<p>The growing complexity of scientific research demands further development of advanced gene regulation systems. For instance, the ultimate goal of tissue engineering is to develop constructs that functionally and morphologically resemble the native tissue they are expected to replace. This requires patterning of gene expression and control of cellular phenotype within the tissue engineered construct. In the field of synthetic biology, gene circuits are engineered to elucidate mechanisms of gene regulation and predict the behavior of more complex systems. Such systems require robust gene switches that can quickly turn gene expression on or off. Similarly, basic science requires precise genetic control to perturb genetic pathways or understand gene function. Additionally, gene therapy strives to replace or repair genes that are responsible for disease. The safety and efficacy of such therapies require control of when and where the delivered gene is expressed in vivo.</p><p>Unfortunately, these fields are limited by the lack of gene regulation systems that enable both robust and flexible cellular control. Most current gene regulation systems do not allow for the manipulation of gene expression that is spatially defined, temporally controlled, reversible, and repeatable. Rather, they provide incomplete control that forces the user to choose to control gene expression in either space or time, and whether the system will be reversible or irreversible.</p><p>The recent emergence of the field of optogenetics--the ability to control gene expression using light--has made it possible to regulate gene expression with spatial, temporal, and dynamic control. Light-inducible systems provide the tools necessary to overcome the limitations of other gene regulation systems, which can be slow, imprecise, or cumbersome to work with. However, emerging light-inducible systems require further optimization to increase their efficiency, reliability, and ease of use.</p><p>Initially, we engineered a light-inducible gene regulation system that combines zinc finger protein technology and the light-inducible interaction between Arabidopsis thaliana plant proteins GIGANTEA (GI) and the light oxygen voltage (LOV) domain of FKF1. Zinc finger proteins (ZFPs) can be engineered to target almost any DNA sequence through tandem assembly of individual zinc finger domains that recognize a specific three base-pair DNA sequence. Fusion of three different ZFPs to GI (GI-ZFP) successfully targeted the fusion protein to the specific DNA target sequence of the ZFP. Due to the interaction between GI and LOV, co-expression of GI-ZFP with a fusion protein consisting of LOV fused to three copies of the VP16 transactivation domain (LOV-VP16) enabled blue-light dependent recruitment of LOV-VP16 to the ZFP target sequence. We showed that placement of three to nine copies of a ZFP target sequence upstream of a luciferase or eGFP transgene enabled expression of the transgene in response to blue-light. Gene activation was both reversible and tunable based on duration of light exposure, illumination intensity, and the number of ZFP binding sites upstream of the transgene. Gene expression could also be spatially patterned by illuminating the cell culture through photomasks containing various patterns.</p><p>Although this system was useful for controlling the expression of a transgene, for many applications it is useful to control the expression of a gene in its natural chromosomal position. Therefore we capitalized on recent advances in programmed gene activation to engineer an optogenetic tool that could easily be targeted to new, endogenous DNA sequences without re-engineering the light inducible proteins. This approach took advantage of CRISPR/Cas9 technology, which uses a gene-specific guide RNA (gRNA) to facilitate Cas9 targeting and binding to a desired sequence, and the light-inducible heterodimerizers CRY2 and CIB1 from Arabidopsis thaliana to engineer a light-activated CRISPR/Cas9 effector (LACE) system. We fused the full-length (FL) CRY2 to the transcriptional activator VP64 (CRY2FL-VP64) and the N-terminal fragment of CIB1 to the N-, C-, or N- and C- terminus of a catalytically inactive Cas9. When CRY2-VP64 and one of the CIBN/dCas9 fusion proteins are expressed with a gRNA, the CIBN/dCas9 fusion protein localizes to the gRNA target. In the presence of blue light, CRY2FL binds to CIBN, which translocates CRY2FL-VP64 to the gene target and activates transcription. Unlike other optogenetic systems, the LACE system can be targeted to new endogenous loci by solely manipulating the specificity of the gRNA without having to re-engineer the light-inducible proteins. We achieved light-dependent activation of the IL1RN, HBG1/2, or ASCL1 genes by delivery of the LACE system and four gene-specific gRNAs per promoter region. For some gene targets, we achieved equivalent activation levels to cells that were transfected with the same gRNAs and the synthetic transcription factor dCas9-VP64. Gene activation was also shown to be reversible and repeatable through modulation of the duration of blue light exposure, and spatial patterning of gene expression was achieved using an eGFP reporter and a photomask. </p><p>Finally, we engineered a light-activated genetic "on" switch (LAGOS) that provides permanent gene expression in response to an initial dose of blue light illumination. LAGOS is a lentiviral vector that expresses a transgene only upon Cre recombinase-mediated DNA recombination. We showed that this vector, when used in conjunction with a light-inducible Cre recombinase system,1 could be used to express MyoD or the synthetic transcription factor VP64-MyoD2 in response to light in multiple mammalian cell lines, including primary mouse embryonic fibroblasts. We achieved light-mediated upregulation of downstream myogenic markers myogenin, desmin, troponin T, and myosin heavy chains I and II as well as fusion of C3H10T½ cells into myotubes that resembled a skeletal muscle cell phenotype. We also demonstrated LAGOS functionality in vivo by engineering the vector to express human VEGF165 and human ANG1 in response to light. HEK 293T cells stably expressing the LAGOS vector and transiently expressing the light-inducible Cre recombinase proteins were implanted into mouse dorsal window chambers. Mice that were illuminated with blue light had increased microvessel density compared to mice that were not illuminated. Analysis of human VEGF and human ANG1 levels by enzyme-linked immunosorbent assay (ELISA) revealed statistically higher levels of VEGF and ANG1 in illuminated mice compared to non-illuminated mice.</p><p>In summary, the objective of this work was to engineer robust light-inducible gene regulation systems that can control genes and cellular fate in a spatial and temporal manner. These studies combine the rapid advances in gene targeting and activation technology with natural light-inducible plant protein interactions. Collectively, this thesis presents several optogenetic systems that are expected to facilitate the development of multicellular cell and tissue constructs for use in tissue engineering, synthetic biology, gene therapy, and basic science both in vitro and in vivo.</p> / Dissertation

En complément aux méthodes traditionnelles d’observation et de stimulation en neuroscience, l’optogénétique, combinant l’expression ciblée de protéines photosensibles dans les neurones et l’utilisation de nouvelles techniques de microscopies, a connu un essor important ces dernières années. Ce nouveau procédé permet d’enregistrer de manière non invasive les signaux fonctionnels de circuits intacts tels que les changements de potentiel de membrane ou de concentration intracellulaire de calcium mais également de moduler l’excitabilité des neurones. Pour illuminer ces protéines photosensibles, de nouvelles méthodes de microscopie ont été développées. En particulier, afin d’obtenir une résolution spatiale optimale au sein d’un tissu biologique, il devient nécessaire d’utiliser l’illumination bi-photonique et d’utiliser des techniques permettant la mise en forme du faisceau lumineux pour s’adapter à la morphologie des circuits ou même des neurones étudiés.Au cours de ma thèse, j’ai développé une combinaison de méthodes optiques (associant le contraste de phase généralisé avec la focalisation temporelle) afin d’activer le canal cationique channelrhodopsin-2 en excitation bi-photonique. Ce travail a démontré, pour la première fois, l’activation simultanée de potentiels d’action dans plusieurs cellules tout en conservant une résolution axiale à l’échelle cellulaire (~10 μm).La mise en forme du faisceau lumineux semble très avantageuse pour améliorer la spécificité de l’activation. Il restait à démontrer que les faisceaux ainsi modulés conservaient leur intégrité spatiale en se propageant à l’intérieur de tissus biologiques diffusants. J’ai donc étudié la propagation de faisceaux lasers modulés par les techniques du contraste de phase généralisé et de l’holographie numérique en combinaison avec la focalisation temporelle. L’utilisation de la focalisation temporelle permet aux volumes d’excitation de rester confinés sur l’axe de propagation comme observé précédemment, mais aussi de reconstruire un profil d’excitation en profondeur dans le tissu, qui correspond au profile généré sans milieu diffusant. Cet effet est plus important pour le contraste de phase généralisé que pour l’holographie numérique et se dégrade en fonction de la profondeur à laquelle l’activation a lieu. J’ai démontré pour la première fois, l’activation en profondeur (> 200 μm) de neurones grâces à ces méthodes.Enfin, j’ai testé les mêmes techniques d’illumination sur d’autres protéines photosensibles, telles que la C1V1 et l’halorhodopsin. Après avoir établi les spectres d’activation afin de trouver la longueur d’onde optimale pour l’activation bi-photonique, j’ai exprimé ces protéines dans des tranches de cerveaux. Les deux protéines requièrent une activation à 1040 nm à la limite du laser Ti:Sapphire utilisé dans de nombreux laboratoires biologiques. La C1V1 a généré des courants similaires à la ChR2 en terme d’amplitude tout en conservant la lente cinétique de fermeture caractéristique de ce canal. L’halorhodopsin, quant à elle, reste difficile à activer avec de faibles courants et ne permet pas une inhibition sélective de trains de potentiels d’action. Ce problème est probablement dû à un faible taux d’expression observé dans les neurones étudiés et serait peut-être résolu en changeant de construction virale. / Optogenetics relies on the genetically targeted expression of light sensitive proteins in specific cell populations. This novel field has had a large impact in neuroscience, allowing both monitoring and stimulating the activity of specific neuronal populations, in intact brain preparations. Optogenetic tools have been used to record functional signals, such as changes in membrane potential or intracellular calcium concentration, as well as to modulate the excitability of neurons. To fully exploit the potentiality of optogenetics, new microscopy techniques have been developed to optimize illumination of photo-active compounds in situ. In particular, an important effort has been directed towards improving the spatial and temporal resolution of light stimulation, in order to match the dynamics of physiological processes. In this frame, the use of two-photon excitation becomes necessary to ensure penetration of light in scattering biological tissues, as well as confining the excitation volume and improve the specificity of illumination. My thesis was dedicated to the development and use of advanced optical methods for two-photon excitation of optogenetic tools. In a first project, we combined optical approaches (generalized phase contrast and temporal focusing) to perform two-photon activation of neurons expressing the light-sensitive cationic channel channelrhodopsin-2 (ChR2). Our work demonstrated for the first time the simultaneous generation of action potentials in multiple neurons, while maintaining a micrometric axial and lateral resolution. These results pointed out the advantages of light sculpting to increase both the specificity and the flexibility of photo-stimulation.In order to investigate the potential of this technique for efficient in-depth stimulation, we therefore studied the propagation through scattering biological media of laser beams generated by two different light patterning techniques, generalized phase contrast and digital holography in combination with temporal focusing. We demonstrated that temporal focusing enabled the excitation volumes to maintain micrometric axial confinement, as well as to maintain well defined patterns deep inside tissues. We also demonstrated for the first time the activation of ChR2 at depth over 200 μm.Finally, the last part of my PhD was focused on testing light patterning methods for the activation of two other photosensitive proteins, the excitatory channel C1V1 and the inhibitory pump, halorhodopsin.

Les mammifères, comme par exemple les rongeurs, soumis à des expériences aversives présentent des réponses comportementales de peur caractéristiques notamment une réponse d'immobilisation (freezing) ou d'évitement. Alors que le rôle du cortex préfrontal dorso-médian (CPFdm) dans l’acquisition ainsi que l’expression du freezing a déjà été expérimentalement établi, son implication dans l’encodage des réponses d’évitement de peur ainsi que l’interaction entre les circuits neuronaux préfrontaux impliqués dans le freezing et/ou l’évitement restent mal compris. Afin de répondre à ces questions, nous avons développé au laboratoire un paradigme expérimental permettant à une souris d’acquérir et d’exprimer le freezing ou l’évitement lors de la présentation d'un même stimulus aversif et ceci en fonction du contexte environnant. Ainsi, nous avons pu déterminer si les mêmes circuits neuronaux dans le cortex préfrontal dorso-médian encodent les deux réponses de peur, le freezing et l’évitement. Nous avons mis en oeuvre au cours de ce travail des approches comportementales, de traçage neuroanatomique, d'immunohistochimie, d'enregistrements extracellulaires in vivo et intracellulaires in vitro ainsi que des approches optogénétiques. Nos résultats indiquent que (i) le CPFdm et les régions dorsales de la substance grise périaqueducale sont activés pendant le comportement d'évitement, (ii) une sous population de neurones du CPFdm encode le comportement d'évitement mais pas le freezing, (iii) cette population neuronale projette sur le dl/lPAG, (iv) l'activation et l'inhibition optogénétique de cette projection induit et bloque l'apprentissage de l'évitement, respectivement et (v) l'apprentissage de l'évitement est associé à la mise en place d'une plasticité des afférences préfrontales sur le dl/lPAG. Dans leur ensemble ces résultats démontrent pour la première fois que la plasticité dépendante de l'activité des neurones du CPFdm projettant sur le dl/lPAG contrôle l'apprentissage de l'évitement de peur. / Mammals, including rodents show a broad range of defensive behaviors as a mean of coping with threatful stimuli including freezing and avoidance behaviors. Several studies emphasized the role of the dorsal medial prefrontal cortex (dmPFC) in encoding the acquisition as well as the expression of freezing behavior. However the role of this structure in processing avoidance behavior and the contribution of distinct prefrontal circuits to both freezing and avoidance responses are largely unknown. To further investigate the role of dmPFC circuits in encoding passive and active fear-coping strategies, we developed in the laboratory a novel behavioral paradigm in which a mouse has the possibility to either passively freeze to an aversive stimulus or to actively avoid it as a function of contextual contingencies. Using this behavioral paradigm we investigated whether the same circuits mediate freezing and avoidance behaviors or if distinct neuronal circuits are involved. To address this question, we used a combination of behavioral, neuronal tracing, immunochemistry, single unit and patch clamp recordings and optogenetic approaches. Our results indicate that (i) dmPFC and dorsolateral and lateral periaqueductal grey (dl/lPAG) sub-regions are activated during avoidance behavior, (ii) a subpopulation of dmPFC neurons encode avoidance but not freezing behavior, (iii) this neuronal population project to the dl/lPAG, (iv) the optogenetic activation or inhibition of this pathway promoted and blocked the acquisition of conditioned avoidance and (v) avoidance learning was associated with the development of plasticity at dmPFC to dl/lPAG synapses. Together, these data demonstrate for the first time that activity-dependent plasticity in a subpopulation of dmPFC cells projecting to the dl/lPAG pathway controls avoidance learning.

La stabilité structurale et l'intégrité mécanique sont des éléments clés pour le bon fonctionnement et la préservation des systèmes vivants complexes. Étant en interaction constante avec leur environnement et en ce qui concerne les intrants externes, de tels systèmes doivent pouvoir faire face aux changements afin de prospérer. Ces entrées peuvent affecter le système dans son ensemble. Toute perturbation qui ne peut pas être supportée mécaniquement par le système vivant entraînera un dysfonctionnement crucial ou, en fin de compte, sa mort. Le mécanisme responsable du maintien des conditions physiologiques du système à l'état correct, malgré les variations environnementales, est identifié comme étant l'homéostasie. Plus précisément, le processus connu en mécanobiologie pour préserver l'équilibre mécanique approprié d'un système vivant est appelé homéostasie tensionnelle.Il est important de noter que tout ce qui précède est vrai à la fois à l'échelle du comportement collectif des organismes complexes et jusqu'au niveau de la cellule unique. En fait, c'est en fait cette dernière petite échelle qui nous intéresse. Les cellules font face à des perturbations mécaniques constantes de leur environnement et sont capables de répondre au maintien d'un état mécanique interne relativement stable. L'existence de cet équilibre tensionnel interne est liée à un processus très dynamique avec des boucles de rétroaction constantes entre les machines contractiles biochimiques internes et les forces actives externes générées.Notre intérêt est de comprendre ce mécanisme dynamique en perturbant dynamiquement le système homéostatique tensionnel en étudiant son retour à l'équilibre. / The structural stability and mechanical integrity are key elements for the proper functioning and preservation of complex living systems. Being in constant interaction with their surroundings and subjected to external inputs, such systems need to be able to face changes in order to thrive. These inputs can affect the system both in a localized way or disturb it as a whole. Any perturbations that cannot be mechanically withstand by the living system will result in a crucial malfunctioning or, ultimately, in its death. The mechanism responsible for maintaining the system’s physiological conditions at the proper state, despite environmental variations, is identified as homeostasis. More specifically, the process known in mechanobiology to preserve the appropriate mechanical equilibrium of a living system is called tensional homeostasis.It is important to note that all of the above stated holds true both at the scale of collective behaviour of complex organisms, and all the way down to the single cell level. In fact, it is actually this last small scale which draws our interest. Cells face constant mechanical perturbations from their surrounding and are able to respond accordingly maintaining a relatively stable internal mechanical state. The existence of this internal tensional equilibrium relies on a very dynamic process with constant feedback loops between the internal biochemical contractile machinery and the external active generated forces.Our interest is to understand better this active mechanism by dynamically perturbing the tensional homeostatic system while studying its return to equilibrium.

Un cadre théorique classique pour expliquer comment les mouvements volontaires sont générés et optimisés implique l'existence d'un modèle interne basé sur les conséquences sensorielles de ses propres actions. Le cervelet est souvent considéré comme une structure où ces modèles pourraient être efficacement stockés et mis-à-jour. Parmi tous les systèmes sensoriels, le système vestibulaire est probablement celui où la plus grande proportion de stimuli est auto-générés et pourtant peu étudié en conditions actifs. Pour appréhender le rôle du vestibulo-cervelet, nous avons enregistré des cellules de Purkinje du nodulus en condition active chez le rongeur, associé à l'enregistrement quantitatif des signaux inertiels produits par les mouvements de la tête. Cela a nécessité le développent d'outils de mesure adaptés au petit animal. Ces outils, absents du commerce, sont capable d'enregistrer, et cela sans aucun câble, les mouvements inertiels (accélération linéaire et vitesse angulaire) de celui ci offrant une représentation des informations vestibulaires. Les résultats présentés dans cette thèse montrent que, au moins dans des conditions actives, les cellules de Purkinje présentent une sensibilité sélective à certaines composantes du mouvement de la tête. La diversité des réponses observées démontre de plus que chaque cellule possède son propre " champ récepteur vestibulaire ". Il a ainsi été montré que certaines cellules avaient un champ récepteur en coordonnées égocentriques et d'autres allocentriques. Cette distinction s'inscrit dans le problème général de la transformation par le cervelet des coordonnées vestibulaires et de la représentation de l'environnement. / A classical and theoretical explaining framework how voluntary movements are generated and optimized implies the existence of an internal model based on the sensory consequences of own actions. The cerebellum is often considered as a structure where the models could be effectively stored and made-to-day. Of all the sensory systems, the vestibular system is probably one where the largest proportion of stimuli are self-generated but yet little studied in active conditions. To understand the role of the vestibular-cerebellum, we recorded Purkinje cells from nodulus in active condition in rodents associated with quantitative recording of inertial signals produced by head motion. This required developing the measurement tools adapted to small animals. These tools, absent of trade, are capable of recording, without any cables, the inertial movement (linear acceleration and angular velocity) of this one as a representation of vestibular information. The results presented in this thesis show that, at least in active condition, Purkinje cells exhibit selective sensitivity to certain components of the head movement. The diversity of responses observed further demonstrates that each cell has its own "vestibular receptive field". It has thus been shown that some cells have a receptive field in egocentric coordinates while others allocentric. This results is part of the general problem of the coordinate transformation and of the environment representation by the vestibular cerebellum.

<div><div><div><p>Increased meal size on a western diet is a major contributor to development and maintenance of obesity. This also leads to decreased sensitivity to the satiating effects of the western diet. Excitation of cells during consumption of a meal in the caudal two-thirds of the nucleus solitary tract (cNTS) in the brainstem are thought to produce satiation and inhibit feeding. Currently, it is unknown how excitation of these cells inhibits feeding. A major obstacle has been the inability to selectively manipulate these cells without affecting intermixed cells that mediate other autonomic functions. We propose a novel approach using inducible, activity-dependent chemogenetics or optogenetics to test whether artificial excitation of cells in the caudal two-thirds of the nucleus solitary tract (cNTS) activated during satiation can reduce food intake and could contribute to preventing or reversing obesity in humans.</p><p>We tested four different mouse models with potential for answering this question: double transgenic mice with cFos-tTA & Tet-O-hM3Dq genes, a single transgenic cFos-tTA mouse with a virally delivered hM3Dq gene injected into the cNTS, a double transgenic mice with the TRAP2- tdTomato genes and double transgenic mice with c-Fos-tTA and ChEF genes. Evidence suggested that clozapine-N-oxide might activate satiation-related cells in the absence of the hM3Dq receptor and this should be taken into consideration for future experiments. All four models had promising aspects for studying feeding as well as serious limitations. These limitations will need to be considered when deciding to use any of these models to study any feeding behaviors, especially satiation.</p></div></div></div>

Previous research investigating the neural circuitry underlying memory consolidation has primarily focused on single “nodes” in the circuit rather than the neural connections between brain regions, despite the likely importance of these connections in mediating different aspects or forms of memory. This focus has, in part, been due to technical limitations; however the advent of optogenetics has altered our capabilities in this regard, enabling optical control over neural pathways with temporal and spatial precision. The current set of experiments took advantage of optogenetics to control activity in specific pathways connecting brain regions in rats immediately after different kinds of learning. Chapter 2 first established the use of optogenetics to manipulate activity in the basolateral amygdala (BLA), which has been shown to modulate memory consolidation for a variety of types of learning likely through its connections to various downstream regions. Using a one-trial inhibitory avoidance task, a simple and robust fear learning paradigm, we found that both post-training stimulation and inhibition of BLA activity could enhance or impair later retention of the task, respectively. Enhancement was specific to stimulation using trains of 40, but not 20, Hz light pulses. Chapters 3 and 4 examined the projections from the BLA to the ventral hippocampus (VH) and medial entorhinal cortex (mEC) as the BLA’s ability to influence the consolidation for many types of memory is believed to be mediated through discrete projections to distinct brain regions. Indeed, the BLA innervates both structures, and prior studies suggest that the mEC and VH have distinct roles in memory processing related to contextual and nociceptive (footshock) learning, such as those involved in contextual fear conditioning (CFC). Optogenetic stimulation or inhibition of the BLA-VH or BLA-mEC pathway after training on a modified CFC task, in which the nociceptive or emotional stimulus (the footshock) and the context are separated, enabled experimental manipulations to selectively affect the consolidation for learning about one component and not the other. Optogenetic stimulation/inhibition was given to each candidate pathway immediately after the relevant training to determine its role in influencing consolidation for that component of the CFC learning. Chapter 3 results showed that stimulation of the BLA-VH pathway following footshock, but not context, training enhanced retention, an effect that was specific to trains of 40 Hz stimulation. Post-footshock photoinhibition of the same pathway impaired retention for the task. Similar investigations of the BLA-mEC pathway in Chapter 4 produced complementary findings. Post-context, but not footshock, stimulation of the pathway enhanced retention. In this particular case, only trains of 8 Hz stimulation were effective at enhancing retention. These results are the first, to our knowledge, to find that BLA inputs to different structures selectively modulate consolidation for different aspects of learning, thus enhancing our understanding of the neural connections underlying the consolidation of contextual fear conditioning and providing a critical foundation for future research.

The field of neuroscience has recently seen optogenetics emerge as a highly utilized and powerful method of non-invasive neural activation and inhibition. This thesis seeks to enhance the optogenetic toolbox through the design, construction, and evaluation of a number of hardware and software modules for research in Caenorhabditis elegans neuroscience. In the first aim, we combine optogenetics, microfluidics, and automated image processing, to create a system capable of high-throughput analysis of synaptic function. In the second aim, we develop a multi-modal illumination system for the manipulation of optogenetic reagents. The system is capable of multi-spectral illumination in definable patterns, with the ability to dynamically alter the intensity, color, and shape of the illumination. The illumination system is controlled by a set of software programs introduced in aim three, and is demonstrated through a set of experiments in aim four where we selectively activate and inhibit specific neural nodes expressing optogenetic reagents in freely moving C. elegans. With the ability to target specific nodes in a freely moving animal, we can correlate specific neural states to behaviors allowing for the dissection of neural circuits. Taken together, the developed technologies for optogenetic researchers will allow for experimentation with previously unattainable speed, precision and flexibility.

A principal goal of neural engineering is to control the activation of neural circuits across space and time. The ability to control neural circuits with surrogate inputs is needed for the development of clinical neural prostheses and the experimental interrogation of connectivity between brain regions. Electrical stimulation provides a clinically viable method for activating neural tissue and the emergence of optogenetic stimulation has redefined the limitations on stimulating neural tissue experimentally. However, it remains poorly understood how these tools activate complex neural circuits. The goal of this proposed project was to gain a greater understanding of how to control the activity of neural circuits in-vivo using a combination of experimental and computational approaches. Voltage sensitive dye imaging was used to observe the spatiotemporal activity within the rodent somatosensory cortex in response to systematically varied patterns of sensory, electrical, and optogenetic stimulation. First, the cortical response to simple patterns of sensory and artificial stimuli was characterized and modeled, revealing distinct neural response properties due to the differing synchrony with which the neural circuit was engaged. Then, we specifically designed artificial stimuli to improve the functional relevance of the resulting downstream neural responses. Finally, through direct optogenetic modulation of thalamic state, we demonstrate control of the nonlinear propagation of neural activity within the thalamocortical circuit. The combined experimental and computational approach described in this thesis provides a comprehensive description of the nonlinear dynamics of the thalamocortical circuit to surrogate stimuli. Together, the characterization, modeling, and overall control of downstream neural activity stands to inform the development of central nervous system sensory prostheses, and more generally provides the initial tools and framework for the control of neural activity in-vivo.

This work presents optogenetics and real-time computer vision techniques to non-invasively manipulate and monitor neural activity with high spatiotemporal resolution in awake behaving Caenorhabditis elegans. These methods were employed to dissect the nematode's mechanosensory and motor circuits and to elucidate the neural control of wave propagation during forward locomotion. Additionally, similar computer vision methods were used to automatically detect and decode fluorescing DNA origami nanobarcodes, a new class of fluorescent reporter constructs.