Now showing items 8026-8045 of 20330

    • Fundamental studies in the solid-phase extraction of organic cations and neutral compounds: The role of hydrophobic and ionic interactions

      Burke, Michael F.; Gonzalez, Ricardo Rene (The University of Arizona., 2001)
      The work presented is a systematic investigation of silica-based sorbents using solid-phase extraction (SPE). Properties of various cation exchangers and mixed beds comprised of strong cation exchange particles and alkyl-modified silica particles were explored. The role of ionic and nonpolar interactions was examined in terms of retention and elution of analytes. A series of displacement experiments was used to characterize the interactions and energy-minimized, three-dimensional models were used to illustrate these interactions. Selectivity of cation exchangers was probed by introducing cations differing in size, hydrophobic nature and charge before and after introduction of the analytes. The ionic strength, the solvent composition and the pH of the liquid phase were parameters that were varied in order to define the type of interaction that was responsible for retention, lack of retention, or elution during the SPE procedure. Application of mixed sorbents toward the extraction of basic drugs of abuse, as well as the use of reversed-phase silica and a resin for the extraction of a neutral organonitrogen species were also investigated. With propylene-linked cation exchangers (under appropriate pH conditions), it was shown that the primary mode of interaction is through ionic forces. As a consequence, there is no selectivity of these sorbents for cations based on hydrophobic nature. With ethylbenzene and octylene-linked exchangers, there is an increase in selectivity for cations with increasing hydrophobic nature. The linker chain is adequately long enough to allow for nonpolar interactions with the aliphatic side groups, just as a resin-based exchanger allows. With short and long chain exchangers, there is selectivity proportional to the charge of the ion. The proposed reason for this is a combination of multiplesite attachment of polyprotic species to the surface and increased probability of single-site interaction proportional to the number of charged nitrogen atoms on the molecule. It was shown that mixed sorbent beds offer advantages in operator control over the retention of organic bases in a high ionic strength sample matrix. The retention mechanism was elucidated, demonstrating a clear contribution of nonpolar forces to retention with the mixed sorbents as was observed with the long-chain cation exchangers.
    • Fundamental studies of micromechanics, fracturing progression, and flow properties in tuffaceous rocks for the application of nuclear waste repository in Yucca Mountain.

      Wang, Runqi.; Kemeny, John M.; Poulton, Mary M.; Labrecque, Douglas J.; Harpalani, Satya; Lever, Paul J.A. (The University of Arizona., 1994)
      Yucca Mountain, Nevada is the proposed site for the underground storage of high-level civilian nuclear waste in the United States. The repository must be isolated from the general environment for at least 10,000 years. Ground water and gases are potential carriers of radioactive materials. Fractures and connected pores in the host rock are the major pathways for ground water and gases. Therefore, the mechanical and flow properties of the host rock should be understood and utilized in the design of the underground repository. Samples of Topopah Spring tuff from Yucca Mountain were used in this study. Cylindrical specimens were prepared to perform uniaxial and triaxial "damage" tests where specimens are loaded to a particular stress level to induce damage and fracturing and then unloaded. Mechanisms of microcracking at different fracturing levels have been studied by using both an optical microscope and a Scanning Electron Microscope (SEM). The original rock sample without loading was also observed under the microscopes. Many kinds of defects including pores, preexisting fractures, and soft inclusions were found in the undamaged Apache Leap tuff samples. Pores were determined to be the main microstructures in Topopah Spring tuff that could influence the mechanical and hydrologic properties. Under compressive stresses, microcracking initiates from some of the pores. These microcracks will interact and coalescence to form large microcracks or macroscopic cracks as the load is increased. Crack propagation phenomena, such as pore cracking, pore linking, pore collapse and the formation of en echelon arrays were all found in specimens unloaded prior to complete failure. The failure of tuff specimens is often through a process of shear localization. In summary, the deformation and failure of both tuffs occurred by progressive fracturing, starting from microcracking on the small scale, and ending as fractures coalesced to form macroscopic fractures and shear localization. On the basis of the experimental studies, micromechanical models such as the pore collapse model and the pore linking model have been developed based on fracture mechanics theory. These models are used to predict the constitutive behavior for tuff and the predicted stress-strain curves match well with the experimental curves.
    • Fundamental studies of the deformability and strength of jointed rock masses at three dimensional level.

      Wang, Shuxin.; Kulatilake, Pinnaduwa H.S.W.; Kemeny, John M.; Glass, Charles E.; Contractor, Dinshaw N. (The University of Arizona., 1992)
      The deformability and strength properties of jointed rock masses are two of the fundamental parameters needed for the design and performance estimation of rock structures. Due to the presence of complicated minor discontinuity patterns (joints, bedding planes etc.), jointed rock masses show anisotropic and scale (size) dependent mechanical properties. At present, satisfactory procedures are not available to estimate anisotropic, scale dependent mechanical properties of jointed rock. Because of the statistical nature of joint geometry networks in rock masses, the joint patterns should be characterized statistically. The available joint geometry modeling schemes are reviewed. One of these schemes is used in this dissertation to generate actual joints in rock blocks. Three dimensional distinct element code (3DEC), which is used to perform stress analyses on jointed rock blocks in this study, is introduced and its shortcoming is identified. To overcome the shortcoming of 3DEC, a new technique is developed by introducing fictitious joints into rock blocks. Concerning the introduced fictitious joints, their geometry positions are mathematically determined; the representative mechanical properties for them found at 2D level are reviewed and verified at 3D level. By using the new technique, the deformation and strength properties of the rock blocks with many different joint configurations are found. Then effects of joint geometry parameters on the mechanical properties of jointed rock blocks are investigated. It is found that the joint geometry patterns have significant influences on the mechanical properties of rock blocks. All the joint geometry parameters are then integrated into fracture tensor. The relationships between the mechanical properties of jointed rock blocks and the fracture tensor parameters (its first invariant and directional component) are investigated. The possibility of obtaining the equivalent continuum behavior (REV properties) of jointed rock blocks is explored by using the aforementioned relationships. Finally, based on the research results, a new 3D constitutive model for jointed rock masses is developed to describe their pre-failure behavior. The constitutive model includes the effects of joints in terms of fracture tensor components and it shows the anisotropic and scale dependent natures of jointed rock masses.
    • Fundamental studies on the removal of copper in hydroxylamine based chemistries of interest to copper chemical-mechanical planarization

      Raghavan, Srini; Huang, Wayne Hai-Wei (The University of Arizona., 2003)
      The advancement of IC technology has led to an increasing demand for faster and cheaper microelectronic devices. One of the key processing steps in fabricating ultra-large scale integration devices is copper chemical-mechanical planarization (CMP). Traditional copper CMP slurries use hydrogen peroxide as an oxidant. A novel copper CMP slurry based on hydroxylamine chemistry is being considered as an alternative to hydrogen peroxide based slurries. The main goal of the research reported in this dissertation is to understand the removal of copper in hydroxylamine based chemistries. Copper removal experiments were performed on a regular CMP tool and a specially designed electrochemical abrasion cell (EC-AC). The effects of applied pressure and abrasion speed were investigated on both tools. The electrochemistry of copper in hydroxylamine based chemistry was investigated using electrochemical techniques on the EC-AC tool. The techniques include electrochemical polarization and voltammetry. The effects of solution pH and hydroxylamine concentration on the polarization of copper were systematically investigated. The fate of hydroxylamine and other nitrogen-based species were studied using capillary electrophoresis chromatography. The removal rates of copper obtained from a regular CMP tool were twice as much as the rates obtained from the EC-AC tool. However, the removal rates from both tools showed the same trend with respect to pH. Interestingly, a maximum peak in copper removal rates occurs at a pH value of 6, and a significant decrease in rates occur at pH values deviating from 6. The copper removal results obtained from the EC-AC tool with and without abrasion showed that the high removal rate at pH 6 is largely due to chemical attack. The reactions involved in the oxidation of copper are dependent on the decomposition and complexation behaviors of hydroxylamine. Electrochemical analysis showed the removal of copper may be dependent on the reduction of nitric oxide (NO) to hyponitrous specie (H₂N₂O₂). Capillary electrophoresis chromatography analyses showed the consumption of hydroxylamine and species generated from the autooxidation/reduction of hydroxylamine. In slightly alkaline pH conditions, the removal of copper was predominantly due to mechanical abrasion of the surface oxide. This was supported by the potential-pH diagrams and the analysis of applied pressure and relative velocity. At pH values ranging from 3 to 5, the removal of copper was due to oxidation of Cu to Cu²⁺.
    • The Fundamentality of Fit

      Timmons, Mark; Howard, Christopher; Timmons, Mark; Cohen, Stewart; Horgan, Terence; Rosati, Connie (The University of Arizona., 2017)
      Normative reasons for attitudes are facts that count in favor of those attitudes, but a fact can favor an attitude in two very different ways. One way in which a fact can favor an attitude is by making the attitude fitting (apt, merited, correct). For example, the fact that Sharon spends much of her time doing charity work is a fact that favors admiring Sharon, since it’s a fact that makes her admirable, and so fit to admire. Call any fact that favors an attitude by making it fitting a "fit-related reason." A second way in which a fact can favor an attitude is by making the attitude somehow valuable, or good to have. For example, the fact that an evil dictator will order my execution unless I admire him is a fact that favors my admiring the dictator, since it's a fact that makes my admiring him good. Call any fact that favors an attitude by making it somehow good to have a "value-related reason." This dissertation has two main goals. The first is to develop an ontology of normativity that can accommodate a view on which both fit- and value-related reasons are genuine reasons. Many authors, including Derek Parfit, T.M. Scanlon, and Mark Schroeder, favor a "reasons-first" ontology of normativity: they take reasons to be normatively basic, and claim that all other normative facts, properties, and relations can be analyzed or accounted for in terms of the reason relation. A central alternative, famously defended by G.E. Moore in Principia Ethica, is the "value-first" ontology—an ontology that takes value or goodness to be normatively basic and claims that the rest of the normative can be accounted for in terms of the property of being good. In the opening chapter of my dissertation, "The Fundamentality of Fit," I advance an ontology of normativity, originally suggested by Franz Brentano and A.C. Ewing, according to which fittingness is the basic normative relation, in terms of which the rest of the normative can be explained. I argue that neither the reasons- nor the value-first ontology can accommodate a view on which both fit- and value-related reasons are genuine reasons. Then I explain how my "fittingness-first" ontology can. Of course, any threat to the plausibility of the view that both fit- and value-related reasons are genuine reasons would undermine the case for my ontology of normativity. And so a full defense of my fittingness-first ontology will require a systematic defense of the substantive normative view it's designed to accommodate. The second goal of my dissertation is to provide this defense. A normative view that says that both fit- and value-related reasons are genuine reasons consists in three component claims: (1) that fit-related reasons are genuine reasons; (2) that value-related reasons are genuine reasons; and (3) that fit- and value-related reasons can be compared against one another to yield univocal verdicts concerning what attitudes one ought, all-things-considered, to have. The first of these claims—that fit-related reasons are genuine reasons—is among the most widely shared in contemporary normative theory. The latter two, however, are more controversial. In the second and third chapters of this dissertation, I defend each of these claims in turn. One way to showcase the plausibility of a normative view that says that both fit- and value-related reasons are genuine reasons is to show that it explains our intuitions in a variety of substantive normative debates. This would, in turn, provide support for my fittingness-first ontology, since, relative to its main competitors, my ontology uniquely accommodates and predicts such a view. In the final chapter, I put this methodological observation into practice by testing the substantive normative predictions of my fittingness-first view against our intuitions in the debate concerning what kinds of considerations can provide reasons for love. I argue that acknowledging the existence of both fit- and value-related reasons for love solves a number of persistent problems in this debate.
    • Fundamentals and Application of Porous Media Filtration for the Removal of Nanoparticles from Industrial Wastewater

      Shadman, Farhang; Rottman, Jeffrey J.; Sierra-Alvarez, Reyes; Aspinwall, Craig A.; Shadman, Farhang (The University of Arizona., 2012)
      Increasing use of engineered nanomaterials presents concerns as some nanoparticles appear to be harmful to both human health and the environment. Effective treatment methods are required to remove problematic nanoparticles from (waste)water streams. Porous media filtration, commonly used for the removal of particulate matter, shows promise for nanoparticle treatment. The goal of this work is to investigate the potential of porous media filtration for the abatement of nanoparticles from aqueous waste streams. To this end, an automated method was developed that allows real-time and in-situ monitoring of nanoparticle transport and retention in porous media using online measurement of UV-visible absorbance or fluorescence. Development of fluorescent-core nano-silica (n-SiO₂) in controllable sizes provided an excellent tracer for nanoparticle transport in porous media. Measurement of n-SiO₂ by destructive techniques is complicated by high natural Si background levels. Fluorescence monitoring enables real-time measurement, facilitating rapid evaluation of n-SiO₂ transport. Synthesized n-SiO₂ remain in their primary sizes making an evaluation of the behavioral change of particles due to transition into the "nano" range possible. A comparison of the role of particle size on transport in porous media displayed the importance of particle number concentration as the dominance of site-specific adsorption may be obscured by simple mass concentration evaluation.T he effectiveness of different bed materials, namely, sand, activated carbon (AC), and diatomaceous earth (DE), for the removal of TiO₂ nanoparticles (n-TiO₂) from aqueous streams was investigated. DE proved promising for n-TiO₂ capture shown by its high bed capacity (33.8 mg TiO₂ g⁻¹(medium)) compared to AC (0.23 mg TiO₂ g⁻¹(medium)) or sand (0.004 mg TiO₂ g⁻¹(medium)). The presence of organic and synthetic contaminants produced varying effects on n-TiO₂ retention, mostly due to either enhanced electrostatic or steric interactions. Application of a process simulator combining physical straining with site-specific interactions, delineating physisorption from chemisorption and diffusion limited interactions, enabled the accurate fit of n-TiO₂ transport in sand, AC and DE. The fitting process revealed the advantage of DE due to increased physisorption and physical straining of n-TiO₂. Modeling of this system afforded the elucidation of controlling retention mechanisms and provides a basis for future scaling and system design.
    • Fundamentals and Applications of Organic Electrochemical Transistors for Biosensing

      Ratcliff, Erin; Harris, Jonathan; Savagatrup, Suchol; Printz, Adam; Guzman, Roberto (The University of Arizona., 2021)
      Sensors that interface with biological environments such as human sweat, foods, and biofuels have garnered significant interest in recent years. The primary need in these complex fields is for a sensor device that can provide a real-time data stream in chemically unforgiving environments while also being portable or wearable and consume low power. Electronic devices that include organic semiconductors can begin to address these issues, as they are flexible, biocompatible and scalable materials. Yet, organic semiconductors are still being actively understood. They have relatively complex microstructural transformations when a voltage is applied to them in an electrochemical environment. Further, their unique ability to conduct both electronic charges and ions offer competing design principles when using them in a device. Understanding these processes occurring during device use is crucial for their application. This work first utilizes a model organic semiconductor, poly(3-hexylthiophene), to examine the microstructural changes occurring during electrochemical oxidation, and possible alternatives to improve ion conduction. Then, P3HT is used as the semiconductor channel in a floating gate organic electrochemical transistor modified with an ion gel to prevent degradation. The final device with modifications to each interface is used for sensing of a yeast used in the biofuel process, Yarrowia lipolytica. The critical interfacial factors that contribute to the overall performance of this device are examined, with a particular focus on reproducibility and manufacturability. It’s found that the final device can provide simplicity and amplification above traditional impedance-based sensors.
    • Fundamentals of controllable photochromic technology

      Uhlmann, Donald R.; Gudgel, Todd Jeffrey (The University of Arizona., 1999)
      Recently, a new technology termed the controllable photochromic has emerged within the field of chromogenic technology. This technology represents a novel approach to the control of solar heat gain and adjustable transmission by utilizing a combination of chromogenic and radiation sensitive technologies. By harnessing solar energy for coloration, these systems represent a low-energy approach to controllable transmission glazings when compared to other chromogenic technologies available today. The zero external power required to reduce the glazing transmission and to maintain that state will provide opportunities for applications where today's chromogenic technologies are not well suited. One emphasis of this work was the rationalization of a general framework through which present and future controllable photochromic systems can be discussed. This framework discusses the roles and properties of the system components, necessary and desired for the function of the system, including a radiation sensitive electrode, a chromogenic electrode, and an electrolyte. The framework was also examined through a detailed case study of a system involving an anatase TiO₂ radiation sensitive electrode and a WO₃ chromogenic electrode. While this study involved a particular implementation of the technology, it exposed a great many attributes of this system including kinetics, wavelength sensitivity, influence of construction parameters, sensitivity to non-uniform incident radiation, and control over the photochromic response. While the general framework is useful for discussion of the principles involved in device operation, the detailed mechanisms occurring in a particular implementation will generally be more complex. Through careful study of the example system described in this thesis, the primary mechanisms occurring in the device were identified, and a model is proposed which is consistent with the observed findings. The source of degradation occurring due to prolonged cycling in the devices was studied through investigation of changes occurring in individual device components. While only one implementation of the technology was studied in detail in this investigation, three configurations were discussed in terms of the general framework. These systems exhibit an impressive array of desirable properties; however, it is clear that there is still much to be done to bring the technology to full fruition.
    • Fundamentals of the optical design of multiple aperture telescopes with wide fields of view

      Burge, James H.; Sabatke, Erin Marie (The University of Arizona., 2002)
      This dissertation derives and demonstrates a new approach to the design of wide-field interferometric telescopes. The first part of this dissertation is a tutorial on multiple aperture systems. Design basics such as PSF and OTF, fill factors, resolution, and temporal coherence are investigated. We show that the perfect image for a multiple aperture system is the sum of an image from each aperture and a set of fringes from each pair of apertures. Four example systems are designed by applying the derived design rules. The first system is a rotationally-symmetric Paul system that is then segmented to make a four-aperture system. The low-order design rules in this system are shown to be automatically satisfied. The second system is an array of four afocal telescopes that share a three-mirror combining telescope. Fold flats are used in the inner two arms to satisfy the requirement that the axial pathlengths should match. Linear piston errors are eliminated by forcing the beam configuration into the combiner to be a scaled version of the afocal array. The angles of the fold flats are chosen to eliminate any constant tilt errors. As a third example, the design of a beam combiner for the Large Binocular telescope is explored. By applying the design rules, coherent imaging with a 1 arcminute field of view is achieved with just three reflections. Linear defocus errors appear, but are minimized by bringing the beams to focus as closely together as possible. The sine condition is satisfied for the axial rays so that the linear piston errors are zero. As a fourth example, a space telescope design is presented that utilizes a flat gossamer mirror technology. The system would consist of a primary array of flats, a shared secondary mirror, and a tertiary array with one mirror corresponding to each of the primary flats. Each branch of the system consists of a primary flat, the shared secondary, and a tertiary that brings the beam to the correct image point. The position of the tertiary is chosen to eliminate axial pathlength errors. The RMS wavefront error is calculated as a function of the system parameters. This gives an efficient method for exploring design space for the gossamer systems. The performance of a system of five flats is explored in this way. A few specific five-flat systems are modeled with full interferometric raytraces, and the results show good agreement with the Strehl values predicted by calculation of the RMS wavefront errors. (Abstract shortened by UMI.)
    • Funds of Knowledge and College Ideologies: Lived Experiences among Mexican-American Families

      Rhoades, Gary; Kiyama, Judy Marquez; Rhoades, Gary; Rhoades, Gary; Moll, Luis; Lee, Jenny J. (The University of Arizona., 2008)
      There are a number of factors that contribute to the differences in college access rates of under-represented students compared with their white and Asian American counterparts. Families play a role in whether students experience a college-going culture. In an effort to challenge the dominant literature which focuses primarily on familial deficits, the intent of this research is to understand families from a different model, that of funds of knowledge (Moll, Amanti, Neff, & Gonzalez, 1992). Using a qualitative approach of embedded case studies and oral history interviews, this study explored the funds of knowledge present in six Mexican families in a university outreach program and sought to understand how those funds of knowledge contribute to the development of the college ideologies for their families. Participants are represented by the term household clusters, which includes extensions of families beyond the nuclear household (Vélez-Ibáñez & Greenberg, 2005). Three theoretical frameworks were used for this study. The primary framework utilized is funds of knowledge (Gonzalez, Moll & Amanti, 2005), with social capital (Bourdieu 1973, 1977) and cultural capital (Bourdieu, 1986; Bourdieu & Passerson, 1977) serving as supplemental frameworks. Findings illustrate that funds of knowledge in the form of daily educational practices were present in household clusters and influenced children’s academic experiences and college knowledge. Educational ideologies highlighted the ways in which beliefs around the college-going process were formed and manifested as both helpful and limiting. Finally, it was evident that parental involvement was valued; this also included examples of non-traditional involvement, particularly when mothers worked at their children’s schools.
    • Funds of Knowledge in Transition: Responding to Diverse Student Populations in Summer Bridge Programs

      Miller-Cochran, Susan; Mapes, Aimee C.; Conti Maravillas, Maria; Kimme Hea, Amy C. (The University of Arizona., 2019)
      In examining twenty-two summer bridge program websites across the country, this study focused on a particular type of student support at one of the most historically-contentious positions in a college student’s trajectory—the point of access. Diverse student populations bring specific strengths, resources, skills, and knowledge, or “funds of knowledge,” to the university space from other parts of their lives (Kiyama & Rios-Aguilar, 2018; Moll, Amanti, Neff, & González, 2005). In light of the history of deficit-based explanations for student failure, funds of knowledge approaches to instruction and program design offer models that more fully describe the abilities and potential of diverse groups of students. Drawing on the diametrically opposed frameworks of remediation and funds of knowledge, this qualitative research study sought to answer the following research questions: (1) What do the website descriptions of bridge programs at a range of institutions reveal regarding assumptions about students and support they need?, and (2) In what ways, if any, do these descriptions connect to funds of knowledge?I engage in systematic qualitative coding and analysis of the bridge program websites. The emphasis on academic/study skills, college knowledge, and relationships in the data set (see Chapter 3) positioned bridge programs as the benevolent giver of these things instead of presenting students as capable of building on their skills and existing knowledges. In the figured world (Holland, Lachiotte, Skinner, & Cain, 1998) of summer bridge, the underlying assumption goes as follows: Adjusting to a challenging new environment is possible as long as the university provides students with academic and social integration. Without these supports, students are not likely to succeed on their own due to their demographics as first-generation students, low-income students, or students of color or due to the intensity of their chosen major (in the case of the STEM-affiliated bridge programs). However, eight of the programs were partially aligned with a funds of knowledge approach, especially regarding aspirational knowledge and familial knowledge (see Chapter 4). The funds of knowledge framework is a constructive response to deficit discourse that asks bridge programs and other student success initiatives across the university to rethink their assumptions about students’ prior knowledges and strengths.
    • Fundus Spectroscopy and Studies in Retinal Oximetry Using Intravitreal Illumination

      Chipman, Russel A.; Salyer, David Alan; Chipman, Russel A.; Park, Robert I.; Denninghoff, Kurt R. (The University of Arizona., 2006)
      This dissertation documents the development of a new illumination technique for use in the studies of retinal oximetry and fundus spectroscopy. Intravitreal illumination is a technique where the back of the eye is illuminated trans-sclerally using a scanning monochromator coupled into a fiber optic illuminator. Retinal oximetry is the processof measuring the oxygen saturation of blood contained in retinal vessels by quantitative measurement of the characteristic color shift seen as blood oxygen saturation changes from oxygenated blood (reddish) to deoxygenated blood (bluish). Retinal oximetry was first attempted in 1963 but due to a variety of problems with accuracy and difficulty of measurement, has not matured to the point of clinical acceptabilityor commercial viability.Accurate retinal oximetry relies in part on an adequate understanding of the spectral reflectance characteristics of the fundus. The use of intravitreal illumination allows new investigations into the spectral reflectance properties of the fundus. The results of much research in fundus reflectance and retinal oximetry is detailed in thisdocument, providing new insight into both of these related fields of study.Intravitreal illumination has been used to study retinal vessel oximetry and fundus reflectometry resulting in several important findings that are presented in this document. Studies on enucleated swine eyes have provided new insight into the bidirectional reflectance distribution function of the fundus. Research on live swine hasshown accurate measurement of retinal vessel oxygen saturation and provided the first in vivo spectral transmittance measurement of the sensory retina. A secondary discovery during this research suggests that vitrectomy alters the retinal vasculature,a finding that should spawn new research in its own right.
    • Fungal Community Diversity and Structure from Cave Mineral Surfaces and Bat Guano in Kartchner Caverns, Arizona

      Pryor, Barry M.; Vaughan, Michael Joe Steven; Bronstein, Judith L.; Orbach, Marc J.; Cotty, Peter J.; Arnold, Anne Elizabeth; Pryor, Barry M. (The University of Arizona., 2012)
      Research regarding the distribution and structure of fungal communities in caves is lacking. The current study examines fungal communities in Kartchner Caverns, a mineralogically diverse cave located in the Whetstone Mountains, Arizona, USA. The first study examines culturable fungal diversity from speleothem surfaces. Twenty-one fungal genera represented by 43 genotypes and 53 distinct morphological taxonomic units (MTU) were recovered from 15 speleothems. Analysis of DGGE profiles indicated a significant effect of sampling site on community structure. The second study examined fungal diversity from speleothem and rock wall surfaces using the 454 FLX Titanium sequencing platform using the rDNA internal transcribed spacer 1 (ITS1) as a genetic marker. Fungal diversity was estimated and compared between speleothem and rock wall surfaces and its variation with distance from the natural entrance of the cave was quantified. Effects of environmental factors and nutrient concentrations in speleothem drip water at different sample sites on fungal diversity were also examined. Sequencing revealed 2219 fungal operational taxonomic units (OTUs) at 95% similarity. Speleothems supported a higher fungal richness and diversity than rock walls, but community membership and the taxonomic distribution of fungal OTUs did not differ significantly. OTU richness and diversity were negatively correlated with distance from the natural cave entrance. Community membership and taxonomic distribution of fungal OTUs differed significantly between the front and back of the cave. There was no observed effect of drip water nutrient concentration on fungal community structure. The third study examined fungal community structure from bat guano over the course of a year. There was no significant difference in fungal OTU richness, diversity, or community membership and taxonomic affiliations among sampling times. There were no significant differences in nutrient concentrations of guano samples among sampling times. Nutrient concentration did have a significant effect on community structure, especially the level of nitrogen and calcium.
    • Fungi Associated with Aflatoxin Contamination in Africa

      Cotty, Peter J.; Probst, Claudia; Arnold, Anne Elizabeth; Orbach, Marc J.; Molnar, Istvan; Stock, S. Patricia; Cotty, Peter J. (The University of Arizona., 2011)
      Aflatoxins are secondary metabolites produced by members of the fungal genus Aspergillus. Immunosuppressive and carcinogenic activities of these toxins negatively impact human health especially in developing countries. Severity of contamination is influenced by both fungal community structure and the environment to which the crop is exposed either prior to or after harvest. In 2004, a severe episode of lethal human aflatoxicosis occurred in the Eastern Province of Kenya. Analysis of fungal community structure revealed that this event was caused by a previously unknown fungal lineage closely resembling the S strain morphotype of Aspergillus flavus. Fungal communities associated with maize produced in affected regions of Kenya were invariably dominated by the new fungal lineage and its incidence was strongly correlated with maize aflatoxin content. Analyses of fungal communities of maize grown in adjacent Kenyan provinces showed that incidences of the new lineage are limited outside the Eastern Province where the aflatoxicoses outbreaks occurred. Multi-locus phylogenetic analyses suggest the newly identified Kenyan lineage is closely related to the B and G aflatoxin producing species A. minisclerotigenes, and more distantly related to both the A. flavus S strain and an unnamed taxon with similar morphology endemic in West Africa (strain SBG). Sequence analyses of the cypA aflatoxin biosynthesis gene identified a previously unknown 2.2 kb deletion unique to the Kenyan lineage and coherent with its phylogenetic placement. A polyphasic approach was used to study aflatoxin-producing fungal communities, with emphasis on occurrence of fungi with S strain morphology, in Sub-Saharan Africa. Four phylogenetically distinct groups of fungi with S strain morphology were identified with restrictions to West Africa (strain SBG) or Central and East Africa (A. flavus S strain, A. minisclerotigenes, the new lineage). Aflatoxin production in synthetic media was a poor predictor of aflatoxin production in viable maize grain. An in vitro assay was developed to predict the aflatoxin-producing potential of fungal isolates in maize. This screen was used to identify atoxigenic isolates of A. flavus with potential value for biological control within highly toxic Aspergillus communities associated with maize production in Kenya. These atoxigenic isolates have potential value for mitigating aflatoxin contamination in Kenya.
    • Further studies of the bacterial necrosis of the giant cactus

      Boyle, Alice McLaughlin, 1904- (The University of Arizona., 1948)

      Nakaue, Harry Sadao, 1932- (The University of Arizona., 1966)
    • Fusion and Wildtype Proteins of EWSR1 Interact in a Protein Granule

      Schwartz, Jacob; Ahmed, Nasiha Salma; Schroeder, Joyce; Montfort, Bill; Buchan, Ross; McEvoy, Justina (The University of Arizona., 2020)
      Ewing sarcoma is driven by fusion proteins containing a low complexity (LC) domain that is intrinsically disordered and a powerful transcriptional regulator. The most common fusion protein found in Ewing sarcoma, EWS-FLI1, takes its LC domain from the RNA-binding protein EWSR1 (Ewing Sarcoma RNA-binding protein 1) and a DNA-binding domain from the transcription factor FLI1 (Friend Leukemia Virus Integration 1). The LC domain in EWS-FLI1 can bind RNA polymerase II (RNA Pol II) and can self-assemble through a process known as phase separation. The ability of EWSR1 and related RNA-binding proteins to assemble into ribonucleoprotein granules in cells has been intensely studied but the role of phase separation in EWS-FLI1 activity is less understood. We investigated the overlapping functions of EWSR1 and EWS-FLI1 in controlling gene expression and tumorigenic cell growth in Ewing sarcoma, and our results suggested that these proteins function closely together. We then studied the nature of interactions among EWS-FLI1, EWSR1, and RNA Pol II. We observed EWSR1 and RNA Pol II to be present in protein granules in cells. We then identified protein granules in cells associated with the fusion protein, EWS-FLI1. The tyrosine residues in the LC domain are required for the abilities of EWS-FLI1 to bind its partners, EWSR1 and RNA Pol II, and to incorporate into protein granules. These data suggest that interactions among EWS-FLI1, RNA Pol II, and EWSR1 in Ewing sarcoma can occur in the context of a molecular scaffold found within protein granules in the cell.
    • Fusion of Inverted Repeats Leads to Formation of Dicentric Chromosomes that Cause Genome Instability in Budding Yeast

      Weinert, Ted; Kaochar, Salma; Nagy, Lisa; Dieckmann, Carol; Burd, Gail; Parker, Roy (The University of Arizona., 2010)
      Large-scale changes are common in genomes, and are often associated with pathological disorders. In the work presented in this dissertation, I provide insights into how inverted repeat sequences in budding yeast fuse during replication. Fusion leads to the formation of dicentric chromosomes, a translocation, and other chromosomal rearrangements.Using extensive genetics and some molecular analyses, I demonstrate that dicentric chromosomes are key intermediates in genome instability of a specific chromosome in budding yeast. I provide three pieces of evidence that is consistent with this conclusion. First, I detect a recombination fusion junction that is diagnostic of a dicentric chromosome (using a PCR technique). Second, I show a strong correlation between the amount of the dicentric fragment and the frequency of instability of the entire chromosome. Third, I demonstrate that a mutant known to stabilize dicentric chromosomes suppress instability. Based on these observations, I conclude that dicentric chromosomes are intermediates in causing genome instability in this system.Next, we demonstrate that fusion of inverted repeats is general. Both endogenous and synthetic nearby inverted repeats can fuse. Using genetics, I also show that many DNA repair and checkpoint pathways suppress fusion of nearby inverted repeats and genome instability. Based on our analysis, we propose a novel mechanism for fusion of inverted repeats that we term `faulty template switching.'Lastly, I discuss two genes that are necessary for fusion of nearby inverted repeats. I identified a mutant of the Exonuclease 1 (Exo1) and a mutant of anaphase inhibitor securin (Pds1) that suppress nearby inverted repeat fusion and genome instability. Studies of Exo1 and Pds1 provide us with insights into the molecular mechanisms of fusion.Our finding that nearby inverted repeats can fuse to form dicentric chromosomes that lead to genome instability may have great implications. The generality of this fusion reaction raises the possibility that dicentric chromosomes formed by inverted repeats can lead to genome instability in mammalian cells, and thereby contribute to a cancer phenotype.

      Pace, Hugh Allen, 1943- (The University of Arizona., 1977)
    • Fuzzy adaptive recurrent counterpropagation neural networks: A neural network architecture for qualitative modeling and real-time simulation of dynamic processes.

      Pan, YaDung.; Cellier, F. E.; Rozenblit, Jerzy W.; Sundareshan, M. K. (The University of Arizona., 1995)
      In this dissertation, a new artificial neural network (ANN) architecture called fuzzy adaptive recurrent counterpropagation neural network (FARCNN) is presented. FARCNNs can be directly synthesized from a set of training data, making system behavioral learning extremely fast. FARCNNs can be applied directly and effectively to model both static and dynamic system behavior based on observed input/output behavioral patterns alone without need of knowing anything about the internal structure of the system under study. The FARCNN architecture is derived from the methodology of fuzzy inductive reasoning and a basic form of counterpropagation neural networks (CNNs) for efficient implementation of finite state machines. Analog signals are converted to fuzzy signals by use of a new type of fuzzy A/D converter, thereby keeping the size of the Kohonen layer of the CNN manageably small. Fuzzy inferencing is accomplished by an application-independent feedforward network trained by means of backpropagation. Global feedback is used to represent full system dynamics. The FARCNN architecture combines the advantages of the quantitative approach (neural network) with that of the qualitative approach (fuzzy logic) as an efficient autonomous system modeling methodology. It also makes the simulation of mixed quantitative and qualitative models more feasible. In simulation experiments, we shall show that FARCNNs can be applied directly and easily to different types of systems, including static continuous nonlinear systems, discrete sequential systems, and as part of large dynamic continuous nonlinear control systems, embedding the FARCNN into much larger industry-sized quantitative models, even permitting a feedback structure to be placed around the FARCNN.