• Characterization of a Gene that Responds to Mitochondrial Retrograde Regulation in Arabidopsis thaliana

      Sepulveda, Jennifer; Rhoads, David M.; School of Plant Sciences (2011-11-04)
      The Rhoads Lab found an Arabidopsis gene (At5g40690) that encodes for a protein similar to yeast ATPase Assembly Proteins (AAPs), which is strongly increased in expression by MRR and during plant stresses such as pathogen attack. Characterization of At5g40690 will be performed by the analysis of knock out (KO) lines, constitutive expressor (CE) lines in comparison to wild-type using northern blots. If this gene is an AAP, then this will be the first AAP in plants to be extensively studied in relation to MRR and stress responses, and will provide researchers with a better understanding of MRR and define a new category of proteins involved in stress response. Findings will give a better understanding of heat stress in crops such as Zea mays.
    • Conserve to Enhance: An Innovative Mechanism for Environmental Benefits

      Choate, Brittany Lynn; Nadeau, Joanna; Rupprecht, Candice; Lien, Aaron; Megdal, Sharon B.; Water Resources Research Center (2011-11-04)
      Arizona’s riparian ecosystems have been susceptible to degradation because state water laws do not consider environmental water needs. This lack of legal authority has led to water being diverted away from desert waterways through surface water and groundwater withdrawals (Megdal et al. 2011). To help bring the environment to the table as a water using sector, the University of Arizona Water Resources Research Center (WRRC) has developed the Conserve to Enhance (C2E) program. C2E is an innovative water conservation mechanism that addresses ecological water needs by raising funds through individual donations for river and riparian enhancement projects. The C2E Program invites community members to implement water conservation methods, track their monthly water savings through a Water Conservation Calculator, and then donate those savings to a C2E fund. Tucson is home to the first C2E Pilot Program, which began January 2011 with 60 participants. The goal is to determine if a program like C2E would be successful at a larger, city-wide scale and if such a program is applicable for other water-scarce communities in the Southwest.
    • Database Forensics in the Service of Information Accountability

      Snodgrass, Richard; Pavlou, Kyriacos; Department of Computer Science (2011-11-04)
      Regulations and societal expectations have recently expressed the need to mediate access to valuable databases, even by insiders. At one end of the spectrum is the approach of restricting access to information and on the other that of information accountability. The focus of the proposed work is effecting information accountability of data stored in databases. One way to ensure appropriate use and thus end-to-end accountability of such information is tamper detection in databases via a continuous assurance technology based on cryptographic hashing. In our current research we are working to show how to develop the necessary approaches and ideas to support accountability in high performance databases. This will include the design of a reference architecture for information accountability and several of its variants, the development of forensic analysis algorithms and their cost model, and a systematic formulation of forensic analysis for determining when the tampering occurred and what data were tampered with. Finally, for privacy, we would like to create mechanisms for allowing as well as (temporarily) preventing the physical deletion of records in a monitored database. In order to evaluate our ideas we will design and implement an integrated tamper detection and forensic analysis system. This work will show that information accountability is a viable alternative to information restriction for ensuring the correct storage, use, and maintenance of databases.
    • Deposition of CuInS₂ Absorber Layer for a Prototype Solar Cell

      Fang, Yizhou; Jiang, Feng; Muscat, Anthony J.; Chemical and Environmental Engineering (2011-11-04)
      A copper indium disulfide (CuInS₂ or CIS) film could potentially be used as the absorber layer in a solar cell that converts solar energy into electricity. CuInS₂ was chosen to lower the cost and environmental impact of manufacturing as an alternate to Si solar cells. The objective of this project is to deposit a uniform CuInS₂ film with a thickness of 2-3 μm. Both spin-coating and painting methods were compared. The substrate, oxidation method, and sulfurization temperature were varied and characterized.
    • Design and fabrication of a preclinical adaptive SPECT imaging system : AdaptiSPECT

      Chaix, Cécile; Kovalsky, Stephen; Kupinski, Matthew A.; Barrett, Harrison H.; Furenlid, Lars R.; College of Optical Sciences, University of Arizona; Center for GammaRay Imaging, Department of Medical Imaging, University of Arizona (2014-11-07)
    • Design and Synthesis of Triazabutadiene-based Fluorogenic Probe for Tyrosine-Specific Labeling of Proteins

      Shadmehr, Mehrdad; Jewett, John C.; Department of Chemistry and Biochemistry (2016-02-24)
    • Different Faces, Different Voices: A Film Analysis of Power Imbalance in Gender-Dominated Societies

      Diaz, Kassandra; Department of Physiology (2014-11-07)
      No amount research need be referenced to justify the consensus that a power differential exists among women and men. The outcome that this power differential has created, however, varies from one society to another. The role of women in male-dominated societies is deconstructed through two films, each situated in the drug trafficking industry—one set in Latin America and the other in the United States-Mexico border. While substantial literature explores the gender power differential in the United States and developing countries, little attention is given to the impact of gender participation in the developing world. Each of these countries has diverse expectations with gender politics; that is, some countries have women as leaders in suffrage reforms and corporations, while women in other countries are not even granted the right to divorce. This paper examines the relationship between gender participation of women and their defiance of the power differential as depicted in the Brazilian film City of God and the American film Traffic. While no evidence is independently presented that economic development provides a basis for equal participation, the most important factors such as gender violence and civil liberties provide a means of understanding the gender gap from a sociopolitical perspective.
    • Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival

      Schissler, Grant A.; Li, Qike; Gardeux, Vincent; Achour, Ikbel; Li, Haiquan; Piegorsch, Walter W.; Lussier, Yves A.; GIDP Statistics (2016-02-24)
      Motivation: The conventional approach to personalized medicine relies on molecular data analytics across multiple patients. The path to precision medicine lies with molecular data analytics that can discover interpretable single-subject signals (N-of-1). We developed a global framework, N-of-1-pathways, for a mechanistic-anchored approach to single-subject gene expression data analysis. We previously employed a metric that could prioritize the statistical significance of a deregulated pathway in single subjects, however, it lacked in quantitative interpretability (e.g. the equivalent to a gene expression fold-change). Results: In this study, we extend our previous approach with the application of statistical Mahalanobis distance (MD) to quantify personal pathway-level deregulation. We demonstrate that this approach, N-of-1-pathways Paired Samples MD (N-OF-1-PATHWAYS-MD), detects deregulated pathways (empirical simulations), while not inflating false-positive rate using a study with biological replicates. Finally, we establish that N-OF-1-PATHWAYS-MD scores are, biologically significant, clinically relevant and are predictive of breast cancer survival (P<0.05, n¼80 invasive car- cinoma; TCGA RNA-sequences). Conclusion: N-of-1-pathways MD provides a practical approach towards precision medicine. The method generates the magnitude and the biological significance of personal deregulated pathways results derived solely from the patient’s transcriptome. These pathways offer the opportunities for deriving clinically actionable decisions that have the potential to complement the clinical interpret- ability of personal polymorphisms obtained from DNA acquired or inherited polymorphisms and mutations. In addition, it offers an opportunity for applicability to diseases in which DNA changes may not be relevant, and thus expand the ‘interpretable ‘omics’ of single subjects (e.g. personalome).
    • Epigenetic loss of SLIT2 leads to an autocrine-to-paracrine switch of the SLIT2/ROBO1 signaling axis in pancreatic cancer

      Rheinheimer, Brenna; Vrba, Lukas; Futscher, Bernard; Heimark, Ronald; Cancer Biology Graduate Interdisciplinary Program; Arizona Cancer Center; Department of Pharmacology and Toxicology and Arizona Cancer Center; Department of Surgery and Arizona Cancer Center (2012-11-09)
      Guidance molecules from the Netrin, Slit, Ephrin, and Semaphorin gene families were originally described as cues for the directional guidance of axons in the developing nervous system. More recently, members of these families have been found to have critical roles in epithelial development, angiogenesis and cancer. The SLIT2/ROBO1 signaling axis has properties of a potential tumor suppressor pathway via the inhibition of epithelial cell growth, directional migration, ductal morphogenesis, and is epigenetically silenced in lung, colon and breast cancers. We proposed that changes in SLIT2 and ROBO1 expression in pancreatic ductal adenocarcinoma may mediate ductal expansion following the conversion of PanIN precursor lesions to invasive carcinoma. The SLIT2 receptor, ROBO1, is a member of the immunoglobulin (Ig) superfamily and is required for lung and mammary development in mammals. ROBO1 has an alternative splice variant, DUTT1, and these two variants have different initial exons and initiating codons which may suggest the two proteins have distinct functions. In our studies, we found that all pancreatic cancer cell lines and primary pancreatic cancer specimens express only the DUTT1 isoform. We also determined that as pancreatic cancer cell lines become KRAS-independent, ROBO1 expression increases. Furthermore, using immunohistochemistry (IHC), we found that ROBO1 protein expression in primary pancreatic cancer tissue specimens is localized to the ductal compartment with no stromal staining seen. In normal pancreas, ROBO1 expression is weak while its ligand SLIT2 is strongly expressed in both the acinar and ductal compartments in vitro and in vivo. Mammals encode three SLIT genes (SLIT1-3). The secreted SLIT2 protein is not diffusible, but has a cleavage site within its EGF-like repeats creating two fragments which allow it to act either as a short or long range guidance cue with each fragment appearing to have its own cell-association characteristics. The 5’ promoter of SLIT2 has been shown to be methylated resulting in gene silencing in early stages of several epithelial cancers suggesting a possible tumor suppressor role. miR-218-1 is an intronic microRNA found between exons 15 and 16 of the SLIT2 gene and targets a complimentary sequence in the ROBO1 3’ untranslated region (UTR) indicative of a potential regulation of receptor availability in the presence of ligand. In our studies, we determined that the KRAS-dependent pancreatic cancer cell lines express SLIT2 and ROBO1 in a cell autonomous manner. The KRAS-independent cell lines, however, have silenced SLIT2 and miR-218-1 expression. Using IHC we found that high levels of SLIT2 are seen in normal pancreas localized to the acinar and ductal compartments. Reduced SLIT2 expression is seen in primary pancreatic cancer tissue specimens. We confirmed that loss of SLIT2 mRNA in KRAS-independent lines was due to DNA hypermethylation shown by methylation specific PCR and Sequenom analysis. Chromatin immunoprecipitation analysis shows that silencing histone marks are found in the 5’ promoter of the SLIT2 gene in KRAS-independent lines. Treatment with demethylating agents reactivate SLIT2 and miR-218-1 expression suggesting that epigenetic mechanisms controlling the SLIT2 promoter also regulate miR-218-1 expression. Overall, our data establishes that the SLIT2/ROBO1 signaling axis is a dynamic pathway in pancreatic cancer that can act in the tumor expansion and progression along intrapancreatic neurons that express the SLIT2 ligand.
    • Evaluating Educational Programs for the Children of Seasonal Labor Migrants in India

      Reed, Megan; International Studies (2011-11-04)
      The research examines a government educational outreach initiative for the children of migrant brick kiln workers in Western India. Through interviews with government officials, parent and para-teacher surveys, and participant observation, the researcher was able to compare the pilot initiative in Bhilwara district, Rajasthan with one in Gandhinagar district, Gujarat. The research highlights some of the impediments faced with planning education for migrant children and provides recommendations for the future of the program in Rajasthan and Gujarat.
    • Exploring Holistic Approaches to the Characterization of Particles in the Environment

      Anhalt, Ashley; Peterson, Tawnya; Tratnyek, Paul; Needoba, Joseph; Mather, Amanda (2011-11-04)
      Most of the main determinants of water quality either consist of, or are controlled by, particles. Previous water quality research has focused on particular particles in isolation or in binary combinations. In this project, we are taking a holistic approach to the characterization of the particle load in water, focusing on the collective properties of the particles rather than individual components. Because the characterization of particles is often time-consuming, applying an informatics-based approach could speed up the evaluation of water quality and the assessment of treatment effectiveness. Further, the breadth of potential changes that could be detected using this multiplex approach may far surpass the abilities of current approaches to monitor threats to water quality. Among the instruments capable of rapidly detecting and manipulating cells is imaging flow cytometry, which distinguishes cell shape and unique fluorescence properties associated with cell types. Sets of images and corresponding data from a 1.5-year time series of samples from the Columbia River were studied and the different particle properties analyzed. Principal Component Analysis (Empirical Orthogonal Function analysis) was applied in order to reduce the number of variables and identify patterns in particle characteristics when compared to environmental data collected from the observation station. The first three principal components were extracted and the dominant characteristics identified: the most prominent variables are particle size, particle color, and fluorescent qualities (transparency and phytoplankton pigments). Further work will relate these top principal components to specific environmental factors that determine water quality.
    • Finding Family Health Solutions within the Bhutanese Refugee Community

      Demers, Deirdre; Heckert, Karen A.; Mel & Enid Zuckerman College of Public Health (2011-11-04)
    • The Influence of the Built Environment on the Use of Greenspace and Wellbeing

      Zuniga Teran, Adriana; Arid Lands Resource Sciences (2014-11-07)
    • Knowledge is Empowering Utilizing 21st Century Library Services to Build Annotated Bibliographic Databases that Connect Native American Communities with Environmental Health Information

      Ruddle, David (2013-11-08)
      Is it possible for a student to create an information resource that helps someone in need? In a two month span, the student author conducted research into the availability of environmental articles and collected over 250 academic papers and grey literature. Library tools and services provided by The University of Arizona Libraries on Southwestern Environmental and Health Issues specifically targeting Native American communities were used to near exclusivity. Locating articles for the database was done quicker than expected by a Library Science student (the author) who had some previous familiarity with academic databases such as PubMED™ and Web of Science™. The database itself was designed in Drupal as a Deep Web (not public) Internet project and completed before schedule. Over the course of this research it was discovered that by properly utilizing library resources its possible for motivated students at the collegiate level to create a database of articles that could aid underserved groups with their understanding of desired specialized issues.
    • Laced with Uncertainty: The Impact of Shoe Gear Fastening on Dorsal Shear Stress

      Owl, Joshua; Marin, Ivan; Enriquez, Ana; Armstrong, David; Najafi, Bijan (2016-02-24)
    • Lampung Language Revitalization Program Evaluation

      Putra, Kristian Adi; Second Language Acquisition and Teaching (SLAT) Graduate Interdisciplinary Program (2016-02-24)
      This project was aimed at evaluating the implementation of Lampung language revitalization program in educational settings in Indonesia. The result of this project was used as input for the improvement of the design of the program and for the formulation of language planning and policies that could effectively support the success of the program. Lampung language is an indigenous language primarily spoken in the Province of Lampung, Indonesia. The language has two dialects: Lampung Api and Lampung Nyo. In 2000, Lampung Api had 827,000 speakers, and Lampung Nyo had 180,000 speakers (Lewis, et.al, 2015). In spite of these figures, native Lampung ethnics under 20 years old commonly do not speak the language anymore both at home and outside, as they prefer speaking in Indonesian. Gunarwan (1994) even predicted that in 75 – 100 years, the language could be extinct. Since 1997, the language has been taught for 2 hours a week in grade 1 – 12. However, the result has never been evaluated, although the trend of diglossia remains strong and more massive. This study, then, tried to fill this gap.
    • Modeling Advanced Oxidation Processes for Water Treatment

      Anhalt, Ashley; Sáez, A. Eduardo; Arnold, Robert; Rojas, Mario; Department of Chemical and Environmental Engineering (2012-11-09)
      Civilization is dependent on wastewater treatment plants. However, many conventional wastewater treatment processes only partially remove trace organics that result from human use, such as pharmaceuticals and endocrine disrupters. Advanced oxidation process (AOP) can be used to remove chemicals that may remain in the treated wastewater. AOP is an enhanced alternative to the traditional water treatment processes because it turns water contaminants into carbon dioxide (CO2), as opposed to simply transporting the contaminants across the different treatment phases. In order to model this process, one proposed idea uses ultraviolet light and hydrogen peroxide to oxidize the unwanted organic compounds. Previous mathematical models have been developed to simulate the UV/H2O2 process, however, the model employed in this work has advanced beyond previous efforts. Our UV/H2O2 model aims to characterize the mechanism and kinetics behind the decomposition of nonylphenol (NP) and p-cresol (PC), two chemicals in wastewater that serve as surrogates for endocrine disrupters. The model demonstrates agreement between experimental results and AOP simulations accounting for light intensity, pH, hydrogen peroxide levels, and concentrations of other radical scavengers. Our goal is to improve an already robust UV/H2O2 AOP model by taking into account spatial variations of radical concentrations. Our results take into account time and space, and show significant improvement in the accuracy of the model. This broadens the applications of this model and consequently, the degradation of organic contaminants is predictable over a wide range of conditions. The potential for polishing conventionally treated wastewater is evident.
    • Modeling of nucleation rate of supersaturated calcium sulfate solutions

      Jonathas, David; Department of Chemical and Environmental Engineering (2012-11-09)
    • Modeling the Effect of Shocks and Stresses on the Reliability of Networks with Radial Topologies

      Mangal, Kunal; Larsen, Alexandra; Chryst, Breanne; Rojo, Javier; University of Arizona; Centenary College; University of Utah; Rice University (2011-11-04)
      We consider the impact that various shocks and stresses have on the reliability of networks with radial topology, such as an electrical power grid. We incorporate the effects of aging, geographical risk, and local dependence between components into a model of overall system reliability. We also simulate how the system fares under extreme weather events, such as hurricanes. Our model gives a flexible and general understanding of how outside forces affect network reliability and can be adapted to a range of specific uses. We run a simulation using this model which yields realistic results.