Matching Items (84)
Description
The study of organismal adaptations oftentimes focuses on specific, constant conditions, but environmental parameters are characterized by more or less marked levels of variability, rather than constancy. This is important in environments like soils where microbial activity follows pulses of water availability driven by precipitation. Nowhere are these pulses more variable and unpredictable than in arid soils. Pulses constitute stressful conditions for bacteria because they cause direct cellular damage that must be repaired and they force cells to toggle between dormancy and active physiological states, which is energetically taxing. I hypothesize that arid soil microorganisms are adapted to the variability in wet/dry cycles itself, as determined by the frequency and duration of hydration pulses. To test this, I subjected soil microbiomes from the Chihuahuan Desert to controlled incubations for a total common growth period of 60 hours, but separated into treatments in which the total active time was reached with hydration pulses of different length with intervening periods of desiccation, so as to isolate pulse length and frequency as the varying factors in the experiment. Using 16S rRNA amplicon data, I characterized changes in microbiome growth, diversity, and species composition, and tracked the individual responses to treatment intensity in the 447 most common bacterial species (phylotypes) in the soil. Considering knowledge of extremophile microbiology, I hypothesized that growth yield and diversity would decline with shorter pulses. I found that microbial diversity was indeed a direct function of pulse length, but surprisingly, total yield was an inverse function of it. Pulse regime treatments resulted in progressively more significant differences in community composition with increasing pulse length, as differently adapted phylotypes became more prominent. In fact, more than 30% of the most common bacterial phylotypes demonstrated statistically significant population growth responses to pulse length. Most responsive phylotypes were apparently best adapted to short pulse regimes (known in the literature as Nimble Responders or NIRs), while fewer did better under long pulse regimes (known as TORs or Torpid Responders). Examples of extreme NIRs and TORs could be found among bacteria from different phyla, indicating that these adaptations have occurred multiple times during evolution.
ContributorsKut, Patrick John (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Sala, Osvaldo (Committee member) / Zhu, Qiyun (Committee member) / Arizona State University (Publisher)
Created2023
ContributorsForgey, Sydney (Performer) / Hickman, Miriam, 1955- (Performer) / Smith, David (Performer) / ASU Library. Music Library (Publisher)
Created2020-03-25
Description
A piezoelectric transducer, comprised of electroded and active pad PZT layer atop a backing PZT layer and protected with an acoustic matching layer, and operating under a pulse-echo technique for longitudinal ultrasonic imaging, acts as both source and detector.
Ultrasonic transducer stacks (modules), which had failed or passed during pulse-echo sensitivity testing, were received from Consortium X. With limited background information on these stacks, the central theme was to determine the origin(s) of failure via the use of thermal and physicochemical characterization techniques.
The optical and scanning electron microscopy revealed that contact electrode layers are discontinuous in all samples, while delaminations between electrodes and pad layer were observed in failed samples. The X-ray diffraction data on the pad PZT revealed an overall c/a ratio of 1.022 ratio and morphotropic boundary composition, with significant variations of the Zr to Ti ratio within a sample and between samples. Electron probe microanalysis confirmed that the overall Zr to Ti ratio of the pad PZT was 52/48, and higher amounts of excess PbO in failed samples, whereas, inductively coupled plasma mass spectrometry revealed the presence of Mn, Al, and Sb (dopants) and presence of Cu (sintering aid) in in this hard (pad) PZT. Additionally, three exothermic peaks during thermal analysis was indicative of incomplete calcination of pad PZT. Moreover, transmission electron microscopy and scanning transmission electron microscopy revealed the presence of parylene at the Ag-pad PZT interface and within the pores of pad PZT (in failed samples subjected to electric fields). This further dilutes the electrical, mechanical, and electromechanical properties of the pad PZT, which in turn detrimentally influences the pulse echo sensitivity.
Ultrasonic transducer stacks (modules), which had failed or passed during pulse-echo sensitivity testing, were received from Consortium X. With limited background information on these stacks, the central theme was to determine the origin(s) of failure via the use of thermal and physicochemical characterization techniques.
The optical and scanning electron microscopy revealed that contact electrode layers are discontinuous in all samples, while delaminations between electrodes and pad layer were observed in failed samples. The X-ray diffraction data on the pad PZT revealed an overall c/a ratio of 1.022 ratio and morphotropic boundary composition, with significant variations of the Zr to Ti ratio within a sample and between samples. Electron probe microanalysis confirmed that the overall Zr to Ti ratio of the pad PZT was 52/48, and higher amounts of excess PbO in failed samples, whereas, inductively coupled plasma mass spectrometry revealed the presence of Mn, Al, and Sb (dopants) and presence of Cu (sintering aid) in in this hard (pad) PZT. Additionally, three exothermic peaks during thermal analysis was indicative of incomplete calcination of pad PZT. Moreover, transmission electron microscopy and scanning transmission electron microscopy revealed the presence of parylene at the Ag-pad PZT interface and within the pores of pad PZT (in failed samples subjected to electric fields). This further dilutes the electrical, mechanical, and electromechanical properties of the pad PZT, which in turn detrimentally influences the pulse echo sensitivity.
ContributorsPeri, Prudhvi Ram (Author) / Dey, Sandwip (Thesis advisor) / Smith, David (Committee member) / Alford, Terry (Committee member) / Arizona State University (Publisher)
Created2018
Description
Biological soil crusts (biocrusts) are topsoil communities of organisms that contribute to soil fertility and erosion resistance in drylands. Anthropogenic disturbances can quickly damage these communities and their natural recovery can take decades. With the development of accelerated restoration strategies in mind, I studied physiological mechanisms controlling the establishment of cyanobacteria in biocrusts, since these photoautotrophs are not just the biocrust pioneer organisms, but also largely responsible for improving key soil attributes such as physical stability, nutrient content, water retention and albedo. I started by determining the cyanobacterial community composition of a variety of biocrust types from deserts in the Southwestern US. I then isolated a large number of cyanobacterial strains from these locations, pedigreed them based on their 16SrRNA gene sequences, and selective representatives that matched the most abundant cyanobacterial field populations. I then developed methodologies for large-scale growth of the selected isolates to produce location-specific and genetically autochthonous inoculum for restoration. I also developed and tested viable methodologies to physiologically harden this inoculum and improve its survival under harsh field conditions. My tests proved that in most cases good viability of the inoculum could be attained under field-like conditions. In parallel, I used molecular ecology approaches to show that the biocrust pioneer, Microcoleus vaginatus, shapes its surrounding heterotrophic microbiome, enriching for a compositionally-differentiated “cyanosphere” that concentrates the nitrogen-fixing function. I proposed that a mutualism based on carbon for nitrogen exchange between M. vaginatus and its cyanosphere creates a consortium that constitutes the true pioneer community enabling the colonization of nitrogen-poor, bare soils. Using the right mixture of photosynthetic and diazotrophic cultures will thus likely help in soil restoration. Additionally, using physiological assays and molecular meta-analyses, I demonstrated that the largest contributors to N2-fixation in late successional biocrusts (three genera of heterocystous cyanobacteria) partition their niche along temperature gradients, and that this can explain their geographic patterns of dominance within biocrusts worldwide. This finding can improve restoration strategies by incorporating climate-matched physiological types in inoculum formulations. In all, this dissertation resulted in the establishment of a comprehensive "cyanobacterial biocrust nursery", that includes a culture collection containing 101 strains, isolation and cultivation methods, inoculum design strategies as well as field conditioning protocols. It constitutes a new interdisciplinary application of microbiology in restoration ecology.
ContributorsGiraldo Silva, Ana Maria (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Barger, Nichole N (Committee member) / Bowker, Mathew A (Committee member) / Sala, Osvaldo (Committee member) / Arizona State University (Publisher)
Created2019
Description
Computer assisted language learning (CALL) has become increasingly common as a means of helping learners develop essential skills in a second or foreign language. However, while many CALL programs claim to be based on principles of second language acquisition (SLA) theory and research, evaluation of design and learning outcomes at the level of individual CALL exercises is lacking in the existing literature. The following proposed study will explore the design of computer-based vocabulary matching exercises using both written text and images and the effects of various design manipulations on learning outcomes. The study will use eye-tracking to investigate what users attend to on screen as they work through a series of exercises with different configurations of written words and images. It will ask whether manipulation of text and image features and combinations can have an effect on learners’ attention to the various elements, and if so, whether differences in levels of attention results in higher or lower scores for measures of learning. Specifically, eye-tracking data will be compared to post-test scores for recall and recognition of target vocabulary items to look for a correlation between levels of attention to written forms in-task and post-test gains in scores for vocabulary learning.
ContributorsPatchin, Colleen (Author) / Smith, David (Thesis advisor) / Ross, Andrew (Committee member) / James, Mark (Committee member) / Arizona State University (Publisher)
Created2019
Description
Euendolithic cyanobacteria have the remarkable ability to actively excavate and grow within certain minerals. Their activity leads to increased erosion of marine and terrestrial carbonates, negatively affecting coral reef and bivalve ecology. Despite their environmental relevance, the boring mechanism has remained elusive and paradoxical, in that cyanobacteria alkalinize their surroundings, typically leading to carbonate precipitation, not dissolution. Thus, euendoliths must rely on unique adaptations to bore. Recent work using the filamentous model euendolith Mastigocoleus testarum strain BC008 indicated that excavation relied on transcellular calcium transport mediated by P-type ATPases, but the phenomenon remained unclear. Here I present evidence that excavation in M. testarum involves an unprecedented set of adaptations. Long-range calcium transport is achieved through the coordinated pumping of multiple cells, orchestrated by the localization of calcium ATPases in a repeating annular pattern, positioned at a single cell pole, adjacent to each cell septum along the filament. Additionally, specialized chlorotic cells that I named calcicytes, differentiate and accumulate calcium at concentrations more than 500 fold those of canonical cells, likely allowing for fast calcium flow at non-toxic concentrations through undifferentiated cells. I also show, using 13C stable isotope tracers and NanoSIMS imaging, that endolithic M. testarum derives most of its carbon from the mineral carbonates it dissolves, the first autotroph ever shown to fix mineral carbon, confirming the existence of a direct link between oxidized solid carbon pools and reduced organic pools in the biosphere. Finally, using genomic and transcriptomic approaches, I analyze gene expression searching for additional adaptations related to the endolithic lifestyle. A large and diverse set of genes (24% of 6917 genes) were significantly differentially regulated while boring, including several master regulators and genes expectedly needed under this condition (such as transport, nutrient scavenging, oxidative stress, and calcium-binding protein genes). However, I also discovered the up-regulation of several puzzling gene sets involved in alternative carbon fixation pathways, anaerobic metabolism, and some related to photosynthesis and respiration. This transcriptomic data provides us with several new, readily testable hypotheses regarding adaptations to the endolithic lifestyle. In all, my data clearly show that boring organisms show extraordinarily interesting adaptations.
ContributorsGuida, Brandon Scott (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Chandler, Douglas (Committee member) / Bingham, Scott (Committee member) / Roberson, Robert (Committee member) / Arizona State University (Publisher)
Created2016
Description
Biological soil crusts (BSCs) dominate the soil surface of drylands in the western United States and possess properties thought to influence local hydrology. Little agreement exists, however, on the effects of BSCs on runoff, infiltration, and evaporative rates. This study aims to improve the predictive capability of an ecohydrology model in order to understand how BSCs affect the storage, retention, and infiltration of water into soils characteristic of the Colorado Plateau. A set of soil moisture measurements obtained at a climate manipulation experiment near Moab, Utah, are used for model development and testing. Over five years, different rainfall treatments over experimental plots resulted in the development of BSC cover with different properties that influence soil moisture differently. This study used numerical simulations to isolate the relative roles of different BSC properties on the hydrologic response at the plot-scale. On-site meteorological, soil texture and vegetation property datasets are utilized as inputs into a ecohydrology model, modified to include local processes: (1) temperature-dependent precipitation partitioning, snow accumulation and melt, (2) seasonally-variable potential evapotranspiration, (3) plant species-specific transpiration factors, and (4) a new module to account for the water balance of the BSC. Soil, BSC and vegetation parameters were determined from field measurements or through model calibration to the soil moisture observations using the Shuffled Complex Evolution algorithm. Model performance is assessed against five years of soil moisture measurements at each experimental site, representing a wide range of crust cover properties. Simulation experiments were then carried out using the calibrated ecohydrology model in which BSC parameters were varied according to the level of development of the BSC, as represented by the BSC roughness. These results indicate that BSCs act to both buffer against evaporative soil moisture losses by enhancing BSC moisture evaporation and significantly alter the rates of soil water infiltration by reducing moisture storage and increasing conductivity in the BSC. The simulation results for soil water infiltration, storage and retention across a wide range of meteorological events help explain the conflicting hydrologic outcomes present in the literature on BSCs. In addition, identifying how BSCs mediate infiltration and evaporation processes has implications for dryland ecosystem function in the western United States.
ContributorsWhitney, Kristen M (Author) / Vivoni, Enrique R (Thesis advisor) / Farmer, Jack D (Committee member) / Garcia-Pichel, Ferran (Committee member) / Arizona State University (Publisher)
Created2015
Description
This dissertation describes fundamental studies of hollow carbon nanostructures, which may be used as electrodes for practical energy storage applications such as batteries or supercapacitors. Electron microscopy is heavily utilized for the nanoscale characterization. To control the morphology of hollow carbon nanostructures, ZnO nanowires serve as sacrificial templates. The first part of this dissertation focuses on the optimization of synthesis parameters and the scale-up production of ZnO nanowires by vapor transport method. Uniform ZnO nanowires with 40 nm width can be produced by using 1100 °C reaction temperature and 20 sccm oxygen flow rate, which are the two most important parameters.
The use of ethanol as carbon source with or without water steam provides uniform carbonaceous deposition on ZnO nanowire templates. The amount of as-deposited carbonaceous material can be controlled by reaction temperature and reaction time. Due to the catalytic property of ZnO surface, the thicknesses of carbonaceous layers are typically in nanometers. Different methods to remove the ZnO templates are explored, of which hydrogen reduction at temperatures higher than 700 °C is most efficient. The ZnO templates can also be removed under ethanol environment, but the temperatures need to be higher than 850 °C for practical use.
Characterizations of hollow carbon nanofibers show that the hollow carbon nanostructures have a high specific surface area (>1100 m2/g) with the presence of mesopores (~3.5 nm). The initial data on energy storage as electrodes of electrochemical double layer capacitors show that high specific capacitance (> 220 F/g) can be obtained, which is related to the high surface area and unique porous hollow structure with a thin wall.
The use of ethanol as carbon source with or without water steam provides uniform carbonaceous deposition on ZnO nanowire templates. The amount of as-deposited carbonaceous material can be controlled by reaction temperature and reaction time. Due to the catalytic property of ZnO surface, the thicknesses of carbonaceous layers are typically in nanometers. Different methods to remove the ZnO templates are explored, of which hydrogen reduction at temperatures higher than 700 °C is most efficient. The ZnO templates can also be removed under ethanol environment, but the temperatures need to be higher than 850 °C for practical use.
Characterizations of hollow carbon nanofibers show that the hollow carbon nanostructures have a high specific surface area (>1100 m2/g) with the presence of mesopores (~3.5 nm). The initial data on energy storage as electrodes of electrochemical double layer capacitors show that high specific capacitance (> 220 F/g) can be obtained, which is related to the high surface area and unique porous hollow structure with a thin wall.
ContributorsSong, Yian (Author) / Liu, Jingyue (Committee member) / Smith, David (Committee member) / McCartney, Martha (Committee member) / Chen, Tingyong (Committee member) / Arizona State University (Publisher)
Created2016
Description
This dissertation presents research findings regarding the exploitation of localized surface plasmon (LSP) of epitaxial Ag islands as a means to enhance the photoluminescence (PL) of Germanium (Ge) quantum dots (QDs). The first step of this project was to investigate the growth of Ag islands on Si(100). Two distinct families of Ag islands have been observed. “Big islands” are clearly faceted and have basal dimensions in the few hundred nm to μm range with a variety of basal shapes. “Small islands” are not clearly faceted and have basal diameters in the 10s of nm range. Big islands form via a nucleation and growth mechanism, and small islands form via precipitation of Ag contained in a planar layer between the big islands that is thicker than the Stranski-Krastanov layer existing at room-temperature.
The pseudodielectric functions of epitaxial Ag islands on Si(100) substrates were investigated with spectroscopic ellipsometry. Comparing the experimental pseudodielectric functions obtained for Si with and without Ag islands clearly identifies a plasmon mode with its dipole moment perpendicular to the surface. This observation is confirmed using a simulation based on the thin island film (TIF) theory. Another mode parallel to the surface may be identified by comparing the experimental pseudodielectric functions with the simulated ones from TIF theory. Additional results suggest that the LSP energy of Ag islands can be tuned from the ultra-violet to the infrared range by an amorphous Si (α-Si) cap layer.
Heterostructures were grown that incorporated Ge QDs, an epitaxial Si cap layer and Ag islands grown atop the Si cap layer. Optimum growth conditions for distinct Ge dot ensembles and Si cap layers were obtained. The density of Ag islands grown on the Si cap layer depends on its thickness. Factors contributing to this effect may include the average strain and Ge concentration on the surface of the Si cap layer.
The effects of the Ag LSP on the PL of Ge coherent domes were investigated for both α-Si capped and bare Ag islands. For samples with low-doped substrates, the LSPs reduce the Ge dot-related PL when the Si cap layer is below some critical thickness and have no effect on the PL when the Si cap layer is above the critical thickness. For samples grown on highly-doped wafers, the LSP of bare Ag islands enhanced the PL of Ge QDs by ~ 40%.
The pseudodielectric functions of epitaxial Ag islands on Si(100) substrates were investigated with spectroscopic ellipsometry. Comparing the experimental pseudodielectric functions obtained for Si with and without Ag islands clearly identifies a plasmon mode with its dipole moment perpendicular to the surface. This observation is confirmed using a simulation based on the thin island film (TIF) theory. Another mode parallel to the surface may be identified by comparing the experimental pseudodielectric functions with the simulated ones from TIF theory. Additional results suggest that the LSP energy of Ag islands can be tuned from the ultra-violet to the infrared range by an amorphous Si (α-Si) cap layer.
Heterostructures were grown that incorporated Ge QDs, an epitaxial Si cap layer and Ag islands grown atop the Si cap layer. Optimum growth conditions for distinct Ge dot ensembles and Si cap layers were obtained. The density of Ag islands grown on the Si cap layer depends on its thickness. Factors contributing to this effect may include the average strain and Ge concentration on the surface of the Si cap layer.
The effects of the Ag LSP on the PL of Ge coherent domes were investigated for both α-Si capped and bare Ag islands. For samples with low-doped substrates, the LSPs reduce the Ge dot-related PL when the Si cap layer is below some critical thickness and have no effect on the PL when the Si cap layer is above the critical thickness. For samples grown on highly-doped wafers, the LSP of bare Ag islands enhanced the PL of Ge QDs by ~ 40%.
ContributorsKong, Dexin (Author) / Drucker, Jeffery (Thesis advisor) / Chen, Tingyong (Committee member) / Ros, Robert (Committee member) / Smith, David (Committee member) / Arizona State University (Publisher)
Created2015
Description
Photocatalytic water splitting is a promising technique to produce H2 fuels from water using sustainable solar energy. To better design photocatalysts, the understanding of charge transfer at surfaces/interfaces and the corresponding structure change during the reaction is very important. Local structural and chemical information on nanoparticle surfaces or interfaces can be achieved through characterizations on transmission electron microscopy (TEM). Emphasis should be put on materials structure changes during the reactions in their “working conditions”. Environmental TEM with in situ light illumination system allows the photocatalysts to be studied under light irradiation when exposed to H2O vapor. A set of ex situ and in situ TEM characterizations are carried out on typical types of TiO2 based photocatalysts. The observed structure changes during the reaction are correlated with the H2 production rate for structure-property relationships.
A surface disordering was observed in situ when well-defined anatase TiO2 rhombohedral nanoparticles were exposed to 1 Torr H2O vapor and 10suns light inside the environmental TEM. The disordering is believed to be related to high density of hydroxyl groups formed on surface oxygen vacancies during water splitting reactions.
Pt co-catalyst on TiO2 is able to split pure water producing H2 and O2. The H2 production rate drops during the reaction. Particle size growth during reaction was discovered with Z-contrast images. The particle size growth is believed to be a photo-electro-chemical Ostwald ripening.
Characterizations were also carried out on a more complicated photocatalyst system: Ni/NiO core/shell co-catalyst on TiO2. A decrease of the H2 production rate resulting from photo-corrosion was observed. The Ni is believed to be oxidized to Ni2+ by OH• radicals which are intermediate products of H2O oxidation. The mechanism that the OH• radicals leak into the cores through cracks on NiO shells is more supported by experiments.
Overall this research has done a comprehensive ex situ and in situ TEM characterizations following some typical TiO2 based photocatalysts during reactions. This research has shown the technique availability to study photocatalyst inside TEM in photocatalytic conditions. It also demonstrates the importance to follow structure changes of materials during reactions in understanding deactivation mechanisms.
A surface disordering was observed in situ when well-defined anatase TiO2 rhombohedral nanoparticles were exposed to 1 Torr H2O vapor and 10suns light inside the environmental TEM. The disordering is believed to be related to high density of hydroxyl groups formed on surface oxygen vacancies during water splitting reactions.
Pt co-catalyst on TiO2 is able to split pure water producing H2 and O2. The H2 production rate drops during the reaction. Particle size growth during reaction was discovered with Z-contrast images. The particle size growth is believed to be a photo-electro-chemical Ostwald ripening.
Characterizations were also carried out on a more complicated photocatalyst system: Ni/NiO core/shell co-catalyst on TiO2. A decrease of the H2 production rate resulting from photo-corrosion was observed. The Ni is believed to be oxidized to Ni2+ by OH• radicals which are intermediate products of H2O oxidation. The mechanism that the OH• radicals leak into the cores through cracks on NiO shells is more supported by experiments.
Overall this research has done a comprehensive ex situ and in situ TEM characterizations following some typical TiO2 based photocatalysts during reactions. This research has shown the technique availability to study photocatalyst inside TEM in photocatalytic conditions. It also demonstrates the importance to follow structure changes of materials during reactions in understanding deactivation mechanisms.
ContributorsZhang, Liuxian (Author) / Crozier, Peter (Thesis advisor) / Smith, David (Committee member) / Chan, Candace (Committee member) / Liu, Jingyue (Committee member) / Arizona State University (Publisher)
Created2015