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  • The atmospheric boundary layer (ABL) has been widely investigated due to the complexity of its physical processes and its impact on human life. One of the most challenging yet critical topics in this layer is scalar transport. Many efforts have been dedicated to investigating heat and moisture transport in the ABL using experimental and numerical approaches over the last several decades. However, there are still many knowledge gaps that limit the performance of numerical weather prediction models, in particular over complex terrain. For example, insufficient understanding of near-surface processes has resulted difficulties in parameterizing meteorological variables in numerical models. Hence, the main objective of this work is to gain a better fundamental understanding of flow processes and scalar transport in the surface boundary layer over different types of terrain with the ultimate goal of improving numerical weather forecasting models by developing more accurate surface parameterizations. Three different topics are discussed in this dissertation. The first topic is a study of land-atmosphere interactions over a desert playa to better understand the impacts of spatial and temporal heterogeneity in water availability as part of the short-term hydrologic cycle. High evaporation rates and the exponential decay of these rates are observed following occasional rainfall events. Three main factors explained the fast evaporation observed following rain- fall. The first factor is the existence of a powerful positive feedback mechanisms initialized by rainfall events that leads to increasing volumetric water content, decreasing surface albedo and Bowen ratio, followed by increases in net radiation, and eventually the enhancement of evaporation rates. The second factor is the clay soil texture, which has low permeability and high capacity. The soil property makes more water available near the surface for evaporation. The third factor is the non-negligible nocturnal evaporation rates that are correlated with increasing soil moisture content. Moreover, a higher spatial variability of surface soil moisture and evaporation is observed when the surface is dry. The second topic is articulated around a case study of the mechanisms that modulates the evolution of valley fog. A typical shallow, early-morning, short- lived valley fog is observed in a sheltered alpine valley. This work shows that mountain circulations play a critical role in the formation and development of shallow valley fog by modulating temperature and moisture fields through katabatic flow interactions and gravity waves. In particular, internal gravity waves are shown to modulate fog processes by varying the near-surface temperature within a time period of ≈ 20 min. The purpose of the last topic is to better understand the potential temperature variance budget over three different surfaces, a desert playa (dry lakebed), characterized by a flat surface devoid of vegetation; a vegetated site, characterized by a flat valley floor covered with greasewood vegetation, and a mountain terrain site with a slope angle of 2 -4° and covered by high-elevation vegetation. The analysis reveals the presence of a 5-m layer where the production and dissipation terms of potential temperature variance drop rapidly below this level. Within the 5-m layer, turbulent transport of potential temperature variance acts as a sink term at all sites of interest. The ratio of turbulent transport to production of potential temperature variance remains constant as stability decreases. The imbalance ratio between production and dissipation shows no correlation with the stability conditions.
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  • Production of a functional protein requires coordination and regulation of many factors that control different cellular processes. One of these factors, Spt6, is a highly conserved nuclear protein that has roles in several facets of gene expression. Spt6 is best known for its ability to chaperone histones and modulate chromatin structure, but it also functions as a transcription elongation factor and in mRNA processing and export. Spt6 co-localizes with elongating RNA polymerase II (RNAPII) where it reassembles nucleosomes following RNAPII passage in order to repress aberrant transcription initiation. Furthermore, Spt6 directly stimulates RNAPII elongation rates and coordinates co-transcriptional mRNA processing. Despite the wealth of functional data that implicate Spt6 in these processes, little is known about the mechanistic basis for these activities. In order to gain mechanistic understanding of Spt6 activities, the work presented in this thesis focused on biochemical, structural, and functional characterization of Spt6 interactions with other proteins. These studies reveal the true Spt6 binding site on RNAPII, identify Tom1 as a novel Spt6 binding partner, and demonstrate a specific interaction between Spt6 and histones H3-H4 that is competitive with DNA. The elucidation of the authentic Spt6 binding site on RNAPII has allowed us to develop tools to probe the mechanism of Spt6 recruitment to transcribed regions. Identification of Tom1 iv as a phosphorylated Spt6 binding partner provides a physical link to potential Spt6 functions such as mRNA export, cell cycle regulation, and regulation of histone levels. Characterization of the interaction with H3-H4 brings us closer to a mechanistic understanding of the histone chaperone activity of Spt6. Overall, the data presented in this work advance our knowledge of the interactions that regulate Spt6 function and will aid future studies to further dissect the mechanistic basis for Spt6 roles in gene expression.
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  • The nonsense-mediated mRNA decay (NMD) pathway functions as a quality control mechanism and a feature of post-transcriptional gene regulation. NMD degrades mRNAs containing premature termination codons (PTCs) to prevent the production of potentially harmful truncated proteins, and it also destroys many error-free endogenous mRNAs to limit the expression of these genes. NMD is critical for viability in most complex organisms, highlighting the importance of this pathway; however, it is unknown which of the two NMD functions is the feature essential for viability. Understanding how NMD recognizes and degrades targets may provide insight to uncover the requirement of this pathway for viability, but the molecular mechanisms of NMD target recognition and destruction also remain unclear. Work presented in this dissertation describes genetic analysis in Drosophila to reveal the feature of the NMD pathway that is critical for viability, and refines the model describing the mechanism of NMD target degradation. We screened a collection of heterozygous deficiencies for suppression of the incomplete lethality of a hypomorphic allele of the core NMD factor Upf2. This screen identified three autosomal regions that partially suppress Upf2 mutant lethality when deleted. The endogenous NMD target Gadd45 is located within one suppressing region, and we found that elimination of Gadd45 restores viability to multiple null NMD mutants. Mekk1, a factor that acts downstream of Gadd45, resides in another suppressing region, and loss of Mekk1 also restores viability to NMD mutants. The third suppressing region contains ! ! iv! Arc2, and we found that Arc2 and the closely related Arc1 may also contribute to the lethality of Drosophila lacking NMD activity. In addition, this dissertation describes the first genetic analysis of Drosophila Smg5 mutants, and determines that Smg5 is a critical NMD factor required for viability and all NMD function. Further analysis of the first characterization of double mutants for multiple NMD factors reveals there are multiple mechanisms for NMD target degradation. These findings provide a new foundation for understanding the crucial NMD gene regulatory function and reshape the model of the NMD pathway.
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  • Snow and ice cover exhibits a high degree of spatial and temporal variability. Data from multispectral optical remote sensing instruments such as Landsat are an underutilized resource that can extend our ability for mapping these phenomena. High resolution imagery is used to demonstrate that even at finer spatial resolutions (below 100 m), pixels with partial snow cover are common throughout the year and nearly ubiquitous during the meltout period. This underscores the importance of higher spatial resolution datasets for snow cover monitoring as well as the utility of fractional snow covered area (fSCA) monitoring approaches. Landsat data are used to develop a fully automated approach for mapping persistent ice and snow cover (PISC). This approach relies on the availability of numerous Landsat scenes, an improved technique for automated cloud cover mapping, and a series of automated postprocessing routines. Validation at 12 test sites suggest that the automated PISC mapping approach provides a good approximation of debris-free glacier extent across the Arctic. The PISC mapping approach is then used to produce the first single-source, temporally well-constrained (2010-2014) map of PISC across the conterminous western U.S. The Landsat-derived PISC map is more accurate than both a previously published dataset based on aerial photography acquired during the 1960s, 1970s and 1980s and the National Land Cover Database (NLCD) 2011 extent of perennial snow and ice cover. Further analysis indicates differences between the newly developed Landsat-derived PISC dataset and the previously published glacier dataset can likely be attributed to changes in the extent of PISC over time. Finally, in order to map mean annual snow cover persistence across the entire landscape, we implement a novel canopy adjustment approach designed to improve the accuracy of Landsat-derived fSCA in forested areas. In situ observations indicate canopy-adjusted snow covered area calculated from all available Landsat scenes can provide an accurate estimate of mean annual snow cover duration. The work presented here lays the groundwork for addressing scientific questions regarding the spatial and temporal variability of snow cover, snow accumulation and ablation processes, and the impact of changes in snow cover on physical and ecological systems.
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  • Twenty coprolites recovered from the excavation of Clyde's Cavern, Utah, were examined for dietary components, dietary change through time, and evidence of parasites. The samples are representative of possibly three prehistoric cultures of Utah; Late Archaic (ca. 1120 B.C.-ca. A.D. 1, Levels 1 and 2), possibly Basket-maker Anasazi (BM II ? ca. A.D. 1 - ca. A.D. 475, Level 3), and Fremont (ca. A.D. 400-A.D. 1200, Levels 4 through 8). The small sample size from the earliest occupation levels (Levels 2 and 3) does not permit a generalization about the diet of this period. However, during Fremont occupation the only change in diet is the addition of corn and Indian rice grass. Corn, until Level 8, appears not as a staple but as a component of a composite diet of various seed types and non-seed plant material. Thus, the concept that the Fremont is but a horticultural accretion to Desert Archaic roots is not refuted (see Marwitt 1971). Throughout the human occupation of the cave the diet appears to reflect a pattern characteristic of the Desert Archaic lifeway. At least nine varieties of seeds were utilized together with non-seed plant material and small amounts of animal protein. The evidence of grit in all coprolites, and charcoal in most, suggests that some foods were roasted and milled before being ingested. Prehistoric man at Clyde's Cavern was heavily parasitized by the human pinworm. He may also have been parasitized by species of Strongyloides, and Acanthocephala. The methods of analysis were essentially those utilized by Fry (1970), however, certain modifications were made which added rigor and efficiency to the analysis.
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  • Dr. George Thomas had a long career as an educator in Utah. During his life he occupied several very important educational positions. His most important position, which he held for twenty years, was that of president of the University of Utah. The importance of this position was brought out very well in a tribute to him that appeared in the 1935 issue of the Utonian, the University of Utah annual.
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  • The following writing is a collection of thoughts and explanations of my choreographic thesis project, which was a practice in combining two unique art forms: Drag and modern dance. In this process, I was asked, "Do you have a point of view beyond ‘Drag is good?'" My ideas revolving around my project have shapeshifted and upon reflection of my process and the resulting performance, I have found that in addition to being "good," Drag can be a powerful tool to examine our daily performances of gender. This thesis describes my creative process in combining Drag and modern dance elements, culminating in the performance of my evening-length work "We Gender: And So Can You!" I approached the art forms through the lens of an ex-Mormon invested in queer and feminist theories. I wanted to explore modern dance and Drag because I find the two art forms as transcendent and liberating of the restrictive discourse in which I was raised. Here I illustrate my identity as a repressed homosexual before I discovered both modern dance and Drag. I also investigate self-expression through modern dance. Following my discussion on modern dance, I lay out my creative process of nine performance pieces and discuss the performance at Metro Music Hall in Salt Lake City on March 24, 2017.
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  • The primary objective of this thesis is the cartographic representation of the dominant plant cover types, and a spatial interpretation of the zonal community types , within the upper Bear River drainage. The upper Bear River drainage is located within the western section of the Uinta Mountains, Utah. Two maps, titled "Plant Cover Types, Hayden Fork," and "Plant Cover Types, upper Bear River." were compiled. The two maps were prepared from data derived from field work, aerial photographs at a nominal scale of 1:15,840, and a photo-mosaic. Four broad steps were carried out in the preparation of the maps: (1) reconnaissance of the vegetation units to be mapped; (2) analysis and interpretation of the plant types from aerial photographs; (3) ground checking, which consisted of using transects and quadrants in determining plant cover frequency, transition belts, and boundaries; and (4) construction of the maps through the process of expansion and reduction by proportional squares. Six zonal community types were recognized in the upper Bear River drainage; krummholz, one of the cover types included, is a physiognomic type. Altitudinal distribution of the six zonal cover types are: (1) sagebrush from the Wyoming Basin to 9,800 feet, (2) quaking aspen to an upper altitudinal limit of 9,200 feet, (3) lodge-pole pine from 8,000 to 9,600 feet, (4) spruce-fir from 9,600 to 11,000 feet, (5) krummholz from 10,400 to 11,600 feet, and (6) alpine tunlra from 10,600 feet upward. Under optimum conditions timberline was found to be 11,000 feet and mean timberline in the study area was determined to be 10,500 feet. The upper lints of krummholz was observed at 11,600 feet. Lodge-pole pine was not found to be a component of krummholz, nor were cones found on any of the krummholz stands.
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  • To understand the process of speciation, evolutionary biologists have traditionally researched extant groups of organisms that have undergone adaptive radiation. Studying speciation in this way relies on inferences about past selective events that have shaped contemporary patterns of diversification. A complimentary approach to studying speciation is to experimentally evolve an adaptive radiation from a single population to examine the initial processes driving adaptive divergence. In my dissertation, I used feather lice ( Columbicola columbae) and their avian hosts (Columba livia ) to examine the earliest stages of adaptive radiation. I used domesticated pigeon breeds that vary in size and color as divergent habitats in which to experimentally evolve a single species of feather louse. The first part of my dissertation explored two aspects of host behavior that may be important defenses against lice. First, I tested if the effectiveness of preening improves with experience. I found that pigeons removed about the same number of lice regardless of prior experience. I then tested for an ectoparasite control function of allopreening. My data suggest that allopreening is, indeed, important for ectoparasite control. The remainder of my dissertation focuses on adaptation by lice to new hosts. Specifically, I examined changes in three phenotypic traits of feather lice: louse color, louse size, and louse behavior. First, I explored the evolution of cryptic coloration in lice. I showed that lice transferred to white pigeons evolved significantly lighter coloration than those on darker pigeons. Second, I tested whether louse size is also an adaptation for avoiding host defense. I found that when lice were transferred to larger pigeons they evolved larger size. However, lice transferred to smaller pigeons did not get smaller; instead, these lice altered their behavior to escape preening. I then further explored these changes in louse behavior and found that lice shifted microhabitat when transferred to smaller hosts. However, the direction and magnitude of this shift depended on the preening ecology of their host. Finally, I showed that increases in louse body size on larger hosts directly affects louse mating success. My work demonstrates how local adaptation can drive diversification among host-specific parasites.
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  • JP-10 is a synthetic fuel with high volumetric energy content. One problem with JP-10, is that its combustion kinetics can be too slow for efficient combustion in hypersonic flight applications. Chapter 2 presents a study on the thermal breakdown and catalytic combustion of JP-10 fuel using CeO 2 (ceria) nanoparticles, in a flow tube reactor. In-situ mass spectrometry was used to analyze decomposition products. In the absence of O2, CeO2 efficiently oxidizes JP-10, reducing decomposition onset temperatures by 300 K over that in a clean flow tube. Under conditions with O2 and CeO2 present, oxidation of JP-10 was found to be catalytic; i.e., oxidation is initiated by reaction of JP-10 with CeO2, which is then reoxidized by O2. Boron is of interest as a high energy density fuel as it has one of the highest volumetric heats of combustion known. A major difficulty in getting boron to burn efficiently is that boron surfaces are protected by a native oxide layer. Chapter 3 presents a simple, scalable, one-step, one-pot synthesis method for producing ∼50 nm boron nanoparticles that are largely unoxidized, made soluble in hydrocarbons through oleic acid functionalization, and optionally coated with ceria. Scanning electron microscopy (SEM) and dynamic light scattering (DLS) were used to investigate size distributions, with X-ray photoelectron spectroscopy (XPS) to probe the surface chemistry. Cryogenic methane has been proposed as a fuel for use in hypersonic engines, due to its relatively high energy content; however its poor ignition performance needs to be addressed through use of catalysts. Chapters 4 and 5 investigate the composition, structure, and surface chemistry of several types of Pd/PdO based nano-catalysts designed to be fuel soluble. A combination of high resolution transmission electron microscopy (HRTEM), electron diffraction, scanning transmission electron microscopy/energy dispersive x-ray spectroscopy (STEM/EDX), and XPS were used. In-situ generated particles were found to be primarily crystalline, metallic Pd, in a narrow size distribution around 8 nm. The ignition temperature was lowered ∼150 K by the catalyst, and evidence is presented showing that ignition is correlated with formation of a subnanometer oxidized Pd surface layer at higher temperatures.
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