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Urbanization offers unique challenges for wildlife. The urban landscape is fragmented and changes available resources for wildlife. Human-dominated landscapes can provide food, shelter, or cover through human-subsidized resources. However, to thrive in human-dominated landscapes, wildlife must adapt or disperse, otherwise they will die. In this study, I investigated how the urban landscape and human behavior influence urban wildlife occurrence. I established 35 camera sites during April 2020. I surveyed residential property dwellers around each camera site to determine what behavior they performed that could increase species occurrence. Gray fox and coyote site use decreased with increased isolation while no species responded to patch area. Almost all species investigated responded to attractants but not all showed a positive response. Although number of survey participants was small, site use by wildlife tended to increase with owning a bird feeder and putting out trash the day before pickup.

Disease is not a unique or singular phenomenon. The medical literature contains multiple reports discussing disease interactions and co-occurrence which remains an important issue. Despite this, there has been no systematic investigation of disease co-occurrence in paleopathology. This thesis will begin to fill the gap by producing a detailed analysis of the pathological indicators for scurvy, rickets, and their co-occurrence, focussing on features of co-occurrence and their identification. The Collégiale Saint-Amé collection from 16th to 18th century Douai, France includes 48 individuals ranging from fetal to five years of age. Previous research indicated a large number of potential cases of scurvy and rickets in the juveniles (Devriendt et al. 2010). The current study identified 12 cases of possible co-occurrence based on macroscopic, radiographic, and microscopic techniques; biocultural and historical data supported disease presence. Macroscopic results indicate that lesions associated with scurvy are identifiable and the vascular system is not known to be directly affected by rickets. Rickets features are present but changes are subtle and reduced in prevalence. Radiographs demonstrate features of both diseases but the presence or absence of the line of Fraenkel, a scurvy feature, was useful in identifying the likely dominant disease process. Diagenetic change significantly impacted microscopic investigations but the technique provided some supporting evidence for the presence of rickets. The results clearly demonstrate that cases of co-occurrence of scurvy and rickets are present and identifiable in the archaeological record. Important factors for recognition include the sequence in which conditions develop and duration of illness. Presently only cases with moderately or better developed features of both scurvy and rickets can be identified. Use of multiple techniques was critical to observe subtle changes and build a case for disease presence. Further research on co-occurrence of any diseases is encouraged to create a fuller understanding of past disease. / Thesis / Master of Arts (MA)

Spring dead spot (SDS) is the most destructive disease of bermudagrass and its hybrids, affecting intensively managed bermudagrass turf that is at least three years old. This bermudagrass disease is most prevalent in the United States where winter temperatures become cold enough to induce dormancy. The symptoms of SDS appear as sunken, necrotic patches of turf ranging from several centimeters to greater than 0.5 m in diameter. Field studies were conducted at Old Waverly Golf Club in West Point, MS on a Tifway bermudagrass fairway beginning January of 2005 and concluding December of 2006 to determine the frequency and the effects of soil temperature on occurrence of O. korrae in bermudagrass. Characterization of O. korrae isolates was conducted based on optimal in vitro growth temperatures and greenhouse pathogenicity studies. Cultural, nutritional, and chemical management practices were evaluated on the bermudagrass fairway for the reduction of SDS severity, promotion of improved turf color, quality, root health, and reduction of the thatch/mat layer. Treatments included core aerification with and without topdressing, vertical mowing, manganese, elemental sulfur, and myclobutanil fungicide applications. Each year was divided into seasons (winter, spring, summer, fall) based on the bermudagrass growth cycle in Mississippi. The frequency of O. korrae occurrence ranged from 14% in 2005 to 16% in 2006, and was similar for all treatments. Ophiosphaerella korrae occurrence was greatest in the winter and spring compared to the summer and fall. There was no direct association between mean soil temperature and frequency of O. korrae occurrence. Spring dead spot severity ratings were similar in 2005 and 2006. Vertical mowing had a significant effect on fall turf color in 2005 and fall turf color and quality in 2006. The aggressive cultural practices (i.e. vertical mowing, aerification) were the most consistent treatments for significantly reducing the thatch/mat layer and improving root health.

No description available.

Predators play a critical role in regulating the structure and function of ecosystems by exhibiting top-down forces on lower trophic levels. Despite their important contributions in maintaining ecosystem health, lethal predator control remains a global wildlife management strategy to reduce predation on livestock, culturally and/or economically important species, and species at risk, as well as to reduce conflict with humans. Predator control has received criticism due in part to a paucity of rigorous research on the community-level impacts of this practice, beyond the target prey species. Specifically, there is a lack of understanding of the behavioural consequences of predator control on the wider ecological community. In this thesis, I used a multi-year camera trap dataset to evaluate how government-mandated grey wolf (Canis lupus) population reduction to conserve boreal woodland caribou (Rangifer tarandus caribou) could impact the resource selection of the carnivore community in northeast Alberta, Canada. In my second chapter, I investigated whether perceived persecution risk due to predator control may alter wolf habitat selection. I found that wolves switched from positively associating with roads before predator control to avoiding anthropogenic linear features and selecting for block features after predator control. These results suggest that lethal control may prompt wolves to prioritize local prey acquisition near block features over movement on linear features. In my third chapter, I examined whether coyote, lynx, and black bear exhibited shifts in co-occurrence with habitat features, competitors, and prey consistent with a release from top-down suppression in response to predator control. I found that predator control triggered unexpected behavioural changes among coyote and lynx consistent with a release from top-down suppression, but not among black bears. Non-apex predator response to predator control may depend on the strength of competition between the apex and non-apex predator, emphasizing the need to consider bottom-up processes when trying to understand the indirect effects of predator control. This research demonstrates that predator control can have trickle-down effects within the larger ecological community, specifically affecting how species utilize resources. As predator control continues to be a recommended wildlife management strategy, it is imperative to continue investigating its unintended consequences throughout the ecological community. / Graduate

As technology advances in all areas of society and industry, the technology used to produce one of life's essentials - food - is also improving. The majority of agriculture production in developed countries has gone from family farms to industrial operations. With the advent of large-scale farming, the automation of basic farming operations has increasingly made practical and economic sense. Broccoli, which is still harvested by hand, is one of the most expensive crops to produce. Investing in sensing technology that can provide detailed information about the location, maturity and viability of broccoli heads has the potential to produce great commercial benefits. This technology is also a prerequisite for developing an autonomous harvester that could select and harvest mature heads of broccoli. This thesis details the work done to develop a computer vision algorithm that has the ability to locate the broccoli head within an image of an entire broccoli plant and to distinguish between mature and immature broccoli heads. Locating the head involves the use of a Hough transform to find the leaf stems and, once the stems are found, the location and extent of the broccoli head can be ascertained with the use of contrast texture analysis at the intersection of the stems. A co-occurrence matrix is then produced of the head and statistical texture analysis is performed to determine the maturity of the broccoli head. The conceptual design of a selective autonomous broccoli harvester, as well as suggestions for further research, is also presented. / Master of Science

Soil microbial communities mediate important ecological processes and play essential roles in biogeochemical cycling. Ecosystem disturbances such as surface mining significantly alter soil microbial communities, which could lead to changes or impairment of ecosystem functions. Reforestation procedures were designed to accelerate the reestablishment of plant community and the recovery of the forest ecosystem after reclamation. However, the microbial recovery during reforestation has not been well studied even though this information is essential for evaluating ecosystem restoration success. In addition, the similar starting conditions of mining sites of different ages facilitate a chronosequence approach for studying decades-long microbial community change, which could help generalize theories about ecosystem succession. In this study, the recovery of microbial communities in a chronosequence of reclaimed mine sites spanning 30 years post reforestation along with unmined reference sites was analyzed using next-generation sequencing to characterize soil-microbial abundance, richness, taxonomic composition, interaction patterns and functional genes. Generally, microbial succession followed a trajectory along the chronosequence age, with communities becoming more similar to reference sites with increasing age. However, two major branches of soil microbiota, bacteria and fungi, showed some contrasting dynamics during ecosystem recovery, which are likely related to the difference in their growth rates, tolerance to environmental change and relationships with plants. For example, bacterial communities displayed more intra-annual variability and more complex co-occurrence networks than did fungi. A transition from copiotrophs to oligotrophs during succession, suggested by taxonomic composition shifts, indicated that the nutrient availability is one important factor driving microbial succession. This theory was also supported by metagenomic analysis of the functional genes. For example, the increased abundance of genes involved in virulence, defense and stress response along ages indicated increased competition between microorganisms, which is likely related to a decrease of available nutrients. Metagenomic analysis also revealed that lower relative abundances of methanotrophs and methane monooxygenase at previously-mined sites compared with unmined sites, which supports previous observations that ecological function of methane sink provided by many forest soils has not recovered after 30 years. Because of the difficulty identifying in situ functional mechanisms that link soil microorganisms with environmental change, modeling can be a valuable tool to infer those relationships of microbial communities. However, the extremely high richness of soil microbial communities can result in extremely complicated models that are difficult to interpret. Furthermore, uncertainty about the coherence of ecological function at high microbial taxonomic levels, grouping operational taxonomic units (OTUs) based on phylogenetic linkages can mask trends and relationships of some important OTUs. To investigate other ways to simplify soil microbiome data for modeling, I used co-occurrence patterns of bacterial OTUs to construct functional groups. The resulting groups performed better at characterizing age-related microbial community dynamics and predicted community structures and environmental factors with lower error. / PHD / Disturbances to ecosystems are known to largely impact important ecological functions such as soil carbon loss, decreased nutrient retention and increased greenhouse gas emission. As a result, surface mining, which totally removes the topsoil and original vegetation, has severe negative influences on forest ecosystem function. Reforestation is performed on reclaimed mined sites to accelerate the return of forest vegetation and ecosystem functions. Although considerable research has shown that the plant community can be well developed after 30 years, little is known on whether ecosystem functions are also recovered during a similar time period. As direct mediators of many ecological processes in the environment, soil microorganisms are important for understanding the restoration progress of ecosystems. They could also provide early indications of restoration progress compared to plants. Historically, most soil microorganisms have been difficult to study because they are highly diverse and the majority cannot be cultured in lab, making it difficult to understand changes in the total soil microbiota. However, technological advances such as DNA sequencing have made it feasible to study soil microorganisms in detail. In this work, we studied soil microbial communities from reclaimed mined sites ranging from 5 to 30 years post-reforestation. We found that overall the microbial community was recovering from the disturbances of surface mining, but many differences from unmined soils still remain after 30 years, such as the unrecovered function as methane sink. Two major groups of soil microorganisms, bacteria and fungi, showed different characteristics during recovery, which are likely due to differences between the two groups with regard to growth rates, tolerance to environmental change and relationships with plants. Mathematical modeling is a useful tool for simulating changes and impacts on microbial communities under different conditions, given that actual interactions between microorganisms and their environment can be difficult to measure. However, the high complexity of soil microbial communities becomes an obstacle for modeling that needs to be addressed by simplifying data describing soil microbial community. One approach is grouping organisms based on their natural evolutionary relationships, but this can mask the trends of some microorganisms since all organisms in these groups do not always respond the same to environmental change. Here we used a method of grouping microorganisms based on their co-occurrence patterns, which resulted in better predictions of changes in community structure and environmental factors when applied in modeling.

<p dir="ltr">Human babesiosis is a malaria-like, tick-borne infectious disease of major public health importance with a global distribution. Babesiosis is caused by intraerythrocytic, apicomplexan parasites of the genus Babesia. In the United States, human babesiosis is primarily caused by Babesia microti and Babesia duncani. Of these parasites, B. duncani infection is lethal to susceptible patients. Current treatment for babesiosis includes either the synergistic use of atovaquone and azithromycin or the combination of clindamycin and quinine. However, the side effects and the resistance posed by these parasites called for alternative approaches for the treatment of human babesiosis. Parasite-derived proteases play several functions in the context of parasitic lifestyle and regulate basic biological processes including cell death, cell progression and cell migration. We hypothesized that proteases are promising class of drug targets in Babesia parasites. Using the SYBR-Green assay, we screened a protease inhibitor library consists of 160 compounds against B. duncani in vitro culture at 50µM and identified 13 preliminary hits. Additionally, dose response assays of hit compounds against <i>B. duncani</i> and <i>B. microti</i> in vitro cultures identified 5 compounds as effective inhibitors against parasite growth. Of these 5 compounds, we chose ixazomib, a proteasome inhibitor as a potential drug for further studies based on its lower IC50 of 58nM as well as a higher therapeutic index as compared to other hit compounds. We demonstrated that in a mouse model infected with <i>target,</i>, the most effective inhibitor, the prodrug of ixazomib at a low dose of 2.5mg/kg lowers parasite proliferation without causing any adverse effects in animals. Thus, our studies suggest that Babesia proteasome may be an important drug target, and ixazomib may be a potential compound that may be used for the treatment of human babesiosis.</p>

The carnivores of Madagascar are likely the least studied of the world's carnivores, thus little is known about threats to their persistence. I provide the first long-term assessment of Madagascar's rainforest carnivore community, including: 1) how multiple forms of habitat degradation (i.e., fragmentation, exotic carnivores, human encroachment, and hunting) affect native and exotic carnivore occupancy; 2) how native and exotic carnivore temporal activity overlap and how body size and niche explain these patterns; 3) how native and exotic carnivores spatially co-occur across the landscape and which variables explain these relationships; and 4) how native and exotic carnivores and humans co-occur with lemurs across Madagascar's largest protected landscape: the Masoala-Makira landscape. From 2008 to 2013 I photographically sampled carnivores and conducted line-transect surveys of lemurs at seven study sites with varying degrees of degradation and human encroachment, including repeat surveys of two sites. As degradation increased, exotic carnivores showed increases in activity and occupancy while endemic carnivore, small mammal, and lemur occupancy and/or activity decreased. Wild/feral cats (Felis sp.) and dogs (Canis familiaris) had higher occupancy (0.37 ± SE 0.08 and 0.61 ± SE 0.07, respectively) than half of the endemic carnivore species across the landscape. Additionally, exotic carnivores had both direct and indirect negative effects on native carnivore occupancy. For example, spotted fanaloka (Fossa fossana) occupancy (0.70 ± SE 0.07) was negatively impacted by both wild/feral cat (beta = -2.65) and Indian civets (beta = -1.20). My results revealed intense pressure from hunting (ex. n = 31 fosa Cryptoprocta ferox consumed per year from 2005-2011 across four villages), including evidence that hunters target intact forest where native carnivore and lemur occupancy and/or activity are highest. I found evidence of high temporal overlap between native and exotic carnivores (ex. temporal overlap between brown-tail vontsira Salanoia concolor and dogs is 0.88), including fosa (Cryptoprocta ferox) avoiding dogs and humans across all seasons. However, I found no evidence of body size or correlates of ecological niche explaining temporal overlap among carnivores. Estimates of spatial co-occurrence among native and exotic carnivores in rainforest habitat revealed strong evidence that native and exotic carnivores occur together less often than expected and that exotic carnivores may be replacing native carnivores in forests close to human settlements. For example, falanouc show a strong increase in occupancy when dogs are absent (0.69 ± SE 0.11) compared to when they are present (0.23 ± SE 0.05). Finally, the two-species interaction occupancy models for carnivores and lemurs, revealed a higher number of interactions among species across contiguous forest where carnivore and lemur occupancy were highest. These various anthropogenic pressures and their effects on carnivore and lemur populations, particularly increases in exotic carnivores and hunting, have wide-ranging, global implications and demand effective management plans to target the influx of exotic carnivores and unsustainable hunting affecting carnivore and primate populations across Madagascar and worldwide. / Ph. D.