NIHRDataInsights/HRCSData huggingface dataset:
Title: A community based training programme for cryo-electron microscopy
Funder: Wellcome Trust

Abstract: Recent advances in cryo-electron microscopy/tomography (cryoEM/ET) are transforming structural biology, and thanks to recent investments in infrastructure the EM community has unprecedented access to high-end instrumentation. However, a severe lack of training opportunities means that the skills required to make the most of these instruments are in very short supply. This in turn is slowing progress on many existing projects within EM-focussed laboratories, and limiting access to EM by the mainstream structural and cell biology communities who are desperate to gain access to the cryoEM methodology. Effectively, there is a block on discovery, which is caused in large part by a deficit in knowledge, expertise, and training. To rectify this training shortfall, we propose a coordinated, multi-level programme of training, that complements those training opportunities that do exist, but expands upon them, significantly increasing the amount of ‘hands-on’ EM training available in the UK. This programme, which will encompass introductory “sample work up”, intermediate “high resolution data collection” and advanced “Facility Placements” will provide a path for users with different expertise, and from different scientific backgrounds, to access the training they require, maximise the return on existing and new investments in EM, and drive forward new biological and biomedical discovery.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Diagnosing Diagnosis: a multidisciplinary perspective
Funder: Wellcome Trust

Abstract: Diagnosis is at the heart of the medical encounter, but many features of making, communicating and recording a diagnosis remain poorly understood and little researched. Without greater understanding, we cannot provide adequate guidance to clinicians about what information to share with patients or adequate advice to patients about what questions to ask, and policy incentives to address problems with ‘overdiagnosis’ or ‘misdiagnosis’ are at risk of unintended consequences. Key goals: 1. To examine the process of making, communicating and recording a medical (differential) diagnosis in the acute care setting; 2. To examine institutional influences on the diagnostic process; 3. To examine ethical and philosophical influences on making and communicating diagnoses; 4. To establish an empirically based, ethically grounded framework for making, communicating and recording a diagnosis to improve patient outcomes on both individual and societal levels. Methodology: Qualitative methods including ethnography and interviews will be combined with medical records analysis and quantification of the reach and permanence of diagnostic labelling between health care settings. Integrated with this empirical work, ethical analysis will explore how the interplay between responsibility, uncertainty and trust affects the process and communication of making a medical diagnosis. This is emphatically multidisciplinary research which benefits from combining different perspectives and methodologies.

Lay abstract: No Data Entered

Research activity codes: 7.3 MANAGEMENT AND DECISION MAKING
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Multi-dimensional Diagnostics for Rapid Detection of Infectious Diseases in Developing Countries
Funder: Wellcome Trust

Abstract: Each year there are 50-100 million cases of dengue worldwide, and 40% of the world’spopulation live in affected areas. There is an urgent need for diagnostic tools able toaccurately identify dengue infections at the point-of-care to ensure timely and targetedclinical management. This is especially important in lower-middle income countries,including Thailand, where access to healthcare facilities is limited. We will deliver anovel portable device that can rapidly diagnose dengue from blood and identify itsserotype with very high accuracy, whilst using a cloud connected mobile phone to mapthe location of infection. The technology, which utilises microchip based chemicalsensors, will be validated as part of a diagnostic evaluation within Thai healthcaresettings. To ensure the technology is appropriate for end user requirements it will be codesignedby healthcare workers in Thailand, with guidance from the Ministry of PublicHealth and the Village Health Volunteer system.”

Lay abstract: Each year there are 50-100 million cases of dengue worldwide, and 40% of the world’s population live in affected areas. There is an urgent need for diagnostic tools able to accurately identify dengue infections at the point-of-care to ensure timely and targeted clinical management. This is especially important in lower-middle income countries, including Thailand, where access to healthcare facilities is limited. We will deliver a novel portable device that can rapidly diagnose dengue from blood and identify its serotype with very high accuracy, whilst using a cloud connected mobile phone to map the location of infection. The technology, which utilises microchip based chemical sensors, will be validated as part of a diagnostic evaluation within Thai healthcare settings. To ensure the technology is appropriate for end user requirements it will be co-designed by healthcare workers in Thailand, with guidance from the Ministry of Public Health and the Village Health Volunteer system.

Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: The Aspergillus fumigatus gene and non-coding RNA knockout library
Funder: Wellcome Trust

Abstract: The filamentous fungus, Aspergillus fumigatus is the most common mould pathogen of man. It is thought to be the causative agent in over 600k deaths annually with global incidence of allergic and chronic disease caused by this agent exceeding 4.8 and 3 million respectively. Worldwide expenditure on antifungal drugs will exceed $13.9 billion by 2018. Hospitalisation heightens the financial burden of fungal disease as antifungal agents represents only 17% of the total healthcare cost. Our understanding of the molecular factors underpinning disease and drug resistance is exceptionally limited and is guided primarily by research on non-pathogenic fungi such as the model yeast Saccharomyces cerevisiae. In an attempt to address this shortfall in our knowledge, and to support the A. fumigatus research community, we have begun the process of generating a genome-wide knockout library. To date we have amassed 3872 genetically tagged knockout mutants. Here we propose to complete this resource by finalising the library to include all c 10,000 genes and non-coding RNAs (ncRNAs) and develop methods for their use. In addition we will update genome annotations to include details of ncRNAs and generate comparative data of the essential gene set in a different genetic background of A. fumigatus.

Lay abstract: Fungi, like bacteria and viruses, cause life-threatening diseases. Diseases caused by fungi are a worldwide problem and estimates suggest that they cause as many deaths as malaria and tuberculosis. One of the most prevalent fungal pathogens is Aspergillus fumigatus. Our understanding of how Aspergillus causes disease is limited. Most of our ideas have been informed from experiments in non-pathogenic ‘model’ fungi as there are exceptionally good scientific resources to support research in these models. However, there are obvious limitations to how far one can infer information from a non-pathogenic model. The aim of the project is to provide a collection of gene deletion mutant strains in A. fumigatus to arm researchers with the ability to answer specific questions about the pathogenic nature of this organism to support the development of new strategies for treatment.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Mass spectrometry infrastructure for in-cell structural biology
Funder: Wellcome Trust

Abstract: The goal of this proposal is to establish a cutting-edge in-cell structural proteomics platform at the Astbury Centre that will enable the characterization of biomolecular structure and function in a cellular context. This will inform on the architectures of proteins and protein complexes, including interactions with nucleic acids and small molecules, directly in their native environment. We are requesting funding for the centrepiece of this platform, an Orbitrap Eclipse mass spectrometer with extended mass range and advanced fragmentation technologies. This equipment will enable us to deploy the suite of structural proteomics methods we have developed for in vitro protein studies directly to the cell. These approaches include in-cell covalent labelling to probe protein structure, such as by hydroxyl radical footprinting, and in-cell chemical crosslinking, including using bespoke photocrosslinkers, for interactome analyses. Such methods can only be implemented utilising the most sensitive mass spectrometry instrumentation available, and require advanced fragmentation methods to achieve the highest possible structural resolution. The proposed equipment will transform our ability to study molecular mechanisms of health and disease directly in the cell, and will result in translational opportunities, by identifying novel proteins, complexes and interactions that could be biomarkers or drug targets.

Lay abstract: Proteins are the molecular workhorses of the cell and understanding protein structure and the details of protein interactions with other proteins, nucleic acids and small molecules is essential to understand their function, identify disease mechanisms and uncover new targets for therapies. Moreover, it is vital that we uncover these details directly in cells, as this is where proteins perform their biological functions. New technologies have been developed to label proteins and trap protein-protein interactions in cells, with the results of these experiments detected using a technique called mass spectrometry. However, performing these experiments requires specialised state-of-the-art mass spectrometry instruments. In this proposal we ask for investment to update and transform crucial mass spectrometry infrastructure at Leeds so that we can study protein structure and interactions in the cell. We will use this technology to study the molecular mechanisms of diseases in areas spanning virology, neurobiology and antimicrobial resistance.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: The role of small RNA pathways in regulating aspects of the parasitic lifestyle and host environment by Strongyloides nematodes
Funder: Wellcome Trust

Abstract: Small RNAs (sRNAs) have two possible roles in nematode parasitism: (i) regulating endogenous genes used in parasitism, and (ii) regulating host genes. Based on my current research and pilot data, I hypothesise that Strongyloides parasites use micro(mi)RNA and worm-specific Argonaute (WAGO)-mediated sRNA pathways to regulate key aspects of their parasite biology, including regulating the host environment. I will use empirical and bioinformatics approaches to investigate the role of sRNAs in nematode parasitism using Strongyloides ratti, a gastrointestinal parasite. The proposed work comprises three aims: (1) Identify the endogenous nematode target genes of S. ratti miRNAs, which I have recently identified, using anti-Argonaute co-immunoprecipitation assays and bioinformatic analyses. (2) Characterise WAGOs and WAGO-associated sRNAs with a putative role in parasitism, including co-immunoprecipitation assays, and sequencing sRNA and mRNAs to establish gene expression patterns across different life cycle stages. (3) Identify miRNAs secreted by S. ratti and predict the host genes they target, through sequencing of S. ratti-secreted products and bioinformatic analyses. Together, this work aims to elucidate the role of sRNAs in a nematode parasite, which is interesting from a fundamental biological standpoint, but is also an essential step required for future developments of new nematode treatment and control methods.

Lay abstract: Parasitic worms infect one third of the global population, causing a substantial disease burden. These worms are controlled by anthelmintic drugs but resistance is becoming increasingly widespread. Parasitic worms, like other animals, use small RNAs to regulate gene expression. I will investigate the role of small RNAs in Strongyloides worms, which infect the gut of humans and other animals (the host). Small RNAs may regulate either the worm’s own genes or can be secreted into the host to regulate host genes. Using experimental and computational approaches, I will identify the small RNAs used by Strongyloides worms, and the worm and host genes that they regulate, during an infection. This work aims to elucidate the role of small RNAs in a parasite, which is interesting from a fundamental biological standpoint, but also an essential step required for future developments of new treatment and control methods for parasitic worm infections.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Lost in translation. Dissecting the divergent features of Toxoplasma gondii mitochondrial translation
Funder: Wellcome Trust

Abstract: Apicomplexan parasites cause diseases, including toxoplasmosis and malaria, that require new drugs. Apicomplexan mitochondrial translation is critical for parasite survival. For example, we recently showed that depleting a Toxoplasma mitoribosomal protein results in parasite death. Apicomplexan mitochondrial translation shows striking differences from humans, as many short mitochondrial rRNAs are transcribed rather than two large rRNAs. Additionally, tRNAs are imported into mitochondria rather than mitochondrially encoded. How translation is performed under these conditions is not understood. Using the model apicomplexan Toxoplasma, we will pursue two aims: 1.Study the mitoribosome composition, structure and function. 1.1.Via proteomics and genetics, taking advantage of our cell-lines with tagged or regulated mitoribosomal proteins 1.2.Via structural analysis, exploiting our new mitochondrial macromolecule enrichment protocol, and cryoEM collaboration. 2.Dissect and functionally characterize the mitochondrial tRNA import pathway. 2.1.Through functional analysis of mitochondrial tRNA interactors we have already identified 2.2.tRNA import may occur directly from the nucleus. We will examine the role of novel nuclear-mitochondrial contact sites. This work will provide mechanistic understanding of divergent aspects of apicomplexan mitochondrial translation. The molecular and atomic insights into how mitoribosomes operate and what interactions facilitate tRNA import, may inform the design of new mitochondrial translation inhibitors, thus seeding drug development.

Lay abstract: How do you run a conveyer belt production line when the belt is cut into pieces and the workers are in another room? Apicomplexans, the deadly parasites that cause diseases such as malaria, must face this challenge. The essential production of proteins in their energy generating compartment, the mitochondrion, must take place with a fragmented machine, the mitoribosome, and with building blocks imported from outside the mitochondrion. This is curious because there is no other such case in nature. Moreover, it is very different from human cells, where the mitoribosome backbone consist of two continuous parts and the necessary building blocks are made in the mitochondrion. This project aims to understand what unique parasite factors enable this essential operation, and to elucidate the differences in the mechanisms of apicomplexan versus human mitochondrial translation, which may assist the design of new drugs for these deadly pathogens.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Photonic hyperspectral no-label spotter (PHEnoSPOT)
Funder: Wellcome Trust

Abstract: A comprehensive understanding of communication in both healthy and diseased cells requires new tools to quantify the spatial distribution, onset and rate of protein secretion. To address this challenge, we will develop an in vitro technology that maps the three-dimensional (x, y, time) distribution of multiple cell-secreted molecules, such as chemokines, hormones, and cytokines, with single cell resolution. This technology allows to better characterise the heterogeneity of cell populations in response to stimuli and to define mechanisms of inter-cellular communication. Our innovation exploits the sensitivity of optical resonances to map the secretion of specific proteins without the need for a labelled antibody. Critically, and in contrast to competing technologies, such label-free approaches enable protein detection in real time. The photonic sensor can be fabricated at low-cost and can be integrated into standard commercial microscopes rendering the technology widely applicable. We have already demonstrated the technology and will now optimise its performance, develop its capability to detect at least 3 different types of proteins in parallel and work with a commercial partner to develop a system compatible with a laboratory-standard inverted microscope. We will engage with the community through exemplar projects that span infection and immunity, cancer, haematology and vaccinology.

Lay abstract: The function of cells within our bodies is coordinated by molecules that are passed between them. To properly understand these signalling events, we need tools that allow us to understand how different types of cells secrete these molecules, and how such messages propagate. Current tools either measure secretion from a large number of cells at a single time point, they may interfere with physiological function by using labels, or they have to destroy the cells in order to analyse them. Here, we propose a fundamentally different imaging technique, which we term "Phenospot" and which is based on optical resonances that allow us to monitor the response of live cells in great detail. As a result, we can obtain a better understanding of many processes critical for health including the immune system or cancer progression and provide new ways to help prevent or treat disease, for example through better vaccines.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: A modern cryo-EM instrument for biological samples at Imperial College London
Funder: Wellcome Trust

Abstract: The Centre for Structural Biology at Imperial College London includes a heavily-used electron microscopy facility on the South Kensington campus that features four electron microscopes for single particle and tomographic analysis of biological samples. A large and rapidly-growing Imperial- and London-based user community spanning molecular biology, chemical biology, and drug development, uses these instruments for sample screening, optimisation, and data collection. These instruments, however, are all based on 20+ year-old archetype, resulting in rising maintenance costs and risk become irreparable any day due to inability to source replacement parts. These machines are also bottlenecks, incapable of providing high-throughput screening, optimisation, and data collection needed to feed high-resolution data collection instruments such as Titan Krioses accessible at various UK-based facilities. Our community is in urgent need of a contemporary electron microscope such as a Talos Arctica capable of both single particle and tomography cryoEM, equipped with technology for rapid screening and optimisation and compatibility with Krios sample handling. The instrument will be embedded and managed within the CSB EM facility and accessible by all CSB users on an hourly user rate basis to guarantee full cost recovery, a company-based service contract, and long-term sustainability.

Lay abstract: Imperial College London harbours a Facility for electron microscopy (EM), which allows structural analysis of biological samples down to a scale of near-atomic resolution. In the past 5-10 years, EM underwent a dramatic technical revolution with strong influence on biology, medicine and chemistry. It today allows researchers to get atomic scale-resolved structures of highly complex molecules or cellular sub-structures, in remarkably short time. Our Facility currently has four electron microscopes, which are all technically outdated (pre-2000) and which also increasingly started showing technical issues. These problems sometimes became impossible to repair, due to non-availability of spare parts or service contracts for antiquated equipment. For our very large (>70), mostly College-based crowd of EM users this makes research much less efficient and much less competitive in the fast advancing, international research context. In this application we are therefore requesting financial support for a modern electron microscope for biological samples.

Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Expanding the capabilities and use of the South West Regional Facility for High-Resolution Electron Cryo-microscopy
Funder: Wellcome Trust

Abstract: State-of-the-art direct electron detectors (DEDs) and new image processing strategies enable electron cryo-microscopy (cryoEM) routinely to achieve near-atomic resolution of biological samples. CryoEM has thus become a primary imaging technique, increasing the need for research institutions to provide cutting-edge cryoEM equipment. The Living Systems Institute (LSI) at the University of Exeter is a brand new interdisciplinary research centre, which will develop strategies to study diseases and their prevention. As part of the GW4 group (also including Bristol, Bath and Cardiff), we seek to develop regional research infrastructure on a scale beyond the capabilities of the single institutions. Within this remit, the Wellcome Trust-funded South West Regional Facility for High-Resolution Electron Cryo-microscopy will be established in Bristol, with a 200kV cutting-edge cryo electron microscope at its core. To support this venture and significantly increase the capabilities of the facility for all users within GW4, we plan to contribute a state-of-the art K3 DED with energy-filter. We also plan to establish an entry-level multiuser cryoEM facility at the LSI, supporting the research needs of local users in order to provide samples for further high-resolution analysis in Bristol and at the Wellcome Trust-funded electron Bio-Imaging Centre (eBIC) at Diamond.

Lay abstract: Electron cryo-microscopy (cryoEM) is an extremely powerful imaging method that has recently undergone a revolution, now enabling direct visualisation of individual cells, organelles and even proteins and small molecules at unprecedented resolution. This means that cryoEM can now be used to gather information on a vast array of important scientific questions that were previously thought of as impossible to attain. Only by a complete understanding of cellular biology, from the range of atoms to cells, can we further our understanding of human health and disease. Due to the exciting new avenues that cryoEM opens up for scientists today, it is essential that the methodology is made more widely available. With this proposal, we aim to expand significantly the capabilities and provide much needed support to a regional facility for high-resolution cryoEM in Bristol, whilst establishing a node for the facility in Exeter. Support and expansion of the regional facility will benefit many scientists in the South West and beyond, and will attract national interest and top-class scientists to the region.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFECTION