NIHRDataInsights/HRCSData huggingface dataset:
Title: Structure and Function of ribosomes
Funder: Wellcome Trust

Abstract: With the basic structures of ribosomes from bacteria, eukaryotes and mitochondria established, the focus has now shifted to more complex problems such as initiation, regulation including during stress and mitochondrial protein synthesis. We shall focus on three areas: 1. Eukaryotic initiation. Following our progress on the role of factors in recruiting initiator tRNA to the 40S subunit to form the 43S complex and in start codon recognition, we propose to tackle the structure of the role of the multisubunit factor eIF4F in recruiting the 43S complex to the 5&prime; end of mRNA to form the 48S complex that scans along mRNA until the start codon is reached. 2. Recognition of stalled ribosomes. One of the ways the cell senses aberrant situations is by recognizing stalled ribosomes. Initial work in collaboration with Manu Hegde has suggested that certain factors recognize polysomes in which a trailing ribosome has collided with a leading stalled ribosome. We propose to elucidate the mechanism by which this recognition occurs and leads to downstream regulation. 3. Mitochondrial protein synthesis. We shall investigate how human and yeast mitochondrial ribosomes insert proteins into membranes. We will also investigate how the ~99% of mitochondrial proteins are imported from the cytoplasm.

Lay abstract: The genes in our DNA contain information to make the thousands of proteins that carry out the various functions of the cell. We are attempting to understand how the large molecular machines known as ribosomes translate genetic information to make proteins. The process is highly complex and also highly controlled so that cells make proteins only when they need them and in the right amounts. When the process goes awry, it can lead to various diseases including cancer. In other cases, viruses can hijack the process to make their own proteins. So apart from its fundamental importance to biology, the work may help us understand the basis of certain diseases. In addition, our cells have organelles called mitochondria that make their own proteins. Many genetic diseases are caused by defects in mitochondria so understanding how they make their proteins is also of importance to human health.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Electrifying Life Science
Funder: Wellcome Trust

Abstract: The ability to image life lies at the heart of biology and medicine. Imaging the molecules of life leads directly to discoveries since they can then be understood in atomic detail. For molecular imaging, electrons give more signal for less damage than X-rays, as demonstrated by the current success of single-particle electron cryomicroscopy. The key recent breakthrough underpinning this technology was the development of direct electron detectors for cryoEM, based on silicon computer chip technology from the 1990s. The promise of using electrons in structural biology more broadly is still held back by several technological hurdles. Here we propose a major cross disciplinary effort to develop new technologies that use electrons to revolutionise biology. There are three components: AMPLUS – using electrons to visualise proteins inside cells, (electron cryotomography) at unprecedented resolution, cryoEM100 – a ten-fold cheaper purpose-built cryomicroscope that will democratise single particle imaging, and HEXI – a project that will create a world-leading combined X-ray and electron beamline, enabling structure determination from crystals ranging from the smallest that exhibit Bragg diffraction up to those useable at a microfocus X-ray beamline.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Determining the mechanisms underlying epigenetic inheritance of chromosome structure and gene expression states
Funder: Wellcome Trust

Abstract: Gene expression states and chromosome structure can be stably perpetuated across cell division cycles in a manner that is uncoupled from direct genetic instructions. I aim to understand how chromatin can self-duplicate and be inherited. Defining the mechanisms by which chromatin components are instructive in maintaining memory is fundamental to our understanding of genome stability and cellular differentiation. In the first two aims, I focus on the mammalian centromere which is an excellent model for self-templating epigenetically-inherited chromatin, based on the histone H3 variant CENP-A. I will ask two fundamental questions: i) how can centromeric chromatin be initiated de novo? ii) how is it subsequently stably inherited? In the final aim, I will use my expertise in centromere biology to ask how heritable chromatin contributes to the mitotic transmission of active gene expression. I will employ a unique, interferon-inducible gene expression model that results in long-lasting memory of prior induction. I will discover how local chromatin structure cooperates with the transcriptional machinery to ensure robust, long-term maintenance of active transcription and determine its importance for innate immunity. Combined, our discoveries will define the molecular basis and role of chromatin inheritance in the maintenance of cell identity and genome architecture.

Lay abstract: The collection of our genes is akin to a book, the genome, divided in chapters that carry the instruction to make the different cell types in our body. Cells have ways to physically organize and read the correct chapter, in a process called gene regulation, such that e.g. nerve cells read only the "nerve" chapter. The instructions for which genes to read are remembered by cells even when they are diving, as if cells had a bookmark that prevents them from "forgetting" who they are, otherwise development fails and disease ensues. Remarkably, these instructions, although memorized are not encoded in the DNA, the material of genes, and is therefore said to be "epi"-genetic. I aim to understand what are the molecules involved and how do they work to make sure that the packaging and reading of genes is so robust, even when cells copy themselves and tissues grow.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Institutional Translation Partnership Awards ‘The University of Bristol Translational Partnership Award 3
Funder: Wellcome Trust

Abstract: This University of Bristol-Wellcome Trust Translational Partnership Award (TPA) will build on the successes and insights gained from the past three years of our partnership to deliver a sustained, impactful change in our translational research and culture. Our ambition is to turn University research into real world solutions which transform our society, economy and health. In this award we will continue to try new things, disrupt the status quo and advance the way we support and accelerate translation by taking a bespoke, personalised approach, driving culture change to maximise the impact of our research. We will use this funding to work with researchers at all stages of the career pathway (PhD to Professor) to develop and realise their ambitions to translate their research through: &bull; A Translational Research Hub to enable straightforward access to expertise and funding and facilitate engagement with non-academic partners &bull; Proof of Concept and Translation Accelerator project funding to meet gaps in the translational funding pathway &bull; Early Career Translational Fellowships to provide bespoke support for the most promising individuals and projects &bull; Developing Innovation Networks with partner organisations in priority modalities and areas &bull; Exploiting the translational platforms developed from our cutting-edge synthetic biology and informatics technologies in TPA1 and 2 &bull; Providing training to researchers that embeds learning into practice through follow-up support and individualised action plans


Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE
Title: Exploiting divergent biology of two fission yeasts to understand membrane function
Funder: Wellcome Trust

Abstract: Membrane function is fundamental to life. Deregulation of the membrane lipid repertoire has severe consequences for cellular and organismal fitness. Defining how lipid composition controls membrane organization and cellular physiology remains a major challenge in biology. Membrane lipid composition is subject to complex feedbacks and reflects the metabolic and regulatory capabilities of the specific experimental system. I propose to attack this problem by exploiting the natural divergence in membrane lipid composition between S. pombe and S. japonicus, two related genetically tractable fission yeasts with different lifestyles. I believe that our research program integrating comparative analyses and reverse engineering of cellular mechanisms with biophysics and systems approaches, provides an unmatched discovery platform capable of revealing the core principles that govern membrane organization and function. Our research will explain how changes in the architecture of glycerophospholipid fatty acyl tails affect membrane properties. It will provide insights into the organization and evolution of genetic networks regulating membrane homeostasis. Finally, it will test if acquisition of new lipid metabolic functionalities engenders diversification of cellular pathways and organismal physiology.

Lay abstract: Membranes made of many types of lipid molecules compartmentalize and organize cells. Deregulation of the lipid repertoire has severe consequences for cellular physiology. In humans, it is linked to neurological disorders, cancer and metabolic diseases. Defining how lipid composition controls membrane organization and cellular physiology remains a major challenge in biology. I propose to tackle this problem by exploiting an ‘experiment of nature’. In spite of being closely related, S. pombe and S. japonicus yeasts have different lipid repertoires and exhibit remarkable differences in cellular processes. By analysing and reverse engineering variant aspects of lipid metabolism in these sister species we will probe the core principles that govern membrane organization. We will explain how changes in lipid composition affect membrane properties. We will elucidate the organization and evolution of genetic networks regulating membrane homeostasis. Finally, we will test if the expansion of the lipid repertoire affects cellular physiology and adaptation.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Membrane remodelling during mitotic exit
Funder: Wellcome Trust

Abstract: Cell division is of critical importance to cellular and organismal health, being essential for proliferation, growth and development, and is deregulated in disease states such as cancer. We will perform discovery-research to acquire new knowledge about cell division. Whilst we know much about how the genome is separated, we know far less about how cytoplasmic organelles are separated during division. I will explore the contribution made by a cytoplasmic membrane remodeling machinery, ESCRT-III, to organelle-separation and organelle-regeneration during mitotic exit. Additionally, we will discover new mechanisms by which the assembly of ESCRT-III can be regulated. Firstly, using a combination of structural biology, lipidomics and cell biology, we will identify how the ESCRT-III component CHMP7 binds to ER and nuclear-envelope membranes to enable ESCRT-III-dependent nuclear envelope regeneration. Secondly, we will use in-vitro and in-vivo assays to explore the role of ESCRT-III phosphorylation as a mechanism regulating ESCRT-III assembly. Lastly, we will discover how the ER is remodelled during mitotic exit. We will explore new roles for the ESCRT-III machinery in controlling ER-morphology, and will expose a hitherto unforeseen role for this machinery in regulating ER-separation during mitotic exit.

Lay abstract: Cell division is the process by which a single cell divides into two daughter cells. It is essential for life, being necessary for the growth, development and repair of all tissues in the body. Errors in cell division can lead to diseases such as cancer, however, despite being so important, there are still many things about this process that we don’t understand. As well as containing DNA, cells also contain a number of internal compartments called organelles that help them live. Some of these organelles fragment when cell division begins, to allow DNA separation to occur. As cells finnish dividing, organelles must be divided equally into daughter cells, and organelles that were fragmented must be reassembled. I want to discover how an organelle that encloses the nucleus (and fragments when cells begin division) is reformed as cells finish division; how a large organelle called the endoplasmic reticulum, that fills most of the cell’s interior, is separated during division; and how a group of membrane-binding proteins called ESCRTs assemble into a machinery that shapes, separates and reforms organelles during cell division. We will discover more about how cells work and reveal more about the cellular processes that guard against cancer-development.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Human genome synthesis
Funder: Wellcome Trust

Abstract: The ability to make any human genome would transform hypothesis driven investigations in diverse areas of biology, genetic-archaeology and biotechnologies. However, there are currently no technologies for building human genomes. Moreover, there is a technological void between the state of the art in the creation of synthetic genomes and what will be required to enable the synthesis of human genomes. The current challenge is therefore to bridge this void. The goal of this proposal is to bridge the technological void between the state of the art, which has enabled the synthesis of Mbp-scale microbial genomes, and the technologies that will be required to build a human genome, which is 3 orders of magnitude larger than any synthetic genome that has been created to date. We will establish key technologies for human genome synthesis and exemplify these technologies through the synthesis of a recoded human chromosome.


Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES;1.4 METHODOLOGIES AND MEASUREMENTS
Health categories: GENERIC HEALTH RELEVANCE
Title: The role of glycosphingolipids in modulating membrane protein trafficking
Funder: Wellcome Trust

Abstract: Glycosphingolipids (GSLs) are specialised lipids enriched in the outer leaflet of the plasma membrane (PM) and defects in GSL metabolism underlie a range of devastating diseases. I have shown for the first time a direct link between GSL metabolic defects and changes in the abundance of disease-associated PM proteins. Changes to the cell surface abundance of these proteins are driven by trafficking defects and gene expression changes: pathways that may be mechanistically linked. My preliminary work highlights that the role of GSLs in membrane trafficking has been under-appreciated. I now seek to define the molecular mechanisms that link GSL abundance to disease pathways: how do specific GSL-protein interactions direct membrane trafficking; and what are the consequences of this mistrafficking? We will target specific enzymes in GSL metabolic pathways, monitor lipid and protein changes using quantitative mass spectrometry and visualise co-ordinated protein trafficking from the endoplasmic reticulum using an innovative fluorescence-based secretory assay. Using high-resolution structural techniques we will determine how the specificity of GSL-protein interactions is defined and exploit these insights to feedback into our cell-based assays. My research proposal implements a multidisciplinary strategy that will reveal crucial new insights into how this important class of lipids influence cell fate.

Lay abstract: The cell surface is decorated with a diverse array of proteins and lipids that mediate essential cell-cell contacts and trigger potent signalling pathways. An important class of lipids enriched at the cell surface are glycosphingolipids (GSLs). Imbalances in GSL levels underlie a range of severe disorders from neurodegeneration to cancer. I aim to define how altered GSL metabolism influences cell fate, driving disease pathogenesis. I have established that accumulation of GSLs leads to loss of proteins from the cell surface and identified this may be driven by direct interactions between GSLs and membrane proteins. Using multidisciplinary approaches we will comprehensively establish which proteins are most sensitive to GSL imbalances, identify the mechanisms by which this occurs, and address how these changes influence disease pathways. My work will shed light on this understudied area of biology, providing a deep mechanistic understanding of GSLs in fundamental cellular pathways with clear medical relevance.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Molecular mechanisms of DNA synthesis by the human replisome
Funder: Wellcome Trust

Abstract: Before mitosis, cells must make two accurate and complete copies of their genome, to ensure genetic stability across cellular generations. This challenging biochemical task requires complex molecular systems that duplicate chromosomal DNA and repair lesions that stall DNA synthesis. Sporadic or inherited defects in the cellular apparatus of genomic duplication cause genetic instability, which is responsible for developmental and degenerative pathologies and for cancer predisposition. Our knowledge of the molecular basis of eukaryotic DNA replication and related repair processes is incomplete, and this is especially true of genomic duplication in human cells, the most relevant to our health. Our proposal aims to provide a high-resolution view of the molecular mechanisms of DNA replication, using state-of-the-art biochemical and biophysical approaches. We will focus on components of the human replisome, the multi-protein assembly responsible for DNA synthesis in our cells. There is intense medical interest in the molecular mechanisms responsible for genomic integrity and the rationale for the consequences of their occasional failure. In this respect, the work of our proposal is highly significant as it aims to deliver a comprehensive description in atomic detail of the complex and dynamic processes of DNA replication, when our genome is at its most vulnerable.

Lay abstract: Each time a cell divides, it must duplicate its genome accurately and completely. Genetic inheritance relies on DNA replication, the biochemical process that is responsible for the accurate duplication of our genome and the repair of lesions that might block DNA synthesis or alter the encoded information. We want to understand at molecular level how our cells execute the orderly duplication of the genome and how they cope with DNA damage. We will achieve our goal by working out in atomic detail the shape of the proteins responsible for the duplication process and use this information to explain their mechanism of action. Elucidating the molecular basis of DNA replication is important, because the genomic instability caused by defective replication predisposes to cancer and developmental and neurodegenerative pathologies. Our efforts will advance the molecular understanding of genome biology and our ability to translate such knowledge into medical diagnosis and treatment.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Establishing the basis for selectivity in the SUMO spray
Funder: Wellcome Trust

Abstract: Specificity in the SUMO system appears to be achieved by modification of large groups of proteins by a PIAS E3 ligase mediated SUMO spray. Our aim is to define the mechanism by which PIAS E3 ligases select multiprotein complexes for modification. Proteomic identification of sites of SUMO modification and SUMO ChIPSeq analysis provide evidence that the SUMO spray functions in human induced pluripotent stem cells. Our objectives are to establish the role of the “SUMO spray” in maintaining pluripotency. We will deplete SUMO globally using the ML792 E1 inhibitor and will deplete SUMO locally at specific genomic loci using Cas9-SUMO protease fusions and at multiprotein complexes using nanobody-SUMO protease fusions. We will follow cell fate, changes in histone marks, chromatin accessibility, transcriptional output and the stability of multiprotein complexes. PIAS proteins can be recruited to substrates via DNA, SUMO and specific protein interactions. We will use structural, biochemical and single molecule approaches to describe PIAS mediated SUMO modification. Our ultimate goal is the structural determination of a ternary complex of DNA bound substrate, PIAS protein and SUMO loaded E2. This would be a first in its class structure and would reveal the mechanism of SUMO spray mediated substrate modification.

Lay abstract: Pluripotent stem cells have the potential to generate all the types of cells required to make a human. The pluripotent state is maintained by many factors that regulate how genes are expressed in these cells. One such factor is know as SUMO and it functions by linking to other proteins involved in regulating gene expression and altering their activity. SUMO is not added to single proteins but is "sprayed" onto groups of proteins acting as a protein glue and stabilising the protein complexes. We want to determine how a protein known as the "PIAS SUMO ligase" selects groups of proteins for modification out of the many thousands of proteins contained in the cell. Selecting the correct proteins for tagging is critical. We will try and figure out how PIAS recognises its targets, determine the mechanism by which PIAS accomplishes the modification reaction and establish the consequences of PIAS action.

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