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- Genre: Masters Thesis
Description
Microbially induced calcium carbonate precipitation (MICP) is attracting increasing attention as a sustainable means of soil improvement. While there are several possible MICP mechanisms, microbial denitrification has the potential to become one of the preferred methods for MICP because complete denitrification does not produce toxic byproducts, readily occurs under anoxic conditions, and potentially has a greater carbonate yield per mole of organic electron donor than other MICP processes. Denitrification may be preferable to ureolytic hydrolysis, the MICP process explored most extensively to date, as the byproduct of denitrification is benign nitrogen gas, while the chemical pathways involved in hydrolytic ureolysis processes produce undesirable and potentially toxic byproducts such as ammonium (NH4+). This thesis focuses on bacterial denitrification and presents preliminary results of bench-scale laboratory experiments on denitrification as a candidate calcium carbonate precipitation mechanism. The bench-scale bioreactor and column tests, conducted using the facultative anaerobic bacterium Pseudomonas denitrificans, show that calcite can be precipitated from calcium-rich pore water using denitrification. Experiments also explore the potential for reducing environmental impacts and lowering costs associated with denitrification by reducing the total dissolved solids in the reactors and columns, optimizing the chemical matrix, and addressing the loss of free calcium in the form of calcium phosphate precipitate from the pore fluid. The potential for using MICP to sequester radionuclides and metal contaminants that are migrating in groundwater is also investigated. In the sequestration process, divalent cations and radionuclides are incorporated into the calcite structure via substitution, forming low-strontium calcium carbonate minerals that resist dissolution at a level similar to that of calcite. Work by others using the bacterium Sporosarcina pasteurii has suggested that in-situ sequestration of radionuclides and metal contaminants can be achieved through MICP via hydrolytic ureolysis. MICP through bacterial denitrification seems particularly promising as a means for sequestering radionuclides and metal contaminants in anoxic environments due to the anaerobic nature of the process and the ubiquity of denitrifying bacteria in the subsurface.
ContributorsHamdan, Nasser (Author) / Kavazanjian, Edward (Thesis advisor) / Rittmann, Bruce E. (Thesis advisor) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2013
Description
Dissolved inorganic carbon (DIC) and dissolved organic carbon (DOC) are crucial nutrients for autotrophic and heterotrophic microbial life, respectively, in hydrothermal systems. Biogeochemical processes that control amounts of DIC and DOC in Yellowstone hot springs can be investigated by measuring carbon abundances and respective isotopic values. A decade and a half of field work in 10 regions within Yellowstone National Park and subsequent geochemical lab analyses reveal that sulfate-dominant acidic regions have high DOC (Up to 57 ppm C) and lower DIC (up to 50 ppm C) compared to neutral-chloride regions with low DOC (< 2 ppm C) and higher DIC (up to 100 ppm C). Abundances and isotopic data suggest that sedimentary rock erosion by acidic hydrothermal fluids, fresh snow-derived meteoric water, and exogenous carbon input allowed by local topography may affect DOC levels. Evaluating the isotopic compositions of DIC and DOC in hydrothermal fluids gives insight on the geology and microbial life in the subsurface between different regions. DIC δ13C values range from -4‰ to +5‰ at pH 5-9 and from -10‰ to +3‰ at pH 2-5 with several springs lower than -10‰. DOC δ13C values parkwide range from -10‰ to -30‰. Within this range, neutral-chloride regions in the Lower Geyser Basin have lighter isotopes than sulfate-dominant acidic regions. In hot springs with elevated levels of DOC, the range only varies between -20‰ and -26‰ which may be caused by local exogenous organic matter runoff. Combining other geochemical measurements, such as differences in chloride and sulfate concentrations, demonstrates that some regions contain mixtures of multiple fluids moving through the complex hydrological system in the subsurface. The mixing of these fluids may account for increased levels of DOC in meteoric sulfate-dominant acidic regions. Ultimately, the foundational values of dissolved carbon and their isotopic composition is provided in a parkwide study, so results can be combined with future studies that apply different sequencing analyses to understand specific biogeochemical cycling and microbial communities that occur in individual hot springs.
ContributorsBarnes, Tanner (Author) / Shock, Everett (Thesis advisor) / Meyer-Dombard, D'Arcy (Committee member) / Hartnett, Hilairy (Committee member) / Arizona State University (Publisher)
Created2023
Description
Cocaine induces long-lasting changes in mesolimbic ‘reward’ circuits of the brain after cessation of use. These lingering changes include the neuronal plasticity that is thought to underlie the chronic relapsing nature of substance use disorders. Genes involved in neuronal plasticity also encode circular RNAs (circRNAs), which are stable, non-coding RNAs formed through the back-splicing of pre-mRNA. The Homer1 gene family, which encodes proteins associated with cocaine-induced plasticity, also encodes circHomer1. Based on preliminary evidence from shows cocaine-regulated changes in the ratio of circHomer1 and Homer1b mRNA in the nucleus accumbens (NAc), this study examined the relationship between circHomer1 and incentive motivation for cocaine by using different lengths of abstinence to vary the degree of motivation. Male and female rats were trained to self-administer cocaine (0.75 mg/kg/infusion, IV) or received a yoked saline infusion. Rats proceeded on an increasingly more difficult variable ratio schedule of lever pressing until they reached a variable ratio 5 schedule, which requires an average of 5 lever presses, and light and tone cues were delivered with the drug infusions. Rats were then tested for cocaine-seeking behavior in response to cue presentations without drug delivery either 1 or 21 days after their last self-administration session. They were sacrificed immediately after and circHomer1 and Homer1b expression was then measured from homogenate and synaptosomal fractions of NAc shell using RT-qPCR. Lever pressing during the cue reactivity test increased from 1 to 21 days of abstinence as expected. Results showed no group differences in synaptic circHomer1 expression, however, total circHomer1 expression was downregulated in 21d rats compared to controls. Lack of change in synaptic circHomer1 was likely due to trends toward different temporal changes in males versus females. Total Homer1b expression was higher in females, although there was no effect of cocaine abstinence. Further research investigating the time course of circHomer1 and Homer1b expression is warranted based on the inverse relationship between total circHomer1and cocaine-seeking behavior observed in this study.
ContributorsJohnson, Michael Christian (Author) / Neisewander, Janet L (Thesis advisor) / Perrone-Bizzozero, Nora (Thesis advisor) / Mangone, Marco (Committee member) / Arizona State University (Publisher)
Created2022
Description
MicroRNAs (miRNAs) are 17-22 nucleotide non-coding RNAs that regulate gene expression by targeting non-complementary elements in the 3’ untranslated regions (3’UTRs) of mRNAs. miRNAs, which form complex networks of interaction that differ by tissue and developmental stage, display conservation in their function across metazoan species. Yet much remains unknown regarding their biogenesis, localization, strand selection, and their absolute abundance due to the difficulty of detecting and amplifying such small molecules. Here, I used an updated HT qPCR-based methodology to follow miRNA expression of 5p and 3p strands for all 190 C. elegans miRNAs described in miRBase throughout all six developmental stages in triplicates (total of 9,708 experiments), and studied their expression levels, tissue localization, and the rules underlying miRNA strand selection. My study validated previous findings and identified novel, conserved patterns of miRNA strand expression throughout C. elegans development, which at times correlate with previously observed developmental phenotypes. Additionally, my results highlighted novel structural principles underlying strand selection, which can be applied to higher metazoans.
Though optimized for use in C. elegans, this method can be easily adapted to other eukaryotic systems, allowing for more scalable quantitative investigation of miRNA biology and/or miRNA diagnostics.
ContributorsMeadows, Dalton Alexander (Author) / Mangone, Marco (Thesis advisor) / LaBaer, Joshua (Committee member) / Murugan, Vel (Committee member) / Wilson-Rawls, Jeanne (Committee member) / Arizona State University (Publisher)
Created2023
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 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.
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
Description
The emergence of invasive non-Typhoidal Salmonella (iNTS) infections belonging to sequence type (ST) 313 are associated with severe bacteremia and high mortality in sub-Saharan Africa. Distinct features of ST313 strains include resistance to multiple antibiotics, extensive genomic degradation, and atypical clinical diagnosis including bloodstream infections, respiratory symptoms, and fever. Herein, I report the use of dynamic bioreactor technology to profile the impact of physiological fluid shear levels on the pathogenesis-related responses of ST313 pathovar, 5579. I show that culture of 5579 under these conditions induces profoundly different pathogenesis-related phenotypes than those normally observed when cultures are grown conventionally. Surprisingly, in response to physiological fluid shear, 5579 exhibited positive swimming motility, which was unexpected, since this strain was initially thought to be non-motile. Moreover, fluid shear altered the resistance of 5579 to acid, oxidative and bile stress, as well as its ability to colonize human colonic epithelial cells. This work leverages from and advances studies over the past 16 years in the Nickerson lab, which are at the forefront of bacterial mechanosensation and further demonstrates that bacterial pathogens are “hardwired” to respond to the force of fluid shear in ways that are not observed during conventional culture, and stresses the importance of mimicking the dynamic physical force microenvironment when studying host-pathogen interactions. The results from this study lay the foundation for future work to determine the underlying mechanisms operative in 5579 that are responsible for these phenotypic observations.
ContributorsCastro, Christian (Author) / Nickerson, Cheryl A. (Thesis advisor) / Ott, C. Mark (Committee member) / Roland, Kenneth (Committee member) / Barrila, Jennifer (Committee member) / Arizona State University (Publisher)
Created2016
Description
Organic compounds are influenced by hydrothermal conditions in both marine and terrestrial environments. Sedimentary organic reservoirs make up the largest share of organic carbon in the carbon cycle, leading to petroleum generation and to chemoautotrophic microbial communities. There have been numerous studies on the reactivity of organic compounds in water at elevated temperatures, but these studies rarely explore the consequences of inorganic solutes in hydrothermal fluids. The experiments in this thesis explore new reaction pathways of organic compounds mediated by aqueous and solid phase metals, mainly Earth-abundant copper. These experiments show that copper species have the potential to oxidize benzene and toluene, which are typically viewed as unreactive. These pathways add to the growing list of known organic transformations that are possible in natural hydrothermal systems. In addition to the characterization of reactions in natural systems, there has been recent interest in using hydrothermal conditions to facilitate organic transformations that would be useful in an applied, industrial or synthetic setting. This thesis identifies two sets of conditions that may serve as alternatives to commonplace industrial processes. The first process is the oxidation of benzene with copper to form phenol and chlorobenzene. The second is the copper mediated dehalogenation of aryl halides. Both of these processes apply the concepts of geomimicry by carrying out organic reactions under Earth-like conditions. Only water and copper are needed to implement these processes and there is no need for exotic catalysts or toxic reagents.
ContributorsLoescher, Grant (Author) / Shock, Everett (Thesis advisor) / Hartnett, Hilairy (Committee member) / Gould, Ian (Committee member) / Arizona State University (Publisher)
Created2020