published_or_final_version / abstract / Microbiology / Master / Master of Philosophy

published_or_final_version / Medicine / Doctoral / Doctor of Philosophy

Proteins are the fundamental unit of computation and signal processing in biological systems. A quantitative understanding of protein biophysics is of paramount importance, since even slight malfunction of proteins can lead to diverse and severe disease states. However, developing accurate and useful mechanistic models of protein function can be strikingly elusive. I demonstrate that the adoption of Bayesian statistical methods can greatly aid in modeling protein systems. I first discuss the pitfall of parameter non-identifiability and how a Bayesian approach to modeling can yield reliable and meaningful models of molecular systems. I then delve into a particular case of non-identifiability within the context of an emerging experimental technique called single molecule photobleaching. I show that the interpretation of this data is non-trivial and provide a rigorous inference model for the analysis of this pervasive experimental tool. Finally, I introduce the use of nonparametric Bayesian inference for the analysis of single molecule time series. These methods aim to circumvent problems of model selection and parameter identifiability and are demonstrated with diverse applications in single molecule biophysics. The adoption of sophisticated inference methods will lead to a more detailed understanding of biophysical systems. / text

Migraine is one of the most common neurological disorders. The pathological conditions that initiate and sensitize afferent pain signaling are poorly understood. The goal of this study is to identify the ion channels and signaling proteins underlying activation and sensitization of meningeal nociceptors.In trigeminal neurons retrogradely labeled from the cranial meninges, approximately 80% responded to a pH 6.0 application with a rapidly activating and desensitizing ASIC-like current. Pharmacological experiments and kinetics analysis demonstrated that dural afferent pH-sensitive currents were mediated via activation of ASIC3. In addition, applications of decreased pH solutions were able to excite these neurons and generate action potentials. In awake animals, application of decreased pH solutions to the dura produced dose-dependent facial and hindpaw allodynia, which was also mediated through activation of ASIC3. Accumulating evidence indicates that meningeal inflammation induced sensitization of dural afferents contributes to migraine headache. We have demonstrated here that in the presence of mast cell mediators, dural afferents showed a decreased pH threshold and increased activity in response to pH stimuli both in vivo and in vitro. These data provide a cellular mechanism by which decreased pH in the meninges directly excites afferent pain-sensing neurons potentially contributing to migraine headache. It also indicates that inflammatory events within the meninges could sensitize afferent pain signaling and result in increased sensitivity of dural afferents.Intracranial Interleukin-6 (IL-6) levels have been shown to be elevated during migraine attacks, suggesting that this cytokine may facilitate pain signaling from the meninges. Here we reported that in awake animals, direct application of IL-6 to the dura produced dose-dependent facial and hindpaw allodynia via activation of the ERK signaling pathway. IL-6 application was also able to increase neuronal excitability in a manner consistent with phosphorylation of Nav1.7. These data provide a cellular mechanism by which IL-6 in the meninges causes sensitization of dural afferents therefore contributing to the pathogenesis of migraine.These findings are discussed in relation to how activation and sensitization of primary afferent neurons might initiate migraine pain signaling and how the research included in this dissertation relates to the development of new therapeutic strategies for migraine.

Hyperkalemic periodic paralysis is characterized by myotonic discharges followed by paralysis. Caused by a mutation in the gene encoding for NaV1.4 channel, patients do not experience symptoms during infancy, but the onset starts between 1-10 years of age. The symptoms severity then increases with age until adolescence. A large increase in gene expression marked by an increase in oxidative capacity of muscles has also been reported in HyperKPP. It is possible that the onset of symptoms is related solely to NaV1.4 channel content/activity reaching a critical level. It is also possible that the onset of some symptoms are due to defective NaV1.4, while other symptoms and the increase in severity with age are related to changes in membrane components as a result of changes in gene expression. To test these possibilities, the progression of paralysis and changes in fiber types were followed with age in HyperKPP mice in relation to changes in NaV1.4 content and activity. Changes in fiber types (index of changes in gene expression), started after the onset of paralysis was observed, which coincided with NaV1.4 channels reaching maximum expression. Therefore, the onset of symptoms was related to defective NaV1.4 channels.

The deep cerebellar nuclei (DCN) function as output gates for a large majority of the Purkinje cells of the cerebellar cortex and thereby determine how the cerebellum influences the rest of the brain and body. In my PhD programme I have investigated how the DCN process two kinds of input patterns received from Purkinje cells: irregularity of spike intervals and pauses in Purkinje cell activity resulting from the recognition of patterns received at the synapses with the upstream parallel fibres (PFs). To that objective I have created a network system of biophysically realistic Purkinje cell and DCN neuron models that enables the exploration of a wide range of network structure and cell physiology parameters. With this system I have performed simulations that show how the DCN neuron changes the information modality of its input, consisting of varying regularity in Purkinje cell spike intervals, to varying spike rates in its output to the nervous system outside of the cerebellum. This was confirmed in simulations where I exchanged the artificial Purkinje cell trains for those received from experimental collaborators. In pattern recognition simulations I have found that the morphological arrangement present in the cerebellum, where multiple Purkinje cells connect to each DCN neuron, has the effect of amplifying pattern recognition already performed in the Purkinje cells. Using the metric of signal-to-noise ratio I show that PF patterns previously encountered and stored in PF - Purkinje cell synapses are most clearly distinguished from those novel to the system by a 10-20 ms shortened burst firing of the DCN neuron. This result suggests that the effect on downstream targets of these excitatory projection neurons is a decreased excitation when a stored as opposed to novel pattern is received. My work has contributed to a better understanding of information processing in the cerebellum, with implications for human motor control as well as the increasingly recognised non-motor functions of the cerebellum.

Sudden cardiac death due to the development of lethal arrhythmias is the dominant cause of mortality in the UK, yet the mechanisms underlying their onset, maintenance and termination are still poorly understood. Therefore biomarkers are used to determine arrhythmic risk within patients and of new drug compounds. In recent years, the magnitude of variations in the length of successive beats, measured over a short period of time, has been shown to be a powerful predictor of arrhythmic risk. This beat-to-beat variability is thought to be the manifestation of the random opening and closing dynamics of individual ion channels that lie within the membrane of cardiac cells. Computational models have become an important tool in understanding the electrophysiology of the heart. However, current state-of-the-art electrophysiology models do not incorporate this intrinsic stochastic behaviour of ion channels. Those that do use computationally costly methods, restricting their use in complex tissue scale simulations, or employ stochastic simulation methods that result in negative numbers of channels and so are inaccurate. Therefore, using current stochastic modelling techniques to investigate the role of stochastic ion channel behaviour in beat-to-beat variability presents difficulties. In this thesis we take a mathematically rigorous and novel approach to develop accurate and computationally efficient models of stochastic ion channel dynamics that can be incorporated into existing electrophysiology models. Two different models of stochastic ion channel behaviour, both based on a system of stochastic differential equations (SDEs), are developed and compared. The first model is based on an existing SDE model from population dynamics called the Wright-Fisher model. The second approach incorporates boundary conditions into the SDE model of ion channel dynamics that is obtained in the limit from the discrete-state Markov chain model, and is called a reflected SDE. Of these two methods, the reflected SDE is found to more accurately capture the stochastic dynamics of the discrete-stateMarkov chain, seen as the ‘gold-standard’ model and also provides substantial computational speed up. Thus the reflected SDE is an accurate and efficient model of stochastic ion channel dynamics and so allows for detailed investigation into beat-to-beat variability using complex computational electrophysiology models. We illustrate the potential power of this method by incorporating it into a state-of-the-art canine cardiac cell electrophsyiology model so as to explore the effects of stochastic ion channel behaviour on beat-to-beat variability. The stochastic models presented in this thesis fulfil an important role in elucidating the effects of stochastic ion channel behaviour on beat-to-beat variability, a potentially important biomarker of arrhythmic risk.

KirBac channels are prokaryotic homologs of eukaryotic inwardly-rectifying potassium channels, which have served as models for gaining insight into the structure of eukaryotic channels. This thesis focuses on the structure-function relationship in these channels. The first part of this study concerns a novel KirBac channel, KirBac9.2, which contains a unique amino acid sequence in the place of the canonical GYG selectivity filter. Although expressed and purified in a stable and functional form, the protein did not form well-diffracting crystals. Functional studies suggest that KirBac9.2 is non-selective for monovalent cations and a random mutagenesis screen identified a number of activatory mutants in the cytoplasmic domains of the channel. A full electrophysiological investigation of KirBac9.2 channel function is beyond the scope of this study. However, initial studies suggest that it is possible to record currents from KirBac9.2 channels reconstituted into lipid bilayers. The second part of this thesis investigates KirBac3.1, which is a classical KirBac channel containing the consensus GYG sequence for potassium selectivity. Five high resolution structures of a mutant channel are reported, which suggest a new feature in the gating mechanism of KirBac3.1 where a rotation of the cytoplasmic domains is linked to a change in the electrostatic environment of the cytoplasmic cavity. In addition, a functional study of the KirBac3.1 showed that the channel is highly pH sensitive.

Le peptide natriurétique de type B (BNP) est une hormone cardiaque fortement impliquée dans l'insuffisance cardiaque (IC). En clinique, le BNP est un bio-marqueur de diagnostic et de pronostic de l'IC; son taux sanguin augmentant avec la progression du remodelage cardiaque, de la dysfonction du ventricule gauche (VG) et des altérations du couplage excitation-contraction (CEC). Administré sous une forme recombinante, le nésiritide, pour ses effets hémodynamiques vasorelaxants, chez des patients en IC aiguë décompensée, il a montré des effets controversés avec un risque d'augmentation de la mortalité. Pour comprendre l'implication du BNP dans le remodelage cardiaque post-ischémique et son efficacité thérapeutique, nous avons étudié les effets cardiaques in vivo et sur le CEC d'un traitement chronique au BNP (0,03 µg/kg/min) sur deux groupes expérimentaux : i) des souris saines, Sham, pendant 14 jours et ii) des souris PMI (Post-Myocardial Infarction) en stade précoce, après ligature de l'artère coronaire gauche (pendant 7 et 14 jours). Chez les Sham, le BNP a engendré une suractivation du système nerveux sympathique, une hypertrophie cardiaque, des altérations électrophysiologiques in vivo et des mouvements calciques dans les cardiomyocytes du VG, à l'origine d'arythmies cellulaires et cardiaques. Les effets délétères du BNP ont été prévenus par une combinaison de ce traitement avec un β-bloqueur : le métoprolol. Chez les PMI, la supplémentation en BNP a réduit l'inotropisme positif précoce acquis par une modification des mouvements calciques, a accéléré l'apparition des altérations des protéines du CEC et la survenue des arythmies. Le BNP accélère la décompensation cardiaque et pourrait être à déconseiller, du moins en monothérapie, en traitement clinique. / BNP is a natriuretic peptide released in excess in the blood during heart failure (HF) to reduce blood volume and pressure. A recombinant form of human BNP, nesiritide, is used for patients with acute decompensated HF but deleterious cardiac effects have been reported. We aimed to investigate the cardiac effects of chronic BNP supplementation (0.03 µg/kg/min) on: i) healthy mice (Sham) for 14 days and ii) mice subjected to myocardial infarction (MI) induced by coronary artery ligation (PMI) for 7 (D7) and (D14) 14 days. Sham treated animals (Sham-BNP) showed an increase in ventricular arrhythmias occurrence in consequence of sympathetic tone increase and Ca2+ handling alterations observed at cellular and protein levels in the left ventricle (LV). Most of these effects were reduced in Sham-BNP by the selective beta1-adrenergic blocker metoprolol. In the PMI group, at early stages after ligation, we showed an increase in cardiomyocytes contraction and Ca2+ handling at D7 and D14. But this response was attenuated in PMI-BNP. In PMI, alterations in Ca2+ handling proteins, particularly SERCA2a and RyR2 appeared at D14 but not D7. But BNP supplementation accelerated these alterations which appeared since D7 in the PMI-BNP group, in parallel with spontaneous arrhythmias occurrence at D7. BNP infusion attenuates compensatory "inotropism" intrinsic to the LV cardiomyocytes and promotes arrhythmias. Our results show that BNP, at least in monotherapy, may be hazardous for the treatment of patients with decompensated HF.

Ligand-gated and ligand-modulated ion channel (IC) sensors have received increased attention for their ability to transduce ligand-binding events into a readily measurable electrical signal. Ligand-binding to an IC modulates the ion flux properties of the channel in label-free manner, often with single-molecule sensitivity and selectivity. As a result, ICs are attractive sensing elements in biosensoring platforms, especially for ligands lacking optical (e.g. fluorescent) or electrochemical properties. Despite the growing number of available ligand-gated and ligand-modulated ICs and artificial lipid bilayer platforms for IC reconstitution, significant work remains in defining the analytical performance capabilities of IC sensors. Particularly, few studies have described platforms for making measurements with rapid temporal resolution and high sensitivity. In this work, we describe an artificial lipid bilayer platform which enables rapid measurement of ion channel activity, a key parameter for developing IC sensors suitable for studying biological events, e.g. single cell exocytosis (Chapter 2 and 3). Additionally, we developed expression, purification, and reconstitution protocols for Kir6.2, a model ligand-gated ion channel, for use in sensor development (Chapter 4). The final goal is to reconstitute ion channel-coupled receptors (ICCRs), G protein-coupled receptor-Kir6.2 fusion proteins, into artificial lipid bilayers to detect small molecules and hormones targeting GPCRs. Towards this goal, we characterized the expression and function of two ICCRs, M2-Kir and D2-Kir, in HEK293 cells (Chapter 5).