Bone marrow oedema is a term used to define the appearance of regions of low signal on T1 weighted and high signal on T2 weighted fat-suppressed magnetic resonance images. The potential association between bone marrow oedema and prognosis in pathologies such as osteoarthritis is becoming increasingly recognised through clinical studies. A limited number of clinical studies have linked bone marrow oedema to altered bone density or altered bone marrow perfusion. The principal aims of this study were to investigate these findings in vitro, using the equine forelimb. The presence of bone marrow oedema within the equine forelimb was initially confirmed by undertaking magnetic resonance imaging scans. Bone samples were selected from 10 animals, 5 exhibiting the presence of bone marrow oedema-type abnormalities (BMOA) at the distal metacarpal. Raman microspectroscopy was used to determine the chemical composition of bone and projection radiography to provide a measure of bone density. Micro computed x-ray tomography was undertaken on a subset of three bone samples exhibiting BMOA. A second component of the study utilised contrast enhanced magnetic resonance imaging to enable comparison of perfusion to bone marrow with and without evidence of oedema. A saline flushing agent containing Evan’s blue was used so that subsequent sectioning of the bone would enable visualisation of the distribution of contrast agent as part of a histological examination of the oedematous region. An initial observation was that the majority of bone marrow oedema that was observed in the distal metacarpal appeared in a consistent location, namely the postero-inferior aspect of the bone, corresponding to the point of greatest load thereby suggesting a potential relationship to forces upon the joint. The principal observations were that there appears to be increased bone volume densities in those bone samples with evidence of bone marrow oedema. The Raman microspectroscopy did not demonstrate any statistically significant differences in the chemical composition of bone. Hence the overall impression is that bone marrow oedema is associated with a greater volume of bone, although of similar maturity and composition. There was limited evidence of increased perfusion (suggestive of increased vascularity and / or hyperpermeability) in those samples with bone marrow oedema. This work suggests that these particular bone marrow oedema lesions are associated with bone changes and potentially vascular changes although the aetiology is currently unclear. Further work is needed to determine the clinical significance and prognosis associated with these particular lesions, and whether these findings can be replicated for bone marrow oedema demonstrated at other anatomical locations.

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.

Carcinome hépatocellulaire (CHC) est le sixième cancer et la deuxième cause de mortalité par cancer dans le monde. Dans la majorité des cas, le CHC se développe sur une maladie chronique associée à des étiologies variées telles que l'infection par le virus de l'hépatite B ou l’hépatite C, la consommation excessive d'alcool et des maladies métaboliques. Le développement des maladies chroniques du foie qui conduisent à la cirrhose puis au cancer induisent des modifications de la composition chimique des cellules et des tissus. En effet, la carcinogenèse hépatique est un processus en plusieurs étapes caractérisé par la progression de nodules de régénération, de nodules dysplasiques de bas grade puis de grade et enfin du CHC. Le traitement du CHC reste difficile et la transplantation du foie est la seule option thérapeutique curative à long terme. Le problème est qu'il n'y a pas de marqueur objectifs et quantifiables pour contrôler la qualité d’un greffon. Des biomarqueurs spécifiques marquant la progression du CHC font également défauts.Dans ce travail de thèse, nous avons évalué l’intérêt de la microspectroscopie infrarouge (IR) pour le diagnostic de la stéatose, qui est le facteur le plus important affectant la reprise de la fonction hépatique après greffe de foie. La microspectroscopie infrarouge permet de détecter de façon qualitative et quantitative les caractéristiques biochimiques liées aux différents constituants moléculaires présents dans l'échantillon biologique. Nos travaux ont montré que la progression de la stéatose hépatique correspond non seulement à l'accumulation de lipides, mais également à des changements spectaculaires dans la composition qualitative du tissu. En effet, le bas grade de stéatose présente une diminution de la teneur en glycogène et une augmentation concomitante de lipides par rapport au foie normal. La stéatose intermédiaire montre une augmentation de glycogène et des changements majeurs sont observés en ce qui concerne les lipides, avec une contribution significative des acides gras estérifiés, des chaînes de carbone allongées et des lipides insaturés. Ces caractéristiques sont encore plus prononcées dans les hauts degrés de stéatose. De plus, nous avons mis en évidence que des changements biochimiques majeurs se produisent dans la partie non-stéatosique du tissu malgré son aspect normal sur le plan histologique, ce qui suggère que l’organe dans son ensemble reflète le degré de la stéatose.La deuxième partie de la thèse est focalisée la carcinogenèse hépatique. Il s’agit d’un processus en plusieurs étapes qui se caractérise dans la plupart des foies cirrhotiques par la progression de nodules hyperplasiques de régénération vers des lésions précancéreuses telles que les nodules dysplasiques de bas grade puis de haut grade et enfin le CHC. Le diagnostic différentiel entre nodules dysplasiques en particulier de haut garde et CHC reste extrêmement difficile. Nous avons abordé le potentiel de la microspectroscopie IR pour le diagnostic des nodules cirrhotiques. Nous avons observé de profondes modifications de la composition biochimique du foie pathologique. En effet, des changements importants ont été détectés dans la composition des lipides, des protéines et des sucres mettant en évidence la reprogrammation métabolique dans la carcinogenèse. Les principaux changements ont été observés dans le domaine de fréquence 950-1480 cm-1 dans lequel plusieurs bandes permettaient la discrimination des nodules cirrhotiques, dysplasiques et tumoraux. Enfin, nous avons montré que le diagnostic peut être réalisé à l’aide d’un microscope de laboratoire qui peut être facilement mis en œuvre en milieu hospitalier. / Hepatocellular carcinoma (HCC) is the sixth most common neoplasm and the second most common cause of death in the world. Hepatocarcinogenesis is a multistep process characterized in patients with chronic liver diseases by a spectrum of hepatic nodules that mark the progression from regenerative nodules to dysplastic lesions followed by HCC. Liver transplantation remains the curative therapeutic option able to treat both the HCC and the underlying liver disease. The issue is that there is no objective and quantifiable marker for quality control of liver graft. Specific biomarkers of early stages of HCC are also an unmet need.In this study, we have evaluated the potential of infrared (IR) microspectroscopy for the diagnosis of steatosis, one of the most important factors affecting the liver allograft function. Vibrational microspectroscopy, such as Fourier transform infrared microspectroscopy (FTIR), allows detecting spectral characteristics associated with different molecular components present in the biological sample, both qualitatively and quantitatively. Our first working hypothesis was that the progression of liver steatosis corresponds not only to the accumulation of lipids but also to dramatic changes in the qualitative composition of tissue. Indeed, a lower grade of steatosis showed a decrease in glycogen content and concomitant increase in lipids in comparison with normal liver. Intermediate steatosis exhibited an increase in glycogen and major changes in lipids, with a significant contribution of esterified fatty acids with elongated carbon chains and unsaturated lipids, and these features were more pronounced in a high grade of steatosis. Furthermore, we have shown, that FTIR approach allows a systemic discrimination of morphological features, leading to a separate investigation of steatotic vesicles and the non-steatotic counterpart of the tissue. This highlighted the fact that dramatic biochemical changes occur in the non-steatotic part of the tissue also despite its normal histological aspect, suggesting that the whole tissue reflects the grade of steatosis. The second part of the thesis focused on hepatocarcinogenesis; a multistep process that is characterized in most cirrhotic livers by the progression from hyperplastic regenerative nodules to low grade dysplastic nodules (LGDN), high grade dysplastic nodules (HGDN) and finally small HCC which corresponds either to vaguely nodular well differentiated HCC so called early HCC or to distinctly nodular moderately differentiated hepatocellular carcinomas. Since the differential diagnosis between precancerous dysplastic nodules and early HCC remains extremely difficult, we addressed the potential of FTIR microspectroscopy for grading cirrhotic nodules. The study was focused on 39 surgical specimens including normal livers as controls, dysplastic nodules, early HCC and the progressed HCC. Profound alterations of the biochemical composition of the pathological liver were demonstrated by FTIR microspectroscopy. Indeed, dramatic changes were observed in lipids, proteins and sugars highlighting the metabolic reprogramming in carcinogenesis. The major changes were observed in the frequency domain 950-1480 cm-1 in which several bands allowed significant discrimination of cirrhotic nodules, dysplastic lesions and HCC. Finally, a significant discrimination between benign, dysplastic nodules and early HCC remained possible using a FTIR microscope equipped with a laboratory-based infrared source that can be easily implemented in hospital environment. In conclusion, our study positions FTIR microspectroscopy as a versatile and powerful approach for investigating liver diseases, such as steatosis, dysplastic lesions and cancer. Further studies on larger series of patients as well as on biopsies will allow confirming the clinical reliability of such spectral signatures. Therefore, we anticipate that FTIR microspectroscopy will open new avenue in clinical diagnosis.

The incidences of obesity and type 2 diabetes and their complications are increasing globally. The presence of elevated circulating free fatty acids has been associated with the initial dysfunction of pancreatic beta cells and microvascular endothelial cells followed later by their demise. The aim of this thesis was to investigate the mechanisms by which demise occurs, and how it may be prevented. Palmitate, a saturated fatty acid, caused cell death in both INS-1 beta cells and HCMec/D3 microvascular cells, whereas the unsaturated fatty acid oleic acid did not cause cell death, and also protected against palmitate-induced toxicity. Etomoxir, the mitochondrial CPT1 inhibitor did not rescue INS-1 or HCMec/D3 cells from palmitate-induced toxicity suggesting that palmitate-induced toxicity does not occur via entry into the mitochondria. Cells were exposed to 2-bromopalmitate, a non-metabolisable fatty acid used to reduce the pool of cytoplasmic CoA, to determine whether palmitate-induced toxicity might be mediated by its ability to be activated. Pre-incubation with 2-bromopalmitate in INS-1 cells significantly prevented palmitate-induced cell death. These data suggest that the activation of palmitate with CoA might mediate cell death. Cell cycle analysis found that neither oleic acid nor palmitate caused an increase or decrease in cell proliferation in both INS-1 and HCMec/D3 cells. The data suggest that the mechanism of oleic acid-induced cytoprotection might not be via a pro-proliferative mechanism. INS-1 cells were imaged using spontaneous Raman microspectroscopy after 24-hour exposure to esterified and non-esterified fatty acids. Uni- and multi-variate analysis and spectral decomposition were carried out using a methodology optimised and validated which is presented in this thesis. The aim was to quantify changes, if any, in lipid disposition: distribution, intensity (as a measure of concentration) and composition after exogenous exposure to these fatty acids. Exposure to 0.125 mM palmitate showed a significant decrease in the percentage of lipid within the cells and a corresponding increase in the intensity of this lipid. This suggests that palmitate, alone, might be shuttled into lipid droplets. This was not observed when the cells were exposed to oleic acid, whereby an increase in the intensity of lipid was observed even though no significant change was observed in the percentage of lipid within the cells. When palmitate and oleic acid were combined, the composition of the lipid droplets changed such that the levels of palmitate decreased and the levels of oleic acid increased. These data suggest that oleic acid does not shuttle palmitate into lipid droplets. These data do not support the hypothesis that oleic acid protects against palmitate-induced cytotoxicity by shuttling palmitate into lipid droplets. The methyl esters of palmitate and oleic acid were employed to determine whether they would affect lipid disposition. No change in lipid distribution or intensity was observed when the cells were exposed to these fatty acids, validating the requirement for the free carboxyl oxygen for the covalent binding to glycerol for the formation of lipid droplets. These data also suggest that INS-1 cells cannot de-esterify esterified fatty acids.

Miniaturization of devices to study chemical interactions and processes in liquid samples has led to the emergence of microfluidics and construction of lab-on-a-chip systems. Present work was devoted to implementation, development and testing of microfluidic systems with detection by confocal Raman microscopy and surface enhanced Raman scattering under the conditions of training department. Several options of performing standard macroscopic measurements in microscopic scales were explored. A method for measuring thermal stability of biopolymers in microsystems with contactless detection of temperature has been designed and tested. Furthermore, possibilites for studying the SERS effect within microfluidic channels were explored. It was demonstrated that the microfluidic chips provide promising opportunity to study hydrodynamics of liquids at microscopic level and chemical reactions and kinetics.

Biological tissues were studied with synchrotron infrared (IR) microspectroscopy, a technique that allows the spatially resolved determination and mapping of multiple components in situ at high spatial resolution. The first project involved studying brain tissue from TgCRND8 mice, a transgenic model of Alzheimer’s disease (AD). AD is the main cause of dementia in the ageing population, marked by the deposition of plaques composed of the Aβ peptide. Dense-cored and diffuse plaques were IR mapped and the results correlated with histochemistry and immunostaining. Spectral analysis confirmed that congophilic plaque cores were composed of highly aggregated protein in a β-sheet conformation. The amide I maximum of plaque cores was 1623 cm-1; there was no evidence of the high frequency (1680-1690 cm-1) peak seen in in vitro Aβ fibrils and attributed to anti-parallel β-sheet. A significant elevation in phospholipids was found around dense-cored plaques in TgCRND8 mice ranging in age from 5 to 21 months. This was due to an increase in cellular membranes from dystrophic neurites and glial cells around the core, but could also contribute to Aβ aggregation through the interaction of newly secreted Aβ with phospholipids. In contrast, diffuse plaques were not associated with infrared detectable changes in protein secondary structure or relative concentrations of other tissue components. In addition, focally elevated deposits of creatine, a molecule with a crucial role in energy metabolism, were discovered in AD brain tissue with IR microspectroscopy. The creatine deposits may be a previously undiscovered disease marker. A second project was part of a larger Natural Sciences and Engineering Research Council Collaborative Health Research Project (NSERC-CHRP) to test the hypothesis that treatment with anti-oxidants, L-2-oxo-thiazolidine-4-carboxylate (OTC) and quercetin, following spinal surgery may reduce oxidative stress, inflammation, and scarring. The effect of OTC and quercetin on scar tissue formation was evaluated in rats that had undergone laminectomy. Synchrotron IR microspectroscopy data were collected on scar tissue from OTC, quercetin and saline (control) treated animals, sacrificed at 3 and 21 days post-surgery. Spectral differences could be correlated with the stages of wound healing. / May 2007

Esta tesis describe el diseño, la fabricación y la caracterización óptica de sistemas plasmónicos resonantes capaces de confinar y aumentar campos de luz en la escala manométrica. En primer lugar, se utilizaron modelos numéricos 3D para diseñar diferentes geometras de nanoestructuras plasmónicas acopladas, a través del cálculo de la respuesta óptica de su campo lejano y cercano. Sobre la base de estas simulaciones se fabricaron las nanoestructuras por litografía de haz electrónico. Se puso especial énfasis en el aumento de la resolución y la optimización de la reproducibilidad de parámetros críticos como la forma de las partículas y el gap entre ellas. Por último, se empleó espectroscopía de campo lejano combinada con espectroscopía de luminiscencia inducida por dos fotones (TPL) para sondar la respuesta óptica local de las geometrías optimizadas. Hemos centrado nuestra atención en diferentes tipos de estructuras metálicas: dímeros, antenas con gap, conjuntos finitos de partículas en cadenas y en forma de estrella. Los dímeros tienen una fuerte amplificación del campo en su gap nanométrico por el acoplamiento en campo cercano de sus resonancias plasmonicas dipolares. Análogamente, antenas con gap, formadas por dos barras de oro adyacentes que soportan resonancias multipolares, pueden acoplar de manera eficiente la luz y concentrarla en volúmenes pequeños. Se ha demostrado que cadenas finitas de partículas son buenos candidatos para guiar la luz a través de secciones transversales por debajo de la longitud de onda y aquí demostramos que también se pueden utilizar como nanolentes capaces de concentrar la luz en su extremo. La distribución del campo cercano en conjuntos de partículas de oro en forma de estrella presenta una fuerte dependencia con la polarización del campo incidente que puede ser explotada para dirigirse dinámicamente a nano-objetos. La espectroscopía de campo lejano de conjuntos de dímeros y de cadenas finitas de partculas se comparó con la espectroscopía de TPL. Nuestro principal resultado es mostrar que la TPL es preferentemente sensible a los campos locales, permitiendo evaluar características espectrosc ópicas que no podrían resolverse de otro modo. A fin de superar las limitaciones de las medidas de conjuntos, en una segunda etapa se dedicó un considerable esfuerzo a construir y optimizar un montaje óptico para medir la señal de TPL de estructuras únicas. El uso de la micro-espectroscopía de TPL permitió obtener mapas espectrales de los modos de antenas aisladas con resolución espacial. Como se predijo mediante cálculos, hemos sido capaces de visualizar directamente, en la resonancia, la señal de TPL amplificada dentro del gap. Nuestros resultados muestran cómo las medidas de TPL pueden compararse directamente con la distribución de la cuarta potencia del campo local calculado. Mediante el análisis de la evolución de la señal de TPL en función de la longitud de onda incidente en el gap y en las extremidades de la antena tenemos más conocimiento sobre el mecanismo físico detrás de la resonancia de la antena. Finalmente, la microscopía de TPL se utilizó para sondar el campo cercano para diferentes orientaciones de la polarización lineal incidente sobre los conjuntos de partículas en forma de estrella. Se demuestra que, a diferencia del espectro de dispersión, la distribución de TPL en la estructura depende drásticamente del estado de polarización incidente. Nuestro estudio aporta una contribución significativa al campo de la óptica de plasmones, proponiendo nuevas geometrías para confinar de manera eficiente los campos ópticos a la escala nanometrica, aportando un profundo conocimiento sobre el uso de micro-espectroscopa de TPL como sonda óptica local. Nuestros resultados tendrán importancia en aplicaciones tales como espectroscopía mejorada, biosensores y la interacción luz-materia, donde se necesita evaluar el campo experimentado por una pequeña cantidad de materia cercana a la nanoestructura. / This thesis describes the design, fabrication and the optical characterization of plasmon-resonant systems able to confine and enhance light fields down to the sub-wavelength scale. Extensive 3D numerical modeling was first used to design different geometries of coupled plasmonic nanostructures through the calculation of their far-field and near-field optical response. On the basis of simulations, the nanostructures were fabricated by e-beam lithography and thin film deposition. Special efforts were devoted to increasing the resolution and optimizing the reproducibility of critical parameters such as particle shape and interparticle gaps. Finally, far-field spectroscopy combined with two-photon induced luminescence (TPL) spectroscopy was used to probe the local optical response of the optimized architectures. We focused our attention on different families of structures: metal dimers, bar antennas, finite chains of nanoparticles and star-like particle arrangements. Particle dimers feature strong field enhancements in their sub-wavelength gap due to near-field coupling of their dipolar localized plasmon resonances. Based on the same physics, gap antennas, formed by two adjacent gold bars supporting multipolar resonances can efficiently couple to propagating light and concentrate it into tiny volumes. While finite particle chains were previously shown by other authors to be good candidates to guide light through subwavelength cross-sections, we show here that they can also be used as efficient nanolenses able to concentrate light at their extremity. Finally, the near-field distribution in star-like arrangements of gold nanoparticles exhibits a strong dependence with the incident field polarization which can be exploited for dynamical optical addressing of nano-objects. We have compared the far field spectroscopy of large ensembles of dimers and finite chains to TPL spectroscopy. Our main result is to show that TPL is preferentially sensitive to local fields and that it enables the assessment of spectroscopic features which cannot be resolved otherwise. In order to overcome the limitations of measurements on large ensembles a considerable effort was dedicated to mounting and optimizing an optical set-up enabling TPL measurement of single structures. Using the developed TPL micro-spectroscopy, spatially resolved spectral mode mapping on single resonant gap-antennas was achieved. As predicted by calculations, we were able to directly visualize at resonance the strongly enhanced TPL signal within the gap. Our results show how TPL scans can be directly compared with the convoluted distribution of the fourth power of the calculated local mode field. By monitoring the evolution with the incident wavelength of the TPL signal within the gap and at the antenna extremities we got further insight in the physical mechanism behind the buildup of the antenna’s resonance. Finally, TPL microscopy was used to probe the local fields under different orientations of the incident linear polarization near star-like arrangement of gold disks. It is shown that, unlike the scattering spectrum, the TPL distribution over the structure is found to depend drastically on the incident polarization state. Our study brings a significant contribution to the field of Plasmon optics by proposing novel geometries able to efficiently confine optical fields down to the nanometric scale, but also by providing deep insight into the use of TPL microspectroscopy to probe their local optical response. Our findings are foreseen to be important in applications such as enhanced spectroscopy, bio-sensing and enhanced light-matter interaction, where one needs to assess the actual field experienced by small amounts of matter.

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.

Mid-infrared (MIR) spectroscopy has been recognized as an important analytical technique, and is widely applied for qualitative and quantitative analysis of materials with an increasing interest in addressing complex organic or biologic constituents. In the presented thesis, (a) the fundamental principles for IR spectroscopic applications via in vivo catheters in combination with multivariate data analysis technique were developed, and (b) the combination with a second analytical technique ¨C scanning electrochemical microscopy (SECM) - for enhancing the information obtained at complex or frequently changing matrices was demonstrated. The first part of this thesis focused on the combination of different MIR measurment techniques with specific focus on evanescent field absorption spectroscopy along with multivariate data analysis methods, for the discrimination of atherosclerotic and normal rabbit aorta tissues. Atherosclerotic and normal rabbit aorta tissues are characterized by marked differences in chemical composition governed by their water, lipid, and protein content. Strongly overlapping infrared absorption features of the different constituents and the complexity of the tissue matrix render the direct evaluation of molecular spectroscopic characteristics obtained from IR measurements challenging for classification. We have successfully applied multivariate data analysis and classification techniques based on principal component analysis (PCA), partial least squares regression (PLS), and linear discriminant analysis (LDA) to IR spectroscopic data obtained by infrared attenuated total reflectance (IR-ATR) measurements, reflection IR microscopy, and a recently developed IR-ATR catheter prototype for future in vivo diagnostic applications. Training and test data were collected ex vivo at atherosclerotic and normal rabbit aorta samples. The successful classification results at atherosclerotic and normal aorta samples utilizing the developed data evaluation routines reveals the potential of IR spectroscopy combined with multivariate classification strategies for in vitro, and ¨C in future - in vivo applications. The second part of this thesis aimed at the development of a novel multifunctional analytical platform by combining SECM with single-bounce IR-ATR spectroscopy for in situ studies of electrochemically active or electrochemically induced processes at the IR waveguide surface via simultaneous evanescent field absorption spectroscopy. The utility of the developed SECM-IR-ATR platform was demonstrated by spectroscopically monitoring microstructured polymer depositions induced via feedback mode SECM experiments using a 25μm Pt disk ultramicroelectrode (UME). The surface of a ZnSe ATR crystal was coated with a thin layer of 2,5-di-(2-thienyl)-pyrrole (SNS), which was then polymerized in a Ru(bpy) ₃ ² ⁺-mediated feedback mode SECM experiment. The polymerization reaction was simultaneously spectroscopically monitored by recording the absorption intensity changes of specific IR bands characteristic for SNS, thereby providing information on the polymerization progress, mechanism, and level of surface modification. Furthermore, a novel current-independent approach mechanism for positioning the UME in aqueous electrolyte solution was demonstrated by monitoring IR absorption changes of borosilicate glass (BSG) shielding the UME, and of water within the penetration depth of the evanescent field.

Biological tissues were studied with synchrotron infrared (IR) microspectroscopy, a technique that allows the spatially resolved determination and mapping of multiple components in situ at high spatial resolution. The first project involved studying brain tissue from TgCRND8 mice, a transgenic model of Alzheimer’s disease (AD). AD is the main cause of dementia in the ageing population, marked by the deposition of plaques composed of the Aβ peptide. Dense-cored and diffuse plaques were IR mapped and the results correlated with histochemistry and immunostaining. Spectral analysis confirmed that congophilic plaque cores were composed of highly aggregated protein in a β-sheet conformation. The amide I maximum of plaque cores was 1623 cm-1; there was no evidence of the high frequency (1680-1690 cm-1) peak seen in in vitro Aβ fibrils and attributed to anti-parallel β-sheet. A significant elevation in phospholipids was found around dense-cored plaques in TgCRND8 mice ranging in age from 5 to 21 months. This was due to an increase in cellular membranes from dystrophic neurites and glial cells around the core, but could also contribute to Aβ aggregation through the interaction of newly secreted Aβ with phospholipids. In contrast, diffuse plaques were not associated with infrared detectable changes in protein secondary structure or relative concentrations of other tissue components. In addition, focally elevated deposits of creatine, a molecule with a crucial role in energy metabolism, were discovered in AD brain tissue with IR microspectroscopy. The creatine deposits may be a previously undiscovered disease marker. A second project was part of a larger Natural Sciences and Engineering Research Council Collaborative Health Research Project (NSERC-CHRP) to test the hypothesis that treatment with anti-oxidants, L-2-oxo-thiazolidine-4-carboxylate (OTC) and quercetin, following spinal surgery may reduce oxidative stress, inflammation, and scarring. The effect of OTC and quercetin on scar tissue formation was evaluated in rats that had undergone laminectomy. Synchrotron IR microspectroscopy data were collected on scar tissue from OTC, quercetin and saline (control) treated animals, sacrificed at 3 and 21 days post-surgery. Spectral differences could be correlated with the stages of wound healing.