NIHRDataInsights/HRCSData huggingface dataset:
Title: CDK-containing macromolecular assemblies
Funder: Medical Research Council

Abstract: Cyclin-dependent protein kinases (CDKs) play an orchestrating role in cellular processes that include transcriptional regulation and the control of cell-cycle progression. Aberrant CDK activity is implicated in diverse clinical conditions including cancer, stroke, neurodegeneration and HIV infection. Whereas CDKs isolated ex vivo are found in large, multi-protein complexes, the prevailing understanding of the CDK structure-function relationship has largely been deduced from the study of variously phosphorylated monomeric or cyclin-bound CDKs. We aim to extend available understanding of the composition, structure and functional properties of the multiprotein complexes that characterise the different CDKs. In particular we will develop a structural view of the complexes that localise and regulate CDK7 and CDK9 activity in transcriptional control, selected complexes that contain CDK4 and CDK6 and coordinate cell-cycle progression with checkpoint and apoptotic pathways, and complexes of CDKs 1 and 2 that coordinate their activity with the ubiquitin-proteolysis system.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Development of a Methodology Hub for the island of Ireland
Funder: Medical Research Council

Abstract: The overarching aim of this proposal is to develop a Methodology Hub, based in Belfast, which will lead the development of clinical trial methodology on the island of Ireland. The Methodology Hub, when established, will: 1) Develop beacons of excellence in specific areas of trial methodology research. 2) Build training capacity, on an all-island basis, in novel methodologies that span a range of complex intervention types, with an emphasis on translation to improve practice and health outcomes. 3) Improve patient care by strengthening the relevance and validity of the healthcare evidence base, with specific reference to healthcare needs and priorities on the island of Ireland. 4) Establish strong collaborative networks with established Methodology Hubs within the UK and with centres with relevant expertise throughout Ireland. This proposal seeks to build on existing clinical research infrastructure and investment to facilitate the development of a world-class environment for conducting methodological research. The Hub will aim to improve the design, conduct and analysis of clinical trials and will establish training programmes to develop the next generation of clinical trialists, trial methodologists and clinical trial personnel. A programme of work will be carried out to increase the validity and relevance of early and late phase clinical trials through improved design, conduct and analysis, initially in relation to cancer, vision, public health and nutrition, with a particular emphasis on behavioural modification and complex interventions. The Director and other Hub staff will develop a balanced methodological research portfolio, generated and supported by a broad team of clinical investigators. Mutually beneficial collaborations will be developed with industry where appropriate, and strong linkages with trialists and policy makers throughout Ireland and the UK in order to ensure the dissemination and rapid application of research findings. These linkages will ensure that a research agenda for trial methodology can be maintained which is informed by the needs of the research community.


Research activity codes: 8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES)
Health categories: GENERIC HEALTH RELEVANCE
Title: Transcription factor dynamics in control of pluripotent cell function and identity
Funder: Medical Research Council

Abstract: We have shown that undifferentiated ES cells fluctuate between states in which they do or do not express the transcription factor Nanog and that these states are differentially responsiveness to differentiation cues. This raises several questions that form the basis of this proposal. Our overarching aim is to examine the function of pluripotency transcription factors at genes that critically modulate self-renewal efficiency. This will allow us to determine how the pluripotent population is compartmentalised into cells that self-renew efficiently and cells that are responsive to differentiation cues. Such knowledge is important because safe application of stem cells for regenerative therapies demands strict control of stem cells, so that their behaviour can be predictably and uniformly directed. We start from the premise that the molecular machinery of distinct pluripotent cell compartments is controlled by transcription factors that direct expression of the appropriate gene set. We will analyse the interdependencies of chromatin binding of pluripotency transcription factors and will identify genes that distinguish between ES cells of high and low self-renewal efficiency. We will determine which of the differentially expressed genes is responsible for the differences in phenotype by modulating the expression of these target genes. We will determine whether enforced expression of pluripotency regulators that control such target genes can complement the self-renewal efficiency of the low-efficiency compartment. We will analyse transcriptional controls operating at the Nanog gene that may influence Nanog heterogeneity and will relate these to chromatin states in Nanog expressing and Nanog non-expressing cells. We will assess single cells to determine the co-ordination between Nanog and other fluctuating genes and will assess the effect of altering transcription factor stability on the dynamics of heterogeneity. We will also extend our studies to epiblast stem cells cultured in vitro to determine whether overlapping mechanisms govern the identity of cells which can readily and quickly be derived from ES cells and will examine hypotheses that arise in the course of the studies to determine the relevance of our findings to cells in the embryo. We anticipate that these studies will lead to a deeper understanding of the mechanisms governing pluripotent cell function and that such knowledge can be used to advance the safe application of pluripotent cells for regenerative medicine.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Analysis of SNARE protein spatio-temporal dynamics during exocytosis in living cells
Funder: Medical Research Council

Abstract: Mammalian regulated exocytosis requires an essential set of proteins; the plasma membrane tSNAREs syntaxin and SNAP-25 and the vesicle resident vSNARE synaptobrevin. The interactions between these proteins have been well characterised in vitro. However, the cellular temporal and spatial organisation of these interactions remains unknown. In order to address this, we will determine the following, using a variety of complimentary techniques, in living neuroendocrine cells in real time: 1. What is the spatio-temporal organisation of the binary tSNARE complex in cells? 2. Do SNARE cluster heterogeneities influence docking site selection? 3. How are the SNARE proteins arranged when an LDCV is present? 4. How are SNARE spatio-temporal interactions influenced by accessory proteins? In this project we aim to deliver a detailed description of tSNARE protein dynamic interactions in living cells, before and after the moment of vesicle fusion, and examine any effects accessory proteins may have on these interactions. These data are essential to further our understanding of exocytosis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Maintaining Genome Stability: Genetic Recombination, DNA Repair and Chromosome Biology Initiated by DNA Misfolding
Funder: Medical Research Council

Abstract: Controlled DNA misfolding is a powerful new tool to initiate DNA repair at a precise chromosomal locus. Our current programme has taken us to the point where we have substantial understanding of the processing pathways of misfolded DNA in the model organism E. coli. For the first time, this knowledge enables us to use DNA misfolding in the chromosome to investigate fundamental aspects of genetic recombination, DNA repair and chromosome segregation. This work is essential, as little is currently known about the physical or cell biological aspects of these processes in a chromosomal context. We will use DNA palindromes to study DNA double-strand break repair (DSBR) and the mechanism of chromosome segregation, whereas we will use trinucleotide repeats to investigate DNA mismatch repair. We will determine the nature of the intermediates generated during DSBR, visualise the repair in real time in live cells using fluorescence microscopy and relate this to protein-DNA and protein-protein interactions. Importantly, the palindrome system is unique as it generates DNA double-strand breaks at a high frequency (once per replication cycle) and on only one of the replicated sister chromosomes, which ensures efficient repair from the un-cleaved sister. Coupling this system with DNA analysis on gels and by flow cytometry, new methods of investigating protein-DNA and protein-protein interactions using Solexa DNA sequencing and mass spectroscopy and new methods of visualisation using fluorescently labelled repressor proteins bound to copies of their operator sites (FROS) provides a powerful and integrated way to investigate DSBR. Similar approaches will be taken for the study of DNA mismatch repair at trinucleotide repeat sequences. We will investigate whether the accumulation of single-stranded DNA caused by a ?futile? mismatch repair reaction relates to the origin of chromosome fragility. Finally, we will determine the genetic basis for the segregation of leading- and lagging-strands to specific cellular destinations and distinguish regions of the chromosome that segregate through pulling or pushing forces. By using the very simple and powerful E. coli system, we can push back the boundaries of fundamental knowledge. To validate our understanding in a eukaryotic cell and to extend our understanding in the context of chromatin, we will transfer and investigate our constructs in the fission yeast S. pombe. Through this work, we will generate understanding relevant to both prokaryotic and eukaryotic biology and to human health


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Tools for Characterizing Multi-Pollutant Patterns of Exposure for Use in Environmental Health Studies
Funder: Medical Research Council

Abstract: There is now extensively reviewed evidence linking chronic air pollution exposures to all-cause, cardiovascular and respiratory mortality. However, such studies typically examine pollutants singly or in two pollutant models since the highly inter-correlated nature of air pollutants makes it difficult to examine their combined effects on health. However, air pollutants occur in complex mixtures consisting of highly correlated combinations of individual components, which makes marginal, single pollutant models inadequate. The objectives of this proposal therefore focus on the development of new, advanced multi-pollutant methods for investigating the health effects of gaseous and particulate air pollution exposures including metal components of particulate matter, and demonstrating their use in examining the combined effect of these pollutants on health outcomes and associations with deprivation. The methods will be developed and applied as part of the new MRC-HPA Centre for Environment and Health at Imperial College London and King s College London. Our overall modelling approach is to cluster joint patterns of air pollution exposures, denoted as an air pollution profile, utilizing recently developed powerful Bayesian dimension-reduction techniques to characterize the pollutant patterns. For some applications, we will then link clusters of exposure profiles to outcomes of interest via a regression model, taking into account relevant confounders. Inference is then based on the joint pattern of pollution exposures and will be implemented via a unified Bayesian modelling framework. We will demonstrate the benefit of using multi-pollutant profiling methods to characterize patterns of air pollution exposures and relate these exposure patterns to indicators of health and socio-economic status using data from the Office for National Statistics. Exposure estimates of NO2, NOx, PM2.5, PM10, and Ozone will be made available from the Environmental Research Group, King?s College London. Health and deprivation data for London will come from the Small Area Health Statistics Unit (SAHSU) at Imperial College, which holds postcoded mortality, hospital admission and cancer registration data and Census derived small area level measures of deprivation. Further, we will exploit the methods developed to examine relationships between traffic concentration and patterns of metal exposures obtained from 16 monitors placed throughout London. The methods developed in this project will be made available to other researchers for use on their datasets, and the substantive results obtained will be of value to health researchers and policy makers. The research programme has thus a strong methodological as well as substantive component, which we believe will help advance this important field.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: GENERIC HEALTH RELEVANCE
Title: Chromosome dynamics during the G2/M transition in meiosis
Funder: Medical Research Council

Abstract: The synaptonemal complex is a tripartite proteinaceous structure that connects homologous chromosomes lengthwise during midprophase/pachytene. Its disassembly is the first, dramatic hallmark of the progression of cells to the first meiotic nuclear division. At this time, crossovers are observed in molecular assays and chiasmata become cytologically distinguishable. Monopolin loading has also taken place, facilitating that sister kinetochores co-orient. All of these events promote homologous chromosomes to segregate to opposite poles during the first meiotic division, thereby avoiding aneuploidy formation in the gametes. We propose to determine how these events coordinated with cell cycle progression. We have recently demonstrated that two highly conserved kinases, Ipl1/Aurora kinase and Cdc5/Polo-like kinase, promote SC disassembly. In ipl1Aurora mutants, SCs are retained in 80% of cells that have transited to diplotene or metaphase I. However, crossover completion and cell cycle progression occur normally, suggesting that Ipl1Aurora links SC disassembly to other events occurring upon pachytene exit. The SC disassembly defect is different in cdc5Polo mutants: numerous, distinct, SC foci are retained at post-pachytene stages. These observations suggest that SCs may not be homogenous structures and that at least two mechanisms promote disassembly. In this programme of work, we propose to study SC disassembly and the integration with crossover formation in the model organism budding yeast. Budding yeast has proved a very good model for understanding crossing over and the SC in higher organisms, including mammals. We have designed cytological, molecular, and proteomic experiments to assess how the SC disassembles, where in the genome Zip1 is retained in the ipl1Aurora and cdc5Polo mutants and how Ipl1Aurora might be regulated. Furthermore, we have developed protein kinase assays that should allow us to identify Ipl1Aurora and Cdc5Polo-specific phosphorylation events, with a view to understand the mechanistic regulation of SC disassembly and crossover formation. We have set up relevant collaborations for the various techniques with world leaders in their fields in order to maximize the probability of success. We envision that our studies will provide valuable insights into a basic biological phenomenon in addition to generating a good model system for understanding meiotic regulation in humans.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Structure, folding and evolution of alpha-helical transmembrane proteins
Funder: Medical Research Council

Abstract: Transmembrane (TM) proteins are involved in a wide range of important biological processes such as cellular signalling, transport, communication and adhesion. Many are also prime drug targets - it has been estimated that over half of all drugs currently on the market target TM proteins. However, due to experimental difficulties, this class of protein is severely under-represented in structural databases, making up less than 2% of known structures in the PDB. The biological and pharmacological importance of TM proteins highlights the need for accurate theoretical structure prediction methods for TM proteins to address this shortfall. In the absence of structural data, bioinformatic strategies turn to sequence- based prediction methods. In this project, I will develop novel prediction tools to aid the identification of structural features involved in pore formation and oligomeric interactions, which, when combined with my topology and helix packing tools, will allow prediction of TM protein quaternary structure for the first time. A genome scan for TM proteins containing pore-forming structures may lead to the identification of novel ion channels which represent an important class of targets for pharmaceutical intervention in a range of diseases including diabetes, hypertension and epilepsy. An analysis of TM protein subunit interactions, combined with a systems biology approach, will also provide insight into TM protein evolution, quaternary structure symmetry and assembly pathways - areas where, compared to soluble proteins, relatively little is known. Additionally, I will analyse stoichiometry and symmetry, implicated in function and regulation, while furthering our understanding of protein aggregation within membranes which is linked to a plethora of clinical syndromes including Alzheimer‘s and Parkinson‘s disease. By combining our novel prediction tools, I will adapt and optimise the FRAGFOLD ab initio method to predict TM protein three-dimensional structure. This will also involve the development of TM protein-specific energy functions and the use of molecular dynamics simulations in order to accurately assess model quality. Collaboration with NMR and X-ray crystallography groups will provide opportunities to validate our methods. This project has the potential to significantly enhance the accuracy of current structural models of TM proteins, which today are largely restricted to two-dimensional topology maps. Recently we have modelled the Batten disease protein which has helped direct further experimental work into this incurable illness. With novel tools we hope to model such disease related proteins at higher resolutions to the point where the application of medicinal chemistry becomes a reality.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: New computational methods for protein function prediction using structural, binding and sequence data
Funder: Medical Research Council

Abstract: Structural Genomics projects determine a large number of protein structures that have little or no functional information associated with them. Therefore, there is an increasing need for tools to analyse and characterise the possible functional attributes of such structures. The main objective of the proposed research is to investigate, implement and validate new methods for protein function prediction exploiting the fast growing volume of publicly available structural, binding and sequence data. A full suite of protein function prediction tools (ProFunc) based on principles such as having similar sequence, fold or binding sites has been recently developed at the European Bioinformatics Institute (EBI). Experience shows that no single method, either sequence-based or structure-based, provides a high proportion of correct predictions in all cases. Furthermore, methods exploiting binding data are not currently incorporated to this holistic effort. This is in contrast with the imminent availability of StARLite, a medicinal chemistry database containing vast bioactivity data, which constitutes an extremely valuable resource for the development of such methods. In order to fill this gap, a new method for protein function prediction exploiting StARLite binding data will be investigated and ultimately integrated with ProFunc using an automatic consensus protocol. This class of methods are based on the principle that protein binding similar sets of molecules are likely to have similar biochemical function, which means that their effectiveness is limited by our ability to predict protein-ligand binding via docking techniques. The candidate has recently developed a very promising machine learning based improvement to docking. The massive volume of structural and binding data that will be used for machine learning training, allied with the availability CREDO?s detailed characterisation of inter-molecular interactions, means that the methodology will be made even more accurate in the course of the fellowship. The successful outcome of the proposed research will represent a major advance in our ability to predict the biochemical function of new structures from Structural Genomics projects. Also, this investigation is expected to increase our understanding of what combination of structural, binding and sequence features confer biochemical function. Furthermore, the proposed chemogenomics studies will improve drug target validation and polypharmacological drug lead profiling. In addition, improved docking will permit more effective identification of biologically active molecules as a way to reduce expensive and slow empirical High-Throughput Screening. Overall, the widespread application of these methodologies would strongly contribute to the understanding and exploitation of biological systems (e.g. pharmaceutical discovery).


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