Theses and Dissertations at Montana State University (MSU)
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Item Genetic dissection of malt quality in barley: an examination of hydration index and metabolite QTL(Montana State University - Bozeman, College of Agriculture, 2024) Jensen, Joseph Riley; Chairperson, Graduate Committee: Jamie Sherman; This is a manuscript style paper that includes co-authored chapters.Malting barley is a high value crop for American farmers. Through the malting process grain is turned into malt which is primarily used in brewing but can also be a flavor and nutritional additive for the food industry. During the malting process hydration of the endosperm is a rate limiting step resulting in increased time and water usage if a third water immersion is needed during steeping. To better understand the genetics of endosperm hydration we used a genome wide association (GWAS) population to map quantitative trait loci (QTL) for malt quality, hydration index (endosperm hydration), and seed morphology traits. We found six hydration index QTL with three related to seed size (qHYI1H, qHYI3H.a, and qHYI3H.b), two improving malt quality (qHYI2H and qHYI6H), and the last (qHYI7H) wasn't related to any other traits. We then wanted to see the relationship between hydration index and dormancy because dormancy is needed to prevent preharvest sprouting. Preharvest sprouting in malt barley results in extreme price reductions for producers however the dormancy genes needed to prevent this negatively impact malt quality. Using a biparental mapping population we were able to map two hydration index QTL and relate them to the dormancy gene SD2. Our results confirmed SD2 negatively impacts malt quality but when the positive alleles for hydration index are present, they negate dormancy's negative effects on quality. The results from these two studies show hydration index can benefit growers and maltsters with barley and malt production. Our third study looked at metabolite variation in the GWAS population to see if we could identify QTL related to malt flavor. This would help craft malt houses and breweries which are usually in search of unique flavors. We were able to identify 827 metabolite QTL however the most impactful to flavor were amino acid, saccharide, and maltol QTL which totaled 39. The three maltol QTL which are directly related to flavor all co-located with maltol precursors (amino acids and saccharides) showing these QTL would be good targets for marker assisted selection to create maltol variation.Item Unveiling the photophysics in solid-state organic materials: a study on BODIPY, porphyrin, and PBI based materials(Montana State University - Bozeman, College of Letters & Science, 2024) King, Alexander James; Chairperson, Graduate Committee: Erik Grumstrup; This is a manuscript style paper that includes co-authored chapters.Organic semiconductors have applications in optoelectronics, light harvesting, and sensing as soft matter materials. One of the biggest challenges to overcome with organic-based materials is structural heterogeneity that arises from the self-assembly of monomers upon solid-state deposition. In this work we have investigated solid-state organic semiconductors with three levels of solution-phase processing: i) materials prepared from drop casting with no solution-phase processing on BODIPY systems ii) films prepared from pre-aggregation of the monomers with porphyrin systems iii) films prepared from aggregated monomers that were covalently stapled with perylene bisimide systems. In the BODIPY systems, we found that: i) the electronic states are highly coupled with a major redshift from 583 nm in the solution to 614 nm in the solid. ii) Through interpretation of the broadband transient absorption spectrum, the initial excited state is delocalized and localizes within the first 10 femtoseconds. iii) Using two color pump probe, we measured ultrafast diffusion at 14.37 + or - 2.79 cm 2 s -1 that abruptly halts after 10 ps. In the porphyrin systems with level 2 solution-phase processing, we have also shown that the lifetime of the excited state is correlated with the degree of structural order. The monomer exhibits the longest lifetime with an average lifetime of 1.26 ns, the aggregate is much shorter with a lifetime of 349 ps, and the films show substantially faster relaxation, with the film fabricated from the monomer having a 72.56 ps average lifetime, and the film composed of the aggregate having a 26 ps average lifetime. These results suggest that the lifetime decreases as the order and electronic coupling of the system increases, so much so that the lifetime is two orders of magnitude different. In the perylene bisimide systems, we did a direct spectroscopic comparison between thin films formed from noncovalent assemblies and from covalently tethered molecular assemblies. This indicates that interchromophore coupling is enhanced in the covalently tethered film. We saw a 73% increase in excited state transport compared to the control film, as well as a shorter and more homogenous excited state lifetime. Covalent tethering proves to be the best strategy for generating homogeneous materials.Item Versatility of cryo-electron microscopy as a structural technique informs iron mineral nucleation and growth in a mini-ferritin(Montana State University - Bozeman, College of Letters & Science, 2024) Gauvin, Colin Charles; Chairperson, Graduate Committee: C. Martin LawrenceIron is an enigmatic element. While necessary for life, it also contributes to the generation of reactive oxygen species via the Fenton reaction. To mitigate this, cellular life has evolved the ferritin family of proteins, including the 24 subunit ferritins and bacterioferritins, and the 12 subunit DPSL "mini-ferritins". Each of these catalyze the controlled oxidation and sequestration of iron as a hydrous ferric oxyhydroxide within their hollow protein cores. While there is a wealth of structural information on the unmineralized ferritins, little is known about the structures of the biomineralized forms, and the mechanism of ferric oxyhydroxide nucleation and growth. Here we report structural and biochemical characterization of a DPS-Like protein from Pyrococcus furiosus. This "thioferritin" utilizes a bacterioferritin-like ferroxidase center, but adopts the mini-ferritin quaternary structure, and is thus thought to sit at the evolutionary boundary between mini- and maxi-ferritins. In addition to the unmineralized structure, we report the 1.91 angstrom structure of P. furiosus thioferritin as it nucleates iron-oxyhydroxide distal to the ferroxidase site. In this very low iron form, a pair of conserved glutamate residues and unsaturated carbonyls at the 3-fold axis serve to template initial nucleation. We also determine structures of higher iron forms with a biomineralized ferrihydrite core, where C-terminal residues 170-176 interact directly with the initial mineral surface, which then grows towards the particle center. These studies provide important new insight into biological mechanisms for the controlled nucleation, growth and storage of ferric oxyhydroxide in this thioferritin specifically, and the ferritin superfamily as a whole.Item A black spot on the narcotics map drug policy in twentieth century Montana(Montana State University - Bozeman, College of Letters & Science, 2024) McLain, Kathryn Kohn; Chairperson, Graduate Committee: Molly ToddThis research examines cycles of drug policy from the federal down to the local level in Montana. I show how drug policy, and the people and organizations that influence that policy, are part of a broader historical and geographical process. If drug use and drug policy are cyclical, as so many policy makers point out, then using a historical methodology to examine them can offer stronger and more nuanced policy analysis. This scholarship is important in understanding past practices to improve our future relationship with drugs in our communities. Specific case studies show the influence of women's clubs on public opinion and policy in Montana in the 1930s. I unpack the long history of methamphetamine leading to the rise of a graphic prevention campaign in Montana at the turn of the twenty-first century. This work addresses the intersections of federal and local drug policies, drawing on professional expertise from my work with the federal government as well as my scholarly research in the field.Item Geobiological feedbacks and the evolution of thermophiles in Yellowstone National Park hot springs(Montana State University - Bozeman, College of Agriculture, 2024) Fernandes Martins, Maria Clara; Chairperson, Graduate Committee: Eric Boyd; This is a manuscript style paper that includes co-authored chapters.This dissertation focuses on identifying the geobiological feedbacks that shaped the evolutionary ecology of thermophiles in Yellowstone National Park (YNP) hot springs. Hot springs can generally be grouped as acidic, moderately acidic, and neutral to alkaline. Although the geochemistry and microbiology of YNP hot springs have been studied for over a century, fundamental gaps in the understanding of the feedbacks between them remain. Here, the influence of fluid mixing regime on geochemistry, microbial diversity, and productivity was investigated in three geographically co-localized springs whose communities are supported by chemical energy. The results indicate that a higher degree of disequilibrium in electron donor/acceptor pairs due to mixing of highly reduced volcanic gases and oxidized near surface waters was present in the moderately acidic hot spring, which supported higher biodiversity and primary productivity. In contrast, the acidic hot spring had the lowest biodiversity and productivity. Interestingly, acidic springs are generally dominated by members of the archaeal order Sulfolobales which have been suggested to mediate the acidification of these environments through aerobic elemental sulfur (S 8 0 ) oxidation that produces sulfuric acid (H2 SO4 ). Intriguingly, Sulfolobales encode the protein sulfide:quinone oxidoreductase (SQR), proposed to catalyze the oxidation of sulfide (H2 S). However, this metabolism has yet to be demonstrated. Five novel Sulfolobales strains were isolated under H 2S-oxidizing conditions from YNP. This activity was coupled to growth and H 2SO 4 production, expanding the role of Sulfolobales in the oxidative sulfur cycle. S 8 0 oxidation in these strains was also investigated due to the observation that nearly half of Sulfolobales don't encode sulfur oxidoreductase (SOR), the canonical pathway of S 80 oxidation in Sulfolobales. Two Sulfolobales strains were selected, one of which encoded SOR and the other of which did not. SOR disproportionates S 8 0 , yielding H 2S as a product. Since H 2S can react with S 8 0 , promoting its solubilization, it was hypothesized that the strain encoding SOR could grow via indirect contact to the mineral while the non-SOR encoding would need direct contact. This was confirmed through experiments where S 8 0 was sequestered in dialysis membranes. Interestingly, the non-SOR strain was able to grow via indirect contact when H 2S was added to the culture media to mimic SOR mechanism. The results shown here provide new insight into the geological and biological feedbacks that shaped the evolution, ecology, and physiology of thermophiles.Item Multi- and many-objective factored evolutionary algorithms(Montana State University - Bozeman, College of Engineering, 2023) Peerlinck, Amy; Chairperson, Graduate Committee: John SheppardMulti-Objective Optimization (MOO) is the problem of optimizing two or more competing objectives, where problems dealing with more than three competing objectives are termed as Many-Objective (MaOO). Such problems occur naturally in the real world. For example, many engineering design problems have to deal with competing objectives, such as cost versus quality in product design. How do we handle these competing objectives? To answer this question, population-based meta-heuristic algorithms that find a set of Pareto optimal solutions have become a popular approach. However, with the increase in complexity of problems, a single population approach may not be the most efficient to solve MOO problems. For this reason, co-operative co-evolutionary algorithms (CCEA) are used, which split the population into subpopulations optimizing over subsets of variables that can now be optimized simultaneously. Factored Evolutionary Algorithms (FEA) extends CCEA by including overlap in the subpopulations. This dissertation extends FEA to MOO, thus creating the Multi-Objective FEA (MOFEA). We apply MOFEA to different problems in the MOO family with positive results; these problems include combinatorial and continuous benchmarks as well as problems in the real-world domain of Precision Agriculture. Furthermore, we investigate the influence of different grouping techniques on continuous large-scale, MOO, and MaOO problems to help guide research to use the appropriate techniques for specific problems. Based on these results, we find that some MaOO problems lead to large sets of non-dominated solutions. From this, an Objective Archive Management (OAM) strategy is presented that creates separate archives for each objective based on performance and diversity criteria. OAM successfully reduces large solution sets to a more manageable size to help end-users make more informed decisions. The presented research makes four main contributions to the field of Computer Science: the creation of a new Multi-Objective framework to create and use subpopulation in a co-operative manner including the ability to use overlapping populations, the analysis of different grouping strategies and their influence on continuous optimization in both large- scale and multi-objective optimization, the introduction of a post-optimization solution set reduction approach, and the inclusion of an environmental objective into a real-world Precision Agriculture application.Item Ichnology and sedimentology of the non-marine Frontier Formation (upper Cretaceous) of southwestern Montana(Montana State University - Bozeman, College of Letters & Science, 2023) Panasci, Giulio; Chairperson, Graduate Committee: David J. Varricchio; This is a manuscript style paper that includes co-authored chapters.The Frontier Formation of southwestern Montana (USA) is comprised of rocks assigned to the early Upper Cretaceous (Cenomanian- Santonian), and has recently yielded a notable fossil record, mostly comprised of dinosaur tracks and invertebrate trace fossils. This fossil record lays within a poorly understood period of the Upper Cretaceous, also known as the middle Cretaceous, valued as critical to understand the evolution of terrestrial ecosystems in North America at the end of the Mesozoic Era. This study aims to describe and analyze preservation and distribution of the Frontier trace fossils record. Twelve stratigraphic sections are measured and sedimentology, taphonomy, and stratigraphic framework described for the main fossiliferous sites. Sixty-five dinosaur tracks and associated invertebrate traces are described. Three tracks are further analyzed by combining anatomical characters and track morphological features to infer a more specific producer. Photogrammetry, tridimensional models, and color elevation maps are generated to document significant specimens and to map two excavated track sites. A concise description and classification of a freshwater turtle is also included to enhance paleoecological and paleodepositional reconstructions. A Coniacian age is provided for the Frontier Formation, main fossiliferous sites. Sedimentology and fossil record suggest the establishment of a rich ecosystem in alluvial plains and wetlands extending between the offshoots of the uplifting Rocky Mountains to the east and the Cody Sea to the east. Facies distribution across the southwest-northeast transect suggests that fossil distribution and preservation is mainly controlled by autogenic and allogenic processes seen in foreland basin systems. Tracks and invertebrate trace fossils preservation was likely favored by high sedimentation rates and variations of the ground water table. Dinosaur track assemblage is comparable to those reported in other middle Cretaceous formations of western North America and include derived hadrosauriform ornithopods, ankylosaurians, and theropods. The integration of body fossil data would suggest the presence of a fauna that included elements (i.e. Neurankylus sp.) shared with Campanian and Maastrichtian formations, suggesting that the Coniacian ecosystems across southwestern Montana was likely undergoing a process of provincialisms as seen in North America at the end of the Cretaceous.Item Improving detection and treatment of anxiety and depression in a southwest Montana women's clinic: a quality improvement project(Montana State University - Bozeman, College of Nursing, 2023) Waldeisen, Hillary Joi; Chairperson, Graduate Committee: Alice RunningBackground: Depression and anxiety are the most prevalent mental health disorders affecting women. Primary care providers predominantly screen for and manage depression and anxiety, improving detection and treatment when adequate systems are in place. As many as 30% of women utilize an OBGYN provider for primary care yet are not typically screened for either diagnosis. Local problem: Rates of anxiety and depression in Montana are higher than the national average. Women utilizing the clinic's OBGYN providers for primary care were not being screened for these disorders. Methods: Over five weeks, Plan-Do-Study-Act cycles were completed weekly. Participants included women utilizing the clinic for annual wellness exams. Data gathered during the project included documented PHQ-9 and GAD-7 scores, and management metrics including behavioral health or psychiatry referrals, prescribed medications, immediate evaluations, and monitored patients. Interventions: Staff education occurred before the implementation date. PHQ-9 and GAD-7 scores were entered into the EHR during wellness exams. Staff surveys were emailed weekly to elicit feedback. PDSA cycles were performed utilizing data from chart audits and survey results. Results: The implementation was well received by both staff and patients. In the first five weeks following the implementation, chart audits demonstrated an average of 86 % of PHQ-9 and 81% of GAD-7 scores entered into the EHR. In addition, management metrics showed improvement in the last week of data collection. Conclusions: Implementation of screening for anxiety and depression during annual wellness exams allowed for early identification and treatment after shared decision-making. Screening was considered a valuable addition to the care provided by the clinic.Item Forecasting vertebrate species habitat suitability and ecoregion types under future climate change scenarios using Species Distribution Modeling (SDM)(Montana State University - Bozeman, College of Letters & Science, 2023) Veneros Guevara, Jaris Emmanuel; Chairperson, Graduate Committee: Andrew J. Hansen; This is a manuscript style paper that includes co-authored chapters.Peru, Ecuador, and Colombia have identified a total of 23 threatened species, including mammals, birds, and plants, which are also a part of their reports for SDG 15. These countries are keen to monitor the risk of extinction of these species and ensure their protection. As part of the Life on Land Project, we aim to assist these countries in approximating the IUCN Red List index using species occurrence data, climatic data, and variables such as Human Footprint (HFP) in different climate change scenario. To achieve this, we conducted a general review of climate drivers and climate change for the three countries and explored climate data to estimate the variation of temperature (°C) and annual precipitation (mm) change under current climate conditions and in RCPs-2050 climate change scenarios (2.6, 4.5, and 8.5). Our results indicated that the average annual temperature for 2050, using a baseline of 1970-2000, is expected to increase by over 1 °C in some areas and over 4 °C in others. For annual precipitation, an increase is also predicted, although few global circulation models show a reduction. We also conducted a median comparison to see the differences between the baseline and the RCPs in 2050, indicating that the medians are different. Density plots were used to illustrate the shift to the right for the temperature case, confirming the anticipated temperature increase by 2050 in the three RCPs. Finally, we used the R package (SDM) to estimate habitat suitability probability for the spectacled bear and the paramo ecoregion. Our findings indicated that climate change impacts their areas with high probability of occurrence to a great extent, and their habitats are also affected by HFP. These methods for exploring climate data and assessing habitat suitability are replicable and can be used with other environmental variables.Item The kinematics and dynamics of rifting in south-central Tibet(Montana State University - Bozeman, College of Letters & Science, 2023) Reynolds, Elizabeth Aislin Nicole; Chairperson, Graduate Committee: Andrew K. Laskowski; This is a manuscript style paper that includes co-authored chapters.Southern Tibet is a unique location to study complex interactions between continental collision and extension, or stretching, of the Earth's crust which forms linear structures called rifts. The study of rifts is important because the rocks they expose can record thermal changes in the Earth's crust related to large-scale processes such as shifts in tectonic plates which occur over long timescales and are difficult to observe. Rifts also interact with topography, can influence river systems, and cause changes in rainfall distribution across a landscape by forming topographic drainage divides. Despite their importance, the kinematics and dynamics of rifting, or processes that occur during rift formation and evolution, are not well understood. This study uses field and radiometric dating techniques to investigate the shape, orientation, and timing of extension in southern Tibet by testing kinematic models for two classes of rifts: (1) Tibetan rifts which are defined as rifts that are >150 km in length and crosscut the Lhasa Terrane, and (2) Gangdese rifts that are defined as rifts <50 km long that are isolated within the high topography of the Gangdese Range. Evaluation of rift age across the Tangra Yumco rift and three Gangdese rifts suggests the TYC rift formed through the linkage of smaller normal fault segments into larger and longer structures over time, while Gangdese rifts may have relatively constant lengths. Additionally, interactions between rifts and contractional structures have likely influenced the evolution of topography and drainage patterns in southern Tibet for at least the past sixteen million years. To further investigate structural interactions, a broader compilation of thermochronology ages expands results to include another Tibetan rift, the Lunggar rift. Trends in the data reveal all samples from Gangdese rifts and Tibetan rifts that spatially overlap the Gangdese Range yield ages between ~28-16 Ma, whereas samples north of the Gangdese Range yield ages between ~12-4 Ma. I interpret these results to reflect Gangdese rift initiation at ~28 Ma in conjunction with, and perhaps balancing, uplift driven by the India-Asia collision, while young ages North of the Gangdese Range (~12-4 Ma) reflect extension along Tibetan rifts.