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Legionella pneumophila is a pathogen that can proliferate in premise (i.e., building) plumbing and, when aerosolized during water use, infect the lungs of exposed individuals and cause a deadly form of pneumonia known as Legionnaires' disease. Given that it is one of the primary sources of tap-water associated disease throughout much of the world, this organism has been the subject of intense research, ranging from aiming to understand key aspects of its physiology that allow it to proliferate in premise plumbing, to the specific virulence factors that make it so infectious to humans. The work presented here starts with a comprehensive review of published studies related to the L. pneumophila proteome, i.e., the set of expressed proteins associated with a given strain under a given set of environmental conditions, showing how the field has progressed in parallel to improvements in mass spectrometry technologies and how proteomics can be used as a tool to understand this unique and important organism. Copper is a natural antimicrobial that can be present in drinking water due to passive release from copper pipes or intentionally dosed (e.g., copper-silver ionization systems) for microbial control. However, some L. pneumophila strains have recently been found to exhibit copper resistance, an adaptive process that is not fully understood at the physiological level. Chapter Two describes the copper survivability of three outbreak-associated strains of L. pneumophila and examines the copper-induced proteome of QC1, a strain found to display high resistance to copper. Pairwise comparisons of the proteomes of copper-resistant and copper sensitive strains indicated that L. pneumophila QC1 adapts to copper exposure via the induction of redox and metal homeostasis proteins, while concomitantly inducing motility and pathogenesis related proteins, suggestive that copper induces a search for a host protozoan strain for protection. In 2014 and 2015, Flint, Michigan experienced the largest per capita community-wide Legionnaires' Disease outbreak in US history. The outbreak was associated with a change in the source of the municipal drinking water supply from Detroit water, which was sourced from the Great Lakes and subject to appropriate corrosion control, to the Flint River, which was not appropriately controlled for corrosivity. The underlying drivers of this outbreak have been debated and include: elevated iron in the water serving as a nutrient for L. pneumophila, diminished chlorine in the water due to reactions with iron, reduced copper in the water due to shifts in pH influencing release from copper pipes, and shifts in potentially key components of the microbial community. In Chapter Three of this dissertation, we employ controlled microcosm studies to establish a fundamental understanding of interactive effects of pipe material and water of varying iron bioavailability (ferric chloride, ferrous chloride and ferric pyrophosphate) on the microbial community and its relationship with L. pneumophila numbers. The combination of copper pipes and Flint River water decreased the diversity of the microbial community to a larger degree than copper pipes with Detroit water, implying greater copper bioavailability in the former condition. Several Order were found to be significantly associated with high or low numbers of culturable L. pneumophila recovered from the microcosms. Most notably, the Order Pseudomonadales was significantly associated to the reactors with low culturable L. pneumophila. This order contains Pseudomonas species known to inhibit the growth of L. pneumophila. The findings reported in this dissertation can be used to develop more informed management practices for drinking water systems to reduce the risk of Legionnaires' Disease outbreaks associated with premise plumbing. Specifically, 1) copper might be inducing a more pathogenic form of copper resistant L. pneumophila, 2) the use of corrosive control in municipal water systems goes beyond the influence on lead and copper pipes, but also on the microbial community, which in part influences L. pneumophila, and 3) there are organisms, such as Pseudomonadales species, associated with environments with low culturable L. pneumophila which might be introduced to the drinking water systems as probiotics. / Doctor of Philosophy / Legionella pneumophila is a microbe found in drinking water plumbing systems. This organism causes Legionnaires' Disease, a severe form of pneumonia that particularly affects immunocompromised individuals. Due to its health and economic impact, there are worldwide efforts to understand the biology of this organism, from the conditions that allows it to grow in the drinking water plumbing, to the specific components that allows it to infect humans. In this dissertation, we first review the published studies related to the L. pneumophila proteome, a powerful tool used to functionally describe biological organisms. This first chapter showed how proteomics can be used to understand this unique and important organism. In the next chapter we studied how copper metals may influence the proteome of L. pneumophila. Copper pipes have been extensively used to control the growth of microorganisms in drinking water systems, however some studies have reported that copper may promote the growth of L. pneumophila. In this chapter, we showed that a copper resistant strain of L. pneumophila adapts to copper exposure by inducing motility and pathogenesis related proteins, suggesting that it might be more infectious. In the last chapter of this dissertation, we investigated the combined effect of pipe material and water chemistry, on the microbial community and its relationship with L. pneumophila. The combination of copper pipes and a more corrosive water decreased the diversity to a larger degree, in comparison to the other evaluated conditions. Several organisms were also identified to be significantly associated with the high or low culturable L. pneumophila. This is of particular interest because they might be used as potential probiotics to control the growth of L. pneumophila. The findings reported in this dissertation can help to better understand the significance of water chemistry and pipe material, particularly copper pipes, for the purpose of reducing risk of Legionnaires' Disease outbreaks associated with drinking water systems.

Call number: LD2668 .T4 1985 J36 / Master of Science

Cette thèse porte sur la Néolithisation du Nord-Ouest de la France, abordée à travers l’analyse des industries en silex jurassiques de Normandie. Objet de plusieurs influences environnementales et culturelles, cette région essentielle pour comprendre les dynamiques et les comportements socio-économiques de la Néolithisation de l’Ouest se caractérise par un environnement géologique riche en silex d’excellente qualité exploités durant toute la Préhistoire, utilisés ici comme marqueurs de ces comportements et de leur évolution sur la longue durée. L’objectif est de caractériser les productions liées à ces ressources et leur diffusion, de préciser les contextes chronoculturels dans lesquels elles évoluent, en prenant en compte tous les processus de la chaîne opératoire, depuis l’acquisition des matériaux jusqu’à l’abandon des outils. Restituer une vision cohérente de ces processus suppose un protocole qui croise les approches typo-morphologique, technologique et fonctionnelle des industries pour respecter le lien structurel qui existe entre l’économie des matières premières, la gestion des productions et de l’outillage. L’étude sur la longue durée de l’utilisation d’un type de ressources particulières offre un point de vue spécifique sur la Néolithisation de l’Ouest. Les continuités et les ruptures, la permanence ou la disparition de chaînes opératoires, procédés techniques, ou voies de distribution restituent un pan de l’évolution technique et culturelle de ces sociétés néolithiques. L’analyse critique des sites a permis de dépasser l’hétérogénéité de la documentation pour parvenir à ce but. / This thesis addresses the question of the Neolithisation of the Northwest of France, throught the analysis of the industries based on Jurassic flint from the Neolithic sequence in Normandy. Subject of several environmental and cultural influences, this region is essential for understanding the dynamics and socio-economic behaviors in the Neolithisation process. Normandy is characterized by a geological environment with excellent flint sources used throughout Prehistory, used here as markers of these behaviors and their evolution over the long term. The aim is to characterize the productions related to these sources and their distribution, the chronological and cultural sequence in which they operate, taking into account all the processes of chaîne opératoire, from flints procurement to the abandonment contexts. Restore a coherent vision of the process involves a protocol that melts typo-morphological, functional and technological approaches, to meet the structural link between the economies of raw materials, production and tools management. The study on the long-term use of a particular type of resource gives a specific point of view about Neolithisation of the Northwest of France. Continuities and ruptures, permanence or extinction of chaînes opératoires, technical processes and distribution channels restore a piece of technical evolution and cultural significance of the Neolithic societies.

Master of Arts / Department of Geography / Douglas G. Goodin / My thesis characterizes the temporal and spatial behavior of ozone and fine particulate matter in the Kansas City metropolitan area. I also investigate the capability of a synoptic weather typing scheme, the Spatial Synoptic Classification, to characterize and explain the behavior of ozone and fine particulate matter in the Kansas City area. Daily maximum ozone concentrations from nine active ozone monitoring stations and daily average particulate concentrations six active PM2.5 monitoring stations were compared to daily SSC weather type records from 2004-2010. Analysis of Variance (ANOVA) tests were conducted on the ozone and PM2.5 data to analyze temporal and spatial behavior. A non-parametric recursive partitioning technique was used to create a conditional inference tree-based regression model to analyze the association between the different SSC weather types and the selected pollutants. The ANOVA results showed significant seasonal trends with both pollutants. In general, ozone concentrations are typically lower in the spring and autumn months and higher during the summer months. PM2.5 concentrations were not as dependent on the season, however, they did tend to be higher in the late summer months and lower in the autumn months. The results also showed significant differences for both pollutants in average concentration depending on location. The ozone concentrations generally tended to be higher in the areas that are located downwind of Kansas City and lowest at the station located in the middle of the urban area. Fine particulates also seemed to be highest in the downwind portion of the urban area and lowest in the region upwind of the city. The conditional inference tree showed that higher concentrations of both pollutants are associated with tropical air masses and lower concentrations are associated with polar air masses.

Call number: LD2668 .T4 1938 S56 / Master of Science

Master of Science / Department of Biology / Samantha Wisely / As human populations increase world-wide, land use and land cover are altered to support the rapid anthropogenic expansion. These landscape alterations influence patterns of zoonotic infectious disease emergence and propagation. It is therefore becoming increasingly important to study emerging and re-emerging diseases to predict and manage for future epidemics. Studies of directly-transmitted infectious diseases should consider three components of disease epidemiology: characteristics of the pathogen, ecology of the host, and habitat configuration of the underlying landscape. I studied the influence of both the host ecology of the striped skunk (Mephitis mephitis) and the alteration of the underlying landscape on the epidemiology of rabies virus in the Flint Hills of Kansas. This tall-grass prairie is experiencing woody expansion due to anthropogenic disturbance, altering the landscape on which the rabies virus emerges and spreads. We first studied the behavioral and social ecology of the striped skunk using field and genetic methods. We concluded that 1) striped skunks reached high population densities in anthropogenically disturbed habitats, 2) these individuals were not closely related, and 3) contact rates could be influenced by temperature. Using habitat-specific skunk densities from this initial study, we created spatially-explicit contact networks of skunk populations across the Upper Kansas River Watershed and simulated the emergence and spread of rabies through the system. This modeling approach revealed a threshold of forest habitat beyond which striped skunks became increasingly connected and the rabies virus reached greater extents across the landscape. Based on these findings we recommend fire regimes and land cover alterations to reduce woody encroachment across the Flint Hills and to avoid future disease epidemics in the region.

Master of Arts / Department of Geography / Kendra K. McLauchlan / The quantitative relationship between pollen assemblages in sediment and vegetation cover is largely unknown because many factors influence this relationship. This lack of quantitative relationship is particularly acute in grassland regions, where both past and future climate change have the potential to determine grassland composition and cover. The tool used to reconstruct past grassland cover is the relative abundance of distinct fossil pollen types preserved in sediment. However, the interpretation of grassland pollen assemblages as grassland vegetation types needs to be refined to improve these reconstructions. Using pollen found in the surface sediments from 24 artificially-constructed ponds in the Flint Hills ecoregion of Kansas, USA, I examined relationships between pollen and vegetation in the tallgrass prairie biome, which includes woody components. By comparing the pollen data to field-surveyed vegetation data and land cover classifications taken from Kansas Gap Analysis Program data, I correlated pollen and vegetation in this ecoregion. Pollen productivity estimates for Artemisia, Ambrosia, Asteraceae, Chenopodiaceae, Cornus, Fabaceae, Juniperus, Maclura, Poaceae, Populus, Quercus, and Salix were calculated via the Extended R-Value Model. Common pollen types identified in sediments are mostly herbaceous grassland plant species such as Poaceae, Artemisia, and Ambrosia, but woody plants such as Populus, Quercus, and Juniperus are also represented. PPEs have been calculated for four of these taxa in Europe, and values from the Flint Hills are higher. These are the first PPEs reported for eight of these taxa. This research will further advance quantitative vegetation reconstructions in the Great Plains of North America and refine interpretations of how climate change affects grasslands.

Master of Science / Department of Agricultural Economics / Glynn Tonsor / The purpose of our analysis was to examine production strategies in the backgrounder and stocker segments of the beef industry within the Flint Hills region of Kansas. The time period analyzed encompassed 1996-2015. September and November placements of steers in the backgrounding sector of the industry were analyzed with an intended March sale date. Placements considered included 425, 500, and 575 pound steers. April and May placements of steers were analyzed for the industry’s stocking sector with an intended July sale date. Placements considered included 450, 600, and 750 pound steers. Within our analysis historical ex-post net incomes were analyzed, prediction errors were calculated (net income, revenue, and cost of gain), and market incentives/signals were analyzed. While for our historical ex-post net income analysis we did not identify one of the four placement strategies as superior in all 20 years of our analysis, we did find scenarios that were typically superior to others. In terms of backgrounding, November placements were typically superior to September placements, in terms of stocking April placements were typically superior to May placements, and when comparing backgrounding and stocking scenarios stocking scenarios were typically superior. In terms of prediction errors, we found that revenue errors are the main drivers of net income error. In general, within the backgrounding scenarios typical producers who are representative of our model assumptions generally overestimate net incomes which is detrimental to them (make lower profits than they anticipate making), while in stocking scenarios producers underestimate net incomes which is generally beneficial to them (make larger profits than they anticipate making). Market signal/incentive and ex-post net income analysis both indicated that steer weight at time of sale was a large factor influencing backgrounder profitability and decision making, and that pasture rents were a large factor influencing stocker profitability and decision making. In all four scenarios it proved economically beneficial to place lighter steer rather than heavy steers. Further research may include, but is not limited to; adding bulls and heifers to our model, analyzing different placement weights within our model, and allowing for animal performance variability within our model.

Call number: LD2668 .T4 1954 H4 / Master of Science