This thesis describes the use of in vivo and in vitro models to better understand the molecular correlates of sleep and sleep deprivation. Unlike previous studies, we utilise a timecourse based experimental design throughout, which has the advantage of identifying how the abundance of molecules return to baseline following sleep deprivation. Chapter 3 outlines the transcriptome of mouse cortex collected over 54 hours from mice subjected to varied durations of sleep deprivation. The timecourse experimental design aids in the identification of genes that are induced during both spontaneous and enforced wakefulness, and facilitates the dissociation of genes whose expression is tightly linked to the current wake state of the animal from those whose expression is linked to the total amount of wakefulness recently experienced by the animal. Like previous studies, we identify several genes involved in the unfolded protein response and synaptic function that are upregulated by sleep deprivation. We also find that increasing durations of sleep deprivation progressively reduces the total number of rhythmically expressed genes in mouse cortex, with only a handful of transcripts identified as diurnal following 12 hour sleep deprivation. Chapter 4 outlines the proteomic and metabolomic effects of 12 hour sleep deprivation. Proteomic analyses indicate that the abundance of ribosomal and nucleosomal proteins is suppressed for at least 24 hours following sleep deprivation, whilst the abundance of several phosphodiesterases are acutely increased following sleep deprivation. Metabolomic analyses of sleep deprived mouse cortex identified 3 molecular species whose abundance profile implicate them as sleep homeostats. Finally, we also set out to develop an in vitro model of sleep deprivation based on the optogenetic activation of a neuroblastoma cell line, which is outlined in Chapter 5. Following several rounds of optimisation, the stable expression of an opsin was found to induce intracellular calcium spikes and immediate early gene expression during illumination. Transcriptomic profiling of illuminated SH-SY5Y cells induced large scale transcriptomic changes, and modulated the expression of genes involved in synapses, cholesterol synthesis, the molecular clock and the unfolded protein response. Although these functional classes are reminiscent of those modulated by in vivo sleep deprivation, there was only a slight enrichment of individual genes modulated by in vivo sleep deprivation amongst the blue light sensitive genes, indicating further work is required to more closely model in vivo sleep deprivation.

Motor cortex, basal ganglia (BG), and thalamus are anatomically arranged in a recurrent loop whose activity is hypothesized to be involved in the selection of motor actions. Direct (dSPN) and indirect (iSPN) striatal projection neurons receive excitatory input from cortex, and are thought to oppositely modulate cortical activity via BG output to thalamus. Here, we test the central tenets of this model in head-restrained mice performing an operant conditioning task using optogenetic manipulation of dSPNs and iSPNs to determine the effects of activity in each pathway on primary motor cortex. We find that dSPN and iSPN activation has bidirectional, robust, and rapid effects on motor cortex that are highly context-dependent, with distinct effects of each pathway during quiescent and active periods. Thus, the effects of activity in each pathway are at times antagonistic and consistent with classic models, whereas in other behavioral contexts the two pathways will work in the same direction or have no effect at all. In a separate but related project, we describe a direct projection from the globus pallidus externa (GP), a central nucleus of the BG, to frontal regions of the cerebral cortex (FC), which is not typically included in models of BG function. Two cell types make up the GP-FC projection, distinguished by their electrophysiological properties, cortical projection patterns and expression of choline acyteltransferase (ChAT), a genetic marker for the neurotransmitter acetylcholine. These cholinergic GP cells receive basal ganglia input and bidirectionally modulate firing in FC of awake mice. Since GP-FC cells receive dopamine sensitive inhibition from iSPNs and dSPNs, this circuit reveals a pathway by which neuropsychiatric pharmaceuticals can act in the BG and yet modulate frontal cortices. Together, these two projects expand our understanding of the complexities of basal ganglia circuitry and its interactions with cortex.

L’addiction se caractérise par une recherche et une consommation pathologiques de la drogue, maintenues malgré leurs conséquences néfastes. C’est une pathologie chronique car, le plus souvent, les tentatives de sevrage se soldent par une rechute. L’addiction à la cocaïne se développe chez 15 à 20 % des usagers, après un usage plus ou moins prolongé. Les solutions thérapeutiques font gravement défaut et c’est un enjeu que de comprendre les mécanismes neurobiologiques qui sous-tendent cette addiction. Les études cliniques et précliniques proposent que l’addiction résulte d’un déséquilibre entre les circuits cortico-subcorticaux qui gèrent la valeur motivationnelle de la drogue et ceux qui sont impliqués dans le contrôle cognitif inhibiteur. Des changements séquentiels dans des circuits interconnectés qui incluent notamment le noyau basolatéral de l’amygdale, le noyau accumbens et le cortex préfrontal seraient au cœur de processus motivationnels pathologiques et d’une difficulté à inhiber le craving et la consommation. L’étude de l’addiction, à l’échelle des circuits neuronaux, fait face à plusieurs défis. Techniquement limitée chez l’homme, elle peut bénéficier des modèles animaux, mais seulement s’ils capturent des dimensions de la pathologie. Au cours des dix dernières années, de tels modèles ont été mis en œuvre, mais exclusivement chez le rat. Or, les outils pour l’exploration fonctionnelle fine des circuits neuronaux ont été majoritairement développés chez la souris. Un autre défi consiste à pouvoir questionner la fonctionnalité des circuits, en temps réel, sur l’individu se comportant. Mes travaux de thèse ont eu pour objectif : 1. L’étude de marqueurs de connectivité fonctionnelle chez des rats Addict et des rats Non-addict à la cocaïne. Notre modèle d’addiction à la cocaïne permet d’identifier 15 à 20 % de rats qui, après une période prolongée d’autoadministration intraveineuse de cocaïne, et bien qu’ils aient consommé la même quantité de cocaïne que les autres, montrent une très forte motivation pour la substance, une difficulté à limiter la recherche de drogue, et maintiennent la prise de cocaïne malgré ses conséquences néfastes. L’électrophysiologie in vivo, multi-site, au moyen d’enregistrements unitaires ou de potentiels de champs locaux est un outil de choix pour l’exploration de la connectivité fonctionnelle chez le rongeur. Un défi technique a été de l’adapter pour la coupler à notre modèle d’addiction à la cocaïne chez le rat. Nous avons montré des différences significatives de connectivité fonctionnelle entre rats Addict et Non-addict, suggérant un défaut de fonctionnalité du cortex préfrontal médian (PFM) chez les Addict. 2. L’étude du rôle du cortex prélimbique (PL) dans le contrôle du comportement d’autoadministration de cocaïne chez le rat. Des données récentes de la littérature remettent en cause le dogme selon lequel le PL exerce exclusivement un rôle facilitateur sur les propriétés motivationnelles de la cocaïne. Nous avons cherché à clarifier le rôle du PL dans le comportement d’autoadministration de cocaïne avant que ne se développe une addiction : comprendre son rôle dans l’usage précoce de cocaïne pour, à terme, étudier l’évolution de son implication selon que l’individu développe ou non une addiction. Nous avons montré que l’inactivation du PL peut s’accompagner, chez le même individu, d’une diminution ou d’une exacerbation du comportement de recherche de cocaïne selon les contingences expérimentales. Les neurones du PL émettent des projections vers plusieurs structures. Pour étudier leur rôle dans les effets comportementaux observés, nous avons travaillé à la mise au point d’outils optogénétiques pour la manipulation de l’activité de voies neuronales spécifiques, chez le rat, pour lequel ils sont encore très peu développés. Mes travaux de thèse contribuent tant sur le plan théorique que technique à la compréhension des mécanismes psychobiologiques de l’addiction à la cocaïne. / Drug addiction is characterized by pathological drug seeking and taking, maintained despite their negative consequences. This is a chronic pathology, withdrawal attempts being unsuccessful in most cases. Cocaine addiction develops in about 15 to 20 % of habitual users. For cocaine, therapeutic options are lacking, which could be explained by the relatively poor understanding of the neurobiological mechanisms underlying cocaine addiction to date. Clinical and preclinical studies propose that addiction results from an imbalance between the cortical-subcortical circuits that process motivational value of drug-related stimuli versus those involved in cognitive inhibitory control. Hierarchical sequential changes in distinct, but interconnected circuits, including the basolateral amygdala, the nucleus accumbens and the prefrontal cortex could be at the core of pathological incentive processes and difficulty to control craving and drug taking. Studying addiction at the neuronal circuit level faces many challenges. Technically limited in humans, it can benefit from animal models, but only if they properly capture dimensions of the pathology. Over the last ten years, such models have been developed, but exclusively in rats. However, tools for a refined functional exploration of neuronal circuits have been established mostly in mice, and until recently they have begun to be explored in rats. In addition, another main challenge is the ability to investigate functional connectivity in real time in behaving animals. My thesis work had two objectives: 1. Studying markers of functional connectivity in rats showing a cocaine addiction-like behavior (Addict) or not (Non-addict). Our model of cocaine addiction allows identifying 15-20% of rats that show a high motivation for cocaine, a difficulty to limit drug seeking and that maintain drug taking despite negative consequences. These extreme behaviors occur after prolonged cocaine self-administration and despite that these rats have used a comparable amount of cocaine as compared to the others. In vivo, multi-site electrophysiology recordings, applied to single units or local field potentials, is a tool of choice for studying functional connectivity in rodents. A technical challenge has been to adapt and couple it to our model of cocaine addiction in the rat. We have evidenced significant differences in connectivity between Addict and Non-addict rats, which suggest a default of functionality of the medial prefrontal cortex in the Addict rats. 2. Studying the role of the prelimbic cortex (PL) in cocaine self-administration behavior in the rat. The canonical role of the PL in exclusively promoting drug seeking was recently questioned, with studies involving it also in inhibition of drug seeking. Our first goal was to clarify this role of the PL in early cocaine self-administration, i.e. before addiction-like behavior develops: understanding its early role to eventually compare it to its late role and whether an addiction-like behavior develops or not. We have shown that optogenetic PL inactivation can decrease or increase cocaine seeking in the same individual, according to experimental contingencies. PL neurons project to several remote structures. To study the role of these different neuronal pathways, we have worked in establishing optogenetic tools for the manipulation of specific neuronal pathways, in the rat, for which they are still poorly developed. My thesis work contribute, both theoretically and technically, to the understanding of the psychobiology of cocaine addiction.

Wireless power transfer (WPT) is currently the most efficient way for transmission of power from one port to another, that is popularly used in various applications.This technique can change the previous energy utilization methods in various applications such as electronic devices, implanted medical devices, electrical vehicles and so forth.It mainly helps overcome the limitations of short battery life, limited storage, heavy weight, and high cost of batteries.This paper is based on the design of a transmitter and a receiver to achieve wireless power transfer for applications like optogenetic stimulation in rodents. With inductive coupling, a very high efficiency can be achieved between the transmitting and receiving coils of an antenna at small distances. When the transmitter and receiver are strongly coupled and are working at their resonant frequencies, the range of efficient WPT can be extended. In this work, the simulations are performed in HFSS at a resonating frequency of 13.56 MHz.A 4-port transmitter and a single-port planar receiver model are developed in HFSS, and the simulations are performed to graph the S parameters with a separation distance of 4cm. A Wilkinson power divider is designed using ADS to split the power from the four ports of the transmitter. The design is simulated to compare the S21 at different positions on the TX.

L'hippocampe est une région du cerveau située dans le lobe temporal médian. Avec d'autres structures limbiques, l'hippocampe est impliqué dans des processus d'apprentissage et de mémorisation et possède un rôle crucial dans le traitement spatial de l'information. Les synapses de l'hippocampe formées entre les fibres moussues (fm) originaires du gyrus denté et les neurones pyramidaux de CA3 ont reçu une attention particulière, compte tenu de la position stratégique occupée par le gyrus denté à l'entrée de l'hippocampe. En outre les synapses fm- CA3 sont distinctes de la plupart des autres synapses excitatrices du système nerveux central par leurs propriétés morphologiques et physiologiques uniques. Cela soulève la question de savoir si ces propriétés uniques reflètent aussi un rôle fonctionnel unique dans le traitement de l'information effectué par cette synapse au sein du microcircuit de l'hippocampe. Malheureusement nous ne savons que peu de choses sur la façon dont les cellules granulaires modulent l'activité des neurones de CA3 dans le réseau intact in vivo (Henze et al, 2002 ; Hagena et Manahan - Vaughan, 2010, 2011). Le manque d'information est dû au fait que la manipulation classique des circuits neuronaux par des approches électriques, pharmacologiques et génétiques manque de précisions spatiale et temporelle in vivo. L'utilisation de la stimulation extracellulaire de fibres moussues peut conduire à l'activation polysynaptique de cellules pyramidales de CA3, qui peuvent ensuite contaminer les réponses enregistrées. Par ailleurs, l'utilisation de critères trop conservateurs peut conduire à l'exclusion des réponses provenant des fibres moussues «purs» aux propriétés méconnues (Henze et al., 2000). Toutefois, le développement récent et rapide de l’optogénétique dans les neurosciences a fourni de nouveaux outils offrant une sélectivité spatiale élevée (activation optique spécifique de la cellule), et une grande précision temporelle (à l'échelle de la milliseconde), permettant la dissection et l'étude des circuits neuronaux in vivo. L'objectif de ma thèse était de mieux comprendre les mécanismes et les conséquences physiologiques de la plasticité synaptique à court terme se produisant à la synapse formée entre les fibres moussues et les neurones pyramidaux de CA3 dans le cerveau de souris intact. La présente thèse se compose de deux parties principales. Dans la première partie, j'ai exploré de nouveaux outils optogénétiques dans le but de contrôler l'activité des cellules granulaires à l’aide d’impulsions de lumière. La stimulation optogénétique repose sur l'activation du canal ionique channelrhodopsin - 2 - lumière fermée ( ChR2 ) par une lumière bleue et induit des potentiels d'action sur une large gamme de fréquences de stimulation. J'ai aussi observé que la stimulation optique peut être utilisée pour déclencher la plasticité à court terme au niveau des synapses fm-CA3.Dans la deuxième partie j'ai affiné la méthodologie de stimulation optogénétique in vivo pour la caractérisation non invasive du fonctionnement synaptique des synapses fm- CA3. La fiabilité de la stimulation optogénétique d'une population neuronale génétiquement ciblée ainsi que la résolution d'une seule cellule obtenue en utilisant des enregistrements de cellules entières sont des étapes importantes vers une meilleure compréhension du rôle fonctionnel des fibres moussues dans le réseau de l'hippocampe in vivo. / The hippocampus is a brain region located in the medial temporal lobe. Along with other limbic structures, the hippocampus is involved in learning and memory processes and has a crucial role in spatial information processing. Within the hippocampus synapses made between mossy fibers (mf) originating from the dentate gyrus and CA3 pyramidal neurons have received particular attention, given the strategic position occupied by the dentate gyrus at the entrance of the hippocampus. Moreover mf-CA3 synapses are distinct from most of other excitatory synapses in the central nervous system for their unusual morphological and physiological properties. This raises the question if these unique properties reflect a unique functional role in information processing carried out by this synapse within the microcircuit of the hippocampus. Unfortunately very little is known on how granule cells modulate the activity of CA3 neurons in the intact network in vivo (Henze et al., 2002; Hagena and Manahan-Vaughan, 2010, 2011). The paucity of information is due to the fact that classical manipulation of neuronal circuits using electrical, pharmacological and genetic approaches lack spatial and temporal precision in vivo. The use of bulk extracellular stimulation may lead to polysynaptic activation of CA3 pyramidal cells, which can subsequently contaminate putative mossy fibers synaptic responses measured in CA3 pyramidal cells. The use of overly conservative criteria on the other side may lead to the exclusion of “pure” mossy fibers responses with unexpected properties (Henze et al., 2000).However the recent and fast growth of optogenetics in neuroscience has provided new tools with high spatial selectivity (cell specific optical activation) and temporal precision (at the millisecond scale), allowing the dissection and investigation of neuronal circuits in vivo. The aim of my thesis was to gain insight into the mechanisms and the physiological consequences of short-term synaptic plasticity occurring at mossy fibers to CA3 pyramidal neurons synapses in the intact mouse brain. The present thesis consists of two main parts. In the first part I explored new optogenetic tools to control the activity of granule cells with pulses of light. Optogenetic stimulation, which relies on the activation of the light-gated ion channel channelrhodopsin-2 (ChR2) by blue light reliably induced action potentials over a wide range of frequencies of stimulation. I also found that optical stimulation can be used to trigger short term plasticity at mf-CA3 synapses. In the second part I refined optogenetic stimulation methodology in vivo for non-invasive characterization of synaptic functioning of the mf-CA3 synapses. The reliability of optogenetic stimulation of a genetically targeted neuronal population together with the single cell resolution obtained using whole-cell recordings are important steps towards a better understanding of the functional role of the mossy fibers in the hippocampal network in vivo.

Os neurônios do grupamento catecolaminérgico C1, localizados na porção ventrolateral do bulbo, são classicamente conhecidos por seu envolvimento no controle cardiovascular. O modelo atual propõe que os neurônios C1 são recrutados em situações que ofereçam risco de vida aos indivíduos, desencadeando respostas generalizadas e estereotipadas em defesa da homeostase. Tais respostas envolvem ajustes cardiovasculares, imunológicos, neuroendócrinos, metabólicos, termorregulatórios e respiratórios. Ferramentas anatômicas e funcionais foram utilizadas para investigar se os neurônios C1 contribuem para os ajustes respiratórios induzidos pela hipóxia e pela hipercpania. Os resultados mostram que os neurônios C1 contribuem para a aumento da ventilação induzido pela hipóxia, mas não pela hiperpania, via aumento da frequência da respiratória. Além disso, demonstramos que o aumento da frequência respiratória promovido pela ativação do grupamento C1 depende da ativação de receptores glutamatérgicos, mas não adrenérgicos, localizados na região do complexo pré-Bötzinger. / The catecholaminergic C1 neurons, located in the rostral ventrolateral portion of the medulla, are classically known by their involvement in the cardiovascular control. Recent models suggest that C1 neurons are recruited in situations of life risk, triggering generalized and stereotyped responses to homeostasis. Such responses involve cardiovascular, immunologic, neuroendocrine, metabolic, thermoregulatory and respiratory adjustments. Thus, anatomic and functional tools were used to assess the contribution of C1 neurons to the respiratory adjustments induced by hypoxia and hypercapnia. The results show that these neurons contribute to the increase of ventilation induced by hypoxia, but not by hypercapnia, via an increase of the breathing frequency. Moreover, we demonstrated that increase of breathing frequency promoted by the activation of C1 neurons depend on the activation of glutamatergic receptors, but not adrenergic, located in the pre-Bötzinge complex.

La perception consciente du monde extérieur repose sur la coordination spatiotemporelle de l’activité des neurones corticaux. Les aires corticales primaires chez les mammifères sont organisées en six couches. Il a été proposé que l’information sensorielle soit traitée de façon sérielle à travers les 6 couches du cortex. D’abord au niveau de la couche IV, cible des afférences thalamiques. Ensuite au niveau des couches II/III, innervées par les neurones excitateurs de la couche IV. Et enfin par les neurones des couches profondes, V et VI, qui sont innervés par les cellules pyramidales des couches II/III. Les neurones pyramidaux de la couche V constituant la principale sortie du néocortex.Il a récemment été montré que les neurones des couches profondes reçoivent également des informations sensorielles directement par des afférences thalamiques, ce qui pose la question du rôle de la connectivité interlaminaire dans le traitement sensoriel opéré par le cortex.J’ai ainsi tiré profit de la technique d’électroporation in utero qui permet d’exprimer spécifiquement des protéines photo-activables dans les cellules pyramidales des couches II/III du cortex somesthésique primaire de la souris. En procédant à des enregistrements unitaires des neurones corticaux à la fois chez des animaux anesthésiés et éveillés, j’ai montré que le recrutement des neurones pyramidaux des couches II/III amplifie les réponses sensorielles des neurones de la couche V. Par ailleurs, l’analyse de cette amplification en fonction de l’intensité des stimulations sensorielles indique que la connectivité interlaminaire joue un rôle majeur dans la modulation du gain des neurones de la couche de sortie du cortex. / The sensory perception of the external world relies on the coordinated activity in space and time of cortical neurons. Primary sensory areas of mammals are organized in six layers.It has been suggested that sensory information is processed serially through the six layers of the cortex. Sensory information is supposed to propagate first through the layer IV, principal target of thalamic axonal projections. Cortical layers II/III then receive sensory information relayed by layer IV excitatory neurons. Finally, deep cortical layers V and VI are connected by layer II/III pyramidal cells. Layer V pyramidal neurons are the principal output of the neocortex.Recently, it has been shown that deep layer neurons receive direct thalamic inputs relaying sensory information. The role of the translaminar connectivity during sensory processing remains an opened question.I took the advantage of in utero electroporation to express photo-sensitive proteins specifically in layer II/III pyramidal cells of the mouse primary somatosensory cortex.By proceeding to extracellular recordings of cortical neurons of either anesthetized or awake mice, I have shown that the recruitment of layer II/III pyramidal neurons amplifies layer V neurons sensory responses. Moreover, the analysis of this amplification phenomenon as a function the sensory stimulation intensity suggests that translaminar connectivity can operate a gain modulation of the layer V pyramidal neurons.

Oxidative stress has been implied in a wide variety of diseases, such as cancer, myocardial infarction, and neurodegenerative diseases including Parkinson's diseases (PD). PD is characterized by the degeneration of dopaminergic (DA) neurons; genetic studies have identified gene mutations causal to PD. Accumulating studies hypothesize that these genes protect DA neurons against oxidative stress. However, lack of experimental tools to target oxidative stress in specific cells has prevented direct evaluation of the hypothesis. We established a novel method to use KillerRed (KR), a genetically-encoded protein that generates radicals upon light activation. We showed its efficacy in live animals by cell-specific ablation of neurons in C. elegans. We applied KR to degenerate DA neurons. By controlling the level of stress via activation light, the protective role of PD-gene, LRRK2, against oxidative stress was confirmed. Thus, we established a method to address the role of oxidative stress in a cell-specific manner.

Oxidative stress has been implied in a wide variety of diseases, such as cancer, myocardial infarction, and neurodegenerative diseases including Parkinson's diseases (PD). PD is characterized by the degeneration of dopaminergic (DA) neurons; genetic studies have identified gene mutations causal to PD. Accumulating studies hypothesize that these genes protect DA neurons against oxidative stress. However, lack of experimental tools to target oxidative stress in specific cells has prevented direct evaluation of the hypothesis. We established a novel method to use KillerRed (KR), a genetically-encoded protein that generates radicals upon light activation. We showed its efficacy in live animals by cell-specific ablation of neurons in C. elegans. We applied KR to degenerate DA neurons. By controlling the level of stress via activation light, the protective role of PD-gene, LRRK2, against oxidative stress was confirmed. Thus, we established a method to address the role of oxidative stress in a cell-specific manner.

The dynamic nature of gene expression enables cellular programming, homeostasis and environmental adaptation in living systems. Dissection of causal gene functions in cellular and organismal processes therefore necessitates approaches that enable spatially and temporally precise modulation of gene expression. Recently, a variety of microbial and plant-derived light-sensitive proteins have been engineered as optogenetic actuators, enabling high-precision spatiotemporal control of many cellular functions. However, versatile and robust technologies that enable optical modulation of transcription in the mammalian endogenous genome remain elusive. Here we describe the development of light-inducible transcriptional effectors (LITEs), an optogenetic two-hybrid system integrating the customizable TALE DNA-binding domain with the light-sensitive cryptochrome 2 protein and its interacting partner CIB1 from Arabidopsis thaliana. LITEs do not require additional exogenous chemical cofactors, are easily customized to target many endogenous genomic loci, and can be activated within minutes with reversibility. LITEs can be packaged into viral vectors and genetically targeted to probe specific cell populations. We have applied this system in primary mouse neurons, as well as in the brain of freely behaving mice in vivo to mediate reversible modulation of mammalian endogenous gene expression as well as targeted epigenetic chromatin modifications. We explore the modularity of the LITE approach through the development of CRISPR/Cas9 transcriptional effectors in either constitutively active or light-inducible contexts. The LITE system establishes a novel mode of optogenetic control of endogenous cellular processes and enables direct testing of the causal roles of genetic and epigenetic regulation in normal biological processes and disease states. / Engineering and Applied Sciences