The reactivity of partially reduced metabolites of 2,4,6-trinitrotoluene (TNT), namely arylhydroxylamines and nitrosoarenes, was evaluated with a simple biological system and with components of soil natural organic matter (NOM). This study was carried out to address the long-standing problem of irreversible binding to soil NOM and biomass, commonly observed during the reductive transformation of polynitroaromatic contamination. The study focused on partially reduced metabolites rather than the completely reduced arylamine metabolites that have already been extensively investigated for their role in binding to soil NOM. In the simple bioreduction system of Clostridium acetobutylicum cell-free extract/molecular hydrogen (electron donor), 10% of the initial 14C was found bound to solid proteinaceous material following sequential anaerobic/aerobic treatment. A review of the nitroso and hydroxylamino functional group chemistry revealed that the nitroso-thiol reaction was most likely responsible for the reaction with proteins. The introduction of a model thiol, 1-thioglycerol, into an anaerobic mixture of 4-hydroxylamino-2,6-dinitrotoluene (4HADNT) and 2,4-dihydroxylamino-6-nitrotoluene (DHA6NT) resulted in the formation of a new product, only when the reaction mixture was exposed to air. The results from the model reaction confirmed that thiols could act as competing nucleophiles for nitroso compounds, which are readily formed from hydroxylamino compounds upon exposure to air. The reactivity of arylhydroxylamines and nitrosoarenes with standard humic acids was investigated using 4HADNT and nitrosobenzene as model compounds, respectively. Contrary to results reported by others, 4HADNT was found to be nonreactive towards humic acid at humic acid concentrations in excess of dissolved organic matter concentrations found in nature. Conversely, nitrosobenzene reacted rapidly with humic acids, with the extent of reaction being highest for humic acids that had a high protein content. Humic acids that were pretreated with a thiol derivatizing agent showed diminished capacity for reaction with nitrosobenzene. Since nitroso intermediates from TNT reduction are difficult to synthesize and are rarely observed in nature due to their high instability, their electrophilic characteristics were evaluated using a molecular modeling approach. Molecular models of potential TNT nitroso intermediates were compared with those of the strongly electrophilic nitrosobenzene. The comparison revealed that 2-nitroso-4-hydroxylamino-6-nitrotoluene was more likely to react similarly to nitrosobenzene than 4-nitroso-2,6-dinitrotoluene.

A series of equilibrium cadmium-binding experiments with raw species of Sargassum was performed in order to extend the database on the biosorption performance of this brown algae. The results indicate that their maximum cadmium uptake ranges from approximately 0.7 to 1.0 mmol Cd/gram biomass. A classical method for the extraction of alginate from brown algae was modified and applied to Sargassum species under high-temperature alkaline conditions (80°C, 2.0% Na2CO3). It yields alginate samples of low viscosity suitable for chemical characterization by direct acquisition of well-resolved NMR spectra. This new method also allowed the identification of an acid-soluble fraction not previously isolated by traditional methods, yet capable of binding cadmium. / The 1H-NMR characterization of the alginates, extracted from Sargassum by the modified method, reveals a consistent and unusual enrichment in homopolymeric alpha-L-guluronic acid (G-blocks). These alginates display G-block diad frequency values (FGG) between 0.37 and 0.81. This translates into an enhanced selectivity for cadmium and calcium relative to monovalent ions such as sodium and the proton as well as smaller divalent ions such as magnesium. Results of competitive exchange experiments in the Cd-Ca-alginate system yield selectivity coefficients, K* CdCa, between 0.43 +/- 0.10 and 1.32 +/- 0.02 for a range of FGG, from 0.23 to 0.81. In contrast, much larger selectivity coefficients were obtained for the Mg-Ca-alginate (K*MgCa ≤ 18.0 +/- 1.4) and Mg-Cd-alginate (K*MgCa ≤ 16.0 +/- 0.9) systems with alginates extracted from Sargassum fluitans (FGG = 0.81) and Sargassum thunbergeii (F GG = 0.75). Selectivity studies with mixed-metal pair alginate systems, as opposed to the more common single metal methods, highlight the importance of the specific macromolecular conformation of the alginate polymer in determining metal binding behaviour in multiple-metal systems as well as the performance of Sargassum as an algal biosorbent. The unique composition of the alginates present in species of Sargassum and the resilience of the algae to degradation provide this bio-material with a distinct advantage over other brown algal species when considering its implementation for the strategic removal of toxic heavy metals from contaminated and industrial waste waters.

<p> Benthic macrofauna can play an important role in facilitating some of the microbial mediated processes of nitrogen cycling in estuarine sediments. Declines in benthic macrofauna, like polychaete worms, have been attributed to long-term increases in bottom water hypoxia in Chesapeake Bay. Utilizing a large monitoring dataset including benthic macrofaunal abundance, biomass, and concurrent measures of environmental parameters, I examined how environmental conditions regulate the densities of opportunistic polychaetes in a mesohaline estuarine system. This analysis points to a benthic community dominated by euryhaline, opportunistic polychaete worms (<i>M. viridis, S. benedicti, H. filiformis, A. succinea</i>) which have well adapted but varying responses to hypoxia and other stressful conditions. Results of two laboratory experiments with the opportunistic polychaete <i>Alitta (Neanthes) succinea</i> were used to quantify the short-term influence of density and size of surface-feeding polychaetes on sediment-water fluxes of inorganic nitrogen under varying oxygen conditions. Polychaete enhancements of O₂ and nitrogen fluxes were strongly correlated with total animal biomass. Solute fluxes were stimulated by presence of both larger and smaller worms, but per capita effects were greater for the deep-burrowing larger polychaetes. Utilizing a unique large-scale monitoring dataset collected in the Chesapeake Bay, I employed Classification and Regression Tree (CART) and multiple linear regression (MLR) analyses to assess the relationship between benthic biomass and NH₄⁺ efflux within different regions of the estuary by season. In addition to labile organic matter, oligohaline and mesohaline tributary temperature and salinity control the rate of nitrogen cycling and benthic macrofaunal biomass. In deeper regions of mesohaline tributaries and the mainstem Bay, dissolved oxygen was found to be the dominating parameter regulating sediment nitrogen pathways as well as the structure of the benthic macrofaunal community. With increased macrofaunal biomass, spring regressions indicated an enhancement of NH₄⁺ efflux. In contrast, fall regressions indicated the enhancement of fixed nitrogen removal from sediments. Summer data lacked a significant relationship, but high NH₄⁺ effluxes under hypoxic/anoxic conditions suggested dissolved oxygen is the primary driver of summer nitrogen cycling. This study, using field and laboratory data, concludes that a complex balance between seasonal and regional dissolved oxygen, temperature and salinity conditions shape not only the benthic community but also the relationship between macrofaunal biomass and sediment nitrogen flux in this eutrophic estuarine system.</p>

<p> Selenium (Se) is a trace element of great ecological importance whose environmental distribution is highly impacted by anthropogenic activity. In the 1980s, selenium was recognized as a major aquatic contaminant following widespread deformities and mortality among waterfowl hatchlings near the agricultural drainage evaporation ponds of the Kesterson Reservoir (CA, USA). Today, 400,000 km² in the Western United States are threatened by agricultural selenium contamination, as are parts of Canada, Egypt, Israel, and Mexico. From the soil aggregate to the watershed, from the soils of the Central Valley to the sediments of the Salton Sea, and from Environmental Science to Policy and Management, in this dissertation I explore agricultural selenium contamination across scales, ecosystems, and disciplines. I begin with a review of the science, policy, and management of irrigation-induced selenium contamination in California, the heart of worldwide research on the issue. I then delve into the physical and biogeochemical mechanisms that control selenium reduction and mobility within the structured surface soils that are the source of contamination, using an aggregate-scale combined experimental and reactive transport modeling approach. Finally, I present a diagenetic model for selenium incorporation into the sediment of the Salton Sea, which has been receiving seleniferous agricultural drainage over the last 100 years. </p><p> To extract lessons from the last 30 years of seleniferous drainage management and water quality regulation in California, I reviewed the history and current developments in science, policy, and management of irrigation-induced selenium contamination in California. Specifically, I evaluated improvements in the design of local attenuation methods and the development of programs for selenium load reductions at the regional scale. On the policy side, I assessed the site-specific water quality criteria under development for the San Francisco Bay-Delta in the context of previous regulation. This approach may be a landmark for future legislation on selenium in natural water bodies and I discussed challenges and opportunities in expanding it to other locations such as the Salton Sea. By combining proven management tools with the novel, site-specific policy approach, it may be possible to avoid future events of irrigation-induced selenium contamination. However, the majority of regional selenium load reductions in California were achieved by decreasing drainage volume rather than selenium concentrations. Thus, there appear to be opportunities for additional improvements through management practices that enhance selenium retention in source soils. </p><p> To quantify the likely implications of these experimental results for soils with different degrees of aggregation, I formulated a general mechanistic framework for aggregate scale heterogeneity in selenium reduction. Specifically, I constructed a dynamic 2D model of selenium fate in single idealized aggregates, in which reactions were implemented with double-Monod rate equations coupled to the transport of pyruvate, O₂, and Se-species (selenate, selenite, and elemental selenium). The spatial and temporal dynamics of the model were validated with the experimental data and predictive simulations were performed covering aggregate sizes between 1 and 2.5 cm diameters. Simulations predict that selenium retention scales with aggregate size. Depending on aeration conditions and the input concentrations of selenate and pyruvate, selenium retention was predicted to be 4-23 times higher in 2.5-cm-aggregates compared to 1-cm-aggregates. Under oxic conditions, aggregate size and pyruvate-concentrations were found to have a positive synergistic effect on selenium retention. Promoting soil aggregation on seleniferous agricultural soils may thus help decrease the impacts of selenium contaminated drainage on downstream aquatic ecosystems receiving it. </p><p> This work presents agricultural selenium contamination as a complex problem that crosses ecosystems, scales, and disciplines. From a management perspective, the tension between dispersed non-point sources and hotspots where elevated selenium concentrations and sensitive aquatic ecosystems converge is difficult to address. Differences in biogeochemical conditions and trophic transfer within food webs render traditional regulatory approaches ineffective and force regulators to engage with the science of site-specific selenium transfer between ecological compartments. At the same time, gaps still exist in our mechanistic understanding of selenium's environmental cycling and in our integration of scientific knowledge across different ecosystems and scales. Centimeter scale heterogeneity in the biogeochemical conditions within source soils may fundamentally control selenium emissions across large agricultural areas and thus determine the selenium loading of rivers, lakes, and estuaries. Within aquatic environments receiving seleniferous drainage, the first few centimeters of surface sediment may control selenium exposure for entire food webs. Improved understanding at this level holds the potential to simultaneously reduce selenium emissions and respond more effectively to pollution where it occurs. In order to preserve sensitive habitat while also meeting agricultural drainage needs in seleniferous regions we must bridge the gaps between ecosystems, scales, and disciplines.</p><p> (Abstract shortened by UMI.)</p>

<p> The identification of beige fat within the last decade, its ability to burn energy in adult humans, and its great potential for therapeutic applications has motivated many to work towards understanding how beige fat is made. Although several proteins have been identified as important for beige fat differentiation, it is clear that the differences that distinguish beige fat from other types of fat cannot be explained by the presence of these proteins alone. Additional regulatory proteins, including transcription factors and their co-factor proteins, must be involved. I took advantage of two important developments in the field of fat differentiation to develop two high throughput approaches that identified new transcription factors involved in beige fat: (1) our ability to culture beige fat cells by differentiating white fat pre-adipocytes in the presence of Rosiglitazone and (2) the established role for PRDM16 as required for beige fat differentiation. In brief, I combined RNA-seq data from beige fat cells and proteomics data from Rosiglitazone-dependent PRDM16 protein complexes to identify a set of candidate transcription factors involved in beige fat differentiation. The most promising candidate among this pool of putative beige fat regulatory transcription factors was GTF2IRD1. I determined that GTF2IRD1 is a PRDM16-interacting transcription factor that is enriched in beige and brown fat cells. In vivo, GTF2IRD1 is enriched in brown adipose tissue and is increased in beige and brown fat in response to beta-3-adrenergic stimulus. In the presence of the potent PPARgamma agonist Rosiglitazone, GTF2IRD1 overexpression enhances and shRNA-mediated knockdown reduces beige fat differentiation. GTF2IRD1 represses TGF-beta-mediated inhibition of beige fat differentiation. In summary, my data strongly supports that GTF2IRD1 is an essential regulator of beige fat differentiation through interaction with PRDM16 and inhibition of TGF-beta-mediated repression of differentiation.</p>

Thesis (Ph. D.)--University of Washington, 2007. / Vita. Includes bibliographical references (leaves 141-160).

Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2007. / Source: Dissertation Abstracts International, Volume: 68-07, Section: B, page: 4335. Adviser: Atul K. Jain. Includes bibliographical references (leaves 133-154). Available on microfilm from Pro Quest Information and Learning.

Thesis (master's)--Lund University, 2005. / "February 2006." Includes bibliographical references (p. 43-47). Also issued electronically via World Wide Web in PDF format.

Thesis (Ph. D.)--Oregon State University, 1997. / Typescript (photocopy). Includes bibliographical references. Also available on the World Wide Web.

Thesis (Ph. D.)--Oregon State University, 2004. / Typescript (photocopy). Includes bibliographical references (leaves 143-152). Also available on the World Wide Web.