2016 MU dissertations - Freely available online
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Item Computational methods for protein structure prediction and next-generation sequencing data analysis(University of Missouri--Columbia, 2016) Li, Jilong; Cheng, Jianlin, 1972-With the wide application of next-generation sequencing technologies, the number of protein sequences is increasing exponentially. However, only a tiny portion of proteins have experimentally verified structures. The huge protein sequence-structure gap could be reduced by computational methods including template-based modeling and template-free modeling. Chapter 2 describes a stochastic point cloud sampling method for multi-template protein model generation. The stochastic sampling and simulated annealing protocol in the method has the capability to improve the global quality and reduce atom clashes in protein models. Two popular approaches for improving protein structure prediction include enlarging the sampling space of template-based modeling and integrating template-based modeling with template-free modeling when no good templates or only partial templates can be found for a target protein. Chapters 3 and 4 introduce a large-scale conformation sampling and evaluation system for protein structure prediction which integrates the two methods. Next-generation sequencing of RNAs (RNA-Seq) generates hundreds of millions of short reads. Analyzing these reads is increasingly being used to foster novel discovery in biomedical research. Chapter 5 describes a bioinformatics pipeline for RNA-Seq data analysis, which converts gigabytes of raw RNA-Seq data into kilobytes of valuable biological knowledge through a five-step data mining and knowledge discovery process.Item Effect of far-red induced shade-avoidance responses on carbon allocation in arabidopsis thaliana(University of Missouri--Columbia, 2016) Coffman, Clayton M.; Schultz, Jack C.; Appel, HeidiPlants are a very dominant form of life on earth and a large part of human society is based on growing plants. Plants use photosynthesis to turn sunlight and carbon dioxide in the air into sugar. This sugar is used to grow and make all the parts of the plants we're interested in using. Roots, flowers, fruits, and seeds can't make the sugar they need from light, and young growing leaves can't make enough sugar on their own to support their growth. The plant's decisions about where to put the sugar it makes is important to determining how the plant will grow. Since plants spend their lives rooted in a single location, they must be able to cope with whatever challenge comes their way. Since plants need light to grow, one challenge plants face is competition with other plants for light. Plants can sense they are growing in competition with other plants by the change in the color of light when it is reflected off other nearby plants. When they sense this change in light they alter how they grow to attempt to avoid being shaded. Usually this involved trying to grow taller to avoid being shaded by their neighbors. Putting their limited resources into growing taller comes at the expense of growing the fruits and seeds we need from them, as well as making the toxic chemicals plants use to defend themselves against insect pests. I was interested in how the light signals which trigger this change in growth affect where plants put the sugar they make from photosynthesis. I hypothesized that treating plants with light which could trigger this change in growth would affect how sugar moved through the plant. Using a radioactive form of sugar which I could follow as it moved through the plant, I found that in response to light signals which trigger this change in growth causes young, growing leaves to export less of the sugar they make (keeping more for themselves), but fully mature leaves did not change how much sugar they exported. Agriculture is all about getting plants to turn sunlight into products we need and understanding how plants make decisions about where to put their resources will help us develop crops and other plants which can more efficiently make the food and other plant products we depend on.Item The influence of Bands of America on one high school marching band : a single case study(University of Missouri--Columbia, 2016) Eubanks, Stephen C.; Silvey, Brian A., 1978-The purpose of this research study was to examine the influence of participation in Bands of America competitions (hereafter referred to as BOA) on one central Missouri high school marching band program. I chose to study a Missouri high school marching band that had been involved with BOA for a minimum of five years. Participants in this study were marching band members plus staff of the Camdenton High School marching band (N = 22). My goal was to produce a study that was descriptive of the influence, if any, that participation in BOA had on the Camdenton High School marching band. I sought to discover this through observations of their rehearsals and performances at their marching band contests. I chose to conduct a qualitative, single case study. Data were collected through structured and open-ended interviews, observations, field notes, and my participant researcher journal. To date, there has been limited research on BOA participation by high school marching bands. BOA claims to be the largest and most prestigious national marching competition available to high school marching bands in the United States. BOA has grown nationally from eight contests in 1985 to 20 contests in 2015. When BOA expanded in 1997 to include the St. Louis, Missouri regional championship, only five Missouri bands participated in the event. The number had grown in 2015 to include 25 Missouri bands. During my research, I assumed the role of an active participant and observed the band's music and marching drill preparation, and attended their competitions in order to observe their BOA performances. My research questions focused on the following areas: (a) the key motivators for a high school marching band to participate in BOA, (b) how BOA influences the practices of a high school marching band, and (c) what barriers a rural marching band faces in order to participate in BOA. Through my investigation, I discovered that there were several motivators for the Camdenton High School marching band staff to elect to participate in BOA. The standard of excellence that exists at BOA marching contests is consistent from state to state, and provides the staff and students with an adjudication rubric that serves as a guide for them to rehearse and perform at a higher musical level. Participation in BOA has led the staff to change the design practices of their marching show design. In addition to the planning of the show, the staff has improved their teaching process. This, in turn, has affected the students' attitude and approach toward their rehearsals. They have an increased work ethic and feel responsible for each other. All of these factors exist despite certain obstacles the band faces, including limited resources and an increased cost factor. Other high school band directors who are considering BOA participation might consider the Camdenton High School marching band program as a model. By looking into the reasons why Camdenton chose to participate in BOA and some of the resultant influences, directors might be able to apply them to their own school marching band programs.Item Spatial modeling of aboveground carbon dynamics of the U. S. central hardwood forest(University of Missouri--Columbia, 2016) Jin, Wenchi; He, Hong S.Central Hardwood Forest (CHF) is one of the largest forested biomes in the United States and its aboveground carbon dynamics have both regional and global significances. Thus, the aboveground carbon dynamics of CHF are of substantial interest to researchers, resources managers and policy makers. Among measures and fluxes of aboveground carbon dynamics, aboveground biomass and aboveground net primary production (ANPP) are the most widely used ones. Modeling has been a powerful approach to study aboveground carbon dynamics, however, it is largely unknown whether more complex process-based models could perform better at both plot and regional scales. CHF is currently a carbon sink mainly due to forest regrowth from previous disturbances, yet as forests regrow towards maturity, how long this carbon sink would persist is subject to uncertainty, and it is unclear what role in carbon sequestration the CHF would play after the current carbon sink diminishes. In addition to forest aging, aboveground carbon dynamics may be influenced by environmental factors, such as climate, CO2 concentration, and nitrogen deposition. Furthermore interactions between forest aging and environmental factors can be complex. Chapter II compared predictions of aboveground biomass by simple physiological, complex physiological, and hybrid empirical-physiological models against field data, at both plot and regional scales in the CHF at decadal interval. I found that simple physiological model provided the worst predictions at both plot and regional scales. At plot scale, predictions of aboveground biomass by complex physiological model were the most concordant with field data, suggesting that physiological processes are more influential than forest composition and structure on aboveground biomass at this spatial scale. Hybrid model provided the best predictions at regional scale, suggesting that forest composition and structure may be more influential than physiological processes on aboveground biomass at this spatial scale. Chapter III compared long-term trends of aboveground biomass of the CHF predicted by a landscape model LANDIS PRO 7.0, a hybrid empirical-physiological model LINKAGES v2.2, and a detailed physiological model ED2 under current climate from 2010 to 2300 to determine how long current carbon sink would persist, and what role in carbon sequestration the CHF would play after the current carbon sink diminishes. All models agreed that the current carbon sink would persist at least to 2100s. There were two different patterns of carbon dynamics after carbon increment diminished to zero. LINKAGES and ED both predicted prolonged periods of relatively stable carbon densities, with minor declines, until 2300. While LANDIS PRO predicted a period of carbon source between 2110s and 2260s, followed by another carbon sink period of approximately 100 years, thus a distinct carbon cycling dynamics. In Chapter IV, I used a simple physiological model PnET daily version to study effects of single factor of climate change, CO2 fertilization, nitrogen deposition, as well as all possible combination of these three environmental factors on ANPP in an ecological subsection (Current River Hills) in the CHF from 2010 to 2099. I also used a hybrid empirical-physiological model LINKAGES v2.2 to study the effect of forest aging, and combined effects of forest aging and climate change on ANPP. Predictions of the simple physiological model showed that all three future climate trajectories (CanESM2, GFDL-ESM2M, and MIROC5 under CMIP5 RCP 8.5 pathway) had negative effects on ANPP, both CO2 fertilization and nitrogen deposition had positive effects. CO2 fertilization could noticeably alleviate the negative effects of climate change on ANPP, and can boast positive effect when combined with nitrogen deposition. Combined effects of nitrogen deposition and climate change differed little from that of climate change alone. Combined effects of all three environmental factors showed relatively small change on ANPP. Predictions of the hybrid empirical-physiological model suggested that forest aging did not have significant effect on ANPP in the CHF during the 21st century as ANPP stayed relative stable. And when forest aging was combined with climate change, the stable trend of ANPP still did not show substantial change.Item Design and testing of optimal personal protective equipment for high energy radiation on earth and beyond(University of Missouri--Columbia, 2016) Watermann, Matthew L.; Prelas, Mark; Milstein, OrenThis study incorporates an experimental and an associated modeling investigation of human protective shielding methodologies for two extreme environments: first responders or military personnel in the case of nuclear or radiological incidents (360 Gamma); second a deep space mission (AstroRad). Both solutions utilize selective shielding of organs, tissues, and stem cell niches which are relatively more radiosensitive to either deterministic or stochastic effects depending on the application to derive the greatest biological benefit per unit mass shielding. This is accomplished by allocating the shielding over the surface of the body in a variable thickness architecture which is inversely related to the radio-density of the intervening tissues between the shielding and the organ, tissue, or stem cell niche being targeted for protection. This structural design of shielding placed adjacent to the area of the body being protected and being of a variable thickness which augments the self-shielding of the body at each point on the surface provides the function of optimized use of shielding material to reduce the absorbed doses to the organs, tissues, or stem cell niches targeted for protection. The experimental studies utilized the best available facilities to provide a dose realistic environment and the best available phantoms for dose absorption. MCNP6 and HZETRN were used for the modeling. In the case of the 360 Gamma, the shielding concept experiments matched well with the model. In the case of the AstroRad, experiments verifying the simulations are planned for the near future. The work demonstrated significant reduction in absorbed dose to the organs and tissues targeted for protection in both cases. This study involves human protective shielding in two distinct environments: First, human protection for military personnel or first responders to a nuclear or radiological incident; Second for astronauts on a deep space mission. The two human protection environments will be discussed separately, thereby dividing this dissertation into 2 distinct but related parts beginning with the 360 Gamma study and results followed by the AstroRad study and results because even though there are some commonalities, the environments and needs for protection differ.