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All peripheral sensory information is represented in the thalamus before being transmitted to the cortex, with the exception of olfaction. The thalamus projects to all areas of the neocortex and all neocortical areas project to the thalamus. I am interested in the development of three corticothalamic populations which are anatomically and functionally distinct; they project to different thalamic nuclei and generate different post-synaptic responses. Layer V fibres project exclusively to higher order thalamic nuclei. These projections drive thalamic neuron activity and mediate a trans-thalamic cortico-cortical relay. Layer VI and VIb fibres project to both first order and higher order thalamic nuclei. These projections modulate thalamic neuron activity and mediate feedback to the thalamus. Using three transgenic mouse lines I demonstrate that developing corticothalamic fibres target the specific groups of thalamic nuclei to which they project in adulthood. Rbp4-Cre::tdTomato labels layer V; Ntsr1-Cre::tdTomato labels layer VI; Golli-τ-eGFP labels layer VI and VIb. By P4 layer V fibres arborise densely in higher order nuclei but do not innervate the first order nuclei at any age. In contrast, at this age VI and VIb fibres densely innervate the first order ventral posterior-medial nucleus (VPM), as well as higher order nuclei. Layer VI and VIb fibres accumulate outside the dorsal Lateral Geniculate Nucleus (dLGN) from P2 before entering at P6. During this waiting period, retinal fibres transmit spontaneous waves of activity to the dLGN. To assess whether retinal input regulates corticothalamic circuit development I performed monocular enucleation. I demonstrate that after loss of retinal input, layer VI and VIb fibres enter the dLGN prematurely, by P2. Furthermore layer V fibres which target the retino-recipient superior colliculus also enter prematurely following enucleation. These results suggest there may be a retinal mechanism which regulates the timing of corticofugal ingrowth to joint retinal/cortical targets. The loss of retinal driver input to the dLGN also induces layer V driver fibres to aberrantly enter the first order dLGN. These results are the first to show cross-hierarchical rewiring after losing peripheral sensory input. The role of peripheral activity in the developing nervous system is underscored by activity dependent molecular mechanisms. I therefore performed a microarray gene expression experiment to systematically analyse molecular changes in the dLGN following enucleation. The expression of numerous genes is altered following enucleation including potassium channels Kcnk9 and Kcnn3, kinase pathway mediators, Shc3 and Dgkk, and immediate early genes BDNF, Egr1 and Egr2. The majority of genes regulated by enucleation are regulated in the opposite direction over development indicating that the loss of the retinal input delays maturation of the dLGN transcriptome. In this thesis I demonstrate that early corticothalamic development targets specific thalamic nuclei. Using the visual system as a model I demonstrate that retinal input regulates corticothalamic development and contributes to the transcriptome of thalamic nuclei.

In 2007, a genome wide association study identified a SNP in intron 1 of FTO with increased BMI. Homozygous risk allele carriers are on average three kg heavier than those homozygous for the protective allele. Mouse models have been made, including a conditional knockout, which is lean when globally expressed, as well as a conditional overexpression allele, which has increased body weight when globally expressed. The results from these and other studies suggest that the FTO SNPs lead to weight gain by increasing FTO activity and/or expression. Adult inactivation of Fto using the tamoxifen inducible Cre demonstrated that removal of Fto may be as deleterious as overexpression, with the adult knockout mice having increased fat mass and decreased lean mass. It also supported the role FTO plays in development as adult inactivation of Fto did not increase mortality rates as seen in the global Fto-/- pups. This study also revealed the importance of effective energy expenditure analysis in the mouse. I have confirmed a link between Fto-/- and increased mortality, which may be caused by alterations to developmental processes. Fto-/- reduces cilia formation in MEFs and results in dysregulated cilia formation in specific tissues in Fto-/- embryos. Levels of FTO also appear to affect adipogenic differentiation, which could be due to altered WNT/β-CATENIN signalling. Pharmacological inhibition of FTO was a success in vitro and a compound screen identified FG2216, which could be used in vivo to inhibit FTO. The in vivo effects of FG2216 at 60 mg/kg/2days did not affect body weight or composition in the mouse. My research suggests that there is dysregulation of gut hormones and neuronal signalling pathways in the FTO overexpression mice, which could cause the hyperphagia and increased body weight. These studies add to our current knowledge of FTO function, and suggest a role for FTO in control of body composition, development, and satiety signalling.

The activity of networks subserving memory and learning in the hippocampus is under the control of GABAergic interneurons. In order to test the contribution of distinct cell types, I have recorded extracellularly, labelled, and identified different types of interneuron in area CA3 of the hippocampus, a region implicated in the generation of gamma and theta oscillations, and the initiation of sharp-waves. I present here a detailed analysis of the spike timing of parvalbumin-positive (PV) basket and physiologically identified pyramidal cells in area CA3, relative to various network states recorded in area CA3 and CA1 simultaneously. Additionally, I have shown by detailed analysis that five classes of previously recorded and identified CA1 interneuron fired with cell type specific firing patterns relative to local gamma oscillations. In CA3, PV basket cells fired phase locked to theta and gamma oscillations recorded in CA1 as well as in CA3, and increased their firing rates during CA1 sharp-waves. Pyramidal cells in CA3 were also phase-locked, but fired at phases different from basket cells. During theta oscillations, CA3 pyramidal and PV basket cells were phase locked to both CA1 and CA3 theta equally, suggesting a wide coherence of these oscillations; in contrast, cells fired more strongly phase-locked to gamma oscillations in CA3 than in CA1, suggesting a specific role for CA3 in the generation of this rhythm. In contrast to theta and gamma oscillations, CA3 basket cells were phase-locked to ripples in area CA3 but not in CA1. Overall, my results show that the spike timing of several types of interneuron in CA1, and PV basket cells in CA3, is correlated in a cell- and area-specific manner with the generation of particular states of synchronous activity.

The goal of this thesis is to investigate the functional role of the cortical column architecture within some of the existing brain coding theories. Here I focus on the hierarchical models of predictive coding and the 'phase of firing' coding hypothesis. Using an oddball paradigm consisting of a sequence of identical sounds interspersed with rare, unexpected sounds, one can observe a difference between the scalp potentials evoked by oddball and common sounds. This difference has been linked to predictive coding and novelty detection, and Stimulus Specific Adaptation (SSA) has been suggested as a likely substrate at the single neuron level. In order to simultaneously constrain hierarchical models of predictive coding, and so as to investigate the contributions that neural processing within the different cytoarchitectonic layers of the primary auditory cortex (A1) may make to SSA, I simultaneously recorded multi-unit activity and current source density (CSD) profiles across all layers in A1 of the rat in response to standard and oddball tones. Our results suggest that SSA arises at the level of the thalamocortical synapse and is further enhanced in the supragranular layers. The phase of low-frequency Local Field Potentials (LFPs) in primary sensory cortices carries stimulus related information and disambiguates the information about different stimuli evoking similar spike rates. However, it is yet unclear how these informative LFP phase values arise within the laminar organization of cortical columns. To address this issue, I performed CSD recordings in the area A1 of anaesthetized rats during the presentation of complex naturalistic sounds. Information theoretic analysis revealed that most LFP phase information originates from discrete CSD events consisting of strong granular-superficial-layer dipoles, likely triggered by bursts of thalamocortical activation. These events, which occur at rates of 2-4 Hz, reliably reset LFP phases at times of strong network excitation. They therefore provide a useful reference frame to measure neural activity with respect to salient times of stimulus history. CSD events display a diverse, stimulus-dependent morphology: these reflect the outcomes of cortical computations which result in varying extents of activation of infragranular output layers.

Over one in five cancer patients will develop brain metastases and prognosis remains poor. Effective chemotherapeutics for primary systemic tumours have limited access to brain metastases owing to the blood-brain barrier (BBB). The aim of this study was to develop a strategy for specifically permeabilising the BBB at sites of cerebral metastases. Tumour necrosis factor was injected intravenously into mouse models of haematogenously induced brain metastasis. BBB permeability was assessed through histology and in vivo MRI and SPECT. Tumour burden and neuroinflammation were assessed after injection of TNF with Caelyx or a novel therapeutic. Mechanism of permeabilisation was investigated through histology and receptor-specific agonist antibodies. Administration of TNF dose-dependently permeabilised the BBB to exogenous tracers selectively at sites of brain metastasis, with peak effect after six hours. Metastasis-specific uptake of radiolabelled trastuzumab was also demonstrated following systemic cytokine administration. Administration of liposomal doxorubicin formulations in conjunction with TNF reduced tumour burden and mean metastasis size. Localised expression of TNFR1 was evident on the vascular endothelium associated with brain metastases. Human brain metastases displayed a similar TNF receptor profile compared to the mouse model. These findings describe a new approach to selectively permeabilise the BBB at sites of brain metastases, thereby enabling detection of currently invisible micrometastases and facilitating tumour-specific access of chemotherapeutic agents. We hypothesize that this permeabilisation works primarily though TNFR1 activation and, owing to the similar TNFR1 expression profiles in mouse models and human condition, the strategy has the potential for clinical translation.

Regular aerobic exercise has a wide range of positive effects on health and cognition. Exercise has been demonstrated to provide a particularly powerful and replicable method of triggering a wide range of structural changes within both human and animal brains. However, the details and mechanisms of these changes remain poorly understood. This thesis undertakes a comprehensive examination of the relationship between brain plasticity and aerobic exercise. A large, longitudinal experiment was conducted in which healthy but sedentary participants were scanned before and after six-weeks of monitored aerobic exercise. Increases in the volume of the anterior hippocampus were observed, as previously reported in an older cohort after a longer exercise intervention. Multimodal imaging methods allowed an in-depth exploration of the mechanisms underlying this volume change, which proved to be dominated by white matter changes rather than the vascular changes that have been previously reported. A surprising global change in the balance of CSF, blood, and brain tissue within the cranial cavity was also observed. Cross-sectional differences in memory and brain structure associated with fitness were also observed. The volume of the anterior hippocampus was shown to correlate with a measure of working memory. Higher cerebral blood volume throughout the brain was found to correlate with greater fitness and better working memory. Focal associations between fitness and magnetic susceptibility, a measure of iron content, were also observed in the basal ganglia. These findings demonstrate that aerobic fitness is associated with improved cognition and brain structure throughout the lifespan rather than simply acting to mitigate age related brain atrophy or accelerate brain development. Finally, a new pipeline was developed for analysing hippocampal morphometry using high-resolution, 7 Tesla scans. Striking variability in the convolution of the hippocampal surface is reported. This technique shows promise for imaging the precise nature of the change in hippocampal volume associated with aerobic exercise. This thesis adds to the evidence that aerobic exercise is a potent catalyst for behavioural and brain plasticity while also demonstrating that the mechanisms for those plastic changes are likely different than previously supposed. Future work will refine these measurement techniques, perhaps to a point where brain changes can be monitored on a single subject level. This work will provide an important tool to understand how best to utilize aerobic exercise to facilitate adaptive behavioural changes, mitigate the negative effects of ageing and disease on the brain, and maximize the benefits of active lifestyles.

This thesis describes the development of a framework for computational modelling of electromechanics in the mouse, with the purpose of being able to integrate cellular and tissue scale observations in the mouse and investigate physiological hypotheses. Specifically, the framework is applied to interpret electromechanical coupling mechanisms and the progression of heart failure in genetically modified mice. Chapter 1 introduces the field of computational biology and provides context for the topics to be investigated. Chapter 2 reviews the biological background and mathematical bases for electromechanical models, as well as their limitations. In Chapter 3, a set of efficient computational methods for coupled cardiac electromechanics was developed. Among these are a modified Newton method combined with a solution predictor which achieves a 98% reduction in computational time for mechanics problems. In Chapter 4, this computational framework is extended to a multiscale electromechanical model of the mouse. This electromechanical model includes our novel cardiac cellular contraction model for mice, which is able to reproduce murine contraction dynamics at body temperature and high pacing frequencies, and provides a novel explanation for the biphasic force-calcium relation seen in cardiac myocytes. Furthermore, our electromechanical model of the left ventricle of the mouse makes novel predictions on the importance of strong velocity-dependent coupling mechanisms in generating a plateau phase of ventricular pressure transients during ejection. In Chapter 5, the framework was applied to investigate the progression of heart failure in genetically modified 'Serca2 knockout' mice, which have a major disruption in mechanisms governing calcium regulation in cardiac myocytes. Our modelling framework was instrumental in showing for the first time the incompatibility between previously measured cellular calcium transients and ventricular ejection. We were then able to integrate new experimental data collected in response to these observations to show the importance of beta-adrenergic stimulation in the progression of heart failure in these knockout mice. Chapter 6 presents the conclusions and discusses possibilities for future work.

The Moonwalker (Mwk) mouse is a mouse model of cerebellar ataxia that harbours a point mutation in the Trpc3 gene. TRPC3 is a non-selective cation channel, most highly expressed in the Purkinje cells of the cerebellum. The gain-of-function mutation in the TRPC3 protein affects the development of Purkinje cell dendrites by reducing their branching, and also leads to abnormal motor coordination and cerebellar ataxia in Mwk mice at the age of 3 weeks. The aim of this thesis was to determine how the mutation in the TRPC3 channel results in the observed pathology. Proper function of the TRPC3 channel relies on its interaction with other proteins, hence we investigated binding partners of TRPC3. The study revealed PI synthase and CaMKIV as novel interaction partners of TRPC3. PI synthase is implicated in the upstream signalling events leading to TRPC3 activation, whereas CaMKIV is activated by Ca²⁺, possibly due to TRPC3 activation. We have identified alterations in phosphorylation of several key Ca²⁺ signalling proteins (CaMKII, CaMKIV, CREB and ERK), which indicates that there are changes in Ca²⁺ homeostasis in Mwk cerebella. Down-regulation of CaMKIV and up-regulation of CREB phosphorylation occurs as early as P21, which indicates that their abnormal activity could contribute to the Mwk phenotype. Microarray analysis comparing wild-type and Mwk Purkinje cells has revealed gene expression changes, which are likely due to abnormal Ca²⁺ signalling. Genes Ipo5, Opn3 and Sv2c are up-regulated at P11; Car2 and Stk17b are down-regulated at P14; and Cntn3 is up-regulated at P18 in Mwk Purkinje cells. High quality RNA from Purkinje cells was extracted using an optimised laser-capture microdissection method. Work on the Mwk mice points to the importance of TRPC3 activity for the proper development of Purkinje cell dendrites and depicts TRPC3 as a possible target for cerebellar ataxia treatment.

<p>The alpha-2 adrenergic receptor (α₂-AR) subfamily includes three different subtypes, α_2A-, α_2B- and α_2C-AR, all believed to exert their function through heterotrimeric G_i/o-proteins. The present study was undertaken in order to investigate subtype differences in terms of cellular response and to explore other potential signalling pathways of α₂-ARs.</p><p>Evidence is provided for a strong G_s-protein coupling capability of the α_2B-AR, leading to stimulation of adenylyl cyclase (AC). The difference between the α_2A- and α_2B-AR subtypes, in this respect, was shown to be due to differences in the second intracellular loops of the receptor proteins. Substitution of the second loop in α_2A-AR with the corresponding domain of α_2B-AR enrolled the chimeric α_2A/α_2B receptor with functional α_2B-AR properties. Dual G_i and G_s coupling can have different consequences for AC output. Using coexpression of receptors and G-proteins, it was shown that the ultimate cellular response of α_2B-AR activation is largely dependent on the ratio of G_i- to G_s-protein amounts in the cell. Also G_i- and G_o-proteins appear to have different regulatory influences on AC. Heterologous expression of AC2 together with G_i or G_o and the α_2A-AR resulted in receptor-mediated inhibition of protein kinase C-stimulated AC2 activity through G_o, whereas activation of G_i potentiated the activity. </p><p>α₂-ARs mobilize Ca²⁺ in response to agonists in some cell types. This response was shown to depend on tonic purinergic receptor activity in transfected CHO cells. Elimination of the tonic receptor activity almost completely inhibited the Ca²⁺ response of α₂-ARs.</p><p>In conclusion, α₂-ARs can couple to multiple G-proteins, including G_i, G_o and G_s. The cellular response to α₂-AR activation depends on which receptor subtype is expressed, which cellular signalling constituents are engaged (G-proteins and effectors), and the signalling status of the effectors (dormant or primed).</p>