- Total grants
- Total funders
- Total recipients
- Earliest award date
- 17 Jan 2014
- Latest award date
- 30 Sep 2018
- Total GBP grants
- Total GBP awarded
- Largest GBP award
- Smallest GBP award
- Total Non-GBP grants
Assessing the effect of the Xrn1 exoribonuclease on global and specific rates of protein synthesis 27 Apr 2017
Gene expression is a complex process requiring the coordination of transcription, transcript turnover, translation and proteostasis. When coordinated, these processes can be adapted to allow cells to respond to changes in growth rate and during differentiation. How these processes are coordinated remains a long-standing question. The exoribonuclease Xrn1 is proposed to coordinate transcription and translation via control of steady-state RNA levels and may be part of the mechanism. In this proposal we intend to test one aspect of the proposed model: that Xrn1 regulates steady-state RNA levels and this in turn affects steady-state protein levels. We predict that rates of protein synthesis will change as steady-state RNA levels change and this relationship will be disrupted in cells lacking Xrn1. To assess rates of protein synthesis, we will pulse label cells with puromycin and use a specific antibody to assess the degree of global and specific protein puromycylation in the presence and absence of Xrn1. By assessing rates of protein synthesis for specific proteins we will be able to relate this to levels of protein, transcripts and transcription in the WT and xrn1Delta strains, obtain preliminary data to validate our hypothesis and if encouraging to support a larger scale analysis.
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.
Solving the 3D molecular structure of membrane proteins has historically been difficult, but recent technological advances have made many more membrane proteins viable targets. Membrane transporters and ion channels are important in all cells, but are particularly important in the nervous system. This project aims to solve a 3D membrane protein structure using either cryo-electron microscopy or x-ray crystallography, beginning with a set of candidate proteins involved in disease or vital function. These include: ABCC5, a Type 2 diabetes associated protein and transporter of the neurotransmitter glutamate in the brain; ABCA7, an Alzheimer’s disease associated protein, which transports lipids; HCN2, an ion channel associated with neuropathic pain and the CNGs, a family of proteins which form heteromeric ion channels found in the retina and olfactory system. We plan to complement the structural study with activity assays of purified protein in combination with known substrates and modulators.
Investigating principles of the regulatory chromatin context and incorporating them into computational models for gene regulation 30 Sep 2018
The mammalian genome is hierarchically structured into domains that restrict and shape the accessible chromatin environment for every genomic element. This context has fundamental implications for transcriptional regulation, by defining which regulatory elements have access to a gene at any given time. Novel experimental techniques are being used to investigate this folding at high resolution. Current computational methods for analyzing these data and models for predicting properties of gene regulation are limited in capturing the emerging principles of DNA folding. We will investigate the principles of chromatin folding with large scale, high resolution chromatin Capture-C experiments, mapping the regulatory domains of mouse embryonic stem cells and differentiated erythroid cells. We will develop computational methods better suited to analyze these data and explore models for integrating the large scale, three dimensional chromatin context to prediction tasks. We expect this to have a significant impact on our ability to interpret the vast amount of sequence mutations and polymorphism in the regulatory genome.
The regulation of gene expression is fundamental for cellular integrity and is partly achieved by the opposing action of repressive and activating histone modifications. One such histone modification is the tri-methylation of lysine 4 on histone H3 (H3K4me3), which is known to correlate with transcriptional activity. The SET1A complex is responsible for depositing the majority of H3K4me3 in mammalian cells and disrupting its function often leads to gene expression defects. However, the mechanisms by which SET1A regulates gene expression remain unknown. I will use the auxin-inducible degron system to rapidly deplete SET1A levels. A series of genomics technologies, including ChIP-seq and NET-seq will then be used to determine the effects of SET1A loss on chromatin architecture and transcriptional activity. Additionally, proteomics techniques will be used to identify the pathways perturbed upon SET1A loss, hence identifying the mechanisms by which SET1A supports active transcription and furthering our understanding of how gene transcription is regulated. This is essential for the development of novel therapies targeting genetic diseases in which the control of gene expression is perturbed.
The Effect of Priorizing Information in Working Memory on Later Behavioural Interference 31 May 2018
This experiment will investigate how prioritised information is represented in working memory (WM) through looking at the serial dependence effect. Myers and colleagues (2017) have suggested that items which are prioritised in WM are transformed into action-ready representations. Therefore, the theory predicts that the difference between prioritised and non-prioritised representations in WM will be reflected in behavioural findings. The serial dependence effect occurs when visual information from the recent past biases perception and behaviour at the present moment (Fischer & Whitney, 2014). If prioritised WM items were stored in an action-oriented format, we predict it will show these interference effects in behaviour more than non-prioritised information. By using an orientation adjustment paradigm, we will measure the serial dependence effect for prioritised WM items (which have been retro-cued) versus non-prioritised WM items. In addition, we will vary the type of testing (forced choice versus free recall), predicting that more interference will occur when the tests are the same than when different, due to the action-based nature of the WM representation. Initially we will use behavioural measures (reaction times) to measure the interference effects, extending to EEG to measure neural evidence for the carry-over effects.
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.
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.
Myeloid effector cells in inflammation 27 Apr 2017
Dysregulation of inflammation underlies a range of chronic inflammatory disease. By increasing our understanding of inflammatory mechanisms we may be able to identify specific therapeutic targets to treat disease. Using a murine model of acute, resolving inflammation, with zymosan as stimulus, we create a physiological inflammatory system where we can observe the spatiotemporal relationship of monocytes, macrophage and neutrophils which predominate this response. These observations in a controlled setting will give us insights into how these cells interact to orchestrate an inflammatory response. Gain of function IRF5 is associated with a range of autoimmune and inflammatory disease and promotes an pro-inflammatory phenotype in monocytes and macrophages. We will manipulate the system using mice deficient of IRF5 to modulate the monocytes phenotype and will be able to study the impact on neutrophil function and activation. These findings have the potential to be translated into more complex physiological systems and present new pathways for the study of disease.
The input required to control a prosthetic device greatly defines the subsequent precision that can be achieved. Robust mechanisms that are low-cost often use musculoskeletal motion for control. However, this often limits the level of control and applicability issues can arise when the system that is augmented also generates the power and drives the control. A device that is powered and controlled by breathing could expand the product options for patients and address certain requirements that are difficult to meet with the currently available prosthetic solutions. Computational modelling has been applied to asses if a Tesla turbine can be used for power and control. Positive results from the model and subsequent conceptual testing has indicated this innovative concept could indeed provide precision control for prosthetic users. The aim of the project is to design and produce a working prototype and test out the functional capabilities of the system using several predetermined tasks.
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.
Spontaneous and induced network dynamics across cortical layers during waking and sleep in mice 30 Sep 2018
No one can live without sleep. Even if we try very hard to stay awake, we ultimately can’t resist to fall asleep. Various brain functions, such as the abilities to remember and concentrate, decline when we get tired and improve with sleep. Therefore, it is thought that especially the brain needs sleep and determines when it is time to disconnect and recover. The goal of my research is to understand the brain machinery, which controls sleep and wakefulness. My research requires working with mice as I need to use a genetic tool to switch on and off specific brain cells for a short period of time to find out their role in sleep regulation. I will observe whether the brain can still coordinate its systematic shut down when we turn off cells, which are thought to measure the duration of wakefulness and initiate sleep. I aim to find out whether specific cells can measure how long the brain has been awake and send out signals to coordinate the systematic shut down of many brain regions when falling asleep. I hope that my experiments contribute to an understanding of healthy and disturbed sleep.
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.
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.
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.
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.
Over a third of cancer cells have been found to contain multiple times the amount of DNA present in healthy cells. This can happen when cells do not divide properly, however, we think that this can also happen when cells are infected with certain viruses that can make cells merge. We want to study which viruses can make cells merge, and under what conditions this happens. We also want to study the differences between merged cells and cells that are interrupted while they are dividing. We can do this in the lab by making cells that produce the proteins that viruses use on the one hand and using chemicals that interrupt cell division on the other hand. After this we will use microscopy combined with genetic analysis techniques to see if these cells behave like cancer cells. Finally, we will study how these cells change over time by analysing their genetic sequence. As part of this project we will also look at existing cancer datasets to see if we can find evidence of cell fusion. We hope that this work will tell us more about the relationship between viruses and cancer, as well as giving rise to new treatment approaches.
I plan to explore the effect of nicardipine, a brain-penetrant calcium channel antagonist, on mood instability and its cognitive/neural correlates. This research (carried out within the Collaborative Oxford Network for Bipolar Research to Improve Outcomes [CONBRIO]) has a number of goals. In addition to studying effects of L-type calcium channel (LTCC) antagonism on mood instability, I will investigate effects on sleep/cognition, and on brain activity measured by functional imaging. Rationale is provided by (a) considerable evidence for calcium signalling abnormalities in bipolar, (b) current mood stabilisers correct some of these abnormalities, (c) calcium channel genes contribute to the basis of bipolar as well as to memory/sleep. Moreover, LTCC antagonists are used for heart disease and available for experimental studies; there have also been early studies in bipolar disorder but no robust results. I will study volunteers screened for high mood instability and risk CACNA1C genotype, and assess mood, sleep, cognition, and neural activity, before and after randomisation to nicardipine or placebo. Results will inform whether trials of LTCC antagonists for bipolar disorder are indicated, and their likely efficacy/tolerability. I will learn to conduct a randomised trial, principles of experimental medicine, and aspects of cognition, circadian-biology, and functional brain imaging.
First, the structure of the first genome layer of ?6 will be revisited with the goal of better separating the different conformations and obtaining a better resolution for each of them. Next, the pathing of the dsRNA and its interactions with the capsid will be studied to understand its organisation and connection to the inner layers at the molecular level. The calculated orientations will then be used to subtract the density of the first layer from the original images in order to examine the inner layers more accurately. The most important reason to continue examining the inner layers is to locate the RNA-dependent RNA polymerases and solve their structures together with the genome. This would facilitate the understanding of how they interact with the dsRNA and, by using inhibitors, different stages in the lifecycle of the virus could be trapped. As a result, a time-resolved mechanism for the packaging of the genome could be proposed. Consequently, the transcription of the dsRNA will be investigated by studying the viruses upon the incubation with a "reaction buffer". Ultimately, the optimized protocol will be applied to study biomedically more relevant viruses such as the human rotavirus.
Z-DNA is an alternative conformation of the DNA double helix. The existence of proteins containing Z-DNA binding domains (ZBDs) suggests that nucleic acids in this conformation have important but so far uncharacterised biological functions. One such protein is the innate immune protein Z-DNA binding protein-1 (ZBP1/DAI/DLM1). We have evidence that ZBP1 mediates virus-induced necroptosis in a manner dependent on its ZBD. This function of ZBP1 is sensitive to RNase but not DNase treatment, suggesting that the trigger is Z-RNA. We therefore hypothesise that Z-RNA may represent a novel pathogen-associated molecular pattern sensed by ZBP1. The aim of my PhD will be to further characterise this role of ZBP1 and to investigate the source and nature of the Z-RNA being sensed. In particular, we will ask if this Z-RNA is of viral and/or cellular origin, and whether specific sequence motifs are recognised by ZBP1. Another question pertains to the relevance of ZBP1 in diverse human virus infections. In parallel to these in vitro studies, we are developing a knock-in mouse in which the ZBD of ZBP1 is mutated. I predict that these animals will be less able to control viral infection due to a failure of ZBP1-mediated virus-induced necroptosis.