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Recipients:
University of Oxford
Amounts:
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Results

Structural studies of bacterial nucleic acid transport proteins 31 Jan 2017

Horizontal gene transfer contributes to genetic plasticity in bacteria and is of great clinical relevance as it contributes to the spread of antibiotic resistance genes. One mechanism of horizontal gene transfer in bacteria is transformation. While the phenomenon of transformation has been known for many decades, little is known about the mechanistic steps of exogenous DNA uptake into bacterial cells. The most obvious problem is how the DNA gets past the cell envelopes. ComEC is believed to be the protein that forms an aqueous pore that allows transport of DNA into the cytoplasm through the bacterial plasma membrane. The protein represents a novel transport protein, and no structural and very little functional information is available. The aim of the project is to structurally and functionally characterize ComEC proteins using modern protein expression and screening techniques, advanced structural approaches (X-ray crystallography, cryo-electron microscopy) and functional studies (fluorescence microscopy, biophysics), in order to build a model for DNA transport across the plasma membrane into the cytoplasm.

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

KDEL Receptor Stuctural Determination & Biochemical Characterisation 31 Jan 2017

This project aims to characterise the KDEL receptor (KDELR) structurally, biochemically and biophysically. The KDELR is a membrane protein resident in the cis-golgi, where it binds the K-D-E-L amino-acid motif present on resident ER proteins, which have been transported to the Golgi via bulk flow. Once KDELR binds cargo, it initiates transport back to the ER via COPI mediated vesicles, where it releases its cargo, ostensibly because of the differing pH. The molecular mechanisms concerning the actions of the KDELR are largely elusive and would be greatly aided by the structural determination of the KDELR, as well as the structures and characterisations of its interactions with native cargos. Furthermore, KDELR has been predicted to be a GPCR, but does not appear to share homology with proteins in the family. However, distant homology to the SWEET family of sugar transporters has been found, suggesting these ‘receptors’ are in fact transporter like proteins. Furthermore, this project has the potential to involve live cell imaging experiments (in collaboration with Prof. Francis Barr) to test hypothesis borne from the structural and biochemical data.

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

Defining the import mechanism of pyocin AP41 and klebicin G 30 Sep 2018

There is an urgent need to develop new antibiotics against multidrug resistant Gram-negative bacteria such as Pseudomonas aeruginosa and Klebsiella pneumoniae. These organisms are major causes of pneumonia and sepsis, with recent reports identifying hospital isolates of each resistant to all known antibiotics. The present research focuses on the mode of action of a family of antibiotic proteins known as nuclease bacteriocins that have not been developed as antimicrobials, but show promise in animal models of infection. Nuclease bacteriocins are species-specific toxins that are used by bacteria to compete with their neighbours. Although folded proteins these molecules are capable of penetrating the defences of Gram-negative bacteria to deliver an enzyme to the organism’s cytoplasm to degrade essential nucleic acids by an unknown mechanism. Two types of nuclease bacteriocin will be investigated, pyocin AP41 which targets Pseudomonas aeruginosa, and klebicin G which targets Klebsiella pneumoniae. Preliminary computational and experimental work on pyocin AP41 has identified potential candidate proteins involved in its import. This will be followed up with structure and function studies of AP41, a dissection of its import mechanism and new studies on klebicin G, a nuclease bacteriocin that has only recently been identified.

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

Investigating the GWAS-identified target NCX3 in nociception 30 Sep 2018

Evolutionary, pain is a protective sensation. However, it can persist beyond its usefulness and become debilitating for patients. Chronic pain affects up to one half of the population in the UK (Fayaz et al, 2016). Currently, the treatment options are limited and discovering new drug targets is of great importance. In a recent genetic study (genome-wide association study), we identified a gene (SLC8A3 encoding the protein NCX3), which was associated with higher pain sensitivity to experimental pain stimuli in healthy participants. My thesis will therefore focus on studying the function of NCX3 on a molecular, cellular and systems level. NCX3 is an important part of the machinery that moves ions in and out of cells. Its role in pain is poorly understood, but previous reports show that it is involved in regulating Ca2+ levels in pain-sensing neurones. Inhibition of NCX3 can cause increased Ca2+ in these cells leading to higher activation of the central nervous system and increasing pain sensation. To investigate the function of NCX3, I will use genetically modified mice lacking the gene as well as isolated pain-sensing neurones. Our genetic data, combined with published results, makes NCX3 an attractive target for future research and drug discovery.

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

Evidence for a pathogenic link between lung inflammation and autoimmune arthritis 27 Apr 2017

Our overall objective is to experimentally identify the early immunological events which trigger a spontaneous breach of tolerance in genetically susceptible mice, and, which can be linked to the development of arthritis. We will analyse the immunological reactivity of the lungs of susceptible mice to environmental stresses such as microbes. Our purpose is to identify early biomarkers of autoimmune initiation, which will be assessed for suitability as treatment targets with translational relevance. We will seek to determine the benefits of administration of anti-microbial agents for amelioration of lung inflammation with a view to prevention of autoimmune disease progression.

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

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

Exploiting whole genome tagging of trypanosomes to identify new ciliopathy candidate genes in humans 27 Apr 2017

Ciliopathies are a range of human genetic diseases in which the normal functions of cilia/flagella are disrupted or prevented entirely. Ranging from mild to embryonically lethal, these diseases are often difficult to investigate as many do not appear to have clear links with particular genes or molecular mechanisms. This project aims to identify potential ciliopathy protein candidates and their corresponding human ciliary/flagellar genes by identifying previously unrecognised ciliary proteins conserved across eukaryotic life using the human parasite Trypanosoma brucei as a model organism. To start with, I plan to use TrypTag, a major new data resource, to identify which proteins localise to the flagellum and cilium. I shall then use bioinformatics tools and human genetic disease databases to identify which are conserved in humans not yet linked to a ciliopathy. Having excluded known ciliopathy-related proteins, I will then screen T. brucei deletion mutants for defects in flagellum growth, motility or flagellar beat. Those with defective phenotypes have the potential to be involved in human ciliopathies when mutated. The intended goal is to create a list of these novel candidate genes for involvement in human ciliopathies, with evidence for localisation and function in the flagellum/cilium of T. brucei.

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

Learning the Signatures of Cancer 30 Sep 2018

Cancer is a genetic disease that is the second leading cause of death worldwide. Developing effective personalised therapies requires characterisation of the genetic factors driving malignancy. This is challenging as cancer is highly complex, heterogeneous, and dependent on cellular context. Cancer stratification aims to group cancers that share similar features, and are therefore likely to respond similarly to treatment, however, current stratification methods ignore many important genetic and epigenetic markers that likely influence cancer pathology, which would result in sub-optimal treatment. We propose to use whole genome-and-epigenome profiling and machine learning to extract clinically meaningful features of the host and cancer genomes that can be used to improve patient stratification and reveal novel cancer subtypes. As a proof of principle, we will apply these methods to predict the site of origin in patients with metastatic cancer but unknown primary (CUP), which could help improve diagnosis and prognosis for patients with this complex disease. We envision the robust stratification of cancer patients using genome profiling could lead to direct prediction of optimal treatment decision for all cancer patients.

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

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

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

Investigating Spatial Determinants of DNA Replication Timing 30 Sep 2018

Complete and error-free replication of the genome is necessary for the normal development and health of all organisms. However, the sheer scale of the genome necessitates precise regulation of replication: in a human cell, 3 billion bases are replicated in about 8 hours, with replication initiating from between 12,000 and 250,000 origins spread across 23 chromosome pairs (1). Interestingly, not all of these origins fire in any given S phase and of those that do fire, not all fire at the same time. In fact, the replication timing profiles of a range of model organisms have been shown to follow precise temporal orders specific to cell type and differentiation status (2). Deviations from this timing regimen can manifest in a range of consequences including chromosomal aberrations and increased mutational load (3). While a range of factors correlating to the observed replication timing profiles have been found, the composite set of known factors still does not fully recapitulate the observed nuances of replication timing. I hope to study how spatial organization of the genome impacts replication timing, with the goal of better understanding how replication proceeds to be better able to understand how it goes awry in disease such as cancer.

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

Social anxiety in adolescents: Testing aspects of the cognitive model and developing an Internet version of Cognitive Therapy. 30 Sep 2018

While it is common for teenagers to report feeling somewhat self-conscious and worried about what others think of them, for some adolescents social anxiety can be overwhelming and markedly interfere with their day-to-day life. Around 4% of young people experience clinical levels of social anxiety by the age of 18. Their success at school and their relationships with family and friends are all seriously affected. It is therefore essential that we have effective treatments for this disorder. Unfortunately, evidence suggests that many young people do not get better with the talking treatments that are available. In contrast we know that Cognitive Therapy (a type of talking treatment) is very effective with socially anxious adults. Cognitive Therapy was developed to target key factors that cause and maintain the illness in adults. I would therefore like to answer two questions in my research. First, are the factors that are important in maintaining social anxiety in adults also important in adolescent social anxiety? Second, can we develop an accessible and effective version of Cognitive Therapy for adolescents online? We will test if Cognitive Therapy works by comparing its effects to online stress management.

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

Nonlinear modelling of courtship behaviour in Drosophila melanogaster. 17 Jan 2014

The proposed research aims to develop mathematical models to help in understanding the relationship between genes, neuronal circuits, and behaviour. A nonlinear model of Drosophila courtship behaviour will be developed to guide experimental studies by providing testable predications about both neural activity and behaviour. Three projects are proposed, modelling different aspects of courtship. The first project aims to model courtship song, in particular switches between two modes of song: sine and pulse. It will be investigated whether switches in male song are related to locomotion changes in the female. The second project aims to develop and evaluate a model of courtship behaviour. A male fly courts a female by tapping, abdomen quivering, singing and licking. Switches between these behaviours seem random. A nonlinear model may account for these switches. A comprehensive computational model will be used to investigate the underlying neural basis of courtship in the fly. The third project aims to extend the model developed in the second project by including experience as a critical parameter. This bridges courtship and memory research in the fly and suggests the possibility of modulation of innate behaviour by individual experience.

Amount: £450
Funder: The Wellcome Trust
Recipient: University of Oxford