Theses and Dissertations at Montana State University (MSU)

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    THE INTERPLAY BETWEEN THE CENTRAL ENGINE AND THE CIRCUMNUCLEAR ENVIRONMENT IN COMPTON-THIN AGN
    (Montana State University - Bozeman, College of Letters & Science, 2022) Chalise, Sulov; Chairperson, Graduate Committee: Anne Lohfink; This is a manuscript style paper that includes co-authored chapters.
    All massive galaxies harbor a supermassive black hole (SMBH) at their galactic center. If these SMBH are actively feeding then they are called Active galactic nuclei (AGN). Their accretion system contains a corona, an accretion disk and an axisymmetric dusty torus. The torus can be connected physically and dynamically to the circumnuclear disk of the galaxy which acts as a molecular gas reservoir for material to be accreted onto the SMBH. Further, AGN can emit radiation from radio up to the gamma rays. The AGN accretion disk emits photons mostly in the optical/UV band which are Compton up-scattered in the corona to generate X-rays. If present, a jet can produce additional high-energy and Synchrotron emission. In some AGN, a huge amount of material can be stripped away from the accretion disk creating an outowing wind. These --radiation pressure, jet, wind etc.--inject energy back into the host galaxy, regulating the SMBH growth. There exist a complex interplay between the AGN feeding and feedback. Understanding this interaction between the central engine and its circumnuclear environment is vital in context of galaxy evolution. My work aims to study this interaction in low to moderately obscured (or Compton-thin) AGN using their broadband multi-epoch X-ray spectra plus other emission bands whenever appropriate. From the spectral analysis of broad-line radio galaxy 3C 109, I was able to constrain its high-energy cutoff for the first time. In another Seyfert galaxy Mrk 926, I was able to explore the origin of its soft excess, and found that a warm coronal origin was slightly preferred. Finally, I performed a joint multi-wavelength analysis with a physical torus model of a sample of Polar-scattered Seyfert 1 galaxies. I utilized their multi-epoch broadband X-ray spectra along with their infrared spectral/photometric data, and was able to constrain their torus properties. Despite being a sample of similar moderately-inclined Compton-thin AGN, I found a complex and varied distribution of gas and dust in their torus.
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    IN-NII (BISON BISON L.) REINTRODUCTION TO AMSKAPIIPIKINI (BLACKFEET) NATION HOMELAND: RELATIONSHIPS WITH KSAHKO (SOILS)
    (Montana State University - Bozeman, College of Agriculture, 2022) Tatsey, Latrice Dawn; Chairperson, Graduate Committee: Anthony Hartshorn
    In-nii (American Bison) are returning to their Traditional Territories after being nearly wiped out of the Great Plains of North America and Canada. The in-nii are slowly returning to Native American tribes who have the resources to run reintroduction programs like that of the Amskapiipikini (Blackfeet). This in-nii reintroduction presented an opportunity to look at the effects of the return of in-nii to the Amskapiipikini, and what their influences might be on the soils, plants, and water resources of the Blackfeet Nation. This research project was conducted on the Blackfeet Buffalo (In-nii) Ranch and the adjacent RRJ Cattle Ranch, comparing the influence of in-nii and cattle on soil nutrient cycles and soil carbon dynamics. Soil samples were taken from locations on the landscape that were near water sources on lower elevations, mid hillslopes for mid-elevation sites and on hilltops at higher elevations. Soil characteristics included soil organic matter (SOM), nitrate, pH, cation exchange capacity (CEC), and exchangeable calcium, potassium, sodium, and magnesium. Only two (CEC, magnesium) appeared to have been influenced by in-nii and cattle. The remaining soil characteristics were little influenced by grazer type. Substrate-induced respiration was also measured in the lab to see how microbes decomposed SOM (carbohydrates and other molecules) to release energy and CO2; we found no evidence of differences between in-nii- and cattle-influenced soils. Finally, we measured field respiration rates and water infiltration rates at multiple fence line sites; field soil respiration rates increased when soil had water infiltrated after the dry readings, soils also increased the time to absorb water after the first infiltration tests were run. Our preliminary results suggest that the reintroduction of in-nii to these lands has not yet resulted in measurable differences in soil-related properties of the Blackfeet Nation. Even so, the return of the in-nii for the Amskapiipikini is also about understanding the importance of using cultural science when studying the ecology of a system. Doing this can create an understanding of the traditional ways of knowing while bringing cultural healing and restoring connections between Amskapiipikini, in-nii, and land.
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    MICROBIAL ADAPTATION TO CULTIVATION STRESS USING STORAGE COMPOUNDS
    (Montana State University - Bozeman, College of Agriculture, 2022) Arnold, Adrienne Dale; Chairperson, Graduate Committee: Ross Carlson; This is a manuscript style paper that includes co-authored chapters.
    Methanotrophs and green algae are microorganisms that grow on single carbon substrates. Methanotrophs are bacteria that use methane as their carbon source, and green algae are eukaryotic phototrophs that grow on CO 2. They are of interest both as primary producers in the environment and as biological catalysts for the conversion of greenhouse gases into value-added compounds. Understanding how methanotrophs and green algae adapt to cultivation stresses is key to understanding carbon cycling in the environment and in industrial settings. This work uses stoichiometric metabolic modeling to investigate the role of carbon storage compounds in the metabolism of C1-utilizing organisms. Storage compounds are accumulated as intracellular reserves of polysaccharides or lipids, which can be catabolized under stress conditions to provide carbon and energy to the cell. Catabolism of carbon storage compounds often results in the excretion of multi-carbon organic compounds that can be utilized as carbon substrates by other members of the microbial community. In silico metabolic models were developed for methanotroph and algal systems and used to examine the breakdown of storage compounds in response to common cultivation stresses. For the aerobic methanotrophs, predictions focused on the use of polyhydroxybutyrate and glycogen in adaptation to O 2 limitation. For the green algae, starch and triacylglycerol reserves are analyzed as sources for compatible solutes, which are produced by cells in response to high salinity conditions. Metabolic modeling of storage compound utilization by methanotrophs and algae helps elucidate the role of these organisms as primary producers and presents an opportunity for industrial production of multi-carbon compounds from single carbon substrates.
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    ALGAL BIOFILMS AND LIPIDS: BICARBONATE AMENDMENT AND NITRATE STRESS TO STIMULATE LIPID ACCUMULATION IN ALGAL BIOFILMS
    (Montana State University - Bozeman, College of Engineering, 2022) Rathore, Muneeb Soban; Chairperson, Graduate Committee: Brent M. Peyton; This is a manuscript style paper that includes co-authored chapters.
    Algal biofuels are compounds obtained by transesterification of algal lipids to fatty acid methyl esters (FAMEs) which can be used as biodiesel. Algal biofilms have a potential for commercial applications of algal biomass for biofuel production and provide concentrated biomass requiring less water removal to reduce biofuel production costs. Lipid production in algal biofilms is low as compared to planktonic algal growth systems and strategies for enhancing lipid content in algal biofilms need to be developed. The overarching goal of the studies presented herein was to develop lipid accumulation strategies in algal biofilms using nutrient stresses to increase triacylglycerides (TAGs) and FAMEs. First, a reactor was designed for photoautotrophic biofilm growth incorporating a novel algal biomass harvesting mechanism. Chlorella vulgaris biofilm growth was demonstrated to establish the reactor characteristics under three different inorganic carbon regimes and the presence of excess calcium to facilitate biofilm attachment and accumulation. Excess calcium resulted in precipitate formation and increasing ash content in biomass and caused difficulty in biofilm detachment. However, the highest biomass accumulation was observed in the bicarbonate and the bicarbonate with calcium treatments. Second, two different algal strains were tested for lipid accumulation under two nutrient conditions: nitrate limitation and bicarbonate addition. Algal strains included, an extremophilic freshwater diatom RGd-1, a Yellowstone National Park (YNP) isolate, and oleaginous chlorophyte C. vulgaris. High bicarbonate content at low nitrate concentration in the bulk medium provided the highest lipid accumulation as determined by Nile Red fluorescence and Gas Chromatography Mass Spectrometry (GCMS) analysis of extracted FAMEs (7-22 % wt/wt). For prevention of biomass loss and quick response to nutrient stresses to stimulate lipid accumulation, the growth medium was exchanged after initial biofilm accumulation and operated in batch mode. This was implemented to quickly introduce nutrient stresses using fresh medium to vary bicarbonate and nitrate concentrations as needed. Thus, the work presented here demonstrated enhanced lipid production in algal biofilms with nitrate stress and bicarbonate amendment is a viable strategy to increase lipid accumulation. Increased lipid content may help offset the cost for biodiesel production with more lipid product and lower processing requirements for water removal.
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    An evaluation of graph representation of programs for malware detection and categorization using graph-based machine learning methods
    (Montana State University - Bozeman, College of Engineering, 2023) Pearsall, Reese Andersen; Chairperson, Graduate Committee: Clemente Izurieta
    With both new and reused malware being used in cyberattacks everyday, there is a dire need for the ability to detect and categorize malware before damage can be done. Previous research has shown that graph-based machine learning algorithms can learn on graph representations of programs, such as a control flow graph, to better distinguish between malicious and benign programs, and detect malware. With many types of graph representations of programs, there has not been a comparison between these different graphs to see if one performs better than the rest. This thesis provides a comparison between different graph representations of programs for both malware detection and categorization using graph-based machine learning methods. Four different graphs are evaluated: control flow graph generated via disassembly, control flow graph generated via symbolic execution, function call graph, and data dependency graph. This thesis also describes a pipeline for creating a classifier for malware detection and categorization. Graphs are generated using the binary analysis tool angr, and their embeddings are calculated using the Graph2Vec graph embedding algorithm. The embeddings are plotted and clustered using K-means. A classifier is then built by assigning labels to clusters and the points within each cluster. We collected 2500 malicious executables and 2500 benign executables, and each of the four graph types is generated for each executable. Each is plugged into their own individual pipeline. A classifier for each of the four graph types is built, and classification metrics (e.g. F1 score) are calculated. The results show that control flow graphs generated from symbolic execution had the highest F1 score of the four different graph representations. Using the control flow graph generated from symbolic execution pipeline, the classifier was able to most accurately categorize trojan malware.
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    Investigation of the cellular pathology underlying the optic neuropathy in a mouse model of familial Dysautonomia
    (Montana State University - Bozeman, College of Agriculture, 2023) Schultz, Anastasia Mardell; Chairperson, Graduate Committee: R. Steven Stowers; This is a manuscript style paper that includes co-authored chapters.
    Familial dysautonomia (FD) is a rare, recessive, progressive autosomal disorder that affects the nervous system. This neurological disorder is caused by a splice mutation in the Elongator complex I (ELP1) gene. The mutation results in a tissue-specific reduction of ELP1 protein due to unstable mRNA targeted for nonsense-mediated decay. ELP1 is a highly conserved scaffolding protein and core subunit of the six-subunit Elongator complex required for normal translation, neuronal development, and survival. Insufficient ELP1 leads to the developmental death of neurons in the peripheral and autonomic nervous systems in addition to central and peripheral nervous system neurodegeneration. Patients suffer from congenital and progressive neuropathies, such as cardiovascular dysfunction, reduced peripheral sensory function, poor growth, and digestive and respiratory problems. Outside of the risk of death in early adulthood, one of the most debilitating conditions affecting patients' quality of life is progressive blindness marked by continual loss of retinal ganglion cells (RGCs). Within the FD community, there is a concerted effort to develop treatments to prevent the loss of RGCs, thereby improving patients' quality of life. This study aims (1) to elucidate mechanisms underlying the death of RGCs in the absence of Elp1 and (2) to obtain pre-clinical intervention data that can eventually be translated into therapeutics for rescuing RGCs in FD. Using histology and confocal microscopy in conjunction with biochemistry, this study provides evidence for disrupted cellular homeostasis and inflammation preceding RGC death, and as the disease progresses, the retinal cells fail to mount a correct stress response to restore neuronal homeostasis. Furthermore, this study provides first-of-its-kind pre-clinical data using targeted gene therapies to rescue RGCs. Understanding the biological crosstalk and signaling mechanisms underlying the death of RGCs in the absence of Elp1 will allow for more targeted and effective therapeutics that will benefit not only the FD community but also individuals affected by other retinal diseases and neurological diseases that result from a faulty Elongator complex. This study provides a novel characterization of the FD retina and establishes baseline methods to further investigate rescuing RGCs.
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    EVALUATING HABITAT SUITABILITY FOR LESSER PRAIRIE-CHICKEN CONSERVATION IN THE MIXED-GRASS PRAIRIE ECOREGION
    (Montana State University - Bozeman, College of Agriculture, 2022) Solomon, Morgan Jean; Chairperson, Graduate Committee: Lance McNew
    Populations of lesser prairie-chickens (Tympanuchus pallidicinctus; hereafter "prairie-chicken") in the southern Great Plains have declined by an estimated 85% and the species is currently being reconsidered for protections under the federal Endangered Species Act. Despite efforts to increase the quantity, quality, and connectivity of available habitat, prairie-chicken populations in the mixed-grass prairie ecoregion have remained relatively stable-to-declining. To provide information that will assist in providing more appropriate qualifications of available prairie-chicken habitat, I used ensemble modeling approaches and a least-cost path analysis to develop spatially-explicit predictions of prairie-chicken habitat and assess connectivity of identified habitat within the mixed-grass prairie ecoregion. In addition, I provided a critical comparison of the Western Association of Fish & Wildlife Agencies (WAFWA) Habitat Evaluation Guide and research-based field indices used to quantify the amount and quality of habitat for prairie-chicken conservation on a proprety participating in an incentive-based conservation program. I also explored the potential for using ecological site descriptions and relative condition (similarity index) to monitor reproductive habitat for prairie-chickens. Predictions from our ensembled model identified ~4,576 km 2 of potentially suitable prairie-chicken habitat both occupied and unoccupied. Least-cost path analyses revealed a low degree of connectivity between areas of occupied and unoccupied habitat indicating a low probability of natural recolonization. Managers should consider focusing conservation efforts on targeting habitat restoration between, within and around areas of identified occupied and unoccupied habitat. Habitat quality under the HEG habitat assessment protocol showed the property had excellent prairie-chicken habitat quality while research-based estimates showed the property only had marginal habitat quality for prairie-chickens. Differences in habitat quality assessments were in areas that had low percent cover of vegetation species preferred by prairie-chickens and in areas that had recently experienced fire. Thus, managers should consider using components of both habitat assessments protocols when quantifying habitat for prairie-chicken conservation to reduce the probability of producing erroneous estimates of habitat quality. Limited sample size within moderate categories of similarity index across ecological sites prevented us from reliably executing further analyses exploring the utility of using a similarity index as a tool for monitoring prairie-chicken habitat.
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    Bio-trapping ureolytic bacteria on sand to improve the efficiency of biocementation
    (Montana State University - Bozeman, College of Engineering, 2023) Ugur, Gizem Elif; Chairperson, Graduate Committee: Chelsea M. Heveran; Adrienne J. Phillips (co-chair); This is a manuscript style paper that includes co-authored chapters.
    Microbially induced calcium carbonate precipitation (MICP) has emerged as a novel biocementation technique for its potential solution to sustainable construction. Although current MICP approaches have made significant progress, achieving spatial control over biomineralization is challenging due to its complexity, which is affected by many factors, such as microorganisms, reaction kinetics, and environmental factors. Spatially controlling biomineralization for building or targeted repair of materials can significantly improve efficiency and sustainability while achieving desired outcomes. The purpose of this thesis was to assess whether biomineralization can be enhanced through surface pre-treatment of sand using amino silanes, such as 3-aminopropyl-methyl-diethoxysilane (APMDES), which is one form of spatial control of biomineralization through prescribing the location of the microbes. Moreover, a preliminary study was conducted to assess whether biomineralized sand, with and without the APMDES treatment, can be recycled and reused for biomineralization of subsequent generations. The impact of APMDES treatment on bacterial adhesion on sand, growth, and urease activity was analyzed. Biocementation efficiency was evaluated by comparing compressive strength and calcium gain of APMDES-treated sand with untreated sand. APMDES treatment promotes abundant and immediate trapping of bacteria on sand surfaces through increased electrostatic interaction that attracts negatively charged walls of bacteria to positively charged amine groups. While APMDES treatment compromises microbial viability, it preserves the urease enzyme for catalyzing urea hydrolysis. APMDES-treated sand achieved comparable strength with fewer bacterial injections compared to untreated sand. APMDES-treated sand biocemented using three injections of bacteria and cementation media gained the same strength as seven injections. Biomineral gain of APMDES-treated sand was similar compared to untreated sand, which shows calcium accrual in the structure may be influenced by additional factors, such as the distribution of calcite, differences in the calcite precipitation patterns, and morphology. Overall, incorporating APMDES treatment can potentially improve the efficiency and sustainability of MICP by spatially controlling biomineralization.
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    PUTTING THE "A" IN AP: THE EFFECT OF ADVANCED COURSE ACCESS ON AP PARTICIPATION AND PERFORMANCE
    (Montana State University - Bozeman, College of Agriculture, 2022) Callen, Ian Andrew; Co-chairs, Graduate Committee: Christiana Stoddard and Andrew Hill
    This paper investigates the effect of state-level policy regarding access to advanced course curriculum on participation and performance within the Advanced Placement (AP) program. From the early 2000's through 2019, participation in the Advanced Placement (AP) program, the most popular college-preparatory course in the United States, has nearly tripled in size. Today, nearly 20% of all high school students taking at least one AP exam per year. The AP program provides an opportunity for students to potentially earn college credit while still in high school which, at least in theory, reduces the cost of a college education. While the AP program provides many benefits to students, it also presents two major barriers - the ability to access advanced-level courses, and the monetary cost associated with taking the AP exam. We find that when states require schools to offer AP courses and when states fund AP exams, participation within the program increases drastically. For Black and Hispanic students, our estimates indicate a large increase in the number of exams that receive a passing score. These findings indicate that when states reduce the financial burden associated with taking an AP exam, students have the ability to participate and succeed in the program at higher rates than their peers in states without AP curriculum and exam funding.
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    Analysis of energy and savings of using ground loop or steam to change temperature of the bulding heat pump loop in Norm Asbjornson Hall
    (Montana State University - Bozeman, College of Engineering, 2023) Kuikel, Shraddha; Chairperson, Graduate Committee: Kevin Amende
    The need for efficient and sustainable environmental conditioning systems in buildings has become increasingly important in the face of rising energy costs and environmental concerns. This thesis aims to assess the optimization of the control logic to maximize energy savings and costs associated with utilizing ground loop or steam to modify the temperature of a heat pump loop in ground source heat pumps (GSHP) in Norm Asbjornson Hall (NAH) building at Montana State University (MSU). The study begins by providing a comprehensive review of existing literature on GSHP systems, their working principles, and the various methods employed to alter the temperature of the heat pump loop. The research methodology involves determining the conditions under which it is economically viable to operate ground loops and/or a steam heat exchanger to maintain the heat pump loop temperature within a set operating range. This is done by deriving an equation that utilizes the coefficient of performance (COP) and entering water temperature (EWT) of the heat pump loop. Energy and cost analysis is then conducted to assess the energy efficiencies for different cases. The findings reveal that both steam and ground loops can effectively alter the temperature of heat pump loops, providing enhanced temperature control and increased energy efficiency. The analysis shows that each strategy does have important financial and environmental implications, nevertheless. Due to the equipment, infrastructure, and operational expenditures, steam injection is primarily utilized to raise the loop's temperature for heating mode only, and at extreme situations when the ground loop cannot provide enough energy to maintain the heat pump loop temperatures. However, compared to steam injection, ground loops, which can be used for both heating or cooling, offer significant energy savings and lower long-term maintenance costs, albeit needing a sizable initial investment. In summary, the thesis explores how to optimize control logic to save energy and costs using ground loop or steam to adjust building heat pump loop temperature. The study evaluates energy, cost, and environmental impact of the proposed control logic optimization approach. The findings aim to provide insights into informed decision-making regarding the adoption of this alternative method.
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    Effects of de-snaring on the demography and population dynamics of African lions
    (Montana State University - Bozeman, College of Letters & Science, 2023) Banda, Kambwiri; Chairperson, Graduate Committee: Scott Creel
    Lions and other African large carnivores are in decline, due in part to effects of illegal hunting with snares, which can reduce prey availability and directly kill or injure carnivores. It is difficult to effectively remove snares from large ecosystems by patrolling, but an additional approach to reduce effects on large carnivores is to monitor the population closely and de-snare individuals who are found in a snare or have broken free but still carry the wire (often with serious injury). The effectiveness of de-snaring programs to reduce impacts on large carnivores has not been directly tested. Here, we used long-term demographic data from 386 individually identified lions in the Luangwa Valley Ecosystem to test the effects on population growth (lambda) and population size (N) of a program to remove snares from injured lions and treat their wounds. Stochastic Leslie matrix projections for a period of five years showed that the population grew with the benefits of de-snaring but was expected to decline without de-snaring. Mean annual growth (lambda) was 1.037 (growth in 70% of years), closely matching observed changes in population size. Mean annual growth was 0.99 (with growth in 47% of years) for a model that assumed snared animals would have died if not treated, and 0.95 (with growth in 37% of years) for models that also accounted for super-additive effects via the death of dependent cubs and increased infanticide with increased male mortality. De-snaring requires intensive effort, but it can appreciably reduce the effect of snaring on lion population dynamics.
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    MICROBIOMES AND ZOONOSES: DYNAMICS OF THE BLACK FLYING FOX (PTEROPUS ALECTO) GASTROINTESTINAL MICROBIOME
    (Montana State University - Bozeman, College of Agriculture, 2022) Jones, Devin Nicole; Chairperson, Graduate Committee: Raina K. Plowright; This is a manuscript style paper that includes co-authored chapters.
    Land-use change is increasingly recognized as a driver of spillover of zoonotic pathogens. Australian black flying foxes (Pteropus alecto) are experiencing extensive loss of habitat which reduces available food, particularly in winter. Hendra virus (HeV, family: Paramyxoviridae) was isolated from horses and humans in 1994 and P. alecto was later identified as the reservoir host. As habitat loss threatens these bat populations, and Hendra virus continues to spill over to horses annually, it is important to understand factors that influence bat health and viral shedding. Because gastrointestinal tract (GIT) microbiomes are important for host health and are understudied in flying foxes, the goal of this research was to understand the natural dynamics of the P. alecto GIT microbiome and its associations with diet, body composition, markers of inflammation, and viral shedding. We sampled Pteropus alecto near Brisbane from 2018-2020. We captured bats returning from foraging and collected rectal swabs to determine the GIT microbiome using 16S rRNA amplicon sequencing. In addition to feces for dietary analysis, we also collected samples to measure health and infection, including blood to measure neutrophil-to-lymphocyte ratios, urine to detect Hendra virus, and bioelectrical impedance analysis to measure body fat. These data enabled us to determine how the P. alecto GIT microbiome varied within individuals over time and in the context of physiological, ecological, and dietary shifts. Lastly, we asked if we could predict health outcomes using the GIT microbiome. We found that P. alecto GIT microbiomes are highly dynamic over time, through different life stages, between foraging strategies, and that the type of diet is associated with GIT microbiome diversity. Bats consuming native foods had lower GIT microbiome diversity compared to those consuming introduced and cultivated foods. Despite associations between body fat and HeV infection, the GIT microbiome was not able to predict these health outcomes. These results suggest that P. alecto GIT microbiomes are highly dynamic and may not contribute significantly to host health. Future research should incorporate more health metrics or other approaches to microbiome profiling to determine if the GIT microbiome could be used as a biomarker of health.
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    Effects of time, cultivar, and storage environment on winter squash in semiarid Montana
    (Montana State University - Bozeman, College of Agriculture, 2023) Sheild, Victoria Marie; Chairperson, Graduate Committee: Mac Burgess
    Winter squash can be stored for months after harvest while taste, texture, and color attributes improve. The potential for producers to attain greater storage longevity and produce better squash would benefit farmers, consumers, and economies. Due to variation in local climates and the respective vendors' needs, understanding how to control a storage environment can be challenging. This research looks at how storage environment and storage period affect biochemical and physical attributes of ten varieties of winter squash in a semiarid climate. The varieties include three Cucurbita pepo, one Cucurbita moschata, one Cucurbita maxima x moschata hybrid, and five Cucurbita maxima cultivars. Two storage environments were used for analysis. One was located indoors and cooled to 53 degrees F while the other was built into an existing barn with a heating unit and insulation to keep the temperature above freezing. A total of 240 winter squash were placed in each storage space. A completely randomized design was used to assign categorical treatments of storage time to each winter squash, with six levels of treatment being implemented. Each variety of squash (n=4) was analyzed monthly in each storage environment for changes in soluble solids, dry matter, starch content, interior color and exterior color (using CIELAB color values L*, a*, b*), and mass. The temperature and relative humidity of each storage environment were also monitored and recorded hourly during the same period. Cultivar was always the most significant factor. There was no simple effect of the storage environment on dry matter, soluble solids, starch content, or mass. There was a strong significant interaction observed between time and cultivar for each response variable, which shows us that the type of squash and how long it should be stored for are important when discussing quality. Storage did have a significant effect on the a* value of interior color, which is an indicator of quality and nutritional value. The biochemical and physical attributes of each cultivar analyzed varied greatly in its response to the amount of time in storage which in turn influences the taste, texture, and sensory quality of each cultivar uniquely.
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    Integration of Puccinia punctiformis into organic management of Cirsium arvense
    (Montana State University - Bozeman, College of Agriculture, 2023) Chichinsky, Daniel Jacob; Chairperson, Graduate Committee: Fabian D. Menalled; Tim F. Seipel (co-chair)
    Cirsium arvense is a perennial weed that causes significant economic losses in agriculture. An extensive rhizomatous root system makes C. arvense difficult to manage, particularly in organic cropping systems that use tillage as a primary management tool. To improve organic management of C. arvense, there is a need for the development of alternative and integrated weed management toolsets that include C. arvense biological controls. Puccinia punctiformis is a fungal pathogen that systemically infects C. arvense, with the potential to reduce host vigor. The goal of this research was to assess the impacts of P. punctiformis within organic cropping systems, using a greenhouse and a field study that examined integration of the biocontrol with cultural and mechanical management tools. In the greenhouse, P. punctiformis was integrated with a competitive annual cropping sequence, where C. arvense's biomass production and competitive ability was assessed. Cirsium arvense biomass production was significantly reduced when P. punctiformis was integrated with the cultural management tactic, more than individual use of the biocontrol or cultural management alone. Additionally, P. punctiformis reduced the competitive ability of C. arvense over time. In the field, P. punctiformis was integrated with mechanical management, where reduced and standard tillage treatments were evaluated to determine the effects on P. punctiformis and C. arvense abundance. The reduced tillage treatment caused a greater increase in P. punctiformis infected C. arvense stems compared to standard tillage, however there was no impact to asymptomatic C. arvense stem density from either tillage treatment. In both tillage treatments, there was a reduction in asymptomatic C. arvense stem density in samples where P. punctiformis infection was present. Integration of P. punctiformis with cultural and mechanical tools can be an effective way to reduce C. arvense vigor. However, successful integration of the biocontrol can be dependent on a combination of environmental factors and deliberate cropping system management. While P. punctiformis is not a singular management solution, it has potential to be integrated into reduced disturbance cropping systems for long-term and sustainable C. arvense management.
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    OPTO-MECHANICAL DESIGN AND ANALYSIS FOR COHERENT ACTIVE IMAGING
    (Montana State University - Bozeman, College of Engineering, 2022) Neeley, Jaime Branson; Co-chairs, Graduate Committee: Wm. Randall Babbitt and Joseph A. Shaw
    The objective of this thesis project was to design a monostatic lidar transmit (Tx) and receive (Rx) opto-mechanical apparatus for remote sensing at a variable range of 50 m - 500 m. The scope of this project begins from the fiber output of a pre-designed Frequency-Modulated Continuous Wave (FMCW) lidar system. After design criteria for the lidar module are given, the optical and mechanical design is presented, opto-mechanical tolerancing is presented, and assembly, alignment, and testing procedures are covered as well. This thesis shows that the required design criteria of diffraction-limited optical performance was achieved while accounting for predictable manufacturing and assembly errors modeled using a Monte Carlo tolerance analysis. Furthermore, this thesis shows that the modeled and measured optical performance results were in good agreement and recommendations are given for improvements for the next-generation revision of the lidar Tx/Rx module.
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    Effect of process variables on the uncured handleability and formability of stretch broken carbon fiber
    (Montana State University - Bozeman, The Graduate School, 2022) Rezaul, Riad Morshed; Chairperson, Graduate Committee: Cecily A. Ryan
    Carbon fiber is a high-performance reinforcing material used extensively in aerospace composites. Although carbon fiber is used in both continuous and discontinuous form, the continuous carbon fiber is limited by its inability to stretch due to its low strain to failure during manufacturing structures with complex geometries. Stretch broken carbon fiber (SBCF) is a type of discontinuous and aligned carbon fiber which has the potential to solve this limitation of inextensibility of its continuous counterpart. The discontinuous nature of SBCF enhances its stretchability making this material a prime candidate for manufacturing parts with complex curvatures. SBCF is generated by stretching the fibers using a pair of differentially driven rollers, which breaks the fibers at their intrinsic flaws. Although SBCF can be stretched due to being discontinuous, it compromises the tensile strength due to the lack of fiber continuity. Therefore, a polymeric coating known as sizing is applied to the SBCF to reconstruct its tensile strength. In the context of SBCF production, sizing serves two important functions. Firstly, sizing provides uncured carbon fiber the desired handleability and back-tension ability. Secondly, sizing enhances the formability of SBCF, which is a defined as the ease at which a material can be formed into a desired shape without failure. The goal of this work is to investigate the effect of process variables on the generation of stretch broken carbon fiber with consistent and repeatable material properties. The stretch broken carbon fiber research group at Montana State University (MSU) has developed a stretch breaking machine known as 'Bobcat' to generate single tow MSU SBCF. The noteworthy process variables related to MSU SBCF production includes sizing deposition on the tow, stretch ratio, nip force, line speed, fiber length distribution, and tow tenacity. Target amount of sizing deposition on MSU SBCF tow was achieved by choosing an appropriate sizing bath. A temperature-controlled tow tenacity result suggests that MSU SBCF possesses adequate handleability, back-tension ability and formability. MSU SBCF also shows a narrow fiber length distribution and relatively short mean fiber length which indicate improved formability. Reproducibility of these results were observed in the replicate batches of MSU SBCF. Suitable stretch ratio and nip force regimes were identified to optimize MSU SBCF production.
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    The hind limb ontogeny of Troodon formosus
    (Montana State University - Bozeman, College of Letters & Science, 2023) Boekenheide, Harris Russell; Chairperson, Graduate Committee: David J. Varricchio; This is a manuscript style paper that includes co-authored chapters.
    The Campanian theropod Troodon formosus has long been recognized as one of the most exceptional dinosaurs of the Late Cretaceous. Despite its relatively small size, it was a remarkably advanced and specialized creature, with one of the largest encephalization quotients among dinosaurs, serrated teeth with hypertrophied denticles, and long hind limbs suited for agility and energy-efficient locomotion. Yet much is still unknown about members of this species due to the fragmentary and disassociated nature of what has thus far been uncovered. In the hopes of better understanding this species, we used the histology and bone scaling of the pelvic limbs of Troodon and the modern emu to make inferences about its ontogeny. This resulted in the discovery of highly variable growth strategies in Troodon individuals, as well as further evidence that modern cursorial avians are not an apt modern analogue for Troodon ontogeny and locomotion.
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    A deeper look into X-ray-selected AGN candidates in dwarf galaxies with Chandra
    (Montana State University - Bozeman, College of Letters & Science, 2023) Sanchez, Adonis Arismendy; Chairperson, Graduate Committee: Amy E. Reines; This is a manuscript style paper that includes co-authored chapters.
    The ability to accurately discern active massive black holes (BHs) in local dwarf galaxies is paramount to understanding the origins and processes of "seed" BHs in the early universe. We present Chandra X-ray Observatory observations of a sample of three dwarf galaxies (M* < or = 3 x 109 M circled dot, z < or = 0.15) pre-selected by Latimer et al. (2021a) as candidates for hosting active galactic nuclei (AGN). The galaxies were selected from the NASA-Sloan Atlas (NSA) with spatially coincident X-ray detections in the eROSITA Final Equatorial Depth Survey (eFEDS). Our new Chandra data reveal X-ray point sources in two of the three galaxies with luminosities of log(L 2-10keV/[erg s -1]) = 39.1 and 40.4. In the target galaxy with the nondetection, we calculate an upper limit on the luminosity for a potential source. We observed notably higher fluxes and luminosities from the two detected X-ray sources compared to their original eFEDS observations, pointing to possible X-ray variability on the scale of a few years. We plot and fit the spectra of the X-ray sources with a power-law model, finding the likely presence of intrinsic absorption. The X-ray luminosities are above that expected from XRBs, but we cannot definitively rule out stellar-mass compact objects with the data on hand. Assuming the X-ray sources are accreting massive BHs with masses that scale with the stellar mass of the host galaxies, the Eddington ratios are on the order of a few x 10 -3.
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    The expansion and optimization of ZN(II)-mediated intramolecular metalloamination and subsequent CU(I)-catalyzed functionalization for the construction of pyrrolidines and piperidines
    (Montana State University - Bozeman, College of Letters & Science, 2023) Frabitore, Christian Ames; Chairperson, Graduate Committee: Thomas S. Livinghouse; This is a manuscript style paper that includes co-authored chapters.
    Nitrogen-containing heterocycles (azacycles) are ubiquitous in pharmaceutical agents. Their ability to moderate and modulate the activity of drugs in the body make them especially powerful, and thus sought after, synthetic targets. While the synthesis of many popular azacycles has been greatly improved in recent years, the production of pyrrolidines and piperidines has not received as much attention despite their standing as the 1st and 5th most common azacycles in FDA-approved drugs. The intramolecular Zn(II)-mediated metalloamination/cyclization of N,Ndimethylhydrazinoalkenes provides structurally diverse pyrrolidines and piperidines with the added advantage of a subsequent functionalization step, efficiently building molecular complexity in one reaction sequence. Herein, this method is optimized and improved by the addition of a new hydrazone reduction method, the inclusion of 1-bromoalkynes in the functionalization step, and multiple key discoveries in the reagents used to effect these transformations. Furthermore, preliminary results adding N,N-dimethylhydrazinoallenes as substrates for this powerful method are presented.
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    Changing shape: an investigation into allostery and protein conformational ensembles
    (Montana State University - Bozeman, College of Letters & Science, 2023) Mattice, Jenna Rose; Chairperson, Graduate Committee: Brian Bothner; This is a manuscript style paper that includes co-authored chapters.
    Allostery is the mechanism by which action at one site on a protein causes a functional change at a distant site. An allosteric change can manifest as conformational change or a change in protein dynamics. In this way, the study of allostery, protein dynamics, and structural biology are individual, yet related fields. Progress and technical advancements in one field inform and drive the others. In this thesis, four protein complexes 2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC), acetone carboxylase (AC), Replication protein A (RPA), and Radiation sensitive 52 (Rad52) were studied to elucidate conformational change and allostery during catalysis. A variety of orthogonal biophysical approaches were used to study these systems. To infer changes in protein dynamics and conformation, hydrogen-deuterium exchange coupled to mass spectrometry was used in three of these studies. This technique allows for the probing of the hydrogen bonding network based on ligand binding or mutation. Probing of AC, RPA and Rad52 has led to the description of conformational changes essential for function. Ion mobility coupled to native mass spectrometry was used to investigate the available conformations of 2-KPCC during catalysis and led to the discovery of residues essential for modulating those conformations. The concepts of allostery, conformational ensemble, and protein dynamics have evolved since they were first described. Utilizing mass spectrometry-based techniques, my work helped expand the knowledge of several protein systems that contain allosteric networks which are necessary for function. The studies presented in this thesis increase the understanding not only for these protein systems, but also of protein function on a deeper level.
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