- Total grants
- Total funders
- Total recipients
- Earliest award date
- 17 Oct 2005
- Latest award date
- 30 Sep 2020
- Total GBP grants
- Total GBP awarded
- Largest GBP award
- Smallest GBP award
- Total Non-GBP grants
The role of metabolic enzymes in the nucleus 08 Dec 2014
Cells exposed to oxidants re-route their main carbon flow from glycolysis to the pentose phosphate pathway (PPP), by two different mechanisms. One bases on a biochemical block and operates purely on a metabolic level, the other on transcriptional regulation. We found that the two processes compartmentalize over time: After contact with the stressor, the cell induces the metabolic transition in seconds-timescale but it takes minutes until transcripts raise. Remarkably, metabolic changes seem cau sally implicated in regulating this process: induction of the transition activates transcripts of the antioxidant-system. It is the aim of this proposal to identify and analyze regulatory mechanisms which surround the involved metabolic pathways on a genome-scale level. For this, we will develop multiple reaction monitoring (MRM) assays that allow fast quantification of metabolic intermediates, and screen an entire yeast knock-out library composed of 5,200 systematically generated yeast mutants to identify all gene deletions which cause specific changes in the concentration of their intermediates. In a second step, by using a targeted proteomics strategy, these mutants will be screened to identify alterations in the abundance of implicated enzymes. The identified genetic/metabolome interactions are studied for their general importance on metabolism, and analyzed in respect of yeast aging phenotypes.
Functional imaging studies (PET and fMRI) have revealed that human speech is processed along distinct (though interacting) streams, in ways that are analogous to the functional and anatomical auditory streams seen in animal primate studies. I am proposing a series of studies in which aspects of human speech perception and production are investigated, to identify the neural basis of low level and higher-order control of speech perception, the neural basis of production and perception of speech in different masking contexts, and plasticity and individual differences in speech processing. I am particularly interested in how we can apply these results to the understanding of clinical issues (e.g. aphasic stroke and cochlear implantation), and will address the latter with studies of cochlear implant users and simulations. I also aim to extend this work to consider how the importance of social factors, such as how communicative intent affects the neural regions recruited in addition to those involved in the linguistic processing of speech. This is an attempt to integrate the neurobiology of speech perception and production with themes in social neuroscience, and important link to establish, given the central role of speech as a communication tool.
My two main and interrelated research questions are: How are different cargoesselected for incorporation into different transport vesicles? How are organelle biogenesis membrane fusion events regulated? Both processes require the complex interplay between many proteins and must also involve interactions with phospholipid membrane components. In the cell, all of theseinteractions must be temporally and spatially regulated to allow cellular lifeto continue and so we also want to understand how such regulation is achieved.We also wish to investigate how certain pathogens, especially retroviruses, recruit the cell's vesicle trafficking machinery to facilitate infection.
Interdisciplinary Training Programme for Clinicians in Translational Medicine and Therapeutics at the University of Cambridge: Support for the 2014 MPhil Appointments. 15 Dec 2014
<table> <tbody> <tr> <td>We propose an innovative training scheme for Translational Medicine and Therapeutics (TMAT) which builds on the exceptional conjunction on the Cambridge campus of leading scientists and clinical specialists, with an industrial research environment embraced both by international pharmaceutical and local biotech companies. Much of this is found under the same roof, the Addenbrookes Centre for Clinical Investigation (ACCI), with a track record of integrated training: academic with industrial, clinical with scientific, pharmacology & therapeutics with patient-based specialties. The novel TMAT programme will attract the brightest candidates at several levels of seniority, ranging from MB PhD students to clinical lecturers, some wishing translational skills in their chosen specialty, others not yet differentiated who may become future leaders and teachers of TMAT. Each trainee will have a customised programme. Part of this will be a bespoke, modular MSc modelled on the well-known small-group lectures and supervisions of the Cambridge final year undergraduate courses. However the centrepiece for most candidates will be a PhD including formal teaching in a wide range of translational and pharmacological skills, and a project which takes proof-of-concept studies in cell or animal systems forward to proof-of-concept studies in humans. We have assembled an outstanding faculty of PhD supervisors spanning a wide choice of skills and experience in basic and clinical science. All trainees will have the opportunity for hands-on exposure to the design and conduct of experimental medicine studies investigating the therapeutic potential of new drugs, in collaboration with our industrial partner, GlaxoSmithKline (GSK). Our product will be a new generation of clinician scientists with 360-degree vision of the complex landscape of modern therapeutic medicine, who can rise to the challenges and opportunities of 21st century drug development.</td> </tr> </tbody> </table>
<p>Circulating cell free tumour DNA (ctDNA) concentrations correlate very closely with cancer burden. Current techniques can reliably detect ctDNA at frequencies above 2% (as occurs in metastatic disease) however the identification of ctDNA in early malignancy remains a challenge. It is my aim to develop technologies to detect ctDNA at very low allelic frequencies, using a cohort of patients with active early stage breast cancer receiving chemotherapy. Following the identification of tumour mutations by exome sequencing, I will track these mutations within the plasma using microfluidic technologies and targeted sequencing.</p> <p>Concurrently, I will design and initiate a pilot trial to gather serial blood samples from patients with early stage breast cancer who are being treated radically, in order to investigate whether ctDNA is detectable before clinically confirmed disease recurrence. If this is the case, then trials could be designed to determine whether ctDNA can be used as a screening tool for relapse.</p> <p>Finally, using tumour and plasma sequencing, I aim to characterise how a previously treatment naiive tumour evolves when subjected to chemotherapy. Using probabilistic models, this could allow us to predict response to treatment given a certain molecular signature.</p>
<p>Parkinson's disease (PO) is common, affecting between 2-3% of people over the age of 65 with over half of patients developing dementia within ten years. This causes a decline in function and often leads to nursing home care. The involvement of the immune system in PO has been well described but it remains unclear whether this is an epiphenomenon. I hypothesise that the immune response to PO associated pathology contributes to disease progression, increasing the risk of dementia. My PhD will look at the role played by 8 lymphocytes as most research has focused on T lymphocytes or the innate immune system. I aim to characterise the 8 lymphocyte response associated with alpha synuclein pathology in both the mouse and human brain and to identify whether there are perturbations in the systemic 8 cell compartment in patients at high risk of dementia versus those who have a low risk. Using two mouse models of PO I will manipulate B cells to see whether 8cell depletion, antibody depletion or manipulation of 8 cell regulatory activity alters disease course thereby confirming causation in an animal model.</p>
<p>Traumatic axonal injury of the brain (TAlB) is a common and devastating type of acquired brain injury. The injury is mediated through direct axonal damage and a cascade of secondary injury factors including local inflammatory response and energy failure. Understanding the response of axons is important in order to try and salvage injured axons from cell death and prevent progressive neurodegeneration.</p> <p>Hypotheses to be tested:</p> <p> • An <em>in vitro </em>primary culture/organotypic injury model can accurately represent the structural and functional changes found in human TAIB.</p> <p> • TAIB impairs Axonal transport, resulting in</p> <p>o axonal varicosities</p> <p>o failure to deliver axon survival factors resulting in Wallerian degeneration o aberrant protein expression</p> <p>• TAIB induced a proinflammatory cascade of signalling that o Contributes to axonal transport defects</p> <p>o mediates persistent neurodegeneration</p> <p> • Altering the inflammatory/microglial response can</p> <p>o promote neuronal survival and salvage injured neurons o mitigate varicosity formation</p> <p>o terminate aberrant protein expression and long-term neurodegeneration</p> <p>• TAlB triggers a progressive neurodegenerative process</p> <p> I will use stretch models of injury and/or addition of pro-inflammatory cytokines and cytokine blockade in variety of culture subtypes, including dispersed cortical cultures, organotypic slices and cortical explants. I will examine live-iimaging markers of transport in various injury states.</p>
<p>CTCF is a DNA-binding protein that regulates enhancer-promoter interactions and defines transcriptional and chromatin domains. CTCF-binding elements and the location of its chromatin binding sites are much more highly conserved across species than other transcription factors, supporting an integral role of CTCF in genomic stability. Indeed, CTCF has been implicated as a tumour supressor gene: Ctcf haploinsufficient mice develop multiple spontaneous tumours, and CTCF mutations have been identified in human malignancies.<br>My study will investigate how altering the genomic concentration of a major chromatin organising factor impacts genome organisation, stability, and unltimately cancer formation. To accomplish this we will analyse chemically induced tumours in a genetically engineered mouse model using functional genomics and proteomics.In aim 1 we will explore which tumour suppressors and oncogenes are near CTCF binding sites and are sensitive to CTCF depletion. In aim 2 we will explore which chromatin organisation machineries are directly dependant on proper CTCF expression by whole proteome analysis. In aim 3 we will use a chemical carcinogen N-nitrosodiethylamine to examine the effect of CTCF loss on hepatocarcenogenisis. Together my Aims will help reveal the mechanisms by which CTCF controls the genome organisation required for tissue homeostatsis and which molecular players facilitate carcinogenisis.</p>
<p>Recent collaborative work demonstrated that mitochondrial DNA (mtDNA) damage and mitochondrial dysfunction occur early in atherosclerosis and that they are linked to vascular smooth muscle cell (VSMC) senescence and cell death as well as pro-inflammatory signalling through monocytes. Importantly, mitochondrial DNA damage is also correlated with atherosclerosis and features of plaque vulnerability in humans (Yu et al Circulation 2013). However, the mechanisms by which mitochondrial DNA damage and dysfunction are linked to early atherosclerosis are currently not elucidated. While some of these effects are likely mediated through reactive oxygen species (ROS), many are not. In particular, although many genes associated with inflammation are redox-regulated, mitochondrial DNA that has been damaged can also act as a damage associated moleculal pattern (DAMP) further perpetuating inflammation in part via the NLRP3 inflammasome and/or toll­ like receptors. Interestingly recent studies have suggested that inflammation can induce a metabolic shift in cells from oxidative phosphorylation to glycolysis. This so called Warburg effect is observed in cancer cells but more recently was also linked to activation of inflammatory cells.This application will investigate the link between mitochondrial dysfunction, metabolism and inflammation in the early stages of atherosclerosis:</p> <p>1. Identify the time course of mtDNA damage/dysfunction and determine how mitochondrial metabolism alters in early atherosclerosis.</p> <p>2. Identify redox-regulated proteins that are altered in early atherosclerosis and after exposure of smooth muscle cells to known mediators of atherosclerosis and inflammation.</p> <p>3. Determine whether improvement of mitochondrial function by increasing mtDNA copy number prevents atherosclerosis.</p>
Male reproduction provides a rich site for exploring a variety of sociological themes and pressing social issues, including gender, sexuality, sexual orientation, global inequality, eugenics, ethics, epigenetics, environmental degradation, reproductive tourism, state-building, veteran rehabilitation, HIV stigma, and alternative family building. All of these themes will be explored at the upcoming male sterility/infertility meeting, to be held September 11-12, 2014 at the University of Cambridge. The aims of this interdisciplinary meeting are to lay the groundwork for the emerging field of male reproductive studies, advance interdisciplinary dialogue, and identify the theoretical concepts that bridge research across disciplines. Presenters include world-class scholars whose work is dedicated to the socio-historical study of male sterility/infertility. Invited presenters include five historians, five anthropologists, five sociologists, and one psychologist. Each scholar will present a pa per on original research findings and each paper will be discussed and workshopped by the group. The meetings are open to the public and registration is free. Following the conference, papers will be revised and organised into an edited volume.
<p>Neutrophils are key effectors of antibacterial immunity and inflammation. These cells often migrate in a highly co-ordinated and directed manner in order to reach sites of infection. This so-called ‘swarming’ response was shown to depend on self-production of the neutrophil attractant, LTB4. However, the cellular dynamics underlying transition from exploratory, single cell migration to collective and highly directional migration remain unclear. To address this knowledge gap I will use in vivo imaging and genetic manipulations in a zebrafish model. I will first determine the cellular triggers for LTB 4 production by neutrophils <em>in situ</em>. For this I will make transgenic fish expressing a reporter probe for LTB 4 production. Then I will investigate how LTB4 autocrine/paracrine signalling directs neutrophil polarity and migration. For this I will directly monitor autocrine/paracrine signalling using an additional probe for LTB 4 sensing. Finally I aim to spatiotemporally manipulate LTB 4 production and neutrophil swarming in vivo. To this end, I will develop an optogenetic tool to control the production of LTB 4 by light and use this to establish the implications of neutrophil swarming in microbial defence and tissue integrity. Thus, this study will provide a better understanding of how neutrophils self-organise their migration to sites of infection</p>
<p>A critical step in pathogenesis of enteric bacteria such as <em>Salmonella </em>is hijacking the host cell. This event depends on the type three secretion system (T3SS) which enables the delivery of subversive virulence effectors into the host 3,11. A hydrophobic protein called SipB is part of the T3SS and forms the translocon element 3. While the mechanism of effector translocation across the host cell plasma membrane remains elusive, previous work in our lab revealed that SipB is essential for translocation and has liposome fusion activity 7. When fusion is inhibited with a truncated derivative of SipB (SipB428-593), <em>Salmonella </em>entry into host cells is prevented6. The aim of this project is to build upon this foundation to research the mechanism of effector delivery into host cells. We will use established i<em>n vitro </em>liposome fusion assays – together with biochemical reconstitution and high-resolution structural studies – to reveal the mechanism of translocation. Following the successful work with SipB 428-593, we aspire to screen natural extracts and synthetic compound libraries in search of a T3SS inhibitor, which could have therapeutic value. Finally, we will also extend our work onto homologous T3S systems from other pathogens, such as <em>Shigella</em>, <em>Yersinia </em>and <em>E. coli</em>.</p>
Investigating!the!influence!and!therapeutic!potential!of!RNA!G^quadruplex!structures!on!positive! 14 Jul 2014
<p>An!increasing!body!of!evidence!suggests!that!RNA!secondary!structures,!such!as!G] quadruplexes!and!stem]loops,!play!crucial!roles!in!the!regulation!of!translation!and!RNA! replication!during!viral!infection.!Our!ability!to!exploit!such!RNA!structures!therapeutically!is! dependent!upon!our!knowledge!of!how!they!act,!which!remains!unclear.!!One!goal!of!this! research!is!to!systematically!identify!and!examine!the!influence!of!RNA!G]quadruplexes! present!in!the!coding!regions!of!two!widely!used!model!calciviruses.!Using!the!established! reverse!genetic!systems!for!these!viruses,!the!effects!of!mutations!that!alter!the!presence!and! distribution!of!G]quadruplex!structures!can!be!studied,!both!in!terms!of!virus!efficiency!and!rate! of!RNA!synthesis!in!cell!culture.!If!suitable!mutated!viruses!are!obtained,!the!persistence!of! these!viruses!within!a!small!animal!model!will!be!examined!which!will!give!insights!into!the! suitability!of!such!modified!viruses!for!use!as!vaccines.!The!second!goal!of!this!research!is!to! investigate!the!mechanisms!by!which!helicases!control!the!regulation!imposed!by!such!RNA! structures.!Using!a!reconstitution!system!for!translation!initiation!<em>in&vitro</em>,!the!hierarchy!between! different!RNA!secondary!structures!and!the!helicases!that!mediate!their!unwinding!can!be! examined.</p>
<p>One of the main questions still puzzling developmental biologists today is how morphogens direct the patterning and growth of different tissues. To address this question, I plan to study the Bone Morphogenetic Protein 2/4 (BMP2/4)-like ligand Decapentaplegic (Dpp) in <em>Drosophila </em>melanogaster. In the wing imaginal disc, Dpp is secreted from a stripe of cells that is located at the boundary between the anterior (A) and posterior (P) compartments and is thought to form a ong-range signalling gradient. In turn, this gradient regulates the activation of target genes that correctly position wing veins along the AP axis. Many studies have focused on unravelling the mechanism by which Dpp patterns the wing imaginal disc and how this signalling feeds into growth. However, the function of Dpp in regulating growth and proliferation still remains unclear. I will use a conditional allele to genetically remove Dpp from the wing disc at different developmental time points and assess the effect on wing disc growth. My long-term plans include finding a novel way to modulate Dpp signalling (i.e. through optogenetic techniques). By doing this, I hope to gain insight into how morphogens provide cells with positional information in a developing organ.</p>
<table> <tbody> <tr> <td><span style="font-size: medium;"><span style="font-size: medium;"></span></span> <p>The main aim of my research is to develop new techniques for investigating transmission events in influenza A virus. These techniques will be mathematical and computational in nature and revolve around the use of publicly available time-resolved within-host data. Specifically, I propose to use maximum likelihood methods to extract information on transmission bottleneck size and selection based on the time-evolution of genetic variants. As a secondary aim, I wish to extend my methods (and perhaps those of other authors) to allow for analysis of other viral species such as HIV, norovirus and picornavirus (foot-and-mouth disease). Influenza virus is particularly convenient to work with as it has a short lifetime, large population size and lacks homologous recombination, however, other RNA viruses are more complicated in these aspects. As a result of this, my initial algorithm may require important adjustments to reflect this.</p> <p>Key goals:</p> <span style="font-size: medium;"><span style="font-size: medium;"></span></span> <p>? Incorporation of genetic selection to my model developed during research rotation</p> <span style="font-size: medium;"><span style="font-size: medium;"></span></span> <p>? Implementation of Gaussian transmission step in maximum likelihood approach leading to a more tractable algorithm</p> <span style="font-size: medium;"><span style="font-size: medium;"></span></span> <p>? Extension of algorithm to allow for analysis of multiple gene segments</p> <span style="font-size: medium;"><span style="font-size: medium;"></span></span> <p>? Analysis of existing influenza datasets</p> <span style="font-size: medium;"><span style="font-size: medium;"></span></span> <p>? Extension to and analysis of other RNA virus species</p> <p> </p> </td> <td> </td> </tr> </tbody> </table>
<p>This project will develop and apply novel network-theoretic approaches to study the regulation of RNA transcription on the basis of multiple molecular phenotypes. In particular, we seek to more accurately characterise the regulatory mechanisms that drive haematopoiesis (the process during which stem cells differentiate into more function-specific blood cells) by combining complementary -omic datasets.</p> <p>The methodological aims of the project:</p> <p>i. Develop a flexible Bayesian procedure for the estimation of high-dimensional covariance matrices.</p> <p>ii. Apply such inference tools to reconstruct interaction networks.</p> <p>iii. Extend the model to incorporate multiple sources of information.</p> <p>The applied aims:</p> <p>iv. Improve understanding of haematopoiesis by characterising cell differentiation lineages, specifically the lineages of the Megakaryocyte Erythrocyte Progenitor cell and the Neutrophil lineage of the Granulocyte Monocyte Progenitor cell. This will be done using the method in</p> <p>(iii) by combining multi-omic datasets, including RNA-seq and Chip-seq, as well as the physical network provided by promoter capture Hi-C experiments. v. Reconstruct gene-interaction networks based on single-cell sequencing data, taking into account the strong technical variability that characterises these experiments. We expect this analysis to reveal interactions that have been masked by bulk experiments, where only overall expression over thousands of cells is recorded</p>
Lewis Wolpert famously called gastrulation the most important time in your life. During this fascinating process, a pluripotent stem cell population in the early embryo gives rise to the three germ layers from which all organ systems develop. Cell signalling and transcriptional networks are known to regulate aspects of gastrulation, but the precise mechanisms have not been investigated at the single cell level. Thus, new principles remain to be discovered that govern the exit from na ve pluripot ency, epigenetic priming, stochasticity in transcriptional programmes, symmetry breaking, and acquisition of heritable transcriptome patterns. We have brought together a consortium of experts in single cell genomics, mammalian postimplantation development, and computational biology to comprehensively tackle this challenge. We will apply recently established single cell genomics techniques for DNA, RNA, and DNA methylation to profile the majority of the cells in mouse postimplantation embryos. Th is will result in epigenetic and gene expression maps of most cells together with experimentally determined lineage relationships, hence populating a Waddingtonian landscape. Based on such maps, combinations of transcription factors and epigenetic modifiers will be used to experimentally direct differentiation in human iPS cells.