NIHRDataInsights/HRCSData huggingface dataset:
Title: Alpha-helical peptide hydrogels as instructive scaffolds for 3D cell culture and tissue engineering
Funder: Biotechnology and Biological Sciences Research Council

Abstract: To achieve our overall aims of (a) producing a reliable recombinant system for the production and development of fibrous peptide hydrogels, and (b) delivering these to end users in cell biology and tissue engineering, requires a multi-disciplinary project. We will combine state-of-the-art peptide chemistry and design; gene design, synthesis and expression; biophysics, including imaging and rheology; and cell biology. Therefore, this proposal brings together local, national and international experts in peptide and materials design and characterization, and cell culture and tissue engineering. Our primary experimental objectives are: 1. To design and synthesize genes for the peptide components of the hydrogels, and to test these in various constructs and expression systems; 2. To engineer the existing, 1st-generation designs to improve and explore physical properties of the gels such as stiffness, strength and longevity; 3. To add function to the hydrogels by introducing modified peptides that are compatible with fibre assembly and hydrogel formation, and then derivatize these with active peptides through click chemistry; 4. To test the recombinant and redesigned functional hydrogels to support cell growth and differentiation for a broad band of basic and more-specific cell and tissue types; 5. To develop next-generation designed biomaterials, in which new physical properties and biological functions can be incorporated and engineered orthogonally. That is, gel strength or stability can be introduced and altered without compromising biological function and vice versa. To do this, we request two PDRAs in molecular and cell biology, and in peptide design and biophysical characterisation, respectively; and propose collaborations with expert cell biologists, tissue engineers and biophysicists from the UK and Canada.


Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: GENERIC HEALTH RELEVANCE
Title: Early-life environmental effects on ageing in an evolutionary context
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Understanding of the evolutionary mechanisms that shape developmental responses to early-life environment and their consequences for ageing in later life in long-lived vertebrates remains limited. I will test and integrate ultimate and proximate explanations for how and why the environment drives variation in ageing rates in a wild population of Soay sheep on St Kilda. This population has been subject to individual-based study since 1985, yielding repeated measures of reproductive performance, morphology and parasite burden, as well as blood samples, from across the lifetimes of thousands of individuals. I will undertake new laboratory work on blood samples to measure key biomarkers of ageing and immune response. I will measure markers of oxidative stress and inflammation in freshly collected and frozen blood samples. In a larger sample, incorporating blood collected previously during the long-term study, I will measure telomere length by QPCR and titres of self-reactive antibodies and antibodies specific to the major nematode parasites infecting the sheep by ELISA. I will use this unique longitudinal data set to test the 'predictive adaptive response' hypothesis against alternative non-adaptive hypotheses explaining early-life environmental effects on health and ageing. I will also how genetic and environmental variation influence trade-offs between growth, reproduction, immunity and somatic maintenance. The new laboratory data will allow me to test how early-life experience of infection influences immune responses and rates of immunosenescence, as well as how early-life investment in growth, reproduction and immunity influences physiological state in later life. Ultimately, I will determine how and why certain developmental and early life history responses to poor nutrition and infection are favoured by natural selection under different environments and what their consequences are for physiological ageing and lifespan in long-lived mammals.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE
Title: Investigation into factors controlling the efficacy of integration deficient lentiviral vectors for gene delivery
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Integration deficient lentiviral vectors (IDLVs) deliver genes to a wide range of cell types, including non-dividing cells. They have the additional benefit of a reduced risk of insertional mutagenesis compared to integrating viruses. Following reverse transcription and nuclear delivery of the lentiviral payload, IDLVs form stable episomal circles, which provide long-term expression of transgenes in post-mitotic cells. As IDLVs lack an origin of replication, the episomes are diluted out of rapidly dividing cell populations. Consequently, IDLV are effective and safe tools for either long-term or transient expression, depending on the target tissue. It was thought that IDLV would not be affected by position effects that can reduce expression from integrating vectors, but variability and lower expression have also been observed from episomal vectors. The reason for this is unclear; while IDLV work efficiently in brain and retina, expression is generally lower in liver and haematopoietic stem cells, when compared to integrating lentiviruses. The aim of this project is to determine what factors may influence differential levels of expression observed in integrating and non-integrating vectors. Candidate causes include obstruction of viral entry and reverse transcription and nuclear import. Cell-type specific factors such as epigenetic effects influence integrating vectors, so these are also likely to affect gene expression from IDLV. Vector efficacy may also depend on both contents and context of what is encoded on the backbone. Using different target cells in vitro and in vivo we aim to elucidate the influence of factors on transgene expression using several vectors that are identical except for their promoter configuration and their ability to integrate DNA into the host cell genome. Information gained will lead to the development of a safer and more efficient lentiviral vector and applicable to generic vector design.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: GENERIC HEALTH RELEVANCE
Title: Genetic analysis of actin dynamics at epithelial wound edges in vivo
Funder: Biotechnology and Biological Sciences Research Council

Abstract: An epithelium is a sheet of cells that functions as a barrier separating a tissue or organism from its surroundings. Epithelia provide essential protection against infection, toxins and fluid loss, therefore it is vital that wounded epithelia are rapidly repaired. Epithelial repair can be achieved by two mechanisms: 1. A crawling mechanism, in which wound edge cells migrate across the substratum by extension of actin protrusions into the wound. 2. A purse-string mechanism in which a contractile actin cable forms in wound edge cells, constriction of which pulls the wound closed. The method of closure is therefore determined by the mode of actin assembly at the wound edge. The development of therapies to accelerate epithelial repair would greatly benefit human health, and manipulation of signaling pathways controlling actin assembly in wound edge cells is a strategy by which this could be achieved. However, actin signaling will differ between wound edge cells assembling protrusions and cables, therefore if we are to exploit this therapeutic approach, we need to understand under what circumstances each of the two modes of closure is used, and how actin signaling differs between them. This grant will therefore address 2 questions: 1. What determines the mode of actin assembly adopted by wound edge cells? 2. How does signaling differ in wound edge cells exhibiting different modes of actin assembly? We will employ a novel experimental strategy in which we will use genetics and imaging to scrutinise wound healing in two epithelial tissues in the drosophila embryo; the epidermis and the amnioserosa. These two tissues exhibit different modes of actin assembly at wound edges and this project will involve comparative analysis and manipulation of wound healing in these two tissues. We will determine the influence of tension, adhesion and gene expression on actin assembly at the wound edge, and investigate the roles of Rho GTPases and PI 3-kinase in regulating actin dynamics.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Bioorthogonal site-selective protein immobilisation and labelling
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Currently the fabrication of protein arrays is hampered by challenges associated with high-throughput expression and purification of the large numbers of proteins and the lack of effective and simple methodologies that can be used to immobilise these proteins whilst retaining their activity/functionality. Furthermore, the number of features that can be written, addressed and detected on the surface, using standard technology remains small relative to the size of a proteome. We propose to develop an highly efficient method for site-selective immobilisation of proteins on to surfaces using an engineered variant of a phosphopantetheinyl transferase enzyme (PPTase). Our approach will be entirely bioorthogonal, allowing immobilisation of functional proteins, possessing a small peptide (12mer) tag, directly from cell lysates on to surfaces functionalised with coenzyme A (CoA) analogues, circumventing the need for protein purification. We will then demonstrate the application of this method, together with the relevant surface chemistries, by producing nano-scale protein features on surfaces that have been patterned using scanning near-field photolithography and dip-pen nanolithography. Model proteins of interest will be immobilised on to the nanopatterned surfaces and subjected to a range of assays to demonstrate the binding of protein partners, specific DNA sequences and small drug-like molecules. By combining site-selective protein immobilisation and nanolithography, we aim to develop new techniques that will underpin the future development of functional high-density protein arrays, which would be extremely valuable for proteomics research, as well as drug screening and diagnostic applications. Finally, to further underline the general utility of our methodology, we will also demonstrate how the bioorthogonal PPTase enzymes we have engineered can also be used for site-specific labelling of proteins.


Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: GENERIC HEALTH RELEVANCE
Title: Investigating the mechanisms by which amino acid balance and reduced TOR signalling improve healthy lifespan
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Both moderate dietary restriction (dr) and nutrient signaling pathway mutations extend lifespan in a range of organisms We have recently found that nutrient amino acid balance is critical for the beneficial effects of dr in drosophila which is consistent with findings in mice. In other recent research, a new component of TOR signaling in response to amino acids has been discovered: the Rag GTPases. We thus have a new combination of tools to study the molecular events from nutritional balance to enhanced longevity via the amino acid specific signaling activity of TOR. I propose to study the phenotypic and molecular responses to combining alterations in dietary amino acid balance with changes in Rag protein activity. In particular, I propose to characterize the tissue-specific, whole-transcriptome effects of combining these interventions. By combining these molecular data with the observed phenotypes under the same conditions, we will seek candidate molecular mediators of the responses for further testing. One group of evolutionarily conserved proteins that may be involved is the GATA family of transcription factors. In yeast and mosquitoes these mediate a transcriptional output of TOR and in worms they have been shown to alter lifespan. The connection from dietary amino acids to TOR to GATA transcriptional output has to date remained unexplored. I propose that this constitutes at least part of the important molecular changes required for enhanced healthy lifespan.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Identification of genetic factors affecting cellular ageing in fission yeast
Funder: Biotechnology and Biological Sciences Research Council

Abstract: To identify genetic factors affecting cellular ageing in fission yeast, we will apply multiple genome-wide and genetic approaches, including state-of-the-art RNA sequencing and proteomics methods, high-throughput phenotyping of a deletion mutant library and of natural fission yeast isolates, as well as large-scale screening of genetic and regulatory interactions among ageing genes. Chronological lifespan in fission yeast, determined in quiescent cells under limiting nitrogen, will serve as a simple yet powerful system to unravel vital processes mediating cellular ageing and longevity. Integrated mining of the resulting genome-scale data sets will reveal global principles for longevity and will provide predictions for key genetic factors that directly impinge on ageing. We will pursue such promising factors by further targeted experiments. This research will provide 1) detailed insight into transcriptome and proteome modulation during ageing; 2) a systematic functional profiling of genes relating to ageing; 3) a survey of intra-species variation in lifespan and accompanying genome regulation; and 4) a basis for a systems-level understanding of genetic mechanisms underlying the ageing process. Integration of these complementary approaches into a research project will thus provide important insight into genotype-phenotype relationships underpinning cellular ageing and longevity.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: A toolbox for the promotion of healthy ageing: Phenotypic prediction from genes and environment
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The most prevalent non-infectious causes of poor health in companion animals and humans are related to aging and are multifactorial in origin: partly genetic and partly environmental, with these factors acting independently or through complex interactions. Where a substantial proportion of the systematic factors can be identified and modelled it is possible to provide accurate predictions of future life events including specific risks of developing these age-related syndromes or diseases in as yet unaffected individuals or beneficial or adverse drug response in those already affected. Such prediction is potentially a powerful tool to promote healthy ageing in both humans and animals, as it allows increasing effectiveness of interventions, and cost-effectiveness, by stratifying the population into subgroups, e.g. at risk/not at risk, responders and non-responders to particular environmental interventions and then targeting interventions. Key to accurate prediction is our ability to explain as much as possible of the trait variance, both genetic and non-genetic and we propose to develop methods that allow us to make best use of the information recorded in a clinical context or in population studies. This information includes records of environmental exposures, phenotypes of interest and genomic information. We propose improving predictive performance by better using information through: 1) Taking appropriate account of all genetic marker information, not just that from few highly selected markers 2) Using models that account for environment and genomic factors and their interactions 3) Utilising information from correlated traits in a multitrait framework 4) Identifying optimum prediction methods from those specific for problems where the set of predictive variables is much larger than the number of observations We will combine and refine these different methods and demonstrate their efficacy using simulated data and crossvalidation on large-scale GWAS data.


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS;2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: GENERIC HEALTH RELEVANCE
Title: Developing generic scalable and standardised selection methods for human therapeutic cells
Funder: Engineering and Physical Sciences Research Council

Abstract: The broad aims of this project proposal are to advance two new high-throughput, single-use cell selection systems in parallel, namely a 'reverse engineered' cell selection device based on hollow fibre dialysis cartridges with the capability of capturing cells ex vivo or in vivo, together with ex vivo cellular chromatographic systems exploiting cast polymer monoliths featuring derivatised giant convective pores (Gigaporous hyDr.ogel monoliths or GHMs). Our intention is to keep the technologies generic to allow industrial partners to develop them for use in selecting many different cell types, but careful consideration to current regulatory constraints for cellular therapy will guide development. In developing the above affinity cell selection systems, we shall employ monoclonal antibodies, cell lines and three major sources for the primary cells, i.e. heparinised whole peripheral or cord blood; leukapheresis products from routine collection machines. This work will culminate in a pre-clinical model of human endothelial stem cell xenotransplantation to assess the efficacy of the cell selection technology. Revascularisation represents a critical component of tissue repair, with autologous endothelial stem/progenitor cells, their pro-angiogenic counterparts and the products of these cells all being attractive targets for therapeutic intervention.


Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES;5.2 CELLULAR AND GENE THERAPIES
Health categories: GENERIC HEALTH RELEVANCE
Title: Multi-level regulation of mitochondrial function in ageing and under caloric restriction
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Mitochondrial function declines during ageing in many tissues, and interventions that prolong healthy lifespan, including caloric restriction, often compensate for this decline. Multiple lines of evidence suggest that mitochondrial dysfunction is a significant cause for tissue ageing. However, the molecular mechanisms responsible for the decline of mitochondrial function in ageing tissues and for its restoration under caloric restriction are still elusive, limiting our abilities to develop specific and efficient interventions that might extend healthy lifespan. Genome-wide analyses have so far not yet provided coherent datasets encompassing multiple levels of regulation during ageing. For the first time, we will generate genome-wide promoter methylation, transcriptome and mitochondrial proteome datasets from liver and skeletal muscle from mice at different ages, ad-libitum fed and under caloric restriction. Each dataset will be exclusively from the same animal, minimizing the confounding effects of biological variation and maximizing comparability between the levels. We will integrate these datasets with each other and with data characterizing mitochondrial function obtained from the same groups of mice, using a powerful probabilistic functional interaction network tool developed and tested for application in ageing research in our Centre for Integrated Systems Biology of Ageing and Nutrition. This will allow us to (i) define network(s) of interacting mitochondrial proteins that are changed in ageing and under CR; (ii) identify the pre-transcriptional and transcriptional regulation for proteins that influence mitochondrial function; (iii) derive candidate regulatory pathways and model these; (iv) derive candidate nodes from these networks and test their impact on mitochondrial function by inhibition and over-expression experiments. This approach will identify novel candidates for biomarkers of ageing and for efficient and specific intervention concepts.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Accessible resource for integrated epigenomics studies (ARIES)
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Serial samples taken at multiple time points across the lifecourse from 1,000 mother-child pairs from ALSPAC will be used to generate genome-wide DNA methylation. The Illumina 450K human methylation array will be used to analyse samples from birth, age 7 and age 15-17 in 1,000 children and samples taken during pregnancy and 17 years later from their mothers. These data will be complemented by methylome sequencing of both the 5-methylcytosine and 5-hyroxymethylcytosine fractions of the genome which will be isolated by immuno-precipitation and sequenced using a next-generation platform. Tandem genome wide methylation and gene expression analysis will be undertaken in mouse tissues (leukocytes, adipose, muscle, liver) using a custom NimbleGen methylation array and Affymetrix gene ST arrays respectively. Further mouse tissues will be harvested and banked for future investigation upon request. The complex primary data generated will be processed and fully integrated using the Ondex system that has been developed under the SABR initiative. In addition to the facility to view these data in an open access browser, users will have the opportunity to access extensive exposure and phenotype information from the ALSPAC cohort using the existing infrastructure. The project will run for 2 years and be managed by a team of academics who have a proven track record in large scale collaborative research and the provision of data and information to the wider scientific community. An international Scientific Advisory Board of leading scientists in epigenetics and bioinformatics will contribute to the oversight of ARIES.


Research activity codes: 2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY);1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE