Enrichment and Fractionation of Rare Earth Elements in an Estuarine Marsh Soil Receiving Acid Discharges from Legacy Sulfide Mine Wastes

This paper provides new insights into the geochemical cycling of rare earth elements (REEs) in acid sulfate soils developed on salt marsh sediments of the Huelva estuary (Spain) as a result of sulfide mineral oxidation in abandoned ore stockpiles. The study was aimed at determining the REE abundance, fractionation pattern and mineralogical control of the dispersal and retention of REEs in the soil system. Forty-one samples were collected at 13 core sampling sites along two transects extending across the degraded marshland, and they were subjected to XRD, ESEM-EDS and ICP-MS analyses. Measurements revealed that the soil receiving acid discharges has relatively high concentrations of SREEs (174.77 +- 19.77 mg kg1) compared to local baseline concentrations. Shale-normalized REE patterns are generally flat, but a slight middle REE (MREE) enrichment is consistently apparent in all soil samples, involving relatively low LaN/GdN ratios (0.83 +- 0.08) and GdN/LuN ratios up to 1.42. The convex-upward REE pattern supports the possibility that iron oxy-hydroxide minerals play an important role in MREE retention through adsorption and co-precipitation mechanisms. Efflorescent sulfate salts left on the topsoil by the evaporation of acid waters show a strong depletion of light REEs (LaN/GdN = 0.16 +- 0.10) and act as a temporary reservoir of labile MREEs and heavy REEs during dry periods.This work has been partially supported by the Andalusian Regional Government (Spain) through the Research Group on Geology and Environmental Geochemistry (RNM-347)

Soil Acidification, Mineral Neoformation and Heavy Metal Contamination Driven by Weathering of Sulphide Wastes in a Ramsar Wetland

Past waste disposal practices have left large volumes of sulphidic material stockpiled in a Ramsar wetland site on the Atlantic coast of southwestern Spain, leading to severe land degradation. With the aim of addressing this legacy issue, soil core samples were collected along two transects extending from the abandoned stockpiles to the adjacent marshland and subjected to XRD, SEM-EDS, ICP-OES and ICP-MS analyses. Sulphide oxidation has been shown to be a major driver of acid generation and metal leaching into the environment. The marsh soil receiving acid discharges from the sulphide wastes contains elevated levels (in mg kg−1 ) of Pb (up to 9838), As (up to 1538), Zn (up to 1486), Cu (up to 705), Sb (up to 225) and Tl (up to 13), which are retained both in relatively insoluble secondary minerals (mainly metal sulphates and oxides) and in easily soluble hydrated salts that serve as a transitory pool of acidity and available metals. By using a number of enrichment calculation methods that relate the metal concentrations in soil and their baseline concentrations and regulatory thresholds, there is enough evidence to conclude that these pollutants may pose an unacceptable risk to human and ecological receptorsThis work has been partially supported by the Andalusian Regional Government through the Research Group on Geology and Environmental Geochemistry (RNM-347). : We thank Jesús de la Rosa (University of Huelva) for his collaboration during fieldwork and for assistance with chemical analysi

Impacto de los depósitos de pirita abandonados en el antiguo centro mineralúrgico de Corrales sobre el suelo de las marismas del Odiel (Huelva, España)

97 páginas.Trabajo Fin de Máster en Tecnología Ambiental. Tutores: Dr. D. Juan Carlos Fernández Caliani ; Dr. D. Jesús Damián de la Rosa Díaz. La industria minero-metalúrgica milenaria en la provincia de Huelva ha dejado a su paso numerosos pasivos ambientales, cuyos efectos se pueden apreciar incluso hoy en día. El Drenaje Ácido de Mina producido por los residuos mineros acumulados genera aguas ácidas con un alto contenido de sulfatos y de elementos traza potencialmente tóxicos, que contaminan las aguas y los suelos afectados. La situación se agrava cuando se trata de una zona protegida como el Paraje Natural Marismas del Odiel. El presente trabajo estudia el impacto de los depósitos de pirita abandonados en el antiguo centro mineralúrgico de Corrales sobre el suelo de las marismas del río Odiel, en el área periubana de Huelva, mediante una evaluación del grado de acidificación y contaminación por metales pesados. Se han recogido un total de 48 muestras tomadas a distintas profundidades a lo largo de dos transectos paralelos que atraviesan la zona afectada, desde los montones de pirita hasta las marismas, con el objetivo de analizar la acidez y la composición química y mineralógica de los residuos mineros, de los suelos adyacentes y de las eflorescencias salinas. Los resultados obtenidos indican que el 61% de las muestras estudiadas tienen valores de pH ultra-ácido, lo que sugiere una alta movilidad y toxicidad por metales pesados. Se han identificado por DRX y SEM-EDS diversas fases mineralógicas neoformadas por procesos de interacción residuo-agua-suelo, como anglesita, jarosita, yeso y una variedad de sales solubles sulfatadas, como melanterita, szomolnokita, copiapita, coquimbita, halotriquita, epsomita y hexahidrita, potenciales portadoras de elementos pesados que pueden liberar al medio ambiente en los períodos húmedos. Los análisis químicos por ICP-MS revelan concentraciones totales muy elevadas de elementos traza de origen antrópico, particularmente en los suelos más próximos a los residuos, llegando a superar más de 100 veces los niveles genéricos de referencia en el caso del Tl (23,2 mg/kg) y del As (4223 mg/kg), en algunos puntos de muestreo. Los contenidos de otros elementos como Pb (hasta 6216 mg/kg), Sb (hasta 457 mg/kg), Cu (hasta 1958 mg/kg) y Co (hasta 189 mg/kg) son indicativos de que los suelos están potencialmente contaminados y requieren análisis de riesgos. Mediante el uso de diferentes índices geoquímicos que permiten evaluar la calidad ambiental de los suelos en comparación con los valores de fondo local y regional (factor de enriquecimiento, índice de carga contaminante, índice de geoacumulación), se ha llegado a la conclusión de que el suelo afectado presenta una acumulación y un enriquecimiento de grado alto a extremo en As, Pb, Sb, Tl, Cd, Cu y Zn, si bien la acidez y los niveles de contaminación tienden a atenuarse con la profundidad, y lateralmente desde los depósitos de pirita hacia las marismas.The millennia-long mining-metallurgical industry in the province of Huelva has left behind numerous environmental liabilities, the effect of which can still be seen today. The Acid Mine Drainage produced by the accumulated mining waste generates acid waters with a high content of sulfates and potentially toxic trace elements, which contaminate the water and the soil. The situation worsens when it comes to protected areas such as the Marismas del Odiel Natural Park. The present study examines the impact of the abandoned pyrite waste deposits in the old mineralurgical center of Corrales on the soils of the marshlands of the Odiel river, in the periuban area of Huelva. With the aim of analyzing the acidity and the chemical and mineralogical composition of the mining waste, the adjacent soils and the saline efflorescence a total of 48 samples have been collected at different depths along two parallel transects across the affected area, from the pyrite tailings to the marshlands. The results obtained indicate that 61% of the studied samples have ultra-acid pH values, which suggests high mobility and toxicity of heavy metals. Different mineralogical phases, such as anglesite, jarosite, gypsum and a variety of sulfated soluble salts like melanterite, szomolnokite, copiapite, coquimbite, halotrichite, epsomite and hexahydrite, newly formed by waste-water-soil interaction, were identified by XRD and SEM-EDS. These minerals are potential carriers of heavy elements that can be released into the environment during the wet periods. The chemical analysis by ICP-MS reveals very high total concentrations of trace elements of anthropogenic origin, particularly in the soils closest to the mining waste. These exceed more than 100 times the generic reference levels for Tl (23.2 mg/kg) and As (4223 mg/kg) in some samples. The high content of other elements such as Pb (up to 6216 mg/kg), Sb (up to 457 mg/kg), Cu (up to 1958 mg/kg) and Co (up to 189 mg/kg) indicates potentially contaminated soils and require a risk-based assessment. Different geochemical indices that evaluate the environmental quality of soils compared to local and regional background values (enrichment factor, pollutant load index, geoaccumulation index) were used. In conclusion, the affected soils exhibit high to extreme level of accumulation and enrichment in As, Pb, Sb, Tl, Cd, Cu, and Zn, although acidity and contamination levels tend to attenuate with depth, and also laterally from the pyrite waste deposits towards the marshlands

Capillarity-like growth of protein folding nuclei

We analyzed folding routes predicted by a variational model in terms of a generalized formalism of the capillarity scaling theory for 28 two-state proteins. The scaling exponent ranged from 0.2 to 0.45 with an average of 0.33. This average value corresponds to packing of rigid objects.That is, on average the folded core of the nucleus is found to be relatively diffuse. We also studied the growth of the folding nucleus and interface along the folding route in terms of the density or packing fraction. The evolution of the folded core and interface regions can be classified into three patterns of growth depending on how the growth of the folded core is balanced by changes in density of the interface. Finally, we quantified the diffuse versus polarized structure of the critical nucleus through direct calculation of the packing fraction of the folded core and interface regions. Our results support the general picture of describing protein folding as the capillarity-like growth of folding nuclei.Comment: 16 pages,6 figures. Submitted to Proc.Natl.Acad.Sc

Multiple Folding Pathways of the SH3 domain

Experimental observations suggest that proteins follow different pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the SH3 domain over a broad range of temperatures, and identify distinct pathways in the folding transition. We determine the kinetic partition temperature --the temperature for which the SH3 domain undergoes a rapid folding transition with minimal kinetic barriers-- and observe that below this temperature the model protein may undergo a folding transition via multiple folding pathways. The folding kinetics is characterized by slow and fast pathways and the presence of only one or two intermediates. Our findings suggest the hypothesis that the SH3 domain, a protein for which only two-state folding kinetics was observed in previous experiments, may exhibit intermediates states under extreme experimental conditions, such as very low temperatures. A very recent report (Viguera et al., Proc. Natl. Acad. Sci. USA, 100:5730--5735, 2003) of an intermediate in the folding transition of the Bergerac mutant of the alpha-spectrin SH3 domain protein supports this hypothesis.Comment: 16 pages, 4 figures To be published in the "Journal of Molecular Biology

Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse

The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core. This view integrates water expulsion effects into the funnel energy landscape theory of protein folding. Comparisons to experimental results are shown for the SH3 protein. After the folding transition, a near-native intermediate with partially solvated hydrophobic core is found. This transition is followed by a final step that cooperatively squeezes out water molecules from the partially hydrated protein core.Comment: Proceedings of the National Academy of Science, 2002, Vol.99. 685-69

Investigation of routes and funnels in protein folding by free energy functional methods

We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can lower the free energy barrier to folding. Correlating stronger contact energies with entropically likely contacts of a given native structure lowers the barrier, and anticorrelating the energies has the reverse effect. Designing in relatively mild energetic heterogeneity can eliminate the barrier completely at the transition temperature. Sequences with native energies tuned to fold uniformly, as well as sequences tuned to fold by a single or a few routes, are rare. Sequences with weak native energetic heterogeneity are more common; their folding kinetics is more strongly determined by properties of the native structure. Sequences with different distributions of stability throughout the protein may still be good folders to the same structure. A measure of folding route narrowness is introduced which correlates with rate, and which can give information about the intrinsic biases in ordering due to native topology. This theoretical framework allows us to systematically investigate the coupled effects of energy and topology in protein folding, and to interpret recent experiments which investigate these effects.Comment: 12 pages, 1 figure, to appear in Proc. Natl. Acad. Sc

Transition states in protein folding kinetics: Modeling Phi-values of small beta-sheet proteins

Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central question is which structural information on the transition state can be derived from the mutational data. In this article, we model and structurally interpret mutational Phi-values for two small beta-sheet proteins, the PIN and the FBP WW domain. The native structure of these WW domains comprises two beta-hairpins that form a three-stranded beta-sheet. In our model, we assume that the transition state consists of two conformations in which either one of the hairpins is formed. Such a transition state has been recently observed in Molecular Dynamics folding-unfolding simulations of a small designed three-stranded beta-sheet protein. We obtain good agreement with the experimental data (i) by splitting up the mutation-induced free-energy changes into terms for the two hairpins and for the small hydrophobic core of the proteins, and (ii) by fitting a single parameter, the relative degree to which hairpin 1 and 2 are formed in the transition state. The model helps to understand how mutations affect the folding kinetics of WW domains, and captures also negative Phi-values that have been difficult to interpret.Comment: 27 pages, 6 pages, 3 tables; to appear in Biophys.

Effects of HER2 overexpression on cell signaling networks governing proliferation and migration

Although human epidermal growth factor receptor 2 (HER2) overexpression is implicated in tumor progression for a variety of cancer types, how it dysregulates signaling networks governing cell behavioral functions is poorly understood. To address this problem, we use quantitative mass spectrometry to analyze dynamic effects of HER2 overexpression on phosphotyrosine signaling in human mammary epithelial cells stimulated by epidermal growth factor (EGF) or heregulin (HRG). Data generated from this analysis reveal that EGF stimulation of HER2-overexpressing cells activates multiple signaling pathways to stimulate migration, whereas HRG stimulation of these cells results in amplification of a specific subset of the migration signaling network. Self-organizing map analysis of the phosphoproteomic data set permitted elucidation of network modules differentially regulated in HER2-overexpressing cells in comparison with parental cells for EGF and HRG treatment. Partial least-squares regression analysis of the same data set identified quantitative combinations of signals within the networks that strongly correlate with cell proliferation and migration measured under the same battery of conditions. Combining these modeling approaches enabled association of epidermal growth factor receptor family dimerization to activation of specific phosphorylation sites, which appear to most critically regulate proliferation and/or migration