Molecular simulations of metal adsorption to bacterial surfaces

The atomic-scale interactions that occur between cations and the metal-binding cell wall components common to many gram-positive bacteria were investigated using molecular simulations techniques. We examined the adsorption of Cd and Pb onto peptidoglycan and teichoic acid components of the bacterial cell wall using classical energy force field methods. Within the framework of molecular mechanics and the Cerius² modeling software, we used energy minimization, conformational analysis, and molecular dynamics to examine the different components of the cell wall and to determine relative binding energies and structural configurations of the cell wall components, both with and without the metals present. Electronic structure calculations of representative metal-organic complexes validate the more practical classical methods required in simulating the large number of atoms associated with the cell wall components. The classical force field simulations were conducted in both gas phase and solvated periodic cells. Force field-based simulation techniques can adequately describe the interactions of Cd with the cell wall, defining both metal ion coordinations and binding distances. However, the classical force field approach is inconsistent in describing the observed Pb-cell wall interactions due to possible limitations in the force field parameters, the propensity for Pb to form hydroxides at circumneutral pH, or the dominance of other adsorption mechanisms.     

Thermal and isotopic profiling of the Pipeline hydrothermal system: Application to exploration for Carlin-type gold deposits

New exploration techniques are vital to the search for new orebodies in mature terranes, as well as for extensions of existing orebodies. This research focused on application of low-temperature dating techniques (primarily apatite fission-tracks) and stable isotope measurements (carbon and oxygen in carbonate rocks) in and around the Pipeline deposit, a Carlin-type gold system. The primary purpose of the project was to assess whether these techniques could provide exploration vectors that might be used in conjunction with other geologic, geochemical, and geophysical techniques to determine the locus of fossil hydrothermal fluid flow, and the attendant possibility of finding economic mineral deposits.At Pipeline, measurements of apatite fission-tracks and (U − Th) / He geochronometry yield a clear indication of the elevated temperatures associated with the fossil hydrothermal system. The pattern is one of a central target (Pipeline deposit) with decreasing thermal effects as far as several kilometers laterally from the known ore zone. Because of the irregular nature of fluid flow through fractures, a significant number of samples are required to discern this pattern, but the pattern is quite clear from the 32 samples in and around the Pipeline pit.Stable isotope measurements of carbonate rocks yield patterns centered on the Pipeline pit area. Oxygen isotopes in particular are shifted toward lower values as the result of interaction between the hydrothermal fluids and carbonate rocks. Carbon isotopes show a pattern, but it is somewhat more difficult to interpret than the oxygen isotope pattern. As with the geochronometric patterns, isotopic indications of fluid flow are present several kilometers from the ore zone at Pipeline. Also as with the geochronometric data, a relatively large sample set is required to see the pattern. At Pipeline, the patterns are evident in approximately 45 surface samples and very clearly in the cross-sections containing approximately 100 samples.From these data, it is clear that thermal and stable isotopic measurements on rocks at a significant distance from the known Pipeline hydrothermal system record the passage of hot fluids through the rock. Both techniques provide a footprint of the Pipeline system that is several diameters larger than the ore zone (as presently known). Therefore, thermochronologic and stable isotopic measurements can be utilized in conjunction with other techniques as part of an overall exploration strategy for Carlin-type deposits. Although these techniques do not provide a direct indication of the metal content of the fossil hydrothermal fluids, they do provide an indication of the robustness of fluid flow and the potential size of a hydrothermal system.     

Geochemistry of silicic magmas in the Macolod Corridor, SW Luzon, Philippines: evidence of distinct, mantle-derived, crustal sources for silicic magmas

Silicic volcanic deposits (>65 wt% SiO₂), which occur as domes, lavas and pyroclastic deposits, are relatively abundant in the Macolod Corridor, SW Luzon, Philippines. At Makiling stratovolcano, silicic domes occur along the margins of the volcano and are chemically similar to the silicic lavas that comprise part of the volcano. Pyroclastic flows are associated with the Laguna de Bay Caldera and these are chemically distinct from the domes and lavas at Makiling stratovolcano. As a whole, samples from the Laguna de Bay Caldera contain lower concentrations of MgO and higher concentrations of Fe₂O_3(t) than the samples from domes and lavas. The Laguna de Bay samples are more enriched in incompatible trace elements. The silicic rocks from the domes, Makiling Volcano and Laguna de Bay Caldera all contain high alkalis and high K₂O/Na₂O ratios. Melting experiments of primitive basalts and andesites demonstrate that it is difficult to produce high K₂O/Na₂O silicic magmas by fractional crystallization or partial melting of a low K₂O/Na₂O source. However, recent melting experiments (Sisson et al., Contrib Mineral Petrol 148:635–661, 2005) demonstrate that extreme fractional crystallization or partial melting of K-rich basalts can produce these silicic magmas. Our model for the generation of the silicic magmas in the Macolod Corridor requires partial melting of mantle-derived, evolved, moderate to K-rich, crystallized calc-alkaline magmas that ponded and crystallized in the mid-crust. Major and trace element variations, along with oxygen isotopes and ages of the deposits, are consistent with this model. Electronic Supplementary Material Supplementary material is available for this article at     

Diffusion-limited REE uptake by eclogite garnets and its consequences for Lu–Hf and Sm–Nd geochronology

Garnets from the Zermatt-Saas Fee eclogites contain narrow central peaks for Lu + Yb + Tm ± Er and at least one additional small peak towards the rim. The REE Sm + Eu + Gd + Tb ± Dy are depleted in the cores but show one prominent peak close to the rim. These patterns cannot be modeled using Rayleigh fractionation accompanied by mineral breakdown reactions. Instead, the patterns are well explained using a transient matrix diffusion model where REE uptake is limited by diffusion in the matrix surrounding the porphyroblast. Observed profiles are well matched if a roughly linear radius growth rate is used. The secondary peaks in the garnet profiles are interpreted to reflect thermally activated diffusion due to temperature increase during prograde metamorphism. The model predicts anomalously low ¹⁷⁶Lu/¹⁷⁷Hf and ¹⁴⁷Sm/¹⁴⁴Nd ratios in garnets where growth rates are fast compared to diffusion of the REE, and these results have important implications for Lu–Hf and Sm–Nd geochronology using garnet.     

Determining the trophic guilds of fishes and macroinvertebrates in a seagrass food web

We established trophic guilds of macroinvertebrate and fish taxa using correspondence analysis and a hierarchical clustering strategy for a seagrass food web in winter in the northeastern Gulf of Mexico. To create the diet matrix, we characterized the trophic linkages of macroinvertebrate and fish taxa present inHalodule wrightii seagrass habitat areas within the St. Marks National Wildlife Refuge (Florida) using binary data, combining dietary links obtained from relevant literature for macroinvertebrates with stomach analysis of common fishes collected during January and February of 1994. Heirarchical average-linkage cluster analysis of the 73 taxa of fishes and macroinvertebrates in the diet matrix yielded 14 clusters with diet similarity ≥ 0.60. We then used correspondence analysis with three factors to jointly plot the coordinates of the consumers (identified by cluster membership) and of the 33 food sources. Correspondence analysis served as a visualization tool for assigning each taxon to one of eight trophic guilds: herbivores, detritivores, suspension feeders, omnivores, molluscivores, meiobenthos consumers, macrobenthos consumers and piscivores. These trophic groups, corss-classified with major taxonomic groups, were further used to develop consumer compartments in a network analysis model of carbon flow in this seagrass ecosystem. The method presented here should greatly improve the development of future network models of food webs by providing an objective procedure for aggregating trophic groups.     

Pauperizing the pastoral periphery: the marginalization of herding communities in the world's dry lands

Environmental degradation and other socio-economic problems are too often discerned in contemporary pastoral systems in the wake of global economic change. This paper identifies cases where pastoral people respond to external pressures and opportunities in positive ways and adapt to changes. We hope that by doing this a framework of pastoral adaptations can be developed. The first part of this paper focuses on impacts of global economic change, which are mostly negative in nature. Through an extensive literature search in geography, anthropology, range management, and development field, the second part introduces cases that we categorize as positive adaptations.     

Exploration and discovery in Yellowstone Lake: results from high-resolution sonar imaging, seismic reflection profiling, and submersible studies

‘No portion of the American continent is perhaps so rich in wonders as the Yellow Stone’ (F.V. Hayden, September 2, 1874)Discoveries from multi-beam sonar mapping and seismic reflection surveys of the northern, central, and West Thumb basins of Yellowstone Lake provide new insight into the extent of post-collapse volcanism and active hydrothermal processes occurring in a large lake environment above a large magma chamber. Yellowstone Lake has an irregular bottom covered with dozens of features directly related to hydrothermal, tectonic, volcanic, and sedimentary processes. Detailed bathymetric, seismic reflection, and magnetic evidence reveals that rhyolitic lava flows underlie much of Yellowstone Lake and exert fundamental control on lake bathymetry and localization of hydrothermal activity. Many previously unknown features have been identified and include over 250 hydrothermal vents, several very large (>500 m diameter) hydrothermal explosion craters, many small hydrothermal vent craters (1–200 m diameter), domed lacustrine sediments related to hydrothermal activity, elongate fissures cutting post-glacial sediments, siliceous hydrothermal spire structures, sublacustrine landslide deposits, submerged former shorelines, and a recently active graben. Sampling and observations with a submersible remotely operated vehicle confirm and extend our understanding of the identified features. Faults, fissures, hydrothermally inflated domal structures, hydrothermal explosion craters, and sublacustrine landslides constitute potentially significant geologic hazards. Toxic elements derived from hydrothermal processes also may significantly affect the Yellowstone ecosystem.     

A rooftop tuned mass damper frame

This article documents the analytical study and feasibility of placing a tuned mass damper in the form of a limber rooftop moment frame atop relatively stiff structures to reduce seismic acceleration response. Six existing structures were analytically studied using a suite of time history and response spectra records. The analyses indicate that adding mass in conjunction with a limber frame results in an increase in the fundamental period of each structure. The fundamental period increase generally results in a decrease in seismic acceleration response for the same time history and response spectra records. Owing to the limber nature of the rooftop frames, non‐linear analysis methods were required to evaluate the stability of the rooftop tuned mass damper frame. The results indicate the addition of a rooftop tuned mass damper frame reduces the seismic acceleration response for most cases although acceleration response can increase if the rooftop frame is not tuned to accommodate the specific structure's dynamic behaviour and localized soil conditions. Appropriate design of the rooftop tuned mass damper frame can result in decreased seismic acceleration response. This translates to safer structures if used as a retrofit measure or a more economical design if used for new construction. Copyright © 2003 John Wiley & Sons, Ltd.     

Natural Gradient Tracer Test to Evaluate Natural Attenuation of MTBE Under Anaerobic Conditions

A natural gradient tracer test using perdeuterated MTBE was conducted in an anaerobic aquifer to determine the relative importance of dispersion and degradation in reducing MTBE concentrations in ground water. Preliminary ground water chemistry and hydraulic conductivity data were used to place the tracer within an existing dissolved MTBE plume at Port Hueneme, California. Following one year of transport, the tracer plume was characterized in detail.
Longitudinal dispersion was identified as the dominant mechanism for lowering the perdeuterated MTBE concentrations. The method of moments was used to determine the longitudinal and lateral dispersion coefficients (0.85 m²/day and 0.08 m²/day, respectively). A mass-balance analysis, carried out after one year of transport, accounted for 110% of the injected mass and indicated that no significant mass loss occurred. The plume structure created by zones of higher and lower hydraulic conductivity at the site was complex, consisting of several localized areas of high tracer concentration in a lower concentration plume. This is important because the aquifer has generally been characterized as exhibiting fairly minor heterogeneity. In addition, the tracer plume followed a curved flowpath that deviated from the more macroscopic direction of ground water flow inferred from local ground water elevation measurements and the behavior of the existing plume. Understanding the mass balance, plume structure, curvature of the tracer plume, and consequently natural attenuation behavior required the detailed sampling approach employed in this study. These data imply that a detailed understanding of site hydrogeology and an extensive sampling network may be critical for the correct interpretation of monitored natural attenuation of MTBE.