are likely to cause elevated methane emissions that have implications for climate-feedback mechanisms

Discrete cilia modelling with singularity distributions

We discuss in detail techniques for modelling flows due to finite and infinite arrays of beating cilia. An efficient technique, based on concepts from previous ‘singularity models’ is described, that is accurate in both near and far-fields. Cilia are modelled as curved slender ellipsoidal bodies by distributing Stokeslet and potential source dipole singularities along their centrelines, leading to an integral equation that can be solved using a simple and efficient discretisation. The computed velocity on the cilium surface is found to compare favourably with the boundary condition. We then present results for two topics of current interest in biology. 1) We present the first theoretical results showing the mechanism by which rotating embryonic nodal cilia produce a leftward flow by a ‘posterior tilt,’ and track particle motion in an array of three simulated nodal cilia. We find that, contrary to recent suggestions, there is no continuous layer of negative fluid transport close to the ciliated boundary. The mean leftward particle transport is found to be just over 1 μm/s, within experimentally measured ranges. We also discuss the accuracy of models that represent the action of cilia by steady rotlet arrays, in particular, confirming the importance of image systems in the boundary in establishing the far-field fluid transport. Future modelling may lead to understanding of the mechanisms by which morphogen gradients or mechanosensing cilia convert a directional flow to asymmetric gene expression. 2) We develop a more complex and detailed model of flow patterns in the periciliary layer of the airway surface liquid. Our results confirm that shear flow of the mucous layer drives a significant volume of periciliary liquid in the direction of mucus transport even during the recovery stroke of the cilia. Finally, we discuss the advantages and disadvantages of the singularity technique and outline future theoretical and experimental developments required to apply this technique to various other biological problems, particularly in the reproductive system

The evolution of galaxy groups and of galaxies therein

Properties of groups of galaxies depend sensitively on the algorithm for group selection, and even the most recent catalogs of groups built from redshift-space selection should suffer from projections and infalling galaxies. The cosmo-dynamical evolution of groups from initial Hubble expansion to collapse and virialization leads to a fundamental track (FT) in virial-theorem-M/L vs crossing time. The increased rates of mergers, both direct and after dynamical friction, in groups relative to clusters, explain the higher fraction of elliptical galaxies at given local number density in X-ray selected groups, relative to clusters, even when the hierarchical evolution of groups is considered. Galaxies falling into groups and clusters should later travel outwards to typically 2 virial radii, which is somewhat less than the outermost radius where observed galaxy star formation efficiencies are enhanced relative to field galaxies of same morphological type. An ongoing analysis of the internal kinematics of X-ray selected groups suggests that the radial profiles of line of sight velocity dispersion are consistent with isotropic NFW distributions for the total mass density, with higher (lower) concentrations than LambdaCDM predictions in groups of high (low) mass. The critical mass, at M200 ~ 10^13 M_sun is consistent with possible breaks in the X-ray luminosity-temperature and Fundamental Plane relations. The internal kinematics of groups indicate that the M-T relation of groups should agree with that extrapolated from clusters with no break at the group scale. The analyses of observed velocity dispersion profiles and of the FT both suggest that low velocity dispersion groups (compact and loose, X-ray emitting or undetected) are quite contaminated by chance projections.Comment: Invited review, ESO workshop "Groups of Galaxies in the Nearby Universe", held in Santiago, Chile, 5-9 December 2005, ed. I. Saviane, V. Ivanov & J. Borissova, 16 page