This PhD thesis is a study of cortical electrophysiology in two basal ganglia disorders: Parkinson’s disease (PD) and dystonia. Two diseases were chosen as being representative of hypokinetic and hyperkinetic movement disorders, respectively. In addition, current treatments seem to be imperfect to control many aspects of both diseases, hence the interest in exploring potential new therapeutic targets. PD and dystonia are basal ganglia diseases, but there is growing body of evidence of impaired cortical function and particularly of abnormal sensorimotor cortical plasticity in both disorders. We however still lack knowledge about functional significance of these cortical changes. Are they maladaptive or compensatory or of little functional significance? Techniques of Transcranial Magnetic (TMS) were used to determine 1) if clinical asymmetry of early PD is reflected in hemispheric asymmetry of sensorimotor cortical plasticity and intracortical inhibition, and 2) how these electrophysiological measures change with disease progression. We found that the hemisphere contralateral to the less affected side had preserved intracortical inhibition and a larger response to the plasticity protocol, whereas on the more affected hemisphere these were reduced. We further demonstrated that the decline in asymmetry of these measures correlated with the reduction in asymmetry of clinical symptoms, suggesting these were compensatory changes. In dystonia patients, we investigated using TMS 1) if change of afferent input induced by botulinum toxin injections may change response to plasticity protocol in primary dystonia, and if 2) secondary and primary dystonia patients share the same pattern of electrophysiological abnormalities. We demonstrated that sensorimotor cortical plasticity in primary dystonia is not permanent abnormality but may be transitory reduced with botulinum injections treatment. Secondary dystonia patients, as opposed to primary dystonia patients did not have enhanced sensorimotor plasticity or impaired cerebellar function. We provide evidence that different types of dystonia do not necessarily have the same neuroanatomical substrates, which might have therapeutic implications.

Objective: To investigate the neuroprotective approach of controlling mitochondria-dependent apoptosis in Parkinson’s disease cellular models. Background: Parkinson’s disease is a neurodegenerative disease and there is evidence indicating that mitochondria-dependent apoptosis is related to dopaminergic neuron loss. pUL37x1, an immediate early protein expressed during cytomegalovirus infection, modulates mitochondria-dependent apoptosis by inactivating Bcl-2-associated X protein (Bax), and meclizine is believed to increase glycolysis and hyperpolarize mitochondria, which inhibits apoptosis. Methods: The neuroprotective and anti-apoptotic effects of pUL37x1 over-expression and meclizine were investigated in SH-SY5Y, a neuroblastoma cell line and primary rat cortical culture cells. Cell death was induced by either staurosporine or 6-hydroxydopamine and measured by lactate dehydrogenase release and propidium iodide binding assay. Apoptotic markers were measured by the release of cytochrome c and the activation of caspase-3. Mitochondrial membrane potential was measured by Tetramethylrhodamine, methyl ester fluorescence obtained by confocal microscope. Extracellular acidification rate (ECAR), a glycolytic activity parameter and oxygen consumption rate (OCR) were measured by XF analyser. Statistics was performed by either ANOVA with Dunnett’s post-hoc analysis or two-tailed Student’s t-test. Results: Both pUL37x1 over-expression and meclizine significantly protected against toxin-induced cell death in SH-SY5Y and rat primary cortical culture cells. Both approaches also down-regulated apoptosis. In terms of meclizine, the protection resulted from glycolysis-related mitochondrial hyperpolarization. Hyperpolarization and protection would decline following glycolytic inhibition. pUL37x1 over-expression prevented apoptotic cell death by two means: Bax-dependent and glycolysis-dependent mechanisms. First, pUL37x1 over-expression led to Bax mitochondria-translocation, and in contrast to control, Bax silencing did not provide more protection on pUL37x1 over-expressing cells. Second, pUL37x1 over-expression increased cellular glycolysis and hyperpolarized mitochondria, and glycolytic inhibitors attenuated the protection, indicating a glycolysis-dependent protective mechanism. Conclusions: The success of neuroprotection by pUL37x1 and meclizine in Parkinson’s disease cellular models not only confirms the significance of controlling mitochondria-dependent apoptosis, but also indicates two novel approaches to neuroprotection.

Recent genome wide association studies in Alzheimer’s disease have highlighted the importance of the complement cascade in the pathogenesis of Alzheimer’s disease. However, the cellular and molecular roles of these complement proteins are not fully understood. Microglia express complement receptors and the activation of specific receptors may increase Aβ clearance and reduce/prevent neurodegeneration. The work presented in this thesis was aimed at investigating the contribution of Complement receptor 1 (CR1), the second most significant hit in GWAS studies, on microglia to neuronal damage. To explore the consequences of blocking CR1 to microglial-neuronal interactions, primary rat microglia were treated with a CR1 functional blocking antibody together with microglial activators for 24 h. It was found that microglia displaying an activated phenotype demonstrated an increase in CR1 expression. Activation of microglial CR1 was found to be detrimental to neurons and this correlated with an increase in microglial intracellular superoxide generation, nitric oxide (NO) production, tumor necrosis factor-α (TNFα) and interleukin-1 β (IL-1β) secretion. Amyloid-β 1-42 (Aβ1-42)-treated microglia displayed an increased ability to phagocytose dextran beads following antibody blockade of CR1 but a decreased capacity to phagocytose fluorescent-tagged Aβ1-42. CR1 immunoreactivity was investigated by immunohistochemistry in AD and control human post-mortem brain tissue. A higher level of CR1 immunoreactivity was found in areas of high Aβ plaque burden in AD brain tissue. A difference in CR1 expression on red blood cells between individuals was measured by flow cytometry. Together, these results indicate that microglial CR1 plays a role in the neuronal death observed in AD and investigating this further may provide a possible strategy to control neurotoxicity in the AD brain.

Schizophrenia is a devastating mental illness and a huge disease burden in terms of cost. The individual is typically affected in early adulthood, thus loosing the best years of their life. The stigma of mental illness and pattern of downward social drift also results in families and society being adversely affected. With advances in neuroscience and neuroimaging, psychiatrists can advance their understanding of schizophrenia as a disease of the brain using biological models. This thesis investigates how volumetric magnetic resonance imaging (MRI), structural MRI techniques such as magnetisation transfer imaging (MTI), diffusion tensor imaging (DTI), and novel techniques such as optical coherence tomography (OCT) and visual function testing may be used to elucidate the neuropathology of schizophrenia in-vivo, in addition to explaining the cognitive deficits that are commonly observed. . The following studies are included in this thesis: 1) A diffusion tensor imaging (DTI) study to explore white matter abnormalities in first episode psychosis and correlations with cognitive performance. 2) An exploratory study utilizing OCT to investigate whether retinal nerve fibre layer thickness varies between patients with schizophrenia and healthy controls. 3) A longitudinal study using MRI and MTI to examine structural brain changes following first episode psychosis and correlating these findings with cognitive performance. 4) An investigation of chromatic vision in schizophrenia spectrum disorders and correlations between hue discrimination ability and cognitive performance. 5) A cross-sectional comparison study of grey matter volume and associations with oculomotor function in first episode patients and healthy controls.

This thesis examines clinical and radiological aspects of Progressive Supranuclear Palsy (PSP) and related conditions. Significant milestones occur sooner in pathologically confirmed PSP than multiple system atrophy (MSA); older age of onset and shorter duration to first milestone are associated with worse prognosis in both; in PSP, the Richardson’s syndrome phenotype and male gender and in MSA, early autonomic failure and the female gender are also predictive of poorer prognosis. Using objective measurements of bradykinesia we found progressive bradykinesia and hypokinesia in Parkinson’s disease (PD) which correlates with disability and responds to levodopa but hypokinesia without decrement in PSP. Using conventional MRI 72.7% of PSP and 76.9% of MSA are correctly identified. The ‘hummingbird sign’ was highly specific for PSP, but sensitvity was 68.4%. A simple measurement of the midbrain < 9.35mm had 100% specificity for a pathological diagnosis of PSP. In a clinically diagnosed PSP 90.5% had a measurement of < 9.35mm. Using high field 9.4 Tesla MRI, the anatomy of the subthalamic nucleus is clearly defined when compared to histology in post mortem material. The anteromedial portion was hypointense in correlation with Perls stain and there was variability in the volume, shape and location of its borders. The nigrosomes within the substantia nigra were visibile as high intensity bands which correlated with calbindin poor zones on immunohistochemical stains. The volume and anatomy were preserved in PD but not PSP. Multimodal 3 Telsla MRI during life revealed distinct patterns of atrophy in PSP and MSA using voxel-based morphometry. Tract-based spatial statistics revealed abnormalities in the frontal and parieto-occipital white matter changes in PSP more than MSA. Midbrain atrophy and frontal white matter increased mean diffusivity were associated with increasing PSP rating scale score, and frontal white matter reduced fractional anisotropy with disease duration.

The critical brain hypothesis provides a framework for viewing the human brain as a critical system, which may transmit information, reorganise itself and react to external stimuli efficiently. A critical system incorporates structures at a range of spatial and temporal scales, and may be associated with power law distributions of neuronal avalanches and power law scaling functions. In the temporal domain, the critical brain hypothesis is supported by a power law decay of the autocorrelation function of neurophysiological signals, which indicates the presence of long-range temporal correlations (LRTCs). LRTCs have been found to exist in the amplitude envelope of neurophysiological signals such as EEG, EMG and MEG, which reveal patterns of local synchronisation within neuronal pools. Synchronisation is an important tool for communication in the nervous system and can also exist between disparate regions of the nervous system. In this thesis, inter-regional synchronisation is characterised by the rate of change of phase difference between neurophysiological time series at different neuronal regions and investigated using the novel phase synchrony analysis method. The phase synchrony analysis method is shown to recover the DFA exponents in time series where these are known. The method indicates that LRTCs are present in the rate of change of phase difference between time series derived from classical models of criticality at critical parameters, and in particular the Ising model of ferromagnetism and the Kuramoto model of coupled oscillators. The method is also applied to the Cabral model, in which Kuramoto oscillators with natural frequencies close to those of cortical rhythms are embedded in a network based on brain connectivity. It is shown that LRTCs in the rate of change of phase difference are disrupted when the network properties of the system are reorganised. The presence of LRTCs is assessed using detrended fluctuation analysis (DFA), which assumes the linearity of a log-log plot of detrended fluctuation magnitude. In this thesis it is demonstrated that this assumption does not always hold, and a novel heuristic technique, ML-DFA, is introduced for validating DFA results. Finally, the phase synchrony analysis method is applied to EEG, EMG and MEG time series. The presence of LRTCs in the rate of change of phase difference between time series recorded from the left and right motor cortices are shown to exist during resting state, but to be disrupted by a finger tapping task. The findings of this thesis are interpreted in the light of the critical brain hypothesis, and shown to provide motivation for future research in this area.

Down syndrome (DS) is a common, complex disorder caused by having an extra copy of human chromosome 21 (trisomy 21). While clinical presentation varies extensively, Alzheimer disease (AD) pathology is found in brains of virtually all people with DS by 40 years. This increases their dementia risk such that one third of the DS population develops AD by 60 years. Therefore DS allows the investigation of pathogenetic mechanisms underlying its clear genetic form of early-onset AD. To model DS in mice, a ‘transchromosomic’ model, Tc1, was generated carrying a freely segregating copy of human chromosome 21 (Hsa21), which is trisomic for ~75% of Hsa21 genes. However, Tc1 is not functionally trisomic for APP. By crossing Tc1 with the J20 model, a transgenic mouse overexpressing mutant human APP that models amyloid deposition, it is possible to compare contributions of trisomy 21 and APP/Aβ overexpression to phenotypes in the genotypically different offspring. The work presented in this thesis therefore characterises AD-related phenotypes in progeny of the Tc1xJ20 cross. I first established a primary cortical culture model from early postnatal Tc1xJ20 pups, which would allow the in vitro observation and manipulation of cortical neurons in a more accessible system compared to in vivo study. To assess the validity and utility of these cultures, they were characterized for APP expression, Aβ production, proportion of neuronal cells in culture and levels of mosaicism for the Hsa21 chromosome. These in vitro phenotypes obtained were compared with relevant in vivo observations in Tc1xJ20 mice. Secondly, to study neuroinflammation and glial reactivity, I developed a digital analysis protocol to systematically quantify morphological characteristics of microglia and astrocytes visualized by immunohistochemistry in Tc1xJ20 brain sections. To further identify AD-related phenotypes that may be differentially influenced by genotype, I annotated data obtained from a pilot RNA sequencing study of Tc1xJ20 hippocampal tissues, identified gene candidates of interest, and explored functions that may be altered by genotype by clustering differentially expressed genes by associated functions. These results therefore allow for discussion and evaluation of the novel Tc1xJ20 model for identifying novel genetic contributions of trisomy 21 on AD phenotypes, apart from APP.

This thesis concerns the simulation of local field potentials (LFPs) from cortical network activity; network gamma oscillations in particular. Alterations in gamma oscillation measurements are observed in many brain disorders. Understanding these measurements in terms of the underlying neuronal activity is crucial for developing effective therapies. Modelling can help to unravel the details of this relationship. We first investigated a reduced compartmental neuron model for use in network simulations. We showed that reduced models containing <10 compartments could reproduce the LFP characteristics of the equivalent full-scale compartmental models to a reasonable degree of accuracy. Next, we created the Virtual Electrode Recording Tool for EXtracellular Potentials (VERTEX): a Matlab tool for simulating LFPs in large, spatially organised neuronal networks. We used VERTEX to implement a large-scale neocortical slice model exhibiting gamma frequency oscillations under bath kainate application, an experimental preparation frequently used to investigate properties of gamma oscillations. We built the model based on currently available data on neocortical anatomy. By positioning a virtual electrode grid to match Utah array placement in experiments in vitro, we could make a meaningful direct comparison between simulated and experimentally recorded LFPs. We next investigated the spatial properties of the LFP in more detail, using a smaller model of neocortical layer 2/3. We made several observations about the spatial features of the LFP that shed light on past experimental recordings: how gamma power and coherence decays away from an oscillating region, how layer thickness affects the LFP, which neurons contribute most to the LFP signal, and how the LFP power scales with frequency at different model locations. Finally, we discuss the relevance of our simulation results to experimental neuroscience. Our observations on the dominance of parvalbumin-expressing basket interneuron synapses on the LFP are of particular relevance to epilepsy and schizophrenia: changes in parvalbumin expression have been observed in both disorders. We suggest how our results could inform future experiments and aid in the interpretation of their results.

Background: Delayed post-stroke dementia (PSD) affects up to 50% of all stroke survivors, developing months or years after the initial stroke. However, the underlying mechanisms which cause PSD are unclear. Hippocampal atrophy is associated with PSD and vascular dementia, and hippocampal neurons are known to be particularly vulnerable in stroke and cerebrovascular disease. This work aimed to identify neuropathological characteristics and mechanisms contributing to cognitive decline in post-stroke survivors, focusing on the involvement of regional specific hippocampal neurons. Methods: Post-mortem brain tissue from the prospective CogFAST study was analyzed to compare pathological changes in stroke survivors who developed PSD with those who maintained normal cognitive function (PSND). Tissue from elderly controls and pathologically defined dementia groups lzheimer’s disease ( D) vascular dementia (VaD), mixed AD with VaD (MD); were also analysed for comparison with different disease aetiologies. Histological and immunohistochemical staining with quantitative image analysis and 3D morphometric analysis was carried out in paraffin-embedded sections, and protein immunoblotting was used in frozen hippocampal tissue. Key findings: Neuronal volumes in hippocampal subfields CA1-4 were reduced in PSD, VaD and AD subjects compared to elderly controls and PSND. Neuronal volume was also related to post-stroke cognitive function. There were no differences in dendritic length-density, hippocampal myelin loss, or autophagy markers between PSD and PSND. However, neuronal volumes were related to hippocampal tau pathology burden, reactive astrocyte density and myelin density in the alveus. Interestingly, the PSND subjects had greater burden of hippocampal amyloid-β than PSD. There were no quantitative differences in markers for astrocytes or microglia between the post-stroke groups. Conclusion: These findings suggest that neuronal volume loss is associated with post- stroke and ageing-related dementia. There were no relationships between the observed neuronal changes and AD pathology in stroke survivors, suggesting an important role for cerebrovascular disease processes.

This thesis presents an original methodology, as detailed below, applied to the testing of an existing computational model of human rhythm perception. Since the computational model instantiates neural resonance theory (Large and Snyder,2009), the thesis also tests that theory. Neural resonance theory is a key target for testing since, as contrasted with many other theories of human rhythm perception, it has relatively strong physiological plausibility. Rather than simply matching overt features of human rhythm perception, neural resonance theory shows how these features might plausibly emerge from low-level properties of interacting neurons. The thesis tests the theory using several distinct research methods. The model stood up well to each family of tests, subject to limitations that are analysed in detail. Firstly, the responses of the model to several types of polyrhythmic stimuli were compared with existing empirical data on human responses regarding beat identification to the same stimuli, at a variety of tempi. Polyrhythmic stimuli closely resemble real life complex rhythmical stimuli such as music, and were used for the first time to test the model. It was found that the set of categories of response predicted by the model matched human behaviour. Secondly, the model was systematically analysed by exploring the degree of dependence of its behaviour on the values of its parameters (sensitivity analysis). The behaviour of the model was found to retain consistency in the face of systematic numerical manipulation of its parameters. Thirdly, the behaviour of the model was compared to that of related models. In particular, the focal computational model, which balances physiological plausibility with mathematical convenience, was compared with other models that relate more directly to brain physiology. In each case, all relevant behaviours were found to be closely in line. Lastly, the outputs of the model under polyrhythmic stimuli were analysed to make new testable predictions about previously unobserved human behaviour regarding the time it takes for people to perceive beat in polyrhythms. These predictions led to the design and conduction of new human experimental studies. It was found that the model had successfully predicted previously unobserved aspects of human behaviour, more specifically it predicted the timescale within which people start to perceive beat in a given polyrhythmic stimulus.