Several traditional methods have been used to characterise bacteria, such as biochemical, morphological and molecular tests; however, these methods are time-consuming and not always reliable. Recently, modern analytical techniques have emerged as powerful tools offering high-throughput, reliable and rapid analysis in applications, such as clinical and microbiology studies. A variety of modern analytical techniques have been employed for bacterial characterisation, including matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS), liquid chromatography-mass spectrometry (LC-MS), Fourier transform infrared (FT-IR) spectroscopy and Raman spectroscopy. This thesis focused on developing a robust MALDI-TOF-MS methodology to generate mass spectra profiles for the discrimination of clinically-significant bacteria. The data generated from MALDI-TOF-MS analysis are significantly influenced by a number of experimental factors, namely instrument settings, sample preparation, the choice of matrix, matrix additives and matrix preparation as well as sample-matrix deposition methods. The need to optimise experimental variables for bacterial analysis using MALDI-TOF-MS was evident despite the increased application of this analytical tool for clinical microbiology. Experimental optimisation revealed that the choice of matrix is the most important element in MALDI-TOF-MS analysis. Based on this study, a number of different matrices were used to obtain more reproducible mass spectra to classify bacterial samples using a rapid and effective approach. Studies in this thesis indicated that sinapinic acid (SA) is the best matrix for the analysis of proteins from intact bacteria, while 6-aza-2-thiothymine (ATT) and 2,5-dihydroxybenzoic acid (DHB) produced promising results for the analysis of lipid extracts from bacteria. Analytical techniques in combination with multivariate analysis, such as principal components analysis (PCA) and principal component-discriminant function analysis (PC-DFA), were used for bacterial discrimination. Classification was initially undertaken using MALDI-TOF-MS analysis, and subsequently FT-IR spectroscopy, Raman spectroscopy and LC-MS were performed to confirm the classification results. Two main types of bacteria were used for this analysis: 34 strains from seven Bacillus and Brevibacillus species and 35 isolates from 12 Enterococcus faecium strains. The findings showed that the four analytical techniques provide clear discrimination between bacteria at these different levels. Classification of different Bacillus and Brevibacillus bacteria using MALDI-TOF-MS analysis of extracted lipids was confirmed by LC-MS data. In addition, MALDI-TOF-MS data based on extracted lipids and intact bacterial cell proteins were very similar. MALD-TOF-MS analysis of intact enterococci cells produced successful classification with 78% correct classification rate (CCR) at the strain level. FT-IR and Raman spectroscopic data produced very similar bacterial classification with CCR of 89% and 69% at the strain level, respectively. However, classification based on MALDI-TOF-MS data and that based on spectroscopic data were slightly different (Procrustes distance of 0.81, p < 0.001, at the species level). Overall, the findings in this thesis indicate the potential of MALDI-TOF-MS as a rapid, robust and reliable method for the classification of bacteria based on different bacterial preparations.

There is a growing awareness of the risks of pollution in biological systems and one potential problem is the synthetic antioxidants, used for e.g. the stabilisation of polymeric materials. Natural antioxidants are an interesting alternative, if the high efficiency and thermal stability of the synthetic compounds can be reached. In the work described in this thesis, vitamin E (alfa-tocopherol) was studied as a natural antioxidant for the stabilisation of one of the major plastics, polyethylene (PE). The dependence of the surrounding environment for the efficiency of alfa-tocopherol in polyethylene (PE), throughout thermal aging, was characterised by sensitive techniques. Two techniques which have shown a high sensitivity in oxidation detection of polymers; chemiluminescence (CL) and gas chromatographic analysis, were compared with the commonly used methods, infrared spectroscopy (FT-IR) and thermal analysis. Three different additive systems were selected as active domains for -tocopherol in PE. Two of these contained carboxylic acid groups, poly (ethylene-co-acrylic acid) (EAA) and polyTRIM/PAA core-shell particles (Core), and the third, oat starch, had no such groups. The additives containing carboxylic groups improved the long-term efficiency of alfa-tocopherol in PE, according to carbonyl index measurements made by FT-IR, while the additive without carboxylic acid groups gave no improvement. The amount of carboxylic acids emitted from the materials after thermal aging, assessed by head-space solid-phase microextraction (HS-SPME) and gas chromatography-mass spectroscopy (GC-MS), also showed that EAA increased the antioxidant efficiency of alfa-tocopherol, whereas the Core system showed lower antioxidant efficiency. Reference systems containing the synthetic antioxidant Irganox 1076 and EAA or oat starch had the same performance as the materials stabilised with only the antioxidants. CL measurements in an inert atmosphere (TLI) have earlier been shown to give earlier oxidation detection than carbonyl index measurements in unstabilised PE. In this work, the TLI analysis and the carbonyl index measurements had the same sensitivity in the detection of oxidation in the stabilised materials. Assessment of low-molecular weight carboxylic acids in PE during the aging was made by gas chromatographic analysis together with solid-phase extraction. Propanoic acid showed the best correlation with the carbonyl index measurements, even if the carbonyl index showed earlier detection of oxidation. It was also found that TLI and CL in an oxidative atmosphere (CL-OIT) had the same sensitivity and were in accordance for all of the materials, with exception of the materials containing EAA and alfa-tocopherol or Irganox 1076. CL-OIT was also compared to the oxygen induction time determined by thermal analysis. / QC 20100921

[pt] A qualidade dos óleos vegetais utilizados na produção de biocombustíveis está diretamente relacionada à qualidade do produto final. Como metais desempenham um papel significativo na oxidação do óleo vegetal, a sua presença é indesejável, mesmo em baixas concentrações. No presente trabalho, investigou se como a presença de cobre, em diferentes estados de oxidação, cobre(0) ou cobre(II), afeta a estabilidade dos óleos de canola e girassol, auxiliando, assim, na compreensão dos mecanismos de oxidação dos mesmos. Óxido cúprico ou cobre metálico foram adicionados a amostras de óleo gerando suspensões contendo um teor de cobre equivalente a 2000 mg kg 1. As amostras foram mantidas a 90 graus celsius durante catorze dias. Periodicamente, foram retiradas alíquotas, que foram avaliadas quanto à estabilidade oxidativa através da determinação do índice de acidez, índice de iodo, espectroscopias de absorção nas regiões do UV Vis e do infravermelho (FT IR), espectroscopia Raman e do teste Rancimat. Os resultados confirmam que o cobre (não importa a espécie) participa ativamente do processo de degradação dos óleos vegetais, sugerindo que as espécies de metal não apenas influenciam a taxa de oxidação, mas também a extensão dos processos de degradação. Os espectros FT IR das amostras derivadas do óleo de canola mostraram um aumento na razão (I2856/I1747)tx/(I2856/I1747)t0, ou seja, uma diminuição dos grupos éster nas amostras de óleo contaminado com cobre. No entanto, não ocorreram alterações nas bandas com máximo em 1120 e 1098 cm 1, indicando que este metal atua como um catalisador no processo de hidrólise das ligações éster. Além disso, as razões (I2856/I3009)tx/(I2856/I3009)t0 e (I2856/I3010)tx/(I2856/I3010)t0 medidas por espectroscopia no FT IR para o óleo de canola e para o óleo de girassol, respectivamente, e a razão (I2856/I3012)tx/(I2856/I3012)t0 medida por espectroscopia Raman apresentaram um aumento mais pronunciado nas amostras contendo cobre. Contudo, os resultados obtidos sugerem que, durante a oxidação dos triglicerídeos, não ocorreu a quebra de ligações olefínicas, pois, embora tenha sido observado tanto por FT IR como por Raman que a banda relacionada ao v(C-H)cis diminuiu com o progresso da oxidação, não foi verificada significativa diminuição do índice de iodo, indicando que uma grande parte da oxidação nos óleos contaminados com cobre não envolveu diretamente a perda de duplas ligações, e sim a isomerização das duplas ligações cis direcionando a formação de produtos contendo ligações trans. Os dados deste trabalho indicam que o estado de oxidação +2 exerce um maior efeito catalítico do que o cobre na forma de partículas metálicas, uma vez que a diminuição no tempo de indução, assim como o aumento na formação de produtos secundários derivados de oxidação, acompanhada pela medição da absorvância a 270 nm, foi mais pronunciada nas amostras contaminadas com cobre(II). A extensão da isomerização das duplas ligações, acompanhada por FT IR e espectroscopia Raman, apontam neste mesmo sentido. Além disso, a influência de um antioxidante natural, curcumina, também foi avaliada. Verificou se que a sua adição às amostras de óleo contendo cobre(II) elevou a estabilidade frente aos ensaios realizados. / [en] The quality of vegetable oils used in biofuel production is directly related to the quality of the final product. As metals play a significant role in vegetable oil oxidation and degradation, their presence is undesirable, even at low concentrations. The present study investigated how the presence of copper, in different oxidation states, copper(0) or copper(II), affects the stability of canola and sunflower oil, thus aiding in the understanding of oil oxidation mechanisms. Cupric oxide or metallic copper were added to the oil samples generating suspensions containing overall copper amounts equivalent to 2000 mg kg 1. The samples were maintained at 90 celsius degrees for fourteen days. Aliquots were taken periodically and evaluated with regard to oxidative stability, by determining the acid value, iodine value, by absorption UV Vis and Infrared (FT IR) spectroscopy, Raman spectroscopy and the Rancimat test. The results confirm that copper, no matter in what oxidation state, participates actively in vegetable oil degradation, suggesting that the metal species do not only influence the oxidation rate, but also the extent of the degradation processes. The FT IR spectra of samples derived from copper contaminated canola oil showed an increase in the (I2856/I1747)tx/(I2856/I1747)t0 ratio, i.e., a decrease of the ester groups. However, no changes in the bands with maximums at 1120 and 1098 cm 1 were observed, indicating that this metal acts as a catalyst in the hydrolysis process of ester bonds. Furthermore, the (I2856/I3009)tx/(I2856/I3009)t0 and (I2856/I3010)tx/(I2856/I3010)t0 ratios measured by FT IR spectroscopy, for canola and sunflower oil, respectively, and the (I2856/I3012)tx/(I2856 /I3012)t0 ratio measured by Raman spectroscopy showed a more pronounced increase in the copper containing samples. However, the results also suggest that olefinic bonds did not rupture during triglyceride oxidation, since, despite the fact that a decrease in the band related to cis C-H vibration was observed by both FT IR and Raman during the oxidation progress, no reductions in the iodine value were observed, indicating that the majority of the oxidation in the copper containing oils did not involve the loss of double bonds, but the isomerization of cis double bonds, directing the formation of products containing trans bonds. The results reported in this study indicate that copper in the (II) oxidation state exerts a greater catalytic effect than Cu in the form of metal particles, since the decrease in the induction time, as well as the increase in the production of secondary oxidation products, verified by measuring the absorption intensity at 270 nm, was more pronounced in samples contaminated with copper(II). The influence of a natural antioxidant, curcumin, on the oxidation stability of vegetable oils was also evaluated, and its addition to the oil samples containing copper(II) increased oil stability.

Les hydrogels de polysaccharide sont des biomatériaux utilisés comme matrices à libération contrôlée de médicaments et comme structures modèles pour l’étude de nombreux systèmes biologiques dont les biofilms bactériens et les mucus. Dans tous les cas, le transport de médicaments ou de nutriments à l’intérieur d’une matrice d’hydrogel joue un rôle de premier plan. Ainsi, l’étude des propriétés de transport dans les hydrogels s’avère un enjeu très important au niveau de plusieurs applications. Dans cet ouvrage, le curdlan, un polysaccharide neutre d’origine bactérienne et formé d’unités répétitives β-D-(1→3) glucose, est utilisé comme hydrogel modèle. Le curdlan a la propriété de former des thermogels de différentes conformations selon la température à laquelle une suspension aqueuse est incubée. La caractérisation in situ de la formation des hydrogels de curdlan thermoréversibles et thermo-irréversibles a tout d’abord été réalisée par spectroscopie infrarouge à transformée de Fourier (FT-IR) en mode réflexion totale atténuée à température variable. Les résultats ont permis d’optimiser les conditions de gélation, menant ainsi à la formation reproductible des hydrogels. Les caractérisations structurales des hydrogels hydratés, réalisées par imagerie FT-IR, par microscopie électronique à balayage en mode environnemental (eSEM) et par microscopie à force atomique (AFM), ont permis de visualiser les différentes morphologies susceptibles d’influencer la diffusion d’analytes dans les gels. Nos résultats montrent que les deux types d’hydrogels de curdlan ont des architectures distinctes à l’échelle microscopique. La combinaison de la spectroscopie de résonance magnétique nucléaire (RMN) à gradients pulsés et de l’imagerie RMN a permis d’étudier l’autodiffusion et la diffusion mutuelle sur un même système dans des conditions expérimentales similaires. Nous avons observé que la diffusion des molécules dans les gels est ralentie par rapport à celle mesurée en solution aqueuse. Les mesures d’autodiffusion, effectuées sur une série d’analytes de diverses tailles dans les deux types d’hydrogels de curdlan, montrent que le coefficient d’autodiffusion relatif décroit en fonction de la taille de l’analyte. De plus, nos résultats suggèrent que l’équivalence entre les coefficients d’autodiffusion et de diffusion mutuelle dans les hydrogels de curdlan thermo-irréversibles est principalement due au fait que l’environnement sondé par les analytes durant une expérience d’autodiffusion est représentatif de celui exploré durant une expérience de diffusion mutuelle. Dans de telles conditions, nos résultats montrent que la RMN à gradients pulsés peut s’avérer une approche très avantageuse afin de caractériser des systèmes à libération contrôlée de médicaments. D’autres expériences de diffusion mutuelle, menées sur une macromolécule de dextran, montrent un coefficient de diffusion mutuelle inférieur au coefficient d’autodiffusion sur un même gel de curdlan. L’écart mesuré entre les deux modes de transport est attribué au volume différent de l’environnement sondé durant les deux mesures. Les coefficients d’autodiffusion et de diffusion mutuelle similaires, mesurés dans les deux types de gels de curdlan pour les différents analytes étudiés, suggèrent une influence limitée de l’architecture microscopique de ces gels sur leurs propriétés de transport. Il est conclu que les interactions affectant la diffusion des analytes étudiés dans les hydrogels de curdlan se situent à l’échelle moléculaire. / Polysaccharide hydrogels are biomaterials used as controlled drug delivery matrices and serve as model scaffolds for the study of many biological systems like bacterial biofilms and mucus. In every case, the transport of drugs or nutriments across a hydrogel matrix is of prime importance. Therefore, the study of transport properties in hydrogels is an important issue for many fields of application. In this work, curdlan, a neutral bacterial polysaccharide made of β-D-(1→3) glucose repeating units, is used as a model hydrogel. Aqueous suspensions of curdlan can form thermogels of different conformations depending on the incubation temperature. In situ characterization of the preparation of thermo-reversible (low-set) and thermo-irreversible (high-set) curdlan hydrogels was first carried out using variable temperature attenuated total reflection (ATR) Fourier transform infrared spectroscopy (FT-IR). The results allowed optimization of the gelling conditions leading to reproducible gel samples. Structural characterization of fully hydrated hydrogels, carried out by FT-IR imaging, environmental scanning electron microscopy (eSEM) and atomic force microscopy (AFM), allowed visualization of the different gel morphologies susceptible of influencing the diffusion of analytes in hydrogels. Our results show that both types of curdlan hydrogels have distinct microscopic architectures. The combination of pulsed field gradient (PFG) nuclear magnetic resonance (NMR) spectroscopy and NMR profiling allowed the study of self-diffusion and mutual diffusion on the same hydrogel system in similar experimental conditions. We showed that the diffusion of analytes in the gels is slower than in the aqueous solution. The diffusion experiments, carried out on a series of analytes of various sizes in both types of curdlan gels, show a decrease of the relative self-diffusion coefficient as a function of the analyte size. In addition, our results suggest that the equivalence between the self-diffusion and mutual-diffusion coefficients measured in the high-set curdlan gels is mainly due to the fact that the environment probed by the analytes during a self-diffusion experiment is representative of the one probed during a mutual-diffusion experiment. In such conditions, our results show that PFG NMR may present a valuable approach for the characterization of controlled drug release systems. Additional experiments show that the mutual-diffusion coefficient of dextran macromolecules is smaller than its self-diffusion coefficient in the same curdlan hydrogel. The difference between both transport rates is attributed to the different environment volumes probed by the analytes during the measurements. The similarities observed between the self-diffusion and mutual-diffusion coefficients, measured in both types of curdlan gels for all investigated analytes, suggest a limited influence of the microscopic gel architecture on its transport properties. It is therefore concluded that the interactions affecting the diffusion of the investigated analytes in the curdlan hydrogels lie at the molecular scale.

Les hydrogels de polysaccharide sont des biomatériaux utilisés comme matrices à libération contrôlée de médicaments et comme structures modèles pour l’étude de nombreux systèmes biologiques dont les biofilms bactériens et les mucus. Dans tous les cas, le transport de médicaments ou de nutriments à l’intérieur d’une matrice d’hydrogel joue un rôle de premier plan. Ainsi, l’étude des propriétés de transport dans les hydrogels s’avère un enjeu très important au niveau de plusieurs applications. Dans cet ouvrage, le curdlan, un polysaccharide neutre d’origine bactérienne et formé d’unités répétitives β-D-(1→3) glucose, est utilisé comme hydrogel modèle. Le curdlan a la propriété de former des thermogels de différentes conformations selon la température à laquelle une suspension aqueuse est incubée. La caractérisation in situ de la formation des hydrogels de curdlan thermoréversibles et thermo-irréversibles a tout d’abord été réalisée par spectroscopie infrarouge à transformée de Fourier (FT-IR) en mode réflexion totale atténuée à température variable. Les résultats ont permis d’optimiser les conditions de gélation, menant ainsi à la formation reproductible des hydrogels. Les caractérisations structurales des hydrogels hydratés, réalisées par imagerie FT-IR, par microscopie électronique à balayage en mode environnemental (eSEM) et par microscopie à force atomique (AFM), ont permis de visualiser les différentes morphologies susceptibles d’influencer la diffusion d’analytes dans les gels. Nos résultats montrent que les deux types d’hydrogels de curdlan ont des architectures distinctes à l’échelle microscopique. La combinaison de la spectroscopie de résonance magnétique nucléaire (RMN) à gradients pulsés et de l’imagerie RMN a permis d’étudier l’autodiffusion et la diffusion mutuelle sur un même système dans des conditions expérimentales similaires. Nous avons observé que la diffusion des molécules dans les gels est ralentie par rapport à celle mesurée en solution aqueuse. Les mesures d’autodiffusion, effectuées sur une série d’analytes de diverses tailles dans les deux types d’hydrogels de curdlan, montrent que le coefficient d’autodiffusion relatif décroit en fonction de la taille de l’analyte. De plus, nos résultats suggèrent que l’équivalence entre les coefficients d’autodiffusion et de diffusion mutuelle dans les hydrogels de curdlan thermo-irréversibles est principalement due au fait que l’environnement sondé par les analytes durant une expérience d’autodiffusion est représentatif de celui exploré durant une expérience de diffusion mutuelle. Dans de telles conditions, nos résultats montrent que la RMN à gradients pulsés peut s’avérer une approche très avantageuse afin de caractériser des systèmes à libération contrôlée de médicaments. D’autres expériences de diffusion mutuelle, menées sur une macromolécule de dextran, montrent un coefficient de diffusion mutuelle inférieur au coefficient d’autodiffusion sur un même gel de curdlan. L’écart mesuré entre les deux modes de transport est attribué au volume différent de l’environnement sondé durant les deux mesures. Les coefficients d’autodiffusion et de diffusion mutuelle similaires, mesurés dans les deux types de gels de curdlan pour les différents analytes étudiés, suggèrent une influence limitée de l’architecture microscopique de ces gels sur leurs propriétés de transport. Il est conclu que les interactions affectant la diffusion des analytes étudiés dans les hydrogels de curdlan se situent à l’échelle moléculaire. / Polysaccharide hydrogels are biomaterials used as controlled drug delivery matrices and serve as model scaffolds for the study of many biological systems like bacterial biofilms and mucus. In every case, the transport of drugs or nutriments across a hydrogel matrix is of prime importance. Therefore, the study of transport properties in hydrogels is an important issue for many fields of application. In this work, curdlan, a neutral bacterial polysaccharide made of β-D-(1→3) glucose repeating units, is used as a model hydrogel. Aqueous suspensions of curdlan can form thermogels of different conformations depending on the incubation temperature. In situ characterization of the preparation of thermo-reversible (low-set) and thermo-irreversible (high-set) curdlan hydrogels was first carried out using variable temperature attenuated total reflection (ATR) Fourier transform infrared spectroscopy (FT-IR). The results allowed optimization of the gelling conditions leading to reproducible gel samples. Structural characterization of fully hydrated hydrogels, carried out by FT-IR imaging, environmental scanning electron microscopy (eSEM) and atomic force microscopy (AFM), allowed visualization of the different gel morphologies susceptible of influencing the diffusion of analytes in hydrogels. Our results show that both types of curdlan hydrogels have distinct microscopic architectures. The combination of pulsed field gradient (PFG) nuclear magnetic resonance (NMR) spectroscopy and NMR profiling allowed the study of self-diffusion and mutual diffusion on the same hydrogel system in similar experimental conditions. We showed that the diffusion of analytes in the gels is slower than in the aqueous solution. The diffusion experiments, carried out on a series of analytes of various sizes in both types of curdlan gels, show a decrease of the relative self-diffusion coefficient as a function of the analyte size. In addition, our results suggest that the equivalence between the self-diffusion and mutual-diffusion coefficients measured in the high-set curdlan gels is mainly due to the fact that the environment probed by the analytes during a self-diffusion experiment is representative of the one probed during a mutual-diffusion experiment. In such conditions, our results show that PFG NMR may present a valuable approach for the characterization of controlled drug release systems. Additional experiments show that the mutual-diffusion coefficient of dextran macromolecules is smaller than its self-diffusion coefficient in the same curdlan hydrogel. The difference between both transport rates is attributed to the different environment volumes probed by the analytes during the measurements. The similarities observed between the self-diffusion and mutual-diffusion coefficients, measured in both types of curdlan gels for all investigated analytes, suggest a limited influence of the microscopic gel architecture on its transport properties. It is therefore concluded that the interactions affecting the diffusion of the investigated analytes in the curdlan hydrogels lie at the molecular scale.