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PHYSCOMITRIUM PATENS : APPLICATIONS IN SYNTHETIC BIOLOGY AND THE CURATION OF DITERPENOID LIBRARIES
No full textThesis (Ph.D.)--Michigan State University. Genetics and Genome Sciences \u2013 Doctor of Philosophy, 2024The model moss species, Physcomitrium patens (P. patens), provides a unique system for investigating plant development, evolution, and physiology and also serves as an excellent chassis for synthetic biology. Because of the unique phylogeny of P. patens as a bryophyte, and sister to the vascular plants, allows opportunity for understanding shared traits among embryophytic life, early terrestrialization of plants on land 500 million years ago, and the divergences/convergences of plant traits since then. The high prevalence and global distribution of plants and fungi today can in-part be attributed to their long-standing relationship which predates early terrestrialization, and who\u2019s early collaboration likely reduced the initial barriers for both kingdoms to thrive on land. Here, the interaction between P. patens and fungi in the Mortierellaceae family are cocultured together to characterize their physiological and transcriptional responses. These analyses are used to explore possible long-standing interactions between plants and fungi, identify essential traits in plant-fungal communication, and provide foundational exploration into coculturing these systems for metabolite production. P. patens is an effective system for the production of heterologous metabolites, particularly diterpenes, because of its relatively low chemical diversity, many developed synthetic biological tools, and similar machinery/compartments to vascular plants. The large pool of diterpene chemodiversity and bioactivity known today affords these compounds with high humanitarian and economic value, making it an excellent metabolite to develop for expression in P. patens. Work presented in this dissertation focuses on evaluating the effectiveness of a coculture system with P. patens and Mortierellaceae, explores long-standing relationships among plants and fungi, provides schematic and initial testing of novel synthetic biological tools for improving P. patens as a chassis, and evaluates complexities among the total diterpene landscape to-date.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
Incomplete barriers to heterospecific mating among Somatochlora species (Odonata : Corduliidae) as revealed in multi-gene phylogenies
No full textThesis (M.S.)--Michigan State University. Entomology - Master of Science, 2024Somatochlora, commonly known as the striped emeralds, is an enigmatic genus whose systematics have lagged other Odonata genera, with the last revision done by Walker (1925). North American Somatochlora inhabit fens, bogs, and forest streams, with most closely related species sharing a sympatric range. As a result, Somatochlora males have elaborate claspers which are species-specific and provide a morphological barrier to heterospecific mating, but exceptions have been observed. The objective of this project was to investigate the occurrence of heterospecific mating between North American Somatochlora species as inferred from multi-gene phylogenies. We employed the use of two mitochondrial genes (COI and ND3) and two nuclear genes (EF1-\u3b1 and ITS2) to construct well-substantiated phylogenies using a maximum parsimony optimality criterion. Compared to nuclear genes (nDNA), mitochondrial genes (mtDNA) have a high nucleotide substitution rate, thereby allowing for the genetic discrimination of populations and species. Monophyly of mtDNA lineages is expected for closely related species because ancestral mtDNA lineages go extinct after a speciation event four times faster than nDNA lineages. Observation of non-monophyletic mtDNA lineages but monophyletic nDNA lineages between Somatochlora sister-species would indicate mtDNA introgression and suggest heterospecific matings. Our results highlighted three instances of heterospecific mating in the following groups: 1) S. hineana + S. tenebrosa; 2) S. kennedyi + S. forcipata + S. franklini; 3) S. calverti + S. provocans + S. filosa. In addition, the recovered topology accurately reflected previous taxonomic understanding of the genus. These multi-gene phylogenies of North American Somatochlora are the first, providing a foundation for future ecological and evolution studies and knowledge for effective decision-making and public policy, which is especially important for endangered species, Somatochlora hineana.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
DECENTRALIZED WASTEWATER UTILIZATION FOR SUSTAINABLE WATER AND ENERGY MANAGEMENT
No full textThesis (Ph.D.)--Michigan State University. Biosystems Engineering - Doctor of Philosophy, 2024With growing water scarcity as a leading challenge for sustainable development, decentralized wastewater treatment and recycling strategies are emerging as viable solutions to address the water needs of a significant portion of the population. Unlike centralized wastewater treatment facilities, decentralized systems, especially those incorporating the source separation of wastewater, offer cost-effective and efficient ways to treat wastewater.This study first conducted a comprehensive life cycle impact assessment and techno-economic analysis to compare five treatment scenarios for two types of source-separated wastewater: blackwater (from toilets and kitchens) and greywater (from showers and laundry). These scenarios utilized different combinations of three scalable technologies: activated sludge, anaerobic digestion (AD), and membrane filtration. Activated sludge was employed to treat source-separated wastewater, while anaerobic digestion processes sludge into biogas for energy generation. Membrane filtration, including ultrafiltration and reverse osmosis, further purified the treated wastewater for discharge or recycling. The study revealed that using activated sludge and membrane filtration to treat blackwater and greywater separately, followed by anaerobic digestion to reduce the sludge and generate methane energy, offered superior environmental and techno-economic performance among the evaluated scenarios. The study highlighted the importance of biological treatments in removing pharmaceutical and personal care products (PPCPs) from wastewater, thus reducing their environmental impact. A baffled bioreactor (BBR) was utilized for blackwater treatment, showing high removal rates of organic content and inorganic nitrogen, which increased with higher feed amounts. The microbial diversity within the BBR system was also greater at higher feed amounts, facilitating the removal of total solids, total nitrogen, and nitrates. An economic analysis examined the treatment costs under different energy scenarios, including electricity from the grid, propane gas engines for remote communities, and diesel engines for military and extreme environments. Greywater, which can be separated from blackwater due to its lower contaminant concentration, is an excellent candidate for recycling. To optimize greywater treatment, the study evaluated three ultrafiltration membranes: Pittsburgh Plate Glass (PPG), Polyvinylidene Fluoride (PVDF), and Polyethersulfone (PES), using greywater from showers, laundry, and a combination of both as feed water. The PPG membrane demonstrated the fastest flux and least fouling across all water types, while PVDF and PES were more efficient at nutrient removal. The study concluded that a multiple objective optimization (MOO) approach is effective for selecting membranes and designing treatment processes tailored to different greywater sources. Addressing the inherent trade-offs in wastewater treatment of balancing water quality, energy consumption, and cost, the study employed a MOO approach to optimize treatment combinations. The system studied included electrocoagulation (EC) for blackwater treatment, AD for food waste and EC sludge, electrodialysis (ED) for final water treatment, and electricity generation from biogas and photovoltaic (PV) solar energy. The combination of PV, AD, EC, and ED achieved the best performance in terms of water quality, meeting EPA discharge standards, and demonstrated a low global warming potential (GWP) and high energy output. The Pareto frontier analysis highlighted AD+EC+ED and PV+AD+EC+ED as the preferred treatment combinations, prioritizing water quality and overall environmental performance. This integrated approach to decentralized wastewater treatment and recycling not only addresses water scarcity but also offers sustainable and economically viable solutions for various applications, from domestic to industrial and agricultural settings.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
THREE ESSAYS IN DEVELOPMENT ECONOMICS
Get PDFThesis (Ph.D.)--Michigan State University. Economics - Doctor of Philosophy, 2024This dissertation studies the effects of transportation access on outcomes ranging from national identity to maternal health and household income. The first chapter studies how the improvement of infrastructure affects national identity. The post-colonial era in Africa witnessed nation-building efforts aimed at establishing a national identity. Nation building is driven by the need for a united population to prevent conflicts and ensure long-term political stability. One key component of nation building is constructing a sense of belonging to one nation and having a strong sense of national identity. This paper explores the role infrastructure development plays in shaping ethnic and national identity. I use georeferenced data from five Afrobarometer waves, combined with a digitized panel dataset on road quality. As roads are not exogenously distributed and can be allocated based on the location of policymakers' ethnic homelands, I propose an instrumental variable strategy based on a least cost path network. I find that living near a paved road reduces national attachment and increases ethnic attachment. In terms of mechanisms, we find that road paving improves Information and Communications Technology (ICT), thus strengthening social networks created along ethnic lines. I also find an increase in the perception of corruption in governments\u2014both national and local. Infrastructure projects can create opportunities for financial misappropriation, thus weakening respondents\u2019 trust in government and consequently weakening their attachment to the nation.The second chapter studies the relationship between access to paved roads and maternal health. One important aspect of public health in developing countries is maternal and child health. As developing countries continue to invest in the improvement of maternal and child health, studies have found a list of obstacles to improving these two key aspects of public health. One of said obstacles is poor access to infrastructure to access health facilities. This project studies the effect of access to road infrastructure on maternal and child health in sub-Saharan Africa. This paper aims to answer the following question: How does the development of road infrastructure affect maternal and child health? The condition of a road is not static over time. Often, roads are upgraded from unpaved to paved. Using a difference in differences estimation method, I study the extent to which the improvement of a mother\u2019s nearest road increases the likelihood of access to good antenatal and delivery care. When studying the effects of road improvement on child health, the paper studies the extent to which the improvement of a child\u2019s nearest road improves child malnutrition outcomes such as stunting and wasting. I find that women who deliver after a road is paved have more access to skilled midwives. Regarding child malnutrition, I find a reduction in the likelihood of being stunted or underweight, when the child is born after the road is paved. The third chapter studies the introduction of the bus rapid transit in Cape Town and the effects on the residents\u2019 income. As cities grew, planners developed a number of transportation systems to cater to their residents, two of which are Mass Rapid Transit (MRT) and Light Rapid Transit (LRT). While the MRT is represented by the subway or metro system, the LRT can be referred to as the tram or streetcars. A third one, emerging as early as the 1930s is the Bus Rapid Transit system. The BRT is a bus-based transportation system with better capacity and efficiency than standard bus systems. The BRT combines the efficiency of a metro system with the low cost and flexibility of a bus system. Starting in 2010, the city of Cape Town introduced MyCiti, a new Bus Rapid Transit system. It was progressively rolled out across the city. This paper studies the following question: what are the effects of BRT system constructions on income and employment in Cape Town? I use the South Africa National Household Travel Survey, to study employment and income metrics. I find that living near a bus rapid transit station is associated with an increase in personal and household income. When the effects are broken down by racial group, I find that coloured households saw large increases in personal and household income, while there was no change in the personal and household income of black and white residents.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
Parameter estimation for univariate and bivariate Gaussian processes and fields
Get PDFThesis (Ph.D.)--Michigan State University. Statistics - Doctor of Philosophy, 2024Gaussian random fields are widely studied in various subject areas. This dissertation focuses on estimating covariance parameters of stationary Gaussian random fields based on both regularly and irregularly spaced sampling points, as well as investigating the infill asymptotic properties of the estimators.We first consider a bivariate Gaussian random process and propose an increment-based estimator for the smoothness parameter in the cross-covariance function, for which the strong consistency and asymptotic normality hold under the infill asymptotic framework. We further study the joint asymptotic distribution of estimators for smoothness parameters in the cross-covariance and autocovariance functions. Subsequently, we estimate the scale parameter and range parameters of a univariate anisotropic Ornstein-Uhlenbeck field based on quadratic forms of vectors of observations. The estimators we propose are computationally more efficient than the maximum likelihood estimators but have similar infill asymptotic performances with MLEs. Another computational complexity reduction method we use is the Vecchia approximation. We estimate the scale parameter in the Mat\ue9rn covariance function using the maximizer of the likelihood approximated by the standard Vecchia approach. We study the bias resulting from a misspecified range parameter and the conditioning variables of the Vecchia approximation. The theoretical results in this work are illustrated by simulations.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
Study of Flash Lamp Annealing to Promote Crystallization of Indium Tin Oxide Thin Films
No full textThesis (M.S.)--Michigan State University. Electrical and Computer Engineering - Master of Science, 2024The use of flash lamp annealing as a low-temperature alternative or supplement to thermal annealing is investigated. Flash lamp annealing and thermal annealing were conducted on 100 nm thick indium tin oxide (ITO) films deposited on glass to compare the films' properties under different annealing methods. The ITO samples had an initial sheet resistance on average of 50 \u3a9/sq. After flash lamp annealing only the sheet resistance was reduced to 33 \u3a9/sq, while by thermal annealing at 210\ub0C for 30 minutes a sheet resistance of 29 \u3a9/sq was achieved. Using a combination of flash lamp annealing and thermal annealing at 155\ub0C for 5 minutes a sheet resistance of 29 \u3a9/sq was achieved. X-ray diffraction (XRD) analysis confirmed that flash lamp annealing can be used to crystallize ITO. Flash lamp annealing allows for the low-temperature crystallization of ITO on a time scale of seconds. Through electrical and optical characterization, it was determined that flash lamp annealing can achieve similar electrical and optical properties as thermal annealing. Flash lamp offers a method of low-temperature annealing which is particularly suitable for temperature-sensitive substrates.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
ENHANCING YIELD AND QUALITY IN SILAGE AND GRAIN CORN THROUGH IMPROVED UNDERSTANDING OF PLANT-PATHOGEN INTERACTIONS
No full textThesis (Ph.D.)--Michigan State University. Crop and Soil Sciences- Doctor of Philosophy, 2024Corn (Zea mays L.) in Michigan and the Great Lakes Region is prone to biotic stresses resulting in unavoidable yield and quality losses. Infections by ascomycete fungi causing ear or stalk rots and foliar diseases (such as tar spot) have become a major concern for corn growers in recent years. Ear and stalk rots in Michigan corn are primarily a result of Fusarium graminearum and F. verticillioides infections. These fungi not only impact the yield but also produce toxic compounds (mycotoxins), rendering corn unsafe for livestock consumption. Therefore, one of the major goals of this dissertation was to evaluate mycotoxin occurrence in silage corn (whole-plant corn fed to cattle) and explore integrated management strategies such as hybrid selection, fungicide application, planting date, and seeding rate. Samples from growers across Michigan revealed that deoxynivalenol, zearalenone, and fumonisins are the most commonly occurring mycotoxins in Michigan silage corn. Multi-location field trials for silage corn from 2019-2022 showed that the use of effective Bt proteins (such as Vip3A) in hybrid trait selection prevent corn ear injury due to Lepidopteran insects (primarily western bean cutworm), limiting access to ear rot causing fungi, eventually reducing mycotoxin accumulation. Fungicide application reduced ear rot incidence only at two out of eleven site-years and had limited benefit when disease incidence was driven by insect injury. Planting silage corn in late-April to early May and avoiding very high seeding rate (>100,000 seeds ha-1) helped in escaping environmental conditions favorable to insect injury and fungal infections from coinciding with corn silking. Post-harvest ensiling studies showed that an infected silage corn is more prone to continued mycotoxin accumulation especially under low compaction density. Additionally, field trials were conducted for quantifying losses in forage or grain yield and nutritive value as impacted by foliar stresses (primarily tar spot). Evaluations of photosynthetic capacity showed that tar spot has an impact that is proportionally greater than the observed disease symptoms. Variability observed in photosynthetic response to tar spot severity among current hybrids would be useful in future germplasm selection for disease resistance. Overall, this dissertation emphasizes the use of in-field integrated management such as hybrid Bt traits, disease resistance, fungicide application, optimal planting date, and seeding rate as potential solutions to minimize corn yield and quality losses due to multiple biotic stresses.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
Elucidating the role of the energy demands of photorespiration in achieving energy balance
No full textThesis (Ph.D.)--Michigan State University. Plant Biology - Doctor of Philosophy, 2024The current annual food production cannot sustain population growth and is limited by rates of photosynthetic efficiency. Some strategies to improve photosynthetic efficiency include modification of the photorespiratory pathway which could substantially alter metabolic energy demands, specifically the ATP and reductant demands. Such altered energy demands might pose a problem in terms of photosynthetic efficiency because to operate efficiently and without photodamage the energy demand from metabolism must be matched with that supplied in a process referred to as energy balancing. There is a lot of focus on how processes which supply ATP and reductant mediate energy balancing, however, there is much less focus on how changes in metabolic demand drives these responses. In terms of metabolism, photorespiration consumes substantial amounts of energy making the pathway an important component in leaf energetics. The energetic costs of photorespiration are often discussed; however, less emphasis is placed on how the energy demands from photorespiration might be involved in achieving energy balance. Overall, this dissertation explored the role of the energy demands of photorespiration in achieving energy balance. First, I contextualized the energy demands of photorespiration within the greater metabolic network by quantifying the contribution of individual pathways to energy demand. Next, I examined the impact of increased and decreased energy demands from photorespiration on the light reactions and found a novel role for the energy demands of photorespiration in energy balancing. More specifically, the ATP consumption from photorespiration assisted in maintaining photosynthetic efficiency. I leveraged the associated phenotype to create a screening platform which identified candidate genes involved in responding to dynamic shifts energy demand. I also examined whether the decreased photosynthetic efficiency associated with altered energetic demands might restore over time and the regulation surrounding this. Finally, this dissertation concludes with future directions which would begin to address some of the outstanding questions raised throughout.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
UNMASKING THE IMPACT : ANALYZING THE ROLE OF ATHLETIC IDENTITY ON CONCUSSION OUTCOMES IN COLLEGIATE ATHLETES
No full textThesis (Ph.D.)--Michigan State University. Kinesiology - Doctor of Philosophy, 2024Background: A concussion is a concerning injury because of the potential long-term effects to the brain. Typical concussion evaluation and management tools include tests that ensure an athlete is physically ready to return to play (e.g., clinical evaluation, symptom reports, balance assessment). However, psychological factors are often overlooked from these protocols, despite increasing evidence that it may prolong recovery. One psychological factor to consider is athletic identity, which is defined as the exclusivity and strength with which an individual identifies with the athletic role and looks to others for confirmation of that role. Purpose: The purpose of this dissertation was to examine athletic identity in collegiate athletes to predict outcomes following concussion, including concussion symptom scores, days to symptom resolution, and days to full medical clearance (FMC). Methods: This was a prospective, repeated measures design study performed in a university laboratory setting. Participants diagnosed with a concussion were included in the study and asked to complete two testing sessions: (1) within 5 days of their injury (the acute visit), and (2) at the time of FMC (within 3 days; FMC visit). During the acute visit, participants provided informed consent, as well as information regarding demographics (e.g., age, sex), injury characteristics (e.g., mechanism of injury), and medical history questions (e.g., concussion history, diagnosis of depression/anxiety). Additionally, participants completed two surveys, the Athletic Identity Measurement Scale (AIMS) and the symptom checklist of the Sport Concussion Assessment Tool (SCAT5/SCAT6). The AIMS is a 7-item questionnaire that assesses the extent to which the athlete role is a stable and central part of one\u2019s self-identity and includes three subscales: social identity, exclusivity, and negative affectivity. At the FMC visit, participants completed recovery information (i.e., days to symptom resolution and days to FMC) and the same surveys completed at the acute visit. A series of hierarchical multiple regression analyses were conducted in a stepwise fashion to assess the extent to which athletic identity predicted total number of symptoms, symptom severity score, days to symptom recovery and days to FMC. These analyses were evaluated based on an a-priori alpha level <0.05. Results: A total of 92 collegiate athletes (mean age: 20.8+1.6; 39 female, 53 male) completed the study. There was a statistically significant weak and positive relationship between the negative affectivity subscale and total number of symptoms (p < 0.01), symptom severity score (p < 0.01), and days to FMC (p < 0.01). The negative affectivity subscale significantly predicted an increase in total number of symptoms (F(1, 87) = 5.827, p = 0.018, R2 = 0.055) and an increase in symptom severity scores (F(1, 87) = 4.002, p = 0.049, R2 = 0.038), while controlling for sex, history of learning disorder or dyslexia, history of depression/anxiety which are known variables that impact concussion recovery outcomes. The AIMS total score, the social identity subscale and the exclusivity subscale did not predict any concussion recovery outcomes. Conclusion: Among collegiate athletes following concussion, the negative affectivity subscale was positively associated with total number of symptoms, symptom severity score, and days to FMC. Additionally, the negative affectivity subscale predicted more total number of concussion symptoms and higher symptom severity score reported at the acute visit over and above known variables that impact concussion symptom scores. These findings further expand our knowledge and understanding about a specific psychosocial factor (i.e., athletic identity) and its relationship to concussion outcomes. The information gleaned from this study gives clinicians a starting point for addressing collegiate athletes who are stronger in negative affectivity following a concussion, but further research on the psychometric properties of the AIMS in a concussion population is warranted.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references
FROM ADAPTATION AND ACCLIMATION TO ENGINEERING : INVESTIGATING HOW PHOTORESPIRATORY MECHANISMS CONTROL PHOTOSYNTHETIC CARBON FIXATION
No full textThesis (Ph.D.)--Michigan State University. Plant Biology - Doctor of Philosophy, 2024Anthropogenic activities are rapidly changing the composition and thermal conditions of the global atmosphere, leading to fundamental trade-offs in photosynthetic carbon metabolism. Unique challenges of photosynthetic carbon fixation under future climate conditions \u2013 mainly elevated temperatures \u2013 include increased rates of photorespiration, which limit C3 photosynthetic performance. Photorespiration initiates when oxygen binds to rubisco, the enzyme responsible for carbon fixation, instead of carbon dioxide. The resulting oxygenation reaction produces 2-phosphoglycolate, an intermediate that inhibits carbon assimilation and allocation. To reduce the inhibition of carbon metabolism, photorespiration detoxifies and recycles 2-phosphoglycolate through a set of reactions that salvage most of the initial carbon fixed to rubisco. While the rate of photorespiratory influx is set by rubisco, downstream photorespiratory enzymes must process the subsequent photorespiratory intermediates that are produced. If photorespiratory influx outpaces downstream metabolic capacity, a reduction of photosynthetic net carbon fixation is anticipated due to insufficient conversion rate and accumulation of various biologically active intermediates. Managing these photorespiratory intermediates is important to maintain plant vigor, especially in dynamic environments where photorespiratory influx is unpredictable. Currently, it is unclear whether photorespiratory biochemistry, downstream of rubisco, adjusts to handle a greater carbon influx through photorespiration. The work in this dissertation looks past rubisco, which has been a prominent focus in engineering efforts, to explore downstream photorespiratory enzymes that directly manage carbon flux through photorespiration. I first investigate the hallmarks of a temperature-tolerant photorespiratory pathway in Rhazya stricta, a C3 shrub native to the hot-arid regions in the Middle East. I found that R. stricta supports higher rates of photorespiration under elevated temperatures and that these higher rates of photorespiration correlate with increased activity of key photorespiratory enzymes; phosphoglycolate phosphatase and catalase, compared to Nicotiana tabacum. I then studied the acclimation potential of photorespiratory capacity in Betula papyrifera, with particular interest in whether enzyme activities acclimate to changes in photorespiratory influx. I found no plasticity in photorespiratory capacity when B. papyrifera was exposed to 6 different CO2 concentrations and temperatures scenarios, and that a fixed capacity is maintained under each growth condition. The fixed capacity is likely due to the existence of safety factors in the pathway that manages unpredictable photorespiratory influx in dynamic environments. Finally, I explored whether replacing native catalase in Arabidopsis thaliana with a foreign catalase isoform conferred any benefit to photorespiratory carbon recycling efficiency. To explore this question, we generated three transgenic independent expression lines of Heliobacter pylori catalase in A. thaliana cat2-KO to determine their in vivo and in vitro function. I found that two out of the three transgenic lines have similar amounts of CO2 loss from photorespiration compared to wildtype line and were able to rescue the cat2-KO growth phenotype, while having less catalase activity than wildtype. The findings from this dissertation contribute to the long-range goal of engineer photorespiration to improve photosynthetic carbon fixation under future climate conditions in C3 crop systems.Description based on online resource. Title from PDF t.p. (Michigan State University Fedora Repository, viewed ).Includes bibliographical references