Thesis (Ph.D.)--Indiana University, Dept. of Geological Sciences, 2006. / "Title from dissertation home page (viewed June 28, 2007)." Source: Dissertation Abstracts International, Volume: 67-06, Section: B, page: 3014. Advisers: Arndt Schimmelmann; Maria Mastalerz.

The recent discovery of proprotein convertase subtilisin/kexin type 9 as a protein that increases LDL-cholesterol has lead researchers to investigate it as a target for cholesterol-lowering medication. New options for cholesterol-lowering therapies are of particular importance for individuals, such as those with familial hypercholesterolemia and statin intolerance, who are unable to achieve recommended values through other means. Currently, two monoclonal antibodies inhibiting PCSK9 are approved for use; these monoclonal antibodies work well in conjunction with other medications for hypercholesterolemia, such as statins or ezetimibe, and are equivalent in efficacy with high dose statins. Investigation of PCSK9 inhibitors through siRNA may provide additional mechanisms for lowering cholesterol in the future.

abstract: One goal of geobiochemistry is to follow geochemical energy supplies from the external environment to the inside of microbial cells. This can be accomplished by combining thermodynamic calculations of energy supplies from geochemical processes and energy demands for biochemical processes. Progress towards this goal is summarized here. A critique of all thermodynamic data for biochemical compounds involved in the citric acid cycle (CAC) and the formulation of metabolite properties allows predictions of the energy involved in each step of the cycle as well as the full forward and reverse cycles over wide ranges of temperature and pressure. These results allow evaluation of energy demands at the center of many microbial metabolic systems. Field work, sampling, and lab analyses from two low-temperature systems, a serpentinizing system, and a subglacial setting, provide the data used in these thermodynamic analyses of energy supplies. An extensive literature summary of microbial and molecular data from serpentinizing systems found is used to guide the evaluation and ranking of energy supplies used by chemolithoautotrophic microbes. These results constrain models of the distribution of microbial metabolisms throughout the low-temperature serpentinization systems in the Samail ophiolite in Oman (including locales of primary and subsequent alteration processes). Data collected from Robertson Glacier in Alberta, Canada, together with literature data from Lake Vida in Antarctica and bottom seawater, allowed thermodynamic analyses of low-temperature energy supplies in a glacial system. Results for 1460 inorganic redox reactions are used to fully inventory the geochemical energy sources that support the globally extensive cold biosphere. / Dissertation/Thesis / Doctoral Dissertation Geological Sciences 2016

2-ligne ferrihydrite was synthesized under different conditions, then characterized by transmission electron microscopy, by X-ray diffraction and particularly by Mossbauer spectroscopy. Three synthesis media have been investigated: (1) in the presence of Bacillus subtilis bacteria, (2) in the presence of Bacillus licheniformis and (3) abiotic, at different concentrations of iron (1 x 10-3 M, 5 x 10-3 M and 1 x 10-4 M) and different pH, (6, 7, 8 and 9). We have also studied the effects: of two precursor salts in the synthesis (FeCl2·4H 2O and FeNO3·9H2O), of the drying method (wet, air-dried or freeze-dried) and of the aging of the samples. We have found that the presence of bacteria affects the crystallinity and creates structural disorder. At lower iron concentration, the biotic samples show some Fe2+. The concentration and aging variations show opposite trends between biotic and abiotic samples. The type of salt used has an important effect but the pH and the drying method have a much smaller one. The thesis comprises a literature review of the Mossbauer parameters of ferrihydrite.

The study of metal speciation and the role of biogeochemical processes in metal distribution and cycling in lake sediments was carried out in remote lakes from the Huntsville and the Clyde Forks areas, Ontario and Kejimkujik Park, Nova Scotia, Canada. Based on geochemical data and sequential extraction results of trace elements from sediment cores of 20 lakes from the Huntsville region, Ontario, Canada, it was demonstrated that relative affinities to organic matter and mineral fractions (silicates) played an important role in the distribution of total metal values and hence in the shape of the metal concentration profiles. The importance of atmospheric and geological trace metal fluxes was studied by using sediment traps in two circum-neutral remote lakes, Lavant Long Lake and Perch Lake, in Lanark County, southeastern Ontario, Canada, to measure sedimentation rates, to quantify trace element fluxes from watershed and atmospheric sources, and to investigate the distribution of elements amongst component phases of the trapped sediments. The results of this study showed that local watershed sources were the dominant source of Hg, Cu, Al, Fe, Mn, Sb, in both lakes with ratio sometimes exceeding 9:1 (geogenic to atmospheric). The study of the effect of humic substances (HS) content and their transformation on their interaction with metals was carried out in three remote lakes: Lavant Long Lake, Perch Lake; and Big Dam Lake. HS transformation was demonstrated by the increase of HA aromaticity and the decrease of the E4/E6 ratio in Lavant Long Lake, by the increase of 13C resonance signal in the aromatic-C region (105--150 ppm) in Perch Lake, and by the gradual decrease of the HS content with depth in Big Dam Lake. A quantitative study of trace metal cycling between pore waters and sediments using the most comprehensive diagenetic models was carried out using a two-layer diagenesis model to account for the bioturbation zone and the zone below the bioturbation zone. Sulfate reducing bacteria (SRB) populations were determined in the three lakes using the most probable number (MPN) method. In the zone of bioturbation of Perch Lake, Co, Cu, and Hg predicted and observed concentrations in the pore waters were close. In Lavant Long Lake and for the rest of the elements in Perch Lake, trace metal concentrations predicted by the model were generally lower than the observed. (Abstract shortened by UMI.)

Abstract not available.

Mercury is a well known environmental pollutant. Anthropogenic sources include coal combustion, waste incineration and metal processing. In base metal mines, Hg is often left in the mining wastes (i.e., mine tailings). Once disposed of in open-air impoundments, these Hg-containing tailings can undergo various biogeochemical transformations, including Hg methylation. It is the methylated form of mercury (MeHg) that poses a threat to the environment, because it bio-accumulates at each level of the food chain. The present study was undertaken to assess the biogeochemical factors affecting Hg methylation in Cu-Zn and Au mine tailings. The study focused on the role of sulfate-reducing bacteria (SRB) because they are suspected to be associated with Hg methylation. Temperature, sulfate and organic carbon availability, along with SRB activity were tested as potential factors affecting Hg methylation in column experiments containing old Au tailings and fresh Cu-Zn tailings. The results first showed that SRB activity did not enhance Hg methylation in Cu-Zn tailings and Au tailings, indicating that iron reducing bacteria, and not SRB, along with abiotic methylation reactions played an important role. Cold temperatures did not slow down SRB activity and MeHg production, but the accidental freezing and thawing of the Cu-Zn tailings promoted the production of soluble MeHg. The mechanism responsible for this unexpected Hg methylation is however unknown. Elevated organic carbon and sulfate concentrations did enhance SRB activity, but not MeHg formation in the tailings, because increased sulfide production hindered Hg methylation. Tailings mineralogy played a significant role in the production of methyl mercury, Au tailings contained more soluble and solid-bound MeHg than Cu-Zn tailings. These results add to the increasing amount of information on Hg cycling in the environment, and indicate that SRB might not be the dominant Hg methylators in mining environments.

Trace gas analysis in Earth systems plays an important role in planetary research. Bernard (1976) and Whiticar (1999) proposed that biologically produced methane and thermogenically or geologically produced methane could be differentiated in marine environments through isotopic analysis coupled with methane to higher n-alkane gas concentration ratios. This differentiation is important to the study of exobiology; the ability to determine a biological source of atmospheric gas production through isotopic and/or concentration analysis could prove critical to the search for a "second genesis" within our solar system, greatly increasing the probability of life throughout the universe. It is hypothesized that the earliest forms of life on Earth were methanogenic archaea developing in extreme anaerobic conditions. These conditions include high temperature >90°C hydrothermal vents as well as hypersaline environments where archaea have been found to exist in present day (Rasmussen 2000, Huber et al., 1989, Kelley et al., 2005 ). Analogous hypersaline paleoenvironments have been found to exist on Mars (Osterloo, M.M. et al., 2008). Tazaz (2012) proposed an extension to the biogenic isotopic boundaries of methane from hypersaline environments investigated in Baja, Mexico. Here we reconfirm Tazaz's results from Baja while showing a similar isotopic composition of methane in hypersaline environments in Atacama, Chile. Tazaz (2012) also proposed further research into low methane to higher n-alkane gas ratios found in field samples from Baja, Mexico. We show here through lab incubation experiments of sediment collected in Baja, Mexico and Atacama, Chile that these low ratios are primarily due to the biogenic production of ethane in hypersaline environments. Experiments were done with various substrate amendments to investigate the greatest yield of ethane and the effects of inhibiting sulfate reducing bacteria. Given the significance of such findings, it is essential to examine the extremophiles that exist in hypersaline environments to gain a better understanding of the biomarkers in trace gas analysis. / A Thesis submitted to the Department of Earth, Ocean and Atmospheric Science in partial fulfillment of the Master of Science. / Spring Semester, 2015. / January 30, 2015. / Astrobiology, Exobiology, Extremophiles, Hypersaline / Includes bibliographical references. / Jeffery Chanton, Professor Directing Thesis; Olivia Mason, Committee Member; Angela Knapp, Committee Member.

Understanding the role humans play in modifying ecosystems through urban development is central to addressing our current and emerging environmental challenges. Urbanization can drastically modify carbon (C) and nitrogen (N) cycling in terrestrial ecosystems. However, spatiotemporal distribution of these modifications and their impact on ecosystems are not well-quantified. In this dissertation, I combined field and remotely sensed data, models and laboratory analysis, and socioeconomic data to understand the variations in ecosystem characteristics and their socioeconomic covariates along a 100-km urbanization gradient in the Boston region. Vegetation and soil C and N chemistry from 139 field plots show that C and N content increased in soil and decreased in vegetation with urbanization for forest, residential and other-developed land use classes. Landsat normalized difference vegetation index correlated positively with aboveground biomass and foliar N content (but not N concentration), and negatively with impervious surface area (ISA) fraction. Patterns in foliar N concentration are associated more strongly with changes in species composition than with phenotypic plasticity. My results demonstrate the need to account for ISA fraction when scaling vegetation and soil data across urban landscapes. Measured atmospheric inorganic N inputs at nine sites along the gradient correlated significantly with proximity to urban core and modeled on-road CO2 emissions. N leaching rates correlated positively with atmospheric N input rates. A regional model underestimated atmospheric N inputs at urban sites and overestimated it at rural sites, thus highlighting the need to incorporate the effects of urbanization in N deposition models. Analysis of census variables, forestland owner surveys, and biomass highlighted the scale-dependent relationships between socioeconomic variables and vegetation biomass. Owner occupancy showed the strongest and most consistent relationship with biomass across different scales. Combined with either housing age or educational attainment, owner occupancy explained ~80% variance in biomass in different spatial extents of the gradient. Conservation awareness among landowners was higher near the urban core and correlated positively with educational attainment and landholding size. My results demonstrate the complex spatial variations in urban biogeochemistry and help develop a mechanistic understanding of urban ecosystem function and its socioeconomic covariates.

As the Arctic warms, the ~277 Pg of carbon stored in permafrost peatlands faces an uncertain fate. Arctic and Subarctic peatlands are likely to release more methane (CH4) as permafrost thaw releases formerly-frozen carbon, thaw-induced land subsidence and inundation lead to anaerobic conditions, and higher temperatures allow more rapid decomposition. In addition to these effects, CH4 and carbon dioxide (CO2) emissions may also change due to shifts in plant inputs and consequent changes in organic matter quality, but the exact relationships between organic matter and CH4 production are not well understood. In this study, we examined microbial CH4 and CO2 production and their relationship to organic matter chemistry in Stordalen Mire, a thawing Subarctic peatland in northern Sweden. We also used stable carbon isotopes (δ13C) of CH4 and CO2, and their apparent fractionation factor (αC), to examine the effect of thaw on the proportion of methanogenesis by hydrogenotrophic or acetoclastic pathways. At Stordalen, permafrost thaw causes dry, aerobic permafrost plateaus (palsas) to collapse and become inundated. These wet depressions are then colonized first by Sphagnum mosses and then by sedges as permafrost thaw and plant succession progress. In our study, we examined a chronosequence of sites with varying permafrost status and plant community composition. These sites included dry, intact palsas; recently-thawed collapsed palsa sinkholes; partially-thawed Sphagnum-dominated bogs; mostly-thawed poor fens with a combination of Sphagnum and tall sedges; and fully-thawed rich fens with mature stands of tall sedges and no Sphagnum. The changes in potential CH4 and CO2 production along the thaw progression were examined with anaerobic peat incubations, which were all performed with identical temperature and water saturation. These incubations showed increases in potential decomposition rates and CH4/CO2 production ratios along the thaw progression. Methanogenesis pathways also shifted from predominately hydrogenotrophic to acetoclastic, as revealed by lower αC in fens. These shifts are consistent with increasing organic matter bioavailability along the thaw progression, which was confirmed by analyses of peat and dissolved organic matter (DOM) chemistry. These analyses showed that compared to collapsed palsas and bogs, rich fens had lower peat C/N ratios, higher peat humification rates (as determined by Fourier-transform infrared [FTIR] spectroscopy), and more labile DOM compounds (as determined by Fourier-transform ion cyclotron resonance mass spectrometry [FT-ICR MS]). The validity of these incubations for revealing trends in in situ CH4 and CO2 production was determined by comparison with dissolved CH4 and CO2 in field-collected pore water. The incubation CH4/CO2 ratios were compared to both the raw pore water CH4/CO2 concentration ratios, and to the pore water CH4/CO2 production ratios estimated with an isotope mass balance model. In both cases, CH4/CO2 ratios were higher in the incubations than in the pore water; however, the same increases in CH4/CO2 with thaw were observed in both cases. Incubation and field pore water αC were also compared. Incubation αC values were slightly higher than field αC, but αC decreased with thaw in both the incubations and the field. We thus conclude that incubations can reliably estimate relative CH4/CO2 ratios and αC between different sites, though their ability to estimate absolute CH4/CO2 and αC is limited. The changes in DOM chemistry along the thaw progression were examined more closely with a combination of elemental composition (via FT-ICR MS) and optical properties (via UV/Vis absorption and fluorescence spectroscopies). These techniques revealed that the presence of dense Sphagnum moss, which is abundant in collapsed palsa, bog, and poor fen sites, is the main driver of DOM elemental composition and optical properties at Stordalen. Compared to rich fens, DOM from sites with Sphagnum had greater aromaticity, higher average molecular weights, and greater O/C ratios. These properties suggest a higher abundance of phenolic compounds, which are released by Sphagnum and may inhibit decomposition at these sites. In contrast, rich fen DOM had greater saturation, lower O/C ratios, greater N/C and S/C ratios, and optical properties suggesting a higher proportion of microbially-derived DOM. Overall, our results suggest that the changes in plant community due to permafrost thaw at Stordalen lead to greater organic matter lability and higher CH4 production. In inundated sites, these changes are primarily driven by the disappearance of Sphagnum as partially-thawed sites transition to fully-thawed rich fens. Similar plant successions have been observed in other peatlands with thawing permafrost, highlighting the potential importance of these shifts in driving future northern peatland greenhouse gas balances. Future models of climate feedbacks in permafrost peatlands should thus take into account any changes in plant community composition, especially changes in Sphagnum cover, as permafrost thaws. / A Dissertation submitted to the Department of Earth, Ocean, and Atmospheric Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Spring Semester 2016. / February 29, 2016. / decomposition, dissolved organic matter, methane, peat, permafrost / Includes bibliographical references. / Jeffrey P. Chanton, Professor Directing Dissertation; Alan G. Marshall, University Representative; William M. Landing, Committee Member; Yang Wang, Committee Member; William C. Burnett, Committee Member; Patrick M. Crill, Committee Member.