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- Creators: Debussy, Claude, 1862-1918
Description
This dissertation examines two topics of emerging interest in the field of organic geochemistry. The topic of the first portion of the dissertation is cold organic geochemistry on Saturn's moon Titan. Titan has an atmosphere and surface that are rich in organic compounds. Liquid hydrocarbons exist on the surface, most famously as lakes. Photochemical reactions produce solid organics in Titan's atmosphere, and these materials settle onto the surface. At the surface, liquids can interact with solids, and geochemical processes can occur. To better understand these processes, I developed a thermodynamic model that can be used to calculate the solubilities of gases and solids in liquid hydrocarbons at cryogenic temperatures. The model was parameterized using experimental data, and provides a good fit to the data. Application of the model to Titan reveals that the equilibrium composition of surface liquids depends on the abundance of methane in the local atmosphere. The model also indicates that solid acetylene should be quite soluble in surface liquids, which implies that acetylene-rich rocks should be susceptible to chemical erosion, and acetylene evaporites may form on Titan. In the latter half of this dissertation, I focus on hot organic geochemistry below the surface of the Earth. Organic compounds are common in sediments. Burial of sediments leads to changes in physical and chemical conditions, promoting organic reactions. An important organic reaction in subsurface environments is decarboxylation, which generates hydrocarbons and carbon dioxide from simple organic acids. Fundamental knowledge about decarboxylation is required to better understand how the organic and inorganic compositions of sediments evolve in response to changing geochemical conditions. I performed experiments with the model compound phenylacetic acid to obtain information about mechanisms of decarboxylation in hydrothermal fluids. Patterns in rates of decarboxylation of substituted phenylacetic acids point to a mechanism that proceeds through a ring-protonated zwitterion of phenylacetic acid. In contrast, substituted sodium phenylacetates exhibit a different kinetic pattern, one that is consistent with the formation of the benzyl anion as an intermediate. Results from experiments with added hydrochloric acid or sodium hydroxide, and deuterated water agree with these interpretations. Thus, speciation dictates mechanism of decarboxylation.
ContributorsGlein, Christopher R (Author) / Shock, Everett L (Thesis advisor) / Hartnett, Hilairy E (Committee member) / Zolotov, Mikhail Y (Committee member) / Williams, Lynda B (Committee member) / Gould, Ian R (Committee member) / Arizona State University (Publisher)
Created2012
ContributorsDebussy, Claude, 1862-1918 (Composer)
ContributorsDebussy, Claude, 1862-1918 (Composer)
ContributorsDebussy, Claude, 1862-1918 (Composer)
ContributorsDebussy, Claude, 1862-1918 (Composer)
ContributorsDebussy, Claude, 1862-1918 (Composer)
Description
The discovery and development of novel antibacterial agents is essential to address the rising health concern over antibiotic resistant bacteria. This research investigated the antibacterial activity of a natural clay deposit near Crater Lake, Oregon, that is effective at killing antibiotic resistant human pathogens. The primary rock types in the deposit are andesitic pyroclastic materials, which have been hydrothermally altered into argillic clay zones. High-sulfidation (acidic) alteration produced clay zones with elevated pyrite (18%), illite-smectite (I-S) (70% illite), elemental sulfur, kaolinite and carbonates. Low-sulfidation alteration at neutral pH generated clay zones with lower pyrite concentrations pyrite (4-6%), the mixed-layered I-S clay rectorite (R1, I-S) and quartz.
Antibacterial susceptibility testing reveals that hydrated clays containing pyrite and I-S are effective at killing (100%) of the model pathogens tested (E. coli and S. epidermidis) when pH (< 4.2) and Eh (> 450 mV) promote pyrite oxidation and mineral dissolution, releasing > 1 mM concentrations of Fe2+, Fe3+ and Al3+. However, certain oxidized clay zones containing no pyrite still inhibited bacterial growth. These clays buffered solutions to low pH (< 4.7) and oxidizing Eh (> 400 mV) conditions, releasing lower amounts (< 1 mM) of Fe and Al. The presence of carbonate in the clays eliminated antibacterial activity due to increases in pH, which lower pyrite oxidation and mineral dissolution rates.
The antibacterial mechanism of these natural clays was explored using metal toxicity and genetic assays, along with advanced bioimaging techniques. Antibacterial clays provide a continuous reservoir of Fe2+, Fe3+ and Al3+ that synergistically attack pathogens while generating hydrogen peroxide (H2O¬2). Results show that dissolved Fe2+ and Al3+ are adsorbed to bacterial envelopes, causing protein misfolding and oxidation in the outer membrane. Only Fe2+ is taken up by the cells, generating oxidative stress that damages DNA and proteins. Excess Fe2+ oxidizes inside the cell and precipitates Fe3+-oxides, marking the sites of hydroxyl radical (•OH) generation. Recognition of this novel geochemical antibacterial process should inform designs of new mineral based antibacterial agents and could provide a new economic industry for such clays.
Antibacterial susceptibility testing reveals that hydrated clays containing pyrite and I-S are effective at killing (100%) of the model pathogens tested (E. coli and S. epidermidis) when pH (< 4.2) and Eh (> 450 mV) promote pyrite oxidation and mineral dissolution, releasing > 1 mM concentrations of Fe2+, Fe3+ and Al3+. However, certain oxidized clay zones containing no pyrite still inhibited bacterial growth. These clays buffered solutions to low pH (< 4.7) and oxidizing Eh (> 400 mV) conditions, releasing lower amounts (< 1 mM) of Fe and Al. The presence of carbonate in the clays eliminated antibacterial activity due to increases in pH, which lower pyrite oxidation and mineral dissolution rates.
The antibacterial mechanism of these natural clays was explored using metal toxicity and genetic assays, along with advanced bioimaging techniques. Antibacterial clays provide a continuous reservoir of Fe2+, Fe3+ and Al3+ that synergistically attack pathogens while generating hydrogen peroxide (H2O¬2). Results show that dissolved Fe2+ and Al3+ are adsorbed to bacterial envelopes, causing protein misfolding and oxidation in the outer membrane. Only Fe2+ is taken up by the cells, generating oxidative stress that damages DNA and proteins. Excess Fe2+ oxidizes inside the cell and precipitates Fe3+-oxides, marking the sites of hydroxyl radical (•OH) generation. Recognition of this novel geochemical antibacterial process should inform designs of new mineral based antibacterial agents and could provide a new economic industry for such clays.
ContributorsMorrison, Keith D (Author) / Williams, Lynda B (Thesis advisor) / Williams, Stanley N (Thesis advisor) / Misra, Rajeev (Committee member) / Shock, Everett (Committee member) / Anbar, Ariel (Committee member) / Arizona State University (Publisher)
Created2015
Description
Variations of 238U/235U in sedimentary carbonate rocks are being explored as a tool for reconstructing oceanic anoxia through time. However, the fidelity of this novel paleoredox proxy relies on characterization of uranium isotope geochemistry via laboratory experimental studies and field work in modern analog environmental settings. This dissertation systematically examines the fidelity of 238U/235U in sedimentary carbonate rocks as a paleoredox proxy focusing on the following issues: (1) U isotope fractionation during U incorporation into primary abiotic and biogenic calcium carbonates; (2) diagenetic effects on U isotope fractionation in modern shallow-water carbonate sediments; (3) the effects of anoxic depositional environments on 238U/235U in carbonate sediments.
Variable and positive shifts of 238U/235U were observed during U uptake by primary abiotic and biotic calcium carbonates, carbonate diagenesis, and anoxic deposition of carbonates. Previous CaCO3 coprecipitation experiments demonstrated a small but measurable U isotope fractionation of ~0.10 ‰ during U(VI) incorporation into abiotic calcium carbonates, with 238U preferentially incorporated into the precipitates (Chen et al., 2016). The magnitude of U isotope fractionation depended on aqueous U speciation, which is controlled by water chemistry, including pH, ionic strength, carbonate, and Ca2+ and Mg2+ concentrations. Based on this speciation-dependent isotope fractionation model, the estimated U isotope fractionation in abiotic calcium carbonates induced by secular changes in seawater chemistry through the Phanerozoic was predicted to be 0.11–0.23 ‰. A smaller and variable U isotope fractionation (0–0.09 ‰) was observed in primary biogenic calcium carbonates, which fractionated U isotopes in the same direction as abiotic calcium carbonates. Early diagenesis of modern shallow-water carbonate sediments from the Bahamas shifted δ238U values to be 0.270.14 ‰ (1 SD) higher than contemporaneous seawater. Also, carbonate sediments deposited under anoxic conditions in a redox-stratified lake—Fayetteville Green Lake, New York, USA— exhibited elevated δ238U values by 0.160.12 ‰ (1 SD) relative to surface water carbonates with significant enrichments in U.
The significant U isotope fractionation observed in these studies suggests the need to correct for the U isotopic offset between carbonate sediments and coeval seawater when using δ238U variations in ancient carbonate rocks to reconstruct changes in ocean anoxia. The U isotope fractionation in abiotic and biogenic primary carbonate precipitates, during carbonate diagenesis, and under anoxic depositional environments provide a preliminary guideline to calibrate 238U/235U in sedimentary carbonate rocks as a paleoredox proxy.
Variable and positive shifts of 238U/235U were observed during U uptake by primary abiotic and biotic calcium carbonates, carbonate diagenesis, and anoxic deposition of carbonates. Previous CaCO3 coprecipitation experiments demonstrated a small but measurable U isotope fractionation of ~0.10 ‰ during U(VI) incorporation into abiotic calcium carbonates, with 238U preferentially incorporated into the precipitates (Chen et al., 2016). The magnitude of U isotope fractionation depended on aqueous U speciation, which is controlled by water chemistry, including pH, ionic strength, carbonate, and Ca2+ and Mg2+ concentrations. Based on this speciation-dependent isotope fractionation model, the estimated U isotope fractionation in abiotic calcium carbonates induced by secular changes in seawater chemistry through the Phanerozoic was predicted to be 0.11–0.23 ‰. A smaller and variable U isotope fractionation (0–0.09 ‰) was observed in primary biogenic calcium carbonates, which fractionated U isotopes in the same direction as abiotic calcium carbonates. Early diagenesis of modern shallow-water carbonate sediments from the Bahamas shifted δ238U values to be 0.270.14 ‰ (1 SD) higher than contemporaneous seawater. Also, carbonate sediments deposited under anoxic conditions in a redox-stratified lake—Fayetteville Green Lake, New York, USA— exhibited elevated δ238U values by 0.160.12 ‰ (1 SD) relative to surface water carbonates with significant enrichments in U.
The significant U isotope fractionation observed in these studies suggests the need to correct for the U isotopic offset between carbonate sediments and coeval seawater when using δ238U variations in ancient carbonate rocks to reconstruct changes in ocean anoxia. The U isotope fractionation in abiotic and biogenic primary carbonate precipitates, during carbonate diagenesis, and under anoxic depositional environments provide a preliminary guideline to calibrate 238U/235U in sedimentary carbonate rocks as a paleoredox proxy.
ContributorsChen, Xinming (Author) / Anbar, Ariel D (Thesis advisor) / Williams, Lynda B (Committee member) / Sharp, Thomas (Committee member) / Hervig, Richard (Committee member) / Romaniello, Stephen (Committee member) / Arizona State University (Publisher)
Created2018
Description
Amazonia, inhabited and investigated for millennia, continues to astonish scientists with its cultural and natural diversity. Although Amazonia is rapidly changing, its vast and varied landscape still contains a complex natural pharmacopeia. The Amazonian tribes have accrued valuable environmental and geological knowledge that can be studied. This dissertation demonstrates that Indigenous Knowledge considered alongside Western Science can enhance our understanding of the relationship of people to geological materials and hydrological resources, and reveal mineral medicines with practical applications.
I used methods from anthropology and geology to explore the geological knowledge of the Uitoto, a tribe of the Colombian Amazon. The Uitoto use two metaphors to describe Earth systems: 1. the earth is a body, and 2. the Amazon is a tree. I found that they classify surface-water systems according to observable characteristics and use mineral clays to treat various maladies. I argue that Uitoto knowledge about Amazonian mineral resources and surface water is practical, empirically–based and, in many cases, more nuanced than mainstream scientific knowledge.
I studied the mode of action of a natural antibacterial clay from the Colombian Amazon (AMZ) to discover whether the Uitoto’s claims about the clay’s medicinal values was verifiable using the methods of Western Science. Natural antibacterial clays can inhibit the growth of human pathogens. Methods from microbiology and geochemistry were combined to evaluate the mineral-microbe interactions that inhibit growth of model Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) bacteria. The AMZ antibacterial clay contains 45 % kaolinites and 30 % smectites. Its high surface area maintains an acidic environment (pH 4.5) and releases high concentrations of aluminum. Aluminum accumulates in the outer membrane of E. coli by binding to phospholipids. Furthermore, the membrane’s permeability increases due to synergistic effects between aluminum and transition metals released from the AMZ (i.e. Fe, Cu). The changes in the membrane may compromise its function as a barrier. Understanding the antibacterial mechanism of AMZ is key for its safe use as a natural product. These findings can help us harness the capabilities of antibacterial clays more efficiently.
Lastly, I integrated the results of this work in place-based, cross-cultural educational materials tailored for the tribal schools in the Colombian Amazon. The design of the units was informed by principles of curriculum design and successful pedagogic approaches for Native American students. The purpose of these educational materials is to return the results of research, enhance learning and participation of indigenous peoples in geosciences, and respond to the multicultural and plurilingual educational needs in countries such as Colombia.
I used methods from anthropology and geology to explore the geological knowledge of the Uitoto, a tribe of the Colombian Amazon. The Uitoto use two metaphors to describe Earth systems: 1. the earth is a body, and 2. the Amazon is a tree. I found that they classify surface-water systems according to observable characteristics and use mineral clays to treat various maladies. I argue that Uitoto knowledge about Amazonian mineral resources and surface water is practical, empirically–based and, in many cases, more nuanced than mainstream scientific knowledge.
I studied the mode of action of a natural antibacterial clay from the Colombian Amazon (AMZ) to discover whether the Uitoto’s claims about the clay’s medicinal values was verifiable using the methods of Western Science. Natural antibacterial clays can inhibit the growth of human pathogens. Methods from microbiology and geochemistry were combined to evaluate the mineral-microbe interactions that inhibit growth of model Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) bacteria. The AMZ antibacterial clay contains 45 % kaolinites and 30 % smectites. Its high surface area maintains an acidic environment (pH 4.5) and releases high concentrations of aluminum. Aluminum accumulates in the outer membrane of E. coli by binding to phospholipids. Furthermore, the membrane’s permeability increases due to synergistic effects between aluminum and transition metals released from the AMZ (i.e. Fe, Cu). The changes in the membrane may compromise its function as a barrier. Understanding the antibacterial mechanism of AMZ is key for its safe use as a natural product. These findings can help us harness the capabilities of antibacterial clays more efficiently.
Lastly, I integrated the results of this work in place-based, cross-cultural educational materials tailored for the tribal schools in the Colombian Amazon. The design of the units was informed by principles of curriculum design and successful pedagogic approaches for Native American students. The purpose of these educational materials is to return the results of research, enhance learning and participation of indigenous peoples in geosciences, and respond to the multicultural and plurilingual educational needs in countries such as Colombia.
ContributorsLondoño Arias, Sandra Carolina (Author) / Williams, Lynda B (Thesis advisor) / Semken, Steven (Thesis advisor) / Brandt, Elizabeth A. (Committee member) / Hartnett, Hilairy H (Committee member) / Raymond, Jason (Committee member) / Arizona State University (Publisher)
Created2016
ContributorsDebussy, Claude, 1862-1918 (Composer)