Theses and Dissertations at Montana State University (MSU)

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    Elucidation of mechanisms of host plant resistance to wheat stem sawfly (Cephus cinctus Norton) in relation to antibiosis and the early stem solidness phenotype
    (Montana State University - Bozeman, College of Agriculture, 2023) Hager, Megan Sunshine; Chairperson, Graduate Committee: David K. Weaver; This is a manuscript style paper that includes co-authored chapters.
    In the North American Great Plains, wheat stem sawfly (WSS), Cephus cinctus Norton is a serious pest of cultivated cereals including common bread wheat (Triticum aestivum L.) and durum wheat (Triticum turgidum L. var durum). The solid stem phenotype is usually the basis of an effective management strategy in preventing infestation and yield loss in areas which experience pressure from large and damaging WSS populations. However solid stem expression can be negatively influenced by environmental effects and fully solid stems decrease the effectiveness of biological control of WSS by endemic parasitoids, highlighting a need for new sources of resistance outside of the solid stem phenotype. Here, we use 'omics technologies to comprehensively examine potential mechanisms of resistance including antibiotic resistance in oat, as well as small molecules, transcripts, photosynthetic parameters and volatile organic compounds in spring and durum wheat which help to explain decreased levels of infestation and lower incidence of stem cutting observed with the early solid stem phenotype. Genes and metabolites related to cellular organization, lignin composition and stem tissue structure appear to be involved in the resistance observed in oat and are also related to the early stem solidness phenotype in spring and durum wheat. Additionally, metabolic differences in abundance of lipids and carbohydrates were observed between oat and wheat as well as in spring and durum wheat near isogenic lines. Collectively, this research provides insight into the impacts that plant metabolites and gene expression may have on plant resistance to WSS.
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    Interferometric methods for spatial-spectral holographic signal processing applications
    (Montana State University - Bozeman, College of Letters & Science, 2023) Wolfe, Owen Robert; Chairperson, Graduate Committee: Wm. Randall Babbitt; This is a manuscript style paper that includes co-authored chapters.
    Spatial spectral holographic (SSH) systems have applications in signal processing including spectrum analysis to optical correlation. Beam splitters and material interactions can affect the phase relationships between fields in separate spots in the material (or fields bypassing the material). Interferometric methods allow for these phase shifts to be exploited for two primary uses: the isolation of fields generated by the material and the amplification of signals and the amplification of signals in the chirped readout of programmed spectra. Stimulated photon echoes are used as the basis of SSH material-based optical systems and have been suggested as a protocol for optical quantum memory. These applications require the stimulated echo field to be isolated from a probe field. Current methods take an angular approach to isolating fields. An alternative approach uses interferometric methods to isolate fields in a way that can be implemented in a photonic integrated circuit. This dissertation will present a mathematical model for the isolation of stimulated photon echoes in both a 2-port Mach-Zehnder interferometer and a 4-port interferometer designed to emulate the isolation achieved via the angular "Box-Geometry" using interferometric methods. Experimental stimulated photon echo studies in a Mach-Zehnder interferometer built around a sample of 0.01% Tm 3+ : LiNbO 3 will demonstrate the principle of interferometric isolation of stimulated photon echoes. Maxwell-Bloch simulations will be used to demonstrate the principle of echo isolation in the 4-port interferometer. Use of the chirped interferometric readout of programmed spectra is demonstrated for SSH grating processing and spectrum analysis is shown in experiments in a sample of 0.01% Tm 3+ : LiNbO 3. Improvements to signal-to-noise ratio over traditional readout are seen by using a strong local oscillator in both applications. In spectrum analysis applications, the recovery of the proper spectral line shape is demonstrated, and SNR improvements are shown for a given read power. In the grating experiments, a non-linear noise floor was shown that created a constraint on the usable read power for these experiments. In this case, the interferometric readout was able to produce an improvement in the signal-to-noise ratio that could not be achieved using a stronger read power.
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    Development and optimization of open-source pumps and drop-based split-and-merge microfluidic devices
    (Montana State University - Bozeman, College of Engineering, 2023) Sanchez, Humberto Scott; Chairperson, Graduate Committee: Connie B. Chang; This is a manuscript style paper that includes co-authored chapters.
    Drop-based microfluidics is used to encapsulate small volumes of chemical and biological agents into discrete drops. The contents of these pico-liter sized drops can then be used for biochemical assays. Microfluidic devices are used to manipulate these drops through the removal and addition of drop contents and pumps are used to control the fluid flow within the microfluidic devices. Often, the pumps used to drive fluid flow are prohibitively costly and the fluid dynamics of the devices used to control drop contents are not fully described. This research focuses on de-mystifying both the pump systems and microfluidic devices commonly used in drop-based microfluidics. We focused on developing an open-source pneumatic pressure pump to create microfluidic drops. Pneumatic pressure pumps have been found to be flexible and accurate systems to control fluid flow within microfluidic devices. Our pump system was found to be accurate and fast-responding as well as easy to assemble and control via open-source software. In addition, we developed a design process to develop drop-based split-and-merge (SAM) microfluidic devices. These devices have been commonly used to control drop volumes and add reagents for intra-drop assays. Our design and optimization methodology was then used to develop multiple SAM geometries with various splitting capabilities and the ability to create a broad range of drop volumes. The operating conditions for each SAM device was optimized for different input drop volumes. We also developed an empirical drop model to predict drop volume changes within a SAM device. Our open-source pneumatic pressure pump is a fast responding and accurate system that can be adapted for driving flow in any microfluidic device. Our drop-based SAM devices and the development and modelling process we developed serves as a blueprint for future SAM devices and similar drop manipulation microfluidic devices.
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    Facility-level quality of service analysis methodology for rural highways
    (Montana State University - Bozeman, College of Engineering, 2023) Raza, Sajid; Chairperson, Graduate Committee: Ahmed Al-Kaisy
    Rural highways constitute a significant portion of the national highway system, serving vital mobility and freight movement functions while connecting towns and small cities separated by rural areas. As urban areas expand further from central cities, rural highways are experiencing increased traffic demand, posing challenges to maintaining an acceptable level of operational performance and quality of service. To evaluate the operational performance and quality of service of highways, the Highway Capacity Manual (HCM) offers a comprehensive set of tools and methodologies. It incorporates analytical methodologies to perform operational analyses for individual highway components (segments and intersections). It also offers facility-level analysis methodologies for freeways and urban streets only. In this context, a facility is defined as a stretch of highway consisting of multiple components. However, the current HCM lacks a facility-level analysis methodology for rural highways which is essential for evaluating extended lengths of rural highways. A rural highway facility consists of any combination of two-lane highway segments, multilane highway segments, and intersections (signal, stop control, or roundabout intersections). To address this limitation within the HCM framework, this research aims to develop a methodology for facility-level analysis of the quality of service for rural highways, thus adding to the existing tools and capabilities of the HCM. The proposed methodology, intended for inclusion in the next HCM edition, focuses on the interaction between contiguous segments and the operational impact of intersections on connected segments. In the course of developing the analysis methodology for rural highway facilities, this research needed to develop procedures for facility segmentation, which is a critical step in developing and applying the proposed methodology. To this end, the research used extensive vehicle trajectory data from multiple sites in estimating the upstream and downstream influence areas for three different types of intersections: signalized intersections, stop-controlled intersections, and roundabouts. Specifically, quantile regression models were developed to estimate the influence areas for the three different types of rural intersections. The proposed analysis methodology significantly enhances the ability of transportation analysts to assess operations along extended lengths of rural routes, allowing more effective planning and management of these important highway facilities.
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    From cross faults to lake deposits: geologic evidence of past and present hazards
    (Montana State University - Bozeman, College of Letters & Science, 2023) Giri, Bibek; Chairperson, Graduate Committee: Mary S. Hubbard; This is a manuscript style paper that includes co-authored chapters.
    The Everest region in the eastern Nepal Himalaya is a natural laboratory for Earth sciences research as it consists of spectacular rock exposures, glaciers, lakes, rivers, and rockslide zones. While a plethora of research has been conducted in the region, a geomorphic and a tectonic feature remained unnoticed until recently. In 2017, a segment of a young (<12 Ma), NNE-striking cross fault, later named the Benkar Fault Zone (BFZ), was recognized and examined within the Everest region. Cross faults are faults that strike at a high angle to the trend of the orogen. The BFZ remained unexplored towards the south. Secondly, there are a number of layered, sandy deposits, around the Namche-Phortse areas, perched high on hillsides with no obvious connection to a modern depositional basin. The goals of my dissertation are to explore these unanswered questions in order to: 1) understand the southern continuity and genesis of the BFZ; and 2) constrain depositional ages for those sandy deposits and understand their depositional settings. To achieve my first goal, I mapped the BFZ towards the south from the Everest region and augmented the mapping results with kinematic and petrographic analysis. I find that the BFZ is a ~100 km long, segmented cross fault zone that possibly cuts across the entire width of the eastern Nepal Himalaya. The BFZ is a composite of a series of deformational events and might continue further towards the south into the foreland basin. This fault, like other Himalayan cross faults, likely contributes to seismic and landslide hazards. Through an extensive literature review, I have synthesized the occurrences and drivers of cross faults and lateral heterogeneity in several mountain belts around the world. For my second goal, I constrained the depositional ages of six sedimentary deposits by utilizing infrared stimulated luminescence analysis and integrated the ages (~13-42 ka) with their geomorphic setting. I interpret that some of them were likely deposited in localized, landslide- and/or moraine-related, ephemeral lakes/ponds. Such deposits provide invaluable agricultural land in these extreme topographies.
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    Childhood trauma and health: an investigation of physiological, behavioral, cognitive, and emotional pathways.
    (Montana State University - Bozeman, College of Letters & Science, 2023) Counts, Cory Joe; Chairperson, Graduate Committee: Neha John-Henderson
    Childhood trauma poses serious risk for overall health. Prior research has identified major pathways connecting childhood trauma to increased risk for poor health across many domains of health. The current project builds on this literature. Some prior research suggests that physiological stress responses in adulthood are blunted for individuals who experience childhood trauma compared to those who have not. Theory suggests that different patterns of physiological stress reactivity may be linked to different perceptions of environmental demands and resources to cope. The project aimed to investigate childhood trauma and blunted physiological reactivity to stress mediated by dissociative responses. Dissociation is a psychological and physiological mechanism thought to protect an individual from stressors that are inescapable or outweigh an individual's abilities to overcome stress. Separately, the perception of childhood trauma burden later in life may predict the degree to which childhood trauma affect health-relevant outcomes in adulthood. Previous research has shown that individuals who perceived their childhood trauma as more burdensome may be at higher risk for poor mental health. In separate research, emotion regulation strategy usage is related to mental health. The possibility exists that differences in childhood trauma burden and emotion regulation strategies used to cope with emotions may interact to inform differences in mental health. The current project addresses the following. Study 1 tested whether childhood trauma is linked to blunted physiological responses to a social-evaluative in-lab stressor, and proposed to test whether this relationship is in part mediated by increased dissociative responses to the stressor. Study 2 tested whether childhood trauma was linked to more dissociative responses to daily stressors, and whether childhood trauma and dissociative responses to daily stressors interacted to predict objective markers of sleep quality in a 6-day data collection period. Study 3 explored the relationship between perceived childhood trauma burden, emotion regulations strategies, and mental health in a sample of American Indian adults nationwide. The findings from Study 1+2 did not confirm hypotheses. The implications of the results are discussed. Study 3 was exploratory and the observed results are discussed. The implications, limitations, and future directions for the 3-part study results are discussed.
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    Distribution, diversity, and physiology of uncultured MCR-encoding microbial populations in Yellowstone Hot Springs
    (Montana State University - Bozeman, College of Letters & Science, 2023) Lynes, Mackenzie Morgan; Chairperson, Graduate Committee: Roland Hatzenpichler; This is a manuscript style paper that includes co-authored chapters.
    Methane, a climate active gas, is an integral component to the global carbon cycle. Microbial activity mediates the transformations of carbon, with methanogenic archaea driving the conversion of organic matter to methane in anoxic environments. Understanding the distribution and activity of methanogenic archaea is essential for estimating their contribution to the carbon cycle and global methane emissions. In the last decade, metagenomic sequencing has expedited the formulation of hypotheses regarding archaea classified outside of established methanogenic lineages, which possess genes responsible for methane production. However, the verification of these hypotheses is often hindered by the difficulties encountered in culturing these organisms. Additionally, these organisms often encode other energy conserving pathways, thus underscoring the necessity for experimental validation of their metabolism. This dissertation is dedicated to exploring the diversity and physiology of methanogenic populations in hot springs of Yellowstone National Park beginning with the collection of primary data from previously uncharacterized geothermal features. To date, this has resulted in the most extensive geochemical and microbiological survey conducted within the Yellowstone geothermal complex. This dataset served as a foundational basis for investigating uncultured methanogenic lineages and their activities in geothermal environments. Through the integration of amplicon sequencing, metagenomics, and mesocosm experiments, the presence and diversity of methanogenic communities in hot springs was revealed and novel lineages were stimulated under methanogenic conditions, resulting in their enrichment. This study emphasizes the impact able to be achieved by combining environmental metagenomics with laboratory-based experiments. To further explore the methanogenic potential revealed by these experiments, our focus shifted towards enriching a novel methanogenic lineage. Through our efforts, we were successful in cultivating the first methanogenic member of the family Archaeoglobaceae, providing genomic and transcriptomic evidence to validate its ability to live as a methyl-reducing methanogen, reducing methylamines to methane. Comprehensively, the work presented here broadens our understanding of methanogenic communities in Yellowstone National Park and contributes to the broader understanding of methanogenesis in geothermal environments.
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    Ecological interactions and environmental stressors: assessing dietary dynamics and population stability of burbot amid non-native trout and warming winter temperatures
    (Montana State University - Bozeman, College of Letters & Science, 2024) Eckelbecker, Robert William; Chairperson, Graduate Committee: Christopher S. Guy
    Burbot Lota lota are a cold-water specialist that have a circumpolar distribution. Though historically widespread, many populations are experiencing declines, including the burbot population in the Torrey Creek drainage, Wyoming, which occurs at the southwest most extent of their native range. One hypothesis for the decline observed in burbot abundance within the drainage is the presence of non-native piscivorous predators (i.e., brown trout Salmo trutta and lake trout Salvelinus namaycush). Using diet composition, bioenergetics, and population modeling, I evaluated the effects non-native trout are having on burbot. There was little dietary overlap among all species combinations. Predation of burbot was not observed by lake trout and was minimal by brown trout, estimated at 7.9 - 37.6 kg annual for the drainage. Nevertheless, I modified a previously developed model to investigate how much predation would be necessary to negatively influence the burbot population. Both the observed and increased predation scenarios yielded positive population growth rates. However, when demographic stochasticity and parameter uncertainty were introduced, every simulation carried a risk of extirpation for burbot within a century, primarily attributed to the high uncertainty associated with the adult mortality estimate. In addition to predation effects, I investigated water temperature induced recruitment failure using a model where egg survival decreased from 86.7% at 2ºC to 47.9% at 4ºC. This critical water temperature, 4ºC, was observed to occur during the putative embryogenesis period of 2022 - 2023 for burbot in the Torrey Creek drainage. The addition of the recruitment penalty to the population models decreased the probability of persistence for all simulation and reduced mean population growth. However, the reduction in recruitment even when occurring annually resulted in higher lambda estimates than the increased predation simulation without the occurrence of a recruitment penalty, indicating that juvenile survival has a greater proportional effect on the population growth rate than the reduction in recruitment as modeled by the recruitment penalty. With the findings from the bioenergetics modeling coupled with the population modeling, direct predations and intraguild predation from brown trout and lake trout are currently not a key factor contributing to the decline of burbot within the drainage.
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    Structure-performance relationship in sutured photopolymer composite films with tunable mechanical heterogeneity
    (Montana State University - Bozeman, College of Engineering, 2024) Darabi-Noferesti, Amir; Chairperson, Graduate Committee: Lewis M. Cox; This is a manuscript style paper that includes co-authored chapters.
    This dissertation investigates the structure-performance relationships of bioinspired materials using photopolymer films. Nature utilizes mechanical heterogeneity in a variety of design architectures to tune biological materials considering their environmental and loading conditions. Compliant interlayers within stiff matrices, often referred to as sutures, are prevalent in biological structures, offering enhanced mechanical performance often despite their weaker material properties. To mimic nature's architecture in engineering materials, understanding the mechanisms through which biological structures achieve their outstanding properties is necessary. Previous manufacturing processes were unable to replicate the complex designs of biological structures, and literature in this field was bound by this limitation. Advancements in the field of photopolymers have enabled the development of mechanical heterogeneity in a defect-free network, facilitating explorations into bioinspired structures, eliminating many of the challenges associated with previous additive manufacturing techniques. In this work, we employ a two-stage reactive polymer (TSRP) system to investigate the structure performance relationship of bioinspired sutured composites, but first, a thorough understanding of the material system is deemed necessary. Through thickness characterization of the photopolymer system demonstrated complexities in material properties, providing details on our control over the material system. The TSRP system is then used to incorporate compliant sutures into stiff matrices to study the impact of mechanical heterogeneity. First, we investigated composites embedded with a single suture joint of sinusoidal geometries. Variations in geometrical features of the sinusoidal wave were explored with respect to the applied tensile load and empirical relationships were developed to correlate the composite performance to the geometrical features of the embedded suture. Further analysis of the failure of suture composites revealed toughening mechanisms such as crack guiding and crack arrest that significantly enhance the composite toughness. Then, we explored composite films embedded with periodic patterns of stiff and compliant interlayers at various length scales. Additional discussion on the fracture toughness of composite films explained the differences observed for composite performance at different length scales. The findings of this research offer fundamental insights into the complexity of nature's architecture and enable a framework for engineering composites and bio-inspired structures in the future.
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    Interrogating the role of transmembrane TNF (tmTNF) in TLR2 or TLR4 activated macrophages during Staphylococcus aureus infection
    (Montana State University - Bozeman, College of Agriculture, 2024) Luu, Abby My; Chairperson, Graduate Committee: Agnieszka Rynda-Apple; Mark T. Quinn (co-chair); This is a manuscript style paper that includes co-authored chapters.
    Tumor Necrosis Factor alpha (TNF) is a cytokine involved in diverse cellular processes such as cell survival, proliferation, differentiation, immune defense, and cell death. TNF produced during an immune response is typically associated with the generation and propagation of inflammation. This association with inflammation is particularly strong for soluble TNF (sTNF), one of two bioactive TNF protein forms, but not transmembrane TNF (tmTNF), the second bioactive TNF protein form. Typically, tmTNF is more closely associated with anti- inflammatory or proliferative responses. As a result, much less is known about the role and extent to which tmTNF participates in host immune responses, particularly as it pertains to host defense. During infection, macrophages are known to secrete large amounts of TNF in response to pathogen detection via Toll-Like-Receptor (TLR) stimulation. In this dissertation research, we investigated the role of sTNF and tmTNF on macrophage priming following TLR2 or TLR4 stimulation and how this priming influenced macrophage ability to clear a subsequent Staphylococcus aureus infection. In vitro cell culture assays demonstrated that TLR stimulated WT bone marrow derived macrophages (BMDMs) became significantly more efficient at clearing a subsequent S. aureus infection. Transcriptomic and protein analysis revealed upregulation of both sTNF and tmTNF following TLR stimulation. We demonstrated that depletion of sTNF, but not tmTNF, during TLR stimulation did not influence BMDM priming which led to improved clearance of a subsequent bacterial infection. Conversely, supplementing exogenous sTNF to TLR2 stimulated TNF-/- BMDMs prior to infection did not improve S. aureus clearance. This indicated that sTNF signaling was not required for BMDM priming. Further, this suggested that TLR-induced tmTNF priming could contribute to improved S. aureus clearance. TmTNF preferentially signals through TNFR2. Indeed, blocking TNFR2 following TLR2 stimulation led to increased overall S. aureus bacterial burden. To mechanistically elucidate how tmTNF could be priming BMDMs prior to S. aureus infection, we investigated the potential of tmTNF reverse signaling. These studies provide valuable insight into the differential involvement of sTNF and tmTNF signaling following TLR stimulation of BMDMs which has implications for downstream response to infection.
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