xvi, 156 p. A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. / This dissertation examined a number of general vegetation-modeling issues, and the sensitivity of terrestrial net primary productivity (NPP), soil moisture and actual evapotranspiration (ET) to climatic variations in China. The specific issues addressed included: (1) the sensitivity of the performance of an equilibrium vegetation model to the choice of monthly-mean climatologies, observed validation data sets, and three map-comparison approaches; and (2) the limitations of existing map-comparison approaches in vegetation modeling; and the variation and climate sensitivity of (3) terrestrial NPP and (4) soil moisture and actual ET in China. To address the first issue, BIOME4 (Kaplan et al., 2002), a typical example of an equilibrium vegetation model, was used along with a set of 19 different monthly-mean climatologies, three validation data sets, and several map-comparison methods. To address the second issue, the "opposite and identity" (01) index (Tang, 2008) was developed for evaluating the correspondence of two simulation results. To examine the third issue, a set of historical NPP dynamics were derived from normalized-difference vegetation index data by modifying the CASA (Potter et al., 1999) approach and then were linked to the variation of temperature and precipitation to analyze the climatic effects on terrestrial NPP in China. To examine the fourth issue, a stand-alone water balance model, LH (LPJ-hydrology), was developed by modifying the LPJ dynamic global vegetation model (Sitch et al., 2003), and applying it to a China case study. The results of these analyses indicate that (1) the 30-year mean-climatology preceding the observed data produces the most accurate vegetation simulations; (2) the OI index is a useful tool to compare two simulation results or to evaluate simulation results against observed spatiotemporal data; (3) climate and land-use change jointly controlled NPP dynamics in the eastern monsoon zone of China. In contrast, NPP dynamics in the north-west and zone and in the Tibet Plateau frigid zone depended more on climatic variation; and (4) the spatial patterns of soil moisture and ET in China were correlated with the variation of temperature and precipitation. However, the strength of such relationship varies spatially. This dissertation includes my published and coauthored materials. / Adviser: Patrick J. Bartlein

abstract: The transmembrane subunit (gp41) of the envelope glycoprotein of HIV-1 associates noncovalently with the surface subunit (gp120) and together they play essential roles in viral mucosal transmission and infection of target cells. The membrane proximal region (MPR, residues 649-683) of gp41 is highly conserved and contains epitopes of broadly neutralizing antibodies. The transmembrane (TM) domain (residues 684-705) of gp41 not only anchors the envelope glycoprotein complex in the viral membrane but also dynamically affects the interactions of the MPR with the membrane. While high-resolution X-ray structures of some segments of the MPR were solved in the past, they represent the pre-fusion and post-fusion conformations, most of which could not react with the broadly neutralizing antibodies 2F5 and 4E10. Structural information on the TM domain of gp41 is scant and at low resolution. This thesis describes the structural studies of MPR-TM (residues 649-705) of HIV-1 gp41 by X-ray crystallography. MPR-TM was fused with different fusion proteins to improve the membrane protein overexpression. The expression level of MPR-TM was improved by fusion to the C-terminus of the Mistic protein, yielding ∼1 mg of pure MPR-TM protein per liter cell culture. The fusion partner Mistic was removed for final crystallization. The isolated MPR-TM protein was biophysically characterized and is a monodisperse candidate for crystallization. However, no crystal with diffraction quality was obtained even after extensive crystallization screens. A novel construct was designed to overexpress MPR-TM as a maltose binding protein (MBP) fusion. About 60 mg of MBP/MPR-TM recombinant protein was obtained from 1 liter of cell culture. Crystals of MBP/MPR-TM recombinant protein could not be obtained when MBP and MPR-TM were separated by a 42 amino acid (aa)-long linker but were obtained after changing the linker to three alanine residues. The crystals diffracted to 2.5 Å after crystallization optimization. Further analysis of the diffraction data indicated that the crystals are twinned. The final structure demonstrated that MBP crystallized as a dimer of trimers, but the electron density did not extend beyond the linker region. We determined by SDS-PAGE and MALDI-TOF MS that the crystals contained MBP only. The MPR-TM of gp41 might be cleaved during or after the process of crystallization. Comparison of the MBP trimer reported here with published trimeric MBP fusion structures indicated that MBP might form such a trimeric conformation under the effect of MPR-TM. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2014

abstract: In enzyme induced carbonate precipitation (EICP), calcium carbonate (CaCO3) precipitation is catalyzed by plant-derived urease enzyme. In EICP, urea hydrolyzes into ammonia and inorganic carbon, altering geochemical conditions in a manner that promotes carbonate mineral precipitation. The calcium source in this process comes from calcium chloride (CaCl2) in aqueous solution. Research work conducted for this dissertation has demonstrated that EICP can be employed for a variety of geotechnical purposes, including mass soil stabilization, columnar soil stabilization, and stabilization of erodible surficial soils. The research presented herein also shows that the optimal ratio of urea to CaCl2 at ionic strengths of less than 1 molar is approximately 1.75:1. EICP solutions of very high initial ionic strength (i.e. 6 M) as well as high urea concentrations (> 2 M) resulted in enzyme precipitation (salting-out) which hindered carbonate precipitation. In addition, the production of NH4+ may also result in enzyme precipitation. However, enzyme precipitation appeared to be reversible to some extent. Mass soil stabilization was demonstrated via percolation and mix-and-compact methods using coarse silica sand (Ottawa 20-30) and medium-fine silica sand (F-60) to produce cemented soil specimens whose strength improvement correlated with CaCO3 content, independent of the method employed to prepare the specimen. Columnar stabilization, i.e. creating columns of soil cemented by carbonate precipitation, using Ottawa 20-30, F-60, and native AZ soil was demonstrated at several scales beginning with small columns (102-mm diameter) and culminating in a 1-m3 soil-filled box. Wind tunnel tests demonstrated that surficial soil stabilization equivalent to that provided by thoroughly wetting the soil can be achieved through a topically-applied solution of CaCl2, urea, and the urease enzyme. The topically applied solution was shown to form an erosion-resistant CaCO3 crust on fine sand and silty soils. Cementation of erodible surficial soils was also achieved via EICP by including a biodegradable hydrogel in the stabilization solution. A dilute hydrogel solution extended the time frame over which the precipitation reaction could occur and provided improved spatial control of the EICP solution. / Dissertation/Thesis / Doctoral Dissertation Civil and Environmental Engineering 2015

abstract: Despite the breadth of studies investigating ecosystem development, an underlying theory guiding this process remains elusive. Several principles have been proposed to explain ecosystem development, though few have garnered broad support in the literature. I used boreal wetland soils as a study system to test a notable goal oriented principle: The Maximum Power Principle (MPP). The MPP posits that ecosystems, and in fact all energy systems, develop to maximize power production or the rate of energy production. I conducted theoretical and empirical investigations to test the MPP in northern wetlands. Permafrost degradation is leading to rapid wetland formation in northern peatland ecosystems, altering the role of these ecosystems in the global carbon cycle. I reviewed the literature on the history of the MPP theory, including tracing its origins to The Second Law of Thermodynamics. To empirically test the MPP, I collected soils along a gradient of ecosystem development and: 1) quantified the rate of adenosine triphosphate (ATP) production--literally cellular energy--to test the MPP; 2) quantified greenhouse gas production (CO2, CH4, and N2O) and microbial genes that produce enzymes catalyzing greenhouse gas production, and; 3) sequenced the 16s rRNA gene from soil microbes to investigate microbial community composition across the chronosequence of wetland development. My results suggested that the MPP and other related theoretical constructs have strong potential to further inform our understanding of ecosystem development. Soil system power (ATP) decreased temporarily as the ecosystem reorganized after disturbance to rates of power production that approached pre-disturbance levels. Rates of CH4 and N2O production were higher at the newly formed bog and microbial genes involved with greenhouse gas production were strongly related to the amount of greenhouse gas produced. DNA sequencing results showed that across the chronosequence of development, the two relatively mature ecosystems--the peatland forest ecosystem prior to permafrost degradation and the oldest bog--were more similar to one another than to the intermediate, less mature bog. Collectively, my results suggest that ecosystem age, rather than ecosystem state, was a more important driver for ecosystem structure and function. / Dissertation/Thesis / Doctoral Dissertation Biology 2015

abstract: The focus of this thesis is to study dissolved organic carbon composition and reactivity along the Colorado and Green Rivers. Dissolved organic carbon (DOC) in large-scale, managed rivers is relatively poorly studied as most literature has focused on pristine unmanaged rivers. The Colorado River System is the 7th largest in the North America; there are seventeen large dams along the Colorado and Green River. DOC in rivers and in the lakes formed by dams (reservoirs) undergo photo-chemical and bio-degradation. DOC concentration and composition in these systems were investigated using bulk concentration, optical properties, and fluorescence spectroscopy. The riverine DOC concentration decreased from upstream to downstream but there was no change in the specific ultraviolet absorbance at 254 nm (SUVA254). Total fluorescence also decreased along the river. In general, the fluorescence index (FI) increased slightly, the humification index (HIX) decreased, and the freshness index (β/α) increased from upstream to downstream. Photo-oxidation and biodegradation experiments were used to determine if the observed changes in DOC composition along the river could be driven by these biogeochemical alteration processes. In two-week natural sunlight photo-oxidation experiments the DOC concentration did not change, while the SUVA254 and TF decreased. In addition, the FI and ‘freshness’ increased and HIX decreased during photo-oxidation. Photo-oxidation can explain the upstream to downstream trends for TF, FI, HIX, and freshness observed in river water. Serial photo-oxidation and biodegradation experiments were performed on water collected from three sites along the Colorado River. Bulk DOC concentration in all samples decreased during the biodegradation portion of the study, but DOC bioavailability was lower in samples that were photo-oxidized prior to the bioavailability study. The upstream to downstream trends in DOC concentration and composition along the river can be explained by a combination of photo-chemical and microbial degradation. The bulk DOC concentration change is primarily driven by microbial degradation, while the changes in the composition of the fluorescent DOC are driven by photo-oxidation. / Dissertation/Thesis / Masters Thesis Chemistry 2015

abstract: As a result of growing populations and uncertain resource availability, urban areas are facing pressure from federal and state agencies, as well as residents, to promote conservation programs that provide services for people and mitigate environmental harm. Current strategies in US cities aim to reduce the impact of municipal and household resource use, including programs to promote water conservation. One common conservation program incentivizes the replacement of water-intensive turfgrass lawns with landscapes that use less water consisting of interspersed drought-tolerant shrubs and trees with rock or mulch groundcover (e.g. xeriscapes, rain gardens, water-wise landscapes). A handful of previous studies in experimental landscapes have shown that converting a turfgrass yard to a shrub-dominated landscape has the potential to increase rates of nitrate (NO3-) leaching. However, no studies have examined the drivers or patterns across diverse management practices. In this research, I compared soil nutrient retention and cycling in turfgrass and lawn-alternative xeriscaped yards along a chronosequence of time since land cover change in Tempe, Arizona, in the semi-arid US Southwest. Soil inorganic extractable nitrogen (N) pools were greater in xeriscapes compared to turfgrass lawns. On average xeriscapes contained 2.5±0.4 g NO3--N/m2 in the first 45 cm of soil, compared to 0.6±0.7 g NO3--N/m2 in lawns. Soil NO3--N pools in xeriscaped yards also varied significantly with time: pools were largest 9-13 years after cover change and declined to levels comparable to turfgrass at 18-21 years. Variation in soil extractable NO3--N with landscape age was strongly influenced by management practices that control soil water availability, including shrub cover, the presence of sub-surface plastic sheeting, and the frequency of irrigation. This research is the first to explore the ecological outcomes and temporal dynamics of an increasingly common, ‘sustainable’ land use practice that is universally promoted in US cities. Our findings show that transitioning from turfgrass to water-efficient residential landscaping can lead to an accumulation of NO3--N that may be lost from the soil rooting zone over time, through leaching following irrigation or rainfall. These results have implications for best management practices to optimize the benefits of water-conserving residential yards. / Dissertation/Thesis / Masters Thesis Biology 2015

abstract: 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. / Dissertation/Thesis / Doctoral Dissertation Geological Sciences 2015

abstract: The Middle Stone Age archaeological record from the south coast of South Africa contains significant evidence for early modern human behavior. The south coast is within the modern Greater Cape Floristic Region (GCFR), which in the present-day encompasses the entirety of South Africa’s Winter Rainfall Zone (WRZ) and contains unique vegetation elements that have been hypothesized to be of high utility to hunter-gatherer populations. Extant paleoenvironmental proxy records for the Pleistocene in the region often indicate evidence for more open environments during the past than occur in the area in the present-day, while climate models suggest glacial presence of the WRZ that would support maintenance of C3-predominant GCFR vegetation. These paleoenvironmental proxies sample past environments at geographic scales that are often regional. The GCFR flora is hyper-diverse, and glacial climate change-driven impacts on local vegetation could have been highly variable over relatively small geographic scales. Proxy records that are circumscribed in their geographic scale are thus key to our understanding of ancient environments at particular MSA archaeological localities. Micromammal fossil teeth are now recognized as an abundant potential reservoir of paleoenvironmental proxy data at an extremely local scale. This study analyzed modern micromammal teeth obtained from raptor pellets at three locations on the south coast. Stable carbon isotope analysis indicates that the modern micromammals from the taxa sampled consume a wide range of δ13Cplant on the landscape when it is available, and thus stable carbon isotope analysis of micromammal teeth should act as a proxy for the range of available δ13Cdiet in a circumscribed area of vegetation. Micromammal stable carbon isotope data obtained from specimens from one of the few well-dated MIS6-MIS5 sequences in the region (Pinnacle Point sites 13B, 30, and 9C). δ13Cenamel values for the taxa sampled indicate diets that are primarily C3, and there is almost no evidence for a dietary C4 grass component in any of the sampled specimens. This indicates that, at a minimum, pockets of C3 vegetation associated with the GCFR were likely available to hunter-gatherers at Pinnacle Point throughout the Middle and Late Pleistocene. / Dissertation/Thesis / Doctoral Dissertation Anthropology 2015

abstract: The Basin and Range province of southwestern USA are composed of different grassland and shrubland ecosystems. Particularly understudied ecosystems in this region are playas, which are ephemerally-flooded wetlands located in topographic low areas of hydrologically-closed dryland catchments. There is not much known about the ecological functioning of playas and the role of playas within desert basins. Even less is known about how global change drivers may affect playas in the future. The main objective of this thesis was to better understand the ecological functioning and the impact of climate change on desert playa wetlands. I collected new data, used existing long-term data, and used simulation modelling techniques to address this objective. I compared playa soils to upland soils and found that playas were hotspots of soil organic carbon and nutrient storage within a desert basin. I also used existing data to analyze the response of above-ground net primary productivity (ANPP) to annual precipitation in playas and upland ecosystems. I found that playa ANPP responded in a non-linear concave-down relationship with annual precipitation amount. Playa ANPP peaked in moderately wet years and declined in very wet years, which was most likely due to flooding; whereas, upland ANPP increased linearly with precipitation. I measured soil organic carbon and nitrogen concentrations in a representative subset of playas and measured the biophysical characteristics of the upland catchments associated with each playa. I found that both catchment geomorphology and vegetation cover were correlated to differences in soil organic carbon and nitrogen among playas. These results showed the importance external soil-inputs delivered via surface runon to playas. Finally, I empirically measured groundwater recharge beneath playas and combined these empirical data with modelling data to forecast how playa groundwater recharge may change in the future. I concluded that playas contribute to groundwater recharge in desert aquifers, playa runon is a strong predictor of playa groundwater recharge, and climate change will have a net-positive impact on groundwater recharge beneath playas. Overall, my thesis research increased the understanding of the role of desert playas on the functioning of dryland ecosystems. / Dissertation/Thesis / Doctoral Dissertation Biology 2016

abstract: This project investigates social mobility in premodern states through a contextualized program of isotopic research at the archaeological site of Teotihuacan, Mexico. Due to the lack of a concrete methodology that can be used to recover information concerning rates of social mobility from archaeological remains, many traditional archaeological models either ignore social mobility or assume that boundaries between socioeconomic strata within archaic states were largely impermeable. In this research, I develop a new methodological approach to the identification of socially mobile individuals in the archaeological record based on changes in the diet across the lifecourse that can be detected through isotopic paleodietary indicators. Drawing upon cross-cultural research surrounding the relationship between diet and socioeconomic status and established methodologies in the biogeochemical analysis of human remains, this methodological approach provides a basis for broader comparative studies evaluating the nature of social mobility within archaic states. I then test the practical application of this methodology by applying it to a mortuary sample including individuals from distinctive socioeconomic groups from the pre-Hispanic city of Teotihuacan, Mexico. The study recovers and uses the dietary isotope ratios within bone and tooth samples from 81 individuals buried throughout the city 1) to define the dietary correlates of wealth and status at Teotihuacan and 2) to identify individuals displaying lifetime dietary changes consistent with changes in socioeconomic status. In addition to supplementing our current understanding of Teotihuacan foodways and processes of geographic migration into the city, I identify an adult male individual from the La Ventilla B apartment compound who displays dietary changes throughout his life that are consistent with downward socioeconomic mobility from a high status socioeconomic group in early adolescence to an intermediate status group later in adulthood. I conclude by identifying ways to move forward with the comparative archaeology of socioeconomic mobility in premodern contexts and highlight the applicability of archaeological information to our understanding of present-day processes of social mobility. / Dissertation/Thesis / Doctoral Dissertation Anthropology 2017