Strains of pathogens are typically described as virulent or non-virulent. However, in the majority of pathogens, strains often vary continuously and quantitatively in their virulence and pathogencity. Biofilm formation is one of the recently recognized virulence factors in many human pathogens and little is known about the variation and evolution of biofilms among natural strains. In this study, I examined quantitative variation of biofilms among natural strains of the human pathogenic yeast Candida albicans. A total of 115 natural strains of C. albicans from three sources (vaginal, oral and environmental) were quantified by two mebods: (i) the XTT tetrazolium reduction assay, and (ii) optical density following staining by crystal violet dye. Mature biofilm was confirmed by observation using confocal laser scanning microscopy. My analyses indicated that strains from each of the three scurces varied widely in biofilm formation abilities and that biofilm formation ability was positively correlated to cell surface hydrophobicity (CSH). For each strain, multilocus genotypes were determined by PCR-RFLP, my comparative genotype and biofilm analyses denonstrated that natural clones and clonal lineages of C. albicans exhibited extensive quantitative variation for biofilm formation. I also examined potential interactions among strains within C. albicans and between different Candida species. My preliminary results suggest significant variation and complex patterns of strains or species interaction during Candida biofilm development. / Thesis / Master of Science (MS)

Mushrooms and insects are both integral components of ecosystems worldwide. Interactions between these two groups of organisms are particularly interesting to study due to the transient nature of mushroom fruiting bodies, which form for a short period of time when environmental conditions are optimal to allow the fungus to distribute its spores. Despite this unpredictability in where and when mushrooms will grow, a variety of insect species use mushrooms as a food source and a substrate on which to lay their eggs. Interactions between these two groups of organisms have been documented extensively in Europe. However, little is known about the diversity of insects that associate with mushrooms in Canada. In this study, 1,017 mushrooms were collected from forests in Hamilton and the Tillsonburg, Ontario regions between fall 2018 and fall 2019. Mushrooms and their associated insects were identified through DNA barcoding using sequences of the nuclear ITS region and the mitochondrial CO1 gene for the mushrooms and insects, respectively. In total, more than 100 insect species from at least 35 families and five orders were identified from the approximately 200 mushroom species collected. While some insect species displayed evidence of specificity in their choice of mushroom host, the larger network of associations was moderately generalized and many insect species inhabited mushrooms from multiple families and orders. This study highlights the incredible diversity of organisms that rely on mushrooms for survival and contributes to our overall understanding of mushroom-insect associations in this region of Southern Ontario. / Thesis / Master of Science (MSc) / Mushrooms and insects are both highly important organisms within ecosystems around the world. Mushrooms play key roles in breaking down organic matter within forests and contributing to plant health, while insects are important decomposers and pollinators. This project involved collecting over 1,000 mushrooms from two regions in Southern Ontario and identifying the insect species found living within these mushrooms in order to examine patterns in the interactions. To our knowledge, this is the first time a survey of mushroom-insect associations has been conducted in Canada. The collected mushrooms were inhabited by a diverse range of insect species, which included mostly flies and beetles, and each of the main sampling locations had their own unique mushroom and insect communities. Some insect species displayed preference in their choice of mushroom host. Overall, this study contributes greatly to our current understanding of mushroom and insect diversity in this part of Canada.

With the traditional fracture mechanics approaches, an initial crack and self-similar progression of cracks are assumed. In this treatise, theoretical and numerical tools are developed to mathematically describe non-self-similar progression of cracks without specifying an initial crack. A cohesive-decohesive zone model, similar to the cohesive zone model known in fracture mechanics as Dugdale-Barenblatt model, is adopted to represent the degradation of the material ahead of the crack tip. This model unifies strength-based crack initiation and fracture based crack progression. The cohesive-decohesive zone model is implemented with an interfacial surface material that consists of an upper and lower surface connected by a continuous distribution of normal and tangential nonlinear elastic springs that act to resist either Mode I opening, Mode II sliding, Mode III sliding, or mixed mode. The initiation of fracture is determined by the interfacial strength and the progression of fracture is determined by the critical energy release rate. The material between two adjacent laminae of a laminated composite structure or the material between the adherend and the adhesive is idealized with an interfacial surface material to predict interfacial fracture. The interfacial surface material is positioned within the bulk material to predict discrete cohesive cracks. The proper work-conjugacy relations between the stress and deformation measures are identified for the interfacial surface theory. In the principle of virtual work, the interfacial cohesive-decohesive tractions are conjugate to the displacement jumps across the upper and lower surfaces. A finite deformation kinematics theory is developed for the description of the upper and lower surface such that the deformation measures are invariant with respect to superposed rigid body translation and rotation. Various mechanical softening constitutive laws thermodynamically consistent with damage mechanics are postulated that relate the interfacial tractions to the displacement jump. An exponential function is used for the constitutive law such that it satisfies a multi-axial stress criterion for the onset of delamination, and satisfies a mixed mode fracture criterion for the progression of delamination. A damage parameter is included to prevent the restoration of the previous cohesive state between the interfacial surfaces. In addition, interfacial constitutive laws are developed to describe the contact-friction behavior. Interface elements applicable to two dimensional and three dimensional analyses are formulated for the analyses of contact, friction, and delamination problems. The consistent form of the interface element internal force vector and the tangent stiffness matrix are considered in the formulation. We investigate computational issues related to interfacial interpenetration, mesh sensitivity, the number of integrations points and the integration scheme, mathematical form of the softening constitutive law, and the convergence characteristics of the nonlinear solution procedure when cohesive-decohesive constitutive laws are used. To demonstrate the predictive capability of the interface finite element formulation, steadystate crack growth is simulated for quasi-static loading of various fracture test configurations loaded under Mode I, Mode II, Mode III, and mixed-mode loading. The finite element results are in agreement with the analytical results available in the literature and those developed in this work. A progressive failure methodology is developed and demonstrated to simulate the initiation and material degradation of a laminated panel due to intralaminar and interlaminar failures. Initiation of intralaminar failure can be by a matrix-cracking mode, a fiber-matrix shear mode, and a fiber failure mode. Subsequent material degradation is modeled using damage parameters for each mode to selectively reduce lamina material properties. The interlaminar failure mechanism such as delamination is simulated by positioning interface elements between adjacent sublaminates. The methodology is validated with respect to experimental data available in the literature on the response and failure of quasi-isotropic panels with centrally located circular cutouts. Very good agreement between the progressive failure analysis and the experiments is achieved if the failure analyses includes the interaction of intralaminar and interlaminar failures in the postbuckling response of the panels. In addition, ideas concerning the implementation of a fatigue model incorporated with a cohesive zone model are discussed. / Ph. D.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Ce travail est consacré à l’élaboration de luminophores à base de polyphosphates d’ions alcalins et de terres rares, stœchiométriques ou activés en ions Eu3+ et Sm3+, émetteurs de fluorescence sous excitation VUV. Ces matériaux, de formulation LixNa1-xY1-yEuy(PO3)4 (x = 0 ; 0,25 ; 0,5 ; 0,75 ; 1 et 0,01 ≤ y ≤ 1), LixNa1-xLa(PO3)4 : 5 % Eu3+ (x = 0 ; 0,1 ; 0,2 ; 0,8 ; 0,9 ; 1), NaxK1-xLa(PO3)4 : 5 % Eu3+ (x = 0 ; 0,1 ; 0,2 ; 0,8 ; 0,9 ; 1) et LixNa1-xSm(PO3)4 (x = 0 ; 0,5 ; 1), ont été synthétisés par voie céramique et caractérisés principalement par diffraction des rayons X, spectroscopies infrarouge et Raman et analyses thermiques. Les analyses physico-chimiques et optiques, notamment grâce aux propriétés de sonde structurale de l’ion Eu3+, démontrent que la substitution croisée des ions alcalins Li+, Na+ et K+ n’est possible que dans une proportion relativement faible, ce qui lié aux différences de structures cristallographiques de ces matériaux. L’analyse des données spectroscopiques de l’ion Eu3+ selon la théorie de Judd et Ofelt confirme le lien étroit existant entre les propriétés optiques et structurales dans ces matériaux. Les spectres d’excitation sont caractérisés par une bande intense localisée dans le domaine VUV, respectivement due au mécanisme de transfert de charge Y3+-O2- et Eu3+-O2- dans les phases à l’yttrium dopées en ions Eu3+ et aux bandes 4f-5d pour les matériaux concentrés en ions Sm3+. Les matériaux concentrés en ions Eu3+ et Sm3+ sont émetteurs d’une intense fluorescence rouge et orange respectivement, démontrant l’absence d’extinction par concentration. / This work is devoted to the development of phosphors based on polyphosphates of alkaline and rare earth ions, stoichiometric or activated with Eu3+ and Sm3+ ions, considered as light emitters under VUV excitation. These materials, with formula LixNa1-xY1-yEuy(PO3)4 (x = 0; 0.25; 0.5; 0.75; 1 and 0.01 ≤ y ≤ 1), LixNa1-xLa(PO3)4 : 5 % Eu3+ (x = 0; 0.1; 0.2; 0.8; 0.9; 1), NaxK1-xLa(PO3)4 : 5 % Eu3+ (x = 0; 0.1; 0.2; 0.8; 0.9; 1) and LixNa1-xSm(PO3)4 (x = 0; 0.5; 1), were synthesized in the solid state and characterized mainly by X-ray diffraction, infrared and Raman spectroscopies and thermal analysis. Physical-chemical and optical analyses, in particular using the Eu3+ ion as a structural probe, show that the cross-substitution of Li+, Na+ and K+ alkaline ions is possible only in a relatively small proportion, which is linked to the differences in crystallographic structures of these materials. The analysis of the Eu3+ ion spectroscopic data according to Judd and Ofelt theory confirms the close link between optical and structural properties in these materials. Excitation spectra are characterized by an intense band localized in the VUV domain, respectively due to the charge transfer mechanism Y3+-O2- and Eu3+-O2- for the Eu3+ doped yttrium materials and to the 4f-5d inter-configuration for the Sm3+ concentrated materials. Materials concentrated in Eu3+ and Sm3+ ions emit intense red and orange fluorescence respectively, demonstrating the absence of concentration quenching.

Este trabalho foi desenvolvido com a finalidade de testar alterações nas metodologias in vitro de produção de gases (diferentes proporções de inóculo) e incorporação de 32P (velocidade de centrifugação, número de lavagens e diferentes tipos de inóculos) para adequá-las às condições climáticas e às especificidades da microbiota dos ruminantes mantidos no clima tropical brasileiro. Além dessas técnicas utilizadas, foram feitas determinações de análise bromatológica com posterior análise de nutrientes digestíveis totais, degradabilidade ruminal in situ e digestibilidade in vitro a partir da técnica dos dois estágios. Os substratos testados foram divididos em, fibrosos (feno de alfafa e capim colonião), concentrados (milho grão e farelo de soja) e fermentado (silagem de milho). O delineamento experimental utilizado foi inteiramente casualizado, todos os substratos foram avaliados para cada uma das variáveis com pelo menos três repetições no tempo. Cada variável foi comparada por análise de variância considerando a hipótese de nulidade dentro dos substratos. As correlações entre as metodologias foram testadas quando biologicamente significantes e compatíveis. A técnica de incorporação in vitro de 32P, obteve resultados satisfatórios (P<0,05) em relação à velocidade de centrifugação e número de lavagens. Os diferentes tipos de inóculos testados (100% fase líquida do rúmen, 50% fase líquida e 50% fase sólida) não apresentaram diferença significativa (P>0,05). As diferentes proporções do inóculo testado na técnica in vitro de produção de gases (A contendo 100% de fase líquida e 0% de fase sólida; inóculo B, 75% de fase líquida e 25% de fase sólida; inóculo C, 67% de fase líquida e 33% de fase sólida; inóculo D, 50% de fase líquida e 50% de fase sólida) apresentaram diferença significativa (P<0,01); os fatores analisados permitiram a interpretação de que usando o inóculo com maior porcentagem de fase sólida, o processo fermentativo foi mais parecido ao potencial de produção de gases. Para a técnica in vitro de incorporação de 32P sugere-se usar uma velocidade de centrifugação de 39.907g, 4 lavagens e um inóculo com apenas a fase líquida do conteúdo ruminal. É sugerido que para a técnica in vitro de produção de gases pode ser usado um inóculo contendo 50% de fase sólida e 50% de fase líquida do conteúdo ruminal. / This study was developed to test the adaptations in in vitro methodologies of gas production (different proportion of solid phase in the inoculum) and 32P incorporation technique (centrifugation speed, number of washings and different kinds of inoculum) to adequate them to the climate condition and to the microbiota specifications of the ruminants kept in the Brazilian tropical climate. Besides these techniques, bromatological analysis determinations were made with further total digestible nutrients and also, in situ rumen degradability and in vitro digestibility from the two-stage technique. The tested substrata were divided in fibrous (Panicum grass and Lucerne hay), concentrated (soybean meal and corn grain) and fermented (corn silage). The experimental design was completely randomized, where all the substrata were evaluated for each of the variables with at least three repetitions. Each variable was compared for analysis of variance considering the hypothesis, within substrata. The correlations between methodologies were tested when biologically significant and compatible. The 32P in vitro incorporation technique obtained satisfactory results (P<0,05) in relation to the centrifugation speed and the number of washings. The two different kinds of tested inocula (100% rumen liquid phase, and 50% both liquid and solid phase) showed no significant difference (P>0,05). The different inoculum proportion tested for in vitro gas production (inoculum A containing 100% liquid phase and 0% solid phase; inoculum B, 75% liquid phase and 25% solid phase; inoculum C, 67% liquid phase and 33% solid phase; and inoculum D, 50% both liquid and solid phases) showed significant difference; the analyzed factors allowed the interpretation that using the inoculum with higher solid phase percentage, the fermentation process was more similar to the gas production potential. In the in vitro 32P incorporation technique it is suggested to use a centrifugation speed of 39,907g, 4 washings and an inoculum with only liquid phase from the rumen. It is suggested that for the in vitro gas production technique can be used an inoculum containing 50% of solid phase and 50% of liquid phase.

L'agriculture urbaine dans la zone des Niayes de Dakar fournit 60% des besoins en légumes de cette région à fort taux d'urbanisation. Les maraîchers de cette zone ont de plus en plus recours aux pesticides pour lutter contre les ravageurs et maladies des cultures. Les objectifs de ce travail sont de tenter de répondre à la problématique suivante : les pratiques d'utilisation des pesticides ont-elles un impact sur la qualité des ressources environnementales dans cette zone? La consommation des produits horticoles et des eaux souterraines de cette zone comporte-t-elle un risque pour les populations? Nous avons tenté de répondre à ces questions par le biais d'enquêtes de terrain et d'analyses. Les résultats des enquêtes ont mis en évidence l'application de diverses matières actives appartenant aux organophosphorés, organochlorés, carbamates et pyréthrinoïdes sur une variété de spéculations. Les pesticides appliqués ne sont pas généralement homologués et certains d'entre eux sont des polluants organiques persistants et donc interdits d'utilisation au Sénégal. Les pratiques d'utilisation (fréquences, quantités appliquées, conditions de stockage, méthodes d'élimination des emballages) ne respectent pas les règles prescrites par les bonnes pratiques agricoles. Les analyses ont porté sur 80 échantillons d'eaux souterraines, 119 de sol, et 175 de légumes, collectés au niveau des sites de Niaga, de Thiaroye, de Cambérène et de Malika sur quatre campagnes. Les résultats montrent des niveaux de contamination environnementale élevés de la zone des Niayes avec la détection de 15 (eaux souterraines et légumes) et de 17 (sol) pesticides sur 21 recherchés. Dans toutes les matrices, les molécules ayant été détectées à des fréquences élevées sont celles qui avaient enregistré des fréquences de citation d'au minimum 6%. Près de 56% des points d'eau ont présenté au moins une substance dont la concentration moyenne est supérieure à la norme de qualité correspondante et 38% ne respectaient pas la norme de concentration totale. Pour les légumes, des pourcentages de non-conformité variant entre 58 et 76% selon les sites ont été obtenus. Les apports journaliers estimés ont montré que près de 80% des quantités de résidus de pesticide ingérables correspondent aux résidus des trois premières classes de pesticides (extrêmement dangereux, hautement dangereux et modérément dangereux) selon l'OMS. Cette observation montre que le risque lié à l'exposition des populations à l'eau et aux aliments contaminés est réel. / Urban agriculture in the Niayes zone of Dakar provides 60% of the vegetable needs of this region which has a high urbanization rate. Farmers in this area rely heavily on pesticides to protect crops from pests and diseases. The main objectives of this work were to try to answer the following questions : Do pesticide use patterns and management have an impact on the quality of environmental resources of the area? Does consumption of horticultural products and groundwater of this area pose a risk? We tried to bring answers through field surveys and analyses. The survey results showed the application of various pesticides belonging to organophosphates, organochlorines, carbamates and pyrethroids on a variety of speculations. Pesticides applied are not generally approved and some of them are persistent organic pollutants and thus prohibited for use in Senegal. Use practices (frequency, amount, storage conditions, packaging disposal) do not respect the rules of good agricultural practices. The analyses were performed on 80 groundwater samples, 119 of soil samples and 175 of vegetables collected at Niaga, Thiaroye, Cambérène and Malika during 4 campaigns. Results show high contamination levels of the environment with detection of 15 (in groundwater and vegetables) and 17 (in soil) pesticides out of 21. The molecules that have been detected with high frequencies in the matrices are those cited with frequencies greater than 6%. Nearly 56% of groundwater samples showed at least one substance with level exceeding the corresponding standard. 38% did not meet the standard set for total residues concentration. For vegetables, the percentages of exceeding standards ranged between 58 and 76% depending on the site. The estimated daily intake showed that nearly 80% of pesticide residues belong to the following WHO classes (extremely hazardous, highly hazardous and moderately hazardous). This observation evidences the risk of human exposure to contaminated food and water.

Les pseudosuchiens représentent l'ensemble de la lignée des crocodiliens qui s'est différentiée de celle des dinosaures à partir du Trias inférieur (il y en a environ 250 Ma). A l'origine probablement endothermes et terrestres, les pseudosuchiens sont par la suite devenus ectothermes et certains d'entre eux sont retournés vers un mode de vie semi-aquatique lors de la transition Trias-Jurassique (200 Ma): les néosuchiens (formes encore représentées dans le nature actuelle) et les téléosauridés (disparus depuis le Crétacé). À l'image de certains taxons fossiles comme les " stégocéphales ", les pseudosuchiens présentent une ornementation composée de cupules et de sillons à la surface des os dermiques (toit crânien, mandibules et ostéodermes) qui a la particularité de se former par résorption osseuse au sein de ce groupe. L'étude d'os fossilisés et d'os sec par des techniques d'imagerie 3D combinées à des analyses phylogénétiques basées sur des caractères quantitatifs a montré que les formes amphibies présentent un développement accrue de l'ornementation. Par la suite, nos analyses histologiques à partir de prélèvements sur des crocodiliens vivants ont montré que ces cupules hébergent des bouquets vasculaires qui seraient possiblement impliqués dans les échanges de chaleurs en phase émergée et semi-émergée ainsi que dans le tampon, de l'acidité sanguine pendant les phases émergées (en apnée). Concernant les possible implications biomécaniques de l’ornementation, les analyses en éléments finis que nous avons effectuées à partir d’ostéodermes scannés en 3D ont montré que la présence d’ornementation n’avait pas d’influence ni sur la résistance mécanique des ostéodermes ni sur leur capacité à conduire la chaleur. Par conséquent, le rôle fonctionnel de l’ornementation serait strictement d’ordre physiologique en lien avec la mise en place d’un réseau sanguin péri-osseux qui faciliterait à la fois les transferts de chaleur entre l’organisme et l’environnement en phase d’exposition et le stockage du lactate dans les os dermiques en phase d’apnée. De plus, la mise en place de l’ornementation pourrait permettre le maintien de l’équilibre homéostatique phospho-calcique via la succession de résorption superficielle et de dépôt secondaires en périphérie des os dermiques suivant la trajectoire ontogénétique de chaque individu (phase de ponte, jeun prolongé...). / Pseudosuchia is the crocodylian lineage which split up with the dinosaurs since the Early- Triassic (around 250 million years ago). At first probably endothermic and terrestrial, pseudosuchians became secondarily ectothermic and some of them returned to a semi-aquatic lifestyle at the Triassic-Jurassic transition (200 Ma): the neosuchians (still present in current nature) and the teleosaurids (disappeared since the Cretaceous). Like some extinct vertebrate groups (« the stegocephalians »), the pseudosuchians possess a dermal bone ornamentation made of pits and grooves on the skull roof, the mandibles and the osteoderms but with the particularity to be excavated by resorption. The study of both fossil and dry bones combining 3D-data monitoring and quantitative data-based phylogenetic comparative analyses evidenced that the semi-aquatic forms possess a more excavated bone ornamentation. Further, histological analyses based on living animal sampling have revealed that the ornamentation pits always house a vessel proliferation which may be involved in heat exchanges during emerged and semi-emerged periods as well as acidosis buffering during submerged periods (apnea). Concerning the biomechanical and thermal implications, the finite element analyses performed on 3D-modeled osteoderms have proved that the bone ornamentation does not modify the osteoderm heat conduction nor their mechanical resistance. Consequently, we assess that the functional role of bone ornamentation shall mainly concern physiological implications through the set-up of a blood vessel network on the bone periphery (heat transfers, blood acidosis buffering; as hypothesized by previous authors). Secondarily, bone ornamentation may also be involved in phosphor-calcic homeostasis based on the succession of pit resorption and secondary superficial bone deposit in response to the specimens. life-long changes (eggshelling, diets.).