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Item Energy metabolism and mechanotransduction in osteoarthritic chondrocytes: targeted metabolic profiling and flux analysis(Montana State University - Bozeman, College of Engineering, 2023) Erdogan, Ayten Ebru; Chairperson, Graduate Committee: Ronald K. June II; This is a manuscript style paper that includes co-authored chapters.Osteoarthritis (OA) is a prevalent and debilitating disease that affects hundreds of millions people worldwide. One of OAs major consequences is the degradation of articular cartilage, leading to joint pain, stiffness, and loss of function. Currently, there is no treatment for OA. The existing interventions are mostly for suppressing the symptoms: physical therapy, anti-inflammatories, and pain management. The last resort is total joint replacement, which has long-term consequences especially for early-onset OA patients. Thus, researchers are focusing on understanding this complex disease and its molecular components to develop better treatments. Chondrocytes, the sole cell type in articular cartilage, play a crucial role in maintaining tissue homeostasis and responding to mechanical stimuli via synthesis of key structural components like collagen. However, the intracellular pathways underlying chondrocyte mechanotransduction are not fully understood, especially those related to central carbon metabolism. This thesis uses 13C isotopic labeling to trace carbon sources and downstream metabolites related to energy metabolism in vitro. Primary human articular chondrocytes from OA patients exposed to labeled glucose and glutamine, and their global and targeted metabolite profiles are assessed. The results show how both glucose and glutamine utilization as carbon sources flows through the TCA cycle. This work also develops a comprehensive model of mammalian carbon metabolism in OA primary human chondrocytes. The model integrates energy metabolism, amino acid synthesis, and transport reactions contributing to Collagen-II and Collagen-VI production. Using flux balance analysis (FBA), trade-offs between Collagen-II and Collagen-VI synthesis are evaluated based on ATP and carbon source requirements under different oxidative stress conditions. Then, these model predictions are presented with experimental data obtained from OA chondrocytes subjected to shear and compressive mechanical stimulation, which can be integrated in the model later on. These data shed new light on metabolism of primary OA chondrocytes and provides insight into potential therapeutic targets for OA intervention.Item An expanded lava creek tuff eruption: re-mapping the Sour Creek Dome, Yellowstone National Park(Montana State University - Bozeman, College of Letters & Science, 2023) Salazar, Raymond Dale; Chairperson, Graduate Committee: Madison MyersThe ~1000 km 3, ~630 ka Lava Creek Tuff is the product of the younger major caldera- forming eruption of the Yellowstone Volcanic Field. It is currently mapped as two ignimbrite units, hot dense flows of ash, gas, and molten material, termed members A and B, with accompanying widespread ashfalls over the western U.S. This view of the Lava Creek Tuff, and its eruption, was complicated when two, visually distinct, ignimbrites were recognized on the Sour Creek dome in Yellowstone National park (Wilson et al., 2018). These visually distinct ignimbrites on the Sour Creek dome were initially mapped as the older (2.08 Ma) Huckleberry Ridge Tuff, however, when dated by U - Pb on zircon and 40Ar/39Ar on sanidine the ignimbrites returned ages analytically indistinguishable from the Lava Creek Tuff (0.631 Ma). In the newly dated ignimbrites, one unit is found as clasts of dense welded tuff withing a lag deposit which is conformably overlain by a second, cliff-forming, densely welded ignimbrite that contains scoria. This study further complicate matters due to the discovery of two additional, previously unrecognized, ignimbrites while mapping on the Sour Creek dome, bringing the total to four ignimbrites. Physical and chemical evidence suggests there were multiple magma bodies tapped during the eruptions. This project broadens our understanding of the four ignimbrites documenting their spatial distribution and source area(s) and determine how they relate geochemically to the established members A and B. This was done through field mapping, thin section examination, and whole-rock and single crystal geochemistry. This resulted in a revised understanding of the Lava Creek Tuff stratigraphy and holds implications for reevaluating the eastern boundary of the Yellowstone Caldera.Item What's the big eel: highlighting the efforts of scientists to explore the scientific process(Montana State University - Bozeman, College of Arts & Architecture, 2023) Grunder, Amanda Katherine; Chairperson, Graduate Committee: Dennis AigBy highlighting the devoted efforts that science requires, science films can create a long-term impression on their audiences. This thesis showcases how the scientific process can create a more trustworthy and believable documentary, even with an audience having an increasing rate of science denial. By highlighting the passionate dedication it takes to conduct the scientific process, documentaries can create an interest in audiences and retain a sense of trust. This method's success is discussed in a variety of different documentaries, including "My Octopus Teacher", "Particle Fever", "The Thin Blue Line", and my related thesis film "The Eel Problem."Item Integrated weed management in pulse crops(Montana State University - Bozeman, College of Agriculture, 2024) Brar, Akamjot Singh; Chairperson, Graduate Committee: Fabian D. Menalled; Lovreet S. Shergill (co-chair); This is a manuscript style paper that includes co-authored chapters.The wheat-fallow rotation remains a predominant cropping system in the US Great Plains, with heavy reliance on chemical control for weed management. This reliance has resulted in problematic weed infestations, necessitating the exploration of additional weed management options. Crop diversification with pulse crops such as chickpeas and fava beans offer expanded weed management options and several agronomic and soil benefits. However, these crops are poor weed competitors due to their slow early-season growth. Early season weed management, primarily through pre-emergence (PRE) herbicides, is crucial but is challenged by a lack of tillage and limited precipitation for herbicide activation in semi-arid regions. These PRE herbicides can also be applied in the fall to facilitate activation, thereby maintaining residual activity for controlling weed emergence and enhancing crop competition in the spring. Another cultural method to enhance competitiveness is early planting, which can provide the crop with a head start by allowing it to emerge before weeds. Field experiments were conducted across Montana in 2022 and 2023 to study the effect of fall-applied herbicides and the integration of fall-applied herbicides and planting dates on weed management in spring-planted pulses. The results demonstrate that fall-applied herbicides provide early-season weed suppression and improve crop establishment, with certain combinations (e.g., pyroxasulfone + flumioxazin, dimethenamid + pendimethalin, carfentrazone + sulfentrazone) offering consistent residual activity throughout the season. However, the efficacy of some of these treatments (e.g., pyroxasulfone, simazine, ethalfluralin, dimethenamid) diminishes later in the season, necessitating a follow-up post-emergence herbicide application to manage late-emerging weeds. Additionally, the thesis explored the integration of fall-applied herbicides and planting dates, revealing that early planting provided an additional 20 (3.5) % reduction in weed biomass by allowing the crop to emerge before major weed species. The integration of herbicides and early planting yielded a substantial increase in crop yield compared to the untreated check, demonstrating the potential of these programs to improve weed management and crop productivity in pulse rotations. The results highlight the importance of integrating chemical and cultural weed management tactics for increasing cropping systems' sustainability by integrating pulses in the US Great Plains.Item Factors associated with elk (Cervus canadensis) distributions during rifle season and individual responses to harvest risk in a prairie environment(Montana State University - Bozeman, College of Letters & Science, 2024) Krieger, Elisabeth Rachelle; Chairperson, Graduate Committee: Jay J. RotellaHunting pressure alters habitat selection of elk and understanding responses to pressure is important for effective population and habitat management. While elk responses to hunting are well-studied in forested and mountainous environments in the western U.S., little is known about elk habitat selection in more open prairie landscapes. Our objectives were to evaluate the effects of landscape and environmental factors on elk habitat selection during the rifle season, assess individual variability, and investigate relationships between selection and harvest risk for male and female elk in two populations: the Custer Forest and Missouri River Breaks in eastern Montana, USA. We also provided management recommendations for habitat characteristics that allowed elk to mitigate exposure to harvest risk (i.e., security habitat) based on where most elk use occurred. We used resource selection function modeling with a use-available design and added random effects to estimate selection patterns for individual elk. Resource selection coefficients indicated that elk generally selected areas with restricted hunter access, rugged terrain, and greater distances from motorized routes with a few notable differences for elk in the Missouri River Breaks. In particular, canopy cover was consistently associated with large increases in relative probability of use. Estimates of individual random coefficients indicated that while elk typically shared the same direction of selection for a given covariate, individuals varied in the strength of these relationships, likely due, in part, to varying exposure to risk. Individual elk increased selection for habitat features that provided security when faced with higher harvest risk (i.e., the proportion of used locations that fell on publicly accessible lands). Our results indicated canopy cover was a particularly important factor associated with elk selection during the rifle season in our prairie landscapes where available cover is relatively limited. The relative importance of other factors varied depending on study area and sex. Based on where most elk use occurred, we recommend managing for security and preferred security areas with canopy cover > or = 28% and > or = 37% in the Custer Forest and > or = 3% and > or = 5% in the Missouri River Breaks, respectively, during the rifle season in these areas and prairie landscapes with similar habitat attributes.Item Shortest common supersequence with applications(Montana State University - Bozeman, College of Engineering, 2024) Chen, Muzhou; Chairperson, Graduate Committee: Binhai ZhuThe shortest common supersequence problem (SCS) is a classical problem that was first studied by Maier in 1978. Recently, some research on the tree-child network inference problem, developed from the inference of phylogenetic networks, which involves a variant of SCS, has been studied. The variant of the shortest common supersequence problem on permutation strings was introduced to solve the tree-child network problem. In this thesis, we first provide the sketch of the proof of the NP-completeness of the SCS problem on the permutation strings from the feedback vertex set problem. From the reduction, we continue analyzing the inapproximability of this new variation. Then, we study the FPT tractability of SCS using different parameters. With the new reduction developed, which corrected and simplified the former reduction provided by Maier from the Vertex Cover problem, we extended the proof to the non-existence of the FPT algorithm parameterized by the number of the inserting positions in the longest input sequence even if it is fixed to be 3. On the other hand, an FPT algorithm parameterized by the solution size has been explored. Furthermore, we extended our proof on the NP-completeness and W[1] hardness of the k-disjoint-SCS problem as another variant of the SCS. Lastly, a new heuristic algorithm has been constructed for practical use by using the concept of maximum increasing substrings, which can be applied to both permutation strings and non-permutation strings. The empirical results show that both algorithms perform similarly in producing the shortest common supersequence, while our algorithm takes longer runtime on average due to the more complex computation during the process.Item Bat homes in the Big Sky: habitat characteristics of northern Myotis (Myotis septentrionalis) in northeastern Montana(Montana State University - Bozeman, College of Letters & Science, 2024) Melhuish, Jacob James Espey; Chairperson, Graduate Committee: Andrea LittThe northern myotis (Myotis septentrionalis) is one of 9 endangered bat species in the United States but the only one to inhabit Montana and the only resident bat species newly discovered in the state in the last 10 years. The need for conservation efforts is hampered by the large gaps in our understanding about northern myotis in Montana. We started to build our knowledge base by characterising habitat, specifically summer daytime roosts. Summer roosts provide refuge for bats while they give birth, raise young, and prepare for hibernation or migration. We mist-netted for bats from May-August in 2022 and 2023 and attached transmitters to 36 individual northern myotis. We located a total of 76 roosts from 33 tagged individuals. We quantified characteristics of the roost trees, as well as the surrounding patch, and compared these values with the same features at random locations. Bats roosted primarily in eastern cottonwood trees (Populus deltoides) (97% of roosts), which was the most available tree species on the landscape. Bats showed a strong preference for tall trees in patches with a relatively high basal area, containing multiple trees similar to the roost tree. Bats also selected for cottonwoods that were in an early to mid-stage of decay with somewhat less canopy cover. Most consecutive roosts were within a few hundred metres of previous roosts (range = 2-881 m) and each roost was used for 1.7 days on average. Our work supports the notion that northern myotis display some flexibility in roost selection in different parts of their range, with the common theme of selecting areas that provide multiple possible roosts and facilitate their social interactions. This is especially important as studied population is one on the edge of the species known range, and edge populations are shown to be more plastic in behaviour and resilient in the face of change. Improving our understanding of habitat preferences of northern myotis in Montana will provide us with a more developed toolkit to aid in their habitat management and conservation. Managers can then design strategies that protect critical roosts as well as surrounding habitat.Item Exploring variation in diversity of arthropod communities in grasslands of Yellowstone National Park(Montana State University - Bozeman, College of Letters & Science, 2024) Segal, Carlisle Regina; Chairperson, Graduate Committee: Andrea Litt; This is a manuscript style paper that includes co-authored chapters.Community ecologists have proposed many hypotheses to explain the mechanisms that drive patterns of diversity in plants and animals. For arthropods, understanding community assembly may have important conservation implications, given that this group provides many vital ecosystem services, yet many arthropods are in decline globally. We investigated drivers of arthropod diversity by testing the habitat complexity hypothesis, productivity hypothesis, and intermediate disturbance hypothesis in grasslands in the northern range of Yellowstone National Park. We collected data on vegetation (vegetation cover, litter cover, vegetation height, remotely sensed biomass, and the normalized difference vegetation index) and bison movement as explanatory variables, and sampled arthropods to help us test our hypotheses. We used generalized linear models and multivariate methods to explore patterns of richness and composition of arthropod communities among our sites. We found limited evidence for the habitat complexity hypothesis; richness of predators increased with heterogeneity in litter cover. In contrast, richness of multiple functional groups decreased with heterogeneity in vegetation cover and we did not detect any relationships with heterogeneity in vegetation height. We found evidence supporting the productivity hypothesis among herbivores; richness of herbivores overall and chewing herbivores were positively related to net primary productivity, whereas richness of omnivorous arthropods decreased with increased biomass. Although the intermediate disturbance hypothesis predicts that species richness will be maximized at moderate levels of disturbance, we found the lowest richness of all arthropods and that of multiple functional groups at moderate levels of disturbance. Overall, we found that herbivorous arthropods were more affected by quality and quantity of vegetation, whereas upper-trophic feeders were more affected by habitat complexity. These findings highlight that different functional groups of arthropods are driven by different mechanisms. By considering diversity metrics beyond taxonomic classification, we can gain important insights about arthropods - a diverse, understudied taxa.Item Synthesis of ciprofloxacin-coupled AoM esters as pre-cursors for antibacterial applications utilizing click chemistry(Montana State University - Bozeman, College of Letters & Science, 2024) Evans, Ryan Henry; Chairperson, Graduate Committee: Thomas S. Livinghouse; Brian Bothner (co-chair)Biofilm-forming bacteria pose significant challenges in the realm of drug synthesis and delivery, due to their ability to acclimate to extreme environmental conditions and resist effective antibiotics. Ciprofloxacin has traditionally been employed to combat Pseudomonas aeruginosa, a bacterium implicated in diseases such as cystic fibrosis and tuberculosis. However, the increasing resistance to this drug necessitates modification to enhance its efficacy upon cellular entry. One approach involves appending various molecules to the piperazine moiety of ciprofloxacin, thereby altering its antibacterial activity against P. aeruginosa and Staphylococcus aureus. Here, the inclusion of 1,2,3-triazoles and acetoxymethyl (AoM) esters are implemented to the base ciprofloxacin drug, tested against P. aeruginosa and S. aureus, and compared to the base drug for observations of improved potency. The techniques of the copper-catalyzed azide-alkyne cycloaddition (CuAAC) is primarily used to synthesize these novel 1,2,3-triazole compounds.Item Gene expression effect on pea protein accumulation(Montana State University - Bozeman, College of Agriculture, 2024) KC, Shreejana; Chairperson, Graduate Committee: Kevin McPhee; This is a manuscript style paper that includes co-authored chapters.Pea (Pisum sativum L.) is a good source of plant-based protein with important components like globulin, albumin, legumin(11S), prolamin, vicilin(7S), convicilin(8S) and gluteins. It possesses the functional properties like water solubility, hydration, oil holding capacity essential for the formulation of industrial products like Ripptein and protein powder. The study presents an environmental and phenotypic evaluation of pea accessions aimed at estimating the gene expression effect on pea protein accumulation. Understanding gene expression patterns associated with pea protein accumulation is vital to successful crop breeding and plant protein use. Factors impacting breeding and use include gene regulation, developmental biology, environmental factors, and agricultural practices. The experimental design included 300 Plant Identification accessions and four repeated checks planted in an augmented randomized complete block design (RCBD) with one replication in 2021 and two replications in 2022. Phenotypic evaluations included yield, plant height, pod characteristics, and protein content. PI 193837 had the greatest yield (2344 kg/ha) in 2021 and PI 193837 recorded highest yield (3676 kg/ha) in 2022. The average yield was 1536 kg/ha in 2021 and 1867 kg/ha in 2022. PI 269777 PSP had the greatest protein content (36.5%) in 2021 followed by PI 269802 PSP (36.3%) and the average protein content was 25%. In 2022, protein percentage was slightly decreased with PI 404225 PSP having 34% protein. Yield and protein content were significantly correlated (r=-0.2, p = 4.54e -10). Molecular analysis revealed differential gene expression patterns associated with pea protein accumulation, highlighting potential candidate genes and pathways. 456 significant genes were identified. Gene Ontology reveals protein synthesis and translation, stress response, transport function, carbon, propanoate metabolism and glycolysis- gluconeogenesis pathways associated with significant genes. 33 genes associated with storage seed protein in peas was identified. The identified genes and pathways help for genetic manipulation and breeding strategies to enhance nutritional content and functional properties for pea and other leguminous plants.