Matching Items (86)
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Description
Despite the prevalence of coyotes (Canis latrans) little is known about the viruses associated with this species. To assess the extent of viral research that has been conducted on coyotes, a literature review was performed. Over the last six decades, there have been many viruses that have been identified infecting

Despite the prevalence of coyotes (Canis latrans) little is known about the viruses associated with this species. To assess the extent of viral research that has been conducted on coyotes, a literature review was performed. Over the last six decades, there have been many viruses that have been identified infecting coyotes. The pathology of some cases implies that infection is rare and lethal while others have been demonstrated to be endemic to coyotes. In addition, the majority of the prior analyses were done through serological assays that were limited to investigating target viruses. To help expand what is known about coyote-virus dynamics, viral assays were conducted on coyote scat. The samples were collected as part of transects established along the Salt River near Phoenix, Arizona, United States (USA). The recovered viral genomes were clustered with other deoxynucleic acid (DNA) viruses and analyzed to determine phylogeny and genetic identity. From the recovered viral genomes, there are two novel circoviruses, one novel naryavirus, five unclassified cressdnaviruses, and two previously identified species of anelloviruses from the Wawtorquevirus genus. For these viruses, new phylogenies for their groups and pairwise identity plots have been generated. These figures give insight into the potential hosts and the evolutionary history. In the case of the anelloviruses, they likely derived from a wood rat (Neotoma) host, given the anellovirus family’s host specificity and its similarity to another viral genome derived from a wood rat in Arizona, USA. Of the recovered circovirus genomes, one is associated with a viral isolate collected from a dust sample in Arizona, USA. The second circovirus species identified is within a clade that consists of rodent associated circoviruses and canine circovirus. Other recovered genomes expand clusters of unclassified cressdnaviruses. The recovered genomes support further genomic analysis. These findings help support the notion that there is a wealth of viral information to be identified from animals like coyotes. By understanding the viruses that coyotes are associated with, it is possible to better understand the viral impact on the urban environment, domesticated animals, and wildlife in general.
ContributorsHess, Savage Cree (Author) / Varsani, Arvind (Thesis advisor) / Kraberger, Simona (Committee member) / Upham, Nathan S (Committee member) / Arizona State University (Publisher)
Created2023
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Description
Alpha herpesviruses are a family of neuroinvasive viruses that infect multiplevertebrate species. Alpha herpesviruses are responsible for human and livestock infections, most notably Herpes Simplex Virus (HSV), Varicella Zoster virus (VZV), and Pseudorabies Virus (PRV). PRV is a potent swine virus that can infect other mammals, and results in lethal

Alpha herpesviruses are a family of neuroinvasive viruses that infect multiplevertebrate species. Alpha herpesviruses are responsible for human and livestock infections, most notably Herpes Simplex Virus (HSV), Varicella Zoster virus (VZV), and Pseudorabies Virus (PRV). PRV is a potent swine virus that can infect other mammals, and results in lethal encephalitis that can be devastating to livestock and of great financial expense to farmers. HSV, types 1 and 2, and VZV are widespread throughout the global human population, with estimates of the HSV-1 burden at about 60% of people worldwide. The hallmark of alpha herpesvirus infection is a persistent, lifelong infection that can reactivate throughout the lifespan of the host. Currently, the precise mechanisms of how these viruses undergo intracellular trafficking to emerge from the infected cell in epithelial tissues is not well understood. Many insights have been made with PRV in animal neurons, both in culture systems and animal models, about the viral genes and host factors involved in these processes. However, understanding of these mechanisms, and the interplay between viral and host proteins, in the human pathogen HSV-1 is even more lacking. Using recombinant fluorescent virus strains of HSV-1 and Total Internal Reflection Microscopy to image the transport of mature viral progeny in epithelial cells, it was determined that the egress of HSV-1 uses constitutive cellular secretory pathways. Specifically, the viral progeny traffic from the trans-Golgi network to the site of exocytosis at the plasma membrane via Rab6a secretory vesicles. This work will contribute to the understanding of how alpha herpesviruses complete their lifecycles in host cells, particularly at the sites where infection initially occurs and can spread to a new organism. Knowledge of these processes may lead to the development of therapeutics or prophylactics to reduce the burden of these viruses.
ContributorsBergeman, Melissa Hope (Author) / Hogue, Ian B (Thesis advisor) / Hogue, Brenda (Committee member) / Roberson, Robert (Committee member) / Varsani, Arvind (Committee member) / Arizona State University (Publisher)
Created2023
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DescriptionA
ContributorsLund, Michael (Author) / Varsani, Arvind (Thesis advisor) / Upham, Nathan (Committee member) / Harris, Robin (Committee member) / Arizona State University (Publisher)
Created2023
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Description
The human gut microbiome is associated with health outcomes including gastrointestinal and metabolic health, autoimmune disease and cancer. However, the role of the microbiome in many disease processes, including in the preterm gastrointestinal tract and female genital tract, has yet to be defined. Further, the diverse community of viruses within

The human gut microbiome is associated with health outcomes including gastrointestinal and metabolic health, autoimmune disease and cancer. However, the role of the microbiome in many disease processes, including in the preterm gastrointestinal tract and female genital tract, has yet to be defined. Further, the diverse community of viruses within the microbiome (the virome) is understudied compared to bacteria. Here, I examine the microbiome and virome in specific disease models that are poorly understood: necrotizing enterocolitis (NEC), discordant HIV shedding in women living with HIV (WHLIV), female genital tract inflammation and gammaherpesvirus infection. Specifically, I examined the gut virome longitudinally in a cohort of preterm infants at risk for NEC; the female genital tract (FGT) microbiome and virome longitudinally in a cohort of WLHIV from Lima, Peru; the FGT virome in women from Phoenix, Arizona with differing levels of genital inflammation and different microbiome compositions; and the gut microbiome in murine gammaherpesvirus 68 (MHV68) infection. Further, I contributed to research responding to the spread of SARS-CoV-2 in Arizona. I found that 1) gut virome beta diversity decreased before NEC onset in preterm infants, suggesting a role for the virome in NEC; 2) FGT microbiome instability was associated with discordant HIV shedding, while FGT virome composition changed in association with ART duration and immune recovery; 3) FGT virome composition was associated with inflammation and microbiome composition; and 4) MHV68 infection outcomes were independent of microbiome perturbation, which may reflect environmental influences. The results of this research advance understanding of the microbiome and virome in these specific disease processes, and support further investigation of the microbiome and virome in preterm infant gastrointestinal health and FGT health, as well as environmental effects in microbiome research.
ContributorsKaelin, Emily (Author) / Lim, Efrem (Thesis advisor) / Varsani, Arvind (Committee member) / Jacobs, Bertram (Committee member) / McFadden, Grant (Committee member) / Rahman, Masmudur (Committee member) / Arizona State University (Publisher)
Created2024
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Description
Microplastics, plastics smaller than 5 mm, are an emerging concern worldwide due to their potential adverse effects on the environment and human health. Microplastics have the potential to biomagnify through the food chain, and are prone to adsorbing organic pollutants and heavy metals. Therefore, there is an urgent need to

Microplastics, plastics smaller than 5 mm, are an emerging concern worldwide due to their potential adverse effects on the environment and human health. Microplastics have the potential to biomagnify through the food chain, and are prone to adsorbing organic pollutants and heavy metals. Therefore, there is an urgent need to assess the extent of microplastic contamination in different environments. The occurrence of microplastics in the atmosphere of Tempe, AZ was investigated and results show concentrations as high as 1.1 microplastics/m3. The most abundant identified polymer was polyvinyl chloride. However, chemical characterization is fraught with challenges, with a majority of microplastics remaining chemically unidentified. Laboratory experiments simulating weathering of microplastics revealed that Raman spectra of microplastics change over time due to weathering processes. This work also studied the spatial variation of microplastics in soil in Phoenix and the surrounding areas of the Sonoran Desert, and microplastic abundances ranged from 122 to 1299 microplastics/kg with no clear trends between different locations, and substantial total deposition of microplastics occurring in the same location with resuspension and redistribution of deposited microplastics likely contributing to unclear spatial trends. Temporal variation of soil microplastics from 2005 to 2015 show a systematic increase in the abundance of microplastics. Polyethylene was prominent in all soil samples. Further, recreational surface waters were investigated as a potential source of microplastics in aquatic environments. The temporal variation of microplastics in the Salt River, AZ over the course of one day depicted an increase of 8 times in microplastic concentration at peak activity time of 16:00 hr compared to 8:00 hr. Concurrently, microplastic concentrations in surface water samples from apartment community swimming pools in Tempe, AZ depicted substantial variability with concentrations as high as 254,574 MPs/m3. Polyester and Polyamide fibers were prevalent in surface water samples, indicating a release from synthetic fabrics. Finally, a method for distinguishing tire wear microplastics from soot in ambient aerosol samples was developed using Programmed Thermal Analysis, that allows for the quantification of Elemental Carbon. The method was successfully applied on urban aerosol samples with results depicting substantial fractions of tire wear in urban atmospheric environments.
ContributorsChandrakanthan, Kanchana (Author) / Herckes, Pierre (Thesis advisor) / Fraser, Matthew (Committee member) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2024
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Description
Atmospheric particulate matter (PM) has a pronounced effect on our climate, and exposure to PM causes negative health outcomes and elevated mortality rates in urban populations. Reactions that occur in fog can form new secondary organic aerosol material from gas-phase species or primary organic aerosols. It is important to understand

Atmospheric particulate matter (PM) has a pronounced effect on our climate, and exposure to PM causes negative health outcomes and elevated mortality rates in urban populations. Reactions that occur in fog can form new secondary organic aerosol material from gas-phase species or primary organic aerosols. It is important to understand these reactions, as well as how organic material is scavenged and deposited, so that climate and health effects can be fully assessed. Stable carbon isotopes have been used widely in studying gas- and particle-phase atmospheric chemistry. However, the processing of organic matter by fog has not yet been studied, even though stable isotopes can be used to track all aspects of atmospheric processing, from particle formation, particle scavenging, reactions that form secondary organic aerosol material, and particle deposition. Here, carbon isotope analysis is used for the first time to assess the processing of carbonaceous particles by fog.

This work first compares carbon isotope measurements (δ13C) of particulate matter and fog from locations across the globe to assess how different primary aerosol sources are reflected in the atmosphere. Three field campaigns are then discussed that highlight different aspects of PM formation, composition, and processing. In Tempe, AZ, seasonal and size-dependent differences in the δ13C of total carbon and n-alkanes in PM were studied. δ13C was influenced by seasonal trends, including inversion, transport, population density, and photochemical activity. Variations in δ13C among particle size fractions were caused by sources that generate particles in different size modes.

An analysis of PM from urban and suburban sites in northeastern France shows how both fog and rain can cause measurable changes in the δ13C of PM. The δ13C of PM was consistent over time when no weather events occurred, but particles were isotopically depleted by up to 1.1‰ in the presence of fog due to preferential scavenging of larger isotopically enriched particles. Finally, the δ13C of the dissolved organic carbon in fog collected on the coast of Southern California is discussed. Here, temporal depletion of the δ13C of fog by up to 1.2‰ demonstrates its use in observing the scavenging and deposition of organic PM.
ContributorsNapolitano, Denise (Author) / Herckes, Pierre (Thesis advisor) / Fraser, Matthew (Committee member) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2018
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Description
Arachnids belong to the phylum Arthropoda, the largest phylum in the animal kingdom. Ticks are blood-feeding arachnids that vector numerous pathogens of significant medical and veterinary importance, while scorpions have become a common concern in urban desert cities due to the high level of toxicity in their venom. To date,

Arachnids belong to the phylum Arthropoda, the largest phylum in the animal kingdom. Ticks are blood-feeding arachnids that vector numerous pathogens of significant medical and veterinary importance, while scorpions have become a common concern in urban desert cities due to the high level of toxicity in their venom. To date, viruses associated with arachnids have been under sampled and understudied. Here viral metagenomics was used to explore the diversity of viruses present in ticks and scorpions. American dog ticks (Dermacentor variabilis) and blacklegged ticks (Ixodes scapularis) were collected in Pennsylvania while one hairy scorpion (Hadrurus arizonensis) and four bark scorpions (Centruroides sculpturatus) were collected in Phoenix. Novel viral genomes described here belong to the families Polyomaviridae, Anelloviridae, Genomoviridae, and a newly proposed family, Arthropolviridae.

Polyomaviruses are non-enveloped viruses with a small, circular double-stranded DNA (dsDNA) genomes that have been identified in a variety of mammals, birds and fish and are known to cause various diseases. Arthropolviridae is a proposed family of circular, large tumor antigen encoding dsDNA viruses that have a unidirectional genome organization. Genomoviruses and anelloviruses are ssDNA viruses that have circular genomes ranging in size from 2–2.4 kb and 2.1–3.8 kb, respectively. Genomoviruses are ubiquitous in the environment, having been identified in a wide range of animal, plant and environmental samples, while anelloviruses have been associated with a plethora of animals.

Here, 16 novel viruses are reported that span four viral families. Eight novel polyomaviruses were recovered from bark scorpions, three arthropolviruses were recovered from dog ticks and one arthropolvirus from a hairy scorpion. Viruses belonging to the families Polyomaviridae and Arthropolviridae are highly divergent. This is the first more extensive study of these viruses in arachnids. Three genomoviruses were recovered from both dog and deer ticks and one anellovirus was recovered from deer ticks, which are the first records of these viruses being recovered from ticks. This work highlights the diversity of dsDNA and ssDNA viruses in the arachnid population and emphasizes the importance of performing viral surveys on these populations.
ContributorsSchmidlin, Kara (Author) / Varsani, Arvind (Thesis advisor) / Van Doorslaer, Koenraad (Committee member) / Stenglein, Mark (Committee member) / Arizona State University (Publisher)
Created2019
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Description
Chemical and physical interactions of flowing ice and rock have inexorably shaped planetary surfaces. Weathering in glacial environments is a significant link in biogeochemical cycles – carbon and strontium – on Earth, and may have once played an important role in altering Mars’ surface. Despite growing recognition of the importance

Chemical and physical interactions of flowing ice and rock have inexorably shaped planetary surfaces. Weathering in glacial environments is a significant link in biogeochemical cycles – carbon and strontium – on Earth, and may have once played an important role in altering Mars’ surface. Despite growing recognition of the importance of low-temperature chemical weathering, these processes are still not well understood. Debris-coated glaciers are also present on Mars, emphasizing the need to study ice-related processes in the evolution of planetary surfaces. During Earth’s history, subglacial environments are thought to have sheltered communities of microorganisms from extreme climate variations. On Amazonian Mars, glaciers such as lobate debris aprons (LDA) could have hosted chemolithotrophic communities, making Mars’ present glaciers candidates for life preservation. This study characterizes glacial processes on both Earth and Mars.

Chemical weathering at Robertson Glacier, a small alpine glacier in the Canadian Rocky Mountains, is examined with a multidisciplinary approach. The relative proportions of differing dissolution reactions at various stages in the glacial system are empirically determined using aqueous geochemistry. Synthesis of laboratory and orbital thermal infrared spectroscopy allows identification of dissolution rinds on hand samples and characterization of carbonate dissolution signals at orbital scales, while chemical and morphological evidence for thin, discontinuous weathering rinds at microscales are evident from electron microscopy. Subglacial dissolution rates are found to outpace those of the proglacial till plain; biologically-mediated pyrite oxidation drives the bulk of this acidic weathering.

Second, the area-elevation relationship, or hypsometry, of LDA in the midlatitudes of Mars is characterized. These glaciers are believed to have formed ~500 Ma during a climate excursion. Hypsometric measurements of these debris-covered glaciers enable insight into past flow regimes and drive predictions about past climate scenarios. The LDA in this study fall into three major groups, strongly dependent on basal elevation, implying regional and climatic controls on ice formation and flow.

I show that biologically-mediated mineral reactions drive high subglacial dissolution rates, such that variations within the valley can be detected with remote sensing techniques. In future work, these insights can be applied to examining Mars’ glacial regions for signs of chemical alteration and biosignatures.
ContributorsRutledge, Alicia Marie (Author) / Christensen, Philip R. (Thesis advisor) / Shock, Everett (Committee member) / Clarke, Amanda (Committee member) / Sharp, Thomas (Committee member) / Whipple, Kelin (Committee member) / Arizona State University (Publisher)
Created2015
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Description
Natural variations in 238U/235U of marine carbonates might provide a useful way of constraining redox conditions of ancient environments. In order to evaluate the reliability of this proxy, we conducted aragonite and calcite coprecipitation experiments at pH ~7.5 and ~ 8.5 to study possible U isotope fractionation during incorporation into

Natural variations in 238U/235U of marine carbonates might provide a useful way of constraining redox conditions of ancient environments. In order to evaluate the reliability of this proxy, we conducted aragonite and calcite coprecipitation experiments at pH ~7.5 and ~ 8.5 to study possible U isotope fractionation during incorporation into these minerals.

Small but significant U isotope fractionation was observed in aragonite experiments at pH ~ 8.5, with heavier U in the solid phase. 238U/235U of dissolved U in these experiments can be fit by Rayleigh fractionation curves with fractionation factors of 1.00007+0.00002/-0.00003, 1.00005 ± 0.00001, and 1.00003 ± 0.00001. In contrast, no resolvable U isotope fractionation was observed in an aragonite experiment at pH ~7.5 or in calcite experiments at either pH. Equilibrium isotope fractionation among different aqueous U species is the most likely explanation for these findings. Certain charged U species are preferentially incorporated into calcium carbonate relative to the uncharged U species Ca2UO2(CO3)3(aq), which we hypothesize has a lighter equilibrium U isotope composition than most of the charged species. According to this hypothesis, the magnitude of U isotope fractionation should scale with the fraction of dissolved U that is present as Ca2UO2(CO3)3 (aq). This expectation is confirmed by equilibrium speciation modeling of our experiments. Theoretical calculation of the U isotope fractionation factors between different U species could further test this hypothesis and our proposed fractionation mechanism.

These findings suggest that U isotope variations in ancient carbonates could be controlled by changes in the aqueous speciation of seawater U, particularly changes in seawater pH, PCO2, [Ca], or [Mg] concentrations. In general, these effects are likely to be small (<0.13 ‰), but are nevertheless potentially significant because of the small natural range of variation of 238U/235U.
ContributorsChen, Xinming (Author) / Anbar, Ariel (Thesis advisor) / Herckes, Pierre (Committee member) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2015
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Description
The discovery and development of novel antibacterial agents is essential to address the rising health concern over antibiotic resistant bacteria. This research investigated the antibacterial activity of a natural clay deposit near Crater Lake, Oregon, that is effective at killing antibiotic resistant human pathogens. The primary rock types in the

The discovery and development of novel antibacterial agents is essential to address the rising health concern over antibiotic resistant bacteria. This research investigated the antibacterial activity of a natural clay deposit near Crater Lake, Oregon, that is effective at killing antibiotic resistant human pathogens. The primary rock types in the deposit are andesitic pyroclastic materials, which have been hydrothermally altered into argillic clay zones. High-sulfidation (acidic) alteration produced clay zones with elevated pyrite (18%), illite-smectite (I-S) (70% illite), elemental sulfur, kaolinite and carbonates. Low-sulfidation alteration at neutral pH generated clay zones with lower pyrite concentrations pyrite (4-6%), the mixed-layered I-S clay rectorite (R1, I-S) and quartz.

Antibacterial susceptibility testing reveals that hydrated clays containing pyrite and I-S are effective at killing (100%) of the model pathogens tested (E. coli and S. epidermidis) when pH (< 4.2) and Eh (> 450 mV) promote pyrite oxidation and mineral dissolution, releasing > 1 mM concentrations of Fe2+, Fe3+ and Al3+. However, certain oxidized clay zones containing no pyrite still inhibited bacterial growth. These clays buffered solutions to low pH (< 4.7) and oxidizing Eh (> 400 mV) conditions, releasing lower amounts (< 1 mM) of Fe and Al. The presence of carbonate in the clays eliminated antibacterial activity due to increases in pH, which lower pyrite oxidation and mineral dissolution rates.

The antibacterial mechanism of these natural clays was explored using metal toxicity and genetic assays, along with advanced bioimaging techniques. Antibacterial clays provide a continuous reservoir of Fe2+, Fe3+ and Al3+ that synergistically attack pathogens while generating hydrogen peroxide (H2O¬2). Results show that dissolved Fe2+ and Al3+ are adsorbed to bacterial envelopes, causing protein misfolding and oxidation in the outer membrane. Only Fe2+ is taken up by the cells, generating oxidative stress that damages DNA and proteins. Excess Fe2+ oxidizes inside the cell and precipitates Fe3+-oxides, marking the sites of hydroxyl radical (•OH) generation. Recognition of this novel geochemical antibacterial process should inform designs of new mineral based antibacterial agents and could provide a new economic industry for such clays.
ContributorsMorrison, Keith D (Author) / Williams, Lynda B (Thesis advisor) / Williams, Stanley N (Thesis advisor) / Misra, Rajeev (Committee member) / Shock, Everett (Committee member) / Anbar, Ariel (Committee member) / Arizona State University (Publisher)
Created2015