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Multi-omic responses of fish exposed to complex chemical mixtures in the Shenandoah River watershed

To evaluate relationships between different anthropogenic impacts, contaminant occurrence, and fish health, we conducted in situ fish exposures across the Shenandoah River watershed at five sites with different land use. Exposure water was analyzed for over 500 chemical constituents, and organismal, metabolomic, and transcriptomic endpoints were measured in fathead minnows. Adverse reproductive outcomes were observed in fish exposed in the upper watershed at both wastewater treatment plant (WWTP) effluent- and agriculture-impacted sites, including decreased gonadosomatic index and altered secondary sex characteristics. This was accompanied with increased mortality at the site most impacted by agricultural activities. Molecular biomarkers of estrogen exposure were unchanged and consistent with low or non-detectable concentrations of common estrogens, indicating that alternative mechanisms were involved in organismal adverse outcomes. Hepatic metabolomic and transcriptomic profiles were altered in a site-specific manner, consistent with variation in land use and contaminant profiles. Integrated biomarker response data were useful for evaluating mechanistic linkages between contaminants and adverse outcomes, suggesting that reproductive endocrine disruption, altered lipid processes, and immunosuppression may have been involved in these organismal impacts. This study demonstrated linkages between human-impact, contaminant occurrence, and exposure effects in the Shenandoah River watershed and showed increased risk of adverse outcomes in fathead minnows exposed to complex mixtures at sites impacted by municipal wastewater discharges and agricultural practices.

Virginia, West Virginia

Assessing spatial coupling in complex population dynamics using mutual prediction and continuity statistics

A number of important questions in ecology involve the possibility of interactions or ?coupling? among potential components of ecological systems. The basic question of whether two components are coupled (exhibit dynamical interdependence) is relevant to investigations of movement of animals over space, population regulation, food webs and trophic interactions, and is also useful in the design of monitoring programs. For example, in spatially extended systems, coupling among populations in different locations implies the existence of redundant information in the system and the possibility of exploiting this redundancy in the development of spatial sampling designs. One approach to the identification of coupling involves study of the purported mechanisms linking system components. Another approach is based on time series of two potential components of the same system and, in previous ecological work, has relied on linear cross-correlation analysis. Here we present two different attractor-based approaches, continuity and mutual prediction, for determining the degree to which two population time series (e.g., at different spatial locations) are coupled. Both approaches are demonstrated on a one-dimensional predator?prey model system exhibiting complex dynamics. Of particular interest is the spatial asymmetry introduced into the model as linearly declining resource for the prey over the domain of the spatial coordinate. Results from these approaches are then compared to the more standard cross-correlation analysis. In contrast to cross-correlation, both continuity and mutual prediction are clearly able to discern the asymmetry in the flow of information through this system.

Theoretical Population Biology

Range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) in northwestern North America

The dynamic geological and climatic history of northwestern North America has made it a focal region for phylogeography. We conducted a range-wide phylogeographic analysis of the spotted frog complex (Rana luteiventris and Rana pretiosa) across its range in northwestern North America to understand its evolutionary history and the distribution of clades to inform conservation of R. pretiosa and Great Basin R. luteiventris, candidates for listing under the US Endangered Species Act. Mitochondrial DNA sequence data from a segment of the cytochrome b gene were obtained from 308 R. luteiventris and R. pretiosa from 96 sites. Phylogenetic analysis revealed one main R. pretiosa clade and three main R. luteiventris clades, two of which overlapped in southeastern Oregon. The three R. luteiventris clades were separated from each other by high levels of sequence divergence (average of 4.75-4.97%). Two divergent clades were also uncovered within the Great Basin. Low genetic variation in R. pretiosa and the southeastern Oregon clade of R. luteiventris suggests concern about their vulnerability to extinction. ?? 2008 Elsevier Inc.

Molecular Phylogenetics and Evolution

U-Pb geochronology of zircon and polygenetic titanite from the Glastonbury Complex, Connecticut, USA: An integrated SEM, EMPA, TIMS, and SHRIMP study

U-Pb ages for zircon and titanite from a granodioritic gneiss in the Glastonbury Complex, Connecticut, have been determined using both isotope dilution thermal ionization mass spectrometry (TIMS) and the sensitive high resolution ion microprobe (SHRIMP). Zircons occur in three morphologic populations: (1) equant to stubby, multifaceted, colorless, (2) prismatic, dark brown, with numerous cracks, and (3) elongate, prismatic, light tan to colorless. Cathodoluminescence (CL) imaging of the three populations shows simple concentric oscillatory zoning. The zircon TIMS age [weighted average of 207Pb/206Pb ages from Group 3 grains-450.5 ?? 1.6 Ma (MSWD=1.11)] and SHRIMP age [composite of 206Pb/238 U age data from all three groups-448.2 ?? 2.7 Ma (MSWD = 1.3)], are interpreted to suggest a relatively simple crystallization history. Titanite from the granodioritic gneiss occurs as both brown and colorless varieties. Scanning electron microscope backscatter (BSE) images of brown grains show multiple cross-cutting oscillatory zones of variable brightness and dark overgrowths. Colorless grains are unzoned or contain subtle wispy or very faint oscillatory zoning. Electron microprobe analysis (EMPA) clearly distinguishes the two populations. Brown grains contain relatively high concentrations of Fe2O3, Ce2O3 (up to ~ 1.5 wt.%), Nb2O5, and Zr. Cerium concentration is positively correlated with total REE + Y concentration, which together can exceed 3.5 wt.%. Oscillatory zoning in brown titanite is correlated with variations in REE concentrations. In contrast, colorless titanite (both as discrete grains and overgrowths on brown titanite) contains lower concentrations of Y, REE, Fe2O3, and Zr, but somewhat higher Al2O3 and Nb2O5. Uranium concentrations and Th/U discriminate between brown grains (typically 200-400 ppm U; all analyses but one have Th/U between about 0.8 and 2) and colorless grains (10-60 ppm U; Th/U of 0-0.17). In contrast to the zircon U-Pb age results, SHRIMP U-Pb data from titanite indicate multiple growth episodes. In brown grains, oscillatory zoned cores formed at 443 ?? 6 Ma, whereas white (in BSE) cross-cutting zones are 425 ?? 9 Ma. Colorless grains and overgrowths on brown grains yield an age of 265 ?? 8 Ma (using the Total Pb method) or 265 ?? 5 Ma (using the weighted average of the 206Pb/238U ages). However, EMPA chemical data identify zoning that suggests that this colorless titanite may preserve three growth events. Oscillatory zoned portions of brown titanite grains are igneous in origin; white cross-cutting zones probably formed during a previously unrecognized event that caused partial dissolution of earlier titanite and reprecipitation of a slightly younger generation of brown titanite. Colorless titanite replaced and grew over the magmatic titanite during the Permian Alleghanian orogeny. These isotopic data indicate that titanite, like zircon, can contain multiple age components. Coupling SHRIMP microanalysis with EMPA and SEM results on dated zones as presented in this study is an efficient and effective technique to extract additional chronologic ?? 2002 Elsevier Science B.V. All rights reserved.

Chemical Geology

Complexation of copper by aquatic humic substances from different environments

The copper-complexing properties of aquatic humic substances isolated from eighteen different environments were characterized by potentiometric titration, using a cupric ion selective electrode. Potentiometric data were analyzed using FITEQL, a computer program for the determination of chemical equilibrium constants from experimental data. All the aquatic humic substances could be modelled as having two types of Cu(II)-binding sites: one with K equal to about 10 6 and a concentration of 1.0 ± 0.4 × 10 −6 M(mg C) −1 and another with K equal to about 10 8 and a concentration of 2.6 ± 1.6 × 10 −7 M(mg C) −1 . A method is described for estimating the Cu(II)-binding sites associated with dissolved humic substances in natural water based on a measurement of dissolved organic carbon, which may be helpful in evaluating chemical processes controlling speciation of Cu and bioavailability of Cu to aquatic organisms.

Science of the Total Environment

Modeling Np and Pu transport with a surface complexation model and spatially variant sorption capacities: Implications for reactive transport modeling and performance assessments of nuclear waste disposal sites

One-dimensional (1D) geochemical transport modeling is used to demonstrate the effects of speciation and sorption reactions on the ground-water transport of Np and Pu, two redox-sensitive elements. Earlier 1D simulations (Reardon, 1981) considered the kinetically limited dissolution of calcite and its effect on ion-exchange reactions (involving 90 Sr, Ca, Na, Mg and K), and documented the spatial variation of a 90 Sr partition coefficient under both transient and steady-state chemical conditions. In contrast, the simulations presented here assume local equilibrium for all reactions, and consider sorption on constant potential, rather than constant charge, surfaces. Reardon's (1981) seminal findings on the spatial and temporal variability of partitioning (of 90 Sr) are reexamined and found partially caused by his assumption of a kinetically limited reaction. In the present work, sorption is assumed the predominant retardation process controlling Pu and Np transport, and is simulated using a diffuse-double-layer-surface-complexation (DDLSC) model. Transport simulations consider the infiltration of Np- and Pu-contaminated waters into an initially uncontaminated environment, followed by the cleanup of the resultant contamination with uncontaminated water. Simulations are conducted using different spatial distributions of sorption capacities (with the same total potential sorption capacity, but with different variances and spatial correlation structures). Results obtained differ markedly from those that would be obtained in transport simulations using constant K d , Langmuir or Freundlich sorption models. When possible, simulation results (breakthrough curves) are fitted to a constant K d advection–dispersion transport model and compared. Functional differences often are great enough that they prevent a meaningful fit of the simulation results with a constant K d (or even a Langmuir or Freundlich) model, even in the case of Np, a weakly sorbed radionuclide under the simulation conditions. Functional behaviors that cannot be fit include concentration trend reversals and radionuclide desorption spikes. Other simulation results are fit successfully but the fitted parameters ( K d and dispersivity) vary significantly depending on simulation conditions (e.g. “infiltration” vs. “cleanup” conditions). Notably, an increase in the variance of the specified sorption capacities results in a marked increase in the dispersion of the radionuclides. The results presented have implications for the simulation of radionuclide migration in performance assessments of nuclear waste-disposal sites, for the future monitoring of those sites, and more generally for modeling contaminant transport in ground-water environments.

Computers & Geosciences

Formation and failure of volcanic debris dams in the Chakachatna River valley associated with eruptions of the Spurr volcanic complex, Alaska

The formation of lahars and a debris avalanche during Holocene eruptions of the Spurr volcanic complex in south-central Alaska have led to the development of volcanic debris dams in the Chakachatna River valley. Debris dams composed of lahar and debris-avalanche deposits formed at least five times in the last 8000-10,000 years and most recently during eruptions of Crater Peak vent in 1953 and 1992. Water impounded by a large debris avalanche of early Holocene (?) age may have destabilized an upstream glacier-dammed lake causing a catastrophic flood on the Chakachatna River. A large alluvial fan just downstream of the debris-avalanche deposit is strewn with boulders and blocks and is probably the deposit generated by this flood. Application of a physically based dam-break model yields estimates of peak discharge (Qp) attained during failure of the debris-avalanche dam in the range 104 < Qp < 106 m3 s-1 for plausible breach erosion rates of 10-100 m h-1. Smaller, short-lived, lahar dams that formed during historical eruptions in 1953, and 1992, impounded smaller lakes in the upper Chakachatna River valley and peak flows attained during failure of these volcanic debris dams were in the range 103 < Qp < 104 m3 s-1 for plausible breach erosion rates. Volcanic debris dams have formed at other volcanoes in the Cook Inlet region, Aleutian arc, and Wrangell Mountains but apparently did not fail rapidly or result in large or catastrophic outflows. Steep valley topography and frequent eruptions at volcanoes in this region make for significant hazards associated with the formation and failure of volcanic debris dams. Published by Elsevier Science B.V.

Geomorphology

Hatching, dispersal, and bathymetric distribution of age-0 wild lake trout at the Gull Island Shoal complex, Lake Superior

We studied age-0 lake trout ( Salvelinus namaycush ) associated with spawning and nursery areas of the Gull Island Shoal complex in western Lake Superior. Post-emergent age-0 lake trout were captured on rocky spawning substrate with a 3-m beam trawl and at the nursery area with a bottom trawl from June to September 1990 and June to August 1991. Catch data suggested that age-0 lake trout move distances of 7&ndash;11 km to the nursery area over a 3-month period. Water currents, measured at Gull Island Shoal, may be a part of the transport mechanism. Examination of daily-growth increments on the sagittae and back-calculation from the date of capture revealed that most fish hatched between 6 June and 19 July in 1990 and between 30 April and 30 May in 1991. The duration of the hatch was 100 days in 1990 and 120 days in 1991, and the estimated incubation period is about 7 months for lake trout eggs at this site. Similar hatch-date distributions of age-0 captured on different sampling dates suggested that natural mortality was low.

Journal of Great Lakes Research

Cambrian nepheline syenite complex at Jabal Sawda, Midyan region, Kingdom of Saudi Arabia

The only nepheline syenite complex presently known in the Arabian Shield is at Jabal Sawda, about 30 km S of Haql in the extreme NW of Saudi Arabia. It is a post-tectonic, composite intrusion with a crudely concentric structure. A core of leuco-nepheline syenite, a partial ring of mela-nepheline syenite, and an almost complete outer ring of alkali-feldspar syenite are the main rock units. Several mega-inclusions of porphyritic nepheline syenite, nepheline monzosyenite, malignite and ijolite are present in the leuco-nepheline syenite. The chemical composition is notable for very high values of Al 2 O 3 , Na 2 O, Ba, La, Nb, Sr and Zr. U Pb isotope dating indicates an emplacement age of 553 ± 4 Ma, one of an increasing number of reliable Cambrian isotope dates in the northern Red Sea region.

Journal of African Earth Sciences

Learning complex spatial dynamics of wildlife diseases with machine learning-guided partial differential equations

Emerging wildlife pathogens often display geographic variability due to landscape heterogeneity. Modeling approaches capable of learning complex, non-linear spatial dynamics of diseases are needed to rigorously assess and mitigate the effects of pathogens on wildlife health and biodiversity. We propose a novel machine learning (ML)-guided approach that leverages prior physical knowledge of ecological systems, using partial differential equations. We present our approach, taking advantage of the universal function approximation property of neural networks for flexible representation of the underlying dynamics of the geographic spread and growth of wildlife diseases. We demonstrate the benefits of our approach by comparing its forecasting power with commonly used methods and highlighting the obtained insights on disease dynamics. Additionally, we show the theoretical guarantees for the approximation error of our model. We illustrate the implementation of our ML-guided approach using data from white-nose syndrome (WNS) outbreaks in bat populations across the US. WNS is an infectious fungal disease responsible for significant declines in bat populations. Our results on WNS are useful for disease surveillance and bat conservation efforts. Our methods can be broadly used to assess the effects of environmental and anthropogenic drivers impacting wildlife health and biodiversity.

Environmental Data Science

Untargeted lipidomics for determining cellular and sub-cellular responses in Zebrafish (Danio rerio) liver cells following exposure to complex mixtures in U.S. streams

Surface waters often contain a variety of chemical contaminants potentially capable of producing adverse outcomes in both humans and wildlife due to impacts from industrial, urban, and agricultural activity. Here, we report the results of a zebrafish liver (ZFL) cell-based lipidomics approach to assess the potential ecotoxicological effects of complex contaminant mixtures using water collected from eight impacted streams across the United States mainland and Puerto Rico. We initially characterized the ZFL lipidome using high resolution mass spectrometry, resulting in the annotation of 508 lipid species covering 27 classes. We then identified lipid changes induced by all streamwater samples (nonspecific stress indicators) as well as those unique to water samples taken from specific streams. Subcellular impacts were classified based on organelle-specific lipid changes, including increased lipid saturation (endoplasmic reticulum stress), elevated bis(monoacylglycero)phosphate (lysosomal overload), decreased ubiquinone (mitochondrial dysfunction), and elevated ether lipids (peroxisomal stress). Finally, we demonstrate how these results can uniquely inform environmental monitoring and risk assessments of surface waters.

Environmental Science & Technology

Formation of mercury sulfide from Hg(II)−thiolate complexes in natural organic matter

Methylmercury is the environmental form of neurotoxic mercury that is biomagnified in the food chain. Methylation rates are reduced when the metal is sequestered in crystalline mercury sulfides or bound to thiol groups in macromolecular natural organic matter. Mercury sulfide minerals are known to nucleate in anoxic zones, by reaction of the thiol-bound mercury with biogenic sulfide, but not in oxic environments. We present experimental evidence that mercury sulfide forms from thiol-bound mercury alone in aqueous dark systems in contact with air. The maximum amount of nanoparticulate mercury sulfide relative to thiol-bound mercury obtained by reacting dissolved mercury and soil organic matter matches that detected in the organic horizon of a contaminated soil situated downstream from Oak Ridge, TN, in the United States. The nearly identical ratios of the two forms of mercury in field and experimental systems suggest a common reaction mechanism for nucleating the mineral. We identified a chemical reaction mechanism that is thermodynamically favorable in which thiol-bound mercury polymerizes to mercury–sulfur clusters. The clusters form by elimination of sulfur from the thiol complexes via breaking of mercury–sulfur bonds as in an alkylation reaction. Addition of sulfide is not required. This nucleation mechanism provides one explanation for how mercury may be immobilized, and eventually sequestered, in oxygenated surface environments.

Environmental Science & Technology

Surface complexation modeling of U(VI) adsorption by aquifer sediments from a former mill tailings site at Rifle, Colorado

A study of U(VI) adsorption by aquifer sediment samples from a former uranium mill tailings site at Rifle, Colorado, was conducted under oxic conditions as a function of pH, U(VI), Ca, and dissolved carbonate concentration. Batch adsorption experiments were performed using <2mm size sediment fractions, a sand-sized fraction, and artificial groundwater solutions prepared to simulate the field groundwater composition. To encompass the geochemical conditions of the alluvial aquifer at the site, the experimental conditions ranged from 6.8 ?? 10 -8 to 10 -5 M in [U(VI)]tot, 7.2 to 8.0 in pH, 3.0 ?? 10 -3 to 6.0 ?? 10 -3 M in [Ca 2+ ], and 0.05 to 2.6% in partial pressure of carbon dioxide. Surface area normalized U(VI) adsorption Kd values for the sand and <2 mm sediment fraction were similar, suggesting a similar reactive surface coating on both fractions. A two-site two-reaction, nonelectrostatic generalized composite surface complexation model was developed and successfully simulated the U(VI) adsorption data. The model successfully predicted U(VI) adsorption observed from a multilevel sampling well installed at the site. A comparison of the model with the one developed previously for a uranium mill tailings site at Naturita, Colorado, indicated that possible calcite nonequilibrium of dissolved calcium concentration should be evaluated. The modeling results also illustrate the importance of the range of data used in deriving the best fit model parameters. ?? 2009 American Chemical Society.

Environmental Science & Technology

Major histocompatibility complex loci are associated with susceptibility of Atlantic salmon to infectious hematopoietic necrosis virus

Infectious hematopoietic necrosis virus (IHNV) is one of the most significant viral pathogens of salmonids and is a leading cause of death among cultured juvenile fish. Although several vaccine strategies have been developed, some of which are highly protective, the delivery systems are still too costly for general use by the aquaculture industry. More cost effective methods could come from the identification of genes associated with IHNV resistance for use in selective breeding. Further, identification of susceptibility genes may lead to an improved understanding of viral pathogenesis and may therefore aid in the development of preventive and therapeutic measures. Genes of the major histocompatibility complex (MHC), involved in the primary recognition of foreign pathogens in the acquired immune response, are associated with resistance to a variety of diseases in vertebrate organisms. We conducted a preliminary analysis of MHC disease association in which an aquaculture strain of Atlantic salmon was challenged with IHNV at three different doses and individual fish were genotyped at three MHC loci using denaturing gradient gel electrophoresis (PCR-DGGE), followed by sequencing of all differentiated alleles. Nine to fourteen alleles per exon-locus were resolved, and alleles potentially associated with resistance or susceptibility were identified. One allele ( Sasa -B-04) from a potentially non-classical class I locus was highly associated with resistance to infectious hematopoietic necrosis ( p < 0.01). This information can be used to design crosses of specific haplotypes for family analysis of disease associations.

Environmental Biology of Fishes

Application of artificial neural networks to complex groundwater management problems

As water quantity and quality problems become increasingly severe, accurate prediction and effective management of scarcer water resources will become critical. In this paper, the successful application of artificial neural network (ANN) technology is described for three types of groundwater prediction and management problems. In the first example, an ANN was trained with simulation data from a physically based numerical model to predict head (groundwater elevation) at locations of interest under variable pumping and climate conditions. The ANN achieved a high degree of predictive accuracy, and its derived state-transition equations were embedded into a multiobjective optimization formulation and solved to generate a trade-off curve depicting water supply in relation to contamination risk. In the second and third examples, ANNs were developed with real-world hydrologic and climate data for different hydrogeologic environments. For the second problem, an ANN was developed using data collected for a 5-year, 8-month period to predict heads in a multilayered surficial and limestone aquifer system under variable pumping, state, and climate conditions. Using weekly stress periods, the ANN substantially outperformed a well-calibrated numerical flow model for the 71-day validation period, and provided insights into the effects of climate and pumping on water levels. For the third problem, an ANN was developed with data collected automatically over a 6-week period to predict hourly heads in 11 high-capacity public supply wells tapping a semiconfined bedrock aquifer and subject to large well-interference effects. Using hourly stress periods, the ANN accurately predicted heads for 24-hour periods in all public supply wells. These test cases demonstrate that the ANN technology can solve a variety of complex groundwater management problems and overcome many of the problems and limitations associated with traditional physically based flow models.

Natural Resources Research

The complexity of reversals

This chapter contains sections titled: Introduction Some Illustrative Polarity Transition Records The Case for Complexity Conclusions

Geophysical Monograph Series

Aeromagnetic evidence for a volcanic caldera(?) complex beneath the divide of the West Antarctic Ice Sheet

A 1995–96 aeromagnetic survey over part of the Sinuous Ridge (SR) beneath the West Antarctic Ice Sheet (WAIS) divide shows a 70-km diameter circular pattern of 400–1200-nT anomalies suggesting one of the largest volcanic caldera(?) complexes on earth. Radar-ice-sounding (RIS) shows the northern part of this pattern overlies the SR, and extends south over the Bentley Subglacial Trench (BST). Modeled sources of all but one the caldera(?) anomalies are at the base of <1–2-km thick ice and their volcanic edifices have been glacially removed. The exception is a 700-m high, 15-km wide "volcano" producing an 800-nT anomaly over the BST. “Intrusion” of this “volcano” beneath 3 km of ice probably resulted in pillow basalt rather than easily removed hyaloclastite erupted beneath thinner ice. The background area (−300 to −500-nT) surrounding the caldera(?) is possibly caused by a shallow Curie isotherm. We suggest uplift of the SR forced the advance of the WAIS.

Geophysical Research Letters

Geophysical evidence for the evolution of the California Inner Continental Borderland as a metamorphic core complex

We use new seismic and gravity data collected during the 1994 Los Angeles Region Seismic Experiment (LARSE) to discuss the origin of the California Inner Continental Borderland (ICB) as an extended terrain possibly in a metamorphic core complex mode. The data provide detailed crustal structure of the Borderland and its transition to mainland southern California. Using tomographic inversion as well as traditional forward ray tracing to model the wide-angle seismic data, we find little or no sediments, low (≤6.6 km/s) P wave velocity extending down to the crust-mantle boundary, and a thin crust (19 to 23 km thick). Coincident multichannel seismic reflection data show a reflective lower crust under Catalina Ridge. Contrary to other parts of coastal California, we do not find evidence for an underplated fossil oceanic layer at the base of the crust. Coincident gravity data suggest an abrupt increase in crustal thickness under the shelf edge, which represents the transition to the western Transverse Ranges. On the shelf the Palos Verdes Fault merges downward into a landward dipping surface which separates "basement" from low-velocity sediments, but interpretation of this surface as a detachment fault is inconclusive. The seismic velocity structure is interpreted to represent Catalina Schist rocks extending from top to bottom of the crust. This interpretation is compatible with a model for the origin of the ICB as an autochthonous formerly hot highly extended region that was filled with the exhumed metamorphic rocks. The basin and ridge topography and the protracted volcanism probably represent continued extension as a wide rift until ∼13 m.y. ago. Subduction of the young and hot Monterey and Arguello microplates under the Continental Borderland, followed by rotation and translation of the western Transverse Ranges, may have provided the necessary thermomechanical conditions for this extension and crustal inflow.

California