NIHRDataInsights/HRCSData huggingface dataset:
Title: Next-Generation RNA Genotype-Phenotype Mapping
Funder: Wellcome Trust

Abstract: Genome sequencing projects uncover large amounts of noncoding genetic variation, which underlies phenotypic diversity and can cause disease. To understand the mechanisms through which noncoding mutations influence function, we will combine saturation mutagenesis of selected genes with high-throughput assays to measure molecular and cellular phenotypes. In part (1), we will measure the effects of mutations in yeast U3 snoRNA on fitness, U3 abundance, and U3 association with proteins. We will measure fitness in the presence of mutations that decrease the levels of U3-interacting proteins, and in environmental conditions that influence RNA stability and shift the balance between U3 supply and demand. We expect that these experiments will uncover the molecular mechanisms that underlie the U3 fitness landscape. In part (2), we will stably integrate thousands of synonymous variants of GFP into the genome of human cells, and use massively parallel assays to measure the expression of these variants. We will develop computational models to explain expression in terms of sequence properties such as nucleotide composition, codon bias, and specific sequence motifs. By comparing the results in wild-type cells and in cells depleted of specific regulatory proteins, we will study the mechanisms through which codon usage influences gene expression.

Lay abstract: The first human genome sequence was published in 2000, and thousands of genomes have been analysed since that time. To fully use the information contained in these genomes, we need to be able to predict the effects of mutations on molecules (for example, whether mutations influence enzyme function), cells (whether they affect cell growth or differentiation), and organisms (whether they cause disease). To make these predictions, we first need to measure the effects of many mutations on each outcome. In this project, we will develop methods that can be used to study the effects of thousands of mutations in paralel. We will apply these methods to comprehensively study the mutations in a model yeast gene, and try to understand how the different effects of mutations are related to each other. For example, can we predict the effects of mutations on yeast growth from their effects on molecular interactions of the model gene? We will then study a class of mutations that were long thought to have no effect in human: the so-called "synonymous mutations". We have already shown that synonymous mutations influence gene expression, and we will use our data to uncover the mechanisms underlying these effects.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Unshackling Membrane Protein Research : New Amphiphilic Copolymers for Extraction of Stable, Active Membrane Proteins
Funder: Wellcome Trust

Abstract: Membrane proteins provide a multitude of functions essential to the life of the cell, and yet extracting them in an active form remains exceptionally challenging. In recent times an amphiphilic polymer, poly(styrene-co-maleic acid) (SMA) has gained significant traction as an effective agent for extracting and stabilising membrane proteins in phospholipid nanodiscs. Unlike conventional methods based on detergents, the method also extracts the lipids surrounding the protein, helping to preserve native activity. Although the original SMA polymer provided a good solution for demonstrating the utility of this approach it is becoming increasingly clear that further development of the polymer is required to fully capitalise on the unique aspects of the method. This project aims to address this by providing a technical resource for the community for generating improved, bespoke polymers matched to end users need allowing them to: 1) Tune the lipid environment within the nano-particle to optimise protein activity by introducing a variety of comonomers, including aromatic, linear aliphatic and branched aliphatic into the established maleic anhydride copolymer 2) Harness functionalised "plug-n-play polymers" that allow researchers to easily modify the polymers for downstream applications These polymers will be tested by the community and delivered through an integrated commercial supply chain.

Lay abstract: Membrane proteins (MPs) form about 70% of all drug targets, but they are very difficult to isolate in their intact, stable and fully functional form. Since about a decade, three commercially available polymers have been used to transform cell membranes into nanodiscs and it was discovered that these nanodiscs offer interesting possibilities for the isolation of MPs. Although the three commercial polymers work reasonably well, they were never developed specifically for this application and there are several shortcomings that still need to be overcome. In this project, we aim to develop the next generation of amphiphilic copolymers, dedicated for the isolation of MPs. In collaboration with several scientists from the MP field we will enhance the efficiency of the amphiphilic copolymers and also introduce additional functionality that is needed to expand the utilisation of the isolated MPs in the field of drug discovery and beyond.

Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: GENERIC HEALTH RELEVANCE
Title: Selfish selection of de novo mutations in the male germline
Funder: Wellcome Trust

Abstract: Understanding the factors determining the occurrence of de novo mutations (DNMs) in the human genome is central to genetic disease and genome biology. DNMs arise predominantly in the male germline and increase in frequency with paternal-age. Despite the fact that germline mutation rates are intimately linked to spermatogenesis, very little is known about testicular homeostasis in humans. This proposal aims to address this gap in knowledge by focusing on a new disease-mechanism whereby pathogenic DNMs are preferentially transmitted because they hijack the mechanisms controlling spermatogenesis. This selfish selection process relies on principles similar to oncogenesis to explain why some paternally-derived mutations occur spontaneously up to 1000-fold more frequently than background. Exploiting our current knowledge of selfish selection, this proposal will deploy novel methodologies to describe mutations/genes/pathways subject to this phenomenon, including (1) cataloguing DNMs at single-seminiferous tubule resolution, in geographically-mapped testicular biopsies and in sperm; (2) modelling clonal DNM distribution in tubules to describe spermatogonial dynamics; (3) mining large DNM databases from family trios to detect mutational enrichment. We will also investigate 'selfish mitotic drive', a novel mechanism of mutation enrichment. Together these approaches will allow us to assess the significance of selfish selection for human disease and genome evolution.

Lay abstract: Genetic diseases happen when mistakes, known as ‘mutations’, arise in our DNA code. When these mistakes occur in the DNA of eggs or sperm, they can be transmitted to the next-generation and cause disease in newborns. Because most mutations happen in the father during sperm production, studying how sperm is made and how it accumulates DNA mistakes is important to understand genetic diseases. We have previously shown that some mutations can be ‘selfish’. These selfish mutations hijack the way sperm is produced to their own advantage and become more abundant in sperm as men get older. Although so far we have only demonstrated this effect for rare disease mutations, we think it may be more common than currently recognised. In this project, we want to use state-of-the-art technologies to identify new mutations subject to this selfish effect in order to understand why some diseases arise and how our DNA evolves.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: In vivo mechanisms of epithelial tissue morphogenesis
Funder: Wellcome Trust

Abstract: Understanding how a tri-dimensional tissue is built from the genetic blueprint is a key frontier in biology. In addition to genes known to be important in specific aspects of morphogenesis, physical constraints and properties play a major role in building tissues. In this proposal, I aim to understand how the genetic inputs integrate with the mechanical properties of the cells and tissues to produce form. To investigate this, we study the early development of the Drosophila embryo. We have found previously that actomyosin-rich boundaries play an important role in two fundamental and conserved morphogenetic phenomena, axis extension and compartmental boundary formation. We have also found that an extrinsic force contributes to axis extension. We will build on these findings by first investigating how the actomyosin-rich boundaries form and how they might repair genetic patterns during axis extension. Second, we will ask how, during compartmentalisation, they control the planar orientation of cell division and also epithelial folding. Finally, we will examine the impact of actomyosin-rich boundaries and extrinsic forces on epithelial tissue mechanics. Our approaches will be interdisciplinary, combining genetic, quantitative and in silico analyses to find novel and universal morphogenetic rules.

Lay abstract: During animal development, a ball of cells (the blastula) forms from division of a single cell, the egg. This ball elongates to form the main body axis (gastrulation), which becomes divided into repeated regions (segmentation). These processes are important: defects in body axis elongation can lead to neural tube problems in humans (such as spina bifida); the human vertebrate column is made from the embryonic regions generated by segmentation (somites). Our goal is to understand how embryos are shaped, by studying tissue elongation and segmentation in a simple system, the fly embryo. These embryos can be watched live and easily manipulated both genetically and physically (they are also cheap to raise). We will study the role of an essential cellular structure, the actomyosin cytoskeleton, in tissue elongation and segmentation. This structure, which can be thought of as the cell’s ‘muscle’, is a contractile web made of proteins called actin and myosin, closely associated with the cell’s membrane. In tissue elongation and segmentation, the cells redistribute their actomyosin cytoskeleton, so that it is found more commonly along certain sides of the cell. This redistribution can for example cause cells to contract and push past each other, which causes tissue elongation.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: PDBe - Facilitating Open Science in Structural Biology
Funder: Wellcome Trust

Abstract: Established in 1971, the Protein Data Bank (PDB), is the single global archive of macromolecular structures. It is managed by the Worldwide Protein Data Bank (wwPDB), currently consisting of four partner sites across Europe, Asia and the USA. The Protein Data Bank in Europe (PDBe) is a founding member of wwPDB and is an ELIXIR Core Data Resource and deposition database. Structural biology is being transformed by rapid advances in structure-determination techniques (e.g. Electron Microscopy and Integrative/Hybrid Methods) and improved access to large-scale facilities that offer high-throughput methods (e.g. ligand and fragment screens). These developments lead to a continuous increase in the number, size and complexity of structures deposited to the PDB. In this project we aim to address the challenges posed by these advances in structural biology through: 1. Active engagement in worldwide data-archiving activities: i. Development of data-representation standards; ii. Further development of the wwPDB deposition, validation, and biocuration system (OneDep) to accommodate new structure-determination modalities; iii. Interoperability with specialist archives for experimental structural biology data. 2. Maintaining data quality and integrity by fulfilling PDBe’s responsibility to curate all structures produced in Europe and Africa. 3. Development of data-analysis and dissemination tools for improved accessibility. 4. Conducting training, outreach, and public-engagement activities.

Lay abstract: Macromolecular structure data is critical to understand biology at the molecular level and is used by the research community and hundreds of biomedical resources (~1.7 million data downloads/day). Structural biology continues to advance with revolutionary developments in structure-determination techniques and widespread access to large-scale facilities, resulting in vast increases in the number, size and complexity of structures deposited to the PDB. To meet these challenges and ensure continued benefit to advanced life-science research, we will collaborate establish vital data standards and deposition requirements, conduct expert biocuration, and link PDB data to other structural biology resources. We will adapt the deposition and biocuration processes and develop new data-analysis tools and intuitive ways of making structures available to the wider community, impacting areas from discovery of new pharmaceuticals to improving crop resistance. We will further build on our pilot public-engagement project with secondary schools, contributing to their scientific and art curricula.

Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE
Title: A2O - Transforming EMPIAR into an Essential Resource for EM Data Spanning Scales from Atoms to Organisms
Funder: Wellcome Trust

Abstract: The Electron Microscopy Public Image Archive (EMPIAR) was developed following consultations with the cryo-EM community highlighting the pressing need for public dissemination of image data underpinning cryo-EM structures. Since 2014, EMPIAR has quickly grown in volume (286 entries; 284 terabytes as of 01/04/2020) and established its role and value for the community (>180 EMPIAR citations). Its remit now includes micro-crystal electron diffraction (microED), soft-X-ray tomography (SXT), and volume-EM (including Focused Ion Beam and Serial Block-Face SEM) data. The main goals of this grant are to streamline and facilitate the deposition process (encouraging deposition and improving quality and quantity of deposited information) and to enhance and facilitate data reuse. All hardware and IT infrastructure will be provided by EMBL-EBI. Specific aims: 1. Fully support deposition of volume-EM data; 2. Support handling large (tissue- and organism-level) 3D-volumes by pump-priming EMPIAR with flagship connectomics and non-connectomics datasets; 3. Enable efficient and interactive reuse of large 3D-volumes by supporting multiscale imaging formats; 4. Facilitate potential mandatory deposition by simplifying the deposition workflow and enhancing data reuse; 5. Improve support for correlative imaging data, working with stakeholder communities and the EMBL-EBI BioImage Archive; 6. Prepare for rapid growth of data volumes by evaluating and implementing data-compression methods.

Lay abstract: Recent advances in electron microscopy (EM) have made it a key technique for studying the three-dimensional structures of important biological molecules and even cells. This has helped to improve our understanding of biological functions and processes. If the experimental EM data are made publicly available then specialists can use it to improve current methods and to develop new ones for data processing and for checking the accuracy or validity of the results and conclusions. The Electron Microscopy Public Image Archive (EMPIAR) was developed in collaboration with the EM community for this very purpose. In this proposal we aim to improve EMPIAR and also make it possible to store EM data related to much larger biological specimens. By doing this, EMPIAR will become a rich and freely available resource of EM data on scales from atoms and molecules, via cells and tissues to entire organisms.

Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: GENERIC HEALTH RELEVANCE
Title: Actin-like cytoskeletal systems in bacteria and archaea
Funder: Wellcome Trust

Abstract: Bacteria contain proteins that form internal fibres. These proteins have counterparts in all other organisms but the functions of the fibres in bacteria are different. One type of fibres facilitates multiplication of bacteria by dividing them into two daughter cells (FtsZ protein). Others organise the distinct shapes that bacteria adopt (MreB protein). Other types of fibres make sure that certain kinds of parasitic small DNAs, plasmids, are distributed to daughter cells during division (Tubz and ParM proteins), or organise small magnets that form inside certain bacteria, so that they are able to swim guided by earth’s magnetic field (MamK protein). We propose to investigate some of these fibre systems by integrating information at various length scales, ranging from atoms to individual protein molecules and protein fibres, even to entire cells. Methods we will use include X-ray crystallography, electron microscopy and electron tomography. Combining them with methods that reveal information about the system’s dynamics, such as light microscopy, and assembly from their components outside cells, we will be able to investigate how the systems do their work. In longer-term, our new insights might even make it possible to disrupt these processes using new drugs, with the purpose of killing harmful bacteria.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Disentangling relationships between genotype and phenotype in complex genetic disorders, with particular application to liver and kidney disease
Funder: Wellcome Trust

Abstract: The main goal of this research is to develop and apply advanced statistical methods to help elucidate the biological mechanisms and causal pathways underpinning the correlations seen between genotype and phenotype in complex genetic disorders, with specific emphasis on liver and kidney disease. This will allow us to better understand the biological processes leading to disease development, thus enabling the development of potential therapies and cures. Identifying genes and their protein products which alter disease risk will point to potential new drug targets and allow opportunities for re-purposing of existing drugs. We will use measurements of genetic factors and potential intermediate processes like gene expression, DNA methylation and protein levels, available through long-standing collaborations with clinical colleagues. A key goal of our research is to develop methods that integrate these different data types with one another and with similar data from external sources. We will expand the data available through UK-PBC (SNP-genotypes and gene-expression profiling in 100 pre-treatment cases plus 50 controls), by adding CpG-methylation and serum proteomics, enhancing our ability to identify causal pathways in disease development/progression.This will inform disease biology, subsequent treatment response, and the extent to which it can be predicted from baseline measures.

Lay abstract: Genome-wide association studies investigate genetic variation (changes to the DNA sequence) across the entire genome, to see which changes correlate with disease or disease-related outcomes. We want to both detect such correlations and understand the biological mechanisms behind them. We will measure potential intermediate processes like gene expression (where DNA is transcribed to RNA), DNA methylation (the presence or absence of a chemical modification to the DNA sequence) and measurements of proteins (based on the amino acids into which RNA is translated), in a set of diseased and non-diseased individuals. These measurements can also be extrapolated to other diseased and non-diseased individuals with genetic data available. We will develop improved statistical methods (and accompanying software implementations), in order to carry out the required data analyses. The work carried out will allow us to better understand the biological processes leading to disease development, and thus to propose potential therapies and cures.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE
Title: Pandemic preparedness: local and global concepts and practices in tackling disease threats in Africa
Funder: Wellcome Trust

Abstract: Since the Ebola epidemic in West Africa in 2014-15, the notion of disease ‘preparedness’ has gained prominence in global health policy. Yet ‘preparedness’ remains ambiguous, inviting critical scrutiny. Who, or what, exactly, is being prepared for what, and by whom? We propose research to examine the concept of ‘preparedness’ by exploring diverse meanings and uses of the term from an anthropological perspective, with specific focus on any gap between preparedness as understood in global health, and ‘preparedness from below’ (how communities anticipate and deal with disease threats on a daily basis). Three key themes are addressed - risk and uncertainty, knowledge and information, and agency and responsibility. The meanings of ‘preparedness’ globally, and how the idea is mobilised in policy, research and implementation, will be examined. We also ask what concepts and practices of preparedness might be locally salient in two countries, Sierra Leone and Uganda, and how ideas ‘travel’ both upwards and downwards between local, national, regional and global levels. Examining different perspectives on pandemic preparedness via multi-sited ethnography, oral history, focus groups, interviews and participatory methods, we will identify pathways for connecting them, towards more effective preparedness and response approaches informed by a critical medical anthropology.

Lay abstract: Threats from deadly diseases that spread rapidly in our interconnected world to become pandemics are a growing concern, and international, regional and national agencies are putting in place complex strategies to prepare for and head off future outbreaks. Yet who is being prepared for what in these pandemic preparedness efforts? Are local communities in the places most vulnerable to outbreaks being listened to? Our team’s work during the Ebola epidemic showed how community responses to disease that draw on local knowledge and social relations can complement those proposed by outside agencies. We now want to address ‘preparedness from below’, working closely with communities in Sierra Leone and Uganda to explore how they deal with uncertain health-related threats in their everyday lives, comparing their ideas and practices with those emerging globally, and addressing how a more connected approach could help us be better prepared for future pandemics.

Research activity codes: 8.3 POLICY, ETHICS AND RESEARCH GOVERNANCE
Health categories: GENERIC HEALTH RELEVANCE