Despite the scientific progress in the last decades in terms of therapeutic agents to fight cancer there is still the need of developing safer and more effective drugs. Developing an innovative drug is not only very expensive, but also highly time consuming; furthermore, the number of anticancer agents that fail in clinical trials with high attrition rates mainly caused by unexpected toxicity and lack of efficacy far outweighs those considered effective, which indicates that drug screening processes require further improvements. In this project the application of Fourier transform infrared microspectroscopy is evaluated in order to develop a spectral based model that could be used to describe the drug-cell interaction and also to discriminate between the metabolic modifications due to a particular drug and the inherent cell cycle of a cell. A computational method was built using the FTIR spectra from a highly resistant renal cell carcinoma cell line, Caki-2, in order to discriminate between the phases of the continuous cell cycle that cells undergo while proliferating in vitro. Such model enabled the discrimination of early events of the cell cycle (G0/G1 phase cells) from G2/M phase cells with a prediction accuracy of 90% and 92.9% respectively. On the other hand, when the RMieS-corrected FTIR spectra corresponding to G0/G1, S and G2/M phases were modelled, the algorithm was able to retrieve each stage of proliferation with 82.3%, 71.8% and 84.4% accuracy respectively. Although the average accuracy yielded by the method was relatively low compared with what has previously been reported in the literature, these results emphasize the need to correct the data from physical distortions due to size and prove the principle that it is possible to create a method for identifying different events of the cell cycle based on the data that the FTIR spectroscopy provides, as well as using the scattering profile characteristic of each phase of development. Once the underlying biochemistry of proliferating Caki-2 cells were characterised by FTIR, the cells were treated with 5-Fluorouracil and paclitaxel, two widely used cytotoxic agents known to induce cellular damage at S or G2/M phase of the cell cycle respectively. The FTIR spectra collected were analysed via multivariate and bivariate techniques. Results demonstrated that, after 24 hours of treatment at the IC50 concentration of each drug, Caki-2 cells displayed spectral features consistent with early stages of apoptosis. These spectral characteristics did not appear to be linked either to the drug’s mode of action or the cell’s cycle phase. The cell’s proliferation stage was not the main classification trend among the drug-treated spectra; nevertheless, the cell cycle phase of each drug-treated population was successfully retrieved by an optimized model capable to classify such phases with an average accuracy of 77.98%. Altogether, this study offers a new perspective when analysing FTIR data from single cells as a function of the cell cycle and also when investigating the biochemical response of a cell line to a given anticancer agent.

Alzheimer Disease (AD) is a progressive neurodegenerative disorder characterized by memory loss and dementia. Both energy metabolism and the function of creatine kinase are known to be affected in Alzheimer diseased brain. With synchrotron FTIR microscopy, extensive deposits of crystalline creatine (Cr) had been discovered in TgCRND8 mouse brain tissue by previous students in our lab. In this thesis, regions of hippocampus and caudate of 5 pairs of transgenic mice and their non-transgenic littermate controls were mapped using Raman and IR microspectroscopy to find clues to Cr origin in transgenic mouse brain. Raman spectra obtained at higher spatial resolution (1-2 µm) were used for better delineation of the Cr crystalline deposits and their environs. These results indicate that Cr crystals were formed after snap-freezing and desiccation of brain tissue. Therefore, it can be speculated that Cr might be exist in solution form in vivo.

Alzheimer Disease (AD) is a progressive neurodegenerative disorder characterized by memory loss and dementia. Both energy metabolism and the function of creatine kinase are known to be affected in Alzheimer diseased brain. With synchrotron FTIR microscopy, extensive deposits of crystalline creatine (Cr) had been discovered in TgCRND8 mouse brain tissue by previous students in our lab. In this thesis, regions of hippocampus and caudate of 5 pairs of transgenic mice and their non-transgenic littermate controls were mapped using Raman and IR microspectroscopy to find clues to Cr origin in transgenic mouse brain. Raman spectra obtained at higher spatial resolution (1-2 µm) were used for better delineation of the Cr crystalline deposits and their environs. These results indicate that Cr crystals were formed after snap-freezing and desiccation of brain tissue. Therefore, it can be speculated that Cr might be exist in solution form in vivo.

Esta dissertação de mestrado aborda dois estudos que foram desenvolvidos utilizando a técnica de microscopia FTIR (micro-FTIR): a reatividade do grafeno funcionalizado e a eletroquímica in-situ com micro-FTIR para avaliação de reações redox. A reatividade e a distribuição de cargas em materiais 2D, mais especificamente em folhas individuais de grafeno, têm sido alvo de muita investigação na última década. No entanto, ainda não é conhecido como elas se apresentam em grafeno com grandes áreas, uma vez que a maioria dos estudos utilizam áreas muito pequenas (~μm2). Neste estudo, investigou-se experimentalmente como um eletrodo formado por uma única folha de grafeno se comporta quando sua estrutura é alterada por funcionalização covalente. Utilizando microespectroscopia na região do infravermelho, avaliou-se a funcionalização de grafeno com unidades de ácido benzoico no grafeno ancorados eletroquimicamente. O mapeamento químico mostrou que a distribuição espacial dessas unidades não ocorre uniformemente, ao invés disso, existem pontos específicos de ancoramento. Por fim, observou-se que a funcionalização ocorre mais intensamente na borda da folha de grafeno, alterando as propriedades óticas e eletroquímicas deste material, reduzindo o ganho ótico proporcionado pelos plásmons e aumentando a resistência de transferência heterogênea de elétrons. Para o segundo capítulo dessa dissertação, aplicou-se a microespectroscopia FTIR multiplex ao estudo da mudança química de um eletrodo de ouro modificado com azul da prússia (AP). Para isso, observou-se que uma etapa limitante era a confecção de um porta-amostra que reduzisse a camada de eletrólito ao mínimo de forma que a água não mais absorvesse a radiação de forma majoritária. Logo, foi possível o estudo vibracional de vários pontos da superfície do eletrodo, observando-se a influência do potencial aplicado, onde tem-se uma grande dependência dos sinais referentes ao estiramento C≡N do AP com a condição de potencial imprimida no eletrodo. / This Masters dissertation approaches two studies developed using the FTIR microspectroscopy technique (micro-FTIR): the activity of graphene functionalized and the in-situ electrochemistry with micro-FTIR for the evaluation of redox reactions. Reactivity and charge distribution in 2D materials, especially in single graphene sheets, have been the focus of extensive investigation during the last decade. However, there is still no knowledge on how large-area graphene behaves, since most of the studies utilize too small areas (~μm2). In this study, we aim to investigate experimentally how an electrode composed of only one single sheet of graphene behaves when its structure is changed by covalent functionalization. Using infrared microspectroscopy, the electrochemically induced covalent functionalization of graphene with benzoic acid unities was evaluated. The chemical mapping showed that the spatial distribution of these unities does not occur uniformly, instead, there are specific anchoring points. Lastly, it was observed that the functionalization occurs more intensely on the edges of the graphene sheet and that the covalent, affecting its optical and electrochemical properties, reducing the optical gain provided by the plasmons and increasing the resistance of heterogeneous electron transfer. In the second chapter of this dissertation, multiplex FTIR microspectroscopy was applied to the study of the chemical changes of a gold electrode modified with Prussian blue (PB). It was observed that the limiting step for this type of analysis was the building of a sample holder that reduces the electrolyte layer to the minimum in a way that water did not absorb the radiation in majority. Therefore, a vibrational study of several points of the electrode surface was possible evaluating the influence of the applied potential, where there is a dependence of the signals related to the C≡N stretching mode from PB on the potential condition applied to the electrode.

Fourier transform infrared (FTIR) microscopy has shown promise as an analytical tool for detecting changes in cells and tissues, such as those due to viral infection, apoptosis induction or malignancy. In many cases, diagnosis via FTIR microscopy can be undertaken on a timescale shorter than that required for other physical or histological techniques. In this work we have used FTIR microscopy to study Vero cells that have been infected with herpes simplex virus (type I) and adenovirus. We have studied cellular samples at various time intervals following exposure to the virus. Several spectral regions were identified that allow discrimination between infected and uninfected Vero cell samples at 24 hours post exposure to both HSV1 and adenovirus. Spectral features were also identified that could be used to discriminate infected cells within 2-6 hours after exposure to both viruses. FTIR microscopy is therefore a useful tool for following the kinetics of viral infection in the 2-24 hours time range, at least at the levels of infection used in this study. In a second type of study, FTIR microscopy was used to study apoptosis induction in acute lymphoblastic leukemia T-cells. Apoptosis was induced in T-cells in three different ways. We show that FTIR microscopy can be used to distinguish T-cells in the early stages of apoptosis from normal cells. We also provide data that may suggest that FTIR microscopy can distinguish cells that have undergone apoptosis via different pathways. For most of the FTIR microscopic studies on cellular samples we have focused on the collection of spectral data in the 1500-800 cm-1 region. Spectra were collected for control cells and variously treated cells. The two sets of cells were then analyzed statistically using: 1) pair-wise comparison, 2) logistic regression, 3) partial least square regression, 4) principle component fed linear discriminant analysis and 5) hierarchical cluster analysis. The statistical analyses rigorously quantify to what extent treated and untreated cells can be distinguished. Since different statistical methods give differing results for the same data, it is important the right statistical method should be applied. The basis for these differences is discussed.

Esta dissertação de mestrado aborda dois estudos que foram desenvolvidos utilizando a técnica de microscopia FTIR (micro-FTIR): a reatividade do grafeno funcionalizado e a eletroquímica in-situ com micro-FTIR para avaliação de reações redox. A reatividade e a distribuição de cargas em materiais 2D, mais especificamente em folhas individuais de grafeno, têm sido alvo de muita investigação na última década. No entanto, ainda não é conhecido como elas se apresentam em grafeno com grandes áreas, uma vez que a maioria dos estudos utilizam áreas muito pequenas (~μm2). Neste estudo, investigou-se experimentalmente como um eletrodo formado por uma única folha de grafeno se comporta quando sua estrutura é alterada por funcionalização covalente. Utilizando microespectroscopia na região do infravermelho, avaliou-se a funcionalização de grafeno com unidades de ácido benzoico no grafeno ancorados eletroquimicamente. O mapeamento químico mostrou que a distribuição espacial dessas unidades não ocorre uniformemente, ao invés disso, existem pontos específicos de ancoramento. Por fim, observou-se que a funcionalização ocorre mais intensamente na borda da folha de grafeno, alterando as propriedades óticas e eletroquímicas deste material, reduzindo o ganho ótico proporcionado pelos plásmons e aumentando a resistência de transferência heterogênea de elétrons. Para o segundo capítulo dessa dissertação, aplicou-se a microespectroscopia FTIR multiplex ao estudo da mudança química de um eletrodo de ouro modificado com azul da prússia (AP). Para isso, observou-se que uma etapa limitante era a confecção de um porta-amostra que reduzisse a camada de eletrólito ao mínimo de forma que a água não mais absorvesse a radiação de forma majoritária. Logo, foi possível o estudo vibracional de vários pontos da superfície do eletrodo, observando-se a influência do potencial aplicado, onde tem-se uma grande dependência dos sinais referentes ao estiramento C≡N do AP com a condição de potencial imprimida no eletrodo. / This Masters dissertation approaches two studies developed using the FTIR microspectroscopy technique (micro-FTIR): the activity of graphene functionalized and the in-situ electrochemistry with micro-FTIR for the evaluation of redox reactions. Reactivity and charge distribution in 2D materials, especially in single graphene sheets, have been the focus of extensive investigation during the last decade. However, there is still no knowledge on how large-area graphene behaves, since most of the studies utilize too small areas (~μm2). In this study, we aim to investigate experimentally how an electrode composed of only one single sheet of graphene behaves when its structure is changed by covalent functionalization. Using infrared microspectroscopy, the electrochemically induced covalent functionalization of graphene with benzoic acid unities was evaluated. The chemical mapping showed that the spatial distribution of these unities does not occur uniformly, instead, there are specific anchoring points. Lastly, it was observed that the functionalization occurs more intensely on the edges of the graphene sheet and that the covalent, affecting its optical and electrochemical properties, reducing the optical gain provided by the plasmons and increasing the resistance of heterogeneous electron transfer. In the second chapter of this dissertation, multiplex FTIR microspectroscopy was applied to the study of the chemical changes of a gold electrode modified with Prussian blue (PB). It was observed that the limiting step for this type of analysis was the building of a sample holder that reduces the electrolyte layer to the minimum in a way that water did not absorb the radiation in majority. Therefore, a vibrational study of several points of the electrode surface was possible evaluating the influence of the applied potential, where there is a dependence of the signals related to the C≡N stretching mode from PB on the potential condition applied to the electrode.

Disease- and drug-related bone disorders are rapidly increasing in the population. The drugs which are used for the treatment of neurodegenerative diseases and metabolic derangements, may have negative or positive effects on bone tissues. In the first study, the possible side-effects of Carbamazepine and epileptic seizures on bone structure and composition were investigated by FTIR and synchrotron-FTIR microspectroscopy, AFM and micro- and nano-hardness analysis. The effects on the blood parameters, bone turnover and vitamin D metabolism were also investigated by ELISA and western blot analysis. The current study provides the first report on differentiation of the effects of both epileptic seizures and AED therapy on bones. Besides Carbamazepine treatment, seizures also caused a decrease in the strength of bone. The biochemical data showed that both the epileptic and drug-treated groups decreased vitamin D levels by increasing the vitamin D catabolism enzyme / 25-hydroxyvitamin D-24-hydroxylase. In the second study, the possible pleiotropic (positive) effects of cholesterol lowering drug / Simvastatin on bones were investigated by ATR-FTIR spectroscopy. The current study provides the first report on dose-dependent effects of simvastatin on protein structure and lipid conformation of bones. ATR-FTIR studies showed that although both high and low dose simvastatin strengthen bones, low dose simvastatin treatment is much more effective in increasing bone strength. Neural network analysis revealed an increased antiparallel and aggregated beta sheet and random coil in the protein secondary structure of high dose group implying a protein denaturation. Moreover, high dose may induce lipid peroxidation which limit the pleiotropic effects of high dose treatment on bones. This study clearly demonstrated that using low dose simvastatin is safer and more effective for bone health than high dose simvastatin treatment.

Le stratum corneum (SC), couche supérieure de l’épiderme, est composé principalement de cornéocytes entourés d’une matrice lipidique. Cette structure particulière confère au SC son rôle de barrière et protège l’organisme de la perte en eau, de la pénétration de substances exogènes et de l’irradiation ultra-violette (UV). La matrice lipidique du SC est constituée de trois lipides majeurs : les céramides, les acides gras et le cholestérol organisés en phase cristalline. Cette matrice est la principale voie de pénétration des molécules exogènes à travers la peau. L’estimation de l’absorption cutanée pour l’analyse du risque des produits cosmétiques est basée sur les recommandations de l’Organisation de Coopération et de Développement Économiques (OCDE) qui prend en compte les propriétés physicochimiques des molécules i.e. Log Pow (lipophilie) et MW (masse moléculaire). En effet, l’OCDE considère une absorption de 100% pour une molécule ayant une MW inférieure à 500g/mol et un Log Pow compris en -1 et +4. En dehors de ces valeurs, l’OCDE applique une estimation de 10%. Hors, cette estimation est bien souvent loin de la réalité et a besoin d’être affinée. Notre travail s’est focalisé sur le développement d’un critère d’évaluation de la pénétration cutanée afin de moduler les données de l’OCDE par trois approches différentes : chromatographie d’affinité, spectroscopie de fluorescence et microspectroscopie infra-rouge à transformée de Fourier (FTIR) avec une source synchrotron. Etant donné que les propriétés barrières de la peau sont étroitement liées à la composition en céramides du SC, les méthodes développées en chromatographie d’affinité et spectroscopie de fluorescence se sont focalisées sur l’interaction céramide-molécules. Un critère prédictif de la pénétration percutanée a été défini avec chacune de ces méthodes :  et I. La troisième méthodologie a consisté à développer un autre critère (Sindex) par microspectroscopie FTIR avec une source synchrotron. La distribution cutanée des molécules a été suivie sur coupes microtomées de biopsies humaines. A partir de Sindex, une cartographie prédictive de la pénétration percutanée des molécules a été établie. Notre design expérimental comprenait des molécules (filtres UV, conservateurs, actifs cosmétiques) avec des Log Pow et MW variés (cf annexe 1). La pénétration cutanée de ces molécules a été étudiée avec une méthode de référence : cellules de Franz couplées à la chromatographie. Ces données de référence ont servi à valider les modèles et critères prédictifs développés. Ce travail a permis d’explorer de nouvelles pistes pour l’étude prédictive de la pénétration percutanée et de développer ainsi de nouveaux critères. Utilisés en complément des propriétés physicochimiques des molécules, ces nouveaux critères permettent d’affiner l’estimation de la pénétration cutanée de molécules exogènes pour l’analyse du risque. / The stratum corneum (SC) is the upper skin layer and due to its particular composition, corneocytes embedded in a lipidic matrix, it owns a role of barrier function and protects our body against water loss, penetration of exogenous molecules and UV irradiation. Its lipidic matrix is composed of three major lipids: fatty acids, cholesterol and ceramides, organised in liquid crystalline phase. This high cohesion creates cement between corneocytes. This cement is the principal pathway taken by the exogenous molecules to penetrate the skin. Percutaneous penetration estimation of cosmetic products is today based on the Organisation for Economic Co-operation and Development (OECD) recommendations, regarding molecules structural characteristics i.e. Log Pow (polarity) and MW (molecular weight). The OECD claims that 100% dermal absorption may be assumed if the exogenous molecule molecular mass is lower than 500 g/mol and Log Pow ranged between -1 and +4. Besides these values, a 10% coefficient is applied. This approach is sometimes far from reality. Our work focused on developing new evaluation criteria of percutaneous penetration from three different approaches: affinity chromatography, fluorescence spectroscopy and FTIR microspectroscopy with a synchrotron source in order to modulate OECD predictions. Considering that skin barrier properties are closely linked to ceramide composition and conformation within the SC, two methods were developed to study the interaction between ceramides and exogenous molecules by affinity chromatography and fluorescence spectroscopy. A predictive criterion of percutaneous penetration was developed from each of these methods:  and I. The third methodology consisted of developing a predictive criterion, Sindex, by FTIR microspectroscopy with a synchrotron source, on microtomized cuts of human skin biopsies. A predictive cartography was build from Sindex. Our experimental design included exogenous molecules (e.g. UV filters, preservatives, cosmetic actives) with various Log Pow and MW (cf annexe 1). Molecules skin penetration was studied with a Franz cell device coupled to HPLC analysis. These results served as reference data to validate our predictive models and criteria.This work permitted to set up new methods for predicting skin penetration of exogenous molecules and to develop complementary predictive criterion to Log Pow and MW. These new criterion will serve to modulate OECD predictions.

Naphthenic acids (NAs) are toxic organic acid compounds released during the caustic hot-water extraction of crude oil from oil sands in north-eastern Alberta, Canada. NAs subsequently accumulate in the large volume of oil sands process water (OSPW) produced daily by oil sands operations. The complexity of dealing with a mixture of over 200 individual NA compounds, combined with their acute aquatic toxicity and large volume of production has made them an emerging pollutant of concern for western Canada. The following thesis outlines a variety of experiments designed to determine the potential to use wetland plants to enhance the dissipation of NAs from OSPW (phytoremediation). <p>Investigations were carried out with three native emergent macrophyte species cattail (<i>Typha latifolia</i>), common reed (<i>Phragmites australis </i>subsp. <i>americanus</i>), and hard-stem bulrush (<i>Scirpus acutus</i>) to see if they enhanced the dissipation of NAs from a hydroponic system. Dissipation of NAs (at 30 mg L-1 and 60 mg L-1) was investigated with both a commercially available NA mixture as well as with a NA mixture extracted from the OSPW. Dissipation of NAs was also investigated under the different ionized forms of NAs (ionized, pH = 7.8; and non-ionized, pH = 5.0) to better elucidate the mechanisms of NA uptake and toxicity in plants. Phytotoxicity of NAs was investigated in hydroponic experiments through fresh weight gain and evapotranspiration was monitored throughout the experiment by water uptake. Commercially available NA mixture was more phytotoxic than oil sands NAs mixture. As well, NAs were found to be more phytotoxic in their non-ionized form therefore indicating that they may be taken up through an ion-trap‟ mechanism. However despite this, no significant dissipation of total NAs was observed from planted hydroponic systems. Nevertheless there was a significant change in the distribution (percent abundance) of individual NA families of certain size. These changes were related to the one- and two-ring NA compounds (Z = -2 and Z = -4). Despite not detecting any dissipation of total NAs from the systems, plants were able to reduce the toxicity of a NA system over 30 days by 45% as determined by Daphnia magna acute toxicity bioassays; a 11% greater reduction than unplanted systems.<p> Studies were also conducted investigating the microbial community inhabiting cattail roots exposed to NAs. It was observed that the rhizosphere community changed with NA exposure, with a general increase in potentially pathogenic bacteria and a decrease in bacteria previously found to be beneficial to plant growth. The observed microbial community change could be an indirect effect of the Phytotoxicity experienced by aquatic macrophytes exposed to NAs. Synchrotron-sourced, fourier transform microspectroscopy analysis of root cross sections revealed that there were significant physiological changes to those roots exposed to NAs. These changes were identified as being cell death in the plant root epidermis as well as a change in the chemistry of parenchyma cells in the root pith. It is not known if these changes are a direct effect of NAs to the plant or due to changes of the associated rhizosphere community in the roots or some combination of both these factors.

Naphthenic acids (NAs) are toxic organic acid compounds released during the caustic hot-water extraction of crude oil from oil sands in north-eastern Alberta, Canada. NAs subsequently accumulate in the large volume of oil sands process water (OSPW) produced daily by oil sands operations. The complexity of dealing with a mixture of over 200 individual NA compounds, combined with their acute aquatic toxicity and large volume of production has made them an emerging pollutant of concern for western Canada. The following thesis outlines a variety of experiments designed to determine the potential to use wetland plants to enhance the dissipation of NAs from OSPW (phytoremediation). <p>Investigations were carried out with three native emergent macrophyte species cattail (<i>Typha latifolia</i>), common reed (<i>Phragmites australis </i>subsp. <i>americanus</i>), and hard-stem bulrush (<i>Scirpus acutus</i>) to see if they enhanced the dissipation of NAs from a hydroponic system. Dissipation of NAs (at 30 mg L-1 and 60 mg L-1) was investigated with both a commercially available NA mixture as well as with a NA mixture extracted from the OSPW. Dissipation of NAs was also investigated under the different ionized forms of NAs (ionized, pH = 7.8; and non-ionized, pH = 5.0) to better elucidate the mechanisms of NA uptake and toxicity in plants. Phytotoxicity of NAs was investigated in hydroponic experiments through fresh weight gain and evapotranspiration was monitored throughout the experiment by water uptake. Commercially available NA mixture was more phytotoxic than oil sands NAs mixture. As well, NAs were found to be more phytotoxic in their non-ionized form therefore indicating that they may be taken up through an ion-trap‟ mechanism. However despite this, no significant dissipation of total NAs was observed from planted hydroponic systems. Nevertheless there was a significant change in the distribution (percent abundance) of individual NA families of certain size. These changes were related to the one- and two-ring NA compounds (Z = -2 and Z = -4). Despite not detecting any dissipation of total NAs from the systems, plants were able to reduce the toxicity of a NA system over 30 days by 45% as determined by Daphnia magna acute toxicity bioassays; a 11% greater reduction than unplanted systems.<p> Studies were also conducted investigating the microbial community inhabiting cattail roots exposed to NAs. It was observed that the rhizosphere community changed with NA exposure, with a general increase in potentially pathogenic bacteria and a decrease in bacteria previously found to be beneficial to plant growth. The observed microbial community change could be an indirect effect of the Phytotoxicity experienced by aquatic macrophytes exposed to NAs. Synchrotron-sourced, fourier transform microspectroscopy analysis of root cross sections revealed that there were significant physiological changes to those roots exposed to NAs. These changes were identified as being cell death in the plant root epidermis as well as a change in the chemistry of parenchyma cells in the root pith. It is not known if these changes are a direct effect of NAs to the plant or due to changes of the associated rhizosphere community in the roots or some combination of both these factors.