High- and low-affinity binding sites for Cd on the bacterial cell walls of Bacillus subtilis and Shewanella oneidensis

Bulk Cd adsorption isotherm experiments, thermodynamic equilibrium modeling, and Cd K edge EXAFS were used to constrain the mechanisms of proton and Cd adsorption to bacterial cells of the commonly occurring Gram-positive and Gram-negative bacteria, Bacillus subtilis and Shewanella oneidensis, respectively. Potentiometric titrations were used to characterize the functional group reactivity of the S. oneidensis cells, and we model the titration data using the same type of non-electrostatic surface complexation approach as was applied to titrations of B. subtilis suspensions by Fein et al. (2005). Similar to the results for B. subtilis, the S. oneidensis cells exhibit buffering behavior from approximately pH 3-9 that requires the presence of four distinct sites, with pK_a values of 3.3 ± 0.2, 4.8 ± 0.2, 6.7 ± 0.4, and 9.4 ± 0.5, and site concentrations of 8.9(±2.6) × 10⁻⁵, 1.3(±0.2) × 10⁻⁴, 5.9(±3.3) × 10⁻⁵, and 1.1(±0.6) × 10⁻⁴ moles/g bacteria (wet mass), respectively. The bulk Cd isotherm adsorption data for both species, conducted at pH 5.9 as a function of Cd concentration at a fixed biomass concentration, were best modeled by reactions with a Cd:site stoichiometry of 1:1. EXAFS data were collected for both bacterial species as a function of Cd concentration at pH 5.9 and 10 g/L bacteria. The EXAFS results show that the same types of binding sites are responsible for Cd sorption to both bacterial species at all Cd loadings tested (1-200 ppm). Carboxyl sites are responsible for the binding at intermediate Cd loadings. Phosphoryl ligands are more important than carboxyl ligands for Cd binding at high Cd loadings. For the lowest Cd loadings studied here, a sulfhydryl site was found to dominate the bound Cd budgets for both species, in addition to the carboxyl and phosphoryl sites that dominate the higher loadings. The EXAFS results suggest that both Gram-positive and Gram-negative bacterial cell walls have a low concentration of very high-affinity sulfhydryl sites which become masked by the more abundant carboxyl and phosphoryl sites at higher metal:bacteria ratios. This study demonstrates that metal loading plays a vital role in determining the important metal-binding reactions that occur on bacterial cell walls, and that high affinity, low-density sites can be revealed by spectroscopy of biomass samples. Such sites may control the fate and transport of metals in realistic geologic settings, where metal concentrations are low.     

Utilization of a multicriteria least cost path model in an aquatic environment

A critical component of maintaining biodiversity in fragmented habitats is maintaining connectivity among the usable fragments. Least cost path (LCP) analysis is a tool that can be used for predicting the ability of an organism to move from one habitat patch to another, based on geographical features of the landscape and life history traits of the organism. While this analysis has been utilized for terrestrial habitats, it is rarely applied to aquatic environments. Aquatic hypoxic conditions occur when dissolved oxygen falls below 2 mg/L. These conditions can create barriers in the water column that can either force fish to leave a habitat, or avoid that habitat altogether. Using the lower St. Johns River (LSJR) estuary in Florida, USA, as a study system, the ability of an adult silver perch, Bairdiella chrysoura, to escape a large-scale hypoxic event was modeled using a multicriteria LCP approach. Criteria-specific cost grids were constructed based upon current speed, risk of predation, and whether oxygen levels in the habitat area were normoxic (>5.5 mg/L), or hypoxic (<2.0–1.5 mg/L) as a function of water depth for the LSJR. The criteria cost grids were combined using relative weighting to produce the multicriteria cost grid used to implement the LCP analysis. Three origin and destination point locations within the LSJR study area were selected for modeling whether or not a silver perch would be able to escape a hypoxic zone. Since the LCP model will always determine a LCP from the specified origin point location, ecologically relevant swimming capacities for silver perch under normoxic and hypoxic conditions were then applied to assess the model, and to determine whether the fish would be able to reach areas unimpacted by hypoxia. The LCP model and the swimming capacity results for this study predict that under normoxic conditions, fish movement was unimpeded. During the rapidly developing hypoxic event that was modeled, the results from the LCP model indicate that the fish could move outside the hypoxic zone, but when swimming capacities were applied to the model, the silver perch could not escape. Ecologically, the results of this study suggest that silver perch would experience high mortality under a rapidly developing hypoxic event. Additionally, the results of this study indicate that a LCP model can be applied to an aquatic habitat, as long as the cost grids incorporate relevant abiotic and biotic factors.     

Training Images from Process-Imitating Methods

The lack of a suitable training image is one of the main limitations of the application of multiple-point statistics (MPS) for the characterization of heterogeneity in real case studies. Process-imitating facies modeling techniques can potentially provide training images. However, the parameterization of these process-imitating techniques is not straightforward. Moreover, reproducing the resulting heterogeneous patterns with standard MPS can be challenging. Here the statistical properties of the paleoclimatic data set are used to select the best parameter sets for the process-imitating methods. The data set is composed of 278 lithological logs drilled in the lower Namoi catchment, New South Wales, Australia. A good understanding of the hydrogeological connectivity of this aquifer is needed to tackle groundwater management issues. The spatial variability of the facies within the lithological logs and calculated models is measured using fractal dimension, transition probability, and vertical facies proportion. To accommodate the vertical proportions trend of the data set, four different training images are simulated. The grain size is simulated alongside the lithological codes and used as an auxiliary variable in the direct sampling implementation of MPS. In this way, one can obtain conditional MPS simulations that preserve the quality and the realism of the training images simulated with the process-imitating method. The main outcome of this study is the possibility of obtaining MPS simulations that respect the statistical properties observed in the real data set and honor the observed conditioning data, while preserving the complex heterogeneity generated by the process-imitating method. In addition, it is demonstrated that an equilibrium of good fit among all the statistical properties of the data set should be considered when selecting a suitable set of parameters for the process-imitating simulations.     

What is a flux tube? On the magnetic field topology of buoyant flux structures

We study the topology of field lines threading buoyant magnetic flux structures. The magnetic structures, visually resembling idealized magnetic flux tubes, are generated self-consistently by numerical simulation of the interaction of magnetic buoyancy and a localized velocity shear in a stably stratified atmosphere. Depending on the parameters, the system exhibits varying degrees of symmetry. By integrating along magnetic field lines and constructing return maps, we show that, depending on the type of underlying behaviour, the stages of the evolution, and therefore the degree of symmetry, the resulting magnetic structures can have field lines with one of three distinct topologies. When the x -translational and y -reflectional symmetries remain intact, magnetic field lines lie on surfaces but individual lines do not cover the surface. When the y symmetry is broken, magnetic field lines lie on surfaces and individual lines do cover the surface. When both x and y symmetries are broken, magnetic field lines wander chaotically over a large volume of the magnetically active region. We discuss how these results impact our simple ideas of a magnetic flux tube as an object with an inside and an outside, and introduce the concept of 'leaky' tubes.     

Variable Grid Method: An Intuitive Approach for Simultaneously Quantifying and Visualizing Spatial Data and Uncertainty

Efforts to develop applications and methods that effectively quantify and communicate uncertainty associated with spatial data remains a focus within many scientific communities. However, the inherent complexity of uncertainty makes it difficult to define, characterize, and represent. Frequently, the products of spatial and spatio‐temporal data are presented without a clear explanation of the inherent uncertainty underlying the data. As uses and applications for spatial data and their products continues to increase, so does the importance for utilizing reliable approaches to effectively communicate spatial data along with their inherent uncertainties. To address this need, the Variable Grid Method (VGM) was developed as an intuitive approach that simultaneously communicates both spatial patterns and trends and the uncertainty associated with data or their analyses. This article details the VGM approach and demonstrates the utility of the VGM to provide critical information about the relationship between uncertainty and spatial data, necessary to support the increasing utilization of spatial information for a wide range of research and other needs.     

The High-Resolution Coronal Imager (Hi-C)

The High-Resolution Coronal Imager (Hi-C) was flown on a NASA sounding rocket on 11 July 2012. The goal of the Hi-C mission was to obtain high-resolution (≈?0.3?–?0.4′′), high-cadence (≈?5 seconds) images of a solar active region to investigate the dynamics of solar coronal structures at small spatial scales. The instrument consists of a normal-incidence telescope with the optics coated with multilayers to reflect a narrow wavelength range around 19.3 nm (including the Fe xii 19.5-nm spectral line) and a 4096×4096 camera with a plate scale of 0.1′′?pixel^?1. The target of the Hi-C rocket flight was Active Region 11520. Hi-C obtained 37 full-frame images and 86 partial-frame images during the rocket flight. Analysis of the Hi-C data indicates the corona is structured on scales smaller than currently resolved by existing satellite missions.     

H2 in molecular shocks: observations from 2 to 12 microns

We present spectroscopy of the molecular shock in the supernova remnant IC 443. The H₂ level populations in IC 443 are nearly identical to Orion Peak 1 (Brand et al. 1988; Parmar et al. 1994) and are consistent with a partially dissociative J-shock. The similarity with Orion suggests the shock processes which dominate the emission in both regions are essentially identical.     

Two-body motion in the post-Newtonian approximation

The motion of two massive particles is considered within the framework of the first post-Newtonian approximation. The system Hamiltonian is constructed and normalized through first order using a canonical transformation method of implicit variables. Closed-form solutions for the Delaunay elements in the phase space are obtained. The bridge between the phase space and the state space of the Lagrangian of the motion is provided by a velocity-dependent Legendre transformation. By explicit inversion of this transformation, expressions for the Keplerian elements in the state space are obtained from the Delaunay element solutions.     

Estimating background and threshold nitrate concentrations using probability graphs

Because of the ubiquitous nature of anthropogenic nitrate (NO3(-)) in many parts of the world, determining background concentrations of NO3(-) in shallow ground water from natural sources is probably impossible in most environments. Present-day background must now include diffuse sources of NO3(-) such as disruption of soils and oxidation of organic matter, and atmospheric inputs from products of combustion and evaporation of ammonia from fertilizer and livestock waste. Anomalies can be defined as NO3(-) derived from nitrogen (N) inputs to the environment from anthropogenic activities, including synthetic fertilizers, livestock waste, and septic effluent. Cumulative probability graphs were used to identify threshold concentrations separating background and anomalous NO(3)-N concentrations and to assist in the determination of sources of N contamination for 232 spring water samples and 200 well water samples from karst aquifers. Thresholds were 0.4, 2.5, and 6.7 mg/L for spring water samples, and 0.1, 2.1, and 17 mg/L for well water samples. The 0.4 and 0.1 mg/L values are assumed to represent thresholds for present-day precipitation. Thresholds at 2.5 and 2.1 mg/L are interpreted to represent present-day background concentrations of NO(3)-N. The population of spring water samples with concentrations between 2.5 and 6.7 mg/L represents an amalgam of all sources of NO3(-) in the ground water basins that feed each spring; concentrations > 6.7 mg/L were typically samples collected soon after springtime application of synthetic fertilizer. The 17 mg/L threshold (adjusted to 15 mg/L) for well water samples is interpreted as the level above which livestock wastes dominate the N sources.