Browsing by Author "Stewart, Jane, committee member"
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Item Embargo Characterization and insights into the molecular mechanism of cytokinin-induced priming of plant defenses(Colorado State University. Libraries, 2023) McIntyre, Kathryn, author; Argueso, Cristiana, advisor; Bush, Daniel, committee member; Leach, Jan, committee member; Stewart, Jane, committee member; Reddy, Anireddy, committee memberPlants have developed several mechanisms to cope with pathogenic challenges. One of these mechanisms, known as defense priming can be effective at reducing susceptibility to pathogens. Compared to unprimed plants, the immune response from primed plants, upon pathogen attack, is much stronger. This mechanism of induced disease resistance can be initiated by biological and chemical agents. The major benefit of priming is the induction of a high level of protection with considerably low fitness costs making it an attractive disease management strategy to preserve agricultural output. Recent research has demonstrated that the plant hormone cytokinin (CK) has a priming effect against biotrophic pathogens, a phenomenon referred to here as cytokinin-induced priming (CIP). This dissertation aims to gain further understanding of CIP against the hemibiotrophic bacterial pathogens Pseudomonas syringae pv. tomato (Pst) and Pseudomonas syringae pv. maculicola (Psm) in Arabidopsis thaliana (Arabidopsis) and Brassica napus, respectively as well as the necrotrophic fungal pathogen Botrytis cinerea in Arabidopsis. Chapter 2 focuses on characterizing CIP as a true priming agent by investigating the timeframe in which CIP is most effective at reducing susceptibility to Pst and Psm in both Arabidopsis and its closely related relative, B. napus and the impacts on plant growth due to CIP in these pathosystems. Moreover, we discovered that other known priming agents depend on endogenous CK signaling suggesting CK-mediated processes are involved in the priming of defense responses. The role of CK in primed defenses against B. cinerea is explored in chapter 3 where CIP is demonstrated to reduce necrotic lesion size caused by B. cinerea in a manner dependent on the JA-mediated defenses and partially on SA-mediated defenses. Transcriptome analysis revealed that during the priming stage, CK prepares the plants for pathogenic challenge through the accumulation of cellular components needed for translation and metabolites utilized for energy production and defense. Following B. cinerea inoculation, CIP suppresses defense while increasing photosynthetic-related processes. In the final chapter, molecular mechanisms are explored during CIP against Pst. Through transcriptome changes, priming by CK potentiates gene expression associated with systemic induction of defense, also known as systemic acquired resistance (SAR), following Pst challenge. Using this information, it is demonstrated that CK treatment can also induce SAR and that the known SAR inducer, L-pipecolic acid, is dependent on endogenous CK signaling. Due to the previously identified relationship between CK and source-sink relationships, amino acid transport was demonstrated to have a role in both CIP and CK-induced SAR. New agricultural practices that mitigate crop loss due to plant diseases are beneficial in terms of sustainability and economic costs. The use of CK as a priming agent offers an avenue for a new disease management strategy in that CIP protects plants against a broad range of pathogens with minimal effects on plant growth. The molecular mechanisms underlying CIP discovered here offers new insights into the relationship between plant metabolism and defense, where its exploitation could be used to create disease protection strategies.Item Open Access Complex interactions between dwarf mistletoe, fuel loading, and fire in the lodgepole pine dominated forests of central Colorado(Colorado State University. Libraries, 2016) Ritter, Scott, author; Hoffman, Chad, advisor; Ex, Seth, committee member; Stewart, Jane, committee member; Zimmerman, Tom, committee memberLodgepole pine dwarf mistletoe (Arceuthobium americanum Nutt. ex Engelm) is an obligate hemiparsite that infects lodgepole pine (Pinus contorta Dougl. Ex. Loud) throughout the large majority of lodgepole pine’s range. Lodgepole pine dwarf mistletoe increases mortality rates, alters tree biomass distributions, and slows overall tree growth, which results in substantial losses to stand productivity and wood quality. In lodgepole pine dominated forests, dwarf mistletoe and wildfire are fundamental disturbances that may interact with each other in complex ways. This interaction is bidirectional as wildfire can either positively or negatively affect post-fire dwarf mistletoe populations, and pre-fire dwarf mistletoe populations may influence wildfire severity. Though it has long been assumed that dwarf mistletoe increases potential wildfire severity in lodgepole pine forests through modifications to the fuels complex, empirical data to support this conclusion is lacking. The overall goal of this project was to enhance the understanding of both sides of the fire-dwarf mistletoe interaction through a combination of long-term post-fire data, forest measurements, and simulation of dwarf mistletoe impacts and intensification. Chapter one provides background into dwarf mistletoe biology and pathology, and reviews the existing literature on interactions between fire and dwarf mistletoe. The second chapter documents the results of research into the influence of dwarf mistletoe infestation level on stand structure and fuel parameters that influence potential fire behavior. To evaluate the relationship between infestation severity and stand structure and forest fuels plots were randomly located within stands containing a range of dwarf mistletoe infestation severities. Of primary interest were impacts to canopy base height and the loading of fuels both on the forest floor and in the canopy. Chapter three is a case study documenting the impact of three prescribed crown fires on dwarf mistletoe populations thirty years post-fire. These fires burned across a range of mortality levels allowing for a detailed evaluation of the influence of fire severity on dwarf mistletoe populations. This chapter combines field measurements with forest growth and yield simulations from the United States Forest Service’s Forest Vegetation Simulator to understand longer-term impacts to both the dwarf mistletoe population and stand productivity. Field data from randomly located plots indicate that dwarf mistletoe may have conflicting impacts on parameters influencing crown fire potential and wildfire severity. This finding suggests that the impact of dwarf mistletoe infestation of potential wildfire severity may not conform to the positive linear relationship assumed by many forest pathologists. Infestation level was found to have a strong positive relationship with the loading of surface fuels of all sizes, and was negatively related to canopy base height, and calculated canopy fuel load and canopy bulk density. Impacts to stand structure include significant reductions to live basal area and average tree size, and significant increases to the density and basal area of standing dead trees. The results from the long-term post-fire data set provide experimental evidence showing that fire severity negatively influences future dwarf mistletoe populations, and that long-term population reductions are possible without complete stand replacement. Over multiple fire cycles, feedbacks between fire and dwarf mistletoe may enhance heterogeneity in burn patterns, infestation severity, and stand structures across the landscape.Item Embargo Development and characterizations of mycelium-based composites(Colorado State University. Libraries, 2024) Davis, Morgan N., author; Li, Yan Vivian, advisor; Morris, Kristen, committee member; Stewart, Jane, committee memberThe current materials economy produces linear materials without regard to their end of life. As the demand for these materials rises, the demand for a new textile economy increases: regenerative by design, minimizing resource input, and waste systems. Mycelium-based composites (MBC) is a lightweight biodegradable material, with good thermal insulation, fire resistance, and acoustic attenuation. The role of MBC lies at a crossroads between biology and design, where designers incorporate biological principles and need to understand the mechanisms of material growth. The study's specific aims include the evaluation of the chemical, mechanical, and physical properties of MBC developed in various conditions and nutrient substrates. Essential to this process is the cultivation of the mycelium, where careful considerations of fungal species, nutrient substrate, and growing parameters are critical. A component of the first critical factor emerges: verification of the fungal DNA. The nutrient substrate hemp fabric demonstrates great compatibility, with the fungal species Pleurotus fossulatus, as it has the largest hyphae diameter, and offers solutions to incorporate waste. In contrast to the strong hydrophilic nature inherent in many natural cellose, mycelium exhibits hydrophobic properties, a critical feature in terms of product implication. The results provide insight for the future design and optimization of mycelium-based composites for product development innovation.Item Open Access Evaluation of cover crops in reducing Spongospora subterranea inoculum through qPCR and microscopy assays(Colorado State University. Libraries, 2021) Alaryan, Maryam M., author; Charkowski, Amy, advisor; Stewart, Jane, committee member; Wrighton, Kelly, committee memberCover crops have been used for years as an effective practice to manage soil-borne pathogens. Beside their other beneficial properties in enhancing soil quality and fertility, they can suppress soil-borne pathogens and reduce their populations in the soil. Spongospora subterranea is a soil-borne obligate biotrophic plasmodiophorid that causes powdery scab on potato tubers and gall formation on roots. Powdery scab tuber lesions are filled with resting spores (sporosori) and reduce potato quality and marketability. S. subterranea also vectors Potato mop-top virus, which causes necrotic arcs and spraing in tuber flesh. Currently, there are no effective methods to manage S. subterranea, which has a wide host range in addition to potato. This study was conducted to determine whether cover crops can decrease S. subterranea population levels in the soil. Eighteen cover crops, including legumes and mustards were assessed, and for each plant line, five plants were grown in individual pot that was inoculated with 10 sporosori/g of potting mix by comparison with five plants that were grown in non-inoculated potting mix. After harvest, plant roots were stained using trypan blue and examined under the light microscope, and qPCR was performed to determine S. subterranea inoculum level in the potting mix. The results suggested that S. subterranea invaded all the cover crop roots; however, the pathogen was unable to complete its life cycle on eleven out of eighteen cover crops based on post-harvest qPCR results. To confirm our results, a follow up experiment was conducted by inoculating the potting mix with 40 sporosori/g to better detect the pathogen, in addition to autoclaving the peat moss prior to planting. The roots were stained with DAPI after harvest and examined under the fluorescence microscope and S. subterranea DNA levels was quantified in the eleven cover crops by qPCR. The results showed that buckwheat, barley, and legumes have the potential to stop the pathogen from increasing in the soil where there was no significant increase in the inoculated samples in most of the tested cover crops. The results from this experiment will be used to guide in-field cover crop experiments and to advise farmers on cover crops that may not increase the inoculum levels of S. subterranea in the soil.Item Open Access Modern considerations for the use of naive Bayes in the supervised classification of genetic sequence data(Colorado State University. Libraries, 2021) Lakin, Steven M., author; Abdo, Zaid, advisor; Rajopadhye, Sanjay, committee member; Stenglein, Mark, committee member; Stewart, Jane, committee memberGenetic sequence classification is the task of assigning a known genetic label to an unknown genetic sequence. Often, this is the first step in genetic sequence analysis and is critical to understanding data produced by molecular techniques like high throughput sequencing. Here, we explore an algorithm called naive Bayes that was historically successful in classifying 16S ribosomal gene sequences for microbiome analysis. We extend the naive Bayes classifier to perform the task of general sequence classification by leveraging advancements in computational parallelism and the statistical distributions that underlie naive Bayes. In Chapter 2, we show that our implementation of naive Bayes, called WarpNL, performs within a margin of error of modern classifiers like Kraken2 and local alignment. We discuss five crucial aspects of genetic sequence classification and show how these areas affect classifier performance: the query data, the reference sequence database, the feature encoding method, the classification algorithm, and access to computational resources. In Chapter 3, we cover the critical computational advancements introduced in WarpNL that make it efficient in a modern computing framework. This includes efficient feature encoding, introduction of a log-odds ratio for comparison of naive Bayes posterior estimates, description of schema for parallel and distributed naive Bayes architectures, and use of machine learning classifiers to perform outgroup sequence classification. Finally in Chapter 4, we explore a variant of the Dirichlet multinomial distribution that underlies the naive Bayes likelihood, called the beta-Liouville multinomial. We show that the beta-Liouville multinomial can be used to enhance classifier performance, and we provide mathematical proofs regarding its convergence during maximum likelihood estimation. Overall, this work explores the naive Bayes algorithm in a modern context and shows that it is competitive for genetic sequence classification.Item Open Access Paralogy or reality? Exploring gene assembly errors in a target enrichment dataset(Colorado State University. Libraries, 2022) Rosén, Austin, author; Simmons, Mark P., advisor; Ackerfield, Jennifer, committee member; Richards, Christopher, committee member; Stewart, Jane, committee memberDe novo gene assembly of short read data is inherently difficult – similar to the process of assembling a jigsaw puzzle. I describe three errors that occurred with the assembly of target enrichment data in the genus Cirsium (Asteraceae): inconsistent contig selection, artificial recombination, and inconsistent intron determination leading to over-alignment of non-homologous nucleotides. These errors occurred in 39% of loci in the dataset and were often a by-product of undetected paralogs: assembled loci that likely contained paralogous or homoeologous sequences but did not trigger default paralog warnings by the assembly program, HybPiper. Default HybPiper thresholds for identifying paralogy during the assembly process were insufficient to filter such loci. A custom target file was created in which putative paralogs were separated into independent loci. The custom target file was successful in reducing, but not eliminating, assembly errors in the dataset. A final iteration of quality control was performed to create a dataset largely free of assembly errors. However, phylogenetic inferences applied to this final cleansed dataset were unable to resolve the taxonomic relationships between the sampled specimens. Rather, these results affirm that Cirsium is a taxonomically problematic genus and may require population-level genetic data or integrative taxonomy approaches to delimit species boundaries.Item Open Access Pavement, pests, & parasitoids, oh my! Elm herbivores and their natural enemies in the urban forest(Colorado State University. Libraries, 2022) Buenrostro, Jacqueline, author; Hufbauer, Ruth, advisor; Cranshaw, Whitney, committee member; Redmond, Miranda, committee member; Stewart, Jane, committee memberUrban areas are the fastest growing habitat type in the world, and an increasing proportion of the United States and global population lives in urban areas. Urban forests provide essential ecosystem services to rapidly expanding urban populations, but their health is threatened by damaging herbivory from non-native, invasive insects. To address this problem, my masters research investigated two critical questions that limit our ability to sustainably manage invasive insects in urban forest ecosystems: (1) How do urban environments impact the density of invasive herbivores in the urban forest? and (2) Are predator and parasitoid natural enemies present, and, if so, what is the level of parasitism? I investigated these questions in the context of the elm-herbivore study system, analyzing a globally distributed host tree and its complex of invasive insect pests in Colorado, USA. In my first chapter, I address the first question and explore how a variety of environmental factors that vary across urban habitats influence the density of several invasive insects. Specifically, I evaluate how vegetational complexity, distance to buildings, impervious surface, canopy temperature, host availability, and density of co-occurring herbivores impact three invasive pests of elm trees: the elm leaf beetle Xanthogaleruca luteola Müller (Coleoptera: Chrysomelidae), the European elm flea weevil Orchestes steppensis Korotyaev (Coleoptera: Curculionidae), and the elm leafminer Fenusa ulmi Sundevall (Hymenoptera: Tenthredinidae). I found that insect responses to these factors were species-specific, and all environmental factors were associated with density of at least one pest species except for distance to buildings. Elm leafminer density decreased with higher temperatures and was influenced by an interaction between vegetational complexity and impervious surface. Elm flea weevil density increased with greater host availability, and elm leaf beetle density increased with higher temperatures. Both elm leaf beetle and elm flea weevil density decreased with greater leafminer density, suggesting that insect density is mediated by species interactions. Results of this study can be used to inform future tree planting efforts through the selection of "safe sites", or locations where trees will be less likely to experience damaging outbreaks of insect pests. Additionally, these results can be used to strategize preventative management on trees that are located in outbreak "hotspots", or locations where environmental conditions make trees predisposed to insect outbreaks. Finally, results of this study contribute to our knowledge of the dynamic ways in which multiple invasive insects interact in urban environments. This information will be especially valuable as non-native insect introductions continue to increase into the future. In my second chapter, I narrow my focus to two historically important and particularly damaging pests of elm, the elm leaf beetle and elm flea weevil, to address the second question listed above and explore the complex of natural enemies attacking these two pests. In many areas of these insects' invaded range, outbreaks severely damage elm hosts. Natural enemies are thought to be important in regulating elm leaf beetle and elm flea weevil populations in other regions, but whether natural enemies are present in Colorado is largely unknown. As such, the aim of chapter 2 was to identify which predators and parasitoids of these pests are present in Colorado, a state with frequent pest outbreaks and where the natural enemy community is almost entirely undescribed. In June – August 2021, I identified predators through field observations and laboratory feeding trials, finding seven species of predators from six arthropod orders that fed on elm leaf beetle or elm flea weevil. Additionally, I reared 58 elm leaf beetle egg clusters, 539 elm leaf beetle larvae, and 435 elm flea weevil mines to detect parasitoids. Two parasitoids of elm leaf beetle, the egg parasitoid Oomyzus gallerucae and the larval-adult parasitoid Erynniopsis antennata, are present in Colorado, representing novel records of these species in the state. However, combined parasitism of elm leaf beetle eggs and larvae was low at <3% across the season, with parasitoids nearly absent early in the season and peak parasitism occurring in late summer. I found five families of parasitoid wasps that emerged from leaves containing weevil mines: Chalcididae, Encyrtidae, Eulophidae, Euplemidae, and Pteromalidae. Parasitoids emerged from <20% of leaves containing weevil mines with almost no parasitism early in the season. Given the low parasitism rates and few predators observed in our study, it seems unlikely that predator and parasitoid natural enemies exert effective control over elm leaf beetle and elm flea weevil in Colorado. This finding challenges the assumption that natural enemies are a driving force of elm leaf beetle and elm flea weevil control in Colorado. Additional research is needed to confirm species identifications for parasitoids of the elm flea weevil, disentangle elm leaf beetle and elm flea weevil population dynamics, and establish effective and sustainable control methods amidst frequent pest outbreaks. Together, these two research projects enhance our knowledge of what triggers outbreaks of the elm leaf beetle Xanthogaleruca luteola, the elm flea weevil Orchestes steppensis, and the elm leafminer Fenusa ulmi in urban areas while also laying the groundwork for a renewed interest in biological control of elm leaf beetle and elm flea weevil. It is my hope that this work can be applied to other invasive insect pests in urban forest ecosystems and make urban forests more resilient in an era when they are increasingly vulnerable to insect attack.Item Open Access Phenotypic and experimental variation in Beauveria bassiana isolates from the Rocky Mountain region(Colorado State University. Libraries, 2019) Mann, Andrew, author; Davis, Seth, advisor; Ode, Paul, committee member; Redmond, Miranda, committee member; Stewart, Jane, committee memberThe ubiquitous insect-killing fungus Beauveria bassiana is widely used as a biological control agent to treat a variety of arthropods ranging from mites to beetles. Dendroctonus rufipennis has been responsible for the death of 17 million Picea engelmannii trees over the past two decades and is currently considered to be one of the major forest pests in western North America. Despite the promise that B. bassiana brings as a form of augmentative biological control against D. rufipennis, a recent laboratory evaluation did not lead to successful field application likely due to a lack of cohesion between environmental conditions that D. rufipennis and B. bassiana prefer. Chapter 1 describes the previous literature on B. bassiana as a biological control agent of Hylesinini bark beetles. In 32 studies to date, not one has studied the pathogenicity of potential strains against a range of abiotic and biotic conditions representative of bark beetle habitats. Therefore, I summarize findings of how B. bassiana might respond to abiotic and biotic factors representative of Hylesinini beetle systems extrapolating from findings in other systems. There is a particular dearth of literature in how B. bassiana responds to competition with other microorganisms and plant secondary metabolites. In chapter 2, I tested 14 B. bassiana isolates from the Rocky Mountain region for their growth, pathogenicity, and virulence in a series of environmental assays representative of the D. rufipennis study system such as a range of temperatures, competition with the spruce beetle symbiotic fungus Leptographium abietinum, constitutive and induced concentrations of five Picea engelmannii monoterpenes, varying levels of osmotic potentials, a nutrient limited environment, and sunlight. Three major findings emerged from this chapter: (1) genetically related B. bassiana isolates from similar habitats and sources exhibit considerable variation in their growth response to environmental conditions; (2) low temperatures and monoterpenes are highly inhibitory to B. bassiana growth, pathogenicity, and virulence; and (3) the interpretation of isolate virulence and pathogenicity can differ substantially depending on bioassay design. These collective findings have implications for the field application of B. bassiana as a bark beetle control agent and could help explain discrepancies between laboratory field assessments.