<p> A model of two predators competing for the same prey also involving predation interaction between the two predators is considered. Coexistence in forms of equilibria and periodic orbits is obtained by using bifurcation and dynamical systems theory. Global dynamics is obtained by studying the survival functions and persistence is obtained by using a theorem of Freedman and Waltman. Finally, numerical results for a specific example demonstrate the above. A Hopf bifurcation at the interior equilibrium and its unstable periodic orbit are observed.</p> / Thesis / Master of Science (MSc)

The eastern massasauga rattlesnake, or massasauga, is threatened in Ontario. Massasaugas overwinter in habitat that is sufficiently moist, above the water table, and below the zero-degree isotherm in a physical space conceptualized as a resilience zone. A development project in the Eastern Georgian Bay subpopulation of massasaugas overwintering habitat necessitated restoration. The Toronto Zoo hibernacula design was deemed inappropriate for use in this bedrock dominated landscape, as the limited deep groundwater percolation would result in flooding of the habitat from the fall to spring. Massasaugas in EGB, overwinter above the water table in Sphagnum peat hummocks. The ecohydrological factors of these hummocks in confirmed massasauga habitat were evaluated in a mixed effect linear model. It was found that taller hummocks, taller shrubs, and less WT variability were the best predictor of suitable conditions. This information was combined into a restoration method that moves surficial peat material from a soon to be impacted wetlands to an adjacent depression with mean depths of 40-80 cm, with mean bottom substrates 15-30 cm, and varying proportions of open water and floating peat with different vegetation communities. This design limits water table variability and allows for the growth of tall shrubs. Unforeseen circumstances meant that peat to be used in the project had to be stockpiled, which increased peat bulk density and limited photosynthesis. Despite this, restored habitat had similar mean lengths of unsuitable conditions compared to confirmed massasauga wetland habitat. The physical size of available overwintering habitat, as well as the total duration of unsuitable conditions, was not significantly different between restored wetlands, unconfirmed wetlands, and confirmed wetlands. Amendments to increase the cover of live Sphagnum moss will likely increase the duration and size of suitable conditions in the restored wetlands. Based on this success with degraded materials this new method of restoration design shows great promise in this region. / Thesis / Master of Science (MSc)

Gradient-driven mass diffusion, or species separation, is a transport process which can occur in plasma shocks. Experimental observations of this phenomena are difficult to make, but are of interest to ongoing Inertial Confinement Fusion efforts. This body of work describes the results of two major experimental campaigns conducted at Virginia Tech's Experimental Plasma and Propulsion Laboratory to identify species separation in multi-component plasma shocks. A linear plasma-armature railgun forms and accelerates low temperature, high density, supersonic plasma jets, with the collision between two of these jets shown to induce a collisional plasma shock in the first campaign. The second campaign leverages this experimental setup while employing spatially resolved emission spectroscopy alongside collisional radiative modeling to identify species separation within multi-ion-species plasma shocks consisting of argon, aluminum, and nitrogen. These results are some of the first to be performed in a plasma shock with more than two ion species, and can be used for verification and validation of physics models of fusion plasmas. This body of work was supported by the National Science Foundation under Grant No. PHY-1903442. / Doctor of Philosophy / Plasmas represent the fourth state of matter, where enough energy has been imparted onto a gas for ionization to occur, resulting in a quasi-neutral collection of charged and neutral particles that are subject to both hydrodynamic and electrodynamic effects. Shocks can occur in plasmas, which presents as a transition layer where plasma parameters drastically change over a small region of space. Plasmas hold the key to nuclear fusion, with the topic of gradient-driven mass diffusion, or species separation, in plasma shocks being of great interest to large-scale fusion experiments. This body of work performs experimental measurements using a railgun-based plasma source to create plasma shocks with multiple ion species in the laboratory, and ultimately observe this effect of species separation through the use of spatially resolved spectroscopy. To the author's best knowledge, these measurements represent some of the first to be done in a plasma shock with more than two ion species, and can be used to benchmark physics models of plasmas in fusion experiments.

Steroidal glycoalkaloids (SGAs) are secondary metabolites produced by approximately 350 species in the Solanaceae family. SGAs are reported to be important for pest resistance and flavor enhancement at low concentrations but are toxic to humans and other mammals at high concentrations. Studies on sterol / SGA biosynthesis have implicated squalene synthase as a key regulatory enzyme because it catalyzes an irreversible step from the mevalonic acid pathway. However, the regulatory mechanisms of squalene synthase are not yet known. A study was conducted to elucidate the distribution pattern of SGAs and to clone the squalene synthase gene in order to determine a relationship between SGAs and gene expression levels. Solanum chacoense, a wild potato species was used as a model plant from which tissues were harvested at specified developmental stages and analyzed for SGA content. The results from the SGA analysis suggest a qualitative and quantitative tissue- and age-dependent accumulation of SGAs. Regenerative tissues such as, axiliary shoots, flowers and floral buds had the highest levels of 88, 49 and 63 µmole/g DW, respectively. The roots, stems and tubers showed the lowest amounts of SGAs of 1 to 8, 5 to 15 and 7 to 15 µmole/g DW, respectively. Stolons and tubers accumulated higher amounts of α-chaconine (59 to 67%) than α-solanine (61 to 64%) at all developmental stages analyzed. On the other hand, in young expanding, fully expanded, and old senescing leaves where leptine and leptinines tend to dominate, α-solanine and α-chaconine together accounted for only 8 to 15%, 7 to 15%, and 8 to 45%, respectively. Plant organs that showed the highest biosynthetic activity for SGA production also had high levels of transcripts coding for genes of isoprenoid biosynthesis. The results from the cloning and characterization of squalene synthase suggest that the cloned cDNA fragment is a putative S. chacoense squalene synthase gene with an open reading frame / predicted protein precursor of 411 amino acids. The cloned cDNA has high similarity (68-100%) to known plant squalene synthase genes and contains six deduced peptide domains observed in other species. The 3â untranslated regions of floral buds, young leaves (early vegetative stage), and fully expanded leaves (anthesis) were different in length with, 249, 335, and 202 nucleotides, respectively. The Southern blot analysis suggests a single copy gene although the existence of a gene family cannot be ruled out. / Ph. D.

Fungi of the Crepidotaceae are characterized by saprotrophic habit, filamentous cuticle, and brown-pigmented basidiospores that lack either a germ pore or plage. The majority of species belong to Crepidotus, distinguished by their pleurotoid basidiomata. Because of their diverse morphology, the presence of several conflicting classifications, and lack of data regarding the biology, phenotypic plasticity, or phylogeny of these fungi, the present study sought first to determine phylogenetic relationships among the different taxonomic groups as a basis for addressing other aspects of Crepidotus biology and evolution. Sequencing analyses show the Crepidotaceae is not monophyletic, and the family concept is revised. Crepidotus and its sister genus Simocybe are found to be monophyletic. At least nine phylogenetic lineages within Crepidotus were uncovered, although relationships between them could not be resolved. However, none of the previously proposed infrageneric classifications are reflective of phylogeny. Morphological, biological, and phylogenetic species concepts were compared within a single phylogenetic unit, termed the Sphaerula group, showing an unusual amount of phenotypic plasticity exists within species, and a taxonomic revision of these species proposed. Also reported are several unique or unusual aspects of Crepidotus biology, including presence of a prolonged latent period prior to basidiospore germination; spontaneous reversion of differentiated hymenial cells to vegetative growth; and the revelation that structures previously termed pleurocystidia are actually the expression of secondary growth from basidia. Results from mating system, culture, and type studies, reassessment of morphological characters traditionally applied to agaric taxonomy, and a revised life cycle for the Crepidoti are presented. / Ph. D.

The need for new antibiotics has been highlighted recently with the increasing pace of emergence of drug resistant pathogens (MRSA, XDR-TB, etc.). Modification of existing antibiotics with the additions of side chains or other chemical groups and genomics based drug targeting have been the preferred method of drug development at the corporate level in recent years. These approaches have yielded few viable antibiotics and natural products are once again becoming an area of interest for drug discovery. We examined the antimicrobial "Red Soils" of the Hashemite Kingdom of Jordan that have historically been used to prevent infection and cure rashes by the native peoples. Antimicrobial producing bacteria were present in these soils and found to be the reason for their antibiotic activity. After isolation, these bacteria were found to excrete their antimicrobials into the liquid culture media which we could then attempt to isolate for further study. Adsorbent resins were employed to capture the antimicrobial compounds and then elute them in a more concentrated solution. As part of a drug discovery program, we sought a way to quickly characterize other soils for potential antibiotic producing bacteria. The community level physiologic profile was examined to determine if this approach would allow for a rapid categorizing of soils based on their probability of containing antimicrobial producing microorganisms. This method proved to have a high level of variability that could not be overcome even after mixing using a commercial blender. The role of these antimicrobial producing bacteria within their natural microbial community has largely been confined to microbe-plant interactions. The role of antimicrobial-producing microorganisms in driving the diversity of their community has not been a focus of considerable study. The potential of an antimicrobial-producing bacterium to act as a driver of diversity was examined using an artificial microbial community based in a sand microcosm. The changes in the microbial assemblage indicate that antimicrobial-producing bacteria may act in an allelopathic manner rather than in a predatory role. / Ph. D.

Relationships between nutrient heterogeneity, root foraging behavior and short-term competitive interactions were investigated for six species native to southeastern USA. Monoculture, two- and six-species garden plots were established and fertilized to create spatially homogeneous or heterogeneous nutrient conditions. After 3.5 months, root proliferation in rich patches (precision) and aboveground biomass response to heterogeneity were assessed in monocultures, and competitive outcomes (aboveground biomass) were determined from mixed-species plots. In monoculture plots, two species were relatively precise foragers, but no species showed significant aboveground biomass response to nutrient treatment. Correlations between precision and aboveground biomass were weak (-0.40 < r < 0.17). In two-species plots, interspecific competition was influenced by soil heterogeneity in two of six cases tested (P < 0.05), and precision was the behavior most correlated with competitive success. In six-species plots, spatial pattern of nutrients had no influence on aboveground growth or competition. Results suggest that heterogeneity influences competition, but the influence is context-specific and generally small. Precision may be the foraging behavior that most influences interspecific interactions. / Ph. D.

Biological invasions have been observed throughout the world for centuries, often with major consequences to biodiversity and food security. Tying invasion to species identity and associated traits has led to numerous hypotheses on why, and where, some species are invasive. In recent decades, attention to intraspecific variation among invaders has produced questions about their adaptation to climate, land use, and environmental change. I examined the intraspecific variation of invasive Johnsongrass's (Sorghum halepense (L.) Pers.) seedling stress response, propagule cold tolerance, and large-scale niche dynamics for correlation with populations' climatic and ecotypic (i.e., agricultural vs. non-agricultural) origin. Overall, I found a greater number of home climate effects than ecotypic effects on various traits. Non-agricultural seed from cold climates and agricultural seed from warm climates germinated more and faster, while non-agricultural seedlings showed uniform chlorophyll production regardless of home soil carbon origin, unlike their agricultural counterparts. Neither seedling stress response nor propagule cold tolerance interacted with ecotype identity; however, drought stress varied with population origins' aridity and soil fertility, and seed from warm/humid and cold/dry climates was most germinable. Comparison of seed and rhizome cold tolerance also suggested that the latter is a conserved trait that may be limiting S. halepense poleward range expansion. This physiological limit, an unchanged cold temperature niche boundary between continents and ecotypes, and a narrowed niche following transition to non-agricultural lands all imply low likelihood of spread based on climatic niche shift. Instead, evidence points to range expansion driven primarily by climate change and highlights agriculture's role in facilitating invasibility. This tandem approach to climate and land use as drivers of intraspecific variation is transferable to other taxa and can help refine our conception of and response to invasion in the Anthropocene. / Doctor of Philosophy / Exotic invasive species are a global problem, threatening biodiversity and biosecurity now and in the future. In the last several decades, ecologists have studied many individual invaders and their traits to understand what drives their spread. More recently, abundant differences in traits between populations within an invasive species have raised questions about humans' role in facilitating invasion through climate change, land use, and other disturbances. I studied the invasive Johnsongrass's (Sorghum halepense (L.) Pers.) response to drought, nutrient limitation, and freezing to detect differences between populations based on their climate and ecotype (agricultural vs. non-agricultural) origin. I also tracked differences in the climates the species occupied across the globe and North America and projected its future distribution under climate change. Overall, I found a greater number of home climate effects than ecotypic effects on various traits. Non-agricultural seed from cold climates and agricultural seed from warm climates germinated the most, while non-agricultural seedlings performed consistently regardless of soil carbon origin, unlike their agricultural counterparts. In addition, drought stress varied with population origins' rainfall and soil fertility, and seed germination favored warm/humid and cold/dry origin. Rhizome (underground stem) cold tolerance appears to be a trait that limits S. halepense poleward range expansion. Along with no change in the coldest climates occupied worldwide and no spread to new climates with transition to non-agricultural lands, this implies that Johnsongrass is unlikely to expand its range without external forces. Instead future range expansion will likely be driven by climate change. This coupled approach to climate and land use affecting invasion is transferable to other species and can help refine both our concepts and response strategies.

Interactions are important drivers of selection and community structure, which makes the study of multi-species interactions critical for understanding the ecology and evolution of organisms. This dissertation includes four data chapters that examine the biotic and abiotic mechanisms that shape multi-species interactions in both tropical and temperate ecosystems. The first three data chapters (Chapters 2–4) were completed within a Neotropical rainforest in Costa Rica and focus on one plant genus, Piper (Piperaceae). The final data chapter (Chapter 5) was conducted within a working landscape of soybean (Glycine max) fields in eastern Maryland, USA. In Chapter 2, I explore intra- and inter-specific dietary niche partitioning of Piper fruits among three frugivorous bats, illustrating the importance of fine-scale mechanisms that facilitate species coexistence and influence plant–animal interactions. In Chapter 3, I demonstrate how the chemical ecology of a Neotropical shrub, Piper sancti-felicis, shapes fruit interactions with antagonists (fruit fungi) and mutualists (frugivorous bats and birds), developing a foundation for understanding evolutionary ecology of plant chemical traits based on phytochemical investment patterns. In Chapter 4, I describe the direct and indirect impacts of elevated temperature and CO2 concentration on the plant traits and interactions in Piper generalense, improving our understanding of the effects of climate change on a Neotropical plant–herbivore system. In Chapter 5, I explore the biotic (herbivore-induced plant volatiles) and abiotic (fine-scale weather conditions) drivers affecting insectivorous bat foraging in soybean fields in eastern Maryland, providing a pathway to further investigate new strategies for integrated pest management. As a collective work, this dissertation disentangles the nuances of multi-species interactions, exploring foundational mechanisms underlying biodiversity maintenance as well as answering applied questions to address a changing climate and aid sustainable agriculture. / Doctor of Philosophy / Everything in nature is connected, so studying ecological interactions requires us to view them from many different angles. As with most relationships, ecological interactions are multi-faceted and context-dependent. In this dissertation, I describe both tropical and temperate systems, collecting a variety of measurements from plants, microbes, and animals to explore the complicated relationships that exist between them. In Chapter 2, I explore how three species of fruit-eating bats may divide the use of a shared food resource (tropical pepper fruits in the genus Piper) to maintain separate populations and how those foraging differences may affect Piper plant populations. In Chapter 3, I characterize a chemical compound found in the fruits of a Piper plant species and test the effect of that compound on fruit fungi and fruit-eating bats and birds, leading to a better understanding of the selective pressures affecting fruit chemistry. In Chapter 4, I describe the direct and indirect effects of climate change on a Piper plant in the first study to measure the responses of tropical understory plants to treatments that mimic climate change using active warming and CO2 supplementation. In Chapter 5, I explore the fine-scale drivers of bat activity in soybean fields, including how weather conditions and the specific compounds emitted by insect-damaged plants may affect bat activity. As a collective work, this dissertation describes the complex relationships among plants and their many interactors, exploring questions from biodiversity maintenance to integrated pest management strategies.

Hydrogen sulfide (H2S) has been recognized as a biological signaling molecule for over twenty years now. Since these important findings emerged, many collaborative projects among chemists, biologists, and clinicians have demonstrated the physiological roles and potential therapeutic benefits of exogenous H2S delivery. As our understanding of the active roles H2S plays in biological systems has increased, so has the desire to investigate other related sulfur species (i.e. persulfides, R–SSH) for their physiological interactions with H2S and potential therapeutic efficacy. This recent interest in persulfides has stimulated a flurry of research in the field and created a new set of scientific problems to solve and opportunities to improve our understanding of persulfides in a biological context. With this surge of interest in persulfides, chemists set out to synthesize and characterize a variety of stimuli-responsive compounds that release persulfides under specific, biologically relevant conditions. In order to better understand persulfide reactivity and biological activity, and provide several prodrug platforms that respond to a variety of stimuli, this dissertation describes four persulfide-releasing prodrug systems, a pyrene-based fluorescent probe that measures H2S release in the presence of thiols, and efforts toward a peptide-based system for the release of H2S from a peptide thioacid (C(O)SH). The first four systems described utilize the well-known 1,6-benzyl elimination reaction (sometimes called self-immolation) to trigger release of a persulfide from a small molecule, polymeric, or peptide-based prodrug platform. Importantly, the first self-immolative small molecule persulfide prodrug (termed BDP-NAC) was designed to respond to reactive oxygen species (ROS). Specifically, BDP-NAC utilized a para-positioned boronic acid pinacol ester functionality to selectively react with H2O2, yielding N-acetylcysteine persulfide (NAC-SSH) and p-hydroxybenzyl alcohol as a byproduct. BDP-NAC showed trigger specificity towards H2O2, as determined by the use of a structurally analogous fluorescent probe (termed BDP-fluor). The prodrug also exhibited antioxidant properties in vitro, and served as the first example in the literature of a self-immolative persulfide donor. The second group of donors, self-immolative small molecule and peptide-based persulfide prodrugs (termed SOPD-Pep and SOPD-NAC), were designed to be responsive to superoxide (O2∙–), the primary precursor to all other ROS. In this work, the advantages of attaching small molecule persulfide donors to peptides were explored. In vitro experiments showed that SOPD-Pep mitigated toxicity induced by phorbol 12-myristate 13-acetate (PMA) more effectively than its small molecule counterpart SOPD-NAC and several common H2S donors. It is proposed that peptide scaffolds offer increased cellular uptake due to their nanoscale size, allowing for better antioxidant activity, as confirmed by fluorescence microscopy. The third section of this dissertation compares an esterase-responsive small molecule to an analogous polymeric persulfide releasing prodrug (termed EDP-NAC and polyEDP-NAC) and their abilities to decrease oxidative stress in response to immediate (H2O2) and sustained (5-fluorouracil, 5-FU) forms of ROS. Persulfide release half-lives were characterized using 1H NMR spectroscopy and showed over one order of magnitude difference between EDP-NAC and polyEDP-NAC. In vitro evaluation of the donors showed polyEDP-NAC was better suited to combat sustained production of ROS induced by 5-FU, whereas EDP-NAC was better suited to combat immediately available ROS from H2O2. These discrepancies in antioxidant activity between the two donors were deemed to be a result of their different persulfide release half-lives, indicating that scientists must take these factors into consideration when designing R–SSH prodrugs for specific disease indications. The fourth donor, NDP-NAC, responded to the bacteria-specific enzyme nitroreductase to release its persulfide payload. NDP-NAC elicited gastroprotective effects in mice that were not observed in animals treated with control compounds incapable of persulfide release or in animals treated with Na2S. NDP-NAC induced these effects by the upregulation of beneficial small and medium chain fatty acids and through increasing growth of Turicibacter sanguinis, a beneficial gut bacterium. It also decreased the populations of Synergistales bacteria, opportunistic pathogens implicated in gastrointestinal infections. Lastly, two appendices are provided in this dissertation that briefly describe the synthesis of a pyrene-based H2S sensor and efforts toward a readily accessible peptide-based thioacids as H2S donors. / Doctor of Philosophy / Hydrogen sulfide (H2S), produced naturally in hydrothermal vents and as a byproduct of industrial processes, has historically been known for its potent smell and toxicity. However, the recent discovery of H2S as a naturally-produced signaling molecule (termed gasotransmitter) in mammals has changed the way scientists view this malodorous gas. Our understanding of the biological roles and production of H2S is still growing, and recent research has suggested various links between changes in H2S concentrations in the body and a variety of disease states, including Alzheimer's, cardiovascular disease, and inflammation. Because of this link between various diseases and alterations in natural H2S production, collaborative efforts among chemists, biologists, and pharmacologists have demonstrated the usefulness of therapeutics that contain H2S-donating moieties, in an effort to alleviate these disease conditions. Persulfides (R-SSH), biological signaling molecules related to H2S, have emerged as critical species in sulfur signaling because of the similar observed antioxidative effects compared to H2S. This dissertation focuses on the synthesis and characterization of several compounds that release persulfides in response to specific stimuli (called persulfide donors). The first donor system described here releases persulfides in response to hydrogen peroxide (H2O2), a major cellular oxidant, and reduces oxidative stress in response to H2O2. The second donor system responds to superoxide (O2∙–), a precursor oxidant to H2O2 in cells, to release persulfides. Specifically, two variants of these donors, a small molecule and a peptide-based donor, exhibited antioxidant activity in response to O2∙–, but to varying degrees based on differences in cellular uptake of small molecules and self-assembled peptide nanostructures. The third donor system compares persulfide release from a small molecule and polymeric scaffold, both of which release persulfides in response to esterase enzymes. A large persulfide release half-life range was observed between the two donor systems, and antioxidant activity in response to H2O2 also varied based on the source and timescale of oxidant (H2O2 versus 5-fluorouracil). The fourth section of this dissertation focuses on a persulfide donor that responds to the bacterial enzyme nitroreductase. This donor increased levels of beneficial bacteria and short and medium chain fatty acids in murine models, while simultaneously decreasing levels of a niche subset of harmful bacteria. Taken together, these persulfide donor systems exhibit the strong reducing ability of persulfides in a biological context, showcasing the potential for therapeutic efficacy and avenues for more advanced donors to be synthesized in the future.