NIHRDataInsights/HRCSData huggingface dataset:
Title: Identification and characterization of telomere proteins in Plasmodium falciparum.
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The proposed work will identify and characterise novel telomere-associated proteins in the protozoan parasite Plasmodium falciparum. This parasite (along with other apicomplexans of medical and veterinary importance: Toxoplasma, Cryptosporidium, Eimeria, Babesia and Theileria) belongs to an early-branching, highly-divergent lineage and few of the factors that cap, regulate and maintain its telomeres have been identified by homology with model organisms Telomere maintenance is, however, a vital basic function, and may also represent a novel drug target. This project will use Proteomics of Isolated Chromatin Segments (PICh) to identify the protein complement of telomeric DNA from P. falciparum. The PICh technique, in which cross-linked protein-DNA complexes are isolated via a specific DNA probe before identifying the proteins by mass spectrometry, was recently very successful in identifying known and novel components of the human telomere-binding complex. After identifying the telomeric proteome in wildtype P. falciparum, telomeric proteins in sirtuin-knockout parasites will be identified for comparison. The two 'sirtuin' histone deacetylases play key roles in regulating expression of sub-telomeric virulence genes. I have shown that they also affect telomere length and genome stability, so these enzymes may be central components of a telomere-regulating complex. Telomeric proteins of particular interest will be validated by immunofluorescence with fluorescence in situ hybridisation, to verify their specificity for the telomere. Genetic knockouts will then be generated and phenotyped for an initial characterisation of the roles of these proteins: telomere length and telomere stability in knockout lines will be analysed by Southern blotting and karyotyping. The project will improve our understanding of a fundamental aspect of Plasmodium biology, as well as opening up new avenues for research on Plasmodium and other important apicomplexan parasites.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Mechanisms of mosquito gut homeostasis and the role of NF-kappaB signalling
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The Anopheles gambiae gut is habitat to large and diverse bacterial communities. The total number of bacteria in the gut of a female mosquito increases several folds after ingestion of a bloodmeal. We have shown that the increase of gut bacteria triggers strong immune reactions of the REL2 NF-kappaB signalling pathway, which are important in reducing the bacterial numbers and restoring gut homeostasis, but also limit infections of blood-borne parasites and viruses. This project aims to investigate the molecular mechanisms involved in regulating the mosquito gut flora. To identify genes and mechanisms involved in responses to gut bacteria, we will carry out genome-wide association studies (GWAS) using an Affymetrix SNP chip that we have recently developed and three colonies of A. gambiae mosquitoes that will be orally infected with fluorescently tagged Serratia marcescens and Asaia. Candidate genes identified following sequencing of the GWAS highlighted regions will be silenced using RNAi, and their effect on the total size and composition of the gut flora as well as on infections with malaria parasites and the O'Nyong Nyong virus will be examined. We will also investigate whether these genes function through the REL2 pathway. We have previously shown that the peptidoglycan recognition receptor, PGRPLC, senses gut bacteria and triggers activation of the REL2 pathway. PGRPLC mediates both low-level constitutive activation of REL2 signalling prior to bloodmeal, which is important for homeostasis maintenance, and robust activation of the pathway after a bloodmeal, which is critical in restoring homeostasis. We will experimentally explore our hypothesis that the underlying molecular mechanism involves differential expression of PGRPLC isoforms, linked to infection-regulated alternative splicing of a pool of unspliced PGRPLC transcripts.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: The immunological basis of protection obtained by prime-boost immunisation against bovine tuberculosis
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Although current evidence indicates that Th1 CD4 T cell responses play a central role in immunity against TB, the precise properties of the CD4 T cells that confer immunity are poorly understood. Better knowledge of these parameters is required to rationally design improved vaccines. The recent demonstration that BCG-induced immunity to M. bovis can be enhanced by boosting with viral vectors expressing 85A provides an opportunity to analyse the CD4 T cell responses to a relevant antigen, in order to understand the properties of the specific T cells that mediate immunity. The applicants have recently defined the repertoires of bovine TCR genes and have developed deep sequencing methods to analyse the TRB chain repertoires expressed by responding T cells, thus allowing the clonal composition of T cell responses to be followed over time. This project seeks to exploit these technologies in combination with immunological measurements to analyse in detail the 85A-specific CD4 T-cell response to BCG/rAd85A prime-boost immunisation and subsequent M. bovis challenge. Building on preliminary data indicating that boosting with 85A increases the functional avidity and alters the fine epitope specificity of the responding CD4 T cells, the project will study the frequency, epitope-specificity and functional activity of 85A-specific CD4 T cell responses in relation to their clonotypic composition. The ability to track clonotypes using TCR sequencing provides a novel dimension to TB vaccine studies and will yield important new data on how the response to 85A evolves during vaccination and importantly how this impacts on the ability of the response recalled from vaccine-induced memory populations to mediate protection against subsequent challenge. The latter is particularly important in gaining a better knowledge of how to generate efficacious vaccines and the bovine TB model provides an exceptionally useful model in which to study this in a target species.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Molecular basis of DNA gating by topo IV and gyrase and its inhibition by antimicrobial drugs
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Topo IV and gyrase mediate chromosome unlinking and DNA supercoiling and are targeted by clinically important antibacterial quinolones and other agents. Each enzyme transports a DNA duplex (the T segment) through a DNA gate made in a second DNA helix (the G-gate) in a process that involves the reversible formation of a covalent enzyme-DNA intermediate called the cleavage complex. In recent advances, we have determined the X-ray crystal structures of cleavage complexes of Streptococcus pneumoniae topo IV formed with quinolone and quinazolinediones. Building on these and other structures and new biochemical tools, we aim to examine how DNA is gated through the DNA enzyme complex and how novel drugs interfere with this process. The work will involve a mutidisciplinary approach employing biochemical, X-ray structure, EM and SAXS approaches. Completion of the study will provide new insights on DNA gating during catalysis by topo IV and gyrase and its arrest by anti-topoisomerase therapeutics.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Ecological and socio-economic factors impacting maintenance and dissemination of antibiotic resistance in the Greater Serengeti Ecosystem
Funder: Biotechnology and Biological Sciences Research Council

Abstract: We will develop a novel approach, extending the study of antibiotic resistance from the molecular to the community level, where resistance is least well understood, and focusing on broad patterns of resistance and dissemination of resistance to multiple communities, rather than on patterns of antibiotic resistance for specific pathogens. Underpinning our approach is the use of ecological diversity measures to quantify the distribution of resistance - an approach pioneered by the UK applicants (Matthews, Haydon, Mather) and successfully applied to the analysis of antibiotic resistance patterns. Diversity of resistance phenotypes is quantified using a continuum of ecological diversity measures related to Rényi's entropy measures, that differentially weight the abundance of rare antibiotic resistance phenotypes. The resulting diversity profiles provide a population 'fingerprint' that allows robust comparison of diversity between populations. For the current project we will develop mathematical models that capture the observed patterns of resistance and use them to test our hypotheses about the roles of antibiotic usage versus transfer of resistance within and between reservoir populations as drivers of the observed resistance patterns. Our analyses will: (i) quantify the diversity of resistance profiles; (ii) characterise the connectivity of isolates across different communities and spatio-temporal scales; (iii) identify risk factors for resistance prevalence and diversity; (iv) develop simple dynamic models for the generation and transfer of resistance between populations, and; (v) link socio-economic variables to the modeling outputs to identify differences in household characteristics (e.g., socio-economic status, livestock type and production system) proximity to wildlife, antibiotic usage, and contact patterns that impact on the relative balance between generation and transfer of resistance, thereby identifying modifiable risks.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Development and validation of new reagents and assays to exploit the final steps of peptidoglycan construction
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Penicillin-binding- proteins (PBPS) involved in the construction of peptidoglycan (PG) are the target of important classes of antibiotics, the b-lactams and glycopeptides. Although resistance has arisen to these classes of antibiotic, the formation of peptide cross-links between the glycan backbone of PG by transpeptidation (TP) remains an excellent target for antimicrobial development. Advances have been made in understanding mechanisms underlying the activity of PBPs, however, assay development (let alone high throughput screening) for these enzymes has remained difficult, involving extensive product isolation and characterization. We will extend our development and scale up of novel reagents and target enzymes. Reagents will encompass the chemical diversity that exists in PG structure across bacteria, including, non-cognate substitutions within the linear muramyl pentapeptide, the production of polymeric lipidII where required to prime reactions, and truncation of the C55 lipid tail (using C35 or C20 lipids etc.) to improve in assay solubility and assay function. Interestingly, the required acceptor transpeptidation substrate can be as small as a single amino acid with D-chirality around the alpha-carbon atom. This observation opens up the development of a range of novel more complex (linear/branched) acceptor molecules for use in assays to probe the TP acceptor site structurally and to format assays to identify novel non-lactam TP inhibitors. These reagents will ultimately enable a systematic characterization of the transpeptidase activity of PBPs, the development of co-crystal structures, and provide the foundation for previously unavailable robust assays with direct readouts. Astra Zeneca will work with us to help scale up reagent production, format assays for use in high throughput screens, test sensitivity, and help validate these for industry though IP free access to trial compound libraries.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Transport mechanism of a multidrug transporter from Vibrio cholerae
Funder: Biotechnology and Biological Sciences Research Council

Abstract: In the past decade, crystal structures have been determined for multidrug transporters belonging to four families. However, the structure of members of the final family, that of multidrug and toxic compound extrusion (MATE) proteins, has only recently been determined. MATE transporters may be last in the list of crystallised multidrug transporters, but they are certainly not the least. They are present in all kingdoms of life and, in addition to their role in microbial drug resistance, they are essential for the detoxification of metabolic products in plants and for the excretion of toxins by the liver and kidney in mammals. Over the past decade, crystallographic evidence has been obtained supporting the general concept of alternating access for a variety of membrane transporters, demonstrating that this mechanism has been evolutionarily conserved. However, the structural details and biochemical reactions underlying the necessary conformational changes in multidrug transporters are only partly understood. This is particularly true for MATE transporters, for which very few studies on structure-function relationships have been published to date. In this project we will study the mechanism by which the MATE transporter NorM from Vibrio cholerae mediates antiport between coupling ions and substrates. The involvement of Na(+) in the transport reaction of NorM offers a unique opportunity compared to 'conventional' H(+)/drug antiporters to study the antiport reaction from the perspective of the transported substrate AND coupling ion, as Na(+) can be detected by using radioactive 22Na+. We will identify catalytic residues in NorM that are important for interactions with Na(+) and substrates, and we will challenge NorM's mechanism by relocating these residues to various positions in binding pockets. In this way, we will unravel details of the mechanism of transport and identify possible routes by which multidrug transporters can be inhibited.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Vector competence of British mosquitoes to flaviviruses
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Historically, the UK has been free of viruses biologically-transmitted by mosquitoes. This persists despite the presence of potential mosquito vectors in the UK, and the transmission of arboviruses in neighbouring mainland European countries. Given global changes to climate, landscape, and human and animal demography change, this naive situation is threatened. While several UK native mosquito species and the recently introduced mosquito, Culex modestus, have been named as potential vectors of certain epizootic and zoonotic viruses, vector competence (VC) studies have not been undertaken that firmly implicate these species. The aim of this project is to determine the competence of three UK mosquitoes for two major arboviruses, Japanese encephalitis virus (JEV) and West Nile virus (WNV), using infection assays on field-collected native and invasive mosquitoes. To determine VC, mosquitoes will be assessed for their ability to harbour an infection, disseminate the infection to secondary tissues and transmit the virus by bite. Oral infectious dose needed to infect 50% of a mosquito population will be determined in order to quantify the competence threshold for virus. Temperature has been shown to affect VC by increasing susceptibility of the vector or reducing the extrinsic incubation period. We will assess these temperature effects in infection bioassays. This study aims to identify competent vectors of WNV and JEV in the UK and determine the effect of temperature on their ability to spread these viruses.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: CUKPGP: Streptococcus suis in the pig meat supply chain: from genomics to control strategies.
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Streptococcus suis (SS) is an important zoonotic pathogen of pigs with global relevance to pig productivity and human health. Strategies for SS control are needed to protect human health andto reduce dependence of pig production on antimicrobials. This project aims to identify control points for the prevention of SS related disease in pigs and humans. Longitudinal studies in UK and Chinese farms and abattoirs (intensive and traditional systems), with whole genome sequencing of isolates, will provide guidance to new control points for disease prevention by shedding light on strain diversity, fitness, and antimicrobial resistance along the supply chain. Sequences will be compared to those obtained from pig meat products and those available from human isolates. Risk factors for carriage of SS on consumer-ready pig-meat will be investigated. We will identify avenues for environmental control of SS using transposon directed insertion site sequencing (TraDIS) to explore the genes that underpin environmental survival of SS in the farm, abattoir and meat product context.All partners (Cambridge University, Huazhong Agricultural University (HAU), and Wellcome Trust Sanger Institute (WTSI)) have strong track records in SS research. CU and HAU hold a China Partnering Award, and all 3 work together within the existing BBSRC Longer and Larger funded consortium, 'A single platform diagnostic and multivalent vaccine approach to bacterial respiratory diseases of pigs'.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: INFECTION
Title: Enhancing potency and efficacy of herpesvirus of turkeys-based multivalent vaccines against avian influenza viruses
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Avian influenza (AI) viruses of H5N1 and H9N2 subtypes cause severe losses in poultry and pose risks for zoonotic infections. Currently available inactivated vaccines against these viruses are produced in embryonated eggs and have several disadvantages. We have developed a novel live virus vector-based vaccine exploiting herpesvirus of turkeys (HVT) as vaccine vector. The vaccine was prepared in cultured cells, and a single dose of vaccine delivered into eggs before hatch or after hatch induced life-long immunity in vaccinated chickens. Vaccinated birds showed protection against both highly pathogenic AI and Marek's disease when challenged at six week post vaccination. This project will enhance potency and efficacy of the HVT-based AI vaccines that will protect birds at an early age (within three weeks of hatch). In addition, we plan to develop a trivalent vaccine that will protect vaccinated chickens against both H5 and H9 subtypes of avian influenza viruses and Marek's disease.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: CUKPGP: Epidemio- and immunological perspectives and prophylactic potential of Mycobacterium bovis and M. paratuberculosis co-infections in cattle
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Mycobacterium bovis and M. avium subsp. paratuberculosis (MAP) in cattle, remain major public health and/or economic problems in many countries, including the UK and P.R.China. The incidence of M. bovis infection is well documented whereas information on MAP is poor in many countries. It is likely that mixed infection with these two pathogens occurs with unknown consequences for the progress of both diseases. We have developed a DNA-based microarray that allows simultaneous detection of 13 mycobacterial species, which will be applied in both countries to assess the incidence of infection with the individual pathogens and of mixed infection. We have been interested for some time in the stimulation of the innate immune system shortly after infection and the consequences for subsequent infection by related and unrelated pathogens. The presence of intracellular bacteria in the tissues confers a profound resistance for some time after infection against unrelated pathogens. The outcome of this work is the indication that live, attenuated bacterial vaccines might be used to confer rapid resistance to mycobacterial infection as an emergency protection measure. There is an indication that this approach might also be used therapeutically in some circumstances and has potential application for controlling human infection.. This project will involve (i) use of high throughput microarray technology to survey the incidence of mixed and single mycobacterial infections in China and the UK, and (ii) an assessment of the immunological interaction between M. bovis, MAP and Salmonella early in infection and whether this approach might be used prophylactically to protect against these two mycobacterial pathogens for periods when naïve animals might be exposed to infection.


Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION;3.4 VACCINES
Health categories: INFECTION
Title: 13TSB_SynBio: Engineering immune-cell-targeting bacteria to express vaccines from within the body
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Typhoid is responsible for 22 million cases and 200,000 deaths annually, while ETEC is responsible for 500,000 deaths pa. In 2011, the HPA reported 18,000 cases of infection and 2,000 deaths in the UK. In other parts of the world, the incidence is much higher, due to the emergence of highly toxigenic, antibiotic resistant strains. C. difficile infection causes ~3 million cases of diarrhoea and colitis annually in the USA. Over 80% of C. difficile infections in the UK are in people over 65. Thus, oral vaccination offers a convenient, preventative measure for the ageing population, and is currently no vaccine for C. difficile. Repeated ETEC infection causes malnutrition, growth stunting and cognitive deficits in children in developing countries. In adults, including travellers, diarrhoea can result in gastrointestinal disorders, reactive arthritis and even severe inflammatory bowel disease. There are currently no vaccines approved for ETEC, although the cholera vaccine Dukoral has some cross-reactivity and very limited ETEC strain coverage. Prokarium's Typhetec vaccine promises to cover 100% of the known strains of ETEC. There are currently two types of typhoid vaccines; the injectable Vi vaccine and the oral live attenuated vaccine Vivotif. Based on likely having fewer side effects, lower costs and being orally deliverable, we estimate that Typhetec could initially capture at least 20% of the typhoid travellers market. Vaxonella is a synthetic biology platform that utilises a suite of advanced genetic technologies to re-engineer Salmonella from a pathogen to a precise, rationally designed live bacterial delivery and expression platform. Vaxonella bacteria specifically target the immune cells of the gut, and once engulfed, express their recombinant protein vaccine in a controlled manner. It promises to make many recombinant protein vaccines orally deliverable, while eliminating downstream protein purification and with that the majority of development costs.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION