No description available.

The genome sequencing programs have identified hundreds of thousands of genetic and proteomic targets for which there are presently no ascribed functions. The challenge for researchers now is to characterize them, as well as identify and characterize their natural variants. Historically, this has meant studying each individual target separately. However, due to the recent development of multi-analyte microarray devices, these characterizations can be performed in a combinatorial manner in which a single experiment provides information on thousands of targets at a time. In the past decade, microarray technology has settled in on two major designs. The first entails spotting individual receptor types onto a functionalized glass substrate. This is a simple and inexpensive process; however, due to the limited resolution of the mechanical devices used to do the spotting, the densities of these arrays are relatively low. Moreover, receptor preparation requires substantial time and effort. The second variety of microarray uses photolithographic techniques adapted from the semi-conductor industry to chemically synthesize the receptor elements in situ on the sensing surface. Because lithographic patterning is spatially very precise, these arrays achieve very high densities, with as many as one million features per square centimeter. Although these arrays obviate the necessity for laborious "off chip" probe preparation, they are expensive to produce and are limited to two types of receptors (oligonucleotides and peptides). This dissertation presents the development work performed on a hydrogel-based biosensor platform which provides a high density and low cost alternative to the two aforementioned designs. The array features are fabricated lithographically from a liquid pre-polymer doped with biologically active sensing elements at sizes as small as 50[micrometer]. Each of the feature types is uniquely shaped, which enables the features to be mass-produced in batches, pooled together and then assembled into randomly ordered arrays using highly-parallelized self-assembly techniques. The three-dimensional hydrogel features accommodate a wide variety of sensing elements, such as enzymes, antibodies and cells, which cannot be deployed using the traditional designs. This dissertation presents methods developed to integrate cellular and oligonucleotide sensing elements into the hydrogel features which preserve their biological activity and optimize the sensor's performance. / text

No description available.

A Toxicologia tem desempenhado um importante papel na identificação de efeitos nocivos à população, gerando subsídios para a tomada de decisões na prática clínica, auxiliando desta forma no bom prognóstico de pacientes intoxicados. De acordo com a Pan American Health Organization, o sucesso em qualquer intervenção em saúde somente pode ser obtido com a criação e manutenção de um banco de dados confiável, que seja capaz de predizer as diversas particularidades das intoxicações, como a população-alvo e suas suscetibilidades. Assim, recomenda-se que médicos, especialistas, legisladores e administradores em saúde adotem em sua rotina uma coleta de dados sistêmica e integrada para o mapeamento e caracterização das intoxicações. Neste cenário, técnicas de análises multivariadas poderiam ser empregadas para evidenciar possíveis intercorrelações; entretanto, seu uso ainda não é comum na toxicologia clínica. Neste trabalho foram identificados e quantificados agentes exógenos em amostras biológicas (sangue e urina) provenientes do Centro de Controle de Intoxicações da cidade de São Paulo, correlacionando os dados obtidos dessas análises com o perfil clínico e prognóstico dos pacientes. Fármacos benzodiazepínicos, antidepressivos, anticonvulsivantes, paracetamol, drogas de abuso e praguicidas foram selecionados de acordo com a incidência reportada por esse centro no período de 2013 a 2014. Do total de amostras analisadas (n = 320), 192 foram positivas para alguma substância, sendo 101 positivas para etanol e 131 positivas para as demais substâncias. Os dados obtidos foram submetidos à análise de correspondência múltipla e análise hierárquica de cluster. A partir da análise multivariada foi possível agrupar os indivíduos em 3 clusters, o que correspondeu a 66,5% do total de informações. No primeiro eixo houve a separação dos pacientes do gênero feminino, que se intoxicaram ou foram expostos a medicamentos e drogas de abuso, por tentativa de suicídio, dos pacientes do gênero masculino, de idade entre 30 a 39 anos, que se intoxicaram com drogas de abuso. No segundo eixo fatorial foram agrupados os pacientes que se intoxicaram com etanol isoladamente, juntamente com pacientes que se intoxicaram com diazepam. Este trabalho contribuiu para o mapeamento dos casos de intoxicação atendidos pelo CCI-SP e foi um estudo inicial para a criação de um banco de dados que poderá ser alimentado constantemente e assim, oferecer ao sistema de toxicovigilância uma base para políticas educativas. / Toxicology has played an important role in the identification of harmful effects to the population, generating subsidies for decision making in clinical practice, helping in this way the good prognosis of acutely intoxicated patients. According to the Pan American Health Organization, success in any health intervention can only be achieved by creating and maintaining a reliable database that is capable of predicting the various characteristics of intoxications, such as the target population and their susceptibilities. Thus, it is recommended that doctors, specialists, legislators and health administrators adopt in their routine a systemic and integrated data collection for the mapping and characterization of intoxications. In this scenario, multivariate analysis techniques could be used to evidence possible intercorrelations; however, its use is not yet common in clinical toxicology. In this work, were identified and quantified exogenous agents in biological samples (blood and urine) from the Poison Control Center São Paulo city, correlating the data obtained from these analyzes with the clinical and prognostic profile of the patients. Benzodiazepines, antidepressants, anticonvulsants, acetaminophen, drugs of abuse and pesticides were selected according to the incidence reported by this center in the period from 2013 to 2014. Of the total number of samples analyzed (n = 320), 192 samples have shown to be positive for some of the analytes, from these 100 were positive for ethanol and 131 positive for other substances. The data were submitted to multiple correspondence analysis and hierarchical cluster analysis. From the multivariate analysis it was possible to group the individuals into 3 clusters, which corresponded to 66.5% of the total information. In the first axis, the patients were separated from the female gender, who were intoxicated or were exposed to drugs and suicide attempt of the male patients, aged between 30 and 39 years, who became intoxicated with drugs of abuse. In the second factorial axis were grouped the patients who were intoxicated with ethanol, together with patients who became intoxicated with diazepam. This work contributed to the mapping of intoxication cases attended by the CCI-SP and was a initial study for the creation of a database that could be fed constantly and thus provide the toxicovigilance system with a basis for educational policies.

A Toxicologia tem desempenhado um importante papel na identificação de efeitos nocivos à população, gerando subsídios para a tomada de decisões na prática clínica, auxiliando desta forma no bom prognóstico de pacientes intoxicados. De acordo com a Pan American Health Organization, o sucesso em qualquer intervenção em saúde somente pode ser obtido com a criação e manutenção de um banco de dados confiável, que seja capaz de predizer as diversas particularidades das intoxicações, como a população-alvo e suas suscetibilidades. Assim, recomenda-se que médicos, especialistas, legisladores e administradores em saúde adotem em sua rotina uma coleta de dados sistêmica e integrada para o mapeamento e caracterização das intoxicações. Neste cenário, técnicas de análises multivariadas poderiam ser empregadas para evidenciar possíveis intercorrelações; entretanto, seu uso ainda não é comum na toxicologia clínica. Neste trabalho foram identificados e quantificados agentes exógenos em amostras biológicas (sangue e urina) provenientes do Centro de Controle de Intoxicações da cidade de São Paulo, correlacionando os dados obtidos dessas análises com o perfil clínico e prognóstico dos pacientes. Fármacos benzodiazepínicos, antidepressivos, anticonvulsivantes, paracetamol, drogas de abuso e praguicidas foram selecionados de acordo com a incidência reportada por esse centro no período de 2013 a 2014. Do total de amostras analisadas (n = 320), 192 foram positivas para alguma substância, sendo 101 positivas para etanol e 131 positivas para as demais substâncias. Os dados obtidos foram submetidos à análise de correspondência múltipla e análise hierárquica de cluster. A partir da análise multivariada foi possível agrupar os indivíduos em 3 clusters, o que correspondeu a 66,5% do total de informações. No primeiro eixo houve a separação dos pacientes do gênero feminino, que se intoxicaram ou foram expostos a medicamentos e drogas de abuso, por tentativa de suicídio, dos pacientes do gênero masculino, de idade entre 30 a 39 anos, que se intoxicaram com drogas de abuso. No segundo eixo fatorial foram agrupados os pacientes que se intoxicaram com etanol isoladamente, juntamente com pacientes que se intoxicaram com diazepam. Este trabalho contribuiu para o mapeamento dos casos de intoxicação atendidos pelo CCI-SP e foi um estudo inicial para a criação de um banco de dados que poderá ser alimentado constantemente e assim, oferecer ao sistema de toxicovigilância uma base para políticas educativas. / Toxicology has played an important role in the identification of harmful effects to the population, generating subsidies for decision making in clinical practice, helping in this way the good prognosis of acutely intoxicated patients. According to the Pan American Health Organization, success in any health intervention can only be achieved by creating and maintaining a reliable database that is capable of predicting the various characteristics of intoxications, such as the target population and their susceptibilities. Thus, it is recommended that doctors, specialists, legislators and health administrators adopt in their routine a systemic and integrated data collection for the mapping and characterization of intoxications. In this scenario, multivariate analysis techniques could be used to evidence possible intercorrelations; however, its use is not yet common in clinical toxicology. In this work, were identified and quantified exogenous agents in biological samples (blood and urine) from the Poison Control Center São Paulo city, correlating the data obtained from these analyzes with the clinical and prognostic profile of the patients. Benzodiazepines, antidepressants, anticonvulsants, acetaminophen, drugs of abuse and pesticides were selected according to the incidence reported by this center in the period from 2013 to 2014. Of the total number of samples analyzed (n = 320), 192 samples have shown to be positive for some of the analytes, from these 100 were positive for ethanol and 131 positive for other substances. The data were submitted to multiple correspondence analysis and hierarchical cluster analysis. From the multivariate analysis it was possible to group the individuals into 3 clusters, which corresponded to 66.5% of the total information. In the first axis, the patients were separated from the female gender, who were intoxicated or were exposed to drugs and suicide attempt of the male patients, aged between 30 and 39 years, who became intoxicated with drugs of abuse. In the second factorial axis were grouped the patients who were intoxicated with ethanol, together with patients who became intoxicated with diazepam. This work contributed to the mapping of intoxication cases attended by the CCI-SP and was a initial study for the creation of a database that could be fed constantly and thus provide the toxicovigilance system with a basis for educational policies.

The development of a chip-based sensor array composed of individually addressable polystyrene-polyethylene glycol and agarose microspheres has been demonstrated. The microspheres are selectively arranged in micromachined cavities localized on silicon wafers. These cavities are created with an anisotropic etch and serve as miniaturized reaction vessels and analysis chambers. The cavities possess pyramidal pit shapes with trans-wafer openings that allow for both fluid flow through the microreactors/analysis chambers as well optical access to the chemically sensitive microspheres. Identification and quantification of analytes occurs via colorimetric and fluorescence changes to receptor and indicator molecules that are covalently attached to termination sites on the polymeric microspheres. Spectral data is extracted from the array efficiently using a charge-coupled device (CCD) allowing for the near-real-time digital analysis of complex fluids. The power and utility of this new microbead array detection methodology is demonstrated here for the analysis of complex fluids containing a variety of important classes of analytes including acids, bases, metal cations, sugars and antibody reagents. The application of artificial neural network analyses to the microbead array is demonstrated in the context of pH measurements. To assess the utility of the analysis and gain an understanding of the molecular level design of the sensor, parameters such as the choice of the indicator dyes, array size, data pre-processing techniques, as well as different network types and architectures were evaluated. Additionally, the development of miniaturized chromatographic systems localized within individual polymer microspheres and their incorporation into an array is reported. The integrated chromatographic and detection concept is based on the creation of distinct functional layers within the microspheres. Such beads have been incorporated into the array platform and used for speciation and concentration determination of aqueous metal cation solutions. / text

Résumé : Malgré le nombre croissant de capteurs dans les domaines de la chimie et la biologie, il reste encore à étudier en profondeur la complexité des interactions entre les différentes molécules présentes lors d’une détection à l’interface solide-liquide. Dans ce cadre, il est de tout intérêt de croiser différentes méthodes de détection afin d’obtenir des informations complémentaires. Le principal objectif de cette étude est de dimensionner, fabriquer et caractériser un détecteur optique intégré sur verre basé sur la résonance plasmonique de surface, destiné à terme à être combiné avec d’autres techniques de détection, dont un microcalorimètre. La résonance plasmonique de surface est une technique reconnue pour sa sensibilité adaptée à la détection de surface, qui a l’avantage d’être sans marquage et permet de fournir un suivi en temps réel de la cinétique d’une réaction. L’avantage principal de ce capteur est qu’il a été dimensionné pour une large gamme d’indice de réfraction de l’analyte, allant de 1,33 à 1,48. Ces valeurs correspondent à la plupart des entités biologiques associées à leurs couches d’accroche dont les matrices de polymères, présentés dans ce travail. Étant donné que beaucoup d’études biologiques nécessitent la comparaison de la mesure à une référence ou à une autre mesure, le second objectif du projet est d’étudier le potentiel du système SPR intégré sur verre pour la détection multi-analyte. Les trois premiers chapitres se concentrent sur l’objectif principal du projet. Le dimensionnement du dispositif est ainsi présenté, basé sur deux modélisations différentes, associées à plusieurs outils de calcul analytique et numérique. La première modélisation, basée sur l’approximation des interactions faibles, permet d’obtenir la plupart des informations nécessaires au dimensionnement du dispositif. La seconde modélisation, sans approximation, permet de valider le premier modèle approché et de compléter et affiner le dimensionnement. Le procédé de fabrication de la puce optique sur verre est ensuite décrit, ainsi que les instruments et protocoles de caractérisation. Un dispositif est obtenu présentant des sensibilités volumiques entre 1000 nm/RIU et 6000 nm/RIU suivant l’indice de réfraction de l’analyte. L’intégration 3D du guide grâce à son enterrage sélectif dans le verre confère au dispositif une grande compacité, le rendant adapté à la cointégration avec un microcalorimètre en particulier. Le dernier chapitre de la thèse présente l’étude de plusieurs techniques de multiplexage spectral adaptées à un système SPR intégré, exploitant en particulier la technologie sur verre. L’objectif est de fournir au moins deux détections simultanées. Dans ce cadre, plusieurs solutions sont proposées et les dispositifs associés sont dimensionnés, fabriqués et testés. / Abstract : In spite of the growing number of available biosensors, many biochemical reactions and biological components have not yet been studied in detail. Among them, some require the combination of several detection techniques in order to retrieve enough information to characterize them fully. An unknown reaction based, for example, on DNA hybridization could be characterized with an electrochemical sensor, a mechanical sensor and an optical sensor, each giving a different type of information. The main objective of the work presented here is to design, fabricate and characterize a flexible integrated optical biosensor based on surface plasmon resonance, intended to be then combined with other detection techniques, and in particular, a microcalorimeter. Surface Plasmon Resonance (SPR) is well known to be a sensitive technique for surface-based biochemical detection. It has the advantage to be an unlabeled method and provides real time information on the kinetics of a reaction. The flexibility of the proposed SPR biosensor comes from the fact that it is designed for a large range of analyte refractive indices, from 1.33 to 1.48. These values are suitable for most biological entities and their ligand layers, and especially for hydrophilic polymer matrices used to trap DNA or protein entities and introduced in this work. As several biochemical studies require the simultaneous comparison of measurements to a reference or to another measurement, the second objective of this project is to study the potential of multi-analyte detection in an integrated SPR device on glass. The first three chapters of the thesis are focused on the main objective. The design based on two different models is presented, at the same time as the related simulation tools. The first model is based on the weak coupling approximation and permits to obtain most of the information for the device’s design. The second model, having no approximation, is used to validate the first model and complete and refine the design. The fabrication process of the glass chip is then introduced, as well as the characterization instruments and protocols. A device is obtained, with a volumetric sensitivity between 1000 nm/RIU and 6000 nm/RIU depending on the analyte refractive index. The 3D integration of the waveguide within the glass substrate makes the device extremely compact and adapted to the integration with the microcalorimeter in particular. The last chapter describes the study of several spectral multiplexing techniques adapted to an integrated SPR system using the glass technology. The goal is to provide at least two simultaneous measurements. Several detection techniques are examined and the related devices are designed, fabricated and characterized.

Malgré le nombre croissant de capteurs dans les domaines de la chimie et la biologie, de nombreuses réactions n’ont pas encore été correctement identifiées et étudiées. C’est entre autres le cas des interactions intermoléculaires à l’interface liquide/solide trouvées dans les chimies de surface utilisées pour les méthodes de diagnostics médicaux et l’identification de divers processus biologiques. Afin de correctement comprendre les mécanismes en jeux, il est important de pouvoir croiser différentes méthodes de détection pour obtenir des informations complémentaires.MuLe principal objectif de cette étude est de dimensionner, fabriquer et caractériser un détecteur optique intégré sur verre basé sur la résonance plasmonique de surface, destiné à terme à être combiné avec d’autres techniques de détection. La résonance plasmonique de surface est une technique reconnue pour sa sensibilité adaptée à la détection de surface, qui a l’avantage d’être sans marquage et permet de fournir un suivi en temps réel de la cinétique d’une réaction. L’avantage principal de ce capteur est qu’il a été dimensionné pour une large gamme d’indice de réfraction de l’analyte, allant de 1,33 à 1,48. Ces valeurs correspondent à la plupart des entités biologiques associées à leurs couches d’accroche, particulièrement les matrices de polymères. Ces matrices sont de plus en plus utilisées non seulement pour leur capacité à augmenter la densité d’analytes présents à la surface du capteur, mais aussi pour leurs propriétés favorisant l’adsorption spécifique et leur utilisation comme élément actif de reconnaissance biologique.Étant donné que beaucoup d’études biologiques nécessitent la comparaison de la mesure à une référence ou à une autre mesure, le second objectif du projet est d’étudier le potentiel du système SPR intégré sur verre pour la détection multianalyte.MuLes trois premiers chapitres se concentrent sur l’objectif principal du projet. Le dimensionnement du dispositif suivant un cahier des charges préétabli est présenté, ainsi que les outils de simulation. Le procédé de fabrication de la puce optique sur verre est ensuite décrit, ainsi que les instruments et protocoles de caractérisation. Une comparaison est faite entre les simulations et les résultats expérimentaux, et les performances des outils numériques ainsi que celles du dispositif sont évaluées.Le dernier chapitre de la thèse présente l’étude de plusieurs techniques de multiplexage spectral adaptées à un système SPR intégré, exploitant en particulier la technologie sur verre. L’objectif est de fournir au moins deux détections simultanées. Dans ce cadre, plusieurs solutions sont proposées et les dispositifs associés sont dimensionnés, fabriqués et testés. / In spite of the growing number of available biosensors, many biochemical reactions and biological components have not yet been studied in detail. Among them, some require the combination of several detection techniques in order to retrieve enough information to characterize them fully. An unknown reaction based, for example, on DNA hybridization could be characterized with an electrochemical sensor, a mechanical sensor and an optical sensor, each giving a different type of information.MuThe main objective of the work presented here is to design, fabricate and characterize a flexible integrated optical biosensor based on surface plasmon resonance, intended to be then combined with other detection techniques. Surface Plasmon Resonance (SPR) is well known to be a sensitive technique for surface-based biochemical detection. It has the advantage to be an unlabeled method and provides real time information on the kinetics of a reaction. The use of an integrated technology enables us to integrate several sensors on the same chip for the same sample, making them compact and low-cost. The flexibility of the proposed SPR biosensor comes from the fact that it is designed for a large range of analyte refractive indices, from 1.33 to 1.48 in the 600 nm-1000 nm wavelength range. These values are suitable for most biological entities and their ligand layers, and especially for hydrophilic polymer matrices used to trap DNA or protein entities. These biochemical matrices are used more and more for their ability to trap high densities of analyte, provide a strong binding and serve as an active detection medium with good anti-fouling properties.MuAs several biochemical studies require the simultaneous comparison of measurements to a reference or to another measurement, the second objective of this project is to study the potential of multianalyte detection in an integrated SPR device on glass.The first three chapters of the thesis are focused on the main objective. The design according to predefined specifications is presented, at the same time as the simulation tools. The fabrication process of the glass chip is introduced, as well as the characterization instruments and protocols. Simulation and experimental results are then compared, and the device performance is assessed.The last chapter describes the study of several spectral multiplexing techniques adapted to an integrated SPR system using the glass technology. The goal is to provide at least two simultaneous measurements. Several detection techniques are examined and the related devices are designed, fabricated and characterized.

No description available.

In 2D cell cultures uptake/release of various metabolic analytes such as glucose, lactate or metabolic by-products like hydrogen peroxide from/to the extracellular environment results in concentration gradients. The magnitude, direction, and time scales of these gradients carries information that is essential for internal cellular processes and/or for communication with neighboring cells. This PhD research work focusses on the design, fabrication and characterization of electrochemical microelectrode arrays (MEAs) optimized to be positioned in commonly used 2D cell culture setups. Importantly, by simultaneously measuring accurate concentration transients and associated gradients/uxes near the cell surface (surface concentration) the capability of the device to quantify kinetic rates and distinguish mechanisms involved in various cellular processes is demonstrated. An in-situ transient calibration technique suitable for amperometric MEAs is developed and the technique is validated by quantitatively measuring dynamic concentration profiles with varying spatial (100-800 µm) and time (s to hrs.) scales set up from an electrically controlled diffusion reaction system. With the proposed MEA design and technique three physiological applications are demonstrated. Firstly, the position able 1D MEA was employed real time to quantitatively measure the hydrogen peroxide scavenging rates from astrocyte vs glioblastoma cell cultures. With the ability to extract to dynamic surface concentration and fluxes, the cell lines were shown to have hydrogen peroxide uptake rates dependent on local surface concentrations. Moreover, the cancerous glioblastoma cells demonstrated an upregulated linear peroxide scavenging mechanism as compared to astrocytes. For the next phase, spatial scales of 1D MEA device along the size and functionalization scheme of the electrodes in the MEA was further modified to selectively sense glucose and lactate to enable extracellular metabolic profiling of cancer vs normal cell lines. Secondly, measurement of glucose concentration profiles demonstrated an increased glucose uptake rate in glioblastoma as compared to astrocytes. Additionally, sigmoidal (allosteric) vs Michaelis - Menten glucose uptake kinetics was observed in glioblastoma vs astrocytes. Moreover, the presence of a glucose sensing mechanism was observed in glioblastoma cells due to the dependence of the glucose uptake rate on initial exposed concentration rather than surface concentration. Finally, simultaneous multi-analyte (glucose and lactate) gradient measurements were performed on genetically modified mouse pancreatic cancer cell lines. While glucose uptake rate was shown to increase with increasing extracellular glucose concentration for one of the cell lines, the lactate release rate was observed to be independent of the initial extracellular glucose dose.