Matching Items (40)

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Quantifying Whole-Reach Denitrification in Arizona Streams

Description

Elevated nitrate (NO3-) concentration in streams and rivers has contributed to environmental problems such as downstream eutrophication and loss of biodiversity. Sycamore Creek in Arizona is nitrogen limited, but previous

Elevated nitrate (NO3-) concentration in streams and rivers has contributed to environmental problems such as downstream eutrophication and loss of biodiversity. Sycamore Creek in Arizona is nitrogen limited, but previous studies have demonstrated high potential for denitrification, a microbial process in which biologically active NO3- is reduced to relatively inert dinitrogen (N2) gas. Oak Creek is similarly nitrogen limited, but NO3- concentration in reaches surrounded by agriculture can be double that of other reaches. We employed a denitrification enzyme assay (DEA) to compare potential denitrification rate between differing land uses in Oak Creek and measured whole system N2 flux using a membrane inlet mass spectrometer to compare differences in actual denitrification rates at Sycamore and Oak Creek. We anticipated that NO3- would be an important limiting factor for denitrifiers; consequentially, agricultural land use reaches within Oak Creek would have the highest potential denitrification rate. We expected in situ denitrification rate to be higher in Oak Creek than Sycamore Creek due to elevated NO3- concentration, higher discharge, and larger streambed surface area. DEA results are forthcoming, but analysis of potassium chloride (KCl) extraction data showed that there were no significant differences between sites in sediment extractable NO3- on either a dry mass or organic mass basis. Whole-reach denitrification rate was inconclusive in Oak Creek, and though a significant positive flux in N2 from upstream to downstream was measured in Sycamore Creek, the denitrification rate was not significantly different from 0 after accounting for reaeration, suggesting that denitrification does not account for a significant portion of the NO3- uptake in Sycamore Creek. Future work is needed to address the specific factors limiting denitrification in this system.

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Date Created
  • 2018-05

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Coupled Abiotic and Biotic Cycling of Nitrous Oxide

Description

Nitrous oxide (N2O) is an important greenhouse gas and an oxidant respired by a

diverse range of anaerobic microbes, but its sources and sinks are poorly understood. The overarching goal of

Nitrous oxide (N2O) is an important greenhouse gas and an oxidant respired by a

diverse range of anaerobic microbes, but its sources and sinks are poorly understood. The overarching goal of my dissertation is to explore abiotic N2O formation and microbial N2O consumption across reducing environments of the early and modern Earth. By combining experiments as well as diffusion and atmospheric modeling, I present evidence that N2O production can be catalyzed on iron mineral surfaces that may have been present in shallow waters of the Archean ocean. Using photochemical models, I showed that tropospheric N2O concentrations close to modern ones (ppb range) were possible before O2 accumulated. In peatlands of the Amazon basin (modern Earth), unexpected abiotic activity became apparent under anoxic conditions. However, care has to be taken to adequately disentangle abiotic from biotic reactions. I identified significant sterilant-induced changes in Fe2+ and dissolved organic matter pools (determined by fluorescence spectroscopy). Among all chemical and physical sterilants tested, γ - irradiation showed the least effect on reactant pools. Targeting geochemically diverse peatlands across Central and South America, I present evidence that coupled abiotic and biotic cycling of N2O could be a widespread phenomenon. Using isotopic tracers in the field, I showed that abiotic N2O fluxes rival biotic ones under in-situ conditions. Moreover, once N2O is produced, it is rapidly consumed by N2O-reducing microbes. Using amplicon sequencing and metagenomics, I demonstrated that this surprising N2O sink potential is associated with diverse bacteria, including the recently discovered clade II that is present in high proportions at Amazonian sites based on nosZ quantities. Finally, to evaluate the impact of nitrogen oxides on methane production in peatlands, I characterized soil nitrite (NO2–) and N2O abundances along soil profiles. I complemented field analyses with molecular work by deploying amplicon-based 16S rRNA and mcrA sequencing. The diversity and activity of soil methanogens was affected by the presence of NO2– and N2O, suggesting that methane emissions could be influenced by N2O cycling dynamics. Overall, my work proposes a key role for N2O in Earth systems across time and a central position in tropical microbial ecosystems.

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Date Created
  • 2020

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Kinetics, thermodynamics, and habitability of microbial iron redox cycling

Description

Many acidic hot springs in Yellowstone National Park support microbial iron oxidation, reduction, or microbial iron redox cycling (MIRC), as determined by microcosm rate experiments. Microbial dissimilatory iron reduction (DIR)

Many acidic hot springs in Yellowstone National Park support microbial iron oxidation, reduction, or microbial iron redox cycling (MIRC), as determined by microcosm rate experiments. Microbial dissimilatory iron reduction (DIR) was detected in numerous systems with a pH < 4. Rates of DIR are influenced by the availability of ferric minerals and organic carbon. Microbial iron oxidation (MIO) was detected from pH 2 – 5.5. In systems with abundant Fe (II), dissolved oxygen controls the presence of MIO. Rates generally increase with increased Fe(II) concentrations, but rate constants are not significantly altered by additions of Fe(II). MIRC was detected in systems with abundant ferric mineral deposition.

The rates of microbial and abiological iron oxidation were determined in a variety of cold (T= 9-12°C), circumneutral (pH = 5.5-9) environments in the Swiss Alps. Rates of MIO were measured in systems up to a pH of 7.4; only abiotic processes were detected at higher pH values. Iron oxidizing bacteria (FeOB) were responsible for 39-89% of the net oxidation rate at locations where biological iron oxidation was detected. Members of putative iron oxidizing genera, especially Gallionella, are abundant in systems where MIO was measured. Speciation calculations reveal that ferrous iron typically exists as FeCO30, FeHCO3+, FeSO40 or Fe2+ in these systems. The presence of ferrous (bi)carbonate species appear to increase abiotic iron oxidation rates relative to locations without significant concentrations. This approach, integrating geochemistry, rates, and community composition, reveals biogeochemical conditions that permit MIO, and locations where the abiotic rate is too fast for the biotic process to compete.

For a reaction to provide habitability for microbes in a given environment, it must energy yield and this energy must dissipate slowly enough to remain bioavailable. Thermodynamic boundaries exist at conditions where reactions do not yield energy, and can be quantified by calculations of chemical energy. Likewise, kinetic boundaries exist at conditions where the abiotic reaction rate is so fast that reactants are not bioavailable; this boundary can be quantified by measurements biological and abiological rates. The first habitability maps were drawn, using iron oxidation as an example, by quantifying these boundaries in geochemical space.

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Agent

Created

Date Created
  • 2017

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Effects of Grazing Management on Carbon Stocks in an Arid Rangeland

Description

Rangelands are an extensive land cover type that cover about 40% of earth’s ice-free surface, expanding into many biomes. Moreover, managing rangelands is crucial for long-term sustainability of the vital

Rangelands are an extensive land cover type that cover about 40% of earth’s ice-free surface, expanding into many biomes. Moreover, managing rangelands is crucial for long-term sustainability of the vital ecosystem services they provide including carbon (C) storage via soil organic carbon (SOC) and animal agriculture. Arid rangelands are particularly susceptible to dramatic shifts in vegetation cover, physical and chemical soil properties, and erosion due to grazing pressure. Many studies have documented these effects, but studies focusing on grazing impacts on soil properties, namely SOC, are less common. Furthermore, studies testing effects of different levels of grazing intensities on SOC pools and distribution yield mixed results with little alignment. The primary objective of this thesis was to have a better understanding of the role of grazing intensity on arid rangeland soil C storage. I conducted research in long established pastures in Jornada Experimental Range (JER). I established a 1500m transect in three pastures originating at water points and analyzed vegetation cover and SOC on points along these transects to see the effect of grazing on C storage on a grazing gradient. I used the line-point intercept method to measure and categorize vegetation into grass, bare, and shrub. Since soil adjacent to each of these three cover types will likely contain differing SOC content, I then used this vegetation cover data to calculate the contribution of each cover type to SOC. I found shrub cover and total vegetation cover to decrease, while grass and bare cover increased with decreasing proximity to the water source. I found areal (g/m2) and percent (go SOC to be highest in the first 200m of the transects when accounting for the contribution of the three vegetation cover types. I concluded that SOC is being redistributed toward the water source via foraging and defecation and foraging, due to a negative trend of both total vegetation cover and percent SOC (g/g). With the decreasing trends of vegetation cover and SOC further from pasture water sources, my thesis research contributes to the understanding of storage and distribution of SOC stocks in arid rangelands.

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Created

Date Created
  • 2018

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Ritual Violence and the Perception of Social Difference: Migration and Human Sacrifice in the Epiclassic Basin of Mexico

Description

Archaeologists have long contended that large-scale human migrations played an essential role in the cultural development of pre-Hispanic central Mexico. During the Epiclassic period (600-900 CE), migration is implicated in

Archaeologists have long contended that large-scale human migrations played an essential role in the cultural development of pre-Hispanic central Mexico. During the Epiclassic period (600-900 CE), migration is implicated in the appearance of new forms of material culture, sociopolitical disruptions, and the emergence of new regional polities. Sweeping social changes accompanied these developments, including demographic reorganization and increased levels of violence. Research across the social sciences finds that violence directed at individuals perceived as categorically distinct also typically increases during such periods of socio-political upheaval. This dissertation investigates identity-based violence in the Epiclassic Basin of Mexico to consider how diverse social identities contributed to the selection of victims of ritual violence.

This research examines the skeletal remains from a sacrificial deposit at the Epiclassic shrine site of Non-Grid 4 in the Basin of Mexico, where a minimum of 180 human crania were interred as ritual offerings. The project reconstructs patterns of paleomobility and biological relatedness to determine whether individuals with distinct categorical social identities were more likely to become victims of human sacrifice. It answers the questions: (1) Were the sacrificed individuals predominantly locals who lived in the Basin of Mexico throughout their lives?; (2) Were the sacrificed individuals comprised of a single kin-group biologically continuous with pre-extant populations in the Basin of Mexico?; and (3) If victims were migrants biologically discontinuous with antecedent populations, from where in ancient Mesoamerica did they originate?

Results indicate that a majority of sacrificial victims were immigrants originating north and south of the Basin of Mexico. Biogeochemical analyses of sacrificed individuals find that 80% are non-local migrants into the Basin, suggesting that they were likely targeted for violence based on their divergent residential histories. Multi-scalar biodistance analyses of Non-Grid 4 sacrificial victims demonstrate that they represent two biologically distinct groups. There was evidence, however, for both biological continuity among victims and pre-extant central Mexican populations, as well as for migration from northern and southern Mexico. This project therefore not only improves knowledge of migration during the central Mexican Epiclassic, but also contributes to broader anthropological understandings of the social context of violence.

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Created

Date Created
  • 2020

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Traveling monastic paths : mobility and religion in medieval Ireland at five early and late medieval Irish monasteries

Description

Mobility is an important aspect of the lives of religious individuals described by medieval texts in early and late medieval Ireland, and biogeochemical methods can be used to detect mobility

Mobility is an important aspect of the lives of religious individuals described by medieval texts in early and late medieval Ireland, and biogeochemical methods can be used to detect mobility in archaeological populations. Stories are recorded of monks and nuns traveling and founding monasteries across Ireland, Scotland, England, Wales, and other areas of Europe. However, these texts rarely address the quotidian lives of average monks and nuns who lived in monastic communities. This dissertation seeks to understand if travel was a typical part of the experiences of religious and lay people in early and late medieval Ireland. It also aims to increase understanding of how monastic communities related to the local lay communities, including addressing if the monastery was populated by those who grew up in the local area. Another methodological aim of this dissertation is to advance the field of archaeological biogeochemistry by (1) adding to the bioavailable strontium baseline in Ireland and (2) quantifying the contribution of ocean-derived strontium to coastal environments. These topics are explored through the biogeochemical analysis of 88 individuals buried at 5 early and late medieval monasteries in Ireland and the analysis of a total of 85 plant samples from four counties in Ireland. The three papers in this dissertation present: (1) a summary of the mobility of religious and lay people buried at the monasteries (Chapter 2), (2) a case study presenting evidence for fosterage of a local child at the early medieval monastery of Illaunloughan, Co. Kerry (Chapter 3), and (3) a study designed to quantify the impact of sea spray on bioavailable strontium in coastal environments (Chapter 4). The majority of lay and religious individuals studied were estimated to be local, indicating that medieval Irish Christianity was strongly rooted in the local community. The study of ocean-derived strontium in a coastal environment indicates that sea spray has a non-uniform impact on bioavailable strontium in coastal regions. These findings shed new light on medieval monastic and lay life in Ireland through the application of biogeochemical methods, contributing to the growth of the field of archaeological chemistry in Ireland.

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Created

Date Created
  • 2018

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Sources and Decomposition of Dissolved Organic Matter in Desert Streams

Description

Dissolved organic matter (DOM) is an important part of aquatic foodwebs because it contains carbon, nitrogen, and other elements required by heterotrophic organisms. It has many sources that determine its

Dissolved organic matter (DOM) is an important part of aquatic foodwebs because it contains carbon, nitrogen, and other elements required by heterotrophic organisms. It has many sources that determine its molecular composition, nutrient content, and biological lability and in turn, influence whether it is retained and processed in the stream reach or exported downstream. I examined the composition of DOM from vascular wetland plants, filamentous algae, and riparian tree leaf litter in Sonoran Desert streams and its decomposition by stream microbes. I used a combination of field observations, in-situ experiments, and a manipulative laboratory incubation to test (1) how dominant primary producers influence DOM chemical composition and ecosystem metabolism at the reach scale and (2) how DOM composition and nitrogen (N) content control microbial decomposition and stream uptake of DOM. I found that differences in streamwater DOM composition between two distinct reaches of Sycamore Creek did not affect in-situ stream respiration and gross primary production rates. Stream sediment microbial respiration rates did not differ significantly when incubated in the laboratory with DOM from wetland plants, algae, and leaf litter, thus all sources were similarly labile. However, whole-stream uptake of DOM increased from leaf to algal to wetland plant leachate. Desert streams have the potential to process DOM from leaf, wetland, and algal sources, though algal and wetland DOM, due to their more labile composition, can be more readily retained and mineralized.

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Agent

Created

Date Created
  • 2018

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Engineering Open Chromatin with Synthetic Pioneer Factors:: Enhancing Mammalian Transgene Expression and Improving Cas9-Mediated Genome Editing in Closed Chromatin

Description

Chromatin is the dynamic structure of proteins and nucleic acids into which eukaryotic genomes are organized. For those looking to engineer mammalian genomes, chromatin is both an opportunity and an

Chromatin is the dynamic structure of proteins and nucleic acids into which eukaryotic genomes are organized. For those looking to engineer mammalian genomes, chromatin is both an opportunity and an obstacle. While chromatin provides another tool with which to control gene expression, regional density can lead to variability in genome editing efficiency by CRISPR/Cas9 systems. Many groups have attempted to de-silence chromatin to regulate genes and enhance DNA's accessibility to nucleases, but inconsistent results leave outstanding questions. Here, I test different types of activators, to analyze changes in chromatin features that result for chromatin opening, and to identify the critical biochemical features that support artificially generated open, transcriptionally active chromatin.

I designed, built, and tested a panel of synthetic pioneer factors (SPiFs) to open condensed, repressive chromatin with the aims of 1) activating repressed transgenes in mammalian cells and 2) reversing the inhibitory effects of closed chromatin on Cas9-endonuclease activity. Pioneer factors are unique in their ability to bind DNA in closed chromatin. In order to repurpose this natural function, I designed SPiFs from a Gal4 DNA binding domain, which has inherent pioneer functionality, fused with chromatin-modifying peptides with distinct functions.

SPiFs with transcriptional activation as their primary mechanism were able to reverse this repression and induced a stably active state. My work also revealed the active site from proto-oncogene MYB as a novel transgene activator. To determine if MYB could be used generally to restore transgene expression, I fused it to a deactivated Cas9 and targeted a silenced transgene in native heterochromatin. The resulting activator was able to reverse silencing and can be chemically controlled with a small molecule drug.

Other SPiFs in my panel did not increase gene expression. However, pretreatment with several of these expression-neutral SPiFs increased Cas9-mediated editing in closed chromatin, suggesting a crucial difference between chromatin that is accessible and that which contains genes being actively transcribed. Understanding this distinction will be vital to the engineering of stable transgenic cell lines for product production and disease modeling, as well as therapeutic applications such as restoring epigenetic order to misregulated disease cells.

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Agent

Created

Date Created
  • 2019

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Scarlet Macaws, Long-Distance Exchange, and Placemaking in the U.S. Southwest and Mexican Northwest, ca 900-1450 CE

Description

Exchange is fundamental to the establishment and maintenance of social institutions and political economies in all scales of societies. While today people rapidly exchange goods and information over great distances,

Exchange is fundamental to the establishment and maintenance of social institutions and political economies in all scales of societies. While today people rapidly exchange goods and information over great distances, in the past, long-distance exchange necessitated the mobilization of vast networks of interaction with substantial transport costs. Objects traded over long distances were often valuable and challenging to obtain, granting them multifaceted significance that is difficult to understand using traditional archaeological approaches.

This research examines human interactions with scarlet macaws (Ara macao) in the United States (U.S.) Southwest and Mexican Northwest (SW/NW) between 900 and 1450 CE. This period saw large-scale cultural change in the form of migrations, rapid population aggregation, and an expansion of long-distance exchange relations in regional centers at Pueblo Bonito (900-1150 CE) in northwestern New Mexico, Wupatki (1085-1220 CE) in north-central Arizona, and Paquimé (1200-1450 CE) in northern Chihuahua. Despite the distant natural habitat of scarlet macaws, their importation, exchange, and sacrifice appear to have played integral roles in the process of placemaking at these three regional centers. Here, I use an Archaeology of the Human Experience approach and combine radiogenic strontium isotope analysis with detailed contextual analyses using a Material Histories theoretical framework to (1) discern whether macaws discovered in the SW/NW were imported or raised locally, (2) characterize the acquisition, treatment and deposition of macaws at Pueblo Bonito, Wupatki, and Paquimé, and (3) identify patterns of continuity or change in acquisition and deposition of macaws over time and across space in the SW/NW.

Findings from radiogenic strontium isotope analysis indicate that scarlet macaws from all case studies were primarily raised locally in the SW/NW, though at Paquimé, macaws were procured from sites in the Casas Grandes region and extra-regionally. Variation in the treatment and deposition of scarlet macaws suggests that despite their prevalence, macaws were interpreted and interacted with in distinctly local ways. Examination of the human experience of transporting and raising macaws reveals previously unconsidered challenges for keeping macaws. Overall, variation in the acquisition and deposition of scarlet macaws indicates changing strategies for placemaking in the SW/NW between 900 and 1450 CE.

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Date Created
  • 2020

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Thermodynamic Cartography in Basalt-Hosted Hydrothermal Systems

Description

Mantle derived basalts along the entirety of the Earth’s Mid-Ocean Ridge (MOR) spreading centers are continuously altered by seawater, allowing the hydrosphere to subsume energy and exchange mass with the

Mantle derived basalts along the entirety of the Earth’s Mid-Ocean Ridge (MOR) spreading centers are continuously altered by seawater, allowing the hydrosphere to subsume energy and exchange mass with the deep, slowly cooling Earth. Compositional heterogeneities inherent to these basalts—the result of innumerable geophysical and geochemical processes in the mantel and crust—generate spatial variation in the equilibrium states toward which these water-rock environments cascade. This alteration results in a unique distribution of precipitate assemblages, hydrothermal fluid chemistries, and energetic landscapes among ecosystems rooted within and above the seafloor. The equilibrium states for the full range of basalt compositional heterogeneity present today are calculated over all appropriate temperatures and extents of reaction with seawater, along with the non-equilibrium mixtures generated when hydrothermal fluids mix back into seawater. These mixes support ancient and diverse ecosystems fed not by the energy of the sun, but by the geochemical energy of the Earth. Facilitated by novel, high throughout code, this effort has yielded a high-resolution compositional database that is mapped back onto all ridge systems. By resolving the chemical and energetic consequences of basalt-seawater interaction to sub-ridge scales, alteration features that are globally homogeneous can be distinguished from those that are locally unique, guiding future field observations with testable geochemical and biochemical predictions.

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Agent

Created

Date Created
  • 2020