- Total grants
- Total funders
- Total recipients
- Earliest award date
- 17 Oct 2005
- Latest award date
- 30 Sep 2018
- Total GBP grants
- Total GBP awarded
- Largest GBP award
- Smallest GBP award
- Total Non-GBP grants
Clinical Characterisation of a Broad Spectrum of Genetic Variation in the General Population 30 Sep 2018
Inborn errors of metabolism (IEM) are severe and extreme changes in metabolism caused by mutations in a single gene. Recent large-scale human studies have shown that genes causal for IEM are associated with nutrients, or ‘metabolites’, in the blood. However, whether these associations cause disease or adverse health outcomes is unknown. In this project, I will use IEM genes identified in these studies to link genetic variation to clinical features in a large human population. To do this, I will assemble a list of IEM genes of interest that were identified in the literature and in large population datasets. I will then test for associations between the variants I find in these genes and a wide range of clinical features found in open-access population datasets. As the IEM genes used in this study have been associated with blood metabolites previously, linking variants in these genes to clinical features will shed light on the molecular mechanisms underlying genes and disease in the general population. Understanding how genetic variation affects disease will help identify novel therapeutic targets and enable health professionals to better manage disease risk.
Extension to A record- funds for sequencing: Measuring the impact of naturally acquired immunity on the expression of Plasmodium falciparum variant surface antigens. 31 Aug 2011
Plasmodium falciparum infected erythrocytes express on their surface, members of a diverse family of parasite molecules called PfEMP1 that are encoded by a family of 60 var genes. These molecules interact with the surface of host cells and mediate parasite sequestration in tissues including the brain, an important step in the pathogenesis of cerebral malaria. Although naturally acquired antibodies to PfEMP1 provide specific protection against the molecular variants that they recognise, PfEMP1 ar e often considered too diverse to be vaccine candidates. However, we and others have shown that parasites infecting children with severe malaria tend to express serotypes that are more broadly recognised suggesting they may be antigenically restricted. Studies of a laboratory isolate suggest that the most broadly recognised PfEMP1 types are encoded by a genetically distinct subset of groupA var genes. By sequencing short var sequence tags expressed in parasites from Kenya, we have shown that expression of sequences with groupA-like features are associated with younger children and that a smaller subset of these sequences are associated with severe malaria. We propose to identify new targets of malaria intervention by characterizing these specific subsets of PfEMP1 that are associated with infections of children with low natural immunity.
Consent to and community engagement in global health research - reviewing and developing research and practice. 18 Oct 2010
This is a proposal for funding to organize a four-day international collaborative workshop bringing together leading groups engaged in research on community engagement and consent in collaborative global health research. The workshop will bring together individuals responsible for introducing or sustaining community engagement activities in developing countries, and for designing and implementing appropriate consent practices in these settings, and those conducting social science research on these topics. The aim will be to: 1. share ideas, experiences and needs regarding community engagement and consent interventions, including monitoring and evaluation, and related social sciencemethodologies 2. review ethical theories and approaches, and recent community engagement andconsent guidelines, and to consider how these frameworks can be incorporated into implementation activities and social science studies. 3. develop proposals for future research, including comparative studies, and to consider transferability of findings of studies conducted to date. 4. discuss the possibility and practicalities of establishing an internationalnetwork of groups working on community engagement and consent which might, for example, agree todevelop online collaborative resources for the sharing of experiences and of training materials.
Analysis of conserved pathways involved in maintaining homeostasis and survival in mammals and Drosophila. 09 Mar 2011
Our aim is to uncover the molecular basis for toxin clearance from animal body fluids. Using a simple tissue, nephrocyte cells, in Drosophila as a model for blood filtration and detoxification in vertebrates we focus on two molecular pathways essential for these functions; Ig domain proteins (Nephrin, Neph1) required for construction of the podocyte filtration slit diaphragm and the cytoplasmic protein (Rudhira), essential for the micropinocytotic activity in reticulo-endothelial cell scavenger s. Drosophila homologues of these proteins are expressed in nephrocytes. Our goals are to exploit ongoing Drosophila screens to identify candidate molecular interactors to establish the protein interactions that regulate the activity of these pathways, to analyse the roles of identified protein networks in nephrocyte filtration and toxin clearance and to extend our analysis into vertebrate tissues. We aim to test vertebrate homologues for conservation of the molecular interactions identified in Drosophila and, using podocyte cell lines and mutant mouse strains to establish the roles of Ig domain and Rudhira interactors, focussing on podocyte filtration. Overall we shall identify molecular activities that are fundamental to the stability and function of the slit diaphragm and for regulated endocytosis and vesicle trafficking.
We will test whether mitophagy (a catabolic process involving recycling of damaged mitochondria) is important in mitochondrial disease. We aim to overcome the technical difficulties of studying mitophagy using: (1) ImageStream (which combines flow cytometry and fluorescence microscopy in a single platform) to investigate patient-derived cell lines. We will explore how mitophagy is affected in cells with defects of mtDNA maintenance, from patients and from the POLG1 deficient Mutator mouse. We will explore whether mtDNA mutant populations can be manipulated by modulating mitophagy, for instance by amino acid starvation and exposure to certain drugs including rapamicin and chloroquine. (2) a mouse model in which mitophagy may be readily detected by florescence microscopy. This involves crossing two existing transgenic strains in order to breed mice in which mitochondria and lysosomes both constitutively express fluorescent markers. Mitophagosomes would thus be detectab le by co-localisation of these signals, providing a marker for response to therapies. This mouse will be crossed with an existing model (the Deletor mouse) to determine how candidate treatments (including ketogenic diet) affect mitophagy. These approaches will be extremely useful tools for investigating multiple mitophagy-related pathologies and mouse models of mtDNA diseases and ageing.
The bacterial endosymbiont Wolbachia protects insects against viral infections. The aim of this project is to understand this new form of antiviral protection, using Drosophila as a model system. Our results will be relevant for attempts to use Wolbachia to control viral diseases of humans and animals that are transmitted by insect vectors. To understand the causes of this antiviral resistance, we will first determine which stage of the viral replication cycle Wolbachia affects (entry into ce lls, replication, translation or exit). In Drosophila, we will screen for host genes and pathways that are required for the antiviral effects of Wolbachia and examine whether the antiviral protection relies upon the insect immune system or other host pathways. From the bacterium s perspective, we will identify Wolbachia genes up-regulated upon host viral infection and test these for their antiviral effects. Additionally, we will use next-generation sequencing to identify genes associated with n aturally occurring variation in the antiviral properties of Wolbachia. Finally, to see if interventions using Wolbachia will be sustainable, we will test whether viruses can evolve to overcome the antiviral effects of Wolbachia and identify the mutations that underlie these changes.
Colour appearance in a dynamic world. 03 Mar 2011
We argue that time-varying signals play a fundamental part in colour constancy, redefining the problem, both in terms of the information available and the nature of the neural mechanisms that might extract this information. This project considers two classes of dynamic information: (a) changes in the spectral and geometric properties of the illumination and (b) saccadic eye-movements that direct to the retina a sequence of discrete samples. Our first goal is to test observers sensitivity to tem poral cues to disambiguate properties of the illumination and of the illuminated objects. Our second goal is to consider how eye-movements modify the computational task of colour constancy and their effect on perception. Multiple mechanisms, ranging from distal to central, automatic to volitional and passive to active, contribute to maintaining constant perception of surface colour. By tracking the on-line updating of observers perceptual hypotheses we aim to (i) dissociate processes operating on different time-scales, (ii) determine the relative utility of spatial versus temporal comparisons in retinal and spatial coordinates, and (iii) assess interactions between surface colour perception and active viewing, all of which provide important information about the neural mechanisms that maintain perceptual stability, and ultimately enhance our understanding of the adaptive brain.
HP1, which exists as three homodimeric isoforms (HP1alpha, beta, gamma), plays a critical role in constitutive heterochromatin, regulation of the expression of heterochromatic and euchromatic genes, and DNA repair. The monomer unit comprises a chromodomain (CD), a homologous chromoshadow domain (CSD), which dimerises, and a connecting hinge region of variable length. Most attention has focussed on binding of HP1 through its CD to the epigenetic mark H3K9Me, but this does not explain all aspec ts of HP1 binding to chromatin. We will focus mainly on two other regions in HP1 the CSD, which interacts with nucleosomal histone H3 at a second (occluded) site in a methylation-independent manner; and the hinge region, which interacts with DNA in vitro. Building on our preliminary work we will determine the structure of the HP1α CSD in complex with a peptide containing the second H3 site by NMR, and characterise the structure and the DNA-binding properties of the HP1 hinge region. We wi ll also study the interaction of full length HP1 with histones H3 and H1, and through a combination of biochemistry and novel NMR we will characterise the nature of HP1 binding to chromatin.
Our overall aim is to describe the molecular mechanism responsible for the ability of P-gp to confer resistance to anti-cancer drugs. Our investigative strategy relies upon electron paramagnetic resonance (EPR) spectroscopic analysis of purified, reconstituted protein with. Key functional regions of P-gp will be subject to site-directed cysteine mutagenesis. This will enable subsequent covalent attachment of the thiol-reactive paramagnetic spectroscopy probe MTSL. The labelled P-gp will be cycle d between different conformation states and EPR spectra obtained for each. EPR spectroscopy will provide information on the relative accessibility, mobility and local environment of each residue addressed. Moreover, measurement at distinct protein states will provide a dynamic understanding of the conformational changes involved in drug translocation. The proposal has been divided into a number of key investigative goals as follows: Expression of mutant P-gp isoforms and their purification in a functional state Description of conformation changes in the transmembrane domains related to drug translocation Generation of a topographical map for TM6 and TM12 Detailing of movements at the nucleotide binding domain interfaces Locating the drug binding sites and description of their reorientation during translocation Using distance measurements to validate and complement the existing structural data for P-gp
Identification of novel genes causing familial juvenile hyperuricaemic (gouty) nephropathy (FJHN). 15 Mar 2011
Familial juvenile hyperuricaemic (gouty) nephropathy (FJHN) is an autosomal dominant disorder characterised by reduced excretion of uric acid which leads to gout, renal fibrosis and chronic renal failure. Three genetic causes of FJHN have been defined to date, which are mutations in the UMOD, REN and HNF-1beta genes encoding uromodulin, renin, and hepatocyte nuclear factor-1beta, respectively. However, these UMOD, REN, and HNF-1beta mutations are found in only ~45% of FJHN patients and the rem aining ~55% of patients have mutations in as-yet-unidentified genes. We have mapped two novel FJHN loci to ~5.5Mbp and ~9.1Mbp on chromosomes 2p22.1-p21 and 5p15.33-15.2, respectively. We now propose to identify these genes causing FJHN by using whole exome capture, as the majority of Mendelian inherited disorders are caused by mutations in coding regions of genes. This exome capture will reveal novel non-synonymous variants and we will investigate these further for co-segregation in affected family members, absence in a normal population, evolutionary conservation and likely deleterious effects on the protein. In addition, we will characterise wild-type and mutant gene products by transfecting cultured cells and performing functional assays. These studies will provide important insights into novel mechanisms of FJHN, renal fibrosis and chronic renal failure.
Does the potential for proteins to be allergenic depend on structural homologies with IgE targets on metazoan parasites? 07 Mar 2011
IgE is found only in mammals, and is presumed to have evolved to combat metazoan endo- and ecto-parasites (helminths and arthropods). Recently, a closer molecular relationship between major allergens and metazoan products has become apparent. We have tabulated the known allergens and found that 8 of the 10 most abundant allergen protein superfamilies are represented in metazoan parasite genomes, although in only 3 cases have metazoan proteins been experimentally verified as IgE targets. We prop ose to study 5 metazoan gene families containing homologues of known allergens, to establish if these are indeed targets of IgE in natural and experimental infections. To fully validate the hypothesis that all allergens contain structural homology to metazoan antigens, we will also analyze the 2 gene families for which homologues with recognizable sequence homology have yet to be found in metazoan parasites. These will be subject to surface structural feature analysis, which will enable us to se arch metazoan genome databases for structural homologues which will then be tested for IgE reactivity. The technique will then be extended to provide a searchable database of the metazoan parasite surface features which can be searched to predict allergenic epitopes in food and environmental organisms.
Many natural products of clinical importance are made by type I polyketide synthases (PKSs), multienzyme systems that comprise modules of covalently linked catalytic domains. The key players in each module are acyl carrier protein (ACP) domains, which serve as attachment points for the growing substrate chain. The details of ACP-mediated delivery of substrate to each active site are central to understanding how new polyketide chains are assembled. Using NMR spectroscopy, we recently discovered t hat the interaction between an ACP from the erythromycin type I PKS and its downstream thioesterase (TE) works in an unexpected way: chain transfer occurs in the absence of a protein-protein interface, with contact limited to the acyl terminus of the substrate. We now aim to build on that success by determining how ACPs communicate with every other type of enzyme domain in the erythromycin-producing DEBS PKS, the paradigm type I modular system. We will then extend our study to the PKS in Mycobac terium ulcerans that synthesizes mycolactone, the causative agent of the disfiguring tropical disease Buruli ulcer.
It is now recognized that Plasmodium has photosynthetic ancestry, being closely related to dinoflagellate algae. It has a remnant chloroplast, including a 35kbp genome, expression of which is essential for Plasmodium viability. The chloroplast is recognised as a target for new antimalarials. Very little is known about transcription and post-transcriptional processing in the Plasmodium chloroplast, although by analogy with other chloroplasts they are expected to be important determinants of gene expression. Although the Plasmodium chloroplast genome encodes some of the subunits of a bacterial-type RNA polymerase, we have identified a nuclear gene for a phage-type RNA polymerase, which algorithms predict is chloroplast targeted (probably in addition to the mitochondrion, and similar to what may be the case for dinoflagellates). Using our experience of chloroplast molecular biology, we have also identified putative genes for other important proteins, including a sigma factor for the bacte rial-type polymerase, an RNA processing enzyme and two RNA binding proteins. All of these are predicted in silico located in the Plasmodium chloroplast, with varying degrees of confidence. We wish to confirm the chloroplast location of these five proteins, and test their function. This will provide a basis for developing a detailed understanding of Plasmodium chloroplast gene expression.
We have established a translational programme of biomarker discovery in a number of autoimmune diseases, recruiting over 500 patients for whom detailed prospective clinical data has been collected, and performing microarray expression analysis on purified cell subsets. Despite having analysed <25% of the samples collected we have discovered a novel CD8 T cell-based biomarker which predicts prognosis in 4 different autoimmune/inflammatory conditions (e.g. McKinney et al. Nat Med 2010; 16:586-58 9), has been patented and will be assessed in clinical trials. We now seek funding to finish the processing and analysis of this cohort, in order to: i. refine the biomarkers already found, creating a practical clinical assay ii. extend the investigation of the current biomarkers into related conditions iii. discover novel diagnostic biomarkers, improving classification of these heterogeneous conditions iv. determine if transcriptional changes in response to therapy predict prognosis v . associate transcriptional pathways with specific patient subgroups or diseases, illuminating both pathogenic mechanisms and suggesting novel targets for treatment The unique nature of this resource, together with substantial preliminary data which demonstrate its promise, underlined the potential for completion of this important work to produce results that could directly impact patient care in the short to medium term.
Analysis of signalling during development has revealed a consistent and pervasive relationship between Notch and Wnt signalling suggesting that they form a single functional module. Notch encodes a member of a family of cell surface receptors that acts as membrane tethered transcription factors while Wnt represents a family of ligands that interact with receptors to modulate cytoskeletal activity and transcription. Work in Drosophila has revealed that Notch has the ability to modulate Wnt signal ling independently of its transcriptional activity and that this effect has an important function in processes of cell fate assignation. Our studies with Drosophila have uncovered an activity of Notch which targets the activated form of -catenin, the effector of the transcriptional activity of Wnt, and modulates its amount and activity. This function relies on the ligand independent traffic of the Notch receptor, provides a buffer for Wnt signalling and suggests a framework to think about Notch as a multifunctional receptor. Here I propose to probe the mechanisms that govern the interactions between Wnt and Notch signalling using Drosophila as a model system.
MHC class II molecules, which present peptide antigens to T-cells, are associated with autoimmune disease, by mechanisms that are incompletely understood. A set of autoreactive T-cells that escape thymic tolerance and induce autoimmune disease has been identified. These Type B T-cells respond to peptide antigen but not to antigen derived by processing in the conventional class II pathway, which supplies antigen to Type A T cells. We have demonstrated that intracellular Salmonella interfere w ith MHC class II presentation, leading to partial loss of mature class II from the cell surface. We propose to investigate whether the disturbance in MHC class II by Salmonella leads to skewing in presentation of self-epitopes to Type B T-cells. We will ask whether Salmonella influences the loading of antigen in early and late compartments. This approach will be supported by investigation of the precise molecular mechanism of MHC Class II down-regulation. In addition, we intend to use a powerful mutant screen to identify genes required for presentation to Type A or Type B T-cells. These experiments would have consequences both for the way in which Salmonella manipulates the immune system as well as understanding of autoimmunity.
Human cytomegalovirus (HCMV) provides a paradigm for how a complex viral pathogen persists and evades immune responses in humans. HCMV evades cytotoxic T cells by downregulating class I MHC, but then has to evade natural killer (NK) cells. We have recently described a novel MHC-like gene unique to clinical isolates that inhibits NK cell lysis by preventing the expression of NK cell activating ligands MICA and ULBP3. Recently we have discovered another viral gene (UL147) that prevent ULBP3 expres sion from very early post-infection. The specific goals of the work proposed are to:(i) Define the mechanism of action of the novel viral NK evasion gene product (UL147) (ii) Analyse the mechanisms that control NK cell recognition of HCMV in latently infected cells and during reactivation as all analysis to date has been on lytically infected cells. (iii) Address whether if particular NK cell subsets are refractory to HCMV mediated immune evasion and efficiently recognise HCMV infected cells?
Mechanisms of associative action learning. 17 Jan 2011
A major challenge in neurobiology is to explain how experiences can alter a brain to incorporate new information about (1) relationships between stimuli and (2) which actions are consequential. Both kinds of associative learning have been extensively studied, but much less is known about the latter. The fly Drosophila can be trained to form associations between a painful heat pulse and a specific motor program. The lack of external stimuli suggests that this associative process employs informati on about the animal s actions. This information is proposed to be carried by (1) the corollary discharge and reafferent signals that arise from motor commands (2) biochemical signaling pathways that mediate neural plasticity and (3) action representation neurons whose activity is modified by conditioning. I will search for these systems with neurogenetic loss-of-function experiments.
Genetic basis of craniofacial malformations. 14 Oct 2010
1. Prospective ascertainment of patients requiring craniofacial surgery at the four participating centres. We will aim to recruit a minimum of 150 patients (with parents) annually. 2. Identification of new monogenic causes of craniofacial malformation within this cohort using massively parallel sequencing. We will use 16 lanes of Illumina-based sequencing of captured whole exomes in patients or parents chosen because of a combination of positive family history, evidence of progressive feature s, distinctive phenotype or suspected de novo mutation. We will use bioinformatic analysis, including knowledge of gene expression and protein interaction networks affected by known craniofacial mutations, to prioritise genes for further sequencing. 3. We will assess the genetic impact of candidate mutations by DNA sequencing and analysis of exon copy number in the larger cohort, to establish the presence of mutations in the wider sample resource, and determine mutation spectrum, prevalence an d genotype-phenotype correlation. 4. We will undertake studies on the expression of identified genes in murine cranial sutures or other craniofacial structures, and relevant functional assays. 5. As a long-term goal we wish to acquire surgical and developmental outcome data linked to genotype.
Regulation of growth and TORC1 signalling by the novel evolutionarily conserved amino acid transporter, SLC38A10: a new player in amino acid sensing?. 14 Oct 2010
We will dissect out the functions and mechanism of action of the growth regulatory SLC38A10 transporter in Drosophila, using the combination of genetic and molecular genetic approaches we have developed in our pioneering studies of amino acid sensing by the PATs. We will employ analysis of mutant animals and somatic mutant clones, RNAi and overexpression studies to determine in which tissues SLC38A10 controls growth (we already know it affects growth in the eye and a viable mutant appears to mod ulate growth in all parts of the adult). This transporter is expressed ubiquitously, but we will generate anti-SLC38A10 antisera to assess this its subcellular localisation and shuttling, properties that are fundamental to the regulation of the PAT amino acid sensing mechanism. We will determine the transport and TORC1-regulatory properties of SLC38A10, using a combination of studies in Drosophila S2 cell culture and microinjected Xenopus oocytes. This will then allow us to design cell culture a nd in vivo overexpression/rescue experiments to test whether SLC38A10 activates TORC1 through amino acid transport or through a so-called transceptor (signalling) mechanism, and to elucidate which features that distinguish SLC38A10 transporters from all other AATs are critical to this molecule s functions.