More than 30,000 theses and dissertations produced at the University of Arizona are included in the UA Theses and Dissertations collections. These items are available open access, and are 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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You can also refer to the Dissertations and Theses in the UA Libraries guide to find materials that are not available online.

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Recent Submissions

  • Geology and ore deposits of the Richmond Basin area, Gila county, Arizona

    Butler, B.S.; Bishop, O.M. (Ottey Manley), 1905- (The University of Arizona., 1935)
  • Transcription Profiling of Angiogensis using DNA Microarrays

    Hoying, James; Budoff, Adam; Williams, Stuart; Galbraith, David (The University of Arizona., 2000)
    Angiogenesis is the process by which new blood vessels form from an existing vasculature. The degree of angiogenesis and the character of the resulting microvascular beds vary between different healing environments such as wound healing and tumor angiogenesis. These differences are due, in part, to qualitative and quantitative differences in the molecular function within the tissue undergoing angiogenesis. For this study, these two types of angiogenic environments were created in mice and characterized on a gene expression level by utilizing cDNA microarrays. A DNA microarray containing 58 mouse genes from many different molecular classes relevant to angiogenesis was manufactured and tested. Optimal conditions and protocols for the use of microarray technology were designed and implemented. Results show that a polymerinduced angiogenic wound healing response differs greatly in its transcription profile from a tumor, suggesting that different types of angiogenesis occur in different environments.
  • A Novel Pathology Device for the Improvement of Intraoperative Breast-Cancer Tissue Gross Examination

    Arabyan, Ara; Kachur, Xenia; (The University of Arizona., 2011)
    The aim of this study was to design and test key aspects of a novel device, consisting of a polymer referencing enclosure (hardware) and a gel component, for the standardization of intraoperative gross pathology examination of excised breast cancer tissue. The proposed device improves the current practice of tissue preparation for radiographic and pathological examination without changing the existing process and without imposing retraining requirements on professional staff involved in the current process. To identify the optimal composition of the gel component to be used, 32 gel formulations were tested to determine setting times and maximum temperature reached during setting. The radiographic properties of 12 gel formulations and 15 plastic materials for potential use in the hardware were also tested. A negative correlation was found to exist between setting time and maximum temperature reached, narrowing down gel selections to those setting in <10 minutes with a temperature peak of <54 °C. The radiographic properties of the tested and downselected gels and plastics were found to be such that these materials are unlikely to interfere with lesion identification in radiological examinations. A completed tissue study for examination of gel effects on tissue properties revealed no effects, thereby clearing this device for potential clinical applications.
  • Closure of Loop-Mediated Isothermal Amplification Chamber on Lab-On-Chip Using Thermal-Responsive Valve

    Szivek, John; Love, Christopher J.; (The University of Arizona., 2012)
    Point-of-care tests for nucleic acids are important for the diagnosis and management of infectious and genetic diseases, biowarfare agents, and for drug research. Recent integration of loop-mediated isothermal amplification (LAMP) onto a lab-on-chip (LOC) platform allows sensitive and specific, detection of target DNA or RNA sequences for point-of-care (POC) applications. However, because of the high risk of contamination to LAMP products, robust and simple methods of hermetically sealing the reaction chamber are essential. In addition, having a method for isolation of nucleic acids at the level of the chip is more effective for POC applications because a laboratory setting is not required to complete the analysis. This report describes an integrated, polymer-based cassette which was designed for detection of DNA/RNA target-sequences by using LAMP and a solid-state nucleic acid purification membrane. The LAMP chamber seals using a self-actuated thermalresponsive valve made from expandable microspheres suspended in Polydimethylsiloxane (PDMS). A flow-through, Flinders Technology Associates membrane (Whatman FT A®) was installed on the cassette with the expectation of providing isolation and purification of nucleic acids. The cassette was designed, fabricated and the efficacy of the valve to seal the LAMP chamber was investigated. The valve underwent expansion and held pressures of233 +/- 5.0 kPa without signs of leakage. A portable, battery-powered, polyimide-based thin film heater, placed outside the cassette, provided thermal control. In addition, a LAMP primer set was designed for the serotonin receptor 5HTRIA promoter gene using Primer Explorer V 4 software (http:/ / for LAMP detection of neurotransmitter serotonin. The integrated, portable LAMP cassette will be attractive in global health-care challenges, mainly in resource-poor locations, where the availability of laboratory equipment and/or trained personal is restricted.
  • Immunoassay-Based Microsensing

    Hoying, James; Jabbour, Maurice Elie; Deymier, Pierre; Guzman, Roberto; Barnaby, Hugh; Cuello, Joel (The University of Arizona., 2005)
    Immunoassay systems are recognized as superior modalities for detecting biological substances. Immunoassay sensing offers the advantages of selectivity and sensitivity. Development of a portable micro-immunoassay system is quite desirable for fieldwork applications. The basis of such portable sensing approach would combine molecular printing techniques with solid-state devices. In this work, I report on advances in attaching and patterning antibodies on Si02 substrates with the aim of retaining their biological functionality. The integration of functional antibodies with conventional photodetectors through direct printing onto the oxide layer of the detector will result in a device with on-chip readout. To that effect, monoclonal IgG antibody was printed onto chemically modified and thermally oxidized silicon substrates. Using a generic immunoassay, I was able to validate the activity of the antibody adsorbed on epoxyterminated silane surface coatings. An assay based on Mouse anti-biotin - Biotin conjugated to horseradish peroxidase interaction was used to show the activity of printed antibody, specifically the molecular orientation of the antibody, on the silane-coated surface. In addition, avalanche photodiodes were used as solid-state detector for light detection. Avalanche photodiodes were able to detect the chemiluminescence, an indication of the sensitivity of the sensor for the immunoassay. Furthermore, there were clear differences between 'control' measurements obtained using a saline buffer solution compared to actual measurements obtained from antibody attachment to the surface of the sensor. This difference in signals is an indication that protein-protein interaction 10 occurred. To that effect, on-chip readout, namely in situ measurement of light detection without the aid of additional detector, was shown. In summary, I present, as a proof of concept, one example of immunoassay-based microsensing through the integration of antibody with avalanche photodiodes. This may have potential application in designing commercial, low cost, and portable biosensors.
  • Maximal Oxygen Consumption Rates in One-Leg and Two-Leg Exercise: A Theoretical Model

    Secomb, Timothy; Patel, Deepa Praful; Cohen, Zoe; Granzier, Henk; Konhilas, John (The University of Arizona., 2011)
    The goal of this project was to create a theoretical model to predict maximal oxygen consumption rates in one-leg and two-leg exercise. A MATLAB code was developed to simulate both capillary-level oxygen transport (in the legs) and systemic oxygen transport. Predicted values for oxygen consumption closely matched experimental data. The model was used to explain the trend of a lower maximal oxygen consumption rate in two-leg exercise compared to one-leg exercise. As activity increases from rest to one-leg exercise to two-leg exercise, the oxygen demand of the active components, the cardiac output, and the blood flow rate also increase. However, the fraction of cardiac output to the active leg(s) decreases when the second leg is activated. At the capillary level, the oxygen extraction is increased at the arteriolar end of each capillary, resulting in regions of hypoxic tissue towards the venous end. Venous oxygen saturation is decreased, leading to lower venous P02 returning to the lungs. The increased cardiac output decreases the time that the deoxygenated blood has in contact with the alveoli. As a result, arterial P 02 for blood exiting the lungs is lower. This decreases the pressure gradient between the tissue and the capillary and limits diffusive transport. In summary, the reduction of oxygen consumption rate per unit muscle mass in two-leg exercise relative to one-leg exercise is accounted for quantitatively by the model and shown to result from the combined effects of reduced flow and reduced oxygen saturation of blood to each leg in two-leg exercise.
  • Modifying Aqueous Humor Dynamics for the Treatment of Glaucoma

    Snyder, Robert; Khatri, Chandra Michelle; Stamer, Dan; Matsunaga, Terry; Pagel, Marty (The University of Arizona., 2011)
    Glaucoma is one of the leading causes of irreversible blindness in the world, and the leading cause in many developing countries. It is a progressive loss of optic nerve tissue typically caused by increased intraocular pressure and treated by lowering the pressure. In developing nations where the disease is most common medications are not affordable and surgery is expensive and unstable. A new surgical approach and drainage device material that could lead to a cost effective, permanent solution were studied. A tube connected to an e-PTFE reservoir shunts fluid from inside the eye to the subconjunctival reservoir. E-PTFE was chosen because it is biocompatible and porous, while promoting angiogenesis and lymphangiogenesis on its surface. The surrounding vessels can carry the fluid back into the systemic circulation. A tangential surgical approach was evaluated because it could spare and protect lymphatic vessels. Recent studies have shown that lymphatics are important in aqueous outflow. Preliminary results showed that theePTFE device could sufficiently lower IOP and that the lymphatics are potentially involved in aqueous outflow after surgery. These results indicate the importance of further evaluating a new surgical approach that addresses the role of lymphatics in fluid outflow from a glaucoma drainage device.
  • Predictive Variables of Counter-Shock During Resuscitation in a Swine Model

    Indik, Julia; Allen, Daniel N.; (The University of Arizona., 2010)
    The purpose of this study was to examine parameters with potential to predict the outcome of counter-shocks during resuscitation. Out-of-hospital discharge rates decline 8-10% per minute of untreated cardiac arrest (3 ,4 ), therefore time wasted during resuscitation for unsuccessful counter-shocks can be reduced if scrutiny is given toward additional variables of predictive ability. Our experiment was designed to find the predictive ability of amplitude spectral area (AMSA), slope, end-tidal carbon dioxide, coronary perfusion pressure, the condition of acute myocardial infarction (MI), and the duration of ventricular fibrillation (VF) induced cardiac arrest preceding resuscitation in a swine model. Variables were tested by logistic regression (a= 0.1). Groups were set up in a 2x2 design: MI versus control; 2 minute vs 8 minute VF. We found AMSA, slope, MI and duration of VF significant predictors of countershock. We also found AMSA, slope, and duration of VF as independent predictors of counter-shock.
  • Formulation of Perfluorocarbon-Filled Droplets for Ultrasound-Mediated Applications

    Matsunaga, Terry; Wong, Vincent; (The University of Arizona., 2011)
    Microbubbles and nanodroplets are tools used in medicine for diagnosis and therapy. Probubbles are initially submicrometer droplets that become microbubbles in tumors as a result of ultrasonic force. The aim of this investigation was to determine vaporization thresholds of perfluorocarbon (PFC) droplets as a function of PFC boiling point and droplet size. PFC droplets with boiling points -1. 7 to 56.6°C were formulated followed by acoustic droplet vaporization (ADV) and stability testing. Under ultrasound acoustic outputs used, perfluorohexane (PFH) droplets did not vaporize while perfluoro(-2- methyl-3-pentanone) (PFMP), perfluoropentane (PFP), and perfluorobutane (PFB) droplets did vaporize. The acoustic output required to vaporize droplets decreased with decreasing boiling point. Vaporization threshold is a function of size with larger diameter droplets requiring less ultrasound output to vaporize. PFH, PFMP, and PFP droplets remained stable after 16 weeks in 4°C and 23°C environments, but PFMP and PFP evaporated entirely in a 40°C oven after 12 weeks.
  • The Functional Role of the N2B Region Within the Elastic Sarcomeric Protein Titin

    Granzier, Henk; Nedrud, Joshua James; (The University of Arizona., 2011)
    Utilizing a N2B knockout (KO) mouse model in which the exon that encodes the cardiac-specific N2B unique sequence (N2B-Us) spring element (exon 49) has been deleted, I investigated the mechanical role of the N2B-Us, one of the three extensible regions of cardiac titin. I was able to show that the extensibility provided by the N2B-Us limits energy loss during stretch and shortening cycles of the heart (i.e., during diastole and systole). In a range of conditions, KO mice showed significant increases in hysteresis, a measure of energy loss determined from the area between the stretch and release force-sarcomere length curves, over wild type (WT) mice. Most prominently, hysteresis increased significantly from 320±46 pJ/mm2 /sarcomere in WT tissue to 650±94 pJ/mm2 /sarcomere in KO tissue that had been preconditioned with a physiological stretch-release protocol (p < 0.005). To complement this KO model, oxidative stress was used to mechanically inactivate portions of the N2B-Us of WT titin through cysteine crosslinking. This inactivation displayed a greater increase in hysteresis response in WT compared to KO tissue, (32.3±5% vs. 12.9±2.2%, p-value < 0.05). The results of this study support the concept that the mechanical function of the N2B-Us of titin is to reduce hysteresis and increase the efficiency of the cardiac cycle.
  • Rapid Detection of Malaria Antigen in Human Whole Blood using a Handheld Lab-On-Chip Device

    Yoon, Jeong-Yeol; Stemple, Charles Christopher; (The University of Arizona., 2011)
    Malaria is a human infectious disease that affects around 250 million people each year. Primarily found in regions of Africa, Asia, and South America, malaria is typically caused by the protozoa Plasmodium falciparum, and results in symptoms ranging from high fever to death. The most common detection methods currently consist of ELISA, PCR, and blood film smears; however, each of these methods requires a full laboratory environment for proper utilization, with assay times ranging from 2-8 hours. In this study, a novel handheld detection device based on the properties of immunoagglutination will be modified to detect malaria in human whole blood through histidine-rich protein 2 (HRP-2), an antigen expressed only by P. falciparum. HRP-2 antibodies are covalently attached to 920 ?m carboxylated polystyrene nanoparticles, which are mixed with the target human whole blood in a lab-on-chip testing environment. Using a 640 nm LED and avalanche photodiode pair, the sample is illuminated and forward light scatter caused by immunoagglutination of the HRP-2 antigen to the antibodies present on the nanoparticles is measured. The final device is compact, battery powered, low-cost, and capable of detecting HRP-2 antigens in human whole blood with a detection limit of 1 pg/ml and an assay time of approximately 8 minutes. The device represents a significant improvement in assay time over current malaria detection methods at a relatively low cost.
  • Adhesion of Myoblasts to RGD-Alginate

    Calvert, Paul; Tanooryan, Mansooreh; (The University of Arizona., 2003)
    Several types of alginate have been developed, but none of them alone are able to interact with mammalian cells. Alginate does not provide anchorage points that are essential for cell growth and proliferation. As this hydrogel meets many requirements for tissue engineering, modification of alginate was proposed in order to stimulate cell adhesion. After recognition of RGD binding site in ECM proteins, synthetic RGD peptides were coupled with alginate via aqueous carbodiimide chemistry. I applied this conjugation and optimized it in terms of various parameters of the coupling reaction. Mouse skeletal Myoblasts were cultured on the surface of the modified alginate. They were attached, spread and differentiated to form myotubes. This showed that an RGD containing peptide has the ability to mimic ECM molecule binding sites and stimulate adhesion to materials that are otherwise unable to interact with cells. I also demonstrated that RGD density enhanced proliferation and spreading. Increasing crosslinker density made stiffer gels and controlled cell differentiation. Including free Ca2+ improved swelling properties of alginate gel, enforced cell attachment and enhanced conversion of myoblasts to myotubes.
  • Sub-Cytotoxic Nanoparticle Exposure to Airway Epithelial Cells Causes Alterations in Cellular Signaling

    Boitano, Scott; McCorkel, Mia; Sierra-Alvarez, Reyes; Pagel, Marty; Lynch, Ron (The University of Arizona., 2011)
    There are strong correlations between ultrafine particle deposition in the lung and chronic respiratory illness. The growing prevalence of engineered nanoparticles (ENPs) in society presents a new lung toxicant exposure that has the potential to cause adverse affects in the lung, and specifically, on lung innate immune function. We examined the cytotoxicity of hafnium oxide (HfO2), cerium oxide (CeO2), and silicon oxide (SiO2) ENPs, and their micron-sized equivalents, to cultured human airway epithelial cells (16HBE14o-) in terms of cell death and reduction in paracrine ATP signaling as a measure of one aspect of innate immune function in lung epithelium. We used high-throughput real time cell analysis (RTCA) assays and fluorescent-based Live/Dead assays to evaluate cell death to establish cytotoxic levels of ENPs to airway epithelium. We used RTCA with digital imaging video microscopy to evaluate changes in ATP-induced cell signaling following exposure to low, non-cytotoxic doses of ENPs (10 - 50 mg/L). ENP induced cytotoxicity occurred only at high exposures, whereas acute (24 hr) incubations with ENPs resulted in altered ATP-induced cellular signaling at low doses of ENPs. We conclude that sub-cytotoxic exposures to ENPs can alter a basic innate immune function in lung epithelial cells that could contribute to respiratory disease. Such measurements of toxicity may be better indicators of potential health hazards of ENPs than simple cell death assays.
  • Synthesis of Upconverting Nanoparticles for Temperature Sensing Applications

    Romanowski, Marek; Joshua, Gihan Sumith; Pagel, Marty; Matsunaga, Terry; Yoon, Jeong-Jeol (The University of Arizona., 2012)
    Lanthanide-doped nanoparticles have been increasingly gaining attention as possible contrast agents due to their unique upconversion luminescence properties. The luminescence of certain emission bands from NaYF4 :Er3+/Yb3+ nanoparticles are also temperature dependent, and can be used as a ratiometric temperature sensor by monitoring the green-to-red emission ratio. The objective of this study was to reproducibly synthesize NaYF4:Er3 +/Yb3+ nanoparticles, use them to create a thin film on a glass surface, and visualize temperature changes on this coated surface. Nanoparticles were prepared via thermal decomposition at 300° C, underwent an acid treatment process to remove the oleate ligands from their surfaces, and were introduced to glass slides that had been functionalized with carboxyl groups. The temperature of the coated glass slide was varied, and images taken using a CCD camera were used to construct the green-tared emission ratio, which showed a linear trend with respect to increasing temperature.
  • Utilizing Micro Computed Tomography Data to Produce Implantable Scaffolds for Orthopedic Tissue Engineering

    Szivek, John; Tellis, Brandi Charmaine; Szivek, John; Geest, Jonathan; Trouard, Ted (The University of Arizona., 2006)
    Tissue engineering requires a three dimensional porous matrix that provides mechanical support and a template for new tissue growth, as well as allowing vascularization for nutrient delivery and waste product removal. Multiple methods exist for producing porous tissue engineering scaffolds from biocompatible materials. The combination of high resolution imaging systems and rapid prototyping techniques, however, has opened the door to producing scaffolds whose pore structures can match that of the tissue being repaired. A micro computed tomography scanner was used to scan trabecular bone samples from adult male canines, producing three dimensional bone models. These data sets were exported to a computer aided drawing program, where further customization of the data was performed. Additional features were added to the trabecular bone-like pore structure to allow the attachment of strain gauges to the scaffold, as well as achieve an anatomical fit with the intended surgical implant site. The customized scaffolds, made of polybutylene terephthalate (PBT), were produced using a fused deposition modeler. Morphological analysis, mechanical testing and degradation studies were performed to compare the trabecular-like scaffolds, to those with conventionally-designed pore structures. Morphological analysis revealed that the trabecular-like scaffolds matched the bone samples from which they were made in porosity only, requiring an improvement in modeler resolution to better match bone properties such as connectivity density and trabecular number. Mechanical testing showed that the trabecular-like scaffolds and simple pore structured scaffolds possessed a compressive stiffness within the range reported for human trabecular bone, with the trabecular-like scaffolds having a greater compressive stiffness than the complex pore structured scaffolds originally produced to duplicate trabecular bone. Degradation studies show that the mechanical properties and morphology of porous scaffolds made of PBT remained constant after three months soaking in a 37°C saline solution.
  • Recombinant Microtubule End-Capping Proteins as Inorganic Surface Ligands

    Deymier, Pierre; Martin, Greg; (The University of Arizona., 2007)
    Microtubules are being investigated as organic templates for nanowire fabrication. Targeted immobilization of the plus and minus ends of the microtubule can be achieved using recombinant end tracking microtubule proteins. This work examines the effects of five recombinant microtubule proteins on microtubule polymerization to determine their usefulness as inorganic surface ligands. GST-GAMMAtubulin was found to retain its microtubule nucleating capacity and anchor microtubules to an inorganic surface. GST-CLIP-170-H2, HISCLIP- 170-H2, GST-P150glued, and GST-EBl were all found to retain their microtubule binding capacity. GST-P150glued and GST-EBl were used to immobilize microtubules to inorganic surfaces. Their activity was enhanced by the presence of the H2 fragments.
  • Bacteria-Based Molecular Assay Detection System (B-Mad)

    Hoying,Jay; Dion, Greg; (The University of Arizona., 2005)
    Bacteria possess natural mechanisms allowing them to adapt to the environment and communicate with each other, processing large amounts of information in parallel. Cyanobacteria survive in a variety of environments and respond to light. Vibrio harveyi, a marine bacteria, and Pseudomonas aureofaciens, a wheat bacteria, communicate using small molecules; V. harveyi bioluminesces in response to an inter-species signaling molecule, while P. aureofaciens produces phenazine in response to its intra-species signaling molecule. These inherent signaling mechanisms can be engineered to create rapid, specific, modular Bacteria-Based Molecular Assay Detection (B-MAD) systems. ABMAD system designed to detect the human pathogen Clostridium perfringens serves as proof of concept for completely biological information processing units. The B-MAD system consists of three engineered cyanobacteria cells used in combination to detect Clostridium perfringens, a causative agent in gas gangrene, food poisoning and antibioticassociated diarrhea. The B-MAD system is activated by blue/UV-A light and responds to AI-2, a small molecule produced by C. perfringens and perfringolysin 0, a C. perfringens pore-forming toxin. It is possible, using the yellow fluorescence and bioluminescence outputs from the B-MAD system, to unambiguously detect C. perfringens. The design of the B-MAD system as well as the fabrication of components for the Blue Light Converter are reported.
  • Optical Studies of Collagen Crosslinking, Angiogenesis and Matrix Metalloproteinases

    Brands, William Rudy; (The University of Arizona., 2007)
    A blood circulatory system (vasculature) is an essential structure in multicellular organisms for distribution of oxygen and nutrients. Angiogenesis, the formation and growth of new blood vessel sprouts from existing vessels, is the process by which additional vascular elements are formed from an initial vascular structure. During angiogenesis, endothelial cells are stimulated to exhibit migratory and proliferative phenotypes, leading to the formation of new vessel sprouts. Sprouting endothelial cells degrade their basement membrane by production of matrix metalloproteinases (MMPs ). In an effort to understand the role of certain MMPs during the sprouting process, the rat fat microvessel fragment 3D model of angiogenesis was used to immunostain for the presence ofMMP-2, MMP-9 and MTl-MMP at several stages of the sprouting process.
  • Restoration of Finger Movement using Functional Electrical Stimulation and Bayes' Theorem

    Fuglevand, Andrew; Seifert, Heather; (The University of Arizona., 2001)
    Various computational approaches have been applied to predict aspects of animal behavior from the recorded activity of populations of neurons. Here we invert this process to predict the requisite neuromuscular activity associated with specified motor behaviors. A probabilistic method based on Bayes' theorem was used to predict the patterns of muscular activity needed to produce various types of desired finger movements. The profiles of predicted activity were then used to drive frequencymodulated muscle stimulators in order to evoke multi-joint finger movements. Comparison of movements generated by electrical stimulation to desired movements yielded root mean squared errors between -18 - 26%. This reasonable correspondence between desired and evoked movements suggests that this approach might serve as a useful strategy to control neuroprosthetic systems that aim to restore movement to paralyzed individuals.

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