- Total grants
- Total funders
- Total recipients
- Earliest award date
- 31 Jan 2017
- Latest award date
- 30 Sep 2018
- Total GBP grants
- Total GBP awarded
- Largest GBP award
- Smallest GBP award
- Total Non-GBP grants
Lung cancer remains the leading cancer-related cause of death in the UK. Early detection and treatment are critical to improving outcomes. Our lab has collected a unique set of lung tissue samples from patients with pre-cancerous disease, some of whom have gone on to develop cancer. By studying the genetic and molecular profiles of these samples we aim to elucidate the mechanisms of progression from pre-cancerous disease to invasive cancer. By doing so we can identify future methods of treatment and prevention. My work focuses on analysis of vast quantities of data produced by this program. We have recently studied the genetics of these samples, including which genes are expressed, which are mutated, and how they are regulated. From these complex networks we identify key signals of instability in the genome, which we believe are driving progression to cancer. These data provide a snapshot of early cancer. The first aim of this project is to investigate the dynamics of this process using longitudinally collected samples, and new techniques which can probe these samples on a single-cell level. The second aim is to study the immunological mechanisms by which some pre-invasive lesions regress and do not become invasive cancer.
Genomic instability triggers catastrophic events that restructure parts of the genome and provide a proliferative advantage to the cancer cell (e.g. through oncogene amplification) in up to 30% of cancers. There is recent evidence that suggests these types of events may also impact immune responses, by affecting genes that are involved in the interaction between cancer cells and their microenvironment. This project aims to study the impact of two well defined catastrophic events, chromothripsis (massive chromosome-wide rearrangements) and kataegis (hypermutated regions), on genes involved in immune-related pathways in oesophageal adenocarcinoma. The student will work with whole-genome sequencing data from 120 samples of oesophageal tumours available from the International Cancer Genome Consortium and will employ bioinformatics approaches to address the following key goals: (1) identify chromothripsis and kataegis events using computational protocols previously established in the group; (2) identify the genes affected by these events via genomic overlap methods; (3) summarise the proportion of the genes affected that are involved in immune signalling pathways (as recorded in relevant pathway databases). This will enable us to assess the likely impact of such catastrophic events on immune system processes and further clarify their implication in immune evasion during cancer development.
Neural circuits in the brain underlie sensory perception and motor control, functions that are often impaired during neurological disorders. However, many aspects of circuit function remain unclear. These include how sensory and motor information is represented and transformed as it flows through neural circuits. In this project, I will study the properties of Golgi cells, a particular type of inhibitory neuron in the cerebellar cortex, a brain area that helps coordinate movements and predict thier sensory consequences. To do this I will use a new high speed 3-dimensional microscope technology that can measure signals as they rapidly flow through complex neural circuits deep within the brain of mice expressing fluorescence reporters of neural activity. By examining how the activity of populations of inhibitory neurons change during different behavioral tasks and during learning, I will determine how these neurons contribute to information processing in the cerebellum. By combining this imaging method with methods for manipulating neuronal activity and network models of circuit function I will identify the underlying mechanisms. This research will lead to fundamental new insights into cerebellar function and will provide a framework for understanding what goes wrong during neurological disorders.
The role of the Trem2 R47H mutation in the development of Alzheimer disease phenotypes in APP knock-in mice 31 May 2018
The field of research into Alzheimer’s disease is lacking a transgenic mouse model which shows progressive degeneration like in humans. Recently, there has been increased interest in the involvement of the immune system of the central nervous system, particularly microglia, which co-localise with amyloid-beta plaques, potentially limiting toxicity. TREM2 is a protein expressed by microglia and the R47H mutation is an identified risk-factor for Alzheimer’s disease. We propose that combining this microglial risk-factor with raising amyloid beta in APP knock-in mice may exacerbate the Alzheimer's phenotype, potentially leading to tau pathology. Initially I will be taught to perform whole-cell voltage-clamp in brain slices. I will then use a novel TREM2(R47H) knock-in mouse and examine variables previously reported as altered in transgenic APP/PSEN1 mice (and confirmed in APP knock-in mice, unpublished). In particular I will record spontaneous and miniature excitatory postsynaptic currents, the frequency of which is dependent on the probability of glutamate release and number of synapses; the amplitude dependant on the number of postsynaptic receptors. These experiments will help to elucidate the effects of microglia in early synaptic changes involved in AD and will provide initial characterisation of the TREM2 mice that will be crossed with APP knock-in mice.
Computational biology aims to answer some of biology’s most complex questions using computational and statistical methods. The field has successfully identified genes involved in disease and has helped to discover drugs for their treatment. My PhD research takes this approach to understand the processes by which we age. Aging is a complex disease — characterised by the progressive loss of function in an organism over time — with huge social and financial cost. Faced with an aging population, breakthroughs in this area are desperately needed. I am attempting to do this using data collected from experiments that measure the lifespan of yeast in different environmental conditions. Whilst we are only distantly related to yeast, it is a useful model of human aging as it shares many cellular processes, but lives for a fraction of the time. Ultimately, I aim to use these data to predict the genes that cause yeast to age. Whilst a handful of aging genes have been identified, more genes are likely to contribute. I use networks and machine learning approaches to make my predictions. Going forward, these will help to deepen our understanding of aging and aid the development of treatments to eventually cure this disease.
Optimisation of carrier materials for the delivery of olfactory ensheathing cells in spinal cord injury 27 Apr 2017
Transplant-mediated repair is a promising method in spinal cord injury (SCI) treatment. This involves transplanting therapeutic cells that promote nerve regeneration at the site of injury. For SCI, one promising therapeutic cell type is olfactory ensheathing cells (OECs). These have been shown to remyelinate demyelinated axons and promote new synapses following injury. They are also easily accessible clinically via trans-nasal endoscopic biopsy, and compelling pre-clinical evidence means that they are now close to being formally tested as part of a first-in-man clinical trial. However, currently these cells are delivered as a simple cell suspension, and this is unlikely to be optimal for creating a permissive and optimised repair environment. Thus, the objective of this project will be to develop and engineer optimised biomaterial scaffolds for OEC delivery. In doing so, it is hoped that a permissive 3D extracellular environment can be created, and the phenotype and behaviour of OECs optimised for spinal cord repair. Promising prospective biomaterials include fibrin, collagen and collagen-fibrin blends. To this end, we will investigate the effect of these promising carrier materials on OEC survival and phenotype, particularly with a focus on changes they may cause on 3D cell morphology.
To attack cells in our body, bacteria make use of toxins that drill holes in the cell membranes. Following a similar strategy, our immune system makes use of such pore forming proteins to target cancerous, virus-infected and bacterial cells. In the course of their action, pore forming proteins are first secreted as monomers, bind to the membrane, and next self-assemble into oligomeric pores. Some of the various open questions are how these pore assembly processes take place on more complicated, composite membranes such as bacterial envelopes. This project will aim to contribute to answering these questions, while providing the student research expertise in nanoscale microscopy methods applied to process that is essential for bacterial attack and immune defence. More precisely, the student will image live bacteria (E. coli) as they are attacked by the membrane attack complex. This is part of on-going atomic force microscopy experiments in the supervisors lab, which offer the possibility to visualise bacterial cell wall degradation in real time. Time permitting, the student will also be exposed to computational approaches to analyse such new data as well as past data on assembly and membrane insertion of immune effector perforin.
This proposed research intends to investigate the brain representation of complex, multilayered three-dimensional environments in free-roaming rodents by detecting electrical neuronal activities. With the assumption that the grid cell can form a lattice representation in a volumetric space, the main goal of this project is to test this hypothesis and construct more detailed mosaic neuronal models. From the previous experimental evidence, the grid cell plays a pivotal role in distance-measuring by forming a grid-like array on a flat surface, however, how this array is remodelled in vertical or tilled surface remains debatable. In this project, rats will be allowed to explore in a giant lattice model with options of climbing up or down, dwelling forwards or backwards while looking for rewards. The neuronal activities in rat's hippocampus will be collected, reconstructed into a 3D model. If the hypothesis is to be correct, the 3D cognition map is suggested to be a multiple evenly-spaced neuron filed distributed volumetrically (figure1, D and E). Otherwise, the field might be distributed in parallel columns vertical to the ground, as the extension of the 2D hexagonal array (figure 1, C).
Investigation of the structural and conformational preferences of ribosome-bound nascent chains using NMR paramagnetic relaxation enhancement measurements 31 May 2018
Co-translational folding is best studied by providing high-resolution structural descriptions of nascent polypeptides (NCs) as they emerge from the ribosome. This is achieved by producing snapshots of the process using ribosome-associated-nascent chains(RNCs) and developing 3D structural models by combining NMR spectroscopy as experimental restraints within MD simulations. The emerging NC is a dynamic entity that searches conformational space in its quest for acquiring its correct structure; it undergoes both transient interactions with itself and the external surface of its ribosome. This Scholarship aims to develop novel distance-based, PRE (paramagnetic-relaxation-enhancement) NMR measurements of RNCs to evaluate these transient processes. Over 8 weeks, this project will enable us to develop strategies to selectively label RNCs with the MTSL "spin-labels" at a single cysteine site, by adapting well-established RNC technology. We will study two RNCs "snapshots" which capture early folding transition for an immunoglobulin protein. We will characterise the structural properties of the modified RNCs using 2D NMR spectroscopy, and quantitate possible transient interactions/compaction events by collecting PRE measurements. We will also initiate MD simulations with the new experimental restraints that have been acquired. These approaches will advance our current 3D structural models to dissect further molecular details of co-translational protein folding.
Integrated interdisciplinary approaches to design new anti-bacterials with novel mechanisms of action to tackle antimicrobial resistance in Tuberculosis 30 Sep 2018
Tuberculosis (TB) remains a serious threat to global health. The World Health Organisation estimate that 10.4 million new cases were contracted in 2015, and that over 500,000 of those cases were resistant to at least one of the antibiotics currently used to treat this condition. The spread of such resistance is a serious concern and as a result there is a need for the development of new drugs to combat TB. Recent work has identified two classes of molecule which have promising anti-tubercular properties: tetrahydroisoquinolines and non-steroidal anti-inflammatory drugs. My project will focus on the development of new anti-bacterials from these classes of molecule while exploring the reasons behind their anti-tubercular properties. This will be achieved through a combination of chemistry and molecular microbiology, making use of both laboratory and computational techniques.
Inhibition in the Periaqueductal Gray 30 Sep 2018
Deciding which action to take, such as whether to cross a busy road, is a critical survival skill. Making decisions requires integrating complex information and identifying the cellular mechanisms of this process is critical for understanding how the brain computes decisions. In this project will investigate neurons that control defensive decisions in mice and focus on inhibitory neurons in the midbrain Periaqueductal Grey (PAG), which have the ability to veto defensive behaviours.The first main goal of the project is to use electrophysiological and advanced molecular techniques, such as RNA sequencing and gene knock-down, to identify the genes and ion channels that control the firing of PAG inhibitory neurons. The second goal is to determine key regulators of the activity of these neurons, in particular neuromodulators and long-range synaptic connections from other brain areas, using techniques such as optogenetics in combination with behavioural assays that exploit the innate defensive behaviours of mice. The results of this work will reveal new the biophysical principles that drive firing in a key population controlling a critical behavioural decision, and provide an entry point for understanding how pathological states such as anxiety lead to maladaptive decisions.
Gene Editing using CRISPR/Cas9 for Gene Correction in Recessive Dystrophic Epidermolysis Bullosa (RDEB) 31 May 2018
Conventional gene therapy approaches rely on the addition of a corrected gene copy via viral vector transduction. Such strategies are currently being applied to recessive dystrophic epidermolysis bullosa (RDEB) where there is defective collagen type VII protein. However, use of constitutive exogenous promoters in viral vectors results in sustained gene expression that is not subject to the normal regulatory mechanisms of C7 expression. Integrating properties of vectors also pose risk for insertional mutagenic-derived events and efficiency of gene transfer has been challenging given the large size of COL7A1 cDNA. Whereas, gene-editing tools can be designed and engineered to target and repair specific defined regions of DNA, thereby alleviating genomic toxicity and maintaining endogenous gene expression control. Existence of well-known mutation hotspots within COL7A1 allows CRISPR reagents to be designed that would target the mutations found in the UK population with RDEB. Investigations outlined in this proposal aim to identify the most effective CRISPR reagent for a chosen mutation hotspot within COL7A1 gene. In skin, keratinocytes predominantly produce collagen type VII. Therefore, this project will evaluate feasibility of gene editing approaches using CRISPR/Cas9 system in HACAT keratinocytes cell line, and help address critical aspects of CRISPR/Cas9 efficiency at a chosen loci.
Proteins must fold into their tertiary structure in order to function. This complex process has been well studied over recent decades. However, most of these studies rely on small isolated proteins; protein folding inside of cells can be very different. In cells during translation, the ribosome synthesises proteins by adding amino acids to the growing polypeptide chain, this eventually extends out of the ribosome tunnel and can can begin to fold while still being synthesised; representing a major difference between historical folding studies and the real picture inside cells. In our lab we aim to characterise the process of protein folding on the ribosome. We are especially interested in how the ribosome may aid proteins to fold efficiently. To do this we use Nuclear Magnetic Resonance (NMR) spectroscopy to generate structural information of proteins attached to ribosomes alongside Cryo Electron Microscopy and Molecular dynamics computer simulations. This PhD project will aim to fully characterise the structure and dynamics of a nascent chain attached to the ribosome using a variety of NMR experiments. We will then analyse a variety of proteins to try and understand why they fold at different points during translation.
Quantifying the activity of cis-regulatory sequences in the hypothalamus using single molecule fluorescence microscopy. 27 Apr 2017
Every cell in the nervous system contains a programme of gene expression that not only determines its morphology and function, but also allows neurons and circuits to respond and adapt to sensory experiences. It is well document that changes in gene expression in response to these stimuli require cis-regulatory DNA sequences (enhancers), which mediate the activation and repression of specific genes. However, how a neuronal network as a whole tunes their transcriptional responses to achieve behavioural changes remain elusive. This project aims to address this by examining how the regulation of the genes arginine vasopressin (AVP) and oxytocin (OT) (neuropeptides that play a role in mammalian social behaviours) can differ between neurons and even gender, by identifying how different enhancer elements contribute to cell-type specific expression. To do this we will combine an enhancer assay with RNA single molecule fluorescence in situ microscopy (smFISH) in the hypothalamus, where these genes are primarily expressed. This will allow us to quantify the activity of specific enhancers in a given context, such as cell type and gender. The results will therefore give an indication of how information is encoded within these enhancer sequences that allows specific expression of the AVP and OT genes.
Developing a behavioural task for measuring the ability of listeners to perform auditory scene analysis. 27 Apr 2017
The auditory brain separates simultaneous sounds arriving at the ear into identifiable and localisable sources by a process known as Auditory Scene Analysis (ASA). The two steps that are involved in ASA are i) segregation of the simultaneous auditory information and ii) the integration of the sounds from the same source into one stream. To understand how these two steps are connected and how different auditory cues interact to shape the scene, this project will develop a behavioural task and analyse the performance of human listeners. A target vowel will be presented alongside with a distractor vowel, and human listeners will identify what the target is. Listeners will only be able to identify the target if they can separate the two sounds: changing the location and pitch of target and distractor will help this. In order find out whether the separation of competing sounds is facilitated by the formation of perceptual streams, the vowels will also be presented as part of a sound sequence. Our hypothesis is that the ability to identify a target vowel will be improved by the formation of two perceptual streams. The long-term goal is to develop a behavioural paradigm suitable for humans and animals.
Investigating notch signalling in patient-derived models of familial Alzheimer's Disease. 31 May 2018
Alzheimer's Disease (AD) is characterised pathologically by extracellular plaques composed of Abeta peptides, which are generated by the successive proteolytic processing of the amyloid precursor protein (APP) by multiple enzymes including the gamma-secretase complex. Human genetics supports a causative role for Abeta in AD: mutations and gene duplications in APP cause familial AD. Further, mutations in PSEN, which forms part of the gamma-secretase complex, are also causative of fAD. However, substantial clinical heterogeneity exists in fAD patients with PSEN1 mutations, the molecular basis of which is not well understood. Our hypothesis is that differential processing of non-APP substrates of gamma secretase may contribute to neurodegeneration in fAD. The aim of this project is to investigate the processing of non-APP substrates of gamma-secretase in fAD, using induced pluripotent stem cell-derived neurons from 7 fAD patients with mutations in APP and PSEN1 and age/sex matched controls. Specifically, we will use western blot to analyse the notch pathway in fAD and control lines and understand if this pathway is dysregulated in AD. This project will allow us to determine if the processing of non-APP substrates of gamma secretase is altered in fAD patient cell models, forming the basis for further mechanistic studies.
Identification and Validation of the Determinants of Variation in T cell Immunity in Health and in Inherited Immunodeficiency Syndromes 30 Sep 2018
Vaccination is a powerful strategy to prevent infectious diseases, by stimulating our immune system to produce antibodies. However, vaccines have not been as successful in boosting immunity against infections that require a different defence called T-cells. This problem is exemplified by tuberculosis, which causes more deaths than any other infection despite the use of the Bacillus Calmette-Guérin (BCG) vaccine, because the protection provided by BCG is variable. I aim to understand why BCG only works in some people. I will investigate the idea that differences in T-cell activation in different people are responsible for differences in the protective effects of BCG. In healthy individuals, I will test T-cell activation in response to a general stimulus. Using these data, I will develop a mathematical model to understand how variation in T-cell responses comes about. I will then In BCG-vaccinate the same individuals and test if my model explains all the variability in responses to BCG and in T-cell control of tuberculosis. These experiments may reveal the molecular switches that are responsible for differences in BCG efficacy. By testing cells from patients with genetic abnormalities in some of these molecules, I will validate their role in providing effective T-cell immunity.
Many proteins bind to metal ions, and rely on these interactions in order to properly carry out their function - indeed failure to do so is responsible for a number of diseases. Understanding the details of how these metal-protein interactions work and developing tools to predict their occurence in newly discovered proteins, as well as predicting sites that are created when proteins interact with one another, will aid our understanting of these diseases. Such knowledge would also allow us to engineer metal binding sites into synthetic proteins, which would have enormous benefits in biosensing, novel pharmaceuticals, and developing synthetic biological circuits. This project will focus specifically on zinc-protein interactions - creating a publicly accessible database resource of known zinc binding sites, and developing sophisticated tools for predicting the location and strength of zinc binding sites in a given protein structure, including sites that occur when two protein chains come together. Ultimately the project seeks to allow a researcher to modify a protein without zinc binding ability, to enable it to bind zinc and to reveal sites for drug design to modify zinc binding.
Childhood epilepsy affects 1 in 200 children with 20% of affected children being unresponsive to available currently medical treatments resulting in significant health morbidity and socioeconomic cost. Genetic causes of epilepsy are increasing recognised with genome sequencing, resulting in further understanding of disease mechanisms. Mutations in the Eukaryotic translation elongation factor 1 alpha 2 (EEF1A2) gene has recently been identified to cause early onset epileptic encephalopathy and intellectual disability. These children suffer medically refractory epilepsy with significant neurodisability and there is clear medical need to develop new treatments for these children. The success of adeno-associated virus (AAV) mediated gene therapy in spinal muscular atrophy and several neurometabolic syndromes provide compelling clinical precedents to develop gene therapy for genetic epilepsies such as EEF1A2 related childhood neurological disease. Professor Schorge's translational neuroscience research group has developed gene therapies for epilepsy towards clinical trial already and we hypothesise that eEF1A2 neuronal function can be restored by AAV9 mediated gene transfer. We will use the EEF1A2 null mouse that has reduced survival to 23 days with vacuolar degeneration in the spinal cord. We will deliver AAV EEF1A2 gene therapy to EEF1A2 null mouse model and evaluate vector biodistribution and effects on nervous system histology.
alpha1-Antitrypsin, a circulating protein inhibitor of neutrophil elastase, is normally secreted by hepatocytes; the most common pathological ('Z') mutant of this protein results in the formation of an ordered aggregate (‘polymer’) that largely accumulates within the cell instead. The result is the formation of insoluble protein deposits within the liver, with a consequent toxic-gain-of-function phenotype (neonatal hepatitis and cirrhosis) and loss-of-function phenotype within the lung (early-onset emphysema, due to a protease-antiprotease imbalance). Recent data suggests that there is a partition between soluble and insoluble polymer populations within the cell. The overall goal of this study is to determine, at a molecular level, the characteristics of these polymer forms, to address the question: is there evidence for a 'decision point' that determines whether a polymer will accumulate in the insoluble fraction and thereby contribute to the liver polymer burden? To achieve this, biochemical and biophysical techniques - including SEC-MALS, immunoassays, native PAGE, and concanavalin A affinity - will be applied to alpha1-antitrypsin polymers (i) induced artificially in vitro, (ii) extracted from a mammalian model cell line, and (iii) previously extracted from a tissue sample. In addition, FRET and filter-trap assays will be used to study the kinetic mechanism in vitro.