- Total grants
- Total funders
- Total recipients
- Earliest award date
- 20 Nov 1998
- Latest award date
- 05 May 2020
- Total GBP grants
- Total GBP awarded
- Largest GBP award
- Smallest GBP award
- Total Non-GBP grants
My research proposal is to continue the development and application of advanced statistical, computational-chemical techniques for macromolecular crystal structure analysis and to extend this research towards other fields ofstructural biology. It has several interlinked, but at the same time independent key goals: (1) Organisation of a database encapsulating the knowledge available in the Protein Data Bank in a usable form for Macromolecular crystallography (2) Automated molecular replacement to integrate this database with software developed in my group, employing statistically robust decision making procedures (3) Improved electron density calculation after refinement by transferring information from the experimentaldata and database of structural features to newly solved structures (4) Completing the structure using knowledge from chemistry, physics and macromolecular structures (5) Optimal fit of an MX model into EM density usingmaximum likelihood combined with prior structural knowledge (6) Ligands and their geometry, quantum chemical optimisation of the geometry of the building blocks of macromolecules and ligands (7) Application of the techniques developed to difficult problems and exploiting feedback from experimenters. The software developed will be made available to the structural biology community via the UK based initiative, CCP4
Phagocytosis is an essential process by which professional phagocytes engulf invading pathogens, apoptotic cells and other foreign particles. Phagocytosis triggers the activation of multiple transmembrane signaling pathways, leading to the reorganization of the actin cytoskeleton and the formation of a sealed intracellular compartment, the phagosome. The newly formed phagosome matures by undergoing multiple fusion events with endocytic organelles and finally fusion events with lysosomes to form the phagolysosome. It is within the phagolysosome that hydrolytic enzymes kill pathogens and allow phagocytosed material to be 'digested'. Pathogen survival mechanisms involve escaping from the phagocytic pathway (Shigella, Listeria), preventing phagolysosome biogenesis (Mycobacterium, Salmonella) or surviving the harsh phagolysosome environment itself (Leishmania). Unlike other endocytic events, the molecular mechanisms in phagosome maturation remain essentially descriptive and in particular, the molecular machinery involved in phagolysosome biogenesis is ill defined. The focus of this proposal is therefore to determine the molecular mechanisms for phagolysosome formation by developing an in vitro phagosome-lysosome fusion assay. The assay in conjunction with genetic and proteomic screens will be used to investigate the mechanism(s) by which pathogens survive intracellularly, in particular those pathogens that arrest phagolysosome formation.
The immunodominant O-antigen and Salmonella enterica pathogenesis: examining the phage origin, distribution, expression and role of a family of O-antigen modification gene clusters. 06 Jul 2006
The bacterial species Salmonella enterica causes typhoid fever and is a major cause of gastroenteritis, or food poisoning, leading to significant costs and health concerns in humans and livestock worldwide. To develop approaches to combat this problem, it is important to identify immunogenic antigens and to determine when these are expressed. This application focuses on the immunodominant O-antigen of the lipopolysaccharide and the diversity of O-antigen modification, specifically glycoslyation encoded by gtr gene clusters. Our hypothesis is that co-existence of different isolates from the same serogroup is facilitated by phase variation of gtr genes and that phage facilitate horizontal distribution of these genes, which together will influence the persistence and spread of this species in the animal hosts. Our Specific Aims are to characterize regulation of gtr expression, and to determine the presence of gtr among serovars and identify linkage with phage related sequences. In selected isolates the biochemical nature of the modification will be characterized and possible effects on type III dependent secretion examined. A better understanding of O-antigen modification in S. enterica can contribute to the development of improved tools for epidemiology and vaccines, and enhance our understanding of the virulence mechanisms of this important pathogen.
The future of A level science - a series of stakeholder conferences aimed at informing practice and policy. 30 Aug 2006
We intend to set up a programme of stakeholder conferences to inform the new Physics, Chemistry, Biology and Psychology A level courses due to be introduced in 2008. The National Science Learning Centre will host four events leading to the publication of a report informing practice and policy, and implementation of the new courses. We anticipate that 240 key education, science and other stakeholders will be involved in the programme directly, and that the outcomes and outputs will affect many thousands over the subsequent years. This systematic approach is long overdue and would help to ensure that the content and approach at A Level better meets the needs of science, the FE and schools sector, young people and industry. The Qualifications and Curriculum Authority has expressed enthusiastic interest in this model and were it to be successful, we would expect it to be adopted more widely as mechanism for informing curriculum development in science and beyond. The Stakeholder Conference Programme will achieve the following objectives: To identify priorities, themes, core issues and contexts for each of the four science A levels, amongst each of the stakeholder groups; To develop a methodology to inform curriculum development that could be replicated and extended; To act as a forum where research scientists can work with science educationalists to illustrate curriculum content with contemporary examples; To professionalise and make more transparent the curriculum development process. Main audience: 1. Conference attendees and the organisations they represent. 2. Post-16 lecturers and teachers. 3. Policymakers.
PROPERTY, PERSONHOOD AND REPRODUCTIVE TECHNOLOGIES This is an interdisciplinary investigation into the liberal concept of property in the person and its applications to reproductive technologies. The central research question is: can the liberal concept of property in the person be adapted or extended to cope with the dispersion of body parts inherent in gamete donation, surrogacy, the freezing and storage of embryos, etc? If not, what should replace it? Year one will focus on the political philosophy of contract theory and property in the person, extending my understanding of the theories, and applying them to reproductive technologies. As ova and embryos become separated from the body, and hence physically alienated from it, there is a potential for them to become commodified. How widespread is this, does it change our perceptions of pregnancy and childbirth, and if so, is this a problem? In year two I will seek to apply some of the ethical issues identified in year one to the clinical application of reproductive technologies. When conflict arises over a particular application of procedures, is property in the person a useful concept in resolving them? In year three I will draw together theoretical and practical considerations to seek an answer to my research question.
Soot, Skin and Dust: A Comparative History of Chimney Sweeps, Occupational Health and Testicular Cancer 1775-1925. 14 Jun 2006
There has been widespread recognition that chimney sweeps, and especially climbing boys, were one of the first groups targeted for medical and philanthropic assistance in late C18 and early C19 England. However, despite folkloric studies by Phillips and general surveys by Strange and Cullingford, there has been no systematic analysis of their history from the perspective of the history of medicine and occupational health. Furthermore there has been no comparative, European study of their health experiences which relates it to their work culture. Nor has any study explored the incidence of chimney sweep's cancer, as scrotal cancer was termed, in other work contexts in the C19 and early C20. This research will thus examine crucial early episodes in the history of occupational medicine and public health reform in a novel and comparative perspective.
The addition or removal of 2-acetamido-2-deoxy-D-glucopyranose (GlcNAc) to serine or threonine residues of many nuclear and cytoplasmic proteins is an important post-translational modification in higher eukaryotes. It is a dynamic balanced system in vivo; the inability to appropriately regulate the balance is implicated in diabetes and neurodegenerative diseases, and an understanding of these regulatory mechanisms could lead to development of therapeutic treatments. The addition of GlcNAc is cat alyzed by a glycosyltransferase, uridine diphosphate-N-acetyl-D-glucosamine: polypeptidyl transferase (OGTase), which recognizes and binds to targets via tetratricopeptide repeat (TPR) domains. TPR domains are believed to bind to linear peptides, but there is no consensus sequence among the modified proteins and the question of how TPR domains recognize a host of proteins remains. This may be accomplished by linear target peptides binding to unique motifs in different regions of the TPR domains. This research aims to identify peptides/proteins that bind to OGTase using phage display, affinity purification and mass spectrometry, to validate their interaction in cells, and to analyze the amino acid motifs recognized by TPR domains using peptide arrays. Peptide binding epitopes or proteins will be co-crystallised with the TPR domains and studied using X-ray crystallography, and the binding affinities will be quantified.
The research will focus on analysing protein-nucleic acid interactions and related molecular events in the framework of large assemblies. Although the main emphasis is on X-ray analysis, several complementary techniques such as electron microscopy, mass spectrometry and analytical ultracentrifugation, which provide insight into the assembly s composition and the strength of interaction, will be involved. Key goals in the main projects: (1) To understand the structure-function relationship for several tRNA modifying enzymes. To characterize protein interactions with tRNA and determine the crystal structures of protein-tRNA complexes by the X-ray analysis. (2) To continue investigations into the mechanism of DNA translocation by double-stranded DNA viruses, using bacteriophage SPP1 as a model system. Determine the X-ray structure of viral ATPase, which powers DNA translocation, and prepare stable complexes and obtain structural information for the complex of ATPase with the portal pr otein and DNA. Use the derived structural data for understanding how chemical events during the ATP hydrolysis are linked to the mechanical events during DNA translocation. (3) To extend studies on the regulatory processes involving multisubunit proteins and multiple-repeated RNA segments, using B.subtilis TRAP/RNA/anti-TRAP as a model system.
A T cell receptor transgenic model for studying CD4+ effector and regulatory T cells in bacterial-induced colitis. 19 Oct 2006
The intestinal bacterial flora and the CD4+ T cell response to these bacteria play an important role in the induction and regulation of chronic intestinal inflammation. The process by which bacteria-specific CD4+ T cell responses are initiated, and the factors that determine pathogenic versus disease-protective CD4+ T cell effector choice, are however not well understood. The objectives of this project are to define the mechanisms by which specific bacterial antigen/CD4+ T cell interactions trig ger colitis in disease-susceptible hosts and suppress its induction in disease-resistant hosts. We will use a newly developed transgenic mouse model based on the T cell receptor of a disease-inducing CD4+ T cell clone specific for the flagellar hook protein (FHP) of Helicobacter hepaticus. This system will enable us to distinguish bacterial from host-directed immune responses and to study the development of pathogenic effector and disease-protective T regulatory (Treg) cells. The goals of the pr oject are to i) identify the process whereby FHP-specific CD4+ T cells trigger inflammation in the intestine of H. hepaticus-infected mice, ii) define the interaction between H. hepaticus and dendritic cells (DCs), and iii) determine whether mucosal DCs can induce the differentiation of FHP-specific CD4+ Treg cells.
Student elective for Sakaria Said Ali. 18 Apr 2007
What are the views of Somali men in Kenya, with regards to the continuation or abandonment of female genital cutting? Female genital cutting is a cultural phenomenon, which has detrimental effects on the health of millions of women. International change efforts to stop this practice have had little impact on the prevalence of this practice. The views and participatory roles of men with regards to female genital cutting are important factors in change efforts, which are often alluded to in the literature, but not extensively researched. Literature on the attitudes and beliefs of men towards FGC is scarce and for most part does not extend beyond feminist discourse. This study will seek to examine the views and positions that Somali men in Kenya hold in the continuity of this practice.
The clustered Hox genes comprise only 39 of the >200 homeobox genes in the human genome. The non-Hox homeobox genes are usually studied in isolation, but in fact some are in gene clusters. We found that three (Gsx, Xlox/Pdx, Cdx) form the ParaHox cluster in amphioxus, human, mouse, Xenopus and basal ray-finned fish, but not in zebrafish and pufferfish (where the constituent genes have dispersed). We will use a combination of comparative genomics and experimental assays to ask: (1) How conserved is the ParaHox gene cluster? To test, we will analyse two species chosen for their positions in vertebrate diversity. (2) When, how and why did the ParaHox cluster disintegrate in teleost fish evolution? We hypothesize that whole genome duplication (WGD) at the base of the teleosts allowed interdigitated ParaHox genes to be dissociated. We will test by comparison between fish branching before and after the WGD, including zebrafish and some non-traditional models. (3) What is the functional reason for the cluster? We hypothesize the genes are trapped by shared enhancers and overlapping gene organisation; we will test this by determining the activity of conserved non-coding regions using Xenopus transgenics. (4) What are the implications for zebrafish as a model?
Treating the patients' records: a preservation and conservation project for the Retreat Archive at the Borthwick Institute, University of York. 16 May 2007
This project will secure The Retreat patients' records from the effects of original poor storage and handling at The Retreat, and enable them to be safely used by medical history researchers. It builds on a successful ResearchResources in Medical History Scheme re-cataloguing project for The Retreat Archive undertaken in 2002-2004, which transformed access to the archive (resulting in a 50% increase in use), and identified many hitherto unknown records, but also brought to light urgent preservation and conservation problems. These must be addressed to prevent further deterioration of already fragile records. The project will focus on the most heavily-used part of the archive: " Case books, admissions, deaths and discharge registers, and other volumes ofpatients' documentation, 1790s-1960s; " Nineteenth-century patients' papers, letters and writings; " Twentieth-century patients' case notes and correspondence files. The project will utilise a number of preservation and conservation measures, including cleaning, repackaging and boxing; and remedial conservation of individual items as appropriate. The end result will be fully conserved and preserved patients' records for thewhole span of The Retreat's history to the 1960s, thereby opening up new sources relating to one of the most influential psychiatric hospitals in the UK for researchers in medical history.
This longitudinal study will follow the development from 3-7 years, of children at family-risk of dyslexia, children with SLI, and controls. It will document the frequency with which children from these groups experience literacy difficulties, the nature of their reading problems and how these relate to underlying language skills. It will address the overlap between dyslexia and SLI at different points in development, identify endophenotypes of dyslexia and assess the extent to which indivi dual, family and environmental factors play a role in determining outcome. The research will use assess two causal hypotheses: 1. that an underlying deficit in auditory processing causes deficits in speech perception, which in turn lead to the phonological processing impairments that underlie reading problems in dyslexia and SLI. 2. that the phonological processing impairments and other language problems that are central to dyslexia and SLI cannot be traced to underlying auditory or speec h perceptual problems but instead reflect problems in more central language or other cognitive systems. The study will also assess the mediators of response to reading intervention in these groups.
Our proposal brings together expertise in biochemistry/structural biology (York), microbiology (Nottingham) and spectroscopy (Norwich) to determine how nuclease colicins penetrate the cell defences of bacteria. The programme has four key goals: (1) To establish the mechanism by which nuclease colicins translocate acrossthe E. coli outer membrane, centred on a structural dissection of the multiprotein, membrane-bound complex that assembles prior to import. (2) To determine the function of the periplasmic Tol-Pal complex in conjunction with how and why it is parasitised by translocating colicins, using microscopy to determine whether colicins target the bacterial septation machinery, biochemical analysis of the overexpressed membrane-bound TolQRA complex, along with functional dissection of TolB through spectroscopic and biophysical analysis. (3) To establish the mechanism by which colicin nucleases retro-translocate across the bacterial inner membrane using a range of mutants, cell-based assays and crosslinking that will probe the role of electrostatics and the AAA+ATPase FtsH in membrane trafficking. (4) To use NMR to define the conformational ensemble of the natively disordered N-terminal domains of Ton- and Tol-dependent colicins that recruit protein partners for import and examine TolB binding mechanism using pre-steady state methods.
This is an application to replace defunct equipment at York with new instrumentation that will service the needs of the 4 Trust-funded applicants and a further 14 staff in the Departments of Biology and Chemistry in their investigations of biomedically and biologically important proteins. Specifically, we request a surface plasmon resonance instrument (SPR) and electrospray ionisation mass spectrometer (ESI-MS), which will together be used to deconstruct the associations of a wide variety of pr otein complexes and so provide much needed biophysical information to complement ongoing structural work. The key objectives of the proposal are: 1. To use SPR to investigate the assembly and binding affinities of protein complexes and probe their underlying kinetics. 2. To use native state ESI-MS to measure molecular weights of complexes from which we can infer subunit and ligand stoichiometries and oligomeric structure. These approaches will allow us to address fundamental questions in ongoing, Trust-funded work that have hitherto been impossible at York. The areas of research that will benefit from the new equipment include host-parasite interactions, host-bacterial pathogen interactions, viral DNA packaging, antibacterial protein translocation, bacterial transcription and cell division, mammalian DNA replication, archaeal DNA segregation, bone cell signalling and protein sorting.
Structure, function and interaction studies of the cell differentiation protein SpoIIE from bacillus subtilis. 10 Jul 2007
SpoIIE plays a key morphogenetic role in spore formation by Bacillus subtilis. In this work we propose to determine the three dimensional structure of fragments of SpoIIE which constitute its functional domains. The purpose is to define SpoIIE s interactions with (i) FtsZ which helps to define the asymmetric cell division septum that forms during sporulation and (ii) the anti-sigma factor antagonist, SpoIIAA~P whose dephosphorylation and activation by SpoIIE leads to the establishment of differe ntial gene expression in the sister cells following septation. We have crystals of the phosphatase domain of SpoIIE that are suitable for structure solution and we have strategies for probing the interactions of this domain with SpoIIAA by biophysical, NMR and/or crystallographic techniques. We plan to use a recently devised exhaustive truncation mutagenesis screen for stable and soluble SpoIIE fragments encompassing the FtsZ-binding domain. These fragments will be overproduced and purified for detailed biochemical and biophysical characterisation and structural studies with the ultimate aim of defining the interactions of SpoIIE with FtsZ.