NIHRDataInsights/HRCSData huggingface dataset:
Title: Molecular mechanisms and regulation of bacterial transcription in vivo
Funder: Wellcome Trust

Abstract: This research focuses on understanding how simple organisms, such as bacteria, control the conversion of their genes into proteins. This delicate control is essential for the survival and reproduction of all organisms, since it allows them to manufacture the right set of proteins at the right time, at the right place, and at the amounts required. We will study the first and most vital step in the control of gene expression: the start of transcription, a process that converts information store d in DNA into an RNA messenger molecule. Our work focuses on timing the control steps by watching directly an individual molecule of the main transcription machine (a protein called RNA polymerase) opening the gene for reading it and completing the first few reading steps. Using ultra-sensitive light microscopes and fluorescent molecules, we will study these mechanisms both outside and inside single living cells. Our work is unique in that it records dynamic movies of transcription as it hap pens, going much beyond studies that provide only static or blurry images of the machines involved. Our work will help scientists understand how the expression of genes is controlled in complex organisms and discover how some important antibiotics work.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Interlocking nanomechanics of kinesins and tubulins
Funder: Wellcome Trust

Abstract: Kinesin-microtubule systems transport intracellular cargo in eukaryotes and are essential for life. Recently, we discovered that dynamic microtubules can respond to kinesin by changing their conformation, lattice spacing, curvature and stability, and conversely that kinesin stepping can sense and respond to conformational shifts in the microtubule lattice. These insights fundamentally redraw our picture of the function of kinesin-microtubule transport systems. I now propose to dissect the mechanical mechanisms by which kinesins and microtubules instruct one another, using protein engineering combined with single molecule optical trapping at unprecedented resolution. Working with both wild-type and mutant kinesins and tubulins, principally from S. pombe, we will determine the structural requirements for different microtubule lattices to control kinesin substeps, backsteps and bidirectionality; and the converse requirements for kinesins to manipulate the conformation and fate of microtubules. Our experiments will reveal how tubulins communicate mechanically with one another and with kinesins. Illuminating the molecular mechanisms of active mechanical feedback in kinesin-microtubule systems will transform understanding of the transport machinery and open the way to improved chemical biological manipulation of its in vivo function.

Lay abstract: Kinesin-microtubule railways transport cargo in cells and are essential for eukaryotic life. The forces generated by these railways originate in the mechanical cycles of their component molecules. The mechanical cycle of tubulin consumes GTP and drives the dynamic instability of microtubules. The mechanical cycle of kinesins consumes ATP and drives them to step directionally along microtubules. We recently discovered that these two mechanical cycles interlock, so that changes in the structure and mechanics of the microtubule can control patterns of kinesin stepping, whilst motile kinesins can control the curvature, stiffness and longevity of microtubules. I propose to illuminate the molecular mechanisms that connect the mechanical cycles of kinesin and tubulin, using protein engineering combined with single molecule mechanics at unprecedented resolution. Defining the mechanisms by which kinesins and tubulins sense, respond to and manipulate each other's mechanics and dynamics will transform our understanding of the machinery of intracellular transport.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Secretory protein folding, modification and the unfolded protein response
Funder: Wellcome Trust

Abstract: Proteins entering the secretory pathway at the endoplasmic reticulum (ER) undergo a vast array of post-translational modifications some of which are essential for correct folding, assembly and secretion. Failure to fulfil these functions results in several diseases due to the lack of secretion of proteins such as insulin and antibodies, or due to cell death triggered by an unfolded protein stress response. The ER provides a unique environment for protein modifications such as disulfide formation and glycosylation. To ensure efficient protein folding and secretion the cell maintains the environment within the ER that ensures these processes occur efficiently and reacts to situations of cell stress. This proposal builds on exciting new observations from my group to dissect molecular mechanisms involved in secretory protein biogenesis. Our particular focus will be on how the cell maintains ER redox balance, how the repertoire of ER folding factors orchestrate correct protein folding and N-linked glycosylation and how the UPR sensor ATF6 is activated following proteotoxic stress. Our aims will be achieved using a combination of innovative new technological approaches and previously established robust assays to follow protein folding and assembly in both reconstituted and cellular systems.

Lay abstract: The endoplasmic reticulum (ER) is the gateway for proteins to exit cells and plays a key role in ensuring only functional proteins are secreted. Several enzymes and molecular chaperones are located in this organelle with the specific purpose to ensure correct protein folding and to prevent the secretion of misfolded proteins. Breakdown of this folding and quality control system leads to diseases such as diabetes, neurodegeneration and cancer. Here we aim to understand the fundamental processes involved when proteins enter the ER, how the cell maintains the correct environment for folding as well as how the cell responds to stress. We reconstitute some of the processes using isolated components which allows us to dissect the sequence of events following entry of proteins into the ER. A greater understanding of the early stages of the secretory pathway informs the underlying causes of disease as well as potential new therapeutics.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Biomechanics of Ciliated Tissues
Funder: Wellcome Trust

Abstract: Many of the paradigmatic events in embryonic development involve geometric or even topological rearrangements of tissues in response to mechanical forces generated within them. While these processes are familiar and much studied from genetic and biochemical perspectives, there is a striking contrast between the great depth of such biological detail and the glaring lack of quantitative mechanical understanding of the forces and responses involved. We propose to close the theory-experiment loop in specific, carefully chosen examples of these problems, to gain a quantitative understanding of the underlying biomechanics. We seek to solve three outstanding problems: (i) the link between cell shape changes and cell sheet morphology as found in gastrulation, neurulation, and related problems in embryogenesis; (ii) the mechanism of generation of cilia orientational polarity in tissues; (iii) the origin of metachronal wave formation in carpets of cilia. The research will combine state-of-the-art light-sheet microscopy, micromanipulation, high-speed imaging and microfluidics with emerging theoretical tools for understanding complex geometrical transformations of tissues and the stochastic nonlinear dynamics of eukaryotic flagella.

Lay abstract: As embryos develop from the initial mass of cells formed shortly after fertilization they go through a series of remarkable transformations to acquire the form of the adult. Many of these changes involve tissues changing shape in response to mechanical forces generated within them. While these processes are familiar and much studied from genetic and biochemical perspectives, we do not yet have a quantitative understanding of those forces and the response of the tissues to them. In the proposed research we aim to achieve a quantitative understanding of the underlying biomechanics by linking theory and experiment in three carefully chosen examples of these problems. We seek to solve three outstanding problems: (i) the link between cell shape changes and cell sheet geometry as found in such problems as gastrulation, which marks the beginning of the formation of the gastric system; (ii) the mechanism by which carpets of cilia, hairlike appendages whose motion generates fluid flow in many places in the body, develop orientational order; (iii) the origin of metachronal waves in carpets of cilia, variations of the beating pattern on the scale of many cilia. The research will combine state-of-the-art microscopy, micromanipulation, and imaging with emerging theoretical tools.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Global dynamics of mRNA accumulation and translation in embryonic development
Funder: Wellcome Trust

Abstract: The ability of cells to generate complex gene expression patterns is fundamental to multicellular life. While global mRNA levels can now be routinely determined using ‘omics technologies, a major gap in our knowledge is how a cell produces these mRNA levels with the correct temporal dynamics. In addition, the fate of individual mRNAs represents another variable that is rarely globally considered. Therefore, the overarching question addressed in this proposal is: How are global mRNA accumulation dynamics and translatability harmonised with developmental timing to control cell fate decisions? We will exploit the rapid development and tractability of Drosophila to address this question in a developing embryo. We will model the dynamics of mRNA synthesis, processing and degradation across early embryogenesis and integrate these data with the export efficiency and translatability of mRNAs. For individual mRNAs the dynamics will be validated in vivo using live imaging and modeled to give single cell spatiotemporal resolution. For key developmental genes we will perturb mRNA production rates and translatability to determine the effect on protein function and the accuracy and robustness of dorsal-ventral patterning. Overall our data will reveal how dynamic regulation at every step in the gene expression pathway drives developmental patterning.

Lay abstract: During development, cells change their gene expression programme to make new, distinct sets of proteins that turn these cells into particular cell types, eg skin, blood cells, etc. There are multiple steps in the gene expression pathway, including transcription, mRNA processing, export, degradation and translation. The experiments in this proposal are aimed at understanding how the efficiency of each of these steps is controlled and coordinated to generate the required amount of each protein, in order that cells can become the correct cell type. It is proposed to generate large data sets and develop new computational tools to extract information about all the steps in the gene expression process. To confirm our findings we will use advanced imaging methods to visualise the different steps in the gene expression process in real time in living cells. We will then change the efficiencies of particular steps to determine how this affects the ability of a cell to become the correct cell type. Results from this study will provide new insight into how each gene expression step is regulated, and be relevant to many other cell types, including stem cells where the ability to manipulate their fate is critical to their therapeutic use.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Regulatory potential of repeat elements in the evolution of tissue-specific transcription
Funder: Wellcome Trust

Abstract: A surprising fraction of the DNA that contains the information required to make a complex organism like humans is composed of sequences that are repeated thousands to tens of thousands of times called repetitive or repeat elements. Every mammalian genome has a unique collection of repeats, which change in number and location quickly during evolution. Our study tests the hypothesis that different types of repeats carry instructions that can alter when, and in which tissues, nearby genes are turned on. Understanding this is important because changes in gene expression can lead to diseases such as cancer, and are thought to be a central mechanism of species divergence. Our proposal integrates experimental and computational analyses of the function and activity of new-born and ancient repeat sequences in four key tissues in ten species of mammals. We then functionally test their activity with powerful new genetic engineering tools to disrupt or introduce candidate repeats that may be influencing how genes are expressed.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Multi-scale mechanisms of microtubule-based transport within cilia and flagella
Funder: Wellcome Trust

Abstract: The goal of this proposal is to obtain mechanistic insight the microtubule-based transport system that enables cilia/flagella to assemble and perform essential functions in cell motility, signaling, and sensing. Strikingly, this process of intraflagellar transport (IFT) involves multi-megadalton polymers, termed IFT 'trains', which move under the power of oppositely-directed microtubule motors dynein-2 and kinesin Kif3. To address outstanding motor mechanisms of IFT, I propose a multi-disciplinary approach spanning three scales. At the scale of individual motors, we will determine structures of the dynein-2 and Kif3 complexes to elucidate how their subunits come together and enable regulated motor activity. At the scale of multi-motor assemblies, we will reconstitute IFT trains with purified proteins to dissect how they polymerize and coordinate bidirectional motility. At the scale of whole cilia, we will determine how dynein-2 powers IFT turnaround at the ciliary tip and define spatial regulators of dynein-2 in mammalian cells. To achieve these goals, we will use reconstitution and cryo-EM to determine structures, fluorescence microscopy to visualize dynamics, and genome editing to interrogate cellular factors. Together, these studies will illuminate the multi-scale mechanisms that cells use to build and signal through cilia/flagella, which I will integrate into a molecular movie.

Lay abstract: To swim, move fluids, and sense their environment, eukaryotic cells construct long, slender organelles on their surface known as cilia. Defects in cilia are associated with a wide range of severe human developmental disorders. Many of these conditions can be traced to failures in a transportation system that moves building blocks and signalling molecules to and from the site of assembly at the ciliary tip. Using a multi-disciplinary approach, I aim to understand the structural mechanisms of the molecular motors powering this system, how they assemble into multi-motor trains, and how these trains are regulated within cilia to switch direction specifically at the tip. This research will generate new reagents, assays, and discoveries that will help us to understand cilia as self-organising organelles and give insight into the molecular basis of ciliopathies. I will communicate the results via a molecular movie.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: How cell migration and differentiation are coordinated during morphogenesis
Funder: Wellcome Trust

Abstract: During development the embryo needs to generate functional organs composed of many different cell types, often originated in different embryonic location. Thus, it is clear that cell differentiation and migration need to be tightly coordinated, although they are often studied as independent processes. Here I will test the hypothesis that cell migration and differentiations are coordinated by tissue mechanics in vivo. Specifically, I will challenge the current view that cell migration is the result of differentiation, by testing instead whether the reverse occurs, i.e. migration controls differentiation. I will use neural crest cell, a multipotent embryonic cell population in which cell differentiation is always linked to cell migration. One of the problems to study biomechanics in vivo is the limited number of tools to measure and modify mechanical properties in vivo. Here I will develop new tools to analyse and change tissue stiffness in vivo. We will analyse how these mechanical changes influence cell migration and differentiation, and we will identify the molecular response elicited in the neural crest cells. We expect that this multidisciplinary project will provide answers to a central yet unresolved question in developmental biology: how cell fate and migration are integrated during embryo development.

Lay abstract: One-third of all birth defects are accounted by head anomalies, making them a primary cause of infant mortality. Craniofacial birth defects are attributed to problems in neural crest development. Therefore, it is essential to understand the mechanisms that regulate the formation, migration and differentiation of neural crest cells as a prelude to understanding the origins of congenital craniofacial defects and their prevention or repair. IN THIS PROJECT WE WILL STUDY HOW MIGRATION AND DIFFERENTIATION ARE COORDINATED IN THE CEPHALIC NEURAL CREST. Most of the studies on neural crest differentiation are focused on the genes that control this process; HERE WE WILL TEST THE HYPOTHESIS THAT CELL MIGRATION INDUCED BY TISSUE MECHANICS ALSO CONTROLS NEURAL CREST DIFFERENTIATION DURING EMBRYO DEVELOPMENT. Although this project focusses on neural crest, it will set the ground for futures experiments on in vivo biomechanics, with wide implications in cell, developmental and cancer biology.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: From patterning signals to growth and back
Funder: Wellcome Trust

Abstract: During development, pattern formation and tissue growth must be coordinated, suggesting that feedback mechanisms exist between these two processes. Indeed, in some systems, the signals that control pattern formation have been found to be required for growth. Tissue growth is also regulated by dedicated - local and systemic - signals that convey information about tissue architecture and nutritional status. We propose to investigate how these pro-growth signals are integrated. As a first step, we will uncover how patterning signals link molecularly with the cellular growth control machinery. As a model system, we will use Drosophila wing imaginal discs. To overcome the delays associated with traditional genetic analysis, we will develop optogenetic and thermo-sensitive means of controlling signal transduction, focusing on Wingless, a Wnt, and Dpp, a TGF-ß. These tools will be used to identify the patterning signals’ immediate early targets that promote growth, perhaps through regulation of known transducers of systemic signals. In addition, we will investigate whether the activity of patterning signals might be affected by the growth rate, as this could account for scaling. These experiments will uncover, in molecular detail, how various signals are integrated to ensure that tissues grow in a timely and proportionate manner.

Lay abstract: As embryos develop, systemic signals, which convey hormonal and nutritional information, control the growth of its various tissues and organs. At the same time, local signals, sometimes called morphogens, are produced within each tissue to organise positional information within that tissue, ensuring that various cell types are produced in the correct pattern. In well documented cases, these patterning signals have been found also to promote growth, perhaps allowing coordination between patterning and growth. These observations show that individual tissues must integrate local and systemic pro-growth signals. So far, relatively little is known about how morphogens promote growth. Here we propose to first develop means of precisely controlling morphogen signal transduction using light or changes in temperature. This will enable us to identify the molecules that mediate the pro-growth activity of morphogens and to find out how this activity is coordinated with that of other pro-growth signals, local and systemic. We will also ask if, conversely, known growth regulators affect morphogen signalling as this could explain the observation that patterns scale with tissue size. Our experiments will uncover, in molecular detail, how various signals are integrated to ensure that tissues grow in a timely and proportionate manner.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Whole-genome history and evolution in a thousand ancient Britons
Funder: Wellcome Trust

Abstract: On the cusp of the era of precision medicine, data from the British population comprise the world’s most well-characterized resource linking human genomes and traits, with vast information already available from over half a million individuals in initiatives such as the UK Biobank. These resources are producing unparalleled insights into human biology, but the evolutionary processes that shaped human genomic variation—and continue to shape them in the future—can only be fully understood with direct data from the past. Cutting-edge ancient DNA technology now provides unprecedented possibilities to retrieve genome sequences from ancient populations, but few ancient whole genomes from Britain have been published. I propose to undertake reconstruction of fine-scale human evolution by extending available genomic data from the British population into a third dimension—the sequencing of 1,000 ancient genomes. This project aims to: 1. Provide an enduring resource of more than 1,000 genomes from 4,500 years of the Britain's past, and information on sex, relatives, ancestry, and pathogen presence for additional ~2,000 samples. 2. Trace ancestry changes through 4,500 years, untangling present-day population stratification hampering medical genetics studies. 3. Characterise natural selection on single variants and polygenic traits through time, including in response to industrialization, epidemics, and environmental changes.

Lay abstract: The British population is currently the world's most well-studied in the field of human medical genetics. This project extends revolutionary resources of individualized DNA information such as the UK Biobank to a 3rd dimension, by sequencing more than 1000 ancient genomes from the skeletal material of people who lived in Britain during the past 4,500 years. Performing the first fine-scale studies of ancient genomes from a single place will allow us to understand human evolution in response to watershed moments in the past, such as epidemics, dietary shifts, urbanization, and industrialization. It will also aid archaeology and medical genetics by untangling the complex and rich ancestry of present-day British populations through Stone Age, Bronze Age, Iron Age, Roman, Anglo-Saxon, Medieval, and later periods. Collaborating closely with archaeologists, the project will contextualise DNA information about studied individuals, creating new ways to understand the complex tapestry of ancestry through the human past.

Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION
Health categories: GENERIC HEALTH RELEVANCE