NIHRDataInsights/HRCSData huggingface dataset:
Title: Mechanisms of cell surface recycling pathways
Funder: Wellcome Trust

Abstract: Cell surface proteins continually recycle through endosomes, where trafficking decisions control protein levels and activity. Yet, we have limited understanding of the mechanisms that regulate this recycling. I have identified a direct trafficking pathway from endosomes back to the plasma membrane in yeast, and have used genetic approaches to identify machinery that controls this. The majority of candidates identified are highly conserved; I now plan to define the fundamental mechanisms used by these molecules to control recycling. My key goal is to understand three specific regulatory units that I hypothesize are required for endosomes to create recycling tubules, into which cargoes are packaged and delivered back to the plasma membrane. I propose experiments to test three specific hypotheses: 1) Nhx1 elevates osmotic pressure in endosomes to drive recycling tubule formation, 2) Rag GTPases catalyse recycling tubule morphogenesis and drive selective cargo sorting, and 3) Ist1 polymerises on endosomes to drive scission of the recycling tubule. These yeast proteins all have clear human orthologues, and a series of experiments is aimed at testing these human versions in recycling. Importantly, I plan to extend these studies in human cells, to validate conserved recycling mechanisms identified in yeast and reveal additional mechanisms.

Lay abstract: The cell surface is very important to the viability of a cell as it represents the barrier between the inside of the cell and the environment. Regulating what molecules are present at the cell surface is therefore critical in determining how a cell interacts with its environment. To achieve this, surface proteins are continually internalized to “endosome” compartments where proteins are physically separated into different categories such as those to be sent back to the surface or those to be kept inside. The recycling from endosomes back to the surface is dysregulated in cells taken from patients with diseases, including diabetes, cancers and cardiovascular disease. Despite its clear physiological importance, little is known about the machinery that regulates recycling. By taking advantage of evolutionary conservation that exists between yeast and humans I have identified the responsible components of this trafficking pathway to the surface. I now propose specific ideas to investigate exactly how this machinery works. Human cells have version of the proteins that I identified in yeast, so I will test their function in human cells, using techniques developed by a collaborator at the institute where I plan to set up my research group.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Extending the Edinburgh super-resolution imaging consortium STED, FCS and SMLM capability and capacity
Funder: Wellcome Trust

Abstract: This proposal seeks support for 2 items of equipment to increase capacity and capability in our exisiting advanced imaging facility. First, we are requesting support for the procurement of a dual-depeletion gated-STED (stimulated emission depletion) microscope platform. Specifically, we have identified the Leica 3X SP8 STED super-resolution system as ideal for our requirements, balancing the flexibility of fluorophore use in STED with 592 nm and 775 nm depletion lasers, sensitive detection with hydrid detectors and high-speed resonant scanner image acquisiion, with cost and ease-of-use. Second, we request support for an upgrade to an existing N-STORM system to permit faster, more flexible single molecule localisation microscopy, for live cell imaging and integration with parallel single molecule spectroscopies. We have an exceptionally broad collaborative user base from each of Scotland's research-intensive universities who have provided specific letters of support detailing their requirement for these equipment items. Our key goals are to continue to provide the best super-resolution imaging expertise, equipment, training and education to our exceptionally broad excellent user base, to drive biology discovery through mutli-disciplinarity and the most sophisticated microscopy possible.

Lay abstract: New sorts of microscopy allow biology researchers to 'see' smaller things inside living cells than previously thought possible. Looking at the tiny structures on a literally astronomically small scale - these objects are as small to the observer as Jupiter is large - allows biologists to look more deeply and directly at the workings of cells and the biological machines inside them, and so determine how they work in health and disease. We have become very adept at developing and using these nanoscopies but only in one colour. New microscopes are now available where we can look at several different nano-structures in the same cell at the same time, so biologists can work out how different parts of the cells are organised. We are seeking support for one of these new instruments here to maintain our competitiveness and our biology discovery.

Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE
Title: University of Glasgow Wellcome Trust Translational Partnership
Funder: Wellcome Trust

Abstract: The University of Glasgow has a tradition of delivering excellent research and aims to develop 'worldclass, world changing' impact across social, economic and cultural areas. Our College of Medical, Veterinary & Life Sciences (MVLS) spans a diversity of disciplines with research into processes at every biological level from genes, to cells, organs, individuals, populations, and ecosystems. MVLS is grounded in the principle that all research can achieve impact, making a constructive difference in some way, and at some time, to ultimately benefit society. Our strategic aim to drive a partnership approach to translation aligns perfectly with Wei/come Trust's ambition for the Translational Partnerships (TP). Together we will further our ambitions to develop real world benefits from our research through the development of a positive and supportive culture in which our researchers and their translational ambitions will thrive. Our TP will enable us to: 1. Grow and develop our translational pipeline - through a programme of research audits and the provision of support tailored to individual project needs 2. Accelerate the journey of our translational projects - by providing researchers with the tools to access relevant resources and to work in partnership with industry, NHS and other stakeholders."


Research activity codes: 5.9 RESOURCES AND INFRASTRUCTURE (TREATMENT DEVELOPMENT)
Health categories: GENERIC HEALTH RELEVANCE
Title: Exploring mitochondrial metabolism in health and disease using targeted biological chemistry
Funder: Wellcome Trust

Abstract: The molecular mechanisms by which mitochondrial reactive species, metabolites and redox signals contribute to physiology and pathology are unclear. This is in large part because these processes are difficult to assess and modulate in vivo. Our goals are to establish general chemical biology approaches to determine the mechanisms of mitochondrial physiology and dysfunction in vivo and from this develop new therapeutic strategies. The aims are based on the success of our previous Joint Investigator Award, but the specific chemical biology approaches to be used, the insights to be attained and the models have been refined and developed, based on our work over the past four years. These goals will be achieved by addressing three research challenges in cells and in vivo: A: Can we determine how mitochondria operate during normal physiology, and are disrupted during pathology, by targeting probes to measure reactive species and alterations to signaling pathways? B: Can targeting bioactive molecules to mitochondria prevent pathological disruption of mitochondrial function and generate potential therapies? C: Can the above methods to monitor and modulate mitochondrial function be assessed in animal models of human diseases and thus drive the development of rational, translatable therapies?

Lay abstract: Within our cells the energy from food is released by cell components called mitochondria. So, problems with mitochondria contribute to a large number of different diseases, such as diabetes, Parkinson's disease, inflammation and also to acute injuries such as heart attack and stroke. To find out more about what goes wrong with mitochondria in these diseases we will make a range of different small molecules that are designed to go to mitochondria within cells. Some of these molecules will be used to report back on what is going wrong with mitochondria. Other molecules will be designed to alter mitochondrial function in ways that tell us how they are contributing to diseases. Finally, we will also develop molecules that are designed to block some of the damage occurring in the mitochondria and this may enable us to come up with new types of drugs for these diseases.

Research activity codes: 5.1 PHARMACEUTICALS
Health categories: GENERIC HEALTH RELEVANCE
Title: State of the art lipidomics
Funder: Wellcome Trust

Abstract: As a result of a close collaboration with Thermo Fisher, and three visits to their factory in San Jose, modifications and designs have been iterated that have resulted in a modified Orbitrap Fusion Lumos tribrid mass spectrometer (MS). Critically this unique MS platform not only retains resolution at both high and low m/z ranges but also enables multiple rounds of tandem MS for state of the art lipidomics. Proof-of-principle data demonstrate that the instrument is capable of maintaining native membrane protein complexes and also, within the same experiment, characterising the lipids/ligands that regulate them. Our goals are to identify critical lipids/ligands through high resolution native MS of membrane protein assemblies as well as multiple rounds of MS/MS (MSn). Additional goals include developing fast fragmentation methods, such as UVPD, to define lipid binding sites within intact assemblies. Effectively this platform enables for the first time, top-down lipidomics directly from membrane protein assemblies. Importantly the direct link between the lipid and the parent protein-complex is maintained throughout the experiment providing a step change over current methods which involve separate lipid extraction and proteomics experiments. There is a high unmet need for this MS platform with multiple users and many exciting applications.

Lay abstract: Background to the research problem: Membrane proteins constitute the gateways to the interior of the cell. As such they have become important drug targets in numerous diseases including cancer, neurodegenerative and heart disease. It has been widely recognised that membrane proteins do not act in isolation but are controlled by their lipid surroundings. There is, as yet, no way of fully characterising the structures of the lipids in direct contact with membrane proteins. Our approach: In conjunction with my co-applicants we will develop a novel mass spectrometer to define the structures of the lipids that regulate membrane proteins, in one experiment, through multiple rounds of tandem MS. Impact: By understanding at the molecular level the connections between lipids and their proteins we will inform drug targets and multi-drug resistance mechanisms. Moreover, by developing these methods, we will inform disease states that result from changes in lipid structures.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Multimodal scanning electron microscope for three-dimensional imaging of biological specimens
Funder: Wellcome Trust

Abstract: We are requesting funds to acquire a focused ion-beam and scanning electron microscope (FIB-SEM) with a cryo transfer system and an attached mass spectrometer for investigating biological material in three dimensions (3D) at high spatial resolution with chemical specificity. This cryo-FIB-SEM will be used for the three distinct purposes -Firstly, serial block face sectioning and imaging of vitreous samples will provide images of key regions of tissues at unprecedented resolution (~5 nm). Secondly, this instrument will enable thick vitreous biological samples to be precisely thinned at cryogenic temperatures, producing lamella at high throughput with automation, which will be used in cryo-tomography applications for in situ structural cell biology. Thirdly, the instrument will have a secondary ion mass spectrometer attached, which will support molecular identification of the specimen, adding chemical specificity to high-resolution EM pictures. This versatile instrument will therefore provide a link between molecular structural data to 3D ultrastructure of cells and tissues, a complete transformational advance for the research of the MRC Laboratory of Molecular Biology (MRC-LMB).This instrument will enable study of the structure and function of molecules in their native environment inside cells, providing insights into fundamental problems related to molecular biology and medicine.

Lay abstract: Recent developments have enabled special microscopes, which include both an electron and an ion beam, to be optimized for biological investigations. These microscopes are revolutionizing biomedical research by allowing scientists to open windows into cells, tissues and organisms, and peek into their inner workings, generating a wealth of biomedically relevant data.We are requesting funds to acquire such a microscope in Cambridge, where it will be used by a large number of laboratories for 3D imaging of cells (e.g. dividing human cells) and tissues (e.g. Drosophila brain) at high-resolution under native conditions.This versatile instrument will provide a link between atomic and molecular structural data on one hand to 3D ultrastructure of tissues on the other, a complete transformational advance for our research. This will lead to new collaborations, ideas and new discoveries at the MRC-LMB and beyond.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Sleeping well in the early modern world: an environmental approach to the history of sleep care
Funder: Wellcome Trust

Abstract: What does it mean to sleep well? This is not just a modern concern but something that has exercised individuals and communities throughout history. This project will be the first to address this question by assessing how people's efforts to sleep well c.1500-1750 were influenced by a distinctive set of environmental relations and linked 'environing practies' in which people engaged with their physical surroundings to optimise their sleep timings, bedding materials, and to prepare soporific tonics. A PI-led team will reconstruct the principal agents, materials, and 'environing' practices that were used to manage sleep in ecologically distinct parts of Britain, Ireland and England's emergent American colonies of Virginia and Newfoundland, alongside the bodies of medical, botanical, climatic and material knowledge associated with them. The research is important because it brings a fresh environmental history perspective to bear upon cross-disciplinary debates about the significance that physical environments play in shaping healthy and unhealthy sleep habits. It will also be the first to assess the immediate and longer-term impacts of early modern processes of environmental change in shaping people's sleep care practices, which will encourage a reassessment of the assumed primacy of 'watershed' moments such as industrialisation in shaping human sleep fortunes.

Lay abstract: How and why did past communities try to optimise their sleep? To answer this question my project will investigate the development of a culture of 'sleep care' c.1500-1750 in Britain, Ireland and England's American colonies and its manifestation in a range of everyday practices. I will show how historic environments played a powerful role in 'sleep care' practices by uncovering how and why people engaged with their physical surroundings to cleanse and scent their bedding textiles, to prepare sleep tonics, and to control the climatic conditions of their sleeping environments. My project will shift the tone of conversations around sleep from 'crisis' to 'care' and assess how 'sleep care' practices changed in a period marked by large-scale agricultural change, urbanisation, and increased mobility. This research offers critical context for health researchers who claim that a growing disconnection between 'nature' and 'culture' is one important cause of our current sleep 'crisis'.

Research activity codes: 8.1 ORGANISATION AND DELIVERY OF SERVICES
Health categories: GENERIC HEALTH RELEVANCE
Title: Probing intra-cellular dynamics with lattice light sheet microscopy
Funder: Wellcome Trust

Abstract: Cell biology is in the midst of a remarkable “resolution revolution” in which the invention of new optical microscope techniques is allowing visualisation of the dynamics of intra-cellular structures at unprecedented spatial and temporal resolution. We are requesting a Lattice Light Sheet Microscope (LLSM) as developed by Eric Betzig (Janelia) - recipient of the 2014 Nobel Prize for his earlier work on super-resolution microscopy - and a dedicated microscope technician. The LLSM enables simultaneous illumination of the entire field of view with an ultrathin sheet of excitation light permitting imaging at hundreds of planes per second with high axial resolution (~230-nm xy and ~370-nm z), negligible out-of-focus background and a dramatic reduction in photobleaching/toxicity/damage. The LLSM thus opens up a completely new horizon, enabling long-term interrogation of the mechanisms of cell biological machines, inside live cells. Our aim is to make this technology available to Warwick’s expanding cell and developmental biological community - nucleated by four Wellcome Investigators (McAinsh, Straube, Balasubramanian & Cross) based in the Centre for Mechanochemical Cell Biology. We will also establish a visitor programme - inspired by the advanced imaging centre at Janelia - to make this technology accessible to the wider community.

Lay abstract: The invention of the light microscope in the seventeenth century led to the discovery that living things are made of cells. 300 years later jellyfish proteins that can emit green light were discovered. These could be fused to parts of the cell allowing cell biologist to follow events in living cells. A major limitation is that shining too much light on these proteins bleaches them and causes cells to die, meaning we can only look for short times. By using very thin sheets of light, we can now observe fluorescent proteins at short time intervals, over long durations in 3D. This will revolutionise our work, which aims to understand how a cell can copy itself into two new daughter cells, how cells change shape, move and interact with each other – amazing processes that are essential for turning a single fertilised egg into 14 trillion cells.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: 3D-FunSites - a virtual encyclopaedia of protein functional sites for assessing variant impacts and drug repurposing
Funder: Wellcome Trust

Abstract: We will significantly expand CATH, widely used by biomedical researchers, and enhance its value for disease analyses. Data on disease-associated genetic variations is vastly increasing but to fully exploit it we must understand how the resulting residue mutations impact protein functional sites and therefore functions. We will use CATH to predict the impact of variants on diseases and drug responses, enabling personalised medicine. CATH-FunFams are functional sub-classifications of CATH evolutionary superfamilies and the only structural resource comprehensively linking variants, structure and vast sequence data for predicting functional sites accurately (FunSites). Close proximity of disease variants (residue mutations) to FunSites, in 3D, is a key indicator of pathogenicity. Our expanded CATH-FunFams and FunSites will enhance machine learning methods to predict functional impacts and drug responses/side effects, including for different genders and ethnicities. We will:- 1. Expand CATH-FunFams and FunSites >5-fold by adding sequence data from metagenomes. 2. Expand CATH-FunSites further by integrating comprehensive data from PDBe-KB, PDBsum and VarSite. 3. Develop machine-learning tools that exploit data from (1) & (2) to predict impacts of genetic variations in different populations. 4. Integrate drug data into FunFams and develop tools to predict drug repurposing/side effects. 5. Develop intuitive webpages reporting functional impacts/drug repurposing/toxicity.

Lay abstract: We will establish computational protocols for detecting mutations in gene coding regions which destabilise or modify the structure/function of the translated protein. Such changes can affect interactions of proteins with compounds or other proteins in their cellular environment, leading to disruption of cellular systems and human disease. We will use our CATH resource to detect these pathogenic mutations. CATH classifies evolutionarily related proteins into sub-families (FunFams) and inherits functional properties across relatives e.g. residues involved in catalytic activity, significantly increasing knowledge of key functional sites beyond the 1% experimentally characterised. We will massively expand FunFams and increase functional site information by integrating data from PDBe-KB. By calculating proximity of disease mutations to functional sites we can predict their pathogenicity. FunFams can also be used to repurpose drugs between relatives sharing high structure similarity, to combat mutation impacts. We will take account of gender/ethnic differences to support personalised medicine.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Re-Engineering Health Policy Research for Fairer Decisions and Better Health
Funder: Wellcome Trust

Abstract: Health inequalities diminish lives and blight communities. Although the determinants of health inequality are well known, policy makers have repeatedly failed to address the issue effectively, and many public health interventions unwittingly worsen inequalities because they disproportionately benefit those with greater resources. This is also a scientific failure. The analytical tools used to inform policy lack a substantial perspective on equity, focusing on averages rather than social distributions, leading to inequitable solutions. In an age of social division driven by rising inequality, new approaches to health policy are urgently required. We propose to re-engineer health policy research. We will develop rigorous methods for measuring the equity impacts of health and social policy interventions, and apply these methods to assess the effectiveness of major public health and healthcare initiatives. In doing so, we will improve our understanding of the structural, behavioural and organizational barriers to delivering equitable health outcomes. Our programme will equip researchers with the necessary tools for measuring equity impacts, and provide policy makers with vital information on who gains and who loses from their decisions. Our ultimate aim is to enable fairer health policy decisions, leading to better health across society.

Lay abstract: No Data Entered

Research activity codes: 8.1 ORGANISATION AND DELIVERY OF SERVICES
Health categories: GENERIC HEALTH RELEVANCE