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 A mess of rotten eggs from the Two Medicine Formation, Montana(Montana State University - Bozeman, College of Letters & Science, 2024) Tucker, Katherine Lydia; Chairperson, Graduate Committee: David J. VarricchioThe Two Medicine Formation of Montana is known for producing many dinosaur eggs in varying states of preservation. An unusual clutch of eggs MOR 11881 was recently found in the formation that exhibits some distinctive preservation features. The purpose of this research is to describe this clutch using multiple techniques to identify and better understand its taphonomic history. To do this the clutch was prepared by removing sediment from around the eggs, then examined using light microscopy, scanning electron microscopy (SEM), cathodoluminescence (CL), energy dispersive x-ray spectroscopy (EDX), and electron backscatter diffraction analysis (EBSD). Preparation uncovered eleven partially compressed ellipsoidal eggs in the clutch. Microscopy of the eggshell revealed that it is made of two structurally distinct layers. The lower layer at the base of the eggshell is here referred to as the blocky layer based on the blocky texture of the crystals in SEM images. This layer is sometimes interrupted by a phosphatic dark region. The second layer is the lobed layer found along the outer surface of the eggshell. It is characterized by lobes of blocky crystals surrounded by smaller radiating crystals. In addition to the eggshell the eggs also preserve a phosphatized eggshell membrane, two distinct types of pellets, large masses of collophane crystals and hyphae like structures. Unaltered eggshell is found in the sediment surrounding the clutch. The eggshell of the MOR 11881 clutch does not match any described ootaxon but is similar to eggshell found at the Egg Mountain quarry which was never identified. The unusual structure of the eggshell could be the result of multiple stages of alteration. Several structures in the eggshell including the lobes and the dark region are most likely the result of alteration. The presence of unaltered eggshell near the eggs indicates that the source of alteration was the decay of the eggs as recorded by their contents. This decay also produced the conditions necessary for the exceptional preservation of the eggshell membrane.Item The paradoxical role of ATP in viral infections and cellular defense(Montana State University - Bozeman, College of Agriculture, 2024) Zahl, Trevor Ronald; Chairperson, Graduate Committee: Blake Wiedenheft; This is a manuscript style paper that includes co-authored chapters.Conflict between prokaryotes and viruses has driven the evolution of diverse defense systems. The study of these systems has not only expanded our knowledge of the mechanisms underlying genetic conflict, but has also revolutionized biotechnologies. I joined the Wiedenheft lab in early 2021 during the height of the SARS-CoV-2 pandemic. As such, the lab was focused on developing technologies to aid in the identification and study of SARS-CoV-2. I joined a team that was actively repurposing a type III CRISPR system as a molecular diagnostic. Type III CRISPRs are RNA targeting systems that unleash antiviral signaling cascades upon recognition of a target. Previous work in the lab had shown that this activity could be repurposed as a molecular diagnostic, but the first generation technology was not sensitive enough for clinical use. To address this need, we developed a technology termed Capture and Concentrate, which utilized 'CRISPR magnets' to concentrate target RNAs from complex mixtures. Using this technology, we increased diagnostic sensitivity by 1,000 fold. In addition to my work at the bench, I developed an in silico model of the diagnostic to inform future development efforts. While type III CRISPRs are unique due to their ability to generate antiviral signaling cascades, they also contain intrinsic endonuclease activity. In 2023 we demonstrated that this activity could be repurposed as an RNA editing technology. Using the type III system from Streptococcus thermophilus, we introduced precise genomic modifications in a recombinant sindbis virus. This technology removed the need for reverse genetics systems, which hampered the study of the rapidly evolving SARS-CoV-2 virus. In the final year of my graduate studies, I worked with a team focused on determining how, PARIS, a bacterial innate immune system, induced host death upon viral infection. PARIS is a two-component system comprised of the ATPase, AriA, and a nuclease, AriB. Previous studies had shown that PARIS induced abortive infection in response to viral proteins, but the mechanism was not known. We determined that upon antigen recognition, AriB is activated and cleaves host tRNAs to induce cell death and prevent community spread.Item Biorecovery of rare earth elements and critical minerals via Gluconobacter oxydans(Montana State University - Bozeman, College of Engineering, 2024) Kessler, Kendall Rhea; Co-chairs, Graduate Committee: Ross Carlson and Ryan AndersonThe depletion of high-grade ore deposits, accumulation of electronic waste, and the geopolitical challenges in sourcing critical materials have emphasized the need for sustainable metal recovery methods and recycling efforts in the United States. Conventional metal recovery approaches, including pyrometallurgy and hydrometallurgy, are not only environmentally unsustainable but also inadequate for the retrieval of metals from low-grade deposits. Biorecovery, defined by microorganism-mediated metal recovery, provides an advantageous alternative to traditional recovery methods due to increased sustainability, lower operational costs, and high efficiencies observed for the recovery of low-grade feedstocks. This study investigates the potential of bioleaching as an eco-friendly alternative in the recycling of two distinct waste feedstocks: magnetic swarf and lithium-ion batteries (LIBs). Cultivation of Gluconobacter oxydans was investigated under varying growth medium compositions, wherein increased concentrations of yeast extract were substituted for KH 2PO 4, to determine the subsequent impact on the base metal and rare earth element recovery through the application of the cell-free biolixiviant. This substitution resulted in increased growth yields and enhanced recovery with respect to magnetic swarf, whereas negligible improvement was observed for LIBs. Biorecovery has also been demonstrated for the recovery of metals from ore, where yields are a function of comminution and concentration efficiencies. Typical compressive comminution practices account for the largest proportion of energy expenditures in a mining process. Transcritical CO 2 (tCO 2) comminution, wherein ore is fractured through overcoming a rock's tensile strength, was examined to determine whether physical differences in particle generation were present as compared to traditional fracture techniques. An ore deposit in British Columbia, rich in a nickel-iron alloy mineral phase called awaruite, was examined through scanning electron microscopy, backscatter electron imaging, and energy dispersive spectroscopy to determine the impact of comminution method on awaruite recovery. Image processing was used to investigate shape factors for the individual particles. Preliminary evidence indicates despite a lack of distinct particle differences, tCO 2 comminution resulted in increased liberation and recovery of awaruite ore. Abiotic leaching studies were conducted to determine whether the method of comminution impacted leaching efficiencies. Although samples could not be quantitatively measured, initial qualitative results indicate tCO 2 comminution provides increased yields.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 Impact of kinship navigator program on rural kin caregiver wellbeing(Montana State University - Bozeman, College of Education, Health & Human Development, 2024) Foluso, Ayomide Adefunke; Chairperson, Graduate Committee: Brianna Routh; This is a manuscript style paper that includes co-authored chapters.More than 2.6 million children live in kinship families without their parents. Kinship caregivers provide care for children whose parents are unable to care for them, yet often face significant challenges that can impact their wellbeing and the caregiving situation. In line with the passing of the Family First Prevention Services Act in 2018, Kinship Navigator Programs are required to submit for evaluation in the Title IV-E Prevention Services Clearinghouse to seek federal reimbursement. This study evaluated the efficacy of the Montana Kinship Navigator Program in improving caregiver wellbeing through its intervention (Enhanced Case Management) compared to a service-as-usual control (Information and Referral only). The quasi- experimental design compared caregivers in the intervention group (n=59) to the control group (n=33) across measures of wellbeing, services accessed, and navigator assistance at case closure. Data was collected through surveys and program records. The preliminary findings support wider implementation of enhanced case management services. Analysis showed significantly higher wellbeing in the intervention group across domains of coping, enjoying life, and average wellbeing compared to controls. Navigator assistance was significantly higher for the intervention group and positively correlated with multiple wellbeing domains across all participants. Financial and health service accessed showed positive associations with improved health wellbeing across participants. Financial resources emerged as particularly important for improving wellbeing for rural kinship caregivers. White non-Hispanic caregivers were more likely to access more services and navigator support compared to Black, Indigenous, and other People of Color, who in turn were more likely report higher stress. This demonstrates the need for training and culturally informed navigator support to promote equitable access. Implementing enhanced intervention could better address the complex needs of kinship families, particularly in underserved rural communities where resources are limited. MTKNP's recognition by the Clearinghouse and state legislators can result in a more sustainably funded program and positive wellbeing outcomes for kin caregivers and their kin children.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.