Le contrôle de l'aérocontamination fongique est devenu un objectif majeur pour préserver la santé humaine et animale. L'évaluation de l'aérocontamination fongique fait classiquement appel aux techniques de mise en culture ou de dosage de composants fongiques présents dans l'air. Ces techniques présentent des inconvénients. C'est la raison pour laquelle, nous nous sommes fixés comme objectif de mettre au point des méthodes d'analyse alternatives utilisant des outils de biologie moléculaire. Dans un premier temps, nous avons comparé plusieurs techniques de prélèvements d'air dans des environnements intérieurs présentant une contamination plus ou moins élevée. Nous avons, par la suite, optimisé les conditions d'extraction de l'ADN fongique à partir de prélèvements d'air. L'ADN extrait a été amplifié par PCR à semi-nichée ? avec des amorces universelles permettant d'amplifier une partie de l'ARNr 18S de champignons. Par la suite, nous avons utilisé la TTGE (Temporal Temperature Gradient Electrophoresis) et la D-HPLC (Denaturing High Performance Liquid Chromatography) pour séparer les amplificats. Chaque produit de PCR a été identifié par séquençage direct après purification. La comparaison des espèces identifiées par ces techniques avec celles qui sont obtenues par la méthode classique (culture) apporte de meilleurs renseignements sur la qualité fongique d'un même prélèvement d'air. L'application de ces techniques dans des environnements à diff'rents niveaux de contamination a permis de déduire que l'étude de l'évaluation de l'aérocontamination fongique se fait par l'association de la culture et des méthodes moléculaires / Fungal spores represent a significant part of the biological contaminants that could be detected in air. Exposure to fungi has been associated with several types of human or animal health problems (mycosis, allergy, mycotoxicosis). To evaluate the relationship between airborne fungi potential and adverse health effect, the fungal types and their relative frequencies in air need to be investigated. Traditional methods for fungal identification (culture and microscopy analysis) are laborious, time-consuming and require expertise. To replace cultivation, several techniques have been proposed. This study showed that molecular techniques (PCR-TTGE or Temporal Temperature Gradient Electrophoresis and PCR-DHPLC or Denaturing High Performance Liquid Chromatography) allowed the separation of amplificons corresponding to distinct fungal species that may be encountered in air. Both methods were proved to be appropriate for analysis of complex fungal communities. The detection and the molecular identification techniques were adapted for the evaluation of indoor airborne fungal contamination. The cultivation method and culture-independent techniques were further compared for the analysis of fungal aerosols from different sites

Important research questions are typically studied and analyzed more than once, often by different research teams in different locations. However, in many instances, the results of these multiple small studies are diverse and conflicting, which makes decision-making difficult. The need to arrive at decisions fostered the momentum towards synthesizing the results of these multiple studies. Therefore, meta-analysis, also referred to as the standard or traditional meta-analysis, is a statistical technique for combining the results or findings from multiple independent studies to address a specific research question. The applications of meta-analysis have been extended to many fields of research including medicine, psychology, ecology, education, business and many others. Prior to carrying out a meta-analysis or statistically synthesizing data, a researcher must undertake a systematic review. Systematic review attempts to collate empirical evidence that fits pre-specified eligibility criteria to answer a specific research question. That is to determine which studies will be included or excluded from the analysis. Standard meta-analysis methods are used to obtain the relative efficacy (or safety) of a particular intervention versus a competing intervention in the presence of a direct or head-to-head comparison. Thus only a pair-wise comparison can be made. The outcome of these interventions could be continuous, binary or count data. A number of methodologies related to meta-analysis, assessments of underlying assumptions and strategies for the presentation of results have been proposed by several researchers. A commonly used model for estimating effect sizes in meta-analysis is the fixed-effect model. However, various factors can determine the performance of the model which needs to be considered before using the results for decision making. This project aimed to investigate the performance of hypothesis properties and estimation properties on selecting data points from an underlying contaminated distribution under different scenarios for modeling a continuous outcome. Different levels of contamination, levels of significance, number of studies, number of individual study sample sizes, standard deviations and effect sizes were investigated in our simulation study for a continuous outcome. The results of our simulation study shows that, the fixed-effect meta-analytic model does not perform well in the presence of contamination. As the level of contamination in the treatment group increases, the properties of estimators and hypothesis are greatly influenced. The method performs well as expected in the absence of contamination but performs poorly as we observe 50% contamination in the treatment group regardless of the individual sample size, the number of studies, the standard deviation and the effect size. / Thesis / Master of Science (MSc)

No description available.

Delta Store #3033 in Indianola, MS is suspected of having had a release of petroleum, which may have contaminated the underlying soil and shallow groundwater. Exploratory boring/monitoring wells were drilled on-site noting all soil formations and groundwater encountered. The soil facies encountered show a fining upward sequence, representative of a fluvial depositional environment. Soil contamination is mostly confined to the surficial soil; however, evaluation of lab data, boring logs, and cross sections suggests it is likely the contamination migrated through the surficial confining layer into the underlying strata. The hydraulic conductivity of 1.2 x 10-5 cm/sec, surficial geology consisting mostly of low and some high plasticity clays (CL and CH), a hydraulic gradient of 0.01 to 0.02 ft/ft, and the presence of an overlying concrete pavement suggests that any recent release of hydrocarbons should be confined to the immediate vicinity under the site.

The overarching objective of this dissertation was to study groundwater resources on global, local, and regional scales. The first objective of this dissertation was to analyze the groundwater nitrate contamination in the Edwards-Trinity and the Southern High-Plains aquifers of Texas. The second was to study groundwater quality in terms of seawater intrusion in the California Coastal Basin, Upper Floridian, and North Atlantic Coastal Plain aquifers. This dissertation also provided a comprehensive overview of the groundwater level in basins at the global scale and further analyzed agricultural activities on groundwater storage in small and large basins. To achieve first objective, Ordinary Least Square (OLS) and Geographically Weighted Regression (GWR) models were used to study the relationship between groundwater nitrate contamination and land use. This dissertation further identified dominant groundwater types using USGS well data and to estimate the extent of seawater intrusion in terms of dominant ions and ocean salinity in the United States coastal aquifers. Finally, groundwater storage anomaly was quantified using Gravity Recovery and Climate Experiment (GRACE) derived variations in total Terrestrial Water Storage (TWS) and the Global Land Data Assimilation System (GLDAS). Land cover data representing a percentage of irrigated lands using groundwater resources was used to study agricultural activities on groundwater storage. Groundwater nitrate contamination was positively associated with cotton production in Southern High-Plains and Edwards-Trinity aquifers. The nitrate concentrations tended to increase as the well-depth decreased in both aquifers. Results showed that the dominant ions in the study area were Na+ and Cl- . The study concluded that Na-Cl and mixed Ca-Mg-Cl were dominant water types in the United States' coastal aquifers. Results also indicated that seawater intrusion is occurring in the US coastal aquifers. Groundwater depletion has increased in southern Asia, western North America, and southwestern Europe due to groundwater withdrawal for agricultural use. However, farming practice is not the main reason for groundwater scarcity in South America, Africa, and Australia.

No description available.

No description available.

The objective of this study was to determine how hole diameter, channel length, test organism motility, concentration and aerosol exposure time affected microbiological contamination of sealed flexible pouches. Nickel microtubes with 10 μm and 20μm hole diameters and lengths of 5 mm and 10 mm were used in various combinations to create seal defects in 128 retortable pouches. A 119,911 cm³, exposure chamber was used to distribute an aerosol with a particle size of 2.68 μm, infected with motile and isogenically mutated nonmotile <i>Pseudomonas fragi</i> TM 849 in concentrations of 10² or 10⁶ cells/mL. Fifteen and 30 minute aerosol exposure times were used. Six pouches tested positive for test organism growth after a 72 hour incubation period. Pouch contamination via microbial ingress was significant (P < .05) for test organism motility (motile) and concentration (10⁶ cells/mL). / Master of Science

L'usage d'animaux axéniques comme modèles a augmenté exponentiellement dans les dernières années en recherche expérimentale. Afin de conserver leur statut axénique, les animaux doivent être contenus dans des isolateurs traditionnels ou des isolateurs au niveau de la cage, incluant la cage scellée à pression positive de Tecniplast : l'Isocage. Cependant, le moyen le plus efficace de confirmer leur statut axénique des animaux reste incertain, particulier pour les isolateurs au niveau de la cage, comportant un plus grand risque de contamination que l'isolateur traditionnel en raison de leur contact plus fréquent avec l'environnement extérieur. Ce projet de maîtrise a pour buts de gérer le risque de contamination associé à l'Isocage en optimisant la désinfection par immersion et en déterminant l'efficacité des mesures de précautions axéniques, puis finalement de déterminer l'efficacité des mesures de détection à démontrer la présence de contaminants en cages axéniques Les travaux d'optimisation de la désinfection par immersion a permis de déterminer la charge microbienne résiduelle retrouvée à la surface des Isocages entre deux changements de cage, d'évaluer l'efficacité sporicide de deux désinfectants, et finalement de déterminer le temps optimal de désinfection pour l'immersion des cages axéniques lors d'un changement de cage selon la concentration du désinfectant utilisé. L'efficacité de mesures de précaution axéniques a été confirmée en comparant les flores microbiennes retrouvées à la surface de cages contenues dans des locaux axéniques et non axéniques. L'efficacité des mesures de détection à démontrer la présence de contaminants en Isocage a été déterminée en développant, validant et optimisant trois différentes méthodes, puis en testant in situ leur efficacité à détecter des contaminants artificiellement introduits dans des cages axéniques. Cet ouvrage constitue un apport important au domaine puisqu'il est l'un des premiers à aborder la gestion des risques et l'efficacité des méthodes de détection lors d'utilisation de l'Isocage et du bassin d'immersion annexé à la station de biosécurité avec des animaux axéniques. / The use of axenic animals as models have increased exponentially in recent years in experimental research. In order to maintain their axenic status, animals must be contained in traditional isolators or isolators at the cage level, which includes Tecniplast's sealed positive pressure Isocage. However, the most effective way to confirm animal axenic status remains uncertain, especially for cage-level isolators, which carry a greater risk of contamination than the traditional isolator due to their most frenquent contact with outer environment. This Master's project aims were to manage the risk of contamination associated with Isocage by optimizing disinfection by immersion and determining the effectiveness of axenic precautionary measures; then finally to determine the effectiveness of the detection measures to demonstrate the presence of microbial contaminants in axenic Isocages. The optimization of disinfection by immersion made it possible to determine the residual microbial load found on the surface of Isocages between two cage changes, to evaluate the sporicidal efficiency of two disinfectants, and finally to determine the optimal disinfection time for the immersion of the axenic cages during a change of cage depending on the concentration of disinfectants used. The effectiveness of axenic precautionary measures has been confirmed by comparing the microbial flora found on the surface of cages contained in axenic and non-axenic rooms. The effectiveness of detection measures to demonstrate the presence of contaminants in Isocage has been determined by developing, validating and optimizing three different methods, then by testing in situ their effectiveness to detect contaminants artificially introduced into axenic cages. This work constitutes an important contribution to the field since it is one of the first to discuss risk management and the effectiveness of detection methods when using Isocage and the immersion basin attached to the biosecurity station with axenic animals.

Thèse ou mémoire avec insertion d’articles. / La consommation d'aliments contaminés par le norovirus humain, tels que les baies et les légumes feuillus, est une cause majeure de gastro-entérite épidémique dans le monde. Par conséquent, les stratégies de contrôle visant à limiter l'adhésion du norovirus à la surface des produits végétaux ont fait l'objet de plusieurs études. Pendant la dernière décennie, les interactions entre les virus entériques et les bactéries commensales de l'intestin des mammifères ont été étudiées. Cependant, peu de travaux ont été réalisés sur les communautés bactériennes associées à la surface des baies et des légumes feuillus et leur rôle dans la transmission du norovirus humain. D'ailleurs, certaines bactéries de la flore commensale des végétaux sont connues pour leur capacité à former des biofilms dans lesquels des substances analogues aux récepteurs des norovirus sont sécrétées. La présence de biofilms bactériens pourrait ainsi contribuer à l'adhésion du norovirus à la surface des végétaux et favoriser sa persistance. Puisque les produits végétaux sont délicats et susceptibles d'être endommagés, les traitements conventionnels ne sont pas toujours appropriés pour inactiver les virus sans compromettre la qualité des aliments. Dans ce mémoire, neuf bactéries associées à la surface des baies et des légumes feuillus sous forme de biofilms ont été étudiées selon leur effet protecteur sur la persistance de deux virus modèles du norovirus humain, le norovirus murin (MNV-1) et le virus Tulane, après un traitement d'inactivation par la lumière pulsée à une fluence de 11,52 J/cm². Aucune différence significative n'a été détectée dans les réductions du titre viral de MNV-1 en présence de biofilms par rapport au MNV-1 seul après le traitement par la lumière pulsée. Le virus Tulane a montré une résistance plus élevée au traitement par la lumière pulsée lorsqu'il était en présence des biofilms formés par Enterobacter cloacae, Escherichia coli, Kocuria kristinae, Pantoae agglomerans et Pseudomonas fluorescens. / Consumption of contaminated food with human norovirus, such as fresh berries and leafy vegetables, is a major cause of epidemic gastroenteritis worldwide. Consequently, several studies have focused on strategies to prevent norovirus attachment to fresh produce. Over the last decade, interactions between enteric viruses and commensal bacteria of the mammalian gut have been investigated, but limited work has been done on the bacterial communities associated with the surface of fresh produce and their role in norovirus transmission. Some bacterial species can form a matrix of extracellular polymeric substances, called biofilm, in which molecules like norovirus receptors can be secreted. Thus, bacterial biofilms associated with the surface of berries and leafy vegetables could interplay with norovirus through direct interactions and modulate its attachment and persistence. Since fresh produce are susceptible to damage, conventional treatments are not always appropriate to inactivate viruses without compromising food quality. Therefore, there is an urgent need to understand how norovirus interacts with epiphytic bacteria, and more specifically with bacterial biofilms. Nine bacterial species were studied in terms of their protective effect on the persistence and infectivity of two norovirus surrogates, murine norovirus 1 (MNV-1) and Tulane virus, when subjected to a pulsed light inactivation treatment at a fluence of 11.52 J/cm². No significant difference was detected in reductions of MNV-1 when attached to bacterial biofilms compared with the control whereas Tulane virus showed a significantly higher resistance to pulsed light treatment when attached to biofilms formed by Enterobacter cloacae, Escherichia coli, Kocuria kristinae, Pantoae agglomerans, and Pseudomonas fluorescens.