NIHRDataInsights/HRCSData huggingface dataset:
Title: Role of STAT1 Cooperative DNA Binding in Interferon Signalling
Funder: Medical Research Council

Abstract: The proposed research seeks to answer the question whether cooperative DNA binding of the transcription factor STAT1 is critical for discriminating signalling of type I IFN from that of type II IFN. Given the often antagonistic activities of both types and their demonstrated different clinical effectiveness against viruses, malignant cell growth, and Multiple Sclerosis, the answer is of importance both for cytokine biology and interferon therapy. Our studies depend upon a novel knockin mouse strain generated in our laboratory. These mice express point-mutated STAT1, whose ability to interact with DNA is unchanged, but which cannot sustain homotypic protein interactions, so that DNA binding cooperativity is lost. This study is thus distinguished by the fact that a transcription factor deficient in cooperative DNA binding is being tested only for the second time in a mammalian system for its ability to carry out its normal in vivo functions. Extensive transcriptome analyses of type I and type II IFN stimulated macrophages expressing WT or the mutated STAT1 will be done using RNA-sequencing. These studies are complemented with STAT1 chromatin binding data from ChIP-sequencing in order to identify the sequence motifs that distinguish the targets for STAT1 dimers and multimers both in type I and type II IFN signalling. To examine the contribution of DNA affinity differences to target gene selectivity we propose to compare the DNA-binding profiles of WT and mutant STAT1. This is done with total internal reflectance fluorescence protein binding microarrays (TIRF-PBM) containing 1 kB-long promoter regions from 200 different IFN-regulated genes. In order to assess the role of STAT1 cooperativity in antimicrobial immunity, and possible differences between type I and type II IFNs in this regard, we propose to study the progression of infections with both bacterial and viral pathogens.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Taking treatment of chronic lifelong conditions to scale: applying the positive deviance approach to health programme management
Funder: Medical Research Council

Abstract: The objective of this proposal is to conduct an interdisciplinary qualitative and quantitative study to address knowledge gaps about retention in care in the antiretroviral therapy (ART) programme in Western Cape, South Africa. This will inform the design of a larger intervention project with stakeholders for improving implementation, at scale, for a national-level programme to achieve high levels of treatment for chronic lifelong conditions (CLLCs). This study will adopt a "positive deviance" approach for implementing health programmes by identifying facilities which are outliers and analysing constraints to good performance for retention in care. We hypothesise that good performance relies on partnerships between the formal health system and community organisations to support disease self-management. The study will address these questions: - What are the most important factors contributing to good performance for retention in care for facilities that are positive deviants in the ART programme? - What are the major constraints to similar performance in other localities and how could an intervention for disseminating lessons from positive deviants help stakeholders overcome them? - Which generic factors from the ART programme could contribute to good performance for other CLLCs? Phase 1 of the study involves desk-based validation of the central database for chronic medication distribution and the routine management data from facilities for HIV. Facilities will be mapped by typology and paired according to an analysis of good and bad performers for retention in care for ART. In Phase 2, facility-level studies will involve investigating the data for HIV and also diabetes, as a tracer condition for all NCD. Qualitative research will explore the reasons for differences between facilities. In Phase 3, data analysis will facilitate communication of lessons learned and Phase 4 will involve a workshop with stakeholders to design a large scale intervention for CLLCs.


Research activity codes: 8.1 ORGANISATION AND DELIVERY OF SERVICES;8.5 RESOURCES AND INFRASTRUCTURE (HEALTH SERVICES)
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: DFID-WT Health Research Capacity Strengthening Initiative in Malawi and Kenya.
Funder: Wellcome Trust

Abstract: DIFD/Wellcome Trust initiative on capacity building in Kenya and Malawi. The initiative for this proposed programme stems from an agreement between Mark Walport of the Wellcome Trust and Mark Lowcock of DFID early in 2004 to seek closer working in areas of common interest in global health research. Such collaboration reflects more general moves towards greater coordination of UK research funding in global health, most clearly marked by the recent establishment of the UK Funders Forum for Health (presently comprising DFID, Wellcome Trust and the MRC). With the establishment of 'centres of excellence' featuring within the strategies of both WT and DFID, it was agreed that the initiative should build upon existing investments and track-record: leading to the decision that the programme should begin its work in Kenya and Malawi. IDRC has a mission to support development through research, and has a track-record in strengthening health systems through enhancement of research capacity and the utilisation of research. This includes implementation of the Tanzanian Essential Health Interventions Project (TEHIP), which demonstrated clear health impacts on District level services of improved knowledge utilisation. Given this track-record, what was initially conceived of as a Wellcome Trust-DFID partnership is now planned as a tripartite venture, with IDRC providing capacity for local implementation and technical support for the initiative. The initiative is conceived of as a single programme that will be implemented in two components; the two components matched to the distinct needs and opportunities in Kenya and Malawi respectively. In Kenya, for example, the Regional East African Community Health (REACH) Policy initiative, provides a unique opportunity for the programme to link with and support a regionally-owned initiative in getting research into heath policy and practice. In Malawi, SWAp implementation and major external investments in human resources and malaria control, provide a differing range of opportunities and needs. Although the two programme components should be coherent with each other in terms of analysis of research capacity issues, the strategies adopted will be distinctive to the extent that they fit with local circumstances.


Research activity codes: 8.5 RESOURCES AND INFRASTRUCTURE (HEALTH SERVICES);8.3 POLICY, ETHICS AND RESEARCH GOVERNANCE
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Interaction of substrates with the E.coli Tat protein export system
Funder: Wellcome Trust

Abstract: The overall aim of this project is to characterise the interactions of Tat substrates with signal peptide binding chaperones and with the TatBC receptor complex, with the intent of using the findings to guide development of assays that can be used in high throughput screening of small drug-like molecules targeting TatBC signal peptide binding. The project will be split into three specific objectives: I. Structural characterisation of the Tat substrate Tor A in complex with its signal peptide binding chaperone TorD using the E. coli and homologous Salmonella protein pairs and using modem structural biology techniques. 2. Investigation of how substrates are handed over to the TatBC complex and development of in vivo and in vitro assays to measure this. 3. Development of an in vitro assay to assess substrate interaction with the TatBC complex that will be used to screen for small molecule inhibitors.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: The fission yeast database PomBase.
Funder: Wellcome Trust

Abstract: Access to accurate and up-to-date annotations of model organisms genomes is a fundamental requirement for both exploratory and hypothesis-driven research. We aim to provide a comprehensively curated Model Organism Database (MOD) for the fission yeast Schizosaccharomyces pombe. Fission yeast is a well-studied fungal eukaryote, for which a large and active research community routinely applies molecular genetic, cell biological, and biochemical techniques (>9000 publications in total). Increasingl y, high-throughput approaches are being applied, generating a concomitant increase in data volume. We request funding (i) to ensure comprehensive and deep curation of the scientific literature, partially supported by an extensive community curation initiative, (ii) to provide a software infrastructure to support curation activities, and (iii) to provide a computational infrastructure to integrate and display the curated data, high-throughput data, and data from other fungal genomes in the co ntext of the Ensembl Genomes project. We will also develop protocols, resources and workflows in support of literature curation activities that will assist other research communities to work with the Chado schema and Ensembl Genomes to construct their own organism-specific databases, for the benefit of their research communities and the biomedical research community as a whole.


Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Membrane remodelling by viral and cellular proteins: Elucidating structure and dynamics of protein complexes in their native environment by cryo electron tomography and complementary approaches.
Funder: Wellcome Trust

Abstract: Each cell in the human body is contained within a surface membrane and its contents is sub-divided into specialised compartments (for example the nucleus) by additional membranes. These biological membranes are not rigid, static walls, but rather they are flexible components of the overall cellular machinery. Using a rather novel structural biology method - cryo electron tomography - we will here aim to analyze how biological membranes are bent and modified in the course of their function. This method allows the visualization of larger complexes of proteins and lipids 'at work' in their native hydrated environment in three dimensions. When combined with light and fluorescent microscopy imaging techniques and high-resolution structural information arising from crystallographic techniques, this provides a powerful tool to analyse the subcellular organisation in new detail. Viruses are able to influence and modify their host cells and to propagate inside them. Studying the way viruses do this, allows not only an understanding of the fine-tuned interactions of viruses with their host cells, but more fundamentally, this provides insights into the organization and regulation of the basic cellular functions.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: In vitro reconstitution and study of Bacillus subtilis DNA replication.
Funder: Wellcome Trust

Abstract: Genomes carry the genetic information for all species. Passing on this genetic information to offspring requires duplication of genomes in an accurate and efficient way. This duplication process necessitates the involvement of a multitude of replication proteins cooperating with each other in a complicated way. Understanding how these proteins act and cooperate with each other at the molecular level is essential if we are to fully understand the process of genome duplication. Bacteria have provi ded model systems to carry out such studies. In particular the B. subtilis bacterium has a duplication mechanism that is similar to the human duplication mechanism employing two polymerases (the enzymes that synthesize new DNA). Here we aim to recreate the complete process of genome duplication in the test tube with all the necessary enzymes. Being able to recapitulate this complicated process in vitro will be an invaluable tool towards our main aim to understand the peculiar and different mecha nisms employed by different species. Revealing such molecular details will aid in the identification of new drug targets and the development of new antibiotics against many pathogenic bacteria that share similar characteristics with the model organism B. subtilis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Polyketide synthases: Structure, specificity and engineering
Funder: Wellcome Trust

Abstract: 1. Expression and engineering of the enzymes responsible for the starter unit of polyether biosynthesis 2. The main focus of the project will be to express genes encoding individual modules involved in the biosynthesis of indanomycin in E.coli and engineer modules of the biosynthetic gene cluster Figure 2- Schematic of domains within modules of multimodular PKS's. Each module will minimally contain a ketosynthase (KS), Acyltransferase (AT) and an acyl carrier protein (ACP). Additionally, they can contain a dehydratase (DH), enoyl reductase (ER) and/or a beta-ketoreductase (KR). These additional domains aid in determination of the extender i.e. keto, hydroxyl, trans double bond or CH2 group. The ACP domain is post-translationally modified by phospho-pantetheinyl transferases (PPTases), aiding in addition of a phospho-pantetheinyl moiety which facilitates chain extension. Chain release is mediated by a C-terminal thioesterase (not pictured above) 3, 4. STU 06/11 Science 8 3. If appropriate, investigate structural characteristics of proteins involved in the biosynthesis of indanomycin


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Genetic and proteomic analysis of human cytomegalovirus-mediated MHC class I immune evasion.
Funder: Wellcome Trust

Abstract: MHC I are protein molecules present on the surface of cells. The immune system uses them to identify cells infected with viruses. Some viruses therefore make their own protein molecules which decrease the expression of MHC I. This helps them evade the immune system. Two such molecules are encoded by the US2 and US11 genes of HCMV. HCMV is a common viral infection of humans, which may cause severe disease in patients with a weakened immune system for example, patients undergoing transplantation , or patients with HIV. US2 and US11 degrade MHC I by hijacking normal cellular machinery. I wish to identify and characterize new components of this cellular machinery. First, I will screen genes in human cells to identify which ones are important for the activity of US2 and US11. Second, I will screen proteins in human cells to identify other targets of US2 and US11. Through investigating how US2 and US11 allow HCMV to evade the immune system, this project will help us understand how cells r egulate the presence of protein molecules on their surfaces under normal circumstances. Such processes are critical for the wellbeing of all cells, and problems with them underlie a range of different diseases.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Molecular architecture of the bacterial actin cytoskeleton.
Funder: Wellcome Trust

Abstract: Bacteria are now known to contain proteins that form fibrous structures on the inside and these proteins are related to similar ones in all other organisms The functions of these fibres in bacteria, however, are different: the two most important functions are facilitating growth by dividing cells into two daughter cells and giving bacteria their distinctive shapes, since they would otherwise be round and spherical. We propose to investigate the second function, cell shape, which is mediated by the MreB protein. MreB is related to another fibrous protein, present in all non-bacterial cells, called actin. We will investigate what fibres MreB forms inside cells by using a microscopy method (electron cryotomography) that allows imaging whole bacterial cells in three dimensions at a magnification that makes molecules visible. We will combine this new knowledge with an investigation of the interactions that MreB forms in cells. Taking all data together, we will be able to determine how the fibres of MreB give bacteria shape. In the future, our knowledge might make it possible to disrupt this process using drugs, killing bacteria.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Phospholipid transport and membrane formation in Plasmodium falciparum: investigation of the phospholipid transfer protein PFA0210c.
Funder: Wellcome Trust

Abstract: I aim to investigate how a protein in the malaria parasite Plasmodium falciparum, called PFA0210c, allows the parasite to grow inside red blood cells. Within red blood cells the parasite forms large structures that aid in the uptake of nutrients. To make them, the parasite needs to provide phospholipids, the building blocks of these structures. PFA0210c has been shown to bind phospholipids and transfer them between membranes, and therefore may play an important role in the formation of these str uctures. The experiments proposed in this application investigate how PFA0210c transfers phospholipids, where exactly it is located in the parasite and the infected red blood cell (which will provide important information regarding its function) and the effect of inhibiting or removing the protein. Ultimately, this may lead to the development of new drugs against malaria.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Neuroendocrine control of environmental stress responses by Drosophila and insect disease vectors
Funder: Wellcome Trust

Abstract: Insects are hugely successful global vectors of disease and can withstand sevesevere environmental stress. This is partly due to a uniquely impermeable cuticle and to adaptive behaviours that minimize water loss; however, osmoregulatory systems may also be adapted for water conservation and alter iotheir functions when challenged by dehydration. Working in Drosophila neuroendocrinology, cell signalling and osmoregulation in the Malpighian em, atubules, the key tissue for fluid transport in insects, we have recently identified a desiccation-responsive G-protein coupled receptor, capaR. This hureceptor modulates whole fly responses to desiccation stress (Terhzaz et al., 2012), demonstrating that minimising water loss through fluid homeostasis by epithelial tissues is a distinct and effective route for desiccation resistance. We also have preliminary evidence that such pathways operate in a Dipteran disease vector, the dengue fever mosquito, A. aegypti, in which capaRsignalling is conserved (Pollock et al., 2004). Understanding environmental stress response mechanisms in insects is of fundamental scientific importance,


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Structure and mechanism of multicomponent protein-nucleic acid assemblies.
Funder: Wellcome Trust

Abstract: Proteins and the nucleic acids, DNA and RNA, play key roles in the function of biological systems in living organisms The way protein-nucleic acid assemblies do their chemistry and work in the body is scientifically both interesting and important but also matters medically, since their mal-functioning is often linked to disease. Our understanding about the way these assemblies work strongly relies on knowing their three-dimensional structure in enough detail to see the atoms involved in their a ctions. At present one of the best ways of visualizing structures of biological molecules and their complexes is X-ray crystallography, in essence providing a microscope through which we can see these molecules magnified around ten million-fold. This can provide detailed structural information about the overall organization, about atoms, their environments and their roles in reactions in the body. I aim to apply X-ray crystallography and complementary biochemical and biophysical techniques to st udy how viruses stuff their capsids with DNA and to understand mechanisms involved in RNA modification. I will also seek how best to translate structural knowledge into medical applications.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Cytoskeletal cargo transport by cytoplasmic dynein: structure and function.
Funder: Wellcome Trust

Abstract: The aim of the research proposed is to categorise and image the interactions between the dynein microtubule motor, the microtubule and the cargo. In the case of this project, the cargo is primarily herpes viral capsids. We aim to reconstitute the processive dynein/dynactin motor complex recombinantly, and assemble it in vitro with track (microtubules) and cargo (capsids) then image it using a combination of electron cryo-microscopy/tomography. Further, this work will be complemented by a slough of techniques that aim primarily to visualise dynein-mediated transport in vivo. These techniques include electroncryo-tomography of cellular samples, correlative cryo-light electron microscopy (CLEM) as well as live-cell fluorescence microscopy. The key goals are: Determine the ultra-structural details of the dynein/dynactin complex bound toassociated cargoes, including that of HSV-1 capsids. Determine the microtubule-bound structure of the dynein/dynactin complex. Attempt reconstitutional assembly of dynein/dynactin-assisted capsid transportalong microtubules in vitro and provide structural information on the interactions. Produce structural information on the complex in a cellular setting, and relate this to global positioning and dynamics in a cellular context.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;INFECTION