Thesis (Ph. D.)--Oregon State University, 2006. / Blank pages 143 and 159 not microfilmed. Includes bibliographical references.

Gerald M. Edelman, Vernon B. Mountcastle ; introd. by Francis O. Schmitt. / Based on papers presented at the fourth intensive study program of the Neurosciences Research Program, held in June 1977. / Includes bibliographies.

abstract: Recombinases are powerful tools for genome engineering and synthetic biology, however recombinases are limited by a lack of user-programmability and often require complex directed-evolution experiments to retarget specificity. Conversely, CRISPR systems have extreme versatility yet can induce off-target mutations and karyotypic destabilization. To address these constraints we developed an RNA-guided recombinase protein by fusing a hyperactive mutant resolvase from transposon TN3 to catalytically inactive Cas9. We validated recombinase-Cas9 (rCas9) function in model eukaryote Saccharomyces cerevisiae using a chromosomally integrated fluorescent reporter. Moreover, we demonstrated cooperative targeting by CRISPR RNAs at spacings of 22 or 40bps is necessary for directing recombination. Using PCR and Sanger sequencing, we confirmed rCas9 targets DNA recombination. With further development we envision rCas9 becoming useful in the development of RNA-programmed genetic circuitry as well as high-specificity genome engineering. / Dissertation/Thesis / Masters Thesis Biology 2018

La mise en place des circuits neuronaux fonctionnels se construit autour d'une grande diversité cellulaire et nécessite l'accomplissement d'une série d'évènements complexes incluant la prolifération, la migration, la différenciation, le guidage axonal, la reconnaissance cellulaire et la synaptogenèse des progéniteurs neuronaux. Dans le cervelet, les interneurones GABAergiques de la couche moléculaire (IGCM) s‘intègrent au cours des deux premières semaines post-natales et se différencient en deux sous-types cellulaires, les cellules en panier (CP) qui innervent le segment initial de la cellule de Purkinje, cellule principale du cervelet, et les cellules étoilées qui innervent l'arbre dendritique de la cellule Purkinje. Bien que ces deux types cellulaires possèdent des morphologies distinctes et innervent des sous-domaines cellulaires spécifiques, aucun marqueur moléculaire ne permet de les discriminer. Depuis près d'un siècle, la controverse existe concernant leur identité et deux théories s'affrontent. La première suggère que ces deux cellules sont des variantes issues d'un même progéniteur et que les différences morphologiques sont dues à un changement progressif de l'environnement cellulaire alors qu'une autre hypothèse suggère que ces deux cellules proviennent de progéniteurs neuronaux différents. Au cours de ma thèse j'ai étudié l'intégration des IGCM au sein de la couche moléculaire (CM) en caractérisant deux étapes clés de la formation des circuits GABAergiques, la migration et l'innervation de leur cible. En utilisant une combinaison de techniques telles que la microscopie bi-photonique et les greffes in vivo de progéniteurs neuronaux, j'ai mis en évidence que durant la première semaine post-natale, les IGCM quittent leur lieu de naissance pour rejoindre la CM en réalisant une seule étape de migration radiale. De manière intéressante certains IGCM accomplissent une étape de migration supplémentaire inédite tangentiellement à la surface piale pendant la deuxième semaine post-natale. Cette nouvelle phase de migration tangentielle des IGCM se déroule au sein de la couche granulaire externe où résident les cellules granulaires pré-migratoires dont les fibres qui expriment TAG-1 jouent un rôle essentiel en tant que support physique et participent à l'établissement des IGCM en mode “inside-out”. De plus, nos résultats suggèrent que seule une sous-population de type cellule étoilée effectuerait cette étape supplémentaire, montrant ainsi une première divergence dans le processus de maturation des IGCM. Par la suite, je me suis intéressée à l'innervation des cellules de Purkinje par les CP nouvellement différenciées. En utilisant des techniques d'immuno-histochimie, j'ai tout d'abord montré que la Neuropiline-1 (NRP1), un des récepteurs de la Sémaphorine-3A, était exprimé au niveau des terminaisons axonales des CP. Enfin, grâce à l'analyse d'un mutant conditionnel pour NRP1, j'ai pu mettre en évidence qu'en plus de son rôle crucial dans le guidage axonal des CP, NRP1 est également impliquée dans l'innervation spécifique du segment initial axonal des cellules de Purkinje en interagissant avec une molécule d'adhésion cellulaire de la famille L1CAM, la Neurofascine. Ces résultats démontrent pour la première fois un rôle de NRP1 dans la transition entre l'étape de guidage avec celle de la reconnaissance cellulaire par les CP. En conclusion, nos résultats suggèrent fortement que les deux sous-types d'IGMC possèdent un programme génétique spécifique leur permettant de s'intégrer de manière unique au sein de la CM. / The establishment of functional neural circuits is built around a large cell diversity and requires the completion of a series of complexe events including proliferation, migration, differentiation, axon guidance, cell recognition and synaptogenesis of neural precursors. In the cerebellum, molecular layer GABAergic interneurons (MLGI) reach their final location during the first two post-natal weeks and differentiate into two cellular subtypes, the basket cells (BC) that innervate the Purkinje cell initial segment and the stellate cells that innervate the dendritic tree of the Purkinje cell, the principal cell of cerebellar cortex. Although these two cell types have distinct morphologies and innervate specific subcellular domains, no molecular marker allows to discriminate between them. For nearly a century, controversy exists concerning their identity and two theories exist. The first one suggests that these two cell types are variants derived from a single progenitor and that morphological divergence is due to a gradual change in the cellular environment while the other hypothesis suggests that these two cell types come from different progenitors. During my thesis, I studied the integration of the MLGI in the molecular layer (ML) characterizing two key steps in the formation of GABAergic circuits, migration and innervation of their target. Using a combination of techniques such as two-photon microscopy and in vivo transplantation of neural progenitors, I highlighted that during the first post-natal week, MLGI leave their birthplace to join the ML by performing a single radial migration step. Interestingly, some MLGI perform an unexpected additional migration step tangentially to the pial surface during the second post-natal week. This new phase of MLGI tangential migration takes place in the external granule cell layer where resident pre-migratory granule cells whose fibers expressing TAG-1 play an essential role as physical support and participate in the establishment of MLGI « inside-out » mode. In addition, our results suggest that only a stellate-like subpopulation would perform this extra step, bringing the first indication of an early divergence during MLGI maturation process. Then, I was interested in the innervation of Purkinje cells by newly differentiated BC. Using immunohistochemistry experiments, I first showed that Neuropilin-1 (NRP1), a Semaphorin-3A receptor, was expressed in the BC axon terminals. Finally, through the analysis of a NRP1 conditional mutant, I brought out that, in addition to its critical implication in axon guidance, NRP1 is also involved in the specific innervation of the Purkinje cell axon initial segment by interacting with a cell adhesion molecule belonging to the L1 family, Neurofascin. These results demonstrate for the first time a role of NRP1 in the transition between the guidance and the cell recognition steps by BC. In conclusion, our results strongly support that the two MLGI subtypes have a specific genetic program allowing them to integrate within the ML in a unique manner.

Dissociated neuronal cell cultures grown on substrate integrated microelectrode arrays (MEAs) generate spontaneous activity that can be recorded for up to several weeks. The signature wave shapes from extracellular recording of neuronal activity display a great variety of shapes with triphasic signals predominating. I characterized extracellular recordings from over 600 neuronal signals. I have preformed a categorical study by dividing wave shapes into two major classes: (type 1) signals in which the large positive peak follows the negative spike, and (type 2) signals in which the large positive peak precedes the negative spike. The former are hypothesized to be active signal propagation that can occur in the axon and possibly in soma or dendrites. The latter are hypothesized to be passive which is generally secluded to soma or dendrites. In order to verify these hypotheses, I pharmacologically targeted ion channels with tetrodotoxin (TTX), tetraethylammonium (TEA), 4-aminopyridine (4-AP), and monensin.

Changes in spontaneous spike activities recorded from murine frontal cortex networks grown on substrate-integrated microelectrodes were used to determine the dissociation constant (KB) of three GABAA antagonists. Neuronal networks were treated with fixed concentrations of GABAA antagonists and titrated with muscimol, a GABAA receptor agonist. Muscimol decreased spike activity in a concentration dependent manner with full efficacy (100% spike inhibition) and a 50% inhibitory concentration (IC50) of 0.14 ± 0.05 µM (mean ± SD, n=6). At 10, 20, 40 and 80 µM bicuculline, the muscimol IC50 values were shifted to 4.3 ± 1.8 µM (n=6), 6.8 ± 1.7 µM (n=6), 19.3 ± 3.54 µM (n=10) and 43.5 µM (n=2), respectively (mean ± SD). Muscimol titration in the presence of 10, 20, 40 µM of gabazine resulted in IC50s values of 20.1 (n=2), 37.17 (n=4), and 120.45 (n=2), respectively. In the presence of 20, 80, and 160 µM of TMPP (trimethylolpropane phosphate) the IC50s were 0.86 (n=2), 3.07 (n=3), 6.67 (n=2) µM, respectively. Increasing concentrations of GABAA antagonists shifted agonist log concentration-response curves to the right with identical efficacies, indicating direct competition for the GABAA receptor. A Schild plot analysis with linear regression resulted in slopes of 1.18 ± 0.18, 1.29 ± 0.23 and 1.05 ± 0.03 for bicuculline, gabazine and TMPP, respectively. The potency of antagonists was determined in terms of pA2 values. The pA2 values were 6.63 (gabazine), 6.21 (bicuculline), and 5.4 (TMPP). This suggests that gabazine has a higher binding affinity to the GABAA receptor than bicuculline and TMPP. Hence, using spike rate data obtained from population responses of spontaneously active neuronal networks, it is possible to determine key pharmacological properties of drug-receptor interactions.

Simple circuits perform simple tasks. Complex circuits can perform more complicated tasks. This is true for artificial circuits and for brain circuits. As is known from artificial networks, a complexity that makes circuits substantially more powerful is distributing learning across multiple layers. In fact, most brain circuits in vertebrate systems are multi-layer circuits (but for few that perform simple reflexes) in which learning is distributed across layers. Despite the crucial contribution of learning in middle layer neurons to the output of the circuits they are embedded in, there is little understanding of the principles defining this contribution. A very common feature in brain circuits is that middle layer neurons generate two types of signals, known as spikes. These middle layer neurons commonly have long dendrites where they generate dendritic spikes. As well, like most neurons, they generate axonal spikes near the cell body. Neurons exhibiting these two spike types include pyramidal cells in the neo-cortex and the hippocampus, the Purkinje cells in the cerebellum and many more. In this thesis I study another circuit that contains middle layer neurons, the electrosensory lateral lobe (ELL) of the mormyrid fish. The ELL is a tractable brain circuit in which the middle layer neurons generate dendritic and axonal spikes. In this thesis I show that these spike types are not two different expressions of the same inputs. Rather, they have a symbiotic relationship. Instead of all inputs triggering both spikes, some inputs can selectively drive dendritic spikes. The dendritic spikes in return modify the synaptic strength of another set of inputs. The modified inputs are then transmitted to downstream neurons via the axonal spikes, which contributes a desired signal to the output of the circuits. Effectively there is a separation of learning and signaling in the middle layer neurons through the two spike types. Having two types of spikes in the same neuron doing different computations enormously expands the computational power of the neuron. But, being in the same neuron means the separation of function is constrained and needs to be supported by biophysical principles. I have thus built a biophysical model to understand the biophysical principles underlying the separation of function. I show that in the middle layer neurons of the ELL, the axonal spikes are strongly reduced in amplitude as they backpropagate to the apical dendrites, yet they remain crucial in driving dendritic spikes. Critically, modulation of inhibitory inputs can selectively dial up or down the ability of the backpropagating axonal spikes to drive dendritic spikes. Thus, a set of inhibitory modulating inputs can selectively modulate dendritic spikes. Having learning in different layers contributing to the outcome of the circuit, naturally leads to asking how the work is divided across layers and neuron types within the circuit. In this thesis I answer this question in the context of the outcome of the ELL circuit. Finally, another signature of a complex circuit is the ability to integrate many different inputs, usually in middle layer neurons, to generate sophisticated outputs. A goal for scientists studying systems neuroscience is to understand how this integration works. In this thesis I provide a coherent model of a learning behavior called vestibulo occular reflex (VOR) adaptation, that depends on the integration of separate inputs to yield a learned behavior. The VOR is a simple reflex generated in the brain stem. Inputs from the brain stem are also sent to an area in the cerebellar cortex called the flocculus. The flocculus also receives another set of inputs that generate a different behavior, called smooth-pursuit. The integration of VOR inputs with smooth-pursuit inputs in the flocculus generate VOR adaptation. Understanding complex circuits is one of the greatest challenges for today's neuroscientists. In this thesis I tackle two such circuits and hope that through a better understandings of these circuits we gain principles that apply to other circuits and thereby advance our understanding of the brain.

The purpose of this thesis was to determine the neuronal circuitry mediating U50,488-induced locomotion in preweanling rats. To this end, preweanling rats received bilateral electrolytic lesions of the ventromedial thalamus or superior colliculus and, two days later, the same rats received a challenge injection of U50,488. It was predicted that bilateral lesions of the ventromedial thalamus or superior colliculus would attenuate the U50,488-induced locomotor activity of 18-day-old rats.

This thesis focuses on one certain process of cooperation of two cooperating robots operating an automatic measuring station. In this process, articles are handled by two industrial robots KUKA KR6/2. The objective of this thesis was to develop, construct and put into operation a measuring station and the associated workstation. For this purpose the appropriate programs controlling the robots and the measuring stations have been developed. The reader will be acquainted with the design of the workstation and its putting into operation. In addition, the thesis describes in detail the control of the robots and their program part. At the conclusion of the paper, opportunities of optimization of the power period are addressed in brief.

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