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Description
Predatory bacteria are a guild of heterotrophs that feed directly on other living bacteria. They belong to several bacterial lineages that evolved this mode of life independently and occur in many microbiomes and environments. Current knowledge of predatory bacteria is based on culture studies and simple detection in natural systems. The ecological consequences of their activity, unlike those of other populational loss factors like viral infection or grazing by protists, are yet to be assessed. During large-scale cultivation of biological soil crusts intended for arid soil rehabilitation, episodes of catastrophic failure were observed in cyanobacterial growth that could be ascribed to the action of an unknown predatory bacterium using bioassays. This predatory bacterium was also present in natural biocrust communities, where it formed clearings (plaques) up to 9 cm in diameter that were visible to the naked eye. Enrichment cultivation and purification by cell-sorting were used to obtain co-cultures of the predator with its cyanobacterial prey, as well as to identify and characterize it genomically, physiologically and ultrastructurally. A Bacteroidetes bacterium, unrelated to any known isolate at the family level, it is endobiotic, non-motile, obligately predatory, displays a complex life cycle and very unusual ultrastructure. Extracellular propagules are small (0.8-1.0 µm) Gram-negative cocci with internal two-membrane-bound compartmentalization. These gain entry to the prey likely using a suite of hydrolytic enzymes, localizing to the cyanobacterial cytoplasm, where growth begins into non-compartmentalized pseudofilaments that undergo secretion of vesicles and simultaneous multiple division to yield new propagules. I formally describe it as Candidatus Cyanoraptor togatus, hereafter Cyanoraptor. Its prey range is restricted to biocrust-forming, filamentous, non-heterocystous, gliding, bundle-making cyanobacteria. Molecular meta-analyses showed its worldwide distribution in biocrusts. Biogeochemical analyses of Cyanoraptor plaques revealed that it causes a complete loss of primary productivity, and significant decreases in other biocrusts properties such as water-retention and dust-trapping capacity. Extensive field surveys in the US Southwest revealed its ubiquity and its dispersal-limited, aggregated spatial distribution and incidence. Overall, its activity reduces biocrust productivity by 10% at the ecosystem scale. My research points to predatory bacteria as a significant, but overlooked, ecological force in shaping soil microbiomes.
ContributorsBethany Rakes, Julie Ann (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Gile, Gillian (Committee member) / Cao, Huansheng (Committee member) / Jacobs, Bertram (Committee member) / Arizona State University (Publisher)
Created2022
Description
The partitioning of photosynthates between their sites of production (source) and their sites of utilization (sink) is a major determinant of crop yield and the potential of regulating this translocation promises substantial opportunities for yield increases. Ubiquitous overexpression of the plant type I proton pyrophosphatase (H+-PPase) in crops improves several valuable traits including salt tolerance and drought resistance, nutrient and water use efficiencies, and increased root biomass and yield. Originally, type I H+-PPases were described as pyrophosphate (PPi)-dependent proton pumps localized exclusively in vacuoles of mesophyll and meristematic tissues. It has been proposed that in the meristematic tissues, the role of this enzyme would be hydrolyzing PPi originated in biosynthetic reactions and favoring sink strength. Interestingly, this enzyme has been also localized at the plasma membrane of companion cells in the phloem which load and transport photosynthates from source leaves to sinks. Of note, the plasma membrane-localized H+-PPase could only function as a PPi-synthase in these cells due to the steep proton gradient between the apoplast and cytosol. The generated PPi would favor active sucrose loading through the sucrose/proton symporter in the phloem by promoting sucrose hydrolysis through the Sucrose Synthase pathway and providing the ATP required to maintain the proton gradient. To better understand these two different roles of type I H+-PPases, a series of Arabidopsis thaliana transgenic plants were generated. By expressing soluble pyrophosphatases in companion cells of Col-0 ecotype and H+-PPase mutants, impaired photosynthates partitioning was observed, suggesting phloem-localized H+-PPase could generate the PPi required for sucrose loading. Col-0 plants expressed with either phloem- or meristem-specific AVP1 overexpression cassette and the cross between the two tissue specific lines (Cross) were generated. The results showed that the phloem-specific AVP1-overexpressing plants had increased root hair elongation under limited nutrient conditions and both phloem- and meristem-overexpression of AVP1 contributed to improved rhizosphere acidification and drought resistance. It was concluded that H+-PPases localized in both sink and source tissues regulate plant growth and performance under stress through its versatile enzymatic functions (PPi hydrolase and synthase).
ContributorsLi, Lin (Author) / Park, Yujin (Thesis advisor) / Mangone, Marco (Committee member) / Roberson, Robert (Committee member) / Vermaas, Willem (Committee member) / Arizona State University (Publisher)
Created2022
Description
Bisphenol-A or BPA is a common chemical pollutant that contaminates the environment, specifically water systems, due its mass production in human-made plastic
items and subsequent improper disposal. BPA is also an endocrine disruptor that has
negative health impacts on organisms exposed to them, ranging from changes in
reproduction to neural activity. In this study I researched the impact of early exposure to
weak levels of BPA on adult zebrafish (Danio rerio) social behavior. Zebrafish are highly
social creatures that rely on group living for protection and resource attainment in the
wild, meaning any alteration to how they interact with their conspecifics can be
detrimental to their survival. For one-week postfertilization, I exposed baby zebrafish to
either 0.01 mg/l BPA, 0.001 mg/l BPA, 0.1% DMSO, or water. I raised the fish to
adulthood and tested their reaction to a social stimulus. I found that early exposure to low
doses of Bisphenol-A led to an increase in zebrafish activity levels (increased distance
and time spent traveling) and a decrease in preference towards the social stimulus (more
time away from the social stimulus). Increases in activity suggest that the long-term
effects of early BPA exposure may be linked to chronic stress. However, all treatment
and control groups spent most of their time near the social stimulus when they had visual
access to it, implying a natural social drive that was not completely blocked by the
exposure to BPA. This also verifies that visual signals are highly important to social
behavior, since fish given olfactory access alone did not spend as much time in proximity
to the social stimulus. Although even short-term exposure to weak BPA has a lasting
impact on zebrafish social behavior, future studies are needed to confirm that these
persistent effects are related to stress.
ContributorsTufarelli, Alyssa (Author) / Martins, Emilia (Thesis advisor) / Suárez-Rodríguez, Monserrat (Committee member) / Conroy-Ben, Otakuye (Committee member) / Arizona State University (Publisher)
Created2022
Description
Modern aircraft propulsion systems such as the ultra high bypass ratio turbofan impose constraints on engine installation below the wing, causing jet–wing interactions. Similar interactions are encountered when a jet-powered aircraft takes off on airport runway or aircraft carrier deck. High-speed jet flow near a solid surface shows markedly different turbulence characteristics compared with free jet, including attached turbulent jet and development of non-equilibrium boundary layer down- stream. Wall pressure fluctuations tend to be more unsteady and stronger, leading to increased vibration affecting aircraft cabin noise and modified jet noise radiation. Large-eddy simulation (LES) is useful to characterize turbulent jet flows over a solid surface as well as wall pressure distribution to promote physical understanding and modeling studies. In this study, LES is performed for an installed setup of a Mach 0.7 turbulent jet where the jet–plate distance is fixed at 2D where D is the nozzle-exit diameter. Unstructured-grid LES is used to validate the corresponding experiment (from literature). In addition, a high-fidelity numerical database is built for further analysis and modeling. Turbulence statistics and energy spectra show that agreement with the experimental measurement for the installed case is encouraging, paving a way for future analysis and modeling.
ContributorsTamhane, Nikhil (Author) / Kim, Jeongale (Thesis advisor) / Peet, Yulia (Thesis advisor) / Jeun, Jinah (Committee member) / Arizona State University (Publisher)
Created2022
Description
Nanostructured (NS, grain size (d) <100nm) and ultrafine grained (UFG, d<500nm) metals possess superior mechanical and electrical properties over coarse grained (CG, d≫1μm) metals. The strength of metals like copper (Cu) has been shown to be significantly improved when engineered to have fine and ultrafine grain sizes via processes such as cryomilling, Cold Isostatic Pressing (CIP) and Continuous Equal Channel Angular Pressing (C-ECAP). This study investigates the mechanical and electrical properties of laboratory scale copper (Cu) conductors manufactured through several steps including cryomilling followed by cold isostatic pressing and finally C-ECAP and how its strength is affected by a variety of parameters when tested in uniaxial tension. The copper material is fabricated through cryomilling, cold isostatic pressing and (C-ECAP). Mechanical characterization is conducted using uniaxial tensile tests, nanoindentation and hardness tests. Pre and Post fabrication examination of the material with 3D-xray tomography, optical and electron microscope were conducted to gain deeper understanding of the effects of the processing parameters on the material during fabrication and the evolution of the microstructure as the powders go through the manufacturing process. Electrical testing is conducted to evaluate the electrical conductivity of the manufactured copper.
While the material showed improved strength and hardness compared to conventional copper material at room temperature, its ductility decreased. Also, higher ECAP temperatures produced materials with higher electrical and mechanical properties.
ContributorsOpoku, Jackson Abankwa (Author) / Ladani, Leila LJL (Thesis advisor) / Razmi, Jafar JR (Committee member) / Li, Xiangjia XL (Committee member) / Arizona State University (Publisher)
Created2022
Description
Material behavior under high strain rate deformation has always been an interesting topic. Under this extreme impact, possible structure changes such as phase transformation, chemical reaction, and densification occur in materials. It is helpful to develop a fundamental understanding of structure-property relationship, which helps to build a theoretical model and speed up the material design process. Although shock experiment techniques have been widely developed, numerical approaches such as first principle calculations and molecular dynamics simulations have demonstrated their power in predicting shock behavior and revealing structure-property relationship in an economic and feasible manner. In this dissertation, the mechanical properties and shock responses of three materials, polyurea, silicate glass, and erythritol were investigated, among which polyurea and silicate glass are proposed to be protective materials, while erythritol is proposedto be a surrogate of the explosive material pentaerythritol tetranitrate. First principle calculations and classical molecular dynamics were carried out to predict the shock Hugoniot, and other thermomechanical properties. The simulations also explored potential shock-induced phase transformations in these three materials and seek to draw connections between shock-driven transformations and the underlying chemical composition and material structure.
composition and material structure.
ContributorsHu, Jing (Author) / Oswald, Jay JO (Thesis advisor) / Muhich, Christopher CM (Committee member) / Zhuang, Houlong HZ (Committee member) / Solanki, Kiran KS (Committee member) / Peralta, Pedro PP (Committee member) / Arizona State University (Publisher)
Created2022
Description
Vanadium-dioxide-based devices show great switchability in their optical properties due to its dramatic thermochromic phase transition from insulator to metal, but generally have concerns due to its relatively high transition temperature at 68 °C. Doping the vanadium dioxide with tungsten has been shown to reduce its transition temperature at the cost lower optical property differences between its insulating and metallic phases. A recipe is developed through parametric experimentation to fabricate tungsten-doped vanadium dioxide consisting of a novel dual target co-sputtering deposition, a furnace oxidation process, and a post-oxidation annealing process. The transmittance spectra of the resulting films are measured via Fourier-transform infrared spectroscopy at different temperatures to confirm the lowered transition temperature and analyze their thermal-optical hysteresis behavior through the transition temperature range. Afterwards, the optical properties of undoped sputtered vanadium films are modeled and effective medium theory is used to explain the effect of tungsten dopants on the observed transmittance decrease of doped vanadium dioxide. The optical modeling is used to predict the performance of tungsten-doped vanadium dioxide devices, in particular a Fabry-Perot infrared emitter and a nanophotonic infrared transmission filter. Both devices show great promise in their optical properties despite a slight performance decrease from the tungsten doping. These results serve to illustrate the excellent performance of the co-sputtered tungsten-doped vanadium dioxide films.
ContributorsChao, Jeremy (Author) / Wang, Liping (Thesis advisor) / Wang, Robert (Committee member) / Tongay, Sefaattin (Committee member) / Arizona State University (Publisher)
Created2022
Description
Increasingly, college courses have transitioned from traditional lecture to student-centered active learning, creating more opportunities for students to interact with each other in class. Recent studies have indicated that these increased interactions in active learning can create situations where students’ identities are more salient, which could result in novel challenges for students with marginalized identities. Christianity has been shown to be a marginalized identity in the context of undergraduate biology courses, but it is unknown whether Christian students experience challenges in their interactions with other students in class. The social psychology framework of concealable stigmatized identity (CSI) was used to explore the experiences of Christian students during peer interactions in undergraduate biology courses. Thirty students were interviewed, and most felt their religious identity was salient during peer interactions in biology. Students also reported that they have more opportunities to reveal their religious identity in courses that incorporate peer discussion than in courses that do not. Students claimed that revealing their religious identity to their peers could be beneficial because they could find other religious students in their courses, grow closer with their peers, and combat stereotypes about religious individuals in science. Though most students anticipated stigma, which caused some students to choose not to reveal their religious identities, comparatively few had experienced stigma during peer interactions in their college biology courses, and even fewer had experienced stigma from peers who knew they were religious. These findings indicate that it be may important to teach students how to be culturally competent to reduce Christian students’ anticipated and experienced stigma in active learning courses.
ContributorsEdwards, Baylee Anne (Author) / Brownell, Sara E. (Thesis advisor) / Barnes, M. Elizabeth (Committee member) / Sterner, Beckett (Committee member) / Cooper, Katelyn M. (Committee member) / Arizona State University (Publisher)
Created2022
Description
A notable challenge when assembling synthetic gene circuits is that modularity often fails to function as intended. A crucial underlying reason for this modularity failure is the existence of competition for shared and limited gene expression resources. By designing a synthetic cascading bistable switches (Syn-CBS) circuit in a single strain with two coupled self-activation modules to achieve successive cell fate transitions, nonlinear resource competition within synthetic gene circuits is unveiled. However, in vivo it can be seen that the transition path was redirected with the activation of one switch always prevailing over that of the other, contradictory to coactivation theoretically expected. This behavior is a result of resource competition between genes and follows a ‘winner-takes-all’ rule, where the winner is determined by the relative connection strength between the two modules. Despite investigation demonstrating that resource competition between gene modules can significantly alter circuit deterministic behaviors, how resource competition contributes to gene expression noise and how this noise can be controlled is still an open issue of fundamental importance in systems biology and biological physics. By utilizing a two-gene circuit, the effects of resource competition on protein expression noise levels can be closely studied. A surprising double-edged role is discovered: the competition for these resources decreases noise while the constraint on resource availability adds its own term of noise into the system, denoted “resource competitive” noise. Noise reduction effects are then studied using orthogonal resources. Results indicate that orthogonal resources are a good strategy for eliminating the contribution of resource competition to gene expression noise.
Noise propagation through a cascading circuit has been considered without resource competition. It has been noted that the noise from upstream genes can be transmitted downstream. However, resource competition’s effects on this cascading noise have yet to be studied. When studied, it is found that resource competition can induce stochastic state
switching and perturb noise propagation. Orthogonal resources can remove some of the resource competitive behavior and allow for a system with less noise.
ContributorsGoetz, Hanah Elizabeth (Author) / Tian, Xiaojun (Thesis advisor) / Wang, Xiao (Committee member) / Lai, Ying-Cheng (Committee member) / Arizona State University (Publisher)
Created2022
Description
Bouteloua eriopoda (Torr.) Torr., also known as black grama, is a perennial bunchgrass native to arid and semiarid ecosystems in the southwestern region of North America. As a result of anthropogenic climate change, this region is predicted to increase in aridity and experience more frequent extreme drought and extreme wet years. This change in precipitation will no doubt affect black grama; however, few studies have investigated how the specific structural components of this grass will respond. The purpose of this study was to examine the effects of years since start of treatment and annual precipitation amount on tiller and stolon densities, and to test for interaction between the two predictor variables. Additionally, the effects of annual precipitation on ramets and axillary buds were investigated. By using 36 experimental plots that have been receiving drought, irrigated, or control treatments since 2007, tiller density was the most responsive component to both annual precipitation amount and years since start of treatment. Years since start of treatment and annual precipitation amount also had a statistically significant interaction, meaning the effect of precipitation amount on tiller density differs depending on how many years have passed since treatments began. Stolon density was the second-most responsive component; the predictor variables were found to have no statistically significant interaction, meaning their effects on stolon density are independent of one another. Ramet density, ramets per stolon, and axillary bud metabolic activity and density were found to be independent of annual precipitation amount for 2021. The results indicate that multiple-year extreme wet and multiple-year extreme dry conditions in the Southwest will both likely reduce tiller and stolon densities in black grama patches. Prolonged drought conditions reduced tiller and stolon production in black grama because of negative legacies from previous years. Reduced production during prolonged wet conditions could be due to increased competition between adjacent plants.
ContributorsSutter, Bryce Madison (Author) / Sala, Osvaldo E (Thesis advisor) / Makings, Elizabeth (Committee member) / Wojciechowski, Martin F (Committee member) / Arizona State University (Publisher)
Created2022