Multiscale Modeling of Neurobiological Systems

The central nervous system (CNS) is one of the most complicated living structures in the universe. A single gene expression, the expression level of a single protein or the concentration of a neurotransmitter could regulate the entire functionality of the CNS. The CNS needs to be investigated as a multiscale system with connections among different levels. The existing technology significantly limits experimental studies, and computational modeling is a useful tool for understanding how parts are connected, regulated, and function together. Ideally, the goal is to develop unified computational methodologies for exploring biological systems at multiple scales ranging from molecular to cellular to tissue level. While rigorous models have been developed at the molecular scale, higher level approaches usually suffer from lack of physical realism and lack of knowledge on model parameters. Molecular level studies can help to define reaction schemes and parameters which could be used in cellular microphysiology models, and image data provide a structural basis for reconstructing the surroundings of the cellular system of interest. This dissertation develops and tests a new multiscale model of dopaminergic signaling and a detailed model of the activation-triggered subunit exchange mechanism of calcium/calmodulin-dependent kinase type II (CaMKII). The goal is to develop and use computational models to understand the molecular mechanisms of neurotransmission, and how disruptions may cause complex disorders and conditions such as drug abuse. The simulations of the dopamine (DA) signaling model show that the addition of the geometry of the environment and localization of individual molecules significantly affect the DA reuptake. Consequently, the formation of DAT clusters reduces the DA clearance rate and increases DA receptor activity. In addition, the effects of the psychostimulants such as cocaine and amphetamine are also investigated. Constructed model and method can potentially serve as an in silico microscope to understand the molecular basis of signaling and regulation events in the CNS. Calibration of CaMKII model shows the limitations of the current parameter estimation methods for large biological models with long simulation times such as hours. The high dimensional parameter space and the limited and noisy data makes the parameter estimation task a challenge

An alternative approach for assessing drug induced seizures, using non-protected larval zebrafish

As many as 9% of epileptic seizures occur as a result of drug toxicity. Identifying compounds with seizurogenic side effects is imperative for assessing compound safety during drug development, however, multiple marketed drugs still have clinical associations with seizures. Moreover, current approaches for assessing seizurogenicity, namely rodent EEG and behavioural studies, are highly resource intensive. This being the case, alternative approaches have been postulated for assessing compound seizurogenicity, including in vitro, in vivo, and in silico methods. In this thesis, experimental work is presented supporting the use of larval zebrafish as a candidate model organism for developing new seizure liability screening approaches. Larval zebrafish are translucent, meaning they are highly amenable to imaging approaches while offering a more ethical alternative to mammalian research. Zebrafish are furthermore highly fecund facilitating capacity for both high replication and high throughput. The primary goal of this thesis was to identify biomarkers in larval zebrafish, both behavioural and physiological, of compounds that increase seizure liability. The efficacy of this model organism for seizure liability testing was assessed through exposure of larval zebrafish to a mechanistically diverse array of compounds, selected for their varying degrees of seizurogenicity. Their central nervous systems were monitored using a variety of different techniques including light sheet microscopy, local field potential recordings, and behavioural monitoring. Data acquired from these measurements were then analysed using a variety of techniques including frequency domain analysis, clustering, functional connectivity, regression, and graph theory. Much of this analysis was exploratory in nature and is reflective of the infancy of the field. Experimental findings suggest that larval zebrafish are indeed sensitive to a wide range of pharmacological mechanisms of action and that drug actions are reflected by behavioural and direct measurements of brain activity. For example, local field potential recordings revealed electrographic responses akin to pre-ictal, inter-ictal and ictal events identified in humans. Ca2+ imaging using light sheet microscopy found global increases in fluorescent intensity and functional connectivity due to seizurogenic drug administration. In addition, [2] further functional connectivity and graph analysis revealed macroscale network changes correlated with drug seizurogenicity and mechanism of action. Finally, analysis of swimming behaviour revealed a strong correlation between high speed swimming behaviours and administration of convulsant compounds. In conclusion, presented herein are data demonstrating the power of functional brain imaging, LFP recordings, and behavioral monitoring in larval zebrafish for assessing the action of neuroactive drugs in a highly relevant vertebrate model. These data help us to understand the relevance of the 4 dpf larval zebrafish for neuropharmacological studies and reveal that even at this early developmental stage, these animals are highly responsive to a wide range of neuroactive compounds across multiple primary mechanisms of action. This represents compelling evidence of the potential utility of larval zebrafish as a model organism for seizure liability testing

Evaluation of EEG-based depth of anaesthesia monitoring

In 2001 a University of Bristol team patented a novel data reduction method of the EEG for characterising categorical changes in consciousness. After pre-whitening the EEG signal with Gaussian white noise a parametric spectral estimation technique was applied. Two frequency domain indices were then proposed: the relative power found between 8Hz to 12Hz and 0.5Hz to 32Hz termed the 'alpha index', and the relative power between 0.5Hz to 4Hz and 0.5Hz to 32Hz termed the 'delta index'. The research and development of a precision EEG monitoring device designed to embody the novel algorithm is described in this thesis. The efficacy of the technique was evaluated using simulated and real EEG data recorded during Propofol anaesthesia. The simulated data showed improvements could be made to the patented method. Real EEG data collected whilst patients were wakeful and data from patients unresponsive to noxious stimuli were cleaned of obvious artefacts and analysed using the proposed algorithm. A Bayesian diagnostic test showed the alpha index had 65% sensitivity and selectivity to patient state. The delta index showed 72% sensitivity and selectivity. Taking a pragmatic approach, the literature is reviewed in this thesis to evaluate the use of EEG in depth of anaesthesia monitoring. Pertinent aspects of the sciences are profiled to identify physiological links to the characteristics of the EEG signal. Methods of data reduction are also reviewed to identify useful features and possible sources of error. In conclusion it is shown that the proposed indices do not provide a robust measure of depth of anaesthesia. An approach for further research is proposed based on the review work.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Form vs. Function: Theory and Models for Neuronal Substrates

The quest for endowing form with function represents the fundamental motivation behind all neural network modeling. In this thesis, we discuss various functional neuronal architectures and their implementation in silico, both on conventional computer systems and on neuromorpic devices. Necessarily, such casting to a particular substrate will constrain their form, either by requiring a simplified description of neuronal dynamics and interactions or by imposing physical limitations on important characteristics such as network connectivity or parameter precision. While our main focus lies on the computational properties of the studied models, we augment our discussion with rigorous mathematical formalism. We start by investigating the behavior of point neurons under synaptic bombardment and provide analytical predictions of single-unit and ensemble statistics. These considerations later become useful when moving to the functional network level, where we study the effects of an imperfect physical substrate on the computational properties of several cortical networks. Finally, we return to the single neuron level to discuss a novel interpretation of spiking activity in the context of probabilistic inference through sampling. We provide analytical derivations for the translation of this ``neural sampling'' framework to networks of biologically plausible and hardware-compatible neurons and later take this concept beyond the realm of brain science when we discuss applications in machine learning and analogies to solid-state systems

Mécanismes développementaux des circuits dopaminergiques et leur implication dans les comportements hyperactifs

Les neurones dopaminergiques du mésencéphale (mDA) sont impliqués de manière critique dans diverses fonctions clés du cerveau, y compris les mouvements volontaires, la récompense, l'attention et l'apprentissage. La bonne spécification des neurones dopaminergique, ainsi que l’établissement des circuits dopaminergiques sont nécessaires à un bon fonctionnement du cerveau. Le dysfonctionnement des circuits dopaminergiques est lié au développement de troubles neuropsychiatriques, y compris le trouble déficitaire de l'attention avec hyperactivité (TDAH), le trouble obsessionnel compulsif (TOC) et les troubles liés aux TOCs, comme le syndrome de Gilles de la Tourette. L’obtention d’un circuit dopaminergique fonctionnel dépend du développement des neurones dopaminergiques. Les facteurs de transcription Lmx1a et Lmx1b font partie de la famille des LIM à homeodomain et sont des déterminants précoces de l’avenir des neurones dopaminergique. Lmx1a/b sont essentiels pour chaque étape de la différenciation des progéniteurs de neurone dopaminergique. Il a été démontré précédemment que les souris Lmx1a/b cKO ont une activité locomotrice augmentée par rapport aux contrôles. Ici, une caractérisation approfondie des souris Lmx1a/b a révélé que ces souris avaient un comportement hyperactif, en lien avec le TDAH, et démontraient des symptômes du type TOC. Au niveau cellulaire, la perte de fonction de Lmx1a/b a induit une réduction de l’arborisation dendritique et de la fréquence des courants postsynaptiques excitateurs miniatures spontanés (mEPSCs) dans les neurones dopaminergiques. Le profil d'expression des gènes chez les souris Lmx1a / b cKO a révélé que Lmx1a/b contrôle l'expression de Slitrk2 et Slitrk5, deux membres de la famille des protéines Slit et Trk (Slitrk). Le gain et la perte de fonction de Slitrk2 et Slitrk5 dans des cultures de neurones dopaminergiques ont montré que Slitrk2 régule positivement et Slitrk5 régulent négativement la croissance dendritique. Également, le gain et la perte de fonction de Slitrk2 ont induit une variation de la densité des punctas synaptiques excitateurs (PSD95 et VGLUT). En conséquence, la perte de fonction de Slitrk2 a réduit la fréquence des mEPSCs, tandis que l'augmentation de l'expression de Slitrk2 a augmenté la fréquence des mEPSCs, sans changement d'amplitude ou dans la fréquence ou de l'amplitude des mIPSCs. Ces données suggèrent un rôle pour Slitrk2 dans la formation de synapses excitatrices fonctionnelles. À l'inverse, le gain et la perte de fonction de Slitrk5 ont induit une modification de la densité des punctas synaptiques inhibiteurs (géphyrine et VGAT). La perte d’expression de Slitrk5 a réduit la fréquence des mIPSCs tandis que l'augmentation de l'expression de Slitrk5 a augmenté la fréquence des mIPSCs, sans changement dans l'amplitude ou de la fréquence et de l'amplitude des mEPSCs. Ces données suggèrent un rôle pour Slitrk5 dans la formation de synapses fonctionnelles inhibitrices. Nous avons également étudié les conséquences sur le comportement de Slitrk2 et Slitrk5 dans les neurones mDA. Les souris, dans lesquelles Slitrk2 a été invalidé dans la VTA, démontrent un changement significatif dans l'activité locomotrice et montrent de l’hyperactivité. À l'inverse, les souris avec une expression réduite de Slitrk5 présentent une activité locomotrice réduite et un comportement analogue à un TOC. Ces changements de comportement peuvent être causés par une modification de l'activité des neurones dopaminergiques. L'inhibition chronique des neurones de la VTA, en utilisant une approche pharmacogénétique, pendant le développement postnatal à induit une activité motrice augmentée, similaire au TDAH, et un comportement analogue à un TOC. Ceci évoque certains aspects du comportement des souris Lmx1a/b cKO. Une inhibition aiguë a entraîné une diminution de l'activité locomotrice, alors que l'inhibition chronique chez des animaux plus âgés n'a eu aucun effet. Ensemble, ces résultats indiquent que Lmx1a/b, Slitrk2, et Slitrk5 sont des acteurs clés du développement des neurones dopaminergique et de la formation des synapses, ce qui peut avoir un impact sur le développement de TDAH et de TOC.Midbrain dopaminergic (mDA) neurons are critically involved in various key functions of the brain, including voluntary movement, reward, attention, and learning. The proper specification of dopaminergic neurons, as well as the establishment of dopaminergic circuits are necessary to a good functioning of the brain. Dopaminergic circuitry dysfunctions are linked to the development of neuropsychiatric disorders, including attention deficit hyperactivity disorder (ADHD), obsessive-compulsive disorder (OCD) and OCD-like disorders, such as Gilles de la Tourette’s syndrome. The LIM-homeodomain transcriptional factors Lmx1a and Lmx1b are early determinants of the dopaminergic fate and are essential for each step of mDA progenitor differentiation. Previously, it has been demonstrated that Lmx1a/b cKO mice show increased locomotor activity. Further characterization of Lmx1a/b cKO mice revealed that these mice had ADHD- and OCD-like behaviour. The loss of function of Lmx1a/b reduced dendritic morphology and frequency of spontaneous miniature excitatory postsynaptic currents (mEPSCs) in mDA neurons. Gene expression profiling in Lmx1a/b cKO mice revealed that Lmx1a/b controls the expression of Slitrk2 and Slitrk5, two members of the Slit and Trk-like (Slitrk) protein family. Gain and loss of function of Slitrk2 and Slitrk5 in mDA neuron cultures showed that Slitrk2 positively regulates and Slitrk5 negatively regulate dendritic growth. Additionally, gain and loss of function of Slitrk2 induced a change in the density of excitatory synaptic puncta (PSD95 and VGLUT). Accordingly, Slitrk2 knockdown reduced the frequency of mEPSCs while increased Slitrk2 expression increased the frequency of mEPSCs, with no change in amplitude or in mIPSCs frequency or amplitude. These data suggest a role for Slitrk2 in the formation of functional excitatory synapses. Inversely, gain and loss of function of Slitrk5 induced a modification in the density of inhibitory synaptic puncta (gephyrin and VGAT). Slitrk5 knockdown reduced the frequency of mIPSCs while increased Slitrk5 expression increased the frequency of mIPSCs, with no change in amplitude or in mEPSCs frequency or amplitude. These data suggest a role for Slitrk5 in the formation of functional inhibitory synapses. We also investigated the consequences on behaviour of Slitrk2 and Slitrk5 reduced expression in mDA neurons. Mice, in which Slitrk2 was knocked down in the VTA, display significant change in locomotor activity and show ADHD. Inversely, mice with reduced expression of Slitrk5 exhibit lower activity and OCD-like behaviour. These behavioural changes might be caused by a change in mDA neuron firing activity. Chronic inhibition of mDA neurons during postnatal development using a pharmacogenetic approach induced ADHD and OCD-like behaviour and mimic some aspects of the Lmx1a/b cKO mice. Acute inhibition resulted in decreased locomotor activity, while chronic inhibition in older animals had no effect. Altogether, these results indicate that Lmx1a/b and Slitrk2/5 are key players of mDA neuron development and synapse formation, which may have an impact on ADHD and OCD-like disorders.Résumé en espagno

Mechanisms Of Dopaminergic, Histaminergic, And Glutamatergic Neuromodulation Within The Medial Entorhinal Cortex

The medial entorhinal cortex (MEC) is a critical region for both limbic functions as well as learning and memory. In addition to these normal processes, the MEC is also implicated in several disorders including epilepsy, Alzheimer’s disease, and several neuropsychiatric disorders. The MEC’s function and role in various disorders is intimately related to its underlying cellular activity. The primary neuronal cell types in this region consist of glutamatergic principle cells and GABAergic local inhibitory interneurons. This dissertation consists of three aims related to the neuromodulation of these cells located in the superficial layers of the MEC—the primary input source to the hippocampus. The first aim addresses how dopamine (DA) alters GABAergic transmission. The second aim also considers GABAergic transmission but examines its modulation by histamine (HA). Finally, the third aim investigates mechanisms of group I metabotropic glutamate receptor(mGluR)-induced increases in layer III principal cell excitability. For Study 1, exogenous application of DA increases spontaneous inhibitory postsynaptic currents (sIPSCs) recorded from layer II neurons. This increase is mediated by a promiscuous interaction with the α1 adrenergic receptors (α1 ARs) found on the MEC interneurons. Application of amphetamine to elevate extracellular DA concentrations mimic theses effects in an α1 AR-dependent fashion. Activation of interneuron α1 AR-induced depolarization is mediated by inhibition of inwardly rectifying K+ channels (Kirs). For Study 2, exogenous application of HA increases sIPSCs recorded from layer II principal neurons. This increase requires both H1 and H2 receptors located on GABAergic interneurons. The magnitude of HA-induced depolarization is significantly larger within one class of tested interneurons and HA-induced depolarization of interneurons involves both the inhibition of (Kirs) and activation of a TTX-insensitive Na+ current. For Study 3, activation of group I mGluRs increases action potential firing, depolarization and generation of inward currents in layer III pyramidal neurons. This increase is sensitive to antagonists for both mGluR1 and mGluR5, indicating the functional presence of both receptors. The mGluR-induced currents are mediated by a non-selective cation channel that contains TRPC4 and TRPC5 subunits