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Nick Talbot - Cardiac Sciences - 'Modulators of the hypoxia-inducible factor (HIF) pathway and cardiorespiratory physiology'
The hypoxia-inducible factor (HIF) signalling pathway regulates the cellular response to hypoxia, but also appears to coordinate systemic responses to hypoxia, including the pulmonary vascular and ventilatory responses. In humans, the role of the HIF pathway in cardiorespiratory physiology has been characterised to date mainly by studying small groups of patients with genetic disorders, for example those with mutations in the HIF proteins themselves, or in the associated prolyl hydroxylase domain (PHD) oxygen sensing enzymes. Recently, a number of drugs have been developed that influence HIF signalling. Roxadustat, for example, is licensed for treatment of renal anaemia, and acts by upregulating the HIF pathway through PHD inhibition. However, the effects of this drug on systemic responses to hypoxia are not well understood. This project, funded in part by a Medical Research Council award to Dr Mary Slingo, will initially examine the effects of roxadustat on physiological responses to hypoxia in healthy volunteers, with a view to longer term studies in patients receiving this drug in the clinical setting.
Nick Talbot - Cardiac Sciences - 'A novel lung function technique for the early detection of Chronic Obstructive Pulmonary Disease (COPD)'
Chronic obstructive pulmonary disease (COPD) affects 400 million people worldwide and is a leading cause of death. Smoking remains the major risk factor for this condition. Unfortunately, there has been little improvement in outcomes for patients with COPD over the last two decades, in part because we currently lack the ability to diagnosis the condition early, before irreversible damage has occurred in the lungs. In Oxford we have over recent years developed a new technology for the non-invasive assessment of lung function, which is based upon quantification of heterogeneity (‘unevenness’) of gas exchange within the lung, rather than measurements of overall lung function. Across several patient groups, including those with asthma, COPD and cystic fibrosis, this is showing promise as a highly-sensitive marker of early lung disease. In this project, we will test the hypothesis that our measurements of lung heterogeneity, which are made during a period of relaxed breathing through a mouthpiece, are sensitive enough to identify early lung disease in smokers in whom conventional measures of lung function are normal. Our aim is to develop a test for early COPD, which will allow therapeutic intervention prior to the development of irreversible lung disease.
Jakub Tomek - Cardiac Sciences - 'How does nuclear calcium rule the heart?'
Cardiac disease remains the leading cause of death in the developed world, and better understanding of heart physiology and disease is needed to advance our prevention and treatment strategies. Many cardiac diseases, such as heart failure, are progressive and involve a complex network of remodelling at the cellular, as well as organ level. Oscillations of calcium levels in the nucleus of cardiac muscle cells are known to control gene transcription and cell health, and their dysregulation is implicated in the development of several disease. However, the ways of how the cardiac cells control their nuclear calcium levels remain relatively poorly understood. In this project, the student will use advanced cell imaging techniques to provide critical insights into how nuclear calcium levels in cardiac muscle cells are controlled, integrating the data in state-of-the-art computational models to provide an integrated understanding of the system. Dysregulation of nuclear calcium handling in disease will be subsequently explored, aiming to identify therapeutical targets to prevent disease progression and pathological remodelling. The ratio of experimental and computational work will be tailored to the student, and training will be provided in either.
Oliver Stone - Development & Cell Biology - 'Understanding cellular heterogeneity in the cardiovascular system'
In this project, you will receive extensive training in cutting edge bioinformatic, single cell genomic, flow cytometry and in vivo gene expression analysis, techniques that are broadly used to address scientific questions across disciplines in academia and industry. Experiments will address two overarching aims that will build on our recent findings. AIM1: Molecular and functional characterization of distinct angioblast populations. We aim to perform a molecular characterisation of distinct angioblast populations and their derivatives using bioinformatic analyses of existing data, single cell multiome analyses of isolated ECs and their progenitors, and histological analyses using in situ hybridisation and immunofluorescence analyses throughout embryonic development. AIM 2: Genetic dissection of angioblast populations using a novel Etv2DreERT2 knock-in mouse model. To determine the functional importance of ECs derived from distinct sources, we will analyse a novel mouse model for intersectional genetics that will allow us to specifically target ECs derived from distinct angioblast populations.
Dan Li - Cardiac Sciences - 'hiPSC-based modelling of cardiovascular diseases and neurocardiac interactions'
Cardiovascular diseases are a leading cause of death worldwide. They result from a variety of factors, including genetics, lifestyle, and environmental exposures. This project aims to investigate the use of human induced pluripotent stem cell (hiPSC) derived cardiomyocytes and cardiac organoids as disease models to explore novel therapeutic avenues for cardiovascular diseases such as cardiac arrhythmia, hypertrophy, and diabetic cardiomyopathy. The core of this project involves developing hiPSC-derived cardiomyocytes and cardiac organoids that faithfully recapitulate disease pathology. Furthermore, our proposal extends to the realm of neurocardiac interactions by introducing hiPSC-derived sympathetic neurons into the model. By establishing neuronal-cardiac co-culture systems, we will gain insights into how the nervous system influences cardiac function in health and disease. Cutting-edge techniques, such as Fluorescence Resonance Energy Transfer (FRET) and calcium imaging will be employed for precise measurement of intracellular signaling dynamics. Additionally, we will use state-of-the-art methodologies, including optical mapping and electrical mapping using a Microelectrode Array (MEA) system, to comprehensively analyze the electrophysiological properties of the models. The results of this project will provide new insights into the mechanisms of cardiac diseases and could ultimately lead to new treatments and prevention strategies.
Armin Lak - Neuroscience - 'Circuit Mechanisms of Learning and Decision Making'
How the brain integrates external sensory signals with internal reward and motivational signals for making decisions? How the brain learns over time to make better decisions? Our aim is to find quantitative circuit-level answers to these questions. We particularly focus on understanding the roles that frontal-striatal circuits play during decision-making, and how neuromodulators, in particular the dopamine signals, shape these circuits to guide learning. We employ a multi-disciplinary approach including high-count electrophysiology, multi-photon imaging, optogenetics, highly-controlled behavioural tasks in mice, and extensive computational modelling. Projects in the lab can be flexible along these themes, and may include experiments as well as computational work.
Simon Butt - Neuroscience - 'Emergent circuit properties of higher order cognition'
The lab is interested in the neurobiology of emergent higher order cognition across all levels of analysis. To date we have largely explored the contribution of locally projecting GABAergic interneurons to early sensory perception in somatosensory (Anastasiades et al., 2016; Baruchin et al., 2022; Ghezzi et al., 2021; Marques-Smith et al., 2016) and visual cortex (Ghezzi et al., in preparation). These studies have identified differences in the construction of formative circuits that mirror the requirements for early function. The lab is now interested in understanding how circuits are co-ordinated at the brain wide level from the molecular to systems level. To this end we are interested in attracting DPhil students who are keen to pursue individually tailored projects using advanced techniques from patch-seq to multi-photon imaging of neurotransmitter dynamics. We collaborate closely with other groups in the department, notably those of Prof. Armin Lak (prefrontal cortex function and behaviour) and Adam Packer (claustrum and advanced optical approaches). Students are welcome to contact Prof. Simon Butt to discuss further but are encouraged to read recent publications from the group and bring their own ideas.
Stephanie Cragg - Neuroscience - 'Neuromodulation of striatal dopamine by neuronal and non-neuronal circuits'
The neurotransmitter dopamine in the striatum is critical to our motivated actions, and is dysregulated in disorders spanning from Parkinson’s disease (PD) to addictions. Midbrain dopamine neurons form intriguing structures: they give rise to colossal axonal arbours that are more branched than any other neuron type, providing opportunities for diverse neuromodulators to act on axons to shape dopamine function. We have discovered striatal circuits that can act on dopamine axons to powerfully transform dopamine output. We are working to better understand the diverse range of striatal neuromodulators and circuits, neuronal and non-neuronal, that act on dopamine axons to govern dopamine output, in mouse brain ex vivo in health and their disturbances in mouse models of PD. Potential DPhil projects will join our effort to reveal the striatal modulators and circuits that govern dopamine transmission, and to understand the dynamic signalling profiles of those neuromodulators and circuits. Research techniques involved will include state-of-the-art methods for the direct detection of neurotransmitters and neuromodulators in real-time, such as imaging genetically encoded fluorescent reporters for neuromodulators (e.g. GRAB sensors to detect amines, neuropeptides, lipid transmitters) or cellular activity (calcium and voltage sensors), alongside fast-scan cyclic voltammetry for real-time detection of dopamine and/or neuronal recordings with electrophysiology, in conjunction with methods to manipulate brain and cells (optogenetics, chemogenetics, pharmacology) in ex vivo brain slices from healthy mice and transgenic models of PD.
Stephen Goodwin - Neuroscience - 'Building a Sexually Dimorphic Nervous System'
Sex differences often represent the most dramatic intraspecific variations seen in nature. Although males and females share the same genome and have similar nervous systems, they differ profoundly in reproductive investments and require distinct morphological, physiological, and behavioural adaptations. Animals determine sex early in development, which initiates many irreversible differentiation events that influence how the genome and environment interact to produce sexspecific behaviours. Across taxa, these events converge to regulate sexually dimorphic gene expression, which specifies sex-typical development and neural circuit function. However, the molecular programs that act during development remain largely unknown. We aim to understand the gene regulatory networks underlying sexually dimorphic neuronal development in the brain of the genetically tractable vinegar fly Drosophila melanogaster. Given the long and fruitful history of using vinegar flies to uncover fundamental principles of developmental biology and behavioural neuroscience, they are ideally suited for studies which bridge these disciplines. The fly's central brain is a remarkably complex tissue composed of approximately 100,000 interconnected neurons, forming the intricate networks necessary to coordinate complex cognitive and motor functions. Tightly regulated molecular programs act over a broad developmental window leading to the diversity of cell types found in the brain. New advances in single-cell technologies have enabled, for the first time, a comprehensive survey of this diversity throughout development. As sex plays distinct roles in different neurons at different developmental times, we only now have the means of studying the emergence of sexual dimorphisms within this complex structure. We will use single-cell technologies to compare the molecular profiles of both males and females in the developing central brain to understand the mechanisms underlying sexual dimorphism in the nervous system. This timely study will also generate the first developmental single-cell gene expression atlas of the Drosophila central brain, an immensely beneficial resource that will be available and accessible to the research community. More broadly, our findings will generate a unique resource to investigate general mechanisms underlying the development and functions of neuronal circuits for the fly community and beyond, given that many of the fundamental biochemical pathways and mechanisms are conserved between flies and humans. The proposed experiments will paint a detailed picture of cellular and molecular diversity in a developing central nervous system. Our data will answer the longstanding question: How are neuron types associated with sexual behaviours born and wired?
Stephen Goodwin - Neuroscience - 'Integrating visual information with an internal sexual arousal state'
Animals must navigate complex visual environments, ensuring they avoid dangers while also foraging for food or finding a mate. To succeed, animals must identify relevant visual cues and interpret them in relation to their external circumstances and internal state, ensuring they respond appropriately. Visual information is perceived non-discriminately in the eye; however, how the animal responds to this information is determined in the brain. Understanding how the brain transforms complex visual stimuli into complex behaviour patterns remains a significant challenge in behavioural neuroscience. The elegant courtship display of the male vinegar fly Drosophila melanogaster is ideally suited to address this challenge. To reproduce successfully, Drosophila males are hardwired, having the ability to navigate complex environments and identify a mate. The interpretation of the female as a potential mate triggers a behavioural switch in males, setting off an elaborate behavioural display: males persistently pursue the female while intermittently singing her a courtship song through the extension and vibration of a single wing. Meanwhile, the female continuously decamps and rejects the male's advances, giving her time to assess his suitability as a mate before she sanctions the mating. This switch in the males' behavioural pattern is triggered when a sexual arousal threshold is reached, a stable internal state ensuring males persist in pursuing the female. Interestingly, this behavioural switch must also be flexible. If males, once aroused, find the female is, in fact, a different species or sex, they must switch back to their pre-arousal behavioural patterns. Studies in the vinegar fly Drosophila melanogaster can provide insights into general principles of how brains use sensory information, like visual stimuli, to guide behaviour and how internal state changes, such as arousal, modify these sensorimotor programs. Working with flies has the advantage of using a vast array of genetic tools that allows us to identify and manipulate relevant neurons in the brain. Using these tools, we will study a group of sexually-dimorphic neurons involved in visual integration critical to male courtship behaviour and reproductive success.This proposal will be an ideal entry point into our understanding of how animals integrate external sensory information with their internal state to make an appropriate context-dependent decision.
Robin Klemm - Cell Physiology - 'How do adipocytes transport fatty acids across the cell surface?'
How fat tissue secretes fatty acids during times of starvation is a big unanswered question in cell physiology. In fact, we know in general relatively little about the mechanisms that traffic free fatty acids into and out of cells. In your project, we tackle this problem with a tissue culture model for adipocytes, using a combination of light and electron microscopy, structural biology, easy metabolite analysis, cell biology and CRISPR-genetics. The experimental set up is easily tractable because the secretion of fatty acids can be readily induced by addition of a small molecule to differentiated adipocytes. You will focus on studying the intracellular re-arrangement of organelles during lipolysis. We will investigate how the lipid storage organelles called lipid droplets are hooked to the cell surface and how this is coupled to efficient secretion of newly mobilized fatty acids. This will be analyzed by light and electron-microscopy, and metabolic essays. To identify factors that move the lipid droplets around in the cell we are going to use organelle purification and proximity specific proteomics methods. A candidate library of potentially important factors will then be subjected to a targeted genetic screen in which we aim to find the machinery that transports fatty acids outside of the cell. These mechanisms have fundamental relevance in systemic energy metabolism and will help to understand the pathophysiology of obesity and diabetes.
Robin Klemm - Development & Cell Biology - 'How the shape and metabolic function of mitochondria control cellular specialization in differentiation'
Mitochondria are best known for their role in energy metabolism but have recently emerged as critical signalling hubs which are important during cellular differentiation from stem cells. Metabolic adaptability is crucial in decision making processes called “fate switches”. The machinery which controls these processes is beginning to emerge but many central questions remain unanswered. We have recently discovered that mitochondrial contact sites with other organelles in the cell are critical in regulating these processes. The contact site factors establish physical interactions with e.g. the endoplasmic reticulum and specialize in importing specific lipids that remodel the shape, function and biochemical activity of mitochondria. These changes in turn determine the fate of the cell and control mechanism that establish new cellular identity. This PhD project will use CRISPR-genetics in combination with fluorescence microscopy and easy to study metabolic readouts to discover the cell biological mechanisms by which mitochondria remodel their function. We focus on a mitochondrial contact site protein, which, according to its phosphorylation status can interact with different organelles in the cell. The selection of preferred binding partners within the mitochondrial neighbourhood has profound consequences on mitochondrial function and cell fate. We have evidence from mass spectrometry experiments that mitochondrial import of specific lipids modulates the mitochondrial function depending on which other organelle is bound. How cell biological mechanisms organize organelle neighbourhoods and inter-organelle communication is an exciting new area in the molecular life sciences and has relevance in all cell-types which are metabolically active such as fat cells, liver, neurons and muscles.
Samira Lakhal-Littleton - Cardiac Sciences - 'More to iron than the erythron'
Historically, understanding of iron’s importance for physiology and medicine has been centred around haemoglobin, and iron deficiency has been synonymous with anaemia. However, the past decade has seen a paradigm shift in our understanding of the physiological importance of iron, and we now know that non-haemoglobin iron is essential for fundamental processes within the cardiovascular system, such as contractile function of the heart and regulation of vascular tone. In clinical practice, the growing recognition of the importance of iron has led to greater focus on the treatment of non-anaemic iron deficiency, particularly in heart failure. However, this change in clinical practice remains uncoupled from mechanistic understanding of where and how iron exerts its effects. To address this problem, our research combines clinical studies of functional and iron parameters in heart failure patients with mechanistic studies in preclinical models of heart failure. Techniques range from proteomic and metabolomic characterisation of patient samples, to advanced MR imaging of Heart function in pre-clinical models, to cell-based work in cardiac and vascular cells. The aim is to understand how non-anaemic iron deficiency affects heart failure patients, and use that understanding to implement optimal iron replacement therapies.
Andrew King - Neuroscience - 'Models of the encoding of sounds by the auditory system'
Neurons in auditory cortex produce patterns of spikes in response to sound. What is the computational mapping from sound to auditory cortical responses? Can we predict the moment-to-moment responses of neurons in the auditory cortex to arbitrary sounds? This computational project involves fitting various models to the mapping from natural sounds to neural responses recorded from the midbrain and auditory cortex. The project will begin with a fitting a simple model, the linear-nonlinear model, and testing its capacity to predict neural responses to a held-out dataset of sounds. The student will then go on to analyse the linear and nonlinear parts of this model to look for different types of neuron and extend this work to include more complex network models that better reflect the physiological properties of auditory neurons and the way information processing changes between the midbrain and cortex. The structure of these more complex networks will be analysed to provide insight into the functional organization of the auditory brain.
Edward Mann - Neuroscience - 'Functional connectivity of hypothalamo-cortical circuits'
Stress exacerbates many psychiatric conditions, and repeated stress contributes to the pathogenesis of disorders such as Post Traumatic Stress Disorder, Panic Disorder and Major Depressive Disorder. The orexin (hypocretin) system is highly reactive to stress, and regulates many physiological processes that are altered in stress-related mental illness, including sleep/wake patterns, appetite and cognition. Changes in orexin levels have been reported in major depression and anxiety disorders, and polymorphisms in the orexin 1 receptor are associated with anxiety spectrum disorders, particularly in women. The orexin system is therefore an attractive target for treating stress-related disorders. Orexinergic neurons have wide projection targets across the nervous system, including hypothalamus, thalamus, cortex, brain stem and spinal cord. The projections to other hypothalamic neurons and subcortical arousal centres are important for modulating arousal, appetite and activity of the Hypothalamic Pituitary Adrenal Axis. The roles of projections to cortical circuits remain less well understood, but may be involved in regulating cortical arousal and the cognitive responses to stress and could represent promising targets for drug development to treat stress-related cognitive dysfunction. The aim of this project is to resolve the mechanisms by which orexinergic neurons directly modulate cortical network activity, using optogenetic stimulation of orexinergic projections in ex vivo cortical brain slices in combination with patch-clamp recordings, multiphoton imaging and high density multielectrode arrays.
Zoltán Molnár - Neuroscience - 'Role of SNARE proteins in cortical development'
Neural communication in the adult nervous system is mediated primarily through chemical synapses, where action potentials elicit Ca2+ signals, which trigger vesicular fusion and neurotransmitter release in the presynaptic compartment. At early stages of development, the brain is shaped by communication via trophic factors and other extracellular signalling, and by contact-mediated cell–cell interactions including chemical synapses. The patterns of early neuronal impulses and spontaneous and regulated neurotransmitter release guide the precise topography of axonal projections and contribute to determining cell survival. We study of the role of specific proteins of the synaptic vesicle release machinery in the establishment, plasticity, and maintenance of neuronal connections during development. We examine mouse models where various members of the N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex have been genetically manipulated (e.g. Snap25 or Munc13). We are focusing on the role of regulated vesicular release and/or cellular excitability in synaptic assembly, development and maintenance of cortical circuits, cell survival, circuit level excitation–inhibition balance, myelination, refinement, and plasticity of key axonal projections from the cerebral cortex. These models are important for understanding various developmental and psychiatric conditions, and neurodegenerative diseases.
Andrew Peters - Neuroscience - 'Neural circuits for learning and executing behaviour'
Behaviour is not learned and driven by single brain regions, but instead arises from cooperation across multiple areas. One prominent circuit of interdependent regions consists of a loop between the cortex, basal ganglia, and thalamus. Together, these regions are critical for learning and executing behaviour, though it is largely unknown how this is accomplished at the level of neural activity. Our lab is interested in discovering fundamental principles of this circuit, and we investigate issues like how activity flows between regions, how it changes with learning, and how activity relates to behaviour. Our experiments combine large-scale imaging and electrophysiology techniques with learned behaviours and neuronal manipulation in mice. We use simple tasks, like stimulus-response associations, to investigate the relationship between activity and behaviour. Projects in the lab can be flexible along these themes, and may typically include recording and analysis from one or more brain regions across learning.
Paul Riley - Cardiac Sciences - 'Investigating the mechanisms of autoimmunity during heart failure'
Heart Failure (HF) is a rapidly growing public health issue with an estimated prevalence of >37.7 million individuals globally and is a major unmet clinical need. HF is underpinned by cardiomyocyte hypertrophy, interstitial fibrosis, pathological remodelling and ultimately death. Current interventions do not prevent disease progression and cannot restore heart function. A critical contributor to chronic decline of cardiac function in HF is the immune system, notably the adaptive immune response. Following tissue damage there is release of cardiac antigens, such as α-myosin heavy chain (α-MHC), which are captured by dendritic cells (DCs) and presented to T-cells in the draining lymph nodes, inducing an auto-reactive T-cell response. This is due, in part, to T-cells escaping central tolerance towards cardiac self-antigens during development in the thymus. Activation of T-cells, primed against cardiac antigens, is seen as a possible mechanism for prolonged cardiac injury well after the initial insult. In support of this, anti-heart autoantibodies against cardiac epitopes are a well-known clinical epiphenomenon during HF and the presence of autoreactive T-cells post-MI has previously been demonstrated. This project will focus on understanding the mechanisms behind T-cells escaping central tolerance towards cardiac self-antigens during development in the thymus, and whether restoring this tolerance improves disease progression in HF.
Filipa Simões - Cardiac Sciences / Development & Cell Biology - 'Decoding spatial heterogeneity in the regenerating heart'
Myocardial infarction (MI) causes permanent heart tissue loss in adult mammals. Following an MI, the injured heart recruits a significant number of monocyte-derived macrophages, essential immune cells that play critical roles in both scar formation and tissue regeneration. However, we still have limited understanding of the specific factors influencing distinct macrophage functions within the damaged heart. This project aims to shed light on how macrophage heterogeneity is linked to their spatial distribution across the heart and how, in turn, this distribution shapes macrophage identity and function. Despite their vital roles in cardiac repair, the intricate local environmental cues and cell-cell interactions governing the diverse roles of macrophages in this context have not been fully deciphered. By comprehending the regenerative microenvironment, where the innate immune response persists while still supporting regeneration, and by targeting macrophage-induced pro-fibrotic pathways, we may develop therapeutic strategies that harness pro-regenerative responses in the injured mammalian heart.
Filipa Simões - Cardiac Sciences / Development & Cell Biology - 'A human vascularised cardiac organoid system for modelling cell-cell interactions and target discovery in heart disease'
A major obstacle to a deeper understanding of how the human heart responds to injury is the lack of human-derived in vitro 2D and 3D cell culture models that faithfully recapitulate the complexity of an in vivo system, where multiple resident and infiltrating cell populations co-exist and interact within the cardiac niche. Our group is working towards the development and application of self-organizing multi-lineage cardiac organoid structures to account for the complex 3D cell-cell interactions occurring between multiple cardiac cell types. We aim to facilitate translational research by enabling genetic screens and pharmacological modulation of disease states by further developing a human 3D vascularised cardiac organoid model that offers a chamber-specific, scalable and highly manipulable multi-lineage human cardiac model that reduces dependence on animal models.