NIHRDataInsights/HRCSData huggingface dataset:
Title: Molecular and cell biological mechanisms mediating re-establishment and maintenance of cell polarity in the developing CNS
Funder: Medical Research Council

Abstract: Cells differentiating into neurons in the developing spinal cord undergo an acute loss of apical polarity during delamination from the neuroepithelium through the regulated process of apical abscission. The nascent neuron must now rapidly re-establish polarity to determine the position of axon outgrowth. Correct positioning of the nascent axon is crucial, as it will ultimately lead to the formation of functional neural circuits. However, the molecular mechanisms that re-specify the first neuron asymmetry following the acute loss of polarity mediated by apical abscission, and how this asymmetry is sustained remain unclear. These important biological questions will be studied using cutting-edge methods to image spinal cord neurogenesis in real time at high spatial and temporal resolution in ex-vivo tissue slices, allowing observation of dynamic cell-biological processes in individual cells within the developing spinal cord. This assay will therefore allow observation and manipulation of neuron repolarisation within the developing tissue, and and has already started to uncover novel and exciting cell biological behaviours that only take place within a tissue context. Specifically, in this project I will: i) Determine the role of the centrosome during neuron repolarisation and axon extension. ii) Determine the role of the primary cilium during neuron repolarisation and axon extension. iii) Determine the molecular events specifying early neuron asymmetry. Overall, this proposal will advance our understanding of the molecular and cell-biological events involved in the reestablishment and maintenance of polarity in newborn neurons in response to extracellular cues from surrounding tissues. Additionally, these studies will ultimately also be valuable for future studies in other contexts where cells undergo repolarisation events, including mesenchymal to epithelial transitions (MET), wound healing and tumour cell metastasis.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Genome-wide exploration of reprogramming mechanisms using CRISPR/Cas9 and DamID technologies
Funder: Medical Research Council

Abstract: Ever since the first generation of iPSCs about a decade ago, the most robust reprogramming strategy to establish a pluripotent state is still induction of the 4 Yamanaka factors. Nevertheless, only a handful of genes have been demonstrated to be detrimental or essential for reprogramming. It has also not been shown which genes are directly targeted by the Yamanaka factors at different stages of reprogramming. Thus, this project aims to illuminate molecular mechanisms of reprogramming by 1) performing CRISPR/Cas9-mediated genome-wide knockout screening and 2) dissecting changes of direct targets of the Yamanaka factors during reprogramming with inducible mouse DamID-seq technology. One of the difficulties to investigate the molecular mechanisms of reprogramming is the low efficiency and heterogeneous cell populations during the process. To circumvent these problems, we have identified cell surface markers that allow us to isolate more homogenous reprogramming intermediate subpopulations than simple time course analyses. In addition, we have established a system where robust and homogenous expression of the Yamanaka factors can be induced in mouse embryonic fibroblasts with constitutive expression of Cas9 by administration of doxycycline. We will apply lentiviral gRNA library containing 90,000 gRNAs targeting all protein coding genes in the mouse genome to identify genes detrimental or essential for efficient reprogramming. For the second objective, we have been optimizing DamID-seq technology, which has often been used in Drosophila, in mouse cells. DamID-seq is a complementary technology to ChIP-seq, with an advantage of being able to perform with smaller starting cell numbers due to the absence of the antibody-mediated pulling down step. Through this project we aim to improve the human iPSC derivation technology and identify molecular mechanisms that can be applicable for the swift and efficient generation of various cell types important for medical applications.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: New Antibiotic Targets in Bacterial DNA Double-strand Break Repair
Funder: Medical Research Council

Abstract: DNA replication and repair is are essential processes in all organisms but are surprisingly different between eukaryotes and eubacteria. This proposal seeks to examine targets within the DNA double-strand break (DSB) repair for antibiotic development. A key component in bacterial DSB repair is the RecBCD/AddAB system that processes broken ends to prepare them for repair by homologous recombination. Using structural information gathered over the last 10 years we have identified a weakness in the AddAB mechanism that might be exploited. Extending our understanding of the mechanism and regulation of these complex systems will likely reveal additional opportunities for antibiotic development. In particular, understanding of specific aspects of regulation of RecBCD may provide opportunities for drug development. Quinolone antibiotics act upon DNA gyrase by stabilising a normally transient DSB during the enzyme mechanism. Mutations of a number of proteins other than DNA gyrase that are involved in DSB repair show sensitivity to quinolones and combinations will be sought that enhance sensitivity to quinolones in strains that carry mutant forms of RecBCD or AddAB that have lost regulation by Chi sequences. Finally, two new players in DSB repair in bacteria have recently been identified. I propose to determine the molecular mechanism of these proteins to seek opportunities for exploitation in drug development.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Elucidating the Cep135 - CPAP- STIL protein interaction network behind primary microcephaly and centriole formation
Funder: Medical Research Council

Abstract: Centrosomes are cell organelles necessary for division, motility and signalling in many species including humans. They organize the mitotic spindle, the microtubule network, cilia and flagella, and defects in their formation are linked to ciliopathies, male sterility or even cancer. Crucially, centrosomes are implicated in hereditary primary microcephaly, a bona fide genetic neurodevelopmental disorder. There, abnormalities in the timing and outcome of cell divisions by neuronal progenitor cells lead to reduced cerebral cortex size. Centrosomes directly control crucial aspects of the cell division process, thus understanding how centrosomes, and their components, centrioles, form has attracted world-wide interest. Structural and functional studies have shown that a single protein, SAS-6, oligomerises into an initial assembly that defines the overall centriolar symmetry. However, we have relatively little mechanistic information on what follows SAS-6 oligomerisation. Here, we propose to study the essential proteins Cep135, CPAP and STIL. These proteins form an interaction network upstream of SAS-6, link to the initial SAS-6 framework and are implicated in primary microcephaly. Our approach initially utilises protein dissection to resolve high-resolution structures (by crystallography or NMR) of individual domains and protein complexes. We then employ biophysical methods (including crosslinking assays and EM) to place the domain and complexes in the context of full-length proteins and of the whole interaction network. The structural and mechanistic insights gained in this manner will then be tested in human cells by collaborating laboratories, thereby checking the functional significance of our models.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Mitochondrial Dynamics in the Control of the Pluripotent States
Funder: Medical Research Council

Abstract: Understanding how pluripotent stem cells initiate differentiation is a key question not only for developmental and stem cell biology, but is also essential for the use of stem cells in regenerative medicine. Over the last few years, significant research efforts have been focussed on analysing the signalling, transcriptional and epigenetic landscape of pluripotent stem cells, as well as unravelling the molecular changes that underpin the initiation of differentiation. In contrast to this, very little is understood about how pluripotent cells adapt their organelle activity to the new environments they face during the onset of differentiation. Of specific interest, given their fundamental role in determining the cells apoptotic response and metabolic output are mitochondria. We have found that at the onset of differentiation, pluripotent stem cells dramatically change their mitochondrial morphology and dynamics, and that accompanying these changes they modify their response to cell death stimuli and metabolism. Here we will investigate in both mouse, and humans, using a combination of stem cell and embryological approaches, the links between these events. In the first place we will study in detail the precise changes that occur in mitochondrial morphology and dynamics as cells exit the pluripotent state. We will then manipulate mitochondrial dynamics and study how this affects the metabolism of pluripotent stem cells, their ability to respond to cell death stimuli, and their developmental potential. Finally, we will exploit the significant knowledge of the signalling pathways that maintain pluripotency and that drive differentiation, to identify novel signalling inputs that regulate mitochondrial dynamics and function in stem cells. Together, these experiments will provide a unique insight into an essential, but understudied aspect of early embryonic development, the dynamics of the mitochondria, as well as addressing how they impact on the process of differentiation.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Three-dimensional interrogation of gene regulation using next generation chromatin conformation capture and super-resolution imaging.
Funder: Medical Research Council

Abstract: Next Generation Sequencing has allowed us to investigate the structure and function of the genome at unprecedented detail. In particular, chromatin accessibility assays (DNAse-seq and ATAC-seq) produce comprehensive maps of the active regions of the genome and ChIP-seq allows sub-classification by chromatin signature which infers potential function. This has revealed an unsuspected level of complexity in the regulatory landscape of the genome with estimates of ~ 2M potential regulatory elements to control ~20,000 genes. GWAS studies have mapped the majority of disease susceptibility variants to the non-coding portion of the genome suggesting that regulatory elements may be their major targets. However finding which genes these regulatory elements are controlling and how this is achieved is a major challenge, mainly due to the unpredictability of both their number and distribution around their cognate genes. It has been shown that although these elements affect multiple genes, they may "ignore" neighbouring genes in favour of more distal genes. Chromosome conformation capture-based technologies link regulatory elements and genes via their physical interaction, but do not explain why some interactions are favoured and others prevented. As the physical interactions of these elements are thought to be required for their function, this represents a fundamental mechanism for specificity and selectivity. Such interactions, in turn, are likely related to the overall 3D structure of the genome. As small changes in non-coding sequence can have major effect on gene expression, and considering the amount of observed genome variation, it is essential to understand the mechanisms by which regulatory elements work. We propose to develop new technologies to visualize specific regulatory interactions at unprecedented levels of sensitivity and resolution, so that regulatory elements can be seen interacting within the context of the surrounding chromosomal landscape.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Comparative evaluation of Spatio-Temporal Exposure Assessment Methods for estimating the health effects of air pollution (STEAM)
Funder: Medical Research Council

Abstract: The aim of this study is to develop, validate and compare three integrated air pollution exposure assessment methods for estimating simultaneously the health effects of short and long-term exposure to outdoor air pollutants. The dispersion model will use CMAQ-urban which couples the USEPA regional model, CMAQ and the Atmospheric Dispersion Modelling System roads model incorporating emissions data. This combined model will provide hourly predictions at 20x20m spatial resolution for Greater London for PM10, PM2.5, NO2 and O3. Spatio-temporal LUR models for PM10, PM2.5, NO2 and O3 will use a semiparametric approach with covariates that vary primarily in space (e.g. distance to major road, traffic counts) and covariates that vary primarily in time (e.g. meteorology) and a bivariate smooth thin plate function for the geographical co-ordinates. New methods, similar to Chudnovsky 2014, will use a hybrid model, with AOD, land use, and meteorological data to estimate daily PM2.5. Spatial predictors will include population and traffic density, land use (Landsat) and emissions as well as time varying predictors (e.g. vegetative index from MODIS, meteorology). Each method will be evaluated using simulation techniques developed from previous work. We propose to construct scenarios where 'true' temporally and spatially resolved air pollution data are associated with health outcomes by a priori defined concentration response functions (such as those proposed by W.H.O. HRAPIE project). Model performance will be assessed under a variety of scenarios using a number of parameters including bias, statistical power and coverage intervals. Finally the model predictions will be used in conjunction with selected health outcomes to demonstrate proof of concept in estimating simultaneous associations between health outcomes and long- and short-term exposure to air pollution.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: The Mechanics of Wound Healing and Tissue Regeneration
Funder: Medical Research Council

Abstract: It is crucial that organisms can sense and respond to wounding in order to maintain tissue continuity. This can involve the superficial closure of a wound or, in some instances, the regeneration of lost structures. Slow or absent wound healing responses can lead to ulceration and increases the risk of infection, while "over-healing" is thought to be a cause of keloidal and hypertrophic scars. Much work has demonstrated that biochemical signals are required for wound healing and regeneration. However, more recently it has become clear that cells also respond to mechanical stimuli. I therefore aim to explore the mechanical basis of wound healing and regeneration. I will live image cell behaviours and cytoskeleton protein localisations in healing and regenerating Drosophila wing imaginal discs. I will quantitatively analyse time-lapse images of cell behaviours and protein localizations over a time course using the recently developed EpiTools software (Mao, Hoppe and Basler groups) to inform on where forces are likely to be acting within the healing tissue. I will also directly measure mechanical forces using a combination of junctional laser ablation, in vivo tension sensors and force inference software. To demonstrate how these forces contribute to the wound healing process, I will combine mechanical perturbation of wing discs with computational modeling. I will stretch healing wing discs using a bespoke device developed by the Mao and Piel groups and test whether the application of an ectopic force alters wound healing dynamics. I will further test how changing the force balance in wing discs might affect wound healing by using a computational vertex model previously developed by Yanlan Mao. By understanding the mechanical basis of wound healing and regeneration, it will then be possible to develop targeted mechanical therapies to treat wound-healing related disorders.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Using a Complex Systems Approach to Understanding Population Mental Health.
Funder: Medical Research Council

Abstract: AIM: The research project will aim to describe, model and explain the implications for general health and mental health of dynamic neighbourhood contextual and compositional factors. This will be achieved using longitudinal and spatial statistical approaches augmented with methods from Urban Informatics. OBJECTIVES: (i) To explain the pattern of flows of individuals between neighbourhoods according to psychological health and its social and biological antecedents, over time. (ii) To analyse the health and socio-economic trajectories of neighbourhoods over time, according to individual exposure to neighbourhood change. (iii) To model the key individual and environmental factors complicit in explaining population change, particularly focusing on neighbourhood systems related to crime and disorder and economic insecurity, and to assess whether these factors exacerbate inequalities in mental health and wellbeing. (iv) To synthesise findings from objectives i-iii in specifying a mathematical model that operationalises the neighbourhood as a dynamic complex system using spatial flows describing population mobility, disaggregated according to neighbourhood health status and trajectory. Population movement will be explored subject to a range of neighbourhood change scenarios that will be developed. METHODOLOGY: The outcomes of interest are: general health (SF-12), psychiatric morbidity (GHQ-12); and positive mental wellbeing (WEMWBS). Exposures of interest relate to changes in the individual and neighbourhood social and biological antecedents of health and wellbeing. The project will make use of the longitudinal survey "Understanding Society", the UK Census of Population for 2001 and 2011, Census Flow data for 2001 and 2011, a range of open and free administrative data resources, authoritative Ordnance Survey Spatial Reference Data, and the newly funded Administrative Data Research Centre for England (ADRC-E) and Consumer Data Research Centre (CDRC).


Research activity codes: 1.2 PSYCHOLOGICAL AND SOCIOECONOMIC PROCESSES
Health categories: GENERIC HEALTH RELEVANCE
Title: Investigating deliberative methods for setting a monetary capability threshold in the context of social care and public health
Funder: Medical Research Council

Abstract: The capability approach is a normative framework which forms a basis for measuring wellbeing. There is increasing interest in using the capability approach in contexts of social care and public health, where reliance on a narrow assessment of health functioning will provide a partial view of the effects of interventions (which are typically broader in their scope and impact). However, as a conceptual framework, the capability approach is incomplete. One unresolved question relates to the choice of decision-rule. Maximisation of health gain is used by NICE; various forms of shortfall sufficiency have been advocated by some capability theorists. The ICECAP-A is one capability measure recommended by NICE for evaluating social care interventions. Tariff values exist for the ICECAP-A, elicited through best-worst scaling and anchored between zero (no capability) and one (full capability). I will use public deliberation methods to elicit a monetary threshold value for use with ICECAP-A. The first phase of the project will involve the public in setting a sufficient level of capability, a level below which individuals would be prioritised for state funded support. The existing tariff values can then be rescaled such that zero is equivalent to no capability and one is equivalent to sufficient capability. From this, we can adopt a common metric of years of sufficient capability. The next phase (again using deliberative methods, but with the public and policy-makers) will elicit an arbitrated societal monetary value for a gain in wellbeing of one year of sufficient capability. This value can be used as the social care equivalent to the £20k-£30k QALY threshold, adopted by NICE for healthcare. An aggregation of individually formed values, elicited through an online survey, will be compared to the arbitrated social value from the workshops. The arbitrated monetary threshold will be applied to a number of case studies where existing data is available.


Research activity codes: 8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES)
Health categories: GENERIC HEALTH RELEVANCE
Title: Understanding and enhancing approaches to quality improvement in small and medium sized private facilities in sub-Saharan Africa
Funder: Medical Research Council

Abstract: Innovative approaches are needed to assess quality and institutionalize quality improvement in private facilities, but rigorous evaluation of such interventions is very limited, with a particular lack of controlled designs. This study will provide new evidence on the PharmAccess model of quality improvement. The research is based on a well-articulated theory of change, linking PharmAccess activities to outputs, outcomes and impacts, and draws on both quantitative and qualitative data: - to examine changes in adherence to SafeCare standards in participating facilities to date, we will analyse the PharmAccess database which contains SafeCare scores across multiple dimensions, facility characteristics and implementation measures for at least two time points for 300 facilities in Kenya and Tanzania, using panel regression methods to identify factors associated with improvements in scores. - to evaluate the impact of PharmAccess on process quality of care we will conduct a prospective randomised controlled trial in Tanzania. Intervention facilities will receive the full PharmAccess package, while control facilities receive SafeCare assessments only with no further action. The primary outcome will be technical process quality at follow-up, with secondary outcomes of SafeCare scores, perceived quality, and business performance. The primary outcome will be measured using standardised (covert) patients and clinical role-playing vignettes. - to understand experiences and perceptions of participating facilities we will conduct in-depth interviews with staff from 30 purposively selected intervention facilities, and 8 implementing staff. - In addition to improving quality in participating facilities, PharmAccess aims to make the broader market and policy environment more conducive to the operation of a high performing private sector. We will investigate these potential effects through 30 key informant interviews with stakeholders in Kenya and Tanzania


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