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More than 38,000 theses and dissertations produced at the University of Arizona are included in the UA Theses and Dissertations collections. These items are publically available and full-text searchable. A small percentage of items are under embargo (restricted).

We have digitized the entire backfile of master's theses and doctoral dissertations that have been submitted to the University of Arizona Libraries - since 1895!

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### Recent Submissions

• #### Amplification of Enterocytozoon hepatopenaei in Penaeus vannamei Hepatopancreas Primary Culture and Immunofluorescence Assay for Detection of Enterocytozoon hepatopenaei

Hepatopancreatic microsporidiosis (HPM) disease leads to retarded growth in shrimp resulting in a major loss for the shrimp industry worldwide. The causative agent of HPM is a microsporidian known as Enterocytozoon hepatopenaei (EHP). It is little understood how EHP infects its host and hijacks its cellular machinery to replicate more organisms. Lack of an immortal cell line is a bottleneck in studying the cellular and molecular basis of EHP infection in shrimp. For this reason, EHP cannot be propagated in in vitro culture and must be propagated in live shrimp. The use of live EHP-infected shrimp remains the only way to study EHP infectivity. It was hypothesized that supplementing EHP with fresh host cells will aid the propagation of EHP in vitro. Further research must be done but with the data collected at this point, this hypothesis is rejected. In addition to the challenges in amplifying EHP in in vitro culture, there is no antibody-based detection method for EHP. EHP infection in a shrimp is examined by Hematoxylin and Eosin (H&E) histology and real-time polymerase chain reaction based detection methods. Monoclonal antibodies that were previously characterized by Riggs and colleagues to detect Cryptosporidium parvum (C. parvum), successfully detected other parasites. Based on this, it was hypothesized that monoclonal antibodies against C. parvum may also detect EHP.
• #### Numerical Investigations of Receptivity, Stability and Transition for High-Speed Boundary Layers

Numerical tools for receptivity and stability investigations in high-speed boundary layers were developed: A local Linear Stability Theory (LST) solver applicable for axisymmetric geometries as well as linear and nonlinear disturbance flow formulation solvers suitable for complex geometries. Explicit, implicit and time-spectral time-integration schemes were considered. Although explicit methods are comparatively simpler to implement for disturbance flow formulation solvers, the allowable time-step for stability reasons can be much smaller than that required by accuracy considerations. This is especially the case for receptivity problems involving sharp nose geometries, such as cones or wedges, because the resolution requirements in the nose region can lead to severe restrictions of the time-step for explicit schemes. The new solvers were verified and validated for a variety of flow conditions, geometries, and instabilities. Three investigations are presented. First, the effects of (small) leading edge bluntness on the linear stability of flat-plate boundary layers was investigated. For the conditions investigated, it was found that very small nose radii had already a significant effect on the stability characteristics. Second, the receptivity of a Mach 10 boundary layer on a 7 degree half-angle cone to freestream acoustic disturbances was considered. A detailed analysis as well as comparisons with LST are provided. For the case considered, slow acoustic waves converted rather naturally into the unstable mode S, while fast acoustic waves followed the trend of mode F until a specific downstream location where a switch occurred. Finally, linear and nonlinear cross-flow instability computations are presented for an infinite span swept wing with biconvex airfoil at Mach 2. The stability characteristics as well as flow structures associated with the linear, secondary instability and nonlinear regimes are presented and discussed.
• #### Germination Response of Twelve Accessions of Bouteloua curtipendula (Michx.) Torr. (Poaceae) to a Simulated Winter Temperature Regime

Twelve accessions of Bouteloua curtipendula were tested in a laboratory growth chamber to examine the effect of simulated winter temperature on the germination response of the selected accessions of B. curtipendula var. curtipendula (Michx.) Torr. and B. curtipendula var. caespitosa Gould & Kapadia, two botanical varieties of disparate origin. Accessions of the variety curtipendula had significantly higher total germination percentages compared to accessions whose variety was var. caespitosa under the winter treatment. Latitude was also significant with accessions whose origin was farther north exhibiting higher relative germination percentages under the winter treatment. Mean total germination percentage was significantly higher for accessions whose grains were from NPGS seed production facilities under the winter treatment compared to the mean of accessions from wild-collected populations. Mean seed (grain) mass was highly correlated (rs = 0.774) with relative germination percentages, suggesting seed vigor may be an important explanatory factor in germination under stressful conditions.

• #### Actin Regulation of the Morphology, Dynamics, and Development of Dendritic Filopodia

Dendritic filopodia (DF) are thin, highly dynamic structures that project from neuronal dendrites. Once a DF finds and latches onto an axon from another neuron, the DF develops into the postsynaptic portion of a mature synapse. Synapses and their development from DF form the foundation of learning and memory and are implicated in many neurological diseases. The dynamics, morphology, and development of DF are heavily dependent on the actin reorganization within them. Because DF are composed of branched actin filaments, DF are distinct from conventional filopodia, which are composed of parallel, straight actin filaments. Thus, the actin regulation of DF is unique. This thesis will consider some of the proteins reported in the literature to be involved in actin regulation in DF, such as profilin, formins, the enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) homology proteins, the actin-related protein 2/3 (Arp2/3) complex, metastasis suppressor 1 (MTSS1)/missing-in-metastasis (MIM), and actin-depolymerizing factor (ADF)/cofilin, and synthesize the information to propose a comprehensive model of DF development. A deeper understanding of the regulation of DF can open the door for future research into the mechanisms of many diseases and new interventions and therapeutics for them.
• #### Subgenome Fractionation in a Homoploid and Allopolyploid Hybrid Complex

Hybridization and polyploidization are common evolutionary processes in vascular plants. Both processes contribute to the evolution of allopolyploid species, but the unique contributions of hybridization versus polyploidy to these species is not clear. This is partly due to the absence of homoploid hybrid species and allopolyploid species from the same parental diploids. Here, I use a unique species complex in Selaginella to explore the impacts of hybridization and polyploidization on genome evolution. Selaginella is one of the largest genera of lycophytes, despite having one of the smallest nuclear genomes found in vascular plants. The southwestern US and mainland Mexico are a center of functional and taxonomic diversity in Selaginella. Here, in the transition zone between the Lower Colorado River Valley and Arizona Upland subdivisions, diploid hybrids, and allopolyploids of S. arizonica ✕ S. eremophila thrive. Both hybrid taxa have distinct levels of desiccation tolerance and occupy more extreme environments than either of the parents. Using a combination of transcriptome and genome data, I assembled and annotated five reference Selaginella genomes, including the two homoploid and allopolyploid taxa. I investigate the relative contributions of each parent to the genomes of the hybrids and compare the impact of hybridization and polyploidy on genome evolution. A genome content analysis using reciprocal best blast hits (RBH) found strong patterns of biased fractionation in the hybrid complex, each biasing between 12-16% towards one parent. Interestingly, this was a reciprocal pattern, the homoploid and allotetraploid each retained more genomic content from the opposite parent. We determined the maternal origin of the plastid organelles through de novo chloroplast genome assembly, alignment, and phylogenetic inference, which further revealed that more genomic content was retained from the maternal parent. In summary, we believe this is one of the only cases of reciprocal biased fractionation in a hybrid complex.
• #### Head and Neck Dynamics: Prediction of Sports Related Head Impact Characteristics

Brain injuries sustained during an impact to the head during sport and recreation related activities are a common occurrence. They can cause adverse effects in injured participants, some of which are identifiable immediately following contact, while others may not manifest for years. The study of concussive and sub-concussive impacts of sport and recreation activities is important in understanding the mechanism of impact, resultant brain response, and how injury manifests to improve risk of injury assessments, game-play decisions, and protective equipment. This study aims to relate the kinematic motion experienced by the head during impact, to the characteristics, magnitude, direction, and location, of the force applied to the head during contact. To investigate this relationship, a pendulum impact device was designed to replicate on-field impacts of contact sports, kinematic data was collected from an anthropomorphic test device during an applied impact, and the resultant kinematics were related to applied generalized force through Euler-Lagrange dynamics of a simplified rigid link model. Through this system of dynamic equations, the characteristics of applied force were predicted within reasonable bounds; the results of this study could lead to better on-field injury assessments and improved protective equipment.