La première partie de cette thèse présente une revue historique sur les méthodes d'enregistrements d'activité neuronale, suivie par une étude sur une nouvelle technique d'imagerie pour le poisson zèbre : la microscopie par nappe laser 2 photon. En combinant, les avantages de la microscopie 2 photon et l'imagerie par nappe de lumière, le microscope par nappe laser 2 photon garantie des enregistrements à haute vitesse avec un faible taux de lésions photoniques et permet d'éviter l'une des principales limitations du microscope à nappe laser 1 photon: la perturbation du système visuel. La deuxième partie de cette thèse traite de la navigation dirigée. Après une revue exhaustive sur la chemotaxis, la phototaxis et la thermotaxis, nous présentons des résultats qui révèlent les bases neuronales de la phototaxis chez le poisson zèbre. Grace à des expériences de comportement en réalité-virtuelle, des enregistrements d'activité neuronale, des méthodes optogénétiques et des approches théoriques, ce travail montre qu'une population auto-oscillante située dans le rhombencéphale appelée l'oscillateur du cerveau postérieur (HBO) fonctionne comme un pacemaker des saccades oculaires et contrôle l'orientation des mouvements de nage du poisson zèbre. Ce HBO répond à la lumière en fonction du contexte moteur, biaisant ainsi la trajectoire du poisson zèbre vers les zones les plus lumineuses de son environnement (phototaxis). La troisième partie propose une discussion sur les bases neuronales des saccades oculaires chez les vertébrés. Nous concluons ce manuscrit avec des résultats préliminaires suggérant que chez le poisson zèbre, le même HBO est impliqué dans les processus de thermotaxis. / The first part of this thesis presents an historical overview of neural recording techniques, followed by a study on the development of a new imaging method for zebrafish neural recording: two-photon light sheet microscopy. Combining the advantages of two-photon point scanning microscopy and light sheet techniques, the two-photon light sheet microscope warrants a high acquisition speed with low photodamage and allows to circumvent the main limitation of one-photon light sheet microscopy: the disturbance of the visual system. The second part of the thesis is focused on goal-directed navigation in zebrafish larvae. After an exhaustive review on chemotaxis, phototaxis and thermotaxis in various animal models, we report a study that reveals the neural computation underlying phototaxis in zebrafish. Combining virtual-reality behavioral assays, volumetric calcium recordings, optogenetic stimulation, and circuit modeling, this work shows that a self-oscillating hindbrain population called the hindbrain oscillator (HBO) acts as a pacemaker for ocular saccades, controls the orientation of successive swim-bouts during zebrafish larva navigation, and is responsive to light in a state-dependent manner such that its response to visual inputs varies with the motor context. This peculiar response to visual inputs biases the fish trajectory towards brighter regions (phototaxis). The third part provides a discussion on the neural basis of ocular saccades in vertebrates. We conclude with some recent preliminary results on heat perception in zebrafish suggesting that the same hindbrain circuit may be at play in thermotaxis as well.

Motile microorganisms navigate through their environment using special molecular machinery in order to sense gradients of various signals: chemotaxis (reactions to chemical compounds) and phototaxis (to light) sensory cascades. Transmembrane receptors play a central role in these cascades as they receive input signals and transmit them inside the cell, where they modulate activity of the kinases CheA, which are tightly bound to their cytoplasmic domains. CheA further phosphorylates the response regulator protein CheY, which regulates the flagella. At the same time, CheA phosphorylates and, by means of this, activates another response regulator, CheB, which, along with the constantly active CheR protein, catalyzes two opposite reactions: methylation and demethylation of the specific glutamic acid residues located at the cytoplasmic domain of the receptors. The latter reactions establish the adaptation mechanism, which allows microbes to sense in a very broad range of the input signal intensities. Many functional, structural and dynamical aspects of the signal propagation through the prokaryotic receptors as well as a mechanism of the signal amplification remain still unclear. In the present thesis we have used various techniques of computational biophysics, chiefly molecular dynamics (MD) simulations, in order to approach these problems. In Chapter 3, we have carried out MD simulations of the isolated linker domain (HAMP) from the E. coli Tsr chemoreceptor. The MD simulations revealed highly dynamical nature of this domain, which allows for interconversion between several metastable states. These metastable states feature a number of structural and dynamical properties, which were previously reported for HAMP domains of various receptors obtained from different organisms. It allowed us to reconcile numerous experimental data and to hypothesize that different HAMP domains share similar mechanism of their action. In Chapter 4, we have performed MD simulations of the whole cytoplasmic domain of the Tsr chemoreceptor. The simulations revealed a mechanism for the inter-domain coupling between the HAMP domain and a part of the cytoplasmic domain adjacent to the HAMP, the adaptation subdomain, by means of the regulated unfolding of a short linker region termed the stutter. Also, we have found that the reversible methylation/demethylation of the cytoplasmic domain affects its flexibility and symmetry. Altogether, these findings suggest a mechanism of signal propagation at the level of an individual chemoreceptor dimer. In Chapter 5, we have built a model of the trimer-of-dimers of the archaeal phototaxis receptor complex (NpSRII:NpHtrII). Subsequent MD simulations revealed an important role of dynamics in signal transduction and, potentially, in the kinase activation. In Chapter 6, we have reconstructed a whole transmembrane lattice formed by the NpSRII:NpHtrII complexes. The concave shape of the obtained lattice naturally explains polar localization of the receptor arrays in prokaryotic cells. At the same time, additional MD simulations of an individual unit of this lattice (a dimer of the photosensor) revealed global motional modes in its transmembrane region, which presumably co-occur with its activation and can spread across the tightly packed transmembrane arrays allowing for the signal amplification.

A distribuição da biomassa do plâncton é a chave para o entendimento de vários processos inclusive a compreensão da migração vertical diurna. Entender a fototaxia positiva, como responsável por esta distribuição, com enfoque na qualidade espectral da luz é uma campo vasto a ser explorado. Investigamos a percepção espectral luminosa do mesozooplâncton marinho através da quantificação de capturas em uma nova arte de coleta com armadilha de luz. Estas armadilhas foram testadas com tratamentos luminosos na cor vermelha, verde, azul e branco. Elas foram fundeadas na enseada do Flamengo e de Ubatuba (Ubatuba-SP) no fim do verão e outono de 2015 durante a lua cheia e lua nova em três noites consecutivas. Foram avaliadas as associações de exposição (fase lunar, local de coleta e esquema de randomização dos tratamentos) baseada nos dados de captura através de gráficos NMDS, teste PERMANOVA e tabelas de contingência de Chi-quadrado. Os táxons mais abundantes nas capturas foram dois gêneros de copépodes Calanoida (Acartia sp e Temora sp) seguidos pela família Podonidae e Brachyura. Demonstramos que os organismos capturados do zooplâncton marinho expressaram seleção espectral induzidos pela fototaxia positiva. O tratamento luminoso verde exerceu maior atração nos organismos em detrimento ao tratamento luminoso vermelho. A influência das fases lunares ou dos esquemas de randomização dos tratamentos luminosos dependem da sensibilidade espectral de cada táxon. Porém local não implicou em diferenças entre as coletas. Estas particularidades da fototaxia positiva seletiva podem explicar a variação vertical da biomassa do zooplâncton marinho na coluna d\'água inclusive no entendimento da MVD. / The distribution of plankton biomass is the key for understanding many processes including diel vertical migration (DVM). Understand the positive phototaxis, as responsible for this distribution, with a focus on spectral quality of light is a vast field to be explored. We investigate the spectral light perception of the marine mesozooplankton through quantification of catches in a new art with light trap. These traps were tested with light treatments in red, green, blue and white. They were anchored in the Flamengo and Ubatuba bay (Ubatuba-SP) in late summer and autumn of 2015 during the full moon and new moon on three consecutive nights. Exposure associations were evaluated (lunar phase, site and treatment randomization scheme) based on the data capture through NMDS graphics, PERMANOVA test and Chi-square contingency tables. Most abundant taxa catched were two kinds of copepods Calanoida (Acartia sp and Temora sp) followed by Podonidae and Brachyura. We have demonstrated that the captured marine zooplankton showed spectral selection induced by positive phototaxis. The green light treatment exerted biggest attraction in organisms over the red light treatment. The influence of lunar phases or randomization schemes of bright treatments depend on the spectral sensitivity of each taxon. But location did not result in differences between collections. These specifics of selective phototaxis may explain the vertical variation of marine zooplankton biomass in water column including the understanding of DVM.

A distribuição da biomassa do plâncton é a chave para o entendimento de vários processos inclusive a compreensão da migração vertical diurna. Entender a fototaxia positiva, como responsável por esta distribuição, com enfoque na qualidade espectral da luz é uma campo vasto a ser explorado. Investigamos a percepção espectral luminosa do mesozooplâncton marinho através da quantificação de capturas em uma nova arte de coleta com armadilha de luz. Estas armadilhas foram testadas com tratamentos luminosos na cor vermelha, verde, azul e branco. Elas foram fundeadas na enseada do Flamengo e de Ubatuba (Ubatuba-SP) no fim do verão e outono de 2015 durante a lua cheia e lua nova em três noites consecutivas. Foram avaliadas as associações de exposição (fase lunar, local de coleta e esquema de randomização dos tratamentos) baseada nos dados de captura através de gráficos NMDS, teste PERMANOVA e tabelas de contingência de Chi-quadrado. Os táxons mais abundantes nas capturas foram dois gêneros de copépodes Calanoida (Acartia sp e Temora sp) seguidos pela família Podonidae e Brachyura. Demonstramos que os organismos capturados do zooplâncton marinho expressaram seleção espectral induzidos pela fototaxia positiva. O tratamento luminoso verde exerceu maior atração nos organismos em detrimento ao tratamento luminoso vermelho. A influência das fases lunares ou dos esquemas de randomização dos tratamentos luminosos dependem da sensibilidade espectral de cada táxon. Porém local não implicou em diferenças entre as coletas. Estas particularidades da fototaxia positiva seletiva podem explicar a variação vertical da biomassa do zooplâncton marinho na coluna d\'água inclusive no entendimento da MVD. / The distribution of plankton biomass is the key for understanding many processes including diel vertical migration (DVM). Understand the positive phototaxis, as responsible for this distribution, with a focus on spectral quality of light is a vast field to be explored. We investigate the spectral light perception of the marine mesozooplankton through quantification of catches in a new art with light trap. These traps were tested with light treatments in red, green, blue and white. They were anchored in the Flamengo and Ubatuba bay (Ubatuba-SP) in late summer and autumn of 2015 during the full moon and new moon on three consecutive nights. Exposure associations were evaluated (lunar phase, site and treatment randomization scheme) based on the data capture through NMDS graphics, PERMANOVA test and Chi-square contingency tables. Most abundant taxa catched were two kinds of copepods Calanoida (Acartia sp and Temora sp) followed by Podonidae and Brachyura. We have demonstrated that the captured marine zooplankton showed spectral selection induced by positive phototaxis. The green light treatment exerted biggest attraction in organisms over the red light treatment. The influence of lunar phases or randomization schemes of bright treatments depend on the spectral sensitivity of each taxon. But location did not result in differences between collections. These specifics of selective phototaxis may explain the vertical variation of marine zooplankton biomass in water column including the understanding of DVM.

This research explores the capacity for functional photoreception in larvae of the mountain pine beetle (Dendroctonus ponderosae), an extremely important forest pest insect that is well adapted for development beneath the bark of pine trees. Phototaxis tests, gene expression analysis and development experiments were integrated to assess mountain pine beetle larvae for light sensitivity. When presented with a phototaxis choice test, larvae preferred dark over light microhabitats, revealing that larvae sense and respond behaviourally to light. Long wavelength opsin transcription was identified in all life stages, including eggs and larvae, suggesting that D. ponderosae possesses extraretinal photosensitive capabilities across its life cycle. The long wavelength opsin could function in phototaxis or the development phenology of immature beetles, while the ultraviolet opsin, only found to be expressed in pupae and adults, is likely to function in dispersal via the compound eyes. Results from two development experiments reveal an effect of photoperiod treatment on beetle development rate when reared from the egg stage, but not when reared from mature larvae, indicating that a critical photosensitive life stage(s) must occur in D. ponderosae prior to the third larval instar. An effect of photoperiod on adult emergence rates, however, appears to be independent of larval rearing conditions. The discovery of opsin expression and negative phototaxis in eyeless mountain pine beetle larvae, in addition to an effect of photoperiod on immature development and adult emergence rates, suggest that light and photoperiodism likely function in survival and life cycle coordination in this species. / Graduate / 2018-10-17