2020-

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https://hdl.handle.net/10217/182111

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Open Access
Path planning for autonomous aerial vehicles using Monte Carlo tree search
(Colorado State University. Libraries, 2024) Vasutapituks, Apichart, author; Chong, Edwin K. P., advisor; Azimi-Sadjadi, Mahmood, committee member; Pinaud, Olivier, committee member; Pezeshki, Ali, committee member
Unmanned aerial vehicles (UAVs), or drones, are widely used in civilian and defense applications, such as search and rescue operations, monitoring and surveillance, and aerial photography. This dissertation focuses on autonomous UAVs for tracking mobile ground targets. Our approach builds on optimization-based artificial intelligence for path planning by calculating approximately optimal trajectories. This approach poses a number of challenges, including the need to search over large solution spaces in real-time. To address these challenges, we adopt a technique involving a rapidly-exploring random tree (RRT) and Monte Carlo tree search (MCTS). The RRT technique increases in computational cost as we increase the number of mobile targets and the complexity of the dynamics. Our MCTS approach executes a tree search based on random sampling to generate trajectories in real time. We develop a variant of MCTS for online path-planning to track ground targets together with an associated algorithm called P-UAV. Our algorithm is based on the framework of partially observable Monte Carlo planning, originally developed in the context of MCTS for Markov decision processes. Our real-time approach exploits a parallel-computing strategy with a heuristic random-sampling process. In our framework, We explicitly incorporate threat evasion, obstacle collision avoidance, and resilience to wind. The approach embodies an exploration-exploitation tradeoff in seeking a near-optimal solution in spite of the huge search space. We provide simulation results to demonstrate the effectiveness of our path-planning method.
Open Access
Stochastic modeling to explore the central dogma of molecular biology and to design more informative single-molecule, live-cell fluorescence microscopy experiments
(Colorado State University. Libraries, 2024) Raymond, William Scott, author; Munsky, Brian, advisor; Stasevich, Timothy J., committee member; Snow, Christopher D., committee member; Ben-Hur, Asa, committee member; Krapf, Diego, committee member
Despite being described nearly a century ago, the Central Dogma of Molecular Biology still harbors many intricacies and mysteries that scientists have yet to unravel. With the convergence of many multidisciplinary scientific advances such as stronger computing power, next-generation sequencing, machine learning, and single-cell and single-molecule experiments, cellular biologists have never had more investigative power. These complex methods often are used in tandem--necessitating a closer relationship between computational biologists, computer scientists, and bench top experimentalists. As practice of this emerging dynamic, my corpus of work spans multiple areas within computational and quantitative biology with the goal to facilitate better computational tools to interpret and design experiment. For my main work at Colorado State University, I have developed the open source Python package "RNA sequence to Nascent protein simulator," rSNAPsim, to simulate Nascent Chain Tracking experiments and used it as a backbone for an entire experiment simulation pipeline to check experiment design feasibility. The rSNAPsim software provides start-to-finish capabilities for model design, model fitting, and model selection so that experimentalists can fit a mechanistic model to the Nascent Chain Tracking single-mRNA translation experiments. Along with this main work, I have provided computational modeling efforts on live-cell data on the first two steps of the Central Dogma, DNA transcription and mRNA translation. For the final entry in my corpus, I have used my interdisciplinary skills acquired at CSU to do machine learning based ncRNA riboswitch classification and discovery within the human genome; This work provides the broader scientific community with a starting point for searching for this important secondary structure within humans, where it has not been described as of time of writing.
Embargo
Advancements in the chemical recyclability of acrylic polymers through investigation of monomer design
(Colorado State University. Libraries, 2024) Gilsdorf, Reid Anthony, author; Chen, Eugene, advisor; Miyake, Garret, committee member; Shores, Matthew, committee member; Herrera-Alonso, Margarita, committee member
Depolymerization is a key avenue of state-of-the-art recycling of polymeric materials. Although many polymers have been investigated for their ability to depolymerize, a subset of polymers has been widely left out of the conversation, polyolefins, or polymers containing C-C bonds in the polymer main-chain. Acrylic polymers are an important class of polyolefins used throughout the world in a variety of applications. One of the key drawbacks of the polymer, however, is their unfavorable depolymerization conditions, requiring high temperatures in expensive reactors. Although much work has been performed on the depolymerization of the most widely used acrylic polymer, poly(methyl methacrylate) (PMMA), there have been few reports on trying to improve upon the recycling methods, such as decreasing depolymerization temperature or gaining control over the depolymerization mechanism. In this work, key mechanistic steps of acrylic polymer depolymerization are investigated to gain fundamental understanding on the limitations faced during depolymerization and try to improve upon them. When poly(α-methylene-γ-butyrolactone) (PMBL) and poly(α-methylene-γ-methyl-γ-butyrolactone) (PMMBL) were investigated, the suppression of side reactions that occurred with PMMA depolymerization were identified, attributed to the pendant lactone tethering radical species together. Employing this tethering effect, the design of new polymers with pendant lactones and lower equilibrium polymerization temperatures (ceiling temperature or TC), was carried out, overall decreasing depolymerization temperatures and improving polymer recyclability. Finally, these new polymers were incorporated into the design of copolymers with PMMA and PMMBL in order to exploit the new polymers' depolymerizability without hindering thermomechanical properties. Overall, this work has shed light onto the importance of polyolefin design in, not just thermomechanical properties, but also polymerization and depolymerization behavior which will benefit the continued development of recyclable-by-design polymers.
Open Access
Brillouin light scattering: a powerful tool for magnonics research
(Colorado State University. Libraries, 2024) Swyt, Mitchell S., author; Buchanan, Kristen S., advisor; Patton, Carl, committee member; Menoni, Carmen, committee member; Field, Stuart, committee member
The slow down in generation-over-generation improvement in CMOS based logic and storage devices has spurred recent exploration into magnonic devices, those based on propagating perturbations of magnetic order called magnons, or spin waves. These devices are of particular interest due to their chargeless, low-power operation, scalability to the nanoscale, and compatibility with existing CMOS technologies. By exploiting spin waves, information may be transferred and operated upon without electrical currents. Magnetic textures like Neel domain walls, chiral transitions between magnetic domains, or skyrmions, magnetic vortices, represent additional avenues in magnonics for data storage and logic devices. Magnonic crystals, artificial crystals made by modulating magnetic properties in a periodic fashion, are one example of magnonic devices that have seen recent interest. With applicability in logic and signal processing, study of how spin waves propagate through these crystals is a necessity in the pursuit of new crystal designs. Brillouin light scattering (BLS) spectroscopy, an inelastic light scattering technique, is a powerful tool in this pursuit, as it allows for the spatial and temporal mapping of spin wave propagation. In this thesis, we will discuss three studies of spin waves by BLS: a 1D magnonic crystal, a 2D magnonic crystal, and a study of the interfacial Dzyaloshinskii-Moriya interaction. First, time-resolved BLS was used to study the band gap formation in a 1D magnonic crystal. By mapping the propagation of spin wave pulses through the crystal, complex two dimensional interference patterns were observed. These patterns are ignored by the simple models used to understand the behavior of this crystal design, and we provide a model to calculate these patterns from the spin wave dispersion relation. The temporal development of interference that forms the basis for band gap formation in this system is also observed. Second, time-resolved BLS was used to study spin wave caustic beams in a 2D magnonic crystal. This crystal design represents a new regime in magnonic crystals, in which the patterning dimensions are much smaller than the spin wave wavelength and generate caustic beams. The formation of a narrow (3 MHz) wide rejection band is observed and the possible mechanisms, including edge effects and interference between caustic beams, are explored. Third, the temperature dependence of the interfacial Dzyaloshinskii-Moriya interaction (iDMI) is measured in a Pt/Co film for temperatures ranging from 15 K to room temperature. Previous studies have been reported for temperatures above room temperature and this study serves to test theory over a greater range of temperatures. The iDMI parameter was quantitatively measured by measuring the frequency difference for counter-propagating surface spin waves by BLS. These three studies demonstrate that BLS is a versatile and powerful tool in the field of magnonics.
Open Access
Precision measurements on a single trapped beryllium ion
(Colorado State University. Libraries, 2024) Fairbank, David M., author; Brewer, Samuel M., advisor; Yost, Dylan, committee member; Sanner, Christian, committee member; Van Orden, Alan, committee member
Precision laser spectroscopy of transitions in simple atoms can be used as a stringent test of many-body quantum electrodynamics (QED) calculations, or to extract subtle information about internal nuclear structure. 9Be+ is a three electron ion which has been the focus of study in ion trap and high energy beam experiments dating back several decades. We present the first measurements of the D-lines in 9Be+ using a single trapped ion, which reduced the experimental uncertainty of both the D1 and D2 transitions by an order of magnitude. A framework for characterization of systematic shifts due to effects like photon recoil and quantum interference in ion trap-based measurements of strong transitions is presented. From the D2 lineshape data, a 2P excited state lifetime was extracted with reduced uncertainty and better agreement with theory, compared to previous work. The first experimental measurement of the unresolved 2P3/2 hyperfine splittings is reported, which helped to uncover a sign error in the theoretical prediction of the 2P3/2 electric quadrupole hyperfine constant. This measurement required development of techniques to selectively isolate and measure the unresolved components, utilizing the exceptional state preparation and control available for trapped ions. The 1.25 GHz 2S1/2 ground state hyperfine splitting was measured with a relative uncertainty of 1.6×10−11 using microwave Ramsey spectroscopy and is in good agreement with previous measurements made in Penning traps at NIST. The technique can be extended to the rare isotope 7Be+, for which the current hyperfine constant uncertainty is four orders of magnitude larger. This planned measurement could enable extraction of an improved value of the 7Be nuclear Zemach radius. D-line measurements on the rare isotopes 7,10Be+ are also planned using the techniques developed for 9Be+. A comparison of the fine structure splitting across the isotope chain can be used to extract the relative nuclear charge radii or test the many-body QED contributions to theory in Li-like ions. A new ion trap was built and direct ablation loading of the ion trap from small 9BeCl2 salt deposits was demonstrated in preparation for loading the rare isotopes from evaporated aqueous solution.
Open Access
Identifying and evaluating factors that enhance former offenders' hiring-related outcomes
(Colorado State University. Libraries, 2024) Anderson, Kemol J., author; Cleveland, Jeanette, advisor; Gibbons, Alyssa, advisor; Dik, Bryan, committee member; Henle, Chris, committee member; Kraiger, Kurt, committee member
Former offenders face several barriers to re-entry into society and the workplace. One such barrier includes employers' negative and unfounded attitudes of former offenders, which may lead to unfair bias in hiring. Crandall and Eshleman's (2003) justification-suppression model (JSM) posits that such prejudicial attitudes can be suppressed. Guided by the JSM theoretical framework, the current two-study project was designed to (1) identify prejudice suppression factors that might increase employers' willingness to hire former offenders – more specifically former minor drug offenders (FMDOs) and (2) test the efficacy of two suppression factors in a hypothetical hiring setting. Study 1 was an interview study of 13 employers, across several industries, on what factors made them more likely to consider hiring FMDOs. Thematic analysis results yielded 30 factors that were classified as situation-related, employer-related, and applicant-related suppression factors. The two most frequently endorsed prejudice suppression factors were: (1) evidence of the applicant's desistance & positive change, and (2) evidence of the applicant's honest disclosure of their background. In Study 2, the efficacy of these two suppression factors (desistance and disclosure) was tested to assess whether FMDOs' hiring-related outcomes were improved by manipulating suppressor evidence (desistance, disclosure, or no suppressor) and the offense type of the applicant (traffic offense, minor drug offense, and serious drug-related offense) in a hypothetical hiring context, for a retail sales associate position. Using a sample of 230 hiring managers in a retail setting, a significant main effect of offense type was found. No significant main effect was found for suppressor evidence on hiring recommendations. Neither offense type nor suppressor evidence was related to participants' concerns about hiring the applicants, or their proposed starting salary for applicants. Implications of these findings, alternative theoretical explanations, limitations, and future directions are discussed.
Embargo
Three essays on the economics of land use and conservation
(Colorado State University. Libraries, 2024) Shartaj, Mostafa, author; Suter, Jordan F., advisor; Manning, Dale T., committee member; Bayham, Jude, committee member; Jones, Kelly, committee member
This dissertation consists of three chapters focused on the economics of land use and conservation. The first chapter investigates the differences in groundwater use among wells irrigating State Land Board (SLB) parcels and nearby private parcels. SLB parcels represent leased parcels with limited tenure length and uncertainty of renewal. In the chapter, we demonstrate that wells irrigating SLB lands pump substantially more groundwater compared to non-SLB wells. The second chapter makes use of a novel dataset of discount rates elicited from agricultural producers across the United States to explore how estimates of discount rates for can be utilized to improve the performance of agri-environmental programs. The final paper examines camping in US Forest Service (USFS) campgrounds during the COVID-19 pandemic. Using data on campground reservations made through recreation.gov, we illustrate how camping on USFS lands was impacted by infection rates, public health restrictions and proximity to metropolitan areas and National Parks (NPs). Imperfect property rights can lead to over-extraction of resources and provide disincentives to invest in conservation of the resource stock. In the first chapter, making use of a natural experiment, we explore the case of groundwater usage on State Land Board (SLB) parcels, relative to nearby private parcels. The SLB of Colorado leases out land to agricultural producers, with groundwater rights tied to the land leases. Leases by the SLB have tenure lengths of 10 years, where the leaseholder is allowed to renew their lease if they can match the highest bid for the next lease term. This generates uncertainty regarding access to future groundwater stocks. We contribute to the literature by demonstrating the causal impact of SLB designation on groundwater use. We show that wells irrigating SLB lands, on average, use 15 to 24 percent more groundwater compared to nearby private lands. Adoption of conservation practices in agriculture often requires upfront costs, while the private benefits are produced in the future. As such, farmers' time preferences can play an important role in adoption decisions. In the second chapter, using elicited discount rates of farmers from 26 US states, we explore the role of farmers' discount rates in cover crop adoption, program participation, and continuation of cover cropping after the contract period. The data reveal that mean observed discount rates are lower both for farmers that adopt cover cropping and for farmers that participate in conservation programs, compared to those who do not. This suggests that time preferences play a key role in conservation adoption decisions. The empirical results are followed by a simulation analysis, which utilizes the discount rate data to explore benefits of tailoring conservation contracts based on discount rates. The simulations point out that a small increase in upfront payments can substantially increase cover cropping during the contract period, but they do little to increase continuation of cover cropping after the contract period. The simulations also reveal that tailoring the contract length and annual payment, according to the discount rate information, can allow policy makers to target higher levels of continuation, which are unattainable under the 5-year status quo contract. In the extreme case where the program administrator can observe individual discount rates, it is possible to dramatically reduce the costs of increasing continual adoption by individually tailoring the contracts. During the COVID-19 pandemic, US public land managers faced the challenge of catering to large increases in camping demand, while maintaining social distancing guidelines. In the final chapter, we use multivariate linear regression to analyze weekly changes in reservations to US Forest Service (USFS) campgrounds between 2019 and 2020. Our sample includes 1,688 individual USFS campgrounds from across the contiguous US. The results illustrate the dramatic increases in camping on USFS land that occurred in the summer of 2020 and demonstrate that increases in local infection rates led to significant increases in camping nights reserved in the summer. The results also illustrate that the increase in camping nights reserved at USFS campgrounds was particularly dramatic for campgrounds located near large metropolitan areas and near National Parks that saw increases in overall recreational visits. These results point to the important role that public lands played during the pandemic and can help guide public land resource allocations for campground maintenance and operation.
Open Access
Stress during pregnancy leads to long-term consequences in the offspring
(Colorado State University. Libraries, 2024) Sheng, Julietta Angelina, author; Tobet, Stuart, advisor; Smith, Bret, advisor; Myers, Brent, committee member; Hale, Taben, committee member; Chanda, Soham, committee member
Neuropsychiatric disorders encompass a wide range of conditions that affect neurological health and brain function and lead to disabilities worldwide. Such disorders include, but are not limited to, Major Depressive Disorder, schizophrenia, and anxiety disorders. Risk factors for developing neuropsychiatric disorders are multifaceted and can range from genetic predisposition, lifestyle, and environmental influences. Exposure to maternal stress is one type of environmental factor that can lead to changes in brain function and signaling pathways and increase susceptibility for related diseases. Maternal stress encompasses a diverse array of environmental stimuli, ranging from acute traumatic events to chronic or day-to-day life stressors. Maternal stressors, experienced by pregnant women, lead to overexposure of stress hormones in the developing fetus and impact short- and long-term neurological health the offspring. These studies evaluated developmental, neuroendocrine, and behavioral outcomes in offspring exposed to different models of maternal stress. Chapter 1 provided a brief history of stress, the development of the hypothalamic-pituitary-adrenal axis that regulates the stress response, and maternal-fetal interactions in stress regulatory systems and related behaviors. Chapter 2 evaluated several models of maternal stress, maternal high fat diet, maternal caloric restriction, maternal exposure to synthetic glucocorticoids. Although there were vast discrepancies between each type of maternal stress, one similarity was an activated immune response with elevated maternal cytokines. Therefore, Chapter 3 characterized a model of maternal immune activation using a toll-like receptor agonist, Resiquimod, that increased maternal and fetal cytokines, produced delayed developmental milestones and stress-related behavioral impairments in prepubertal (social-like) and adult (social-like, depressive-like, anxiety-like) offspring. Because these behavioral phenotypes are partially regulated by the paraventricular nucleus of the hypothalamus (PVN), Chapter 4 examined the neuroendocrine stress response and blood-brain barrier of the PVN. Data showed altered stress response accompanied by impaired blood-brain barrier integrity in the PVN of the adult offspring exposed to maternal injection of Resiquimod. Taken together, Chapters 2, 3, and 4 suggest maternal stress led to negative developmental, behavioral, and cellular pathologies indicative of neuropsychiatric-like disease. By teasing apart these specific programming mechanisms, we can better diagnose and treat progression of neuro-related disorders.
Embargo
The impact of rootstock on peach tree vigor, light environment, fruit quality, and metabolism
(Colorado State University. Libraries, 2024) Pieper, Jeffrey Ross, author; Minas, Ioannis, advisor; Bunning, Marisa, committee member; Caspari, Horst, committee member; Prenni, Jessica, committee member
The key to Colorado's successful peach industry is superb fruit quality. The fruit quality growers achieve allows for the highest premium 'farm-gate' price per pound in the nation. Fruit quality is created in the orchard via the interaction of several pre-harvest factors. One critical pre-harvest factor that has several knock-on effects for orchard management decisions is rootstock selection. Rootstock selection has the potential to impact the longevity, productivity, efficiency, and profitability of an orchard, and is dependent on climatic and edaphic environments as well as the soil microbiome. Rootstock selection may also allow growers to augment orchard design through vigor manipulation. In Colorado, growers are faced with relatively short growing seasons, sudden fall and spring frost events, and calcareous soils which limit the availability of certain nutrients. The unique growing environments coupled with the need for high quality fruit production makes rootstock selection limited. Identifying rootstocks suitable for production in Colorado and determining how they impact fruit quality is paramount. While previous studies have evaluated rootstocks for their performance and relationship to fruit quality, few have limited confounding factors such as crop load, canopy position, and or physiological maturity when assessing fruit. The following experiments evaluated twenty-one genetically diverse rootstocks for their phenotypic and agronomic performance and potential use in Colorado production systems. The nine-year performance review, in chapter one, details the productivity and suitability of seventeen genetically diverse peach rootstocks in Colorado growing conditions. The trial determined rootstock vigor strongly correlates with cumulative yield. However, vigor also showed an inverse relationship with internal fruit quality development measured as dry matter content (DMC) and soluble solids concentration (SSC). The trial showed interspecific peach and non-peach hybrids outperformed peach seedling rootstocks. One interspecific peach rootstock in particular, 'Krymsk® 86', performed exceptionally well and has since been widely adopted by industry. By controlling for several confounding factors, the rootstock vigor trial, chapter two, demonstrated the true impact of vigor and light availability on fruit quality enhancement and primary metabolite profiles. Fruit developing in reduced vigor canopy of the dwarfing rootstock 'Krymsk® 1' had increased light availability and enhanced internal fruit quality parameters (DMC and SSC) at harvest. Mesocarp metabolites relating to internal quality showed they are up and down accumulated by rootstock vigor and the light environment. Several metabolite classes including soluble sugars, cyclitols, flavanols, and chlorogenic acids were associated with 'Krymsk® 1', a low vigor rootstock that had high light availability and enhanced fruit quality profiles. 'Atlas™' and 'Bright's Hybrid® 5', both vigorous rootstocks, showed low light availability and reduced fruit quality. The vigorous rootstocks also showed an increase of amino and fatty acids compared to the standard and dwarfing rootstocks. The six-year physiological and agronomic performance of modern semi-dwarfing rootstocks trial, chapter three, reiterated the impact of vigor on yield, light availability, and fruit quality development. Furthermore, the trial showed increased vigor was related to an increase of gummosis incidence and severity. Also, intra-specific Prunus hybrids had increased rates of proleptic shoot formation, however, some showed they were susceptible to iron chlorosis. Overall, the rootstock trials identify key parameters of performance and suitability in Colorado production systems. The outcomes indicate that rootstocks with increased vigor resulted in higher yields per tree, however, lower light availability in the canopy decreased DMC and SSC. While rootstock genotype and vigor are influencing peach fruit development and quality, their effect on light availability may play a more significant role in achieving optimal yield and fruit quality and augmented metabolite profiles. Additionally, this work demonstrates the importance of controlling for confounding variables when evaluating preharvest factors for their impact on internal fruit quality and metabolite profiles.
Open Access
Mapping Rhizoctonia root and crown rot resistance from sugar beet germplasm FC709-2 using new genomic resources
(Colorado State University. Libraries, 2024) Metz, Nicholas, author; Mason, Esten, advisor; Dorn, Kevin, committee member; Richards, Christopher, committee member; Gaines, Todd, committee member
Sugar beet (Beta vulgaris subsp. Vulgaris) provides about 35% of the refined sugar globally, and over half of the domestic production in the United States. Sugar beet are primarily grown in temperate climates from plantings in late spring and harvest in the fall. In the United States sugar beets are grown in four diverse regions: the upper Midwest (Minnesota and North Dakota), the far west (California, Idaho, Oregon, and Washington, the Great Plains (Colorado, Nebraska, Montana, and Wyoming), and the Great Lakes (Michigan). Multiple pests and pathogens continue to threaten tonnage and recoverable sugar yields. These are controlled through planting genetically resistant cultivars, agronomic cultural practices and chemical applications throughout the growing season. With a shrinking set of chemical and cultural control options to manage these production threats, the need for continued improvement upon host plant resistance is important. Decades of global breeding efforts to improved disease tolerance in sugar beet has been effective, but molecular and genomic guided breeding and disease resistance characterization in sugar beet is only now emerging. The most important root pathogen in sugar beet is Rhizoctonia Root and Crown Rot (RRCR) caused by the fungal pathogen Rhizoctonia solani. This disease is estimated to cause up to 50% localized losses, and regularly causes 57 million dollars in economic losses per year despite the use of tolerant varieties, chemical control, and cultural practices. Public sugar beet pre-breeding has developed hundreds of widely utilized lines with novel traits and combinations of traits, including for RRCR resistance. One such line, FC709-2, displayed exceptional tolerance to Rhizoctonia solani released from the United States Department of Agriculture sugar beet breeding program in Fort Collins, Colorado. This germplasm line is base for many RRCR resistant cultivars used by growers around the world. In this study, new germplasm, genetic, and genomic resources revolving around FC709-2 were developed. These resources include a new germplasm line derived from the purification of FC709-2. By using stricter selection pressure and single seed decent a more homogenous seed lot was created to be used by other breeding programs. A new reference genome created from a single highly RRCR resistant plant using the most recent sequencings and bioinformatic technologies will be used to discover genes that are responsible for a wide array of plant interactions. Last, novel QTLs associated with RRCR resistance were discovered using a bi-parental mapping population and bulk segregate analysis. Collectively, these results show that discovering novel RRCR resistance genes in a highly resistant germplasm line using a purpose-built reference genome is a streamlined and accurate method. With these new resources in place researchers around the world can use them to discover the genes responsible for RRCR resistance, create markers for more accurate selections, and follow the methods described to be implemented in other plant breeding programs.
Embargo
Investigation into the mechanisms of bone loss in a sheep model of osteoporosis
(Colorado State University. Libraries, 2024) Bisazza, Katherine T., author; Easley, Jeremiah T., advisor; Anthony, Russell V., committee member; McGilvray, Kirk, committee member; Goodrich, Laurie R., committee member; Nelson, Bradley B., committee member
Osteoporosis is the most common metabolic bone disease in humans and the leading cause of fragility fractures in the aging population. Given the invasiveness of researching bone diseases in people, appropriate animal models are essential to both build our understanding of the disease as well as examine novel therapeutics. While small animals and rodents are more commonly used as models in bone research, large animal models offer the ability to perform robust, long-term studies on bone quality with higher translational impact. Ovariectomized sheep are a well-established large animal model for osteoporosis because of the comparable bone size and microarchitecture that is shared with humans. While the ovariectomized sheep has been utilized for decades as a model for the study of bone, many gaps in the model characterization remain. Based on results from a preliminary literature search, we developed study objectives and hypotheses to expand upon current knowledge gaps in the characterization of the sheep model of osteoporosis. In order to test these aims, we performed a single 12-month in vivo study utilizing sixteen ewes. Osteoporosis was induced experimentally in ten of these ewes via ovariectomy followed by a 24-week regimen of high dose corticosteroids, while six ewes were used as healthy seasonal controls. In our first aim, we compared the bone density and microarchitectural changes in the osteoporotic animals as compared to healthy controls over the course of a year. Dual-energy x-ray absorptiometry (DXA) scans revealed significant bone density loss in the osteoporotic animals in both the lumbar spine and tibia as compared to control animals. We also noted significant microarchitectural changes in iliac crest bone biopsies of osteoporotic animals as indicated by micro-computed tomography (microCT), including decreased bone volume fraction, trabecular thickness, and trabecular number, as well as increased trabecular spacing. Additionally, we compared the use of quantitative computed tomography (QCT) and DXA to measure bone mineral density and correlated those findings with microarchitectural parameters in the osteoporotic animals. We demonstrated superior QCT sensitivity and specificity to subtle bone changes in the lumbar spine as compared to DXA, as well as demonstrated a higher correlation of QCT with iliac crest biopsy microarchitectural changes. The second aim of our study was to explore the systemic and clinical impacts of osteoporosis model development in our ten sheep compared to the healthy control animals. To test this aim, we collected blood, bone marrow, and body weights throughout the course of the year-long study. Osteoporotic animals demonstrated significant impacts to hematology and serology blood levels over the course of model development, primarily at 3 and 6-months when corticosteroids were at peak use. In particular, we note significant reductions in monocytes, lymphocytes, and eosinophils at 3-months with accompanying neutrophilia, as well as an increase in platelet count and volume. We also observed an increase in serum phosphorus and electrolytes, decrease in kidney enzymes and total protein, and an increase in select liver enzymes at 3 and 6-months in the same animals. Serum cortisol and estradiol were significantly depleted at 3 and 4-months, respectively, in the osteoporotic animals. However, estradiol levels were maintained to control levels for the remainder of the study. All these changes indicate disruptions to multiple physiologic systems over the course of osteoporosis induction in sheep which may highlight the acute effects of administering high-dose glucocorticoids. In the third and final aim of this study, we investigated the morphometrical and proteomic changes in the bone of sheep following osteoporosis induction over the course of a year. Histomorphometry of iliac crest bone biopsies revealed decreases in trabecular bone area in osteoporotic model animals compared to healthy controls, while negligible differences were observed in cortical bone morphometry. Initial global untargeted proteomic outputs identified a total of 4,765 proteins from the iliac bone biopsy samples, 909 of which were determined to be differentially expressed over the course of model development in our osteoporotic sheep. Pathway analysis of differentially expressed proteins (DEPs) revealed unique enriched pathways at all time points. Enrichment of biological processes such as monocyte differentiation, metabolic processes, regulation of chromosome condensation, and immune responses were noted throughout osteoporosis development. When comparing the 909 DEPs between time points, we identified seven downregulated proteins shared between all time points as compared to baseline in the osteoporotic animals (CTR9, INPP5D, CDK6, PPP2R5C, NUP133, ITPRIPL1, W5PH60_SHEEP). Pathway analysis of these shared proteins revealed enrichment of p53 signaling, mRNA surveillance, sphingolipid signaling, and P13K-Akt signaling pathways. This study was the first to report on the proteomic changes of bone in conjunction with morphometry assessments in a sheep model of osteoporosis. All three of our described experiments allowed us to successfully fill in some of the knowledge gaps in the characterization of a large animal model of osteoporosis by further assessing both macro and micro changes in ovariectomized and steroid-dosed sheep over the course of a year. Large animal preclinical models offer researchers the ability to compare bone changes in the same animals over time, allowing for a more comprehensive insight into the progression of postmenopausal and age-related bone loss. Understanding the mechanisms driving bone loss and systemic changes in osteoporosis disease progression could aid in future cellular therapy research and investigation of novel pathway targets for osteoporosis treatment in humans.
Open Access
Bacteriomes of peaches and cover crops
(Colorado State University. Libraries, 2024) Newberger, Derek R., author; Vivanco, Jorge M., advisor; Minas, Ioannis, advisor; Paschke, Mark, committee member; Manter, Daniel, committee member
Replant syndrome (RS) of fruit and nut trees causes reduced tree vigor and crop productivity in orchard systems due to repeated plantings of closely related tree species. Although RS etiology has not been clearly defined, the causal agents are thought to be a complex of soil microorganisms combined with abiotic factors and susceptible tree genetics. Different soil disinfection techniques alleviate RS symptoms by reducing the loads of the deleterious microbiome; however, the positive effect on crop growth is temporary. Here, the current understanding of RS in orchards from a soil microbiome perspective is reviewed. The resolution to RS will require experts to outline explicit descriptions for its symptoms, determine its etiology, identify the primary phytopathogens, and fully explore sustainable treatments which alleviate RS. Two sustainable treatments of RS were selected to explore at a deeper level, soil disinfection and increasing crop diversity to observe what technique could help establish a healthy soil bacteriome. In a greenhouse study, soil disinfection via autoclave was then followed by cover cropping. It was found that soil disinfection increases plant biomass as compared to the control for only the first crop cycle while non-autoclaved soils with a history of cover cropping alleviated RS in RS-susceptible 'Lovell' peach seedlings. Although soil disinfection via autoclave was found to distinctly alter the peach soil bacteriome for the full duration of the study, this sustainable practice mimicking solarization failed to provide relief from RS for peach seedlings. Instead of long-term benefits, differential abundance comparisons displayed a loss of potentially beneficial bacteria due to soil disinfection. Paenibacillus castaneae and Bellilinea caldifistulae were beneficial bacterial species that uniquely colonized peach rhizosphere of non-autoclaved soils with a cover crop history. As a promising sustainable technique, a greater understanding of how inter-/intra-specific competition of cover crops can influence the bulk soil bacteriome was pursued. Alfalfa, brassica, and fescue were grown in 7 different plant combinations (1. alfalfa, 2. brassica, 3. fescue, 4. alfalfa-brassica, 5. alfalfa-fescue, 6. brassica-fescue, 7. alfalfa-brassica-fescue) across 3 density concentrations (low: 1–3 plants, medium: 24 plants, and high: 48 plants) for a greenhouse microcosm experiment. It was found that even in highly competitive conditions beneficial bacteria were enriched, however, there was an apparent trade-off where different plant combinations enriched distinct beneficial bacteria. As an example, even if a free-living nitrogen fixing bacteria such as an Azospirillum spp. was enriched in the bulk soil of alfalfa and brassica monocultures, it was not enriched in the bulk soil of an alfalfa-brassica plant mixture. Instead Pseudarthrobacter phenanthrenivorans, a phytohormone producer, was enriched in alfalfa-brassica plant mixtures. When zooming into the rhizosphere compartment of these microcosms, it was found that regardless of plant neighbor identity or density, a few rhizobacteria were highly correlated with a specific plant species. Meanwhile, certain plant species specific rhizobacteria were enriched only if specific conditions such as plant neighbor identity or density were met. Overall, our research found that growing diverse plant species plants prior to the re-establishment of a peach orchard could alleviate RS symptoms. Furthermore, cover crops can enrich different microbes when grown together as opposed to when grown separately. Lastly, although plants recruit a particular set of bacteria, this recruitment can shift depending on plant neighbor identity or density. Further study of cover crops may identify how they can alleviate RS in orchards worldwide.
Open Access
A novel smoother-based data assimilation method for complex CFD
(Colorado State University. Libraries, 2024) Hurst, Christopher L., author; Gao, Xinfeng, advisor; Guzik, Stephen, advisor; Troxell, Wade, committee member; van Leeuwen, Peter Jan, committee member
Accurate computational fluid dynamics (CFD) modeling of turbulent flows is necessary for improving fluid-driven engineering designs. Traditional CFD often falls short of providing truly accurate solutions due to inherent uncertainties stemming from modeling assumptions and the chaotic nature of fluid flow. To overcome these limitations, we propose the integration of data assimilation (DA) techniques into CFD simulations. DA, which incorporates observational data into numerical models, offers a promising avenue to enhance predictability by reducing uncertainties associated with initial conditions and model parameters. This research aims to advance our understanding and application of DA for CFD modeling of highly chaotic dynamical systems. This dissertation makes several novel contributions in DA and CFD: i) A novel DA algorithm, the maximum likelihood ensemble smoother (MLES), has been developed and implemented to provide better model parameter estimation and assimilate time-integrated observations while addressing nonlinearity, ii) Multigrid-in-time techniques are applied to enhance the computational efficiency of the MLES by improving the optimization processes, and iii) The MLES+CFD framework has been validated by classical test problems such as the Lorenz 96 model and the Kuramoto-Sivashinsky equation. The effectiveness of the MLES has been demonstrated through a few test problems featuring chaos, discontinuity, or high dimensionality.
Open Access
Evolution at the edge: how hibernation, heat waves, and hybridization impact a range expansion
(Colorado State University. Libraries, 2024) Clark, Eliza, author; Hufbauer, Ruth, advisor; Bitume, Ellyn, committee member; Norton, Andrew, committee member; Funk, Chris, committee member
Evolutionary processes shape the diversity of life on earth. Over millennia, species diverge from one another, radiating out into the tree of life. The same processes of evolution are also acting in much shorter periods of time, selecting for traits, mixing genes across populations, and generating new mutations each generation. These rapid evolutionary processes interact with ecological processes, which are happening on similar time scales. Range expansions, or expansions of a population's geographic distribution, were once considered strictly ecological processes of populations interacting with other populations and the environment, unaffected by evolution. However, modern theory understands range expansions to be crucibles of rapid evolution. Rapid evolution shapes the process of range expansion itself, and is also integral to determining the outcomes of range expansion. During range expansions, ecological and evolutionary processes intertwine, combining to shape the dynamics of a range expansion, like where a population can establish, and how quickly the expansion moves. The study of evolution during range expansions has only just begun to make it out of the theory to be tested in wild populations in nature, so we don't yet know how common evolution during range expansion is, or how large its effects might be. Here, I explore how evolution impacts range expansions that are current and ongoing in natural systems in the wild. I focus on the tamarisk beetle (Diorhabda spp.), deliberately introduced in the United States about two decades ago for biological control of a widespread invasive weed. Through its role as a biological control agent, the tamarisk beetle has expanded its range hundreds of kilometers along rivers, colonizing new areas of the invasive weed in environments very different from its original release habitat. The range expansion of the tamarisk beetle provides a unique opportunity to study evolution during an ongoing natural range expansion across an environmental gradient. Through the following four chapters, I document evolution of dispersal ability and life history traits (Chapter 1), evolution of seasonal dormancy and genetic variation of that trait (Chapter 2), evolution of phenotypic plasticity (Chapter 3), and the impacts of hybridization (Chapter 4). Throughout, I discuss the implications for biological control and the tamarisk beetle specifically, and more generally how these results improve our understanding of how evolution is caused by, enables, and alters natural range expansions over short time periods, even in natural range expansions.
Open Access
Occupational noise exposure and hearing assessment of hydraulic fracturing workers: quiet versus conventional fleets
(Colorado State University. Libraries, 2024) Blevens, Melissa S., author; Brazile, William, advisor; Tsai, Candace Su-Jung, committee member; Van Dyke, Michael, committee member; Autenrieth, Daniel, committee member; Lipsey, Tiffany, committee member
Oil and gas extraction companies are exempt from implementing hearing conservation programs for their workers according to the Occupational Safety and Health Administration's (OSHA) noise standard. The occupational noise exposure and hearing status of these workers has not been published in scientific literature before the present study, presumably due to this exemption. In this study, area and personal noise exposures and worker hearing acuity were measured at both conventional and quiet hydraulic fracturing fleets, allowing a comparison between the fleets. Quiet fleets refer to the use of engineering controls to decrease noise levels of the pumps while conventional fleets do not employ these measures. In both fleets, the authors conducted personal noise dosimetry, equipment noise measurements, and pure tone audiometry pre- and post-work shift to determine if there were temporary threshold shifts (TTS) in hearing. Based on the personal noise dosimetry results, 42/50 (84%) of the quiet fleet and 34/34 (100%) of the conventional fleet workers sampled were at or over 100% noise dose according to the American Conference of Governmental Industrial Hygienists' (ACGIH) noise Threshold Limit Value (TLV). Based on the OSHA Permissible Exposure Limit (PEL) noise criteria, 9/50 (18%) of the quiet fleet workers and 15/34 (44.1%) of the conventional fleet workers were at or over 100% noise dose. Workers in both fleets experienced TTS, but no significant difference was observed between the types of fleets in relation to TTS. Most equipment of both fleets exceeded 85 decibels, but the pumps of the quiet fleet were ~14 dB lower than those of the conventional fleet. Although the quiet fleet noise controls reduced personal noise exposure, a portion of the quiet fleet workers sampled still faced noise levels that could increase the risk of hearing loss. The researchers suggest the initiation of a hearing conservation program despite OSHA exemption to safeguard worker health and recommend workers involved in certain job tasks employ dual hearing protection based on the exposure monitoring results.
Open Access
Plant-mediated interactions between herbivory and soil microbial communities in biocontrol programs of Russian knapweed
(Colorado State University. Libraries, 2024) Matos Franco, Giovana, author; Ode, Paul, advisor; Pearse, Ian, committee member; Smith, Melinda, committee member; Trivedi, Pankaj, committee member
Russian knapweed (Rhaponticum repens) is an invasive noxious weed present in the United States and two insect biocontrol agents have been released to assist with its management: the gall midge (Jaapiella ivannikovi) and the gall wasp (Aulacidea acroptilonica). Since their establishment, no concrete impacts of biocontrol agents onto Russian knapweed have been measured, neither their impacts on interactions between Russian knapweed and local microbiomes. To address this knowledge gap, observational and manipulative studies were conducted to investigate the effects of biocontrol agents on Russian knapweed fitness as well as its associated microbiomes. We found that Russian knapweed associates with a core microbiome that can assist with invasion in the introduced range as well as, in root samples collected from sites where gall wasp were present, lower microbiome diversity was observed, indicating potential negative effects on overall plant health. In garden conditions, water availability positively correlated with plant growth, negatively correlated with insect establishment, and shaped microbiomes in root associated tissues. Results of this dissertation highlights how introduction of biocontrol agents shifts pre-established relationships between invasive plants and microbiomes as well as how such relationships could be impacting the success of biocontrol programs.
Embargo
Thermally-assisted frontal polymerization for rapid curing of fiber-reinforced polymer composites
(Colorado State University. Libraries, 2024) Naseri, Iman, author; James, Susan, advisor; Bailey, Travis, committee member; Herrera-Alonso, Margarita, committee member; Ma, Kaka, committee member
Fiber-reinforced polymer composites (FRPCs) are widely used in a variety of applications owing to their excellent specific mechanical properties, chemical stability, and fatigue resistance. However, the state-of-the-art technologies for manufacturing FRPCs are intensive in terms of time and energy, generate a significant carbon footprint, and require costly resources. In addition, FRPCs lack key non-structural functionalities (e.g., de-icing, damage sensing) required for many applications. Despite the enormous efforts made to improve the manufacturability of FRPCs and address the shortcomings associated with the performance of FRPCs, there is still a pressing need for alternative manufacturing technologies to enable the rapid, energy-efficient, and low-cost manufacturing of multifunctional fiber-reinforced polymer composites. In this dissertation, a novel technique for rapid and cost-effective manufacturing of multifunctional fiber-reinforced polymer composites is developed by exploiting the frontal polymerization concept and joule heating of nanostructured materials. A nanostructured paper or fabric is integrated into the composite layup to supply the energy required to trigger frontal polymerization via the Joule heating effect. In addition, the nanostructured paper remains advantageous in in-service conditions and imparts new functionalities to the host composite structure. In the first chapter, the recent developments in material systems, as well as heating techniques reported for improving the manufacturability of FRPCs, are reviewed, and frontal polymerization (FP) as a rapid and energy-efficient technique for curing thermoset matrix composites is introduced. In the second chapter, frontal curing of multifunctional composites via a commercial nanostructured heater (buckypaper) is demonstrated, and the curing behavior of composite laminate is studied under various layup conditions. It is demonstrated that the through-thickness FP manufacturing strategy using an embedded buckypaper surface heater allows for rapid and energy-efficient manufacturing of fully cured composite panels using the conventional tooling materials utilized in the composite industry. However, the temperature profiles developed during the cure cycle, as well as the degree of cure of resin in produced composites, are greatly affected by the thermal properties of the tooling materials, where lower front temperatures and degree of cure are measured for composite panels manufactured using thermally conductive tooling materials such as aluminum. This issue can be effectively addressed by preheating the dry composite layup for a few minutes. Despite the relatively uniform heat generation in nanostructured buckypaper heaters, the infrared thermal imaging of the curing process reveals that the front initiates from multiple locations and propagates in both the through-thickness and in-plane directions. In addition, the de-icing functionality is demonstrated in the cured composite as one of the several possible functionalities imparted to composite structures due to the presence of a buckypaper layer. In the third chapter, a fabric heater is developed by writing laser-induced graphene on aramid fabric using a CO2 laser and used as an integrated heater for manufacturing FRPCs via the through-thickness FP manufacturing technique. A 10 cm × 10 cm composite panel is successfully cured within only 1 minute with a total energy consumption of 4.13 KJ, which is comparable to the time and energy required for producing a similar composite panel using a buckypaper heater. In addition to composite manufacturing, flexible heaters are prepared with the addition of silicone rubber to fabric heaters. Although the addition of electrically insulating rubber negatively affects the electrothermal performance of fabric heaters, it greatly improves the durability of fabric heaters. In the fourth chapter, a facile and rapid technique for the preparation of mechanically robust nanocomposite film heaters is developed based on a frontally polymerizable resin system. The mechanical and electrothermal properties of the nanocomposite film heaters are characterized, and the produced heaters are used for out-of-oven manufacturing composite laminates. In the final chapter, the main research findings are summarized, and the recommendations for future studies are presented.
Open Access
Students with disabilities during the COVID-19 pandemic: how an inverted disaster impacted educational access, student outcomes, and family strain
(Colorado State University. Libraries, 2024) Bendeck, Shawna Lee, author; Cross, Jennifer E., advisor; Malin, Stephanie A., committee member; Hastings, Orestes P., committee member; Hausermann, Heidi, committee member
During the COVID-19 pandemic, school buildings were closed, and education took place through a variety of at-home, virtual, and hybrid learning models. These alternative teaching modalities were especially challenging for students with disabilities. As a socially vulnerable population, children with disabilities and their families are at greater risk of poor outcomes during disasters and disruptions in schooling. The pandemic was also a different type of disaster. In this dissertation, I propose the COVID-19 pandemic was an inverted disaster, defined by the following characteristics: it was temporally and spatially unbounded; it posed a physical yet invisible threat to all human lives; and its ubiquity and invisibility led to the breakdown of institutional and social support systems. As schools were closed, educators were left unprepared for continued learning during such an event. Students with disabilities rely on the consistency of educational and therapeutic services, accommodations, and modifications for their continued learning and growth. The pandemic presents an urgent need to examine the delivery and consequences of education for these students, and to discover best practices for moving forward. This dissertation is guided by the following research questions: 1) How was education altered during the pandemic? 2) How did shifts in education differentially impact students with disabilities and their parents? and, 3) How did parents mitigate the impacts of school closures during the pandemic, despite the unique challenges posed by the disaster? To answer these questions, I conducted a mixed-methods study that included: 1) surveys with 125 parents and caregivers of children in K-8 grades; 2) qualitative in-depth interviews with a subsample of 39 parents in Northern Colorado; and 3) social network analysis with 29 of these parents. Fifty percent of parents who participated had at least one child with a disability. This study represents a total of 248 children, 83 of which were identified as having a disability qualifying them for special education services. First, findings from this dissertation revealed that due to a lack of preparation and planning for an inverted disaster, schools were unable to provide consistent, equitable educational services to students with disabilities throughout waves of the pandemic. These students faced structural barriers to education that limited their access to general and special education, therapeutic services, and their peers and educational support systems. Second, due to these barriers, students with disabilities experienced greater setbacks in their academics, physical and mental health, and their socio-emotional development. Third, parents experienced strain on their roles, their homes, and their relationships. Role conflict was greater for parents who had a child with a disability. Fourth, parents of children with disabilities reported more stress, worry, and lower wellbeing than their peers. The intersectionality of disability with single parenthood, race, socioeconomic status, and work location impacted various aspects of mental health in disproportionate ways. Fifth, parents mitigated the impacts of the pandemic and school closures by altering forms of connection with their social networks and by developing new networks to meet the unique demands of the pandemic. Parents with stronger social support networks (i.e. larger, denser, more diverse, etc.) experienced less mental health strain than parents who had weaker networks. Social networks provided a buffer to the negative impacts of the pandemic and school closures on parents. This dissertation contributes to scholarly literature by introducing the concept of the inverted disaster as a new way to define the pandemic and understand its impacts on educational equity, children with disabilities, and their parents. This research outlines how the characteristics of the inverted disaster led to a breakdown of institutional and support systems and to the exclusion of children with disabilities from vital educational and therapeutic services. It also examines the disproportionate impacts on parents, linking patterns of disadvantage with mental health outcomes. Methodologically, I explore how the strength of social networks can be measured and analyzed as mitigating factors on parental mental health. Based on the findings from this research, I recommend strategies for improved disaster management and educational policies for continued special education during disaster that prioritize children with disabilities. I also propose strategies for community building and strengthening social networks among at-risk families.
Open Access
Uncovering mechanisms driving variation in mutation rates in organellar and nuclear genomes
(Colorado State University. Libraries, 2024) Waneka, Gus, author; Sloan, Daniel B., advisor; Lockridge Mueller, Rachel, committee member; Argueso, Juan Lucas, committee member; Stenglein, Mark, committee member
Mutations are changes to DNA sequences which drive evolution by supplying raw genetic variation for natural selection to act upon. At the same time, mutations tend to have negative fitness consequences and are the source of genetic diseases. Such costs and benefits of mutation create opposing forces of selection on mutation rate modifiers, which are alleles (typically in DNA repair genes) responsible for increases or decreases to mutation rates. Essentially all eukaryotes possess at least two genomes: the nuclear genome (nucDNA) and the endosymbiotically derived mitochondrial genome (mtDNA). Photosynthetic plants and algae additionally possess endosymbiotically derived plastid genomes (cpDNAs). Together, the mtDNA and cpDNA are referred to as organellar genomes. Chapter 1 of this dissertation provides a framework for understanding how DNA repair machinery and mutation rates have evolved in complex eukaryotic cells. Chapters 2 and 3 focus on specific repair pathways active in organellar genomes. Finally, Chapter 4 shifts focus to understand how environmental perturbations in expression level impact mutation in plant nuclear genomes. Repair of organellar genomes is conducted by nuclear-encoded genes that are translated in the cytosol and targeted to the organelles. In terms of evolutionary history, organellar repair machinery is a mosaic network of bacterial-like repair genes, which came into the cell with the organelles, and nuclear repair genes that have been co-opted for organellar function. In some cases, repair proteins are targeted to both the nucDNA and mtDNA (and/or cpDNA in plants) to perform similar functions. This is the case as for many base excision repair (BER) proteins, which identify and remove of chemically damaged bases. In contrast, organellar repair arsenals are thought to lack canonical mismatch-repair (MMR) and nucleotide excision repair (NER), which are both important repair pathways in nuclear genomes. Instead, the diverse eukaryotic lineages have adopted unique strategies for organellar genome maintenance. As a result, there is a tremendous diversity in mtDNA mutation rates, which show over a 4000-fold variation across eukaryotes. Interestingly, much of this variation is driven by the extremely low point mutation rates plant mtDNAs. In addition, plant organellar genomes are more recombinationally active and plant mtDNAs are structurally unstable compared to the mtDNAs of other eukaryotes. Chapter 2 of this dissertation explores the mechanistic basis of low point mutation rates and recombination-mediated repair in plant organellar genomes. We performed high-fidelity Duplex Sequencing on a panel of Arabidopsis thaliana lines lacking specific organellar genome repair genes. We report large point mutation increases in mutant lines lacking MSH1, a mutS homolog that has been proposed to induce double-stranded breaks at the site of DNA mismatches, effectively shuttling such lesions into homologous recombination (HR) pathways that play important roles in plant organellar genome replication and repair. We see smaller point mutation increases in other mutant lines lacking RADA, RECA1 and RECA3. In addition, we generated long-read Oxford Nanopore sequencing to characterize repeat-mediated recombination in several of the mutants in the panel. Our findings provide valuable insights into the mechanisms driving the fascinating patterns of organellar genome evolution in land plants. The aforementioned lack of NER in organellar genomes is surprising given the importance of NER as a 'catchall' for repair of a variety of bulky DNA lesions in nuclear genomes. Chapter 3 focuses in on the fate of photodamage (an important type of bulky DNA damage) in organellar DNA. To do so, we leverage publicly available XR-seq datasets, which were generated to quantify and map active NER excision products in nuclear genomes following UV exposure. The taxonomic scope of chapter is expanded from plants to also include fungi (the brewer's yeast Saccharomyces cerevisiae) and animals (the model fruit fly Drosophila melanogaster). We find that mtDNA-derived XR-seq reads in A. thaliana and S. cerevisiae have distinct and repeatable patterns in terms of length and internal positioning of pyrimidine dimers (known targets of photodamage formation). These data mirror established patterns of NER-derived reads originating from the nuclear genomes, raising the exciting possibility that NER-like repair pathways may exist in for repair of photodamage in organellar genomes. The focus of chapter 4 shifts to understanding how environmental changes impact mutation in plant nuclear genomes. The textbook view of mutation and adaptation is that mutations occur randomly with respect to their environment-specific fitness consequences. However, this view of random mutation is challenged as evidence increasingly establishes a correlation between increased expression and decreased mutation via the coordination of transcription and DNA repair machinery at the molecular level. As a result of this correlation, intragenomic mutation rates likely vary with changing environments given that expression levels are environmentally labile. Therefore, certain genes may be predisposed to higher or lower mutation rates depending on the environment, though the magnitude and importance of this effect remains largely untested. A technical challenge in addressing these questions is that large scale plant mutation datasets are time and resource intensive to generate. A recent plant study relied on low frequency somatic calls from Illumina based shotgun libraries to generate a large number of mutations, but others report that most of these inferred mutations are sequencing errors. To overcome these challenges, we took a novel approach to measuring somatic mutations by using Duplex Sequencing to quantify mutations in targeted regions of the A. thaliana nucDNA. We identified a set of differentially expressed genes in plants grown at different temperatures, which we then targeted for mutation detection using hybrid capture. In addition to wild type (WT) lines, we also studied mutant lines deficient in BER and MMR to test if either of these pathways are responsible for the correlation between expression and mutation in plants. We found large point mutation increases in the MMR mutants compared to WT plants, which displayed surprisingly few mutations at either temperature. Though the small number of WT mutations precluded a meaningful comparison of expression and mutation in a WT background, this result if nonetheless valuable for establishing that the true frequency of somatic mutations in plants is indeed very low suggesting that previous estimates likely conflated Illumina based sequencing artifacts with mutations. Mutation rates vary by over three orders of magnitude across the tree of life. Much of this variation is captured in mitochondrial mutation rates. The chapters of this dissertation provide valuable insights into the molecular processes that drive mutation rate variation in eukaryotic genomes. Such mechanistic understandings are critical for advancing the broader field of mutation rate evolution.
Embargo
Three essays on food policy adoption and economic welfare
(Colorado State University. Libraries, 2024) Kashyap, Pratyoosh, author; Jablonski, Becca B.R., advisor; Suter, Jordan F., committee member; Hill, Alexandra E., committee member; Carolan, Michael S., committee member
This dissertation contains three chapters that empirically explore policies supporting school meals and local food marketing as well as drivers of food demand with the goal of providing comprehensive insights into their complexities and implications, ultimately contributing to a deeper understanding of the food systems. Recognizing school meals as critical safety nets for children in low-income households, many states in the United States (U.S.) are passing legislation to adopt universal free school meals, linking their funding to the Community Eligibility Provision (CEP), a federally funded universal free school meal program. In the first chapter we develop a unique school district-level dataset and use a Cox regression model to demonstrate the importance of federal- and state-level policy factors in increasing the likelihood of CEP adoption. In the second chapter, we examine the relationships among stocks of community wealth, state legislation supporting farm to school (FTS), and the intensity of FTS activities. Leveraging the U.S. Department of Agriculture's 2019 FTS Census, a new disaggregated database on state-level FTS policies, a new dataset of stocks of local wealth, and using a Heckman selection model, we find positive associations between cultural and social capital and FTS intensity, and associations with state FTS policies. In the third chapter, we shift our focus to examining economic welfare implications in the event of an African Swine Fever (ASF) outbreak in the U.S. Although ASF is not a food safety risk and has never been detected in the U.S., little is known about changes in U.S. pork demand in case of an outbreak. Using an online survey experiment, we find that the demand for pork is predicted to shift downward by approximately 31% resulting in an annual welfare loss of $55.46 billion in the pork market, exacerbating the losses to pork producers. Results also indicate that government institutions are most trusted when it comes to sharing news about food safety, strongly suggesting its importance in generating awareness prior to and during an ASF outbreak.