- Total grants
- Total funders
- Total recipients
- Earliest award date
- 24 Jan 2017
- Latest award date
- 30 Dec 2017
- Total GBP grants
- Total GBP awarded
- Largest GBP award
- Smallest GBP award
- Total Non-GBP grants
Myelinating and non-myelinating Schwann cells are reprogrammed after nerve injury into repair Schwann cells, specialized for maintaining survival of injured neurons and supporting axonal regeneration. This process is regulated by Schwann cell-intrinsic signals, such as the transcription factor c-Jun, however few other candidates have been identified. It is, currently, unknown how Schwann cell reprogramming is initiated, but unidentified extrinsic signals from injured axons are likely candidates. I aim to delineate the spatial and temporal regulation of Schwann cell-intrinsic downstream signals in real-time and define their role in repair Schwann cell function and axonal regeneration. Secondly, I aim to test the hypothesis that axon-derived signals initiate Schwann cell reprogramming during nerve injury. I will use cell culture, in vivo mouse models and a live and dynamic zebrafish larval model of nerve injury. This study will be the first to investigate how axon-intrinsic mechanisms of nervous system injury interplay with glial cell molecular responses to nerve damage, in real-time. Using cutting edge techniques in two species, this project will significantly advance our understanding of Schwann cell-axonal biology and tissue repair. Excitingly, this research may identify new potential therapeutic targets to improve poorly regenerating human nerves and treat patients with neuropathies.
This proposal is to develop an end-to-end system for processing samples from viral outbreaks to generate real-time epidemiological information that is interpretable and actionable by public health bodies. Fast evolving RNA viruses (such as Ebola, MERS, SARS, influenza etc) continually accumulate changes in their genomes that can be used to reconstruct the epidemiological processes that drive the epidemic. Based around a recently developed, single-molecule portable sequencing instrument, the MinION, we will create a 'lab-in-a-suitcase' that will be deployed to remote and resource-limited locations. These will be used to sequence viral genomes from infected patients which will then be uploaded to a central database for rapid analysis. We will develop methods for a wide-range of emerging viral diseases. Novel molecular biology methods will allow us to sequence individual viruses within a patient. Bioinformatics tools will be developed simple enough for non-bioinformaticians to use, without reliance on Internet connectivity. We will develop software to integrate these data and associated epidemiological knowledge to reveal the processes of transmission, virus evolution and epidemiological linkage. Finally we will develop a web-based visualization platform where the outputs of the statistical analyses can be interrogated for epidemiological insights within days of samples being taken from patients.
The folding of genomic DNA from the beads-on-a-string like structure of nucleosomes into higher order assemblies is critically linked to nuclear processes, but it is unclear to what degree it is a cause or consequence of function. We aim to understand whether the Nucleosome Remodeling and Deacetylation (NuRD) complex regulates chromatin structure to control transcription, or whether it is NuRD’s regulation of transcription that results in global changes in chromosome structure. We have calculated the first 3D structures of entire mammalian genomes using a new chromosome conformation capture procedure, which combines imaging with Hi-C processing of the same single cell. Our objectives are now: To study: 1) how interphase mammalian genome structure is established in G1; 2) the factors that drive this formation and; 3) how this organisation is regulated by chromatin remodellers (such as the NuRD complex) as mESC’s differentiate. To build a dedicated bespoke microscope for 3D double helix point spread function detection with light sheet activation, optimised for 3D single-molecule/super-resolution imaging of proteins such as the NuRD complex. To combine 3D super-resolution imaging and the biochemical processing steps of single cell Hi-C to directly correlate binding of protein complexes to regions of the structures.
A role for RNA binding and processing proteins in the control of eukaryotic cellular processes and in disease, including cancer, is emerging . I led the initial sequencing of the myeloma genome at the Broad Institute of MIT and Harvard. A key finding was mutations in RNA processing genes, DIS3 or FAM46C in 25% of cases. These findings have been independently corroborated, establishing these mutations as genuine drivers of the disease. DIS3 is the catalytic component of the exosome, an essenti al RNA processing complex. FAM46C is poorly characterized, but available evidence suggests it has roles in RNA processing in a lineage-dependent manner. This proposal seeks to better characterize these genes and mutations. Characterization of FAM46C mutations will be performed by knock-out of the gene from the DT40 cell line, determination of phenotype and rescue experiments. Lineage-dependent transcriptional pathways affected by altered transcript stability will be identified by RNA sequenci ng and confirmed in primary myeloma samples. Known aberrant RNA processing phenotypes associated with DIS3 loss/mutation will be sought by RNA sequencing in primary myeloma samples. The pathways affected by mutant DIS3 in myeloma will be identified using yeast genetic screens and classical yeast complementation experiments.
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.
Unconventional protein secretion is a poorly understood physiological process in which proteins without an N-terminal signal sequence exit the cell. There are currently four proposed pathways by which unconventionally secreted proteins are thought to exit the cell: by direct translocation across the membrane, via secretory lysosomes, by release from exosomes or multivesicular bodies, or through membrane blebbing. No complete mechanism has been described for any of these pathways, representing a significant gap in our knowledge of protein trafficking. Unconventionally secreted proteins play important extracellular roles physiologically, but abnormal levels are associated with several human diseases, including metabolic disease. As such, this mechanism is interesting to gain an insight into disease as well as to broaden our understanding of cell biology. I will investigate the unconventional transport of galectin-3 to the cell surface. Galectin-3 will here be used as a model to understand the mechanism of unconventional secretion. Data-driven and hypothesis-driven approaches will feed into each other to form a picture of how galectin-3 is secreted. A CRISPR-Cas9 screen has identified potential proteins that decrease cell surface galectin-3, providing the starting point for further investigation. Hypothesis-driven experiments will be used to investigate aspects of the models previously proposed.
During both mouse and human embryonic development there are two waves of global DNA demethylation associated with an increase in developmental potential: firstly during the development of the inner cell mass from the gametes, and secondly during the development of primordial germ cells. Although some of these changes in DNA methylation are correlated with gene expression, it is not understood why this epigenetic reprogramming is consistently so extensive. Until recently it was believed that most of this erasure of DNA methylation occurred actively. However, recent research has revealed that regulation of maintenance methylation accounts for the differing rates of demethylation in different reprogramming contexts. Across the majority of these different contexts, the activity of maintenance methylation is controlled by regulation of UHRF1 protein. This project aims to elucidate the mechanism by which UHRF1 protein is regulated during epigenetic reprogramming, then to use this knowledge to assess the importance of this regulation to the acquisition of pluripotency during mammalian embryonic development. This will improve our understanding of developmental and reproductive health and may even shed light on new or improved methods of reprogramming cells for therapeutic applications.
An important area in drug development is understanding low-level molecular processes and pathways that cause diseases. These cellular phenotypes are high-dimensional and are increasingly being captured using single-cell assays and high-content imaging. In understanding natural cell trait variation and engineered variants, we can elucidate the cellular consequences of disease mutations. In my project, I will exploit cellular images in a range of contexts to investigate the link between genetic variation and cell trait variability using both natural genetic variation and engineered variants. To do so, I will develop machine learning methods to extract features from high throughput microscopy data, and to accurately account for genetic, environmental, and experimental sources of variability in them. Furthermore, I will work on integrative approaches using public genomic data to bring in other omics modalities, thereby tackling key challenges in the larger aim of deciphering disease and fostering drug development. I will use existing data from the HipSci project, high throughput drug screens from AstraZeneca, and, in addition, will design and oversee the generation of datasets through high-throughput CRISPR knockouts as part of Leopold Parts’ group at the Wellcome Trust Sanger Institute and Oliver Stegle’s group at the European Bioinformatics Institute.
Single-cell genomics is a fantastic tool for studying developmental biology: it allows unbiased and large-scale study of gene expression at the correct resolution for cell fate decision making. New fluidics systems provide the capability to study tens of thousands of cells simultaneously - as many as there are in the young embryo. For my PhD, I will analyse scRNA-seq data generated on this platform, studying mouse gastrulation between E6.5 and E8. I will be able to study this process at both an exceptional cell-level resolution (thanks to the fluidics) and at an unprecedented time resolution, at 0.1 day intervals. My focus will be on identification of lineage specification, and how cells make their fate choices. I will need to develop new methods to account for the large numbers of cells assayed, the numerous lineage decisions made, and heterogeneity of speeds of development across and between embryos. I hope to produce a map of lineage specification from epiblast (E6.5) cells through to every cell type present at E8. This work will provide a developmental atlas through gastrulation, and general inferences on cell fate decisions may provide insight for cellular reprogramming and regenerative medicine.
Functional proteomic analysis of novel antiviral restriction factors in primary leukocytes 31 Jan 2017
This project aims to identify and characterise novel antiviral restriction factors (ARFs) that play key roles in preventing infection of primary leukocytes. ARFs may function by preventing viral entry or exit at the cell surface, or replication at various intracellular stages. I will focus on the subset of plasma membrane (PM) ARFs, which will be identified by two properties: interferon (IFN) induction and virally-induced downregulation. For this I will employ tandem mass tag-based MS3 mass spectrometry, enabling quantitation of PM proteins in primary leukocytes. Key Goals: 1. Use IFNs and infection with two important human pathogens, human cytomegalovirus and HIV as a functional screen to identify novel cell surface ARFs 2. Investigate how these ARFs inhibit viral infection, and how are they targeted for destruction by viruses. The use of IFN as part of the functional screen will additionally enable exploration of the difference in effects between IFNalpha, beta and lambda at the PM, a subject which is currently surprisingly poorly understood. This will provide important insights into human immunity in its own right. Understanding how viruses interacts with and targets ARFs for destruction will have important implications for therapy.
Attachment and the transgenerational effects of loss, abuse and trauma: Exploring and testing classic ideas through historical analysis and developmental science 02 May 2017
Since it was introduced by John Bowlby, attachment research has been among the most influential paradigms for understanding the social underpinnings of infant mental health and transgenerational mental health. However, an odd artefact of the way a major research instrument was constructed in the 1980s by Mary Main has meant that to date attachment research has largely treated loss, abuse, and trauma as essentially equivalent, despite their very different clinical implications. A multidisciplinary approach will be used to investigate these concepts and examine potential differences. Work Package 1 will comprise a critical re-examination of the concepts of loss, abuse and trauma in the published and unpublished works by John Bowlby and Mary Main, exploring their reflections on how these experiences might impact parenting. In Work Package 2, hypotheses elaborated in Work Package 1 will be tested using Individual Participant Data pooled from 59 attachment studies, representing 4,542 families. Work Package 3 tests explanations for differential effects of unresolved loss, abuse and trauma on parenting and child development using longitudinal data from 400 mothers and children. The study will shed new light on transgenerational mental health processes, and insights will be disseminated to professionals and families.
Obesity and associated diseases such as type 2 diabetes, cardiovascular disease and some cancers represent a significant health burden. My overall aim is to identify new therapeutic strategies for severe obesity. Using extensive genetic and clinical data on unique cohorts of individuals at both extremes of the weight distribution (severe obesity and thinness), we will comprehensively map the molecular networks that maintain energy homeostasis and their disruption in disorders of weight regulation. Building on our previous work, we will focus on dissecting cellular mechanisms that converge on leptin-melanocortin signalling using human stem-cell derived hypothalamic neurons. In human studies, we will characterise the effects of specific pathways on eating behaviour, energy expenditure and substrate utilisation. By uncovering the fundamental mechanisms that control human energy homeostasis, our goal is to identify and validate control points that can be targeted to improve outcomes in obesity associated diseases.
This project will produce a history of marriage and health in early modern England. Marriage is generally understood as an institution governed by legal and religious regulations and social norms that have taken different forms throughout history. In post-Reformation England marriage was increasingly regulated and interrogated. Performing gendered spousal roles was part of religious practice, something perpetuated by the growing culture of conduct manuals. A central obligation of marriage was to care for one another in sickness. This has underpinned histories of domestic medicine that reveal that the early modern family was active in diagnosis and cure. The two major goals of this project are (1) To assess how good health defined a successful marriage in early modern England and (2) To investigate how the social norms and expectations of marriage changed over the course of a union. As part of this inquiry, subsidiary goals will be (3) To interrogate how marital compatibility was measured, (4) How poor health of one spouse affected the other, and (5) How illness impacted on the household as a whole. Finally, this project aims (6) To uncover how cultural expectations shaped the way early modern people wrote about marriage.
Mammalian embryogenesis entails close partnership between embryonic and extra-embryonic tissues to regulate changes in embryo architecture and developmental potency. We aim for an integrated view of how these events progress hand in hand during key stages of mouse and human embryogenesis. The first architectural changes of the embryo are polarisation and compaction that trigger the separation of embryonic and extra-embryonic lineages. Yet their own trigger remains unknown. We will dissect potential triggering pathways and through genetic manipulations determine their importance for cell fate. Embryo remodelling at implantation is intimately associated with pluripotent-state transitions. We will harness our novel techniques for embryo culture throughout implantation to uncover mechanisms behind these events in relation to signalling partnerships between embryonic and extra-embryonic tissues. By arranging partnership between embryonic and extra-embryonic stem cells in 3D-culture we have recapitulated embryo-like morphogenesis and spatio-temporal gene-expression. We will characterise tissue interactions in such stem cell-derived embryos to understand principles of self-organisation. Our work established an unprecedented opportunity to study human early post-implantation embryogenesis in-vitro. We will build the first morphological and transcriptional atlas of human development beyond implantation. This will bring understanding of normal development and shed light upon why many pregnancies fail at early stages.
The development of novel strategies against influenza viruses depends on our understanding of influenza virus replication and pathogenicity. The former largely depends on the activity of the viral RNA polymerase, which copies and transcribes the viral genome, while the latter is multifaceted and influenced by both viral and host factors. Interestingly, recent findings show that the RNA polymerases of highly pathogenic influenza A viruses produce short RNAs, or mini viral RNAs (mvRNAs), which are non-contiguous in the viral genome and strong inducers of the interferon response. Because they are not made by RNA polymerases of seasonal influenza strains, mvRNA synthesis may be a transformational advance in our understanding of the ‘cytokine storm’ that underlies the pathogenicity of virulent influenza viruses. Unfortunately, our basic understanding of the influenza RNA polymerase is limited and it is unclear how the mvRNAs are made. I here plan to use single-molecule FRET, deep-sequencing and structure-guided mutagenesis to advance our basic understanding of influenza virus RNA synthesis, focussing on the molecular mechanics behind i) influenza transcription initiation, ii) the differences between the RNA polymerases of highly pathogenic and seasonal influenza strains, and iii) the action of influenza inhibitors that target the RNA polymerase.
The nuclear envelope (NE) lies at the interface between the nucleus and the cytoskeleton. It forms a complex structure controlling cell compartmentalization and regulates many processes including nucleo-cytoplasmic transport of proteins and RNA, chromatin organization, DNA replication and DNA repair. Hence, defects in NE integrity and nuclear architecture cause drastic changes in cell homeostasis and are associated with a broad range of diseases including cancer, premature ageing syndromes, neurodegenerative diseases or muscular dystrophies, but also with physiological ageing. One of the main challenges is to understand how NE defects lead to so many types of diseases. Previous theories include changes in gene expression and mechanical weakness. My previous work has shown that subcellular processes including microtubule or chromatin organization can modulate NE function, and has identified the acetyltransferase NAT10 as a key regulatory node for control of nuclear architecture. My goal is to now investigate how NAT10 and other factors regulate the NE. I will thereby gain new understanding of how of nuclear architecture is orchestrated and how this is disrupted in age-related diseases including HGPS. This research will not only contribute to our fundamental understanding of nuclear architecture but will also potentially identify new therapeutic strategies for NE-associated syndromes.
Neurophysiology of nutrient rewards 22 Feb 2017
Optimal human food intake goes beyond reactive consumption and involves sophisticated behaviours that fine-tune food acquisition to our specific needs. Every day, we form decisions and consumption-plans to pursue our favourite foods, and model food choices from our social partners. This proposal develops a novel translational approach to study the neural mechanisms for realistic food-intake behaviours involving planning, decision-making, and social learning. We perform single-neuron recordings in amygdala, hypothalamus, and orbitofrontal cortex during feeding behaviour for clinically relevant nutrients, including fats and sugars. Separate research aims focus on two aspects of food intake: (1) planning and decision-making for specific nutrient rewards; (2) social influences on food choice. Neuroimaging with identical foods and behaviours extends single-cell data to brain networks, functional connectivity, individual differences, and real-life eating phenotypes. We advance the field by identifying explicit neuronal signals that underlie formation and pursuit of nutrient consumption-plans; by formalizing behavioural conditions for social nutrient-reward learning; and by identifying neuronal signals that underlie such learning and related social influences on food choice. By studying sophisticated, typical food intake in single neurons, neural systems, and behaviour, we aim to uncover basic neurophysiological mechanisms and lay foundations for clinical studies in obesity.