Matching Items (187)
Description
The North American Monsoon System (NAMS) contributes ~55% of the annual rainfall in the Chihuahuan Desert during the summer months. Relatively frequent, intense storms during the NAMS increase soil moisture, reduce surface temperature and lead to runoff in ephemeral channels. Quantifying these processes, however, is difficult due to the sparse nature of coordinated observations. In this study, I present results from a field network of rain gauges (n = 5), soil probes (n = 48), channel flumes (n = 4), and meteorological equipment in a small desert shrubland watershed (~0.05 km2) in the Jornada Experimental. Using this high-resolution network, I characterize the temporal and spatial variability of rainfall, soil conditions and channel runoff within the watershed from June 2010 to September 2011, covering two NAMS periods. In addition, CO2, water and energy measurements at an eddy covariance tower quantify seasonal, monthly and event-scale changes in land-atmosphere states and fluxes. Results from this study indicate a strong seasonality in water and energy fluxes, with a reduction in Bowen ratio (B, the ratio of sensible to latent heat fluxes) from winter (B = 14) to summer (B = 3.3). This reduction is tied to shallow soil moisture availability during the summer (s = 0.040 m3/m3) as compared to the winter (s = 0.004 m3/m3). During the NAMS, I analyzed four consecutive rainfall-runoff events to quantify the soil moisture and channel flow responses and how water availability impacted the land-atmosphere fluxes. Spatial hydrologic variations during events occur over distances as short as ~15 m. The field network also allowed comparisons of several approaches to estimate evapotranspiration (ET). I found a more accurate ET estimate (a reduction of mean absolute error by 38%) when using distributed soil moisture data, as compared to a standard water balance approach based on the tower site. In addition, use of spatially-varied soil moisture data yielded a more reasonable relationship between ET and soil moisture, an important parameterization in many hydrologic models. The analyses illustrates the value of high-resolution sampling for quantifying seasonal fluxes in desert shrublands and their improvements in closing the water balance in small watersheds.
ContributorsTempleton, Ryan (Author) / Vivoni, Enrique R (Thesis advisor) / Mays, Larry (Committee member) / Fox, Peter (Committee member) / Arizona State University (Publisher)
Created2011
Description
The concept of vaccination dates back further than Edward Jenner's first vaccine using cowpox pustules to confer immunity against smallpox in 1796. Nevertheless, it was Jenner's success that gave vaccines their name and made vaccinia virus (VACV) of particular interest. More than 200 years later there is still the need to understand vaccination from vaccine design to prediction of vaccine efficacy using mathematical models. Post-exposure vaccination with VACV has been suggested to be effective if administered within four days of smallpox exposure although this has not been definitively studied in humans. The first and second chapters analyze post-exposure prophylaxis of VACV in an animal model using v50ΔB13RMγ, a recombinant VACV expressing murine interferon gamma (IFN-γ) also known as type II IFN. While untreated animals infected with wild type VACV die by 10 days post-infection (dpi), animals treated with v50ΔB13RMγ 1 dpi had decreased morbidity and 100% survival. Despite these differences, the viral load was similar in both groups suggesting that v50ΔB13RMγ acts as an immunoregulator rather than as an antiviral. One of the main characteristics of VACV is its resistance to type I IFN, an effect primarily mediated by the E3L protein, which has a Z-DNA binding domain and a double-stranded RNA (dsRNA) binding domain. In the third chapter a VACV that independently expresses both domains of E3L was engineered and compared to wild type in cells in culture. The dual expression virus was unable to replicate in the JC murine cell line where both domains are needed together for replication. Moreover, phosphorylation of the dsRNA dependent protein kinase (PKR) was observed at late times post-infection which indicates that both domains need to be linked together in order to block the IFN response. Because smallpox has already been eradicated, the utility of mathematical modeling as a tool for predicting disease spread and vaccine efficacy was explored in the last chapter using dengue as a disease model. Current modeling approaches were reviewed and the 2000-2001 dengue outbreak in a Peruvian region was analyzed. This last section highlights the importance of interdisciplinary collaboration and how it benefits research on infectious diseases.
ContributorsHolechek, Susan A (Author) / Jacobs, Bertram L (Thesis advisor) / Castillo-Chavez, Carlos (Committee member) / Frasch, Wayne (Committee member) / Hogue, Brenda (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011
Description
HIV/AIDS is the sixth leading cause of death worldwide and the leading cause of death among women of reproductive age living in low-income countries. Clinicians in industrialized nations monitor the efficacy of antiretroviral drugs and HIV disease progression with the HIV-1 viral load assay, which measures the copy number of HIV-1 RNA in blood. However, viral load assays are not widely available in sub-Saharan Africa and cost between 50-$139 USD per test on average where available. To address this problem, a mixed-methods approach was undertaken to design a novel and inexpensive viral load diagnostic for HIV-1 and to evaluate barriers to its adoption in a developing country. The assay was produced based on loop-mediated isothermal amplification (LAMP). Blood samples from twenty-one individuals were spiked with varying concentrations of HIV-1 RNA to evaluate the sensitivity and specificity of LAMP. Under isothermal conditions, LAMP was performed with an initial reverse-transcription step (RT-LAMP) and primers designed for HIV-1 subtype C. Each reaction generated up to a few billion copies of target DNA within an hour. Presence of target was detected through naked-eye observation of a fluorescent indicator and verified by DNA gel electrophoresis and real-time fluorescence. The assay successfully detected the presence of HIV in samples with a broad range of HIV RNA concentration, from over 120,000 copies/reaction to 120 copies/reaction. In order to better understand barriers to adoption of LAMP in developing countries, a feasibility study was undertaken in Tanzania, a low-income country facing significant problems in healthcare. Medical professionals in Northern Tanzania were surveyed for feedback regarding perspectives of current HIV assays, patient treatment strategies, availability of treatment, treatment priorities, HIV transmission, and barriers to adoption of the HIV-1 LAMP assay. The majority of medical providers surveyed indicated that the proposed LAMP assay is too expensive for their patient populations. Significant gender differences were observed in response to some survey questions. Female medical providers were more likely to cite stigma as a source problem of the HIV epidemic than male medical providers while males were more likely to cite lack of education as a source problem than female medical providers.
ContributorsSalamone, Damien Thomas (Author) / Jacobs, Bertram L (Thesis advisor) / Marsiglia, Flavio (Committee member) / Stout, Valerie (Committee member) / Johnson, Crista (Committee member) / Arizona State University (Publisher)
Created2011
Description
Local municipalities in the Phoenix Metropolitan Area have voiced an interest in purchasing alternate source water with lower DBP precursors. Along the primary source is a hydroelectric dam in which water will be diverted from. This project is an assessment of optimizing the potential blends of source water to a water treatment plant in an effort to enable them to more readily meet DBP regulations. To perform this analysis existing water treatment models were used in conjunction with historic water quality sampling data to predict chemical usage necessary to meet DBP regulations. A retrospective analysis was performed for the summer months of 2007 regarding potential for the WTP to reduce cost through optimizing the source water by an average of 30% over the four-month period, accumulating to overall treatment savings of $154 per MG ($82 per AF).
ContributorsRice, Jacelyn (Author) / Westerhoff, Paul (Thesis advisor) / Fox, Peter (Committee member) / Hristovski, Kiril (Committee member) / Arizona State University (Publisher)
Created2011
Description
Overcrowding of Emergency Departments (EDs) put the safety of patients at risk. Decision makers implement Ambulance Diversion (AD) as a way to relieve congestion and ensure timely treatment delivery. However, ineffective design of AD policies reduces the accessibility to emergency care and adverse events may arise. The objective of this dissertation is to propose methods to design and analyze effective AD policies that consider performance measures that are related to patient safety. First, a simulation-based methodology is proposed to evaluate the mean performance and variability of single-factor AD policies in a single hospital environment considering the trade-off between average waiting time and percentage of time spent on diversion. Regression equations are proposed to obtain parameters of AD policies that yield desired performance level. The results suggest that policies based on the total number of patients waiting are more consistent and provide a high precision in predicting policy performance. Then, a Markov Decision Process model is proposed to obtain the optimal AD policy assuming that information to start treatment in a neighboring hospital is available. The model is designed to minimize the average tardiness per patient in the long run. Tardiness is defined as the time that patients have to wait beyond a safety time threshold to start receiving treatment. Theoretical and computational analyses show that there exists an optimal policy that is of threshold type, and diversion can be a good alternative to decrease tardiness when ambulance patients cause excessive congestion in the ED. Furthermore, implementation of AD policies in a simulation model that accounts for several relaxations of the assumptions suggests that the model provides consistent policies under multiple scenarios. Finally, a genetic algorithm is combined with simulation to design effective policies for multiple hospitals simultaneously. The model has the objective of minimizing the time that patients spend in non-value added activities, including transportation, waiting and boarding in the ED. Moreover, the AD policies are combined with simple ambulance destination policies to create ambulance flow control mechanisms. Results show that effective ambulance management can significantly reduce the time that patients have to wait to receive appropriate level of care.
ContributorsRamirez Nafarrate, Adrian (Author) / Fowler, John W. (Thesis advisor) / Wu, Teresa (Thesis advisor) / Gel, Esma S. (Committee member) / Limon, Jorge (Committee member) / Arizona State University (Publisher)
Created2011
Description
Rhodoferax antarcticus strain ANT.BR, a purple nonsulfur bacterium isolated from a microbial mat in Ross Island, Antarctica, is the first described anoxygenic phototrophic bacterium that is adapted to cold habitats and is the first beta-proteobacterium to undergo complete genome sequencing. R. antarcticus has unique absorption spectra and there are no obvious intracytoplasmic membranes in cells grown phototrophically, even under low light intensity. Analysis of the finished genome sequence reveals a single chromosome (3,809,266 bp) and a large plasmid (198,615 bp) that together harbor 4,262 putative genes. The genome contains two types of Rubiscos, Form IAq and Form II, which are known to exhibit quite different kinetic properties in other bacteria. The presence of multiple Rubisco forms could give R. antarcticus high metabolic flexibility in diverse environments. Annotation of the complete genome sequence along with previous experimental results predict the presence of structural genes for three types of light-harvesting (LH) complexes, LH I (B875), LH II (B800/850), and LH III (B800/820). There is evidence that expression of genes for the LH II complex might be inhibited when R. antarcticus is under low temperature and/or low light intensity. These interesting condition-dependent light-harvesting apparatuses and the control of their expression are very valuable for the further understanding of photosynthesis in cold environments. Finally, R. antarcticus exhibits a highly motile lifestyle. The genome content and organization of all putative polar flagella genes are characterized and discussed.
ContributorsZhao, Tingting, M.S (Author) / Touchman, Jeffrey (Thesis advisor) / Rosenberg, Michael (Committee member) / Redding, Kevin (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011
Analysis of photocatalysis for precursor removal and formation inhibition of disinfection byproducts
Description
Disinfection byproducts are the result of reactions between natural organic matter (NOM) and a disinfectant. The formation and speciation of DBP formation is largely dependent on the disinfectant used and the natural organic matter (NOM) concentration and composition. This study examined the use of photocatalysis with titanium dioxide for the oxidation and removal of DBP precursors (NOM) and the inhibition of DBP formation. Water sources were collected from various points in the treatment process, treated with photocatalysis, and chlorinated to analyze the implications on total trihalomethane (TTHM) and the five haloacetic acids (HAA5) formations. The three sub-objectives for this study included: the comparison of enhanced and standard coagulation to photocatalysis for the removal of DBP precursors; the analysis of photocatalysis and characterization of organic matter using size exclusion chromatography and fluorescence spectroscopy and excitation-emission matrices; and the analysis of photocatalysis before GAC filtration. There were consistencies in the trends for each objective including reduced DBP precursors, measured as dissolved organic carbon DOC concentration and UV absorbance at 254 nm. Both of these parameters decreased with increased photocatalytic treatment and could be due in part to the adsorption to as well as the oxidation of NOM on the TiO2 surface. This resulted in lower THM and HAA concentrations at Medium and High photocatalytic treatment levels. However, at No UV exposure and Low photocatalytic treatment levels where oxidation reactions were inherently incomplete, there was an increase in THM and HAA formation potential, in most cases being significantly greater than those found in the raw water or Control samples. The size exclusion chromatography (SEC) results suggest that photocatalysis preferentially degrades the higher molecular mass fraction of NOM releasing lower molecular mass (LMM) compounds that have not been completely oxidized. The molecular weight distributions could explain the THM and HAA formation potentials that decreased at the No UV exposure samples but increased at Low photocatalytic treatment levels. The use of photocatalysis before GAC adsorption appears to increase bed life of the contactors; however, higher photocatalytic treatment levels have been shown to completely mineralize NOM and would therefore not require additional GAC adsorption after photocatalysis.
ContributorsDaugherty, Erin (Author) / Abbaszadegan, Morteza (Thesis advisor) / Fox, Peter (Committee member) / Mayer, Brooke (Committee member) / Arizona State University (Publisher)
Created2011
Description
The oceans play an essential role in global biogeochemical cycles and in regulating climate. The biological carbon pump, the photosynthetic fixation of carbon dioxide by phytoplankton and subsequent sequestration of organic carbon into deep water, combined with the physical carbon pump, make the oceans the only long-term net sink for anthropogenic carbon dioxide. A full understanding of the workings of the biological carbon pump requires a knowledge of the role of different taxonomic groups of phytoplankton (protists and cyanobacteria) to organic carbon export. However, this has been difficult due to the degraded nature of particles sinking into particle traps, the main tools employed by oceanographers to collect sinking particulate matter in the ocean. In this study DNA-based molecular methods, including denaturing gradient gel electrophoresis, cloning and sequencing, and taxon-specific quantitative PCR, allowed for the first time for the identification of which protists and cyanobacteria contributed to the material collected by the traps in relation to their presence in the euphotic zone. I conducted this study at two time-series stations in the subtropical North Atlantic Ocean, one north of the Canary Islands, and one located south of Bermuda. The Bermuda study allowed me to investigate seasonal and interannual changes in the contribution of the plankton community to particle flux. I could also show that small unarmored taxa, including representatives of prasinophytes and cyanobacteria, constituted a significant fraction of sequences recovered from sediment trap material. Prasinophyte sequences alone could account for up to 13% of the clone library sequences of trap material during bloom periods. These observations contradict a long-standing paradigm in biological oceanography that only large taxa with mineral shells are capable of sinking while smaller, unarmored cells are recycled in the euphotic zone through the microbial loop. Climate change and a subsequent warming of the surface ocean may lead to a shift in the protist community toward smaller cell size in the future, but in light of these findings these changes may not necessarily lead to a reduction in the strength of the biological carbon pump.
ContributorsAmacher, Jessica (Author) / Neuer, Susanne (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Lomas, Michael (Committee member) / Wojciechowski, Martin (Committee member) / Stout, Valerie (Committee member) / Arizona State University (Publisher)
Created2011
Description
To address sustainability issues in wastewater treatment (WWT), Siemens Water Technologies (SWT) has designed a "hybrid" process that couples common activated sludge (AS) and anaerobic digestion (AD) technologies with the novel concepts of AD sludge recycle and biosorption. At least 85% of the hybrid's AD sludge is recycled to the AS process, providing additional sorbent for influent particulate chemical oxygen demand (PCOD) biosorption in contact tanks. Biosorbed PCOD is transported to the AD, where it is converted to methane. The aim of this study is to provide mass balance and microbial community analysis (MCA) of SWT's two hybrid and one conventional pilot plant trains and mathematical modeling of the hybrid process including a novel model of biosorption. A detailed mass balance was performed on each tank and the overall system. The mass balance data supports the hybrid process is more sustainable: It produces 1.5 to 5.5x more methane and 50 to 83% less sludge than the conventional train. The hybrid's superior performance is driven by 4 to 8 times longer solid retention times (SRTs) as compared to conventional trains. However, the conversion of influent COD to methane was low at 15 to 22%, and neither train exhibited significant nitrification or denitrification. Data were inconclusive as to the role of biosorption in the processes. MCA indicated the presence of Archaea and nitrifiers throughout both systems. However, it is inconclusive as to how active Archaea and nitrifiers are under anoxic, aerobic, and anaerobic conditions. Mathematical modeling confirms the hybrid process produces 4 to 20 times more methane and 20 to 83% less sludge than the conventional train under various operating conditions. Neither process removes more than 25% of the influent nitrogen or converts more that 13% to nitrogen gas due to biomass washout in the contact tank and short SRTs in the stabilization tank. In addition, a mathematical relationship was developed to describe PCOD biosorption through adsorption to biomass and floc entrapment. Ultimately, process performance is more heavily influenced by the higher AD SRTs attained when sludge is recycled through the system and less influenced by the inclusion of biosorption kinetics.
ContributorsYoung, Michelle Nichole (Author) / Rittmann, Bruce E. (Thesis advisor) / Fox, Peter (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2011
Description
Pathogenic Gram-negative bacteria employ a variety of molecular mechanisms to combat host defenses. Two-component regulatory systems (TCR systems) are the most ubiquitous signal transduction systems which regulate many genes required for virulence and survival of bacteria. In this study, I analyzed different TCR systems in two clinically-relevant Gram-negative bacteria, i.e., oral pathogen Porphyromonas gingivalis and enterobacterial Escherichia coli. P. gingivalis is a major causative agent of periodontal disease as well as systemic illnesses, like cardiovascular disease. A microarray study found that the putative PorY-PorX TCR system controls the secretion and maturation of virulence factors, as well as loci involved in the PorSS secretion system, which secretes proteinases, i.e., gingipains, responsible for periodontal disease. Proteomic analysis (SILAC) was used to improve the microarray data, reverse-transcription PCR to verify the proteomic data, and primer extension assay to determine the promoter regions of specific PorX regulated loci. I was able to characterize multiple genetic loci regulated by this TCR system, many of which play an essential role in hemagglutination and host-cell adhesion, and likely contribute to virulence in this bacterium. Enteric Gram-negative bacteria must withstand many host defenses such as digestive enzymes, low pH, and antimicrobial peptides (AMPs). The CpxR-CpxA TCR system of E. coli has been extensively characterized and shown to be required for protection against AMPs. Most recently, this TCR system has been shown to up-regulate the rfe-rff operon which encodes genes involved in the production of enterobacterial common antigen (ECA), and confers protection against a variety of AMPs. In this study, I utilized primer extension and DNase I footprinting to determine how CpxR regulates the ECA operon. My findings suggest that CpxR modulates transcription by directly binding to the rfe promoter. Multiple genetic and biochemical approaches were used to demonstrate that specific TCR systems contribute to regulation of virulence factors and resistance to host defenses in P. gingivalis and E. coli, respectively. Understanding these genetic circuits provides insight into strategies for pathogenesis and resistance to host defenses in Gram negative bacterial pathogens. Finally, these data provide compelling potential molecular targets for therapeutics to treat P. gingivalis and E. coli infections.
ContributorsLeonetti, Cori (Author) / Shi, Yixin (Thesis advisor) / Stout, Valerie (Committee member) / Nickerson, Cheryl (Committee member) / Sandrin, Todd (Committee member) / Arizona State University (Publisher)
Created2013