Chemical composition of DSDP and ODP cherts

Rare earth element (REE), major, and trace element abundances and relative fractionations in forty nodular cherts sampled by the Deep Sea Drilling Project (DSDP) and Ocean Drilling Program (ODP) indicate that the REE composition of chert records the interplay between terrigenous sources and scavenging from the local seawater. Major and (non-REE) trace element ratios indicate that the aluminosilicate fraction within the chert is similar to NASC (North American Shale Composite), with average Pacific chert including ~7% NASC-like particles, Indian chert ~11% NASC, Atlantic chert ~17% NASC, and southern high latitude (SHL) chert 53% NASC. Using La as a proxy for sum REE, approximations of excessive La (the amount of La in excess of that supplied by the detrital aluminosilicate fraction) indicate that Pacific chert contains the greatest excessive La (85% of total La) and SHL chert the least (38% of total La). As shown by interelement associations, this excessive La is most likely an adsorbed component onto aluminosilicate and phosphatic phases. Accordingly, chert from the large Pacific Ocean, where deposition occurs relatively removed from significant terrigenous input, records a depositional REE signal dominated by adsorption of dissolved REEs from seawater. Pacific chert Ce/Ce* <<1 and normative La/Yb ~ 0.8-1, resulting from adsorption of local Ce-depleted seawater and preferential adsorption of LREEs from seawater (e.g., normative La/Yb ~0.4), which increases the normative La/Yb ratio recorded in chert. Chert from the Atlantic basin, a moderately sized ocean basin lined by passive margins and with more terrigenous input than the Pacific, records a mix of adsorptive and terrigenous REE signals, with moderately negative Ce anomalies and normative La/Yb ratios intermediate to those of the Pacific and those of terrigenous input. Chert from the SHL region is dominated by the large terrigenous input on the Antarctic passive margin, with inherited Ce/Ce* ~1 and inherited normative La/Yb values of ~1.2-1.4. Ce/Ce* does not vary with age, either throughout the entire data base or within a particular basin. Overall, Ce/Ce* does not correlate with P2O5 concentrations, even though phosphatic phases may be an important REE carrier.

The downhole variation of the rock-magnetic properties of DSDP Leg 73 Holes

The magnetic stability and mean intensity of the natural remanent magnetization (NRM) of Leg 73 sediments (Holes 519 to 523) decreases with the age of the sediment. We demonstrate that these variations are linked with physical and chemical changes in the magnetic grains themselves. Alteration of the magnetic component occurs most rapidly shortly after deposition. A significant magnetic alteration over the topmost few meters of the sediments is thought to be the result of oxidation. The modification of the NRM characteristics through the partial dissolution of the carbonate is largely accounted for by the effects of concentraion of the magnetic minerals. We apply the techniques of rock-magnetism and X-ray fluorescence analysis to clarify the physical and chemical mechanisms that affect the magnetic character of the sediment.

Table 1: Soil chemical properties of the analysed depth profiles in the Venice lagoon

Visual traces of iron reduction and oxidation are linked to the redox status of soils and have been used to characterise the quality of agricultural soils.We tested whether this feature could also be used to explain the spatial pattern of the natural vegetation of tidal habitats. If so, an easy assessment of the effect of rising sea level on tidal ecosystems would be possible. Our study was conducted at the salt marshes of the northern lagoon of Venice, which are strongly threatened by erosion and rising sea level and are part of the world heritage 'Venice and its lagoon'. We analysed the abundance of plant species at 255 sampling points along a land-sea gradient. In addition, we surveyed the redox morphology (presence/absence of red iron oxide mottles in the greyish topsoil horizons) of the soils and the presence of disturbances. We used indicator species analysis, correlation trees and multivariate regression trees to analyse relations between soil properties and plant species distribution. Plant species with known sensitivity to anaerobic conditions (e.g. Halimione portulacoides) were identified as indicators for oxic soils (showing iron oxide mottles within a greyish soil matrix). Plant species that tolerate a low redox potential (e.g. Spartina maritima) were identified as indicators for anoxic soils (greyish matrix without oxide mottles). Correlation trees and multivariate regression trees indicate the dominant role of the redox morphology of the soils in plant species distribution. In addition, the distance from the mainland and the presence of disturbances were identified as tree-splitting variables. The small-scale variation of oxygen availability plays a key role for the biodiversity of salt marsh ecosystems. Our results suggest that the redox morphology of salt marsh soils indicates the plant availability of oxygen. Thus, the consideration of this indicator may enable an understanding of the heterogeneity of biological processes in oxygen-limited systems and may be a sensitive and easy-to-use tool to assess human impacts on salt marsh ecosystems.

Understanding and improving the chemical vapor deposition process for solar grade silicon production

Esta Tesis Doctoral se centra en la investigación del proceso de producción de polisilicio para aplicaciones fotovoltaicas (FV) por la vía química; mediante procesos de depósito en fase vapor (CVD). El polisilicio para la industria FV recibe el nombre de silicio de grado solar (SoG Si). Por un lado, el proceso que domina hoy en día la producción de SoG Si está basado en la síntesis, destilación y descomposición de triclorosilano (TCS) en un reactor CVD -denominado reactor Siemens-. El material obtenido mediante este proceso es de muy alta pureza, pero a costa de un elevado consumo energético. Así, para alcanzar los dos principales objetivos de la industria FV basada en silicio, bajos costes de producción y bajo tiempo de retorno de la energía invertida en su fabricación, es esencial disminuir el consumo energético de los reactores Siemens. Por otro lado, una alternativa al proceso Siemens considera la descomposición de monosilano (MS) en un reactor de lecho fluidizado (FBR). Este proceso alternativo tiene un consumo energético mucho menor que el de un reactor Siemens, si bien la calidad del material resultante es también menor; pero ésta puede ser suficiente para la industria FV. A día de hoy los FBR deben aún abordar una serie de retos para que su menor consumo energético sea una ventaja suficiente comparada con otras desventajas de estos reactores. En resumen, la investigación desarrollada se centra en el proceso de depósito de polysilicio por CVD a partir de TCS -reactor Siemens-; pero también se investiga el proceso de producción de SoG Si en los FBR exponiendo las fortalezas y debilidades de esta alternativa. Para poder profundizar en el conocimiento del proceso CVD para la producción de polisilicio es clave el conocimiento de las reacciones químicas fundamentales y cómo éstas influencian la calidad del producto resultante, al mismo tiempo que comprender los fenómenos responsables del consumo energético. Por medio de un reactor Siemens de laboratorio en el que se llevan a cabo un elevado número de experimentos de depósito de polisilicio de forma satisfactoria se adquiere el conocimiento previamente descrito. Se pone de manifiesto la complejidad de los reactores CVD y de los problemas asociados a la pérdidas de calor de estos procesos. Se identifican las contribuciones a las pérdidas de calor de los reactores CVD, éstas pérdidas de calor son debidas principalmente a los fenómenos de radiación y, conducción y convección vía gases. En el caso de los reactores Siemens el fenómeno que contribuye en mayor medida al alto consumo energético son las pérdidas de calor por radiación, mientras que en los FBRs tanto la radiación como el calor transferido por transporte másico contribuyen de forma importante. Se desarrolla un modelo teórico integral para el cálculo de las pérdidas de calor en reactores Siemens. Este modelo está formado a su vez por un modelo para la evaluación de las pérdidas de calor por radiación y modelos para la evaluación de las pérdidas de calor por conducción y convección vía gases. Se ponen de manifiesto una serie de limitaciones del modelo de pérdidas de calor por radiación, y se desarrollan una serie de modificaciones que mejoran el modelo previo. El modelo integral se valida por medio un reactor Siemens de laboratorio, y una vez validado se presenta su extrapolación a la escala industrial. El proceso de conversión de TCS y MS a polisilicio se investiga mediante modelos de fluidodinámica computacional (CFD). Se desarrollan modelados CFD para un reactor Siemens de laboratorio y para un prototipo FBR. Los resultados obtenidos mediante simulación son comparados, en ambos casos, con resultados experimentales. Los modelos desarrollados se convierten en herramientas para la identificación de aquellos parámetros que tienen mayor influencia en los procesos CVD. En el caso del reactor Siemens, ambos modelos -el modelo integral y el modelado CFD permiten el estudio de los parámetros que afectan en mayor medida al elevado consumo energético, y mediante su análisis se sugieren modificaciones para este tipo de reactores que se traducirían en un menor número de kilovatios-hora consumidos por kilogramo de silicio producido. Para el caso del FBR, el modelado CFD permite analizar el efecto de una serie de parámetros sobre la distribución de temperaturas en el lecho fluidizado; y dicha distribución de temperaturas está directamente relacionada con los principales retos de este tipo de reactores. Por último, existen nuevos conceptos de depósito de polisilicio; éstos se aprovechan de la ventaja teórica de un mayor volumen depositado por unidad de tiempo -cuando una mayor superficie de depósito está disponible- con el objetivo de reducir la energía consumida por los reactores Siemens. Estos conceptos se exploran mediante cálculos teóricos y pruebas en el reactor Siemens de laboratorio. ABSTRACT This Doctoral Thesis comprises research on polysilicon production for photovoltaic (PV) applications through the chemical route: chemical vapor deposition (CVD) process. PV polysilicon is named solar grade silicon (SoG Si). On the one hand, the besetting CVD process for SoG Si production is based on the synthesis, distillation, and decomposition of thriclorosilane (TCS) in the so called Siemens reactor; high purity silicon is obtained at the expense of high energy consumption. Thus, lowering the energy consumption of the Siemens process is essential to achieve the two wider objectives for silicon-based PV technology: low production cost and low energy payback time. On the other hand, a valuable variation of this process considers the use of monosilane (MS) in a fluidized bed reactor (FBR); lower output material quality is obtained but it may fulfil the requirements for the PV industry. FBRs demand lower energy consumption than Siemens reactors but further research is necessary to address the actual challenges of these reactors. In short, this work is centered in polysilicon CVD process from TCS -Siemens reactor-; but it also offers insights on the strengths and weaknesses of the FBR for SoG Si production. In order to aid further development in polysilicon CVD is key the understanding of the fundamental reactions and how they influence the product quality, at the same time as to comprehend the phenomena responsible for the energy consumption. Experiments conducted in a laboratory Siemens reactor prove the satisfactory operation of the prototype reactor, and allow to acquire the knowledge that has been described. Complexity of the CVD reactors is stated and the heat loss problem associated with polysilicon CVD is addressed. All contributions to the energy consumption of Siemens reactors and FBRs are put forward; these phenomena are radiation and, conduction and convection via gases heat loss. In a Siemens reactor the major contributor to the energy consumption is radiation heat loss; in case of FBRs radiation and heat transfer due to mass transport are both important contributors. Theoretical models for radiation, conduction and convection heat loss in a Siemens reactor are developed; shaping a comprehensive theoretical model for heat loss in Siemens reactors. Limitations of the radiation heat loss model are put forward, and a novel contribution to the existing model is developed. The comprehensive model for heat loss is validated through a laboratory Siemens reactor, and results are scaled to industrial reactors. The process of conversion of TCS and MS gases to solid polysilicon is investigated by means of computational fluid-dynamics models. CFD models for a laboratory Siemens reactor and a FBR prototype are developed. Simulated results for both CVD prototypes are compared with experimental data. The developed models are used as a tool to investigate the parameters that more strongly influence both processes. For the Siemens reactors, both, the comprehensive theoretical model and the CFD model allow to identify the parameters responsible for the great power consumption, and thus, suggest some modifications that could decrease the ratio kilowatts-hour per kilogram of silicon produced. For the FBR, the CFD model allows to explore the effect of a number of parameters on the thermal distribution of the fluidized bed; that is the main actual challenge of these type of reactors. Finally, there exist new deposition surface concepts that take advantage of higher volume deposited per time unit -when higher deposition area is available- trying to reduce the high energy consumption of the Siemens reactors. These novel concepts are explored by means of theoretical calculations and tests in the laboratory Siemens prototype.

Chemical phenotype matching between a plant and its insect herbivore

Two potential outcomes of a coevolutionary interaction are an escalating arms race and stable cycling. The general expectation has been that arms races predominate in cases of polygenic inheritance of resistance traits and permanent cycling predominates in cases in which resistance is controlled by major genes. In the interaction between Depressaria pastinacella, the parsnip webworm, and Pastinaca sativa, the wild parsnip, traits for plant resistance to insect herbivory (production of defensive furanocoumarins) as well as traits for herbivore “virulence” (ability to metabolize furanocoumarins) are characterized by continuous heritable variation. Furanocoumarin production in plants and rates of metabolism in insects were compared among four midwestern populations; these traits then were classified into four clusters describing multitrait phenotypes occurring in all or most of the populations. When the frequency of plant phenotypes belonging to each of the clusters is compared with the frequency of the insect phenotypes in each of the clusters across populations, a remarkable degree of frequency matching is revealed in three of the populations. That frequencies of phenotypes vary among populations is consistent with the fact that spatial variation occurs in the temporal cycling of phenotypes; such processes contribute in generating a geographic mosaic in this coevolutionary interaction on the landscape scale. Comparisons of contemporary plant phenotype distributions with phenotypes of herbarium specimens collected 9–125 years ago from across a similar latitudinal gradient, however, suggest that for at least one resistance trait—sphondin concentration—interactions with webworms have led to escalatory change.

Chemical defense against predation in an insect egg

The larva of the green lacewing (Ceraeochrysa cubana) (Neuroptera, Chrysopidae) is a natural predator of eggs of Utetheisa ornatrix (Lepidoptera, Arctiidae), a moth that sequesters pyrrolizidine alkaloids from its larval foodplant (Fabaceae, Crotalaria spp.). Utetheisa eggs are ordinarily endowed with the alkaloid. Alkaloid-free Utetheisa eggs, produced experimentally, are pierced by the larva with its sharp tubular jaws and sucked out. Alkaloid-laden eggs, in contrast, are rejected. When attacking an Utetheisa egg cluster (numbering on average 20 eggs), the larva subjects it to an inspection process. It prods and/or pierces a small number of eggs (on average two to three) and, if these contain alkaloid, it passes “negative judgement” on the remainder of the cluster and turns away. Such generalization on the part of the larva makes sense, because the eggs within clusters differ little in alkaloid content. There is, however, considerable between-cluster variation in egg alkaloid content, so clusters in nature can be expected to range widely in palatability. To check each cluster for acceptability must therefore be adaptive for the larva, just as it must be adaptive for Utetheisa to lay its eggs in large clusters and to apportion alkaloid evenly among eggs of a cluster.

Periodic variation in side-chain polarities of T-cell antigenic peptides correlates with their structure and activity.

We present an analysis that synthesizes information on the sequence, structure, and motifs of antigenic peptides, which previously appeared to be in conflict. Fourier analysis of T-cell antigenic peptides indicates a periodic variation in amino acid polarities of 3-3.6 residues per period, suggesting an amphipathic alpha-helical structure. However, the diffraction patterns of major histocompatibility complex (MHC) molecules indicate that their ligands are in an extended non-alpha-helical conformation. We present two mutually consistent structural explanations for the source of the alpha-helical periodicity, based on an observation that the side chains of MHC-bound peptides generally partition with hydrophobic (hydrophilic) side chains pointing into (out of) the cleft. First, an analysis of haplotype-dependent peptide motifs indicates that the locations of their defining residues tend to force a period 3-4 variation in hydrophobicity along the peptide sequence, in a manner consistent with the spacing of pockets in the MHC. Second, recent crystallographic determination of the structure of a peptide bound to a class II MHC molecule reveals an extended but regularly twisted peptide with a rotation angle of about 130 degrees. We show that similar structures with rotation angles of 100-130 degrees are energetically acceptable and also span the length of the MHC cleft. These results provide a sound physical chemical and structural basis for the existence of a haplotype-independent antigenic motif which can be particularly important in limiting the search time for antigenic peptides.

Intra-population variation and geographic correlation in Canthon humectus hidalgoensis using FTIR-ATR spectroscopy

In some cases external morphology is not sufficient to discern between populations of a species, as occurs in the dung beetle Canthon humectus hidalgoensis Bates; and much less to determine phenotypic distances between them. FTIR-ATR spectroscopy show several advantages over other identification techniques (e.g. morphological, genetic, and cuticular hydrocarbons analysis) due to the non-invasive manner of the sample preparation, the relative speed of sample analysis and the low-cost of this technology. The infrared spectrum obtained is recognized to give a unique ‘fingerprint’ because vibrational spectra are specific and unique to the molecular nature of the sample. In our study, results showed that proteins, amino acids and aromatic ethers of insect exocuticle have promising discriminative power to discern between different populations of C. h. hidalgoensis. Furthermore, the correlation between geographic distances between populations and the chemical distances obtained by proteins + amino acids + aromatic ethers was statistically significant, showing that the spectral and spatial information available of the taxa together with appropriated chemometric methods may help to a better understanding of the identity, structure, dynamics and diversity of insect populations.

Chemical and mineral compositions of sediments from ODP Site 127-797

In order to reconstruct past variations in the aeolian dust (Kosa) contribution to the Japan Sea, and to establish a direct link between terrestrial and marine climatic records, we have applied statistical procedures to distinguish and quantify detrital subcomponents within the detrital fraction of the late Quaternary hemipelagic sediments in the Japan Sea. Q-mode factor analysis with varimax and oblique rotation of the factors followed by multiple-regression analysis between mineral composition and factor loadings was conducted using six ''detrital'' elements. Four detrital subcomponents were defined, which are attributed to Kosa derived from ''typical'' loess, Kosa from ''weathered'' loess, and fine and coarse arc-derived detritus, respectively, based on comparisons with the chemical and mineral compositions of probable source materials. Using these detrital subcomponents, the variation in Kosa fraction was reconstructed for the last 200 ky. The results reveal millennial-scale as well as glacial-interglacial scale variations in Kosa contribution. Especially, millennial-scale variability of Kosa contribution suggests the presence of high frequency variation in summer monsoon precipitation in the central to east Asia during the last 200 ky.

Variation in Coral Photosynthesis, Respiration and Growth Characteristics in Contrasting Light Microhabitats: An Analogue to Plants in Forest Gaps and Understoreys?

1. The often complex architecture of coral reefs forms a diversity of light microhabitats. Analogous to patterns in forest plants, light variation may drive strategies for efficient light utilization and metabolism in corals. 2. We investigated the spatial distribution of light regimes in a spur-and-groove reef environment and examine the photophysiology of the coral Montipora monasteriata (Forskal 1775), a species with a wide habitat distribution. Specifically, we examined the variation in tissue and skeletal thickness, and photosynthetic and metabolic responses among contrasting light microhabitats. 3. Daily irradiances reaching corals in caves and under overhangs were 1-5 and 30-40% of those in open habitats at similar depth (3-5 m), respectively. Daily rates of net photosynthesis of corals in cave habitats approximated zero, suggesting more than two orders of magnitude variation in scope for growth across habitats. 4. Three mechanisms of photoadaptation or acclimation were observed in cave and overhang habitats: (1) a 20-50% thinner tissue layer and 40-60% thinner skeletal plates, maximizing light interception per unit mass; (2) a two- to threefold higher photosynthetic efficiency per unit biomass; and (3) low rates of dark respiration. 5. Specimens from open and cave habitats displayed a high capacity to acclimate to downshifts or upshifts in irradiance, respectively. However, specimens in caves displayed limited acclimation to further irradiance reduction, indicating that these live near their irradiance limit. 6. Analogous to patterns for some plant species in forest gaps, the morphological plasticity and physiological flexibility of M. monasteriata enable it to occupy light habitats that vary by more than two orders of magnitude.

The effect of ionic strength variation and anion competition on the development of nitrate accumulations in variable charge subsoils

The leaching of N fertilisers has led to the formation of nitrate (NO3) accumulations in deep subsoils (>5 m depth) of the Johnstone River catchment. This paper outlines the chemical mechanism by which these NO3 accumulations are formed and maintained. This was achieved via a series of column experiments designed to investigate NO3 leaching in relation to the soil charge chemistry and the competition of anions for exchange sites. The presence of variable charge minerals has led to the formation positive surface charge within these profiles. An increase in the soil solution ionic strength accompanying the fertiliser leaching front acts to increase the positive (and negative) charge density, thus providing adsorption sites for NO3. A decrease in the soil solution ionic strength occurs after the fertiliser pulse moves past a point in the profile, due to dilution with incoming rainwater. Nitrate is then released from the exchange back into the soil solution, thus buffering the decrease in the soil solution ionic strength. Since NO3 was adsorbed throughout the profile in this experiment it does not effectively explain the situation occurring in the field. Previous observations of the sulfate (SO4) profile distribution indicated that large SO4 accumulations in the upper profile may influence the NO3 distribution through competition for adsorption sites. A subsequent experiment investigating the effect of SO4 additions on NO3 leaching showed that NO3 adsorption was minimal in the upper profile. Adsorption of NO3 did occur, though only in the region of the profile where SO4 occupancy was low, i.e. in the lower profile. Therefore, the formation of the NO3 accumulations is dependent on the variable charge mineralogy, the variation of charge density with soil solution ionic strength, and the effects of SO4 competition for adsorption sites.

Chemical characterization of earth's most ancient clastic metasediments from the Isua Greenstone Belt, southern West Greenland

New and published major and trace element abundances of elastic metasediments (mainly garnet-biotite-plagioclase schists) from the similar to 3.8 Ga Isua Greenstone Belt (IGB), southern West Greenland, are used in an attempt to identify the compositional characteristics of the protoliths of these sediments. Compositionally, the metasediments are heterogeneous with enrichment of LREE (La/Sm-chord = 1.1-3.9) and variable enrichment and depletion of HREE (Gd/Yb-chord = 0.8-4.3). Chondrite-normalized Eu is also variable, spanning a range from relative Eu depletion to enrichment (Eu/Eu* = 0.6-1.3). A series of geochemical and geological criteria provides conclusive evidence for a sedimentary origin, in disagreement with some previous studies that questioned the presence of genuine elastic metasediments. In particular, trace element systematics of IGB metasediments show strong resemblance to other well-documented Archaean clastic sediments, and are consistent with a provenance consisting of ultramafic, malic and felsic igneous rocks. Two schists, identified as metasomatized mafic igneous rocks from petrographic and field evidence, show distinct compositional differences to the metasediments. Major element systematics document incipient-to-moderate source weathering in the majority of metasediments, while signs of secondary K-addition are rare. Detailed inspection of Eu/Eu*, Fe2O3 and CIW (chemical index of weathering) relationships reveals that elevated iron contents (when compared to averages for continental crust) and strong relative enrichment in Eu may be due to precipitation of marine Fe-oxyhydroxides during deposition or diagenesis on the seafloor. Some of the IGB metasediments have yielded anomalous Nd-142 and W-182 isotopic compositions that were respectively interpreted in terms of early mantle differentiation processes and the presence of a meteorite component. Alternatively, W and possibly Nd isotopes could have been affected by thermal neutron capture on the Hadean surface. The latter process was tested in this study by analysis of Sm isotope compositions, which serve as an effective monitor for neutron capture effects. As no anomalous variation from terrestrial values was detected, we infer that isotope systematics (including W-182 and Nd-142) of IGB metasediments were not affected by neutron capture, but reflect decay of radioactive parent isotopes. Copyright (c) 2005 Elsevier Ltd.

Human sulfotransferases and their role in chemical metabolism

Sulfonation is an important reaction in the metabolism of numerous xenobiotics, drugs, and endogenous compounds. A supergene family of enzymes called sulfotransferases (SULTs) catalyze this reaction. In most cases, the addition of a sulfonate moiety to a compound increases its water solubility and decreases its biological activity. However, many of these enzymes are also capable of bioactivating procarcinogens to reactive electrophiles. In humans three SULT families, SULT1, SULT2, and SULT4, have been identified that contain at least thirteen distinct members. SULTs have a wide tissue distribution and act as a major detoxification enzyme system in adult and the developing human fetus. Nine crystal structures of human cytosolic SULTs have now been determined, and together with site-directed mutagenesis experiments and molecular modeling, we are now beginning to understand the factors that govern distinct but overlapping substrate specificities. These studies have also provided insight into the enzyme kinetics and inhibition characteristics of these enzymes. The regulation of human SULTs remains as one of the least explored areas of research in the field, though there have been some recent advances on the molecular transcription mechanism controlling the individual SULT promoters. Interindividual variation in sulfonation capacity may be important in determining an individual's response to xenobiotics, and recent studies have begun to suggest roles for SULT polymorphism in disease susceptibility. This review aims to provide a summary of our present understanding of the function of human cytosolic sulfotransferases.