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Recipients:
University of Oxford
Amounts:
£0 - £500

Results

Delineating meiotic gene expression of male mice 31 Jan 2017

The mechanisms of meiosis have important consequences for the evolution, fertility, and speciation of sexually reproducing organisms. However, the full gene expression programme of meiosis is not currently known, partly due to heterogeneity of the cell population which is averaged by bulk tissue RNA sequencing or micro-array analysis. It has recently become possible to transcriptionally profile thousands of single cells using RNA sequencing, raising the possibility of identifying the gene expression profile associated with different stages of meiosis and hence delineating the full gene expression programme. The identification of genes expressed in meiosis and its sub-stages may aid in the discovery and understanding of meiotic mechanisms. I will use pseudotime ordering and latent factor analysis type methods to analyse this data and comprehensively define the transcriptional profile of male meiosis.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Using genetic diversity to map fine-scale epidemiology in malaria 31 Jan 2017

The recent evolution of artemisin-resistant strains of P.falciparum in Southeast Asia have highlighted the need for a deeper understanding of the genetic epidemiology of malaria and for more strategic implementation of malaria control resources. Assessment of the efficacy of these control efforts requires accurate and standardised estimates of epidemological parameters, such as transmission intensity. As of now, these estimates are not standarised across regions, are often labor-intensive, and work poorly in low-transmission areas. Genomics, via the sequencing of geolocated patient blood-derived parasites, has the power to provide key insights into the migration and evolution of malaria. Moreover, the rich data provided by genome sequencing represents an attractive alternative from which epidemological parameters can be calculated. To this end, my DPhil will involve the development and benchmarking of genetic epidemological models of malaria built from thousands of spatially-referenced malaria genomes collected from across Africa and Asia. These models will analysze the structure of regional genetic diversity to make estimates of parasite migration, population size and transmission intensity. Estimates will be systematically compared to field gold-standards and against simulated environments of malaria infection. The overarching goal is to guide malaria eradication policy through improved disease survelliance and control effort assessment.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Statistical models of gene-environment interactions 31 Jan 2017

This PhD focuses on developing statistical methods to discover gene – environment (G-E) interactions. To date there has been some interest in testing for G-E interactions in animal models, but limited success in uncovering examples of G-E interactions in humans. This is in part due to the problem of exposure assessment, or rather, because representative data on the environment of a number of individuals over a lifetime has been hard to acquire. However the data recently made available by the UK BioBank, on over 500000 individuals and a wide array of environmental covariates, may now make it possible to detect these interactions. We aim to use a Bayesian methodology to first test a number of known models, such as a random effects model, against the dataset. We will then attempt to use a Gaussian Process Regression model to identify covariates involved in G-E interactions. This approach is advantageous as GPR is non-parametric, thus avoiding the curse of dimensionality, and places no assumptions on the order of interactions. However as this method currently scales in a cubic manner following the number of samples, significant computational challenges remain.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Dissecting Polo kinase recruitment to the centrosome 31 Jan 2017

Polo kinase is an important cell cycle regulator and it is essential for the correct assembly of centrosomes, major cell organisers. Centrosomes are formed by a pair of cylindrical centrioles surrounded by pericentriolar material (PCM). Polo controls PCM assembly (at least in part through Cnn phosphorylation) and also centriole disengagement and assembly. How Polo is recruited to centrioles and centrosomes is mysterious. During my rotation I have obtained evidence that the PCM protein Spd-2 is necessary for Polo recruitment to centrosomes. During my project I aim to characterise if Polo binding to Spd-2 is necessary for Cnn phosphorylation and correct PCM organisation, what happens when Spd-2 cannot bind Polo and what upstream regulators facilitate this interaction. Furthermore, I aim to identify the other centriole/centrosome proteins involved in Polo recruitment. To do this, I will make use of biochemical assays and advanced microscopy techniques, coupled with fly genetics and a powerful mRNA injection assay to rapidly test the effects of different mutants in fly embryos. Ultimately, I hope to be able to describe in molecular detail which proteins are phosphorylated by which kinases to allow Polo to be recruited to fulfil its many functions at the centrioles and centrosomes.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

The role of regulatory T cells in immunity to malaria 31 Jan 2017

In malaria vaccine trials conducted in the target population of semi-immune people from endemic African countries, vaccine immunogenicity is sometimes substantially reduced compared to European malaria-naïve participants. This could result from the suppression of vaccine-induced immune responses by regulatory T cells (Tregs) acquired through prior malaria infections, however there are few studies in man which have previously explored this. Using samples from controlled human malaria infection studies in semi-immune Kenyan individuals, we will investigate how Tregs affect natural immunity to infection and see if increased Treg responses correlate with vaccine efficacy following malaria challenge in participants with varying prior exposures to malaria. We will also directly compare the effect and induction of Tregs in different pre-erythrocytic candidate vaccines and adjuvants to understand how vaccine-specific effects might affect Treg responses. Additionally, we will investigate if malaria-induced Tregs affect responses to other childhood vaccines. Single cell transcriptomic analysis using the Fluidigm platform will be employed to explore the phenotype and functional heterogeneity of Tregs. This will provide insight into the mechanisms by which Tregs are involved in immunity to malaria. This work will have important implications for the design and evaluation of malaria vaccines for use in endemic populations.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Not just a virulence factor: capsule biology across the Neisseria genus 31 Jan 2017

This project seeks to address the relatively unexplored topic of the genetics, function and evolutionary history of the Neisseria polysaccharide capsule, beyond its established role as a virulence factor in Neisseria meningitidis (Nme). This will be achieved by examining capsular types not associated with disease, both from Nme, and capsules recently discovered in the commensal Neisseria species. The first goal is to complete genetic and phenotypic characterisation of the novel commensal capsular types. Once this is established, a key goal is to seek comparisons between these novel capsules and those of Nme within the coding sequences and regulatory regions, and at the structural level. I also plan to address the question of what the role of capsule is in colonisation and transmission, given that it most likely was not selected for its virulence properties. Finally, I seek to build a clearer history of the acquisition and evolution of capsule in Neisseria. This will bring forward new insights into the roles of capsule in normal, healthy colonisation of the nasopharynx, both by Nme and the strictly commensal Neisseria species. This work may also have implications for our interpretation of Nme dynamics and the rare transition to a state of disease.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Signal transduction of the GPCR Smoothened: a key protein in Hedgehog-regulated morphogenesis and oncogenesis 30 Sep 2018

In complex multicellular organisms, cell-to-cell communication is often managed by morphogen gradients. The secreted Hedgehog ligands fall within this class, as they act in this manner during embryonic development. The Hedgehog signalling pathway (stimulated by these morphogens) tightly regulates crucial developmental processes including body patterning and symmetry. Serious developmental disorders result from inactivation of this pathway during embryogenesis, including holoprosencephaly and cyclopia. Hedgehog signalling is also active through stem cell programs throughout adult life, and aberrant Hedgehog activation, either ligand dependent or mutations in pathway components, can lead to cancer including medulloblastoma and basal cell carcinoma. The G-protein coupled receptor (GPCR) Smoothened is a key protein of this pathway, as it initiates the intracellular cascade, and is already targeted by anti-cancer drugs including Vismodegib and Sonidegib. However, the mechanism of signal transduction has only been poorly characterised. This project aims to explore this using both structural and biophysical approaches. We will study the mechanism and interplay of the two identified ligand-binding sites and the dynamics of agonist association with Smoothened. The ultimate goal is to determine the structure of active-state Smoothened and hence describe the mechanism by which its signal is transmitted across the plasma membrane.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

The role of inhibition in generating sparse neural codes for sensory-guided behaviour 30 Sep 2018

The role of an organism’s nervous system is to make sense of the world and generate appropriate behaviours. This process requires that neurons – the cells that form the fundamental building blocks of the nervous system – perform two basic tasks in parallel: First, neurons must make sense of sensory inputs, such as sight, sound and touch, to accurately represent the world. Second, neurons must use this information to inform decisions which guide behaviour. The goal of this project is to use a mouse’s response to whisker touch as a model to understand these two processes. I will use advanced microscopy techniques to record the activity of the mouse’s neurons while it makes decisions based on different objects detected by its whiskers. Simultaneously, I will modify the activity of individual neurons. If these manipulations impact the decision making of the mouse, it will give us insight into how the brain makes decisions in natural environments. Overall, if successful, this project will help to unravel the fundamental principles governing neural processing in the mammalian brain. This is one of the most fascinating mysteries of modern science, and may form the groundwork for future treatments of neurological conditions.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Structural and computational study of cationic amino acid transporters 30 Sep 2018

Cells are surrounded by a lipid membrane, which isolates the cell content from the extracellular solution. The hydrophobic core of the membrane is impermeable to many hydrophilic substances including amino acids. To circumvent this problem, cells use transporters that can translocate amino acids across the membrane. This translocation process can sometimes be proton-coupled, but in some cases, certain transporters appear to function without the need for proton coupling. The reasons why some transporters are proton-coupled while others are not and how the proton coupling works, remain elusive. Humans contain two closely related types of amino acid transporter, the cationic amino acid transporters (CATs), which are proton independent and the proton-coupled amino acid transporters (PATs), which use protons for transport. Recent work in the Newstead laboratory has characterized a bacterial homolog of CATs that is proton-dependent, which was surprising. My DPhil project is trying to understand the mechanism of proton coupling in these transporters using a comparative approach between these two example proteins. Comparison of residues at key locations provides a working hypothesis of which residues may give rise to proton dependence. We will investigate this via the use of biochemical and cell-based transport assays, X-ray crystallography and molecular dynamics simulations.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Structural Characterisation of the Orthobunyaviral Surface Glycoproteins 30 Sep 2018

Orthobunyaviruses present medical and economical threats as they cause haemorrhagic fever and encephalitis in human, and abortion and stillbirth in livestock. Currently, little is known about how orthobunyaviruses infect their hosts and how they achieve cross-species transmission from anthropods to humans. My DPhil research focuses on structurally characterising the glycoproteins utilised by the orthobunyaviruses for infection and screening for neutralising antibodies. Using X-ray crystallography and electron microscopy techniques, I aim to contribute to a more complete understanding of orthobunyavirus-host cell attachment, intracellular trafficking, and membrane fusion. Ultimately, knowledge of host-cell entry mechanism will aid the development of vaccines and inhibitive peptides.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Probing nucleotide interactions with Kir6.2 using fluorescence spectroscopy. 30 Sep 2018

The ATP-sensitive potassium (KATP) channel is a plasma membrane protein present in beta cells of the pacreas which plays a key role in insulin secretion. KATP acts as a metabolic sensor, alerting the beta cells when blood glucose raises too high and stimulating them to release insulin. In diabetes, normal KATP function is disrupted and beta cells no longer secrete insulin properly in response to blood glucose levels. The molecular structure of the channel is closely linked to its function; there have been several genetic studies linking various mutations (which often only affect one molecule in the channel!) to neonatal diabetes or increased propensity to type II diabetes. Our research aims to identify precisely how these small mutations can have such drastic changes in the activity of the channel by using a combination of fluorescent labels and channel current measurements to watch the KATP channel move in real time. We can then try to construct a model of how the channel converts different stimuli into movements, and how this is affected in mutations linked to diabetes.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

High dose iminosugar treatment: Investigation of a new antiviral mechanism of action 30 Sep 2018

Antiviral iminosugars inhibit endoplasmic reticulum (ER) a-glucosidases I and II (a-Glu), which induces misfolding of viral N-linked glycoproteins. ER a-GluII inhibition leads to the release of fewer infectious viruses in vitro and in vivo, and can protect mice from DENV- and influenza lethal challenge. We observed that inhibition of ER a-GluI can lead to similar life-saving effects in mice, even if enzyme inhibition is short lived and achieved by administration of a single dose of the drug. This is sufficient to create long-lived triglucosylated protein species that can prevent secretion of infectious virus for some time. We aim to understand this process. I first will establish cell lines that can be hosts for the viruses I am investigating in which to re-capitulate in vivo observations. I shall then proceed to identify which protein(s) are responsible for the long-lasting antiviral effect, why they are not degraded, and how they can exert an antiviral effect for longer than enzyme inhibition. This work may lead to new ways of treating viral diseases such as dengue, influenza and hepatitis B, prophylactically and/or therapeutically. Moreover, a field trip to Vietnam is planned to take advantage of clinical samples.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

How is transcription factor function impeded during X chromosome silencing? 30 Sep 2018

In the nucleus of every cell DNA is present as pairs of parentally-inherited chromosomes, from which genes are expressed to perform biological functions. In most mammals, including humans and mice, females tend to have two X chromosomes whereas males have one X and a Y chromosome, which lacks most of the genes present on the X. Thus in order to ensure that the dosage of gene expression from essential X-linked genes is similar between both sexes, almost all genes on one female X chromosome are silenced during development. X inactivation is mediated by a long non-coding RNA, Xist, which spreads to coat the chromosome and coordinates silencing through the recruitment of relatively few factors implicated in specific chromatin remodelling pathways. Beyond its intrinsic biological significance in mammalian development, it is a tractable model system for investigating general molecular mechanisms by which chromosomes are silenced. My reseach will focus on the question of how transcription factors that normally bind enhancers and promoters to activate genes are prevented from performing their functions as the X chromosome is silenced. I will investigate this question in cellular and in vivo models of X inactivation, including in mutant cell lines defective for chromosome silencing.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Exploring the mechanisms of centriole growth and ciliogenesis 30 Sep 2018

When cells divide, their genetic material is distributed between the new daughter cells. Problems at this stage can lead to genome instability, which may promote cancer. Centrioles (barrel-shaped structures in animal cells, surrounded by a layer of microtubules) organise cilia and centrosomes, the latter being the organelles that coordinate the mitotic spindle to pull the genetic material apart. Like the genetic material, centrioles must duplicate every cell cycle so each daughter cell inherits one centrosome. Consistently, the nascent centrioles grow until they reach the same length as the older centriole. I aim to gain insight into how this precise growth is achieved by studying CEP104, a protein implicated in centriole growth regulation. I will investigate the effect of Cep104 knockout on centriole growth in Drosophila melanogaster embryos. I will also study CEP104 dynamics in vivo using fluorescently tagged CEP104, and see how this is affected under different conditions and genetic backgrounds. This, together with interaction assays, will offer insight into the interactions occurring between centriolar proteins during centriole growth. Alongside this work, I hope to determine CEP104’s role in promoting cilia formation in quiescent cells, which represents an important switch between the centriole’s role in centrosome versus cilia organisation.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Monocarboxylate Transporter 4: A Potential Therapeutic Target in Refractory Rheumatoid Arthritis 31 May 2018

Rheumatoid Arthritis (RA) occurs as a complex set of interactions between adaptive and innate immune cells and stromal fibroblasts. Using mouse models of RA we have previously shown that tissue fibroblasts can both promote inflammation and tissue repair. Using a combination of immunohistochemistry, multi-parameter cytometry and single cell RNAseq of both primary human biopsy material and mouse RA models we have identified three different populations of fibroblasts, inflammation lining fibroblasts, resolving sub-lining fibroblasts and pericytes. From analysis of gene expression signatures on these different tissue fibroblast populations we have identified difference in metabolic function. One of key proteins we have identified that is up regulated in inflammatory joint fibroblasts is the monocarboxylate transporter 4 (mct4) which has a key role in the export of lactate resulting from glycolysis. This receptor has been shown to a have a key role in cancer metabolism and disease progression which has lead to the development and clinical trial of high affinity inhibitors. The aim of this project will be to further characterise mct4 expression and function in rheumatoid arthritis fibroblasts using gene expression, immunohistochemistry and functional assays to determine if a mct4 inhibitor could potentially make a novel treatment for treatment refractory rheumatoid arthritis.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

What are the brain specialisations underlying human vocal control? 30 Sep 2018

Speech production requires a uniquely human regulation of airflow by fine control of respiratory and articulatory musculature as well as the larynx. It remains open, which features of the human brain can account for vocal control and speech production. I aim to investigate the anatomical and functional organisation of the cortical networks underlying speech production by using a comparative framework across primate species. I will conduct an fMRI study in humans to establish the anatomical location of laryngeal motor cortex (LMC) and its role in different aspects of speech. I will also use various neuroimaging methods like myelin-mapping and tractography to compare the neural architecture of LMC in humans and non-human primates. Non-invasive brain stimulation in humans will explore the functional implications of human-specific neural connections. These studies will help to understand the neural organisation underlying speech as a key specialisation of the human brain.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

The neural network mechanisms of inferential reasoning 30 Sep 2018

The neural network mechanisms of inferential reasoning The ability to make inferences, as defined by conclusions drawn from given evidence (Peirce, 1868), is a hallmark of higher cognitive function (Vasconcelos, 2008) that relies on internal models of past knowledge, including that of experienced environments (Markovits and Vachon, 1990; Piaget, 1987). The neural representation of such mnemonic models is thought to be shaped by life experience (Barlett, 1929, Lee, 2009) but the neural circuit-level mechanisms supporting the neural representation-to-behaviour translation of inferences remain to be identified. The goals of my project are: To investigate the neural circuit mechanisms underlying the ability to make an inference based on prior knowledge with large-scale neural recording techniques in the mouse brain. To test whether dopamine promotes neural mechanisms underlying inferential reasoning using state-of-the art neural manipulation methods.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

The Role of Cyclophilins in Innate Immunity 30 Sep 2018

The Cyclophilins are a widely expressed, broad acting family of proteins defined by their common enzymatic domain. Among their multiple roles, they are reported to be involved in viral infections (including HIV, Hepatitis, and Influenza infections) both to the benefit and the detriment of the host. Despite this, much is still unknown about whether they play a role in the innate immune system. In the past this research has been limited due to the broad reactivity of the innate immune cells. However, with recent progress in stem cell research and CRISPR gene editing technology, we are now capable of manipulating these cells far more effectively. Therefore I intend to use these advances to knock out each member of the Cyclophilin family and then challenge my cells with a range of immune stimulants looking for changes in innate cell activation and protein secretion. Combining my panel with a pharmacological approach targeting virus-cyclophilin interactions, I also intent to determine whether HIV-1 uses only Cyclophilin-A during infection and discover novel Cyclophilin interacting proteins. These studies aim to lead to a better understanding of the fundamental functioning of cells in response to various threats, and may lead to pathogen specific drug therapies targeting Cyclophilins.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Mechanical testing of tendons and ligaments 27 Apr 2017

The mechanism for collagenous connective tissue damage is little understood. The micromechanics of collagenous tissues is important to understand as it may contribute to injury prevention and be useful in designing treatments for pre existing tissue damage. Bontempi et al in 2009 theorised a relationship between the the probability density function of the stretch value of individual fibrils and the 2nd derivative of stress with stretch. This relationship gained experimental backing in 2016. Recent research suggests that fibrils fail in the order they are first recruited. Combining this model with Bontempi's work suggests fibrillar level damage can be found by performing a stress - stretch test in vivo. However the relationship between order of recruitement and failure is yet to be experimentally proven. A collagen fibril is considered recruited once it is straight enough to bear load and be treated as a Hookean material. During my research I will be tracking fibrils from point of first recruitment to failure. A tensile loading rig will be used with a microscope to image the tendons at different stretch levels.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford

Novel statistical methodology for rare variant association in a case-control cohort 30 Sep 2018

Genetic association studies focusing on common variation have uncovered only a fraction of proposed trait heritability. Some of this so-called missing heritability will be found within rare variation in the population. This hypothesis is supported by the facts that recent explosive population growth has increased the population burden of rare variants and deleterious variants are kept at low allele frequencies. All genetic susceptibility to disease is caused by alterations to the genes or their expression and for this reason it seems fruitful to focus an association study on the genes themselves. Any associations found are then directly informative about the molecular basis of disease without the need for fine mapping. The proposed project aims to develop a statistical method to find genes associated with disease by analysing the rare variation present in a case-control cohort. We aim to extend existing methods by including a previously unconsidered parameter; the position of the variants in a gene. In scenarios where differences in clustering or distribution of variants are observed between cases and controls, this method will have a substantial increase in power. This technique will be useful for elucidating the molecular mechanisms causing the disease and thus discovering new therapeutic targets.

Amount: £0
Funder: The Wellcome Trust
Recipient: University of Oxford