Master of Science, The Ohio State University, 1971, Graduate School

Committee: Not Provided (Other) Subjects:

Master of Science, Miami University, 2022, Microbiology

Ecosystems contain a variety of components that each need to be understood to get a complete picture of environmental change. Recently, fungi have become a rising point of interest in aquatic communities, as they have been shown to play roles akin to their soil bound counterparts. Here we explore which fungi may survive in Antarctic lakes in the McMurdo Dry Valleys and what roles these organisms may be performing in this unique ecosystem. We found that early-diverging lineage fungi, such as Cryptomycota, were common in the waters, and performing parasitic roles. Other fungal phyla, such as Ascomycota and Basidiomycota, were also found in higher abundance than previously predicted. In network analysis these unexpected fungi were shown to correlate with several chlorophyll producing organisms. Cryptomycota was found to correlate more with heterotrophic protists. Seasonal analysis showed that the fungal community was dynamic throughout the year, with the winter being heavily dominated by Cryptomycota. Our data suggests that fungi are dynamic players in the McMurdo Dry Valley ecosystem and are participating in several different roles.

Committee: Rachael Morgan-Kiss (Advisor); Annette Bollmann (Committee Member) Subjects: Biology; Ecology; Microbiology

Master of Science in Biological Sciences, Youngstown State University, 2020, Department of Biological Sciences and Chemistry

Talaromyces marneffei is a thermally dimorphic fungus native to Southeastern Asia that primarily infects individuals with compromised immunity. Being thermally dimorphic, the fungus exists in two phases: a mold phase at 25°C and a yeast phase at 37°C. One can obtain talaromycosis, the disease caused by T. marneffei, by the inhalation of the conidia (i.e., spores) produced by the mold phase of the fungus. These conidia subsequently switch phases to grow in the unicellular yeast while inside of the host. Many pathogenic fungi are known to secrete proteins that have the ability to manipulate host intracellular processes that enable growth and survival. Some of these secreted proteins have been found to be cell-wall proteins or associated with the cell wall. Particular cell-wall proteins in fungal species related to T. marneffei are known to be linked with dimorphism and virulence. Using the database FunSecKB2, 538 potentially secreted proteins of the fungus were identified to which primer pairs were designed to selected genes and used to screen for differential gene expression. In the present study, a gene encoding an antigenic cell wall galactomannoprotein in Talaromyces marneffei was shown to be preferentially expressed in the yeast phase. This gene, designated gmpA, has been found to be 25% homologous to the hsbA gene in Aspergillus oryzae, which encodes for a hydrophobic surface binding protein A. The latter plays an important role in adhesion and facilitates the recruitment of lytic enzymes to help degrade hydrophobic materials. Using this information, we hypothesize that GmpA in Talaromyces marneffei is associated with attainment of morphology, essential to phase transition, and involved with the virulence of the fungus. A deletion mutant was constructed to further analyze the function and importance of gmpA in Talaromyces marneffei.

Committee: Chester Cooper PhD (Advisor); David Asch PhD (Committee Member); Jonathan Caguiat PhD (Committee Member); Gary Walker PhD (Committee Member) Subjects: Biology; Molecular Biology

Doctor of Philosophy, The Ohio State University, 2024, Plant Pathology

Soil fungi and plant-parasitic nematodes (PPN) significantly influence crop health and productivity in agricultural systems. Among the most economically important PPN is the soybean cyst nematode (SCN), Heterodera glycines, which is the most yield-limiting pathogen of soybean in North America. Management strategies for this pathogen are limited, and focus primarily on the use of crop rotation and resistant cultivars. Hence, there is a need for additional tools that can aid nematode management. Some fungi have shown promise as potential nematode control agents, however, their effectiveness in the field has been inconsistent. In contrast, there are fungal soybean pathogens that when causing disease alongside SCN can result in more damage to the plant than the addition of the individual nematode and fungal infections alone. Both types of interactions highlight the important role that fungal communities play in plant health outcomes during SCN infestation. This dissertation explores the associations between soil fungi and SCN, focusing on the potential synergistic and antagonistic interactions between them at different spatial scales. Furthermore, the effects of soil legacy on SCN infestation, particularly as influenced by previous cropping history, were examined. In this work, the distribution of SCN and soil fungi in Ohio was examined through a survey experiment that included samples from 171 fields across the state using ITS amplicon sequencing to identify the fungi in the samples. The fungal communities in bulk soil samples were analyzed to determine if SCN infestation had any impact on fungal community composition. The results of this project provided insight into the ecology of soil fungi in Ohio soybean fields. Edaphoclimatic factors were shown to play a significant role in the community composition of soil fungi. However, it was also demonstrated that SCN abundance significantly influenced the fungal community composition of soybean soils in Ohio. It was also (open full item for complete abstract)

Committee: Horacio Lopez-Nicora (Advisor); Maria Soledad Benitez Ponce (Advisor) Subjects: Plant Pathology

Master of Science, The Ohio State University, 1968, Graduate School

Committee: Not Provided (Other) Subjects:

Master of Science, The Ohio State University, 1971, Graduate School

Committee: Not Provided (Other) Subjects:

Master of Science, The Ohio State University, 1969, Graduate School

Committee: Not Provided (Other) Subjects:

Master of Arts, The Ohio State University, 1906, Graduate School

Committee: Not Provided (Other) Subjects:

Master of Science, The Ohio State University, 1951, Graduate School

Committee: Not Provided (Other) Subjects:

Master of Science, The Ohio State University, 2008, Graduate School

Committee: Not Provided (Other) Subjects:

Master of Science, The Ohio State University, 1918, Graduate School

Committee: Not Provided (Other) Subjects:

Doctor of Philosophy, The Ohio State University, 2024, Animal Sciences

The rumen hosts a diverse array of prokaryotic (bacteria and archaea) and eukaryotic (fungi and protozoa) microbes. Collectively, they hydrolyze complex plant cell wall materials into simple sugars, which are further fermented into VFA, representing a substantial source of the host's energy needs. By incorporating inorganic ammonia generated from feed protein and urea, rumen microbes also provide a significant portion of the host's protein requirements. As regulators of the microbial ecosystem, rumen viruses (bacteriophages and eukaryotic viruses) also influence rumen fermentation and microbial protein synthesis. They achieve this by directly lysing microbes, thereby modulating microbial composition or by modifying the metabolism of infected bacterial cells. Additionally, they drive co-evolution between microbes and viruses, acting as vectors for horizontal gene transfer or through dynamic defense and counterdefense interactions with microbes. The anaerobic microbial cultivation techniques developed by Robert Hungate enable rumen microbiologists to explore the diverse spectrum of rumen microbial physiology and metabolism. However, despite continuous efforts in anaerobic cultivation, the culturable rumen microbes (including viruses) represent only a limited fraction of the overall diversity. Moreover, microbial cultures, whether monocultures or mixed cultures, fail to fully replicate the intricate microbial interactions observed in vivo, such as cross-feeding and predatory conditions. Fortunately, multi-omics technologies complement traditional culture-dependent analyses, enabling us to explore microbial ecology by uncovering the genomes (via genome-resolved metagenomics) and metabolism (via metatranscriptomics, metaproteomics and enzymatic activities) of the unculturable majority. Utilizing advancements in multi-omics and bioinformatics, this research aims to bridge the gap in rumen microbial genomics within the context of microbial ecology and rumen fermentation (open full item for complete abstract)

Committee: Zhongtang Yu Dr. (Advisor); Jeffrey Firkins Dr. (Committee Member); Tansol Park Dr. (Committee Member); Chanhee Lee Dr. (Committee Member); Alejandro Relling Dr. (Committee Member) Subjects: Animal Sciences; Bioinformatics; Microbiology

PhD, University of Cincinnati, 2024, Arts and Sciences: Germanic Languages and Literature

My dissertation, Of Mushrooms, Stones, and Stars. Post-Enlightenment Onto-/Epistemologies in 21st Century Art, Literature and Theory, contributes to the field of Anthropocene Studies in the German-speaking context. The man-made climate crisis that unfolds in the age of the Anthropocene poses the urgency of a paradigm shift and a need for new ways of planetary (co-)existence. I propose that the Anthropocene is deeply connected to the Age of Enlightenment: the centrality and particularity of the human subject as well as the conception of Man as the master of nature, which evolve in the Age of Enlightenment, find their cumulation in the contemporary anthropocenic crisis. Since Enlightenment paradigms have so firmly shaped today's world, I subsequently argue that a critical evaluation of Enlightenment thought is necessary to explore ways of being and knowing that allow for a departure from anthropocentrism and the oppression of nature. I focus on three non-human, material-discursive agents – mushrooms, stones and stars – and show how and why they are of particular importance to Anthropocene discourse; how they inspire a critique of Enlightenment ideas (particularly by Immanuel Kant and Rene Descartes); and to what extent they offer onto-/epistemological impulses that mark a departure from these ideas. In exploring these agents, I engage with contemporary theorists such as Leo Bersani, Karen Barad and Elizabeth Povinelli, in dialog with German-language art, film, and literature by Johann Wolfgang von Goethe, Esther Kinsky, Marion Neumann and Ursula Biemann. My chapter on stones deals primarily with ontological questions. I trace the shift from the distinction between the organic and anorganic in the late 18th century to contemporary concepts that question this distinction – particularly Elizabeth Povinelli's Geontology – and engage with Goethe's geological essays from the 1780s as well as his late novel Wilhelm Meister's Wanderjahre (1829) and Esther Kins (open full item for complete abstract)

Committee: Tanja Nusser Ph.D. (Committee Chair); Rolf Parr Ph.D M.A B.A. (Committee Member); Todd Herzog Ph.D. (Committee Member); Thomas Kuepper Ph.D M.A B.A. (Committee Member); Peter Rehberg Ph.D. (Committee Member) Subjects: Germanic Literature

Doctor of Philosophy, The Ohio State University, 2024, Chemistry

My dissertation research develops Raman spectroscopy-based sensors to measure aspects of human and plant health or disease states at the point of need, specifically in areas where current sensing methods are insufficient. The first main project area involves monitoring plant health, specifically soil ecology, in real time without harvesting the plant. Sensors are needed to non-invasively observe chemical changes expressed in plant leaves which result from nutrition conditions in the soil. These sensors would be especially useful to inform fertilization practices, increasing efficiency and sustainability. The second major project area focuses on developing a rapid and accurate diagnostic assay for COVID-19. The limitations of established testing methods, such as at-home antigen tests and polymerase chain reaction (PCR) assays, motivate the exploration of alternative techniques that do not sacrifice accuracy for speed. To tackle these sensing challenges, my research employs Raman spectroscopy, which uses light to probe the molecular composition of a sample. Each molecule has a unique Raman signature, and Raman signal is proportional to the concentration of molecules present in the sample, making the technique highly advantageous for identification and quantification. Raman signals can be collected quickly and non-destructively with minimal sample preparation. To detect low concentrations of analytes or poorly scattering analytes, we use surface enhanced Raman spectroscopy (SERS), a technique in which metal nanostructures amplify the Raman signals of the molecules near the nanostructures. Overall, this dissertation work focuses on optimizing portable Raman and SERS methods to non-invasively assess plant health and to detect COVID, all in a matter of seconds. Chapter 1 introduces the background and motivation for these projects, as well as the analytical techniques used to address them. Chapter 2 describes the development of handheld Raman techniques to monitor th (open full item for complete abstract)

Committee: Zachary Schultz (Advisor) Subjects: Analytical Chemistry; Chemistry

PhD, University of Cincinnati, 2024, Medicine: Pathobiology and Molecular Medicine

Pneumocystis jirovecii pneumonia (PjP) poses a considerable clinical challenge, especially in immunocompromised individuals due to conditions like HIV/AIDS, organ transplantation, and immune-compromising malignancies. Clinical manifestations of PjP range from dyspnea to life-threatening respiratory failure. A significant obstacle is the absence of a facultative culture system for Pneumocystis spp., limiting research on its metabolism, pathogenesis, and therapeutic strategies. Pneumocystis spp. primarily rely on their mammalian hosts for essential nutrients, necessitating in vivo infection models. Each species infects a specific mammalian host, whereas P. jirovecii (Pj) is the species affecting humans, and P. murina (Pm) and P. carinii (Pc) serve as surrogate mouse or rat models for PjP. Extracellular vesicles (EVs) have long been observed in the alveolar lumen in both uninfected and P. carinii-infected rat lungs. We hypothesized that Pc obtains nutrients through host EVs to supplement its metabolic needs. Our research demonstrates active EV uptake by Pc, suggesting their potential role in nutrient acquisition. However, bronchial alveolar lavage fluid (BALF) EVs from Pc-infected rats exhibited toxic effects on Pc viability in vitro, revealing complex host-pathogen interactions. We identified evidence suggesting that Pc and Pm secrete EVs, including electron-dense cell wall-containing EVs and the EV proteome containing of major surface glycoproteins, which are a Pneumocystis-specific superfamily of membrane proteins. While the Pneumocystis EV proteome shows homology to other fungal EV proteomes, further research is required to comprehensively identify the proteome. The precise functions of these EVs remain uncertain but may function in supportive roles EVs play in other fungal organisms. This includes contributing to proper biofilm formation, as observed in Candida albicans and Pichia fermentans. BALF EVs from Pc-infected rats and Pm-infected mice (open full item for complete abstract)

Committee: Melanie Cushion Ph.D. (Committee Chair); David Askew Ph.D. (Committee Member); George Smulian M.D. (Committee Member); Scott Langevin Ph.D. (Committee Member); Michael Borchers Ph.D. (Committee Member) Subjects: Microbiology

Doctor of Philosophy, The Ohio State University, 2024, Environmental Science

Every occupied indoor environment, including spacecraft, has its own unique microbiome. This composition and quantity of the microbiome present in these environments is dependent on many factors including building materials, occupants cleaning habits, presence of pets, and environmental conditions inside. Indoor microbes can be found in dust, which is generated in both Earth- and space-based built environments, a unique nutrient rich substrate that can act as both a source and sink especially in Earth-based buildings with carpet. Unintended microbial growth indoors can affect the health of the occupants and cause premature failure of building materials via biodegradation. Water is the limiting factor for growth, with moisture in the indoor air sufficient to support microbial growth indoors, especially for fungi. However, we need an improved understanding of microbes and their growth in indoor spaces to ensure healthier environments. The goal of this paper is to provide these examples and show how they fit into the concepts of One Space and bioastronautics. One Space is the idea that the built environment and human health are interconnected based on the One Health principles. Bioastronautics is the study of living organisms in spaceflight conditions. These two ideas complement each other and provide ample opportunity for interdisciplinary collaborations that can lead to innovative solutions to making healthier, safer, and more comfortable built environments on Earth and in space. In these studies, we focus on the intersection between microbiology and the built environment, by looking at the indoor dust microbiome in Earth- and space-based built environments like the International Space Station (ISS). We show that bacteriophages in common Earth-based building materials such as carpet and house dust can remain viable and infectious for up to several days making it a potential source of exposure. We also found the viral genetic material (RNA) remained stable for weeks t (open full item for complete abstract)

Committee: Karen Dannemiller (Advisor); John Horack (Committee Member); Michael Bisesi (Committee Member); Natalie Hull (Committee Member) Subjects: Environmental Health; Environmental Science; Microbiology

Doctor of Philosophy, The Ohio State University, 2023, Plant Pathology

Insects are the most diverse animal class worldwide, inhabiting many ecosystems. Insects have developed different mechanisms to protect themselves from the environment and against diverse pathogens. Fungi have developed strategies to overcome insect defense mechanisms and extract nutrients from them. The Cordycipitaceae family has captured scientific interest due to its wide-ranging species diversity, important medicinal value, its potential for biocontrol applications, and its role in discovering bioactive compounds. Many of this family are entomopathogenic fungi, displaying diverse host ranges and infection strategies. For example, Cordyceps militaris is a specialized pathogen of lepidopteran species, while Beauveria bassiana can kill over 700 species across different hosts. Various infection strategies, such as cuticular and oral infection, have been proposed within this family to induce disease. Moreover, certain members of this group not only infect insects through multiple pathways but also can grow endophytically within different plant species. Work described throughout this dissertation explored several research questions related to generalist and specialist insect pathogens within the Cordycipitaceae family. Specifically, this work aimed to (i) identify genomic trait differences, (ii) determine the evolution of a biosynthesis cluster, and (iii) visualize unique patterns in cuticular and oral infections, as well as endophytic abilities. To explore distinct characteristics within generalist and specialist insect pathogens, a 36-genome dataset was created for a comprehensive genomic analysis, which included three newly sequenced C. militaris isolates. Overall, generalist insect pathogens possess significantly more biosynthetic gene clusters (BGCs), degradative gene clusters (DGCs), and bacterial-like toxins than specialists. Additionally, generalist insect pathogens displayed a higher abundance of adhesins. Although the count of chitinases was similar in gener (open full item for complete abstract)

Committee: Jason Slot (Advisor); Jonathan Jacobs (Committee Member); Chad Rappleye (Committee Member); Rachelle Adams (Committee Member) Subjects: Entomology; Plant Pathology

Doctor of Philosophy, The Ohio State University, 2023, Plant Pathology

Endophytic fungi are ubiquitous in plants and play a pivotal role in shaping the complete collection of metabolites within host plant tissues, which is known as the holometabolome. The ability of endophytic fungi to produce and modify diverse metabolites can significantly impact the health and functionality of their host plant. Here we investigate and compare the diverse metabolic abilities of endophytic fungi across a variety of fungal endophyte species. Through genomic analyses, we identify diverse collections of metabolic gene clusters in fungal genomes which underpin the ability to produce secondary metabolite and modify compounds. Through metabolomic analyses, we examine distinct metabolite repertoires produced by different fungal endophyte species under varied conditions, such as when co-cultured with another endophyte or when exposed to specific plant compounds. Our findings suggest that endophytic fungi have enhanced capabilities for secondary metabolite and plant compound degradation, suggests that diverse metabolite capabilities are key to the fungal endophytic lifestyle. We identified several patterns in the distribution of metabolic gene clusters types across fungal species and identified variations in the metabolite profiles dependent on fungal species and cultivation conditions. The distinctions in metabolic abilities between fungal endophyte species sheds light on how the diverse metabolites in host plants drive the composition of endophyte communities, and also how different endophyte communities can uniquely contribute to the holometabolome. Overall, this research contributes our understanding of fungal endophytes and elucidates how endophyte metabolism shapes their ecological interactions with other organisms.

Committee: Jason Slot (Advisor); Pierluigi Enrico Bonello (Committee Member); Maria Soledad Benitez Ponce (Committee Member); Kou-San Ju (Committee Member) Subjects: Bioinformatics; Genetics; Plant Pathology

Doctor of Philosophy, The Ohio State University, 2023, Plant Pathology

Plants continually confront a multitude of environmental challenges that can impede their growth, development, and survival, and thereby have evolved a remarkable array of responses to environmental stresses to ensure their persistence on the landscape and optimize growth. These stress responses are remarkably plastic and adaptable to a changing environment and have been the subject of intense research interest. The study of plant stress responses provides critical insights into fundamental physiological processes and has practical implications for agriculture, conservation, and ecosystem management. Understanding the intricate signaling cascades and molecular components that underlie plant stress responses is essential for developing strategies to enhance stress tolerance in crops, mitigate the impact of climate change on ecosystems, and conserve plant biodiversity. In recurring encounters of tree species with both abiotic stress and pathogenic invasions, delimiting stress responses will be instrumental for conservation and management practices. Building on current understanding of induced resistance in the Pinus nigra - Diplodia spp. pathosystem, we hypothesized that, (1) predisposition of Austrian pine to abiotic stress such as climate change (CC) leads to increased susceptibility to pathogenic infections by Diplodia spp. and this heightened susceptibility is explainable by a detailed analysis of the transcriptional regulation of both the host and pathogen, (2) attack of Austrian pine by D. pinea results in a systemic induced resistance (SIR) phenotype that intensifies over time, and (3) this phenotype is mediated by the accumulation of terpenoids and is explainable by a detailed analysis of signaling pathways involving phytohormones in specific patterns. The test of the first hypothesis is described in Chapter 2. We subjected Austrian pine trees to simulated CC conditions of high temperatures and prolonged water scarcity, followed by infection with either D. p (open full item for complete abstract)

Committee: Pierluigi Bonello (Advisor); Guo-Liang Wang (Committee Member); Tea Meulia (Committee Member); Jason Slot (Committee Member); David Mackey (Committee Member) Subjects: Plant Pathology

Doctor of Philosophy, The Ohio State University, 2023, Translational Plant Sciences

The composition and organization of genomes, or genome architecture, underlies the ecology and adaptability of organisms, though the fundamental evolutionary drivers of divergent genome architecture remain cryptic. Genome architecture varies across life with prokaryotes exhibiting streamlined genomes that are replete with gene clusters comprised of colocalized genes with cooperative functions. In contrast, multicellular eukaryotes trend toward larger genomes with a higher degree of dispersed gene coordination within the genome. Fungi lie along the center of this continuum, which positions the lineage as a model system for identifying the fundamental rules of life that drive divergent genome architecture. In particular, independent evolution of genomic regions apart from evolutionary pressures acting on the genome as a whole, or selfishness, is a controversial proposed driver of divergent genome architecture. Horizontal gene transfer is linked to the transmission of selfish elements and is hypothesized to increase the prevalence of clustered genome architecture by facilitating the dissemination of genomic regions with complex selectable phenotypes. The primary objective of my dissertation is to quantitatively determine the influence of selfishness in shaping divergent gene cluster architecture. In Chapter 1, I synthesize how divergent architecture evolves, the functions and human-utility of different gene clusters, and the implications and models that explain selection on gene cluster architecture. In Chapter 2, I implement a computational framework that harnesses the exponentially-expanding dataset of fungal genomes. I use this platform to standardize downstream large-scale comparative genomic analysis. In Chapter 3, I more comprehensively and accurately identify gene clusters compared to contemporary algorithms by developing an evolution-informed approach to detecting gene clusters. I implement this algorithm to identify overlooked gene clusters de novo, and char (open full item for complete abstract)

Committee: Jason Slot (Advisor); Jessica Cooperstone (Advisor); Jason Stajich (Committee Member); Laura Kubatko (Committee Member); Jonathan Jacobs (Committee Member); Matthew Anderson (Committee Member) Subjects: Biology; Botany; Evolution and Development; Microbiology