Influenza is the infectious agent of the seasonal flu. Flu symptoms from influenza infection are similar to the symptoms caused by bacterial upper respiratory tract infections. This similarity causes the inappropriate diagnosis and prescription of antibiotics, leading to drug resistant bacterial strains. Moreover, the limitations of the current viral detection methods prevent the clinical diagnosis of influenza. The objective of this project is to design a rapid and sensitive influenza diagnostic method based on the highly sensitive Nanostructured microelectrode biosensing assay. The diagnostic method was designed by selecting probe sequences, controlling the quality of the probes and the sensing chips, and optimizing the deposition conditions. This diagnostic method was shown to be capable of differentiating influenza sequences from non-complementary sequences, detecting influenza sequences in the form of ~1000-nucleotide RNA molecules, sensing the target influenza RNA within a complex mixture of cell lysates, and achieving a clinically relevant detection limit.

Influenza is the infectious agent of the seasonal flu. Flu symptoms from influenza infection are similar to the symptoms caused by bacterial upper respiratory tract infections. This similarity causes the inappropriate diagnosis and prescription of antibiotics, leading to drug resistant bacterial strains. Moreover, the limitations of the current viral detection methods prevent the clinical diagnosis of influenza. The objective of this project is to design a rapid and sensitive influenza diagnostic method based on the highly sensitive Nanostructured microelectrode biosensing assay. The diagnostic method was designed by selecting probe sequences, controlling the quality of the probes and the sensing chips, and optimizing the deposition conditions. This diagnostic method was shown to be capable of differentiating influenza sequences from non-complementary sequences, detecting influenza sequences in the form of ~1000-nucleotide RNA molecules, sensing the target influenza RNA within a complex mixture of cell lysates, and achieving a clinically relevant detection limit.

Le système nerveux central est la cible la plus probable d'effets biologiques dûs à l'exposition aux radiofréquences (RF) de la téléphonie mobile. Plusieurs études sur l’EEG (électroencéphalogramme) ont montré des variations dans le spectre de la bande alpha pendant et / ou après l'exposition aux radiofréquences, avec les yeux fermés ou pendant le sommeil. Dans ce contexte, l'observation de l'activité électrique spontanée des réseaux neuronaux sous exposition aux radiofréquences représente un outil efficace pour détecter de possibles effets des RF de faible niveau sur le système nerveux. Dans ce travail de thèse, nous avons développé un dispositif expérimental dédié à l'exposition dans la gamme des GHz de réseaux neuronaux et permettant simultanément l’enregistrement de l'activité électrique des neurones. Une cellule électromagnétique transversale (TEM) a été utilisée afin d'exposer les réseaux neuronaux aux signaux GSM-1800 à un niveau de DAS de 3,2 W / kg. L'enregistrement de l'activité électrique neuronale et la détection en termes de spikes et bursts sous exposition ont été réalisées à l'aide de réseaux de micro-électrodes (MEAs). Ce travail démontre la faisabilité de l’étude (culture de réseaux de neurones primaires, enregistrement de l'activité électrique et analyse des signaux obtenus sous exposition aux radiofréquences) et expose des résultats préliminaires. Dans l'expérience principale (16 cultures), il y avait une diminution réversible de 30% du taux moyen de spikes (MFR) et de bursts (BR) pendant les 3 min d’exposition aux RF. Des expériences supplémentaires sont nécessaires pour mieux caractériser cet effet, notamment en termes d'élévation de la température au niveau microscopique. / The central nervous system is the most likely target of mobile telephony radiofrequency field (RF) exposure in terms of biological effects. Several EEG (electroencephalography) studies have reported variations in the alpha-band power spectrum during and/or after RF exposure, in resting EEG and during sleep. In this context, the observation of the spontaneous electrical activity of neuronal networks under RF exposure can be an efficient tool to detect the occurrence of low-level RF effects on the nervous system. In this thesis research work we developed a dedicated experimental setup in the GHz range for the simultaneous exposure of neuronal networks and monitoring of electrical activity. A transverse electromagnetic (TEM) cell was used to expose the neuronal networks to GSM-1800 signals at a SAR level of 3.2 W/kg. Recording of the neuronal electrical activity and detection of the extracellular spikes and bursts under exposure were performed using Micro Electrode Arrays (MEAs). This work provides the proof of feasibility and preliminary results of the integrated investigation regarding exposure setup, culture of the neuronal network, recording of the electrical activity and analysis of the signals obtained under RF exposure. In the main experiment (16 cultures), there was a 30% reversible decrease in mean firing rate (MFR) and bursting rate (BR) during the 3 min exposures to RF. Additional experiments are needed to further characterize this effect, especially in terms of temperature elevation at the microscopic level.

Cette thèse s'intéresse à l'application d'un modèle mathématique unidimensionnel de formation et de croissance de biofilms multi-espèces. Le modèle se compose d'un système d'équations non linéaires aux dérivées partielles hyperboliques, décrivant la croissance d'espèces microbiennes dans le biofilm, et un système d'équations semi-linéaires aux dérivées partielles paraboliques, qui régit la diffusion de substrat de la phase aqueuse vers la matrice du biofilm. L'ensemble conduit à un problème de valeur limite libre, essentiellement hyperbolique. Dans une première étude, l'analyse et la simulation de la phase initiale de croissance du biofilm ont été examinées. Le problème mathématique résultant a été discuté en utilisant la méthode des caractéristiques et le théorème du point fixe a été utilisé pour déterminer l'existence et l'unicité des solutions mathématiques. Un deuxième aspect de la thèse porte sur l'analyse et la prévision de la dynamique des populations microbienne dans plusieurs types biofilms pour le traitement des eaux usées. Le modèle a été appliqué pour simuler la compétition bactérienne et évaluer l'influence de la diffusion du substrat sur la stratification microbienne des biofilms multi-espèces, en incluant les bactéries nitrifiantes, Anammox et bactéries sulfato-réductrices. Dans les deux cas, la méthode des caractéristiques a été utilisée à des fins numériques et l'équation de conservation de masse joue un rôle crucial pour vérifier l'exactitude des simulations. Les résultats des simulations montrent que le modèle est en mesure d'évaluer correctement les effets des conditions limites qui s'exercent sur la concurrence bactérienne. Enfin, ce modèle a été étendu pour inclure le phénomène de colonisation microbienne. Le nouveau modèle est capable de prendre en compte l'invasion de nouvelles espèces en se basant sur un ensemble d'équations non linéaires aux dérivées partielles hyperboliques pour ce qui concerne le processus de croissance. De plus, le processus d'invasion biologique d'espèces nouvelles dans le biofilm a été modélisé par un système d'équations non linéaires aux dérivées partielles paraboliques. Ce modèle d'invasion a été appliqué avec succès pour simuler l'invasion des bactéries hétérotrophes dans les biofilms autotrophes / This dissertation relates to the applications of a one-dimensional mathematical model for multispecies biofilm formation and growth. The model consists of a system of nonlinear hyperbolic partial differential equations, describing the growth of microbial species in biofilms, and a system of semilinear parabolic partial differential equations, which governs substrate diffusion from the surrounding aqueous phase into the biofilm. Overall, this leads to a free boundary value problem, essentially hyperbolic. In a first study, the analysis and simulations of the initial phase of biofilm growth have been addressed. The resulting mathematical problem has been discussed by using the method of characteristics and the fixed-point theorem has been used to obtain existence, uniqueness and properties of solutions. A second aspect of the thesis deals with the analysis and prediction of population dynamics in multispecies biofilms for wastewater treatment. The model has been applied to simulate the bacterial competition and to evaluate the influence of substrate diffusion on microbial stratification for a nitrifying multispecies biofilm including Anammox bacteria and a sulfate-reducing biofilm. In both cases, the method of characteristics has been used for numerical purposes and the mass conservation equation plays a crucial role in checking the accuracy of simulations. The simulation results reveal that the model is able to evaluate properly the effects that boundary conditions exert on bacterial competition. Finally, the biofilm model has been extended to include the colonization phenomenon. The new model is able to take into account the invasion of new species diffusing from bulk liquid to biofilm, still based on a set of nonlinear hyperbolic partial differential equations for what concerns growth process. Indeed, the biological invasion process of new species into the biofilm has been modeled by a system of nonlinear parabolic partial differential equations. The invasion model has been successfully applied to simulate the invasion of heterotrophic bacteria in a constituted autotrophic biofilm and viceversa

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For almost a century, the electrical properties of the brain and the nervous system have been investigated to gain a better understanding of their mechanisms and to find cures for pathological conditions. Despite the fact that today's advancements in surgical techniques, research, and medical imaging have improved our ability to treat brain disorders, our knowledge of the brain and its functions is still limited. Culturing dissociated cortical neurons on Micro-Electrode Array dishes is a powerful experimental tool for investigating functional and structural characteristics of in-vitro neuronal networks, such as the cellular basis of brain learning, memory and synaptic developmental plasticity. This dissertation focuses on combining MEAs with novel electrophysiology experimental paradigms and statistical data analysis to investigate the mechanisms that regulate brain development at the level of synaptic formation and growth cones. The goal is to use a mathematical approach and specifically designed experiments to investigate whether dissociated neuronal networks can dependably display long and short-term plasticity, which are thought to be the building blocks of memory formation in the brain. Quantifying the functional evolution of dissociated neuronal networks during in- vitro development, using a statistical analysis tool was the first aim of this work. The results of the False Discovery Rate analysis show an evolution in network activity with changes in both the number of statistically significant stimulus/recording pairs as well as the average length of connections and the number of connections per active node. It is therefore proposed that the FDR analysis combined with two metrics, the average connection length and the number of highly connected "supernodes" is a valuable technique for describing neuronal connectivity in MEA dishes. Furthermore, the statistical analysis indicates that cultures dissociated from the same brain tissue display trends in their temporal evolution that are more similar than those obtained with respect to different batches. The second aim of this dissertation was to investigate long and short-term plasticity responsible for memory formation in dissociated neuronal networks. In order to address this issue, a set of experiments was designed and implemented in which the MEA electrode grid was divided into four quadrants, two of which were chronically stimulated, every two days for one hour with a stimulation paradigm that varied over time. Overall network and quadrant responses were then analyzed to quantify what level of plasticity took place in the network and how this was due to the stimulation interruption. The results demonstrate that here were no spatial differences in the stimulus-evoked activity within quadrants. Furthermore, the implemented stimulation protocol induced depression effects in the neuronal networks as demonstrated by the consistently lower network activity following stimulation sessions. Finally, the analysis demonstrated that the inhibitory effects of the stimulation decreased over time, thus suggesting a habituation phenomenon. These findings are sufficient to conclude that electrical stimulation is an important tool to interact with dissociated neuronal cultures, but localized stimuli are not enough to drive spatial synaptic potentiation or depression. On the contrary, the ability to modulate synaptic temporal plasticity was a feasible task to achieve by chronic network stimulation. / Electrical and Computer Engineering

The central nervous system is the most likely target of mobile telephony radiofrequency field (RF) exposure in terms of biological effects. Several EEG (electroencephalography) studies have reported variations in the alpha-band power spectrum during and/or after RF exposure, in resting EEG and during sleep. In this context, the observation of the spontaneous electrical activity of neuronal networks under RF exposure can be an efficient tool to detect the occurrence of low-level RF effects on the nervous system. In this thesis research work we developed a dedicated experimental setup in the GHz range for the simultaneous exposure of neuronal networks and monitoring of electrical activity. A transverse electromagnetic (TEM) cell was used to expose the neuronal networks to GSM-1800 signals at a SAR level of 3.2 W/kg. Recording of the neuronal electrical activity and detection of the extracellular spikes and bursts under exposure were performed using Micro Electrode Arrays (MEAs). This work provides the proof of feasibility and preliminary results of the integrated investigation regarding exposure setup, culture of the neuronal network, recording of the electrical activity and analysis of the signals obtained under RF exposure. In the main experiment (16 cultures), there was a 30% reversible decrease in mean firing rate (MFR) and bursting rate (BR) during the 3 min exposures to RF. Additional experiments are needed to further characterize this effect, especially in terms of temperature elevation at the microscopic level.

L'hétérotopie en bande sous-corticale (SBH) est une malformation caractérisée par la présence d'une bande de neurones ectopiques en regard du cortex normal ou normotopique. La plupart des patients ont une mutation d'un gène encodant une protéine indispensable à la migration des neurones. Les patients présentent une épilepsie pharmacorésistante. La chirurgie ne donne pas de résultats satisfaisants, le foyer épileptogène n'étant jamais clairement délimité. Un modèle de rat reproduisant les caractéristiques observées chez les patients à pu être généré. Même s'il est clair que le cortex normotopique et l'hétérotopie participent aux évènements épileptiformes, leur zone de genèse reste néanmoins inconnue. Le but de cette thèse a été de localiser l'origine de l'activité épileptiforme in vitro sur tranches de cerveau à l'aide d'une technique d'enregistrement multisite.Des activités épileptiformes (ILEs) ont été enregistrées à l'aide d'une technique d'enregistrement extracellulaire multisite à 60 canaux. Un outil d'analyse développé sous Matlab a ensuite permis de caractériser les ILEs et notamment leur origine et étendues spatiales. Après avoir identifié l'importance du cortex normotopique dans la genèse des ILEs, nous en avons supprimé l'excitabilité in vivo. Nous montrons que la surexpression de ces canaux dans les neurones ectopiques n'altère pas la susceptibilité aux crises des animaux concernés alors que la surexpression de ces canaux dans l'hétérotopie et dans le cortex normotopique améliore le phénotype épileptique. Nos résultats suggèrent ainsi un rôle majeur du cortex normotopique dans la genèse des activités épileptiques dans le syndrome du double cortex. / Subcortical Band Heterotopia (SBH) is a cortical malformation formed when neocortical neurons prematurely stop their migration in the white matter, forming a heterotopic band below the normotopic cortex, and is generally associated with intractable epilepsy. Although it is clear that the band heterotopia and the overlying cortex both contribute to creating an abnormal circuit prone to generate epileptic discharges, it is less understood which part of this circuitry is the most critical. Here, we sought to identify the origin of epileptiform activity in a targeted genetic model of SBH in rats.Rats with SBH were generated by knocking‐down the Dcx gene into neocortical progenitors of rat embryos. Origin, spatial extent and laminar profile of bicuculline‐induced interictal‐like activity on neocortical slices were analyzed by using extracellular recordings from 60‐channels microelectrode arrays. Susceptibility to pentylenetetrazole‐induced seizures was assessed by electrocorticography in head‐restrained nonanaesthetized rats. We show that the band heterotopia does not constitute a primary origin for interictal‐like epileptiform activity in vitro and is dispensable for generating induced seizures in vivo. Further, we report that most interictal‐like discharges originating in the overlying cortex secondarily propagates to the band heterotopia. Importantly, we found that in vivo suppression of neuronal excitability in SBH does not alter the higher propensity of Dcx‐KD rats to display seizures. These results suggest a major role of the normotopic cortex over the band heterotopia in generating interictal epileptiform activity and seizures in brains with SBH.

The synthesis of benzo[e]dimethyldihydropyrene (BDHP) photoswitches with ter-27, quarter-36, and quinque-28 thiophene oligomers attached on the same side of the switch was achieved using Stille coupling reactions. BDHP photoswitches with bi-75, ter-76 and quinque-77 thiophene oligomers attached directly to the switch on one side, and via a carbonyl spacer on the opposite side of the switch were also synthesized. Dimethyldihydropyrene (DHP) photoswitches with a naphthoyl functional group in the 2 position were synthesized using a Friedel Crafts reaction, and ter-96, quinque-97 and septi-98 thiophene oligomers were attached on opposite sides of the switch using Stille coupling reactions. All compounds were characterized by NMR, IR UV-vis spectroscopy and mass spectrometry. The relative rates of the photo-opening reactions under excess light conditions and the UV closing reactions versus BDHP were measured. Improvements in the photo-opening properties of the oligothiophene functionalized switches compared to BDHP were observed. The most dramatic photo-opening improvement was found for the quinquethienyl substituted DHP switch 97 which photo-opened when irradiated with visible light over 100 times faster than BDHP. UV closing rates were virtually the same as that of BDHP. However the addition of oligothiophenes led to an increase in the thermal closing reaction rates. Compounds with the naphthoyl functional group in the 2 position of DHP were found to have dramatically increased thermal closing rates. The electrochemical properties of oligothiophene functionalized BDHP and naphthoyl functionalized DHP switches in the closed form were studied by cyclic voltammetry and spectroelectrochemistry. During the oxidation cycle, a closing reaction from the cyclophanediene (CPD) form to the DHP form of the switches occurred which prevented the study of the electrochemical properties of the switches in the open form. Conductivity testing was performed on the quinquethienyl substituted DHP switch 97 using a gold interdigitated micro electrode array. The conductivity of undoped 97 was greater in the closed DHP isomer than in the open CPD isomer. Irradiation with red or blue light allowed for repetitive switching between the more highly conducting closed form and the less conducting open form. When electrochemically doped, 97 showed improved conductivity over the undoped form but only the conductivity of the closed doped form could be measured due to electrochemically induced closing.