NIHRDataInsights/HRCSData huggingface dataset:
Title: The effects of vaccination and immunity on bacterial infection dynamics in vivo: a systems biology analysis
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Salmonella infections are a serious medical and veterinary problem worldwide and a significant issue for the food industry. Control of Salmonella infections using hygiene and biosecurity measures is difficult; many antibiotics are failing due to the emergence of multi-drug resistant isolates. Current vaccines are far from optimal; design and testing of new preparations is performed empirically often based on reductionist research. The aim of the proposed research is to use a coherent systems biology approach, that evolves from our recent work, to understand how immunity and vaccines affect bacterial infection dynamics in vivo. We will use multidisciplinary research approaches to study the infection process at different levels of complexity in vivo, from the direct interaction between bacteria and host cells to the analysis of global heterogeneous traits of bacterial population dynamics in the host. Using multicolour fluorescence microscopy techniques and quantitation of molecularly tagged bacterial subpopulations we will unravel how the bacteria grow, spread, distribute and persist in the face of different types of vaccine and immune responses. Iterative feedbacks between biological work in vivo and a range of mathematical models will allow synthesis across different scales and reconstruction of the system from its individual biological elements. This work, that will be extendable to a range of pathogens and animal species, will strongly impact on human and animal health through improved understanding of the priniciples underlying vaccine design and will allow academia and industry to capitalise on the increasingly large amount of information available on the genetics of bacterial virulence and on the possibility to modulate the immune system towards specific types of response using appropriate adjuvants or vaccine delivery systems


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;3.4 VACCINES
Health categories: INFECTION
Title: Mapping triclabendazole resistance in Fasciola hepatica using next generation sequencing technologies
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Fasciola hepatica causes serious disease in livestock worldwide. It is common in the UK, its prevalence is increasing and the costs of controlling infection have a significant impact on the UK agricultural sector. Resistance to triclabendazole (TCBZ), the most widely used drug for the control of fasciolosis, is reported in the UK, Europe and Australia. This project will take a new approach to identifying markers for resistance that will, in the long term, be useful in the identification of gene(s) encoding resistance and the development of assays to measure the prevalence and spread of resistance. Clonal lines will be generated from resistant and susceptible field isolates and F1 and F2 generations created based on crosses of these lines. A draft genome sequence for F. hepatica will be created using 454 fragment and mate pair libraries at 10x coverage producing a rough assembly (N50 of 30kb) complemented by Solexa reads and the MAKER pipeline used for basic annotation. Resistant and susceptible clonal lines will be resequenced at 20x coverage to identify single nucleotide polymorphisms (SNP) using SOLiD fragment libraries. Differences in SNP allele frequencies will be identified between parasites that have developed after exposure to TCBZ versus unexposed controls. Six pairs of treated vs control populations will be sequenced at 20x coverage using SOLiD fragment libraries. Allele frequencies will be analyzed using logistic regression plotted against the draft genome sequence to identify genomic regions associated with TCBZ resistance. Finally a sample of 150 SNPs linked to TCBZ resistance, plus 100 unlinked controls will be validated. Individual miracidia will be SNP genotyped to determine linkage between markers to indicate if a single locus is responsible for resistance and if TCBZ resistance is a dominant or recessive trait. Finally experimental infections using F2 individuals will be used to confirm linkage of SNPs to TCBZ resistance in vivo.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: INFECTION
Title: Unravelling the role of the male accessory glands in the fertility of the malaria mosquito Anopheles gambiae
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Anopheles gambiae mosquitoes are the major vectors of malaria, a disease with devastating consequences for human health. Given the evolution of insecticide resistance in mosquitoes and the lack of new insecticidal compounds, novel methods for controlling the natural vector populations are urgently needed. A deeper understanding of the processes shaping the biology of these mosquitoes would undoubtedly help to develop tools aimed at limiting the spread of malaria. In this proposal, we will target mosquito reproduction, a major determinant of the An. gambiae capacity to transmit disease. We will focus our analyses on the male accessory gland (MAGs), a major player of mosquito reproduction, in both laboratory and field settings. We will then set the scene for translating this information into the identification of tools for the manipulation of fertility of field populations. The experimental activities will be divided in three objectives. In Objective 1, we will unravel the role of the MAGs in shaping mosquito fertility and behaviour, by performing a combination of transcriptional and functional studies that will reveal the multifaceted activities of these tissues. In Objective 2 we will instead focus on the assessment of the role of peptide hormones produced in the MAGs on the fertility and reproductive behaviour of mosquitoes. Results obtained in both objectives will then be validated in field mosquitoes in Objective 3. This study will reveal as yet unknown molecular mechanisms underlying reproductive success in mosquitoes, considerably increasing our knowledge beyond the state-of-the-art and critically contributing with innovative tools and ideas to the fight against malaria. Our results will also be instrumental for the study of reproduction in other insect pests of medical and agricultural importance.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: INFECTION
Title: Disruption of cytoplasmic membrane-associated functions in Staphylococcus aureus by epicatechin gallate
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The naturally occurring, abundant, polyphenol (-)-epicatechin gallate (ECg) has the capacity to abrogate beta-lactam resistance in multi-drug-resistant Staphylococcus aureus and is able to reduce the secretion of virulence effectors such as toxins and tissue-degrading enzymes, prevent the formation of biofilms and abolish halotolerance in resistant and susceptible strains of this species, making it potentially useful for the control of infections in animals and humans and for food preservation. The proposed study will provide a detailed understanding of the mechanisms responsible for these wide-ranging phenotypic modifications and support the design, synthesis and characterisation of structural analogues with enhanced bioactivities. We have established that ECg intercalates into the cytoplasmic membrane (CM), engenders physical and structural changes to the bilayer and delocalises penicillin binding protein 2 (PBP2) from the septal site of cell division, where it normally cooperates with PBP2a to facilitate continued cell wall synthesis in the presence of beta-lactams We will determine if ECg disrupts the functional PBP2/2a complex such that PBP2a can no longer compensate for beta-lactam-mediated acylation of PBP2 or if it permits continued wall synthesis in the presence of oxacillin by a delocalised functional complex at sites remote from the division septum. We will investigate if ECg produces a sub-optimal lipid environment for key CM-anchored proteins by searching for lipid 'raft' domains and by determining the degree of phospholipid asymmetry across the inner and outer CM leaflets. The potential for distortion of PBP2a, leading to loss of resistance to active site acylation by oxacillin, following interaction of ECg with the CM will be examined. As halotolerance is due at least in part to a functional Na+/H+ CM-located antiporter system, the effect of ECg intercalation into the CM on the activity of this pump will be determined.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Defining the molecular basis of H7 flagellin as an adhesin and mucosal adjuvant for vaccine development
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 is an important food-borne pathogen that causes serious human infections ranging in symptoms from self-limiting diarrhoea or haemorrhagic colitis to life-threatening haemolytic-uremic syndrome. Cattle are the primary asymptomatic reservoir for EHEC O157 and human infections can occur by consumption of contaminated food or drink, direct contact with animals or person-to-person spread. A key objective is to reduce the carriage or prevalence of EHEC O157:H7 in cattle to limit human exposure. Development of effective interventions in cattle will rely on understanding the bacterial factors involved in colonization of the gastrointestinal tract. We have demonstrated that EHEC O157 predominately colonises the terminal rectum of cattle and that H7 flagella functions as an adhesin for EHEC O157 when binding to epithelial cells cultured from this rectal site. Comparative binding studies with other flagella indicate that distinct motifs in the central (D2 and D3) domains are likely to confer the binding specificity. Systemic immunization of cattle with purified H7 flagellin reduces the proportion of animals that become colonised. However, in calves that do become colonised, bacterial shedding levels are at least as high as non-vaccinated controls. Both IgG and IgA are induced following H7 flagellin immunization and inhibit EHEC O157:H7 adherence in vitro. However, IgG blocks TLR5 signalling and this may impact on shedding levels following immunization. The aims are: (1) to define the region of FliC(H7) required for binding specificity and to generate an H7 flagellin fragment or H7 variant that can be used to induce antibodies that block binding but that do not inhibit TLR5 signalling by wild type H7 flagellin; (2) to investigate how systemic vaccination with H7 flagellin results in specific IgA responses and to use this information to generate a mucosal response to a heterologous antigen.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;3.4 VACCINES
Health categories: INFECTION
Title: A longitudinal model for the spread of bovine tuberculosis
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Currently the incidence of bovine tuberculosis in Great Britain is increasing, despite over £100 million per year being spent in surveillance and compensation. Herds are monitored for the disease through slaughterhouse surveillance and through imperfect routine skin testing. Our proposal is to build a longitudinal statistical model to account for within- and between-herd transmission of bTB using information from the VetNet, Vebus and Cattle Tracing System data sets. The aim is to understand better the mechanisms of transmission and ultimately to be able to identify herds with a high-risk of harbouring undetected infection, based on the past history of infection as well as localised incidence and connectedness to other premises, and also to characterise areas or premises of high- or low-risk relative to that due to the cattle network. The system is characterised by a hidden dynamic non-linear infection process overlaid with a probabilistic observation mechanism. We intend to explore the development of data-augmented Markov chain Monte Carlo or sequential filtering methods to fit the model. Localised (environmental) transmission will be dealt with using spatial and non-spatial random effects. A surveillance model of this nature would have a practical use in terms of targeting specific herds with more stringent or more regular testing, and if successful could have substantial impacts on slowing the spread of the disease. However, these methods are computationally intensive, given the large scale and long time frame of the datasets. Recent advances in parallel processing technology, both on multi-core CPUs as well as on graphics processing units (e.g. CUDA/OpenCL) provide an exciting and cost-effective way of approaching this problem. Although the focus here is on bTB, the computational problems of fitting models to large-scale data sets in a robust manner are relevant to a wide range of infectious disease systems


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: INFECTION
Title: Dissecting the mechanism of translational control during calicivirus infection
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Caliciviruses are important pathogens of man and animals, such as the noroviruses which cause major outbreaks of gastroenteritis. We have previously demonstrated that translation initiation on calicivirus mRNA is dependent on the viral protein (VPg) linked to the 5' end of the viral mRNA and that VPg acts as a novel proteinaceous 'cap substitute' to attract ribosomes to the viral mRNA, via its interaction with the cap-binding protein, eIF4E. We have also started to analyse the requirement for other components of the eIF4F complex for FCV and MNV mRNA translation; while we have shown that eIF4A is required for both FCV and MNV translation, the viruses may differ in their requirements for eIF4G. Therefore, our first aim is to conduct a comparative analysis to identify and functionally characterise initiation factors within the FCV and MNV VPg-initiation complexes. We will first use a proteomics approach to identify initiation factors contained within the VPg-initiation complexes and then use a number of complementary biochemical techniques to assess their functional role in VPg-directed translation initiation. Furthermore, we have recently demonstrated that both viruses modulate the eIF4F complex during infection, particularly the activity of eIF4E, and propose that these changes are involved in regulation of viral translation. Therefore, our second aim is to analyse biochemically the effect of calicivirus infection on the eIF4F complex, by characterising the signalling pathways involved in phosphorylation of eIF4E and its regulating protein, 4E-binding protein-1, by using quantitative proteomics (SILAC) to measure the changes to eIF4F during infection and finally to assess the effect of these changes in regulating calicivirus protein synthesis. Understanding the mechanism of calicivirus protein synthesis may lead to the identification of novel antiviral targets for this important group of viruses.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: High resolution phylogenetic analysis of livestock-associated Staphylococcus aureus.
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The emergence of pathogens causing endemic diseases of livestock is an important food security and public health issue. Staphylococcus aureus is an important human and animal pathogen and a major economic burden worldwide. Recent studies indicate that some animal-specific lineages have evolved from human progenitor strains followed by host-adaptive diversification. Importantly, human activities such as domestication and globalization may have contributed to the emergence of livestock-associated S. aureus by providing increased opportunities for cross-species host-jumps and promoting global dissemination. Furthermore, reports that some livestock-associated strains have the capacity to cause human zoonotic infection is a major public health concern. The project represents a high resolution genetic analysis of livestock-associated S. aureus to resolve the evolutionary history of all major livestock-associated S. aureus, including the molecular basis for host adaptation and the timing of predicted host-jumps. For clonal complexes associated with multiple animal and human hosts, this approach will allow us to identify intraclonal genetic variation, determine the geographic distribution of subtypes, and predict their zoonotic potential. Furthermore, the fundamental molecular processes contributing to adaptive genome diversification will be examined and genetic markers for host-specificity identified, leading to the identification of novel targets for the control of S. aureus livestock diseases. Overall, the project will contribute fundamental insights into an endemic pathogen of livestock which could be applied to improve animal health, and protect food security and public health


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Identification and functional analysis of surface factors that enable human pathogens to adhere to and colonise plants.
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The hypothesis to be tested is that bacterial surface-expressed factors mediate interactions between human pathogenic enterobacteria and plants. The project will focus on enterohaemorrhagic E. coli (EHEC) and will characterise functional surface factors the play a role in colonisation and internalisation of plants. Preliminary work has shown several surface factors are induced in planta and indicated a role for the F9 fimbrial cluster. Objectives: 1 - Functional analysis of EHEC F9 fimbriae in bacteria-plant interactions. 2 - Identification of additional surface-expressed factors from EHEC O-island deletion mutants and an EHEC BAC library 3 - Functional analysis of additional EHEC surface expressed factors in bacteria-plant interactions 4 - Determine whether any EHEC surface factors affect the plant host response Libraries of EHEC O-island mutants and BAC clones will be screened to identify surface factors that are functional in planta (available from Prof. Gally, Edinburgh). Functional analysis of F9 fimbriae and additional surface factors will determine their expression in planta, whether they confer specificity to any plant tissue type or species and whether they induce a host response. Surface factors from other EHEC with sequence variation will be tested to determine whether they confer any advantage in plant colonisation. Candidate genes will identified from initial in planta and bioinformatics screens and assessed by microbiology and microscopy. Light and electron microscopy will also be used in functional analysis. Plant infection assays will be routinely carried out on plants associated with fresh produce outbreaks and different time points will distinguish between initial adherence and establishment of colonisation. In addition, the internalised population will be investigated. Infection of edible tissue will be initiated on the roots of growing plants since the rhizosphere is colonised to a far greater extent than the phyllosphere.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Quorum sensing and lifestyle switching in Yersinia.
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Yersinia pseudotuberculosis is an enteric pathogen that has a lifestyle which alternates between the food/water environment and the mammalian gastrointestinal tract. Its virulence depends on the pYV plasmid which harbours the yop virulon, a type III secretion (T3S) system required for subversion of host defences. Some Y.pseudotuberculosis strains form biofilms on the anterior cuticle of Caenorhabditis elegans blocking feeding. This offers a simple means of investigating biofilm development in vivo on a living surface which has the major benefit that both bacterial and host responses can be studied. Previously we discovered that Y. pseudotuberculosis employs quorum sensing (QS) to make lifestyle decisions with respect to motility, T3S, pYV plasmid maintenance, metabolism and biofilm formation on C. elegans. In addition, QS itself appears to be regulated via N-acetylglucosamine (GlcNAc) and we have identified several key C. elegans genes differentially regulated in response to Yersinia biofilms The present project aims to obtain detailed molecular insights into the yersinia signalling pathways involved and the functions of the C. elegans genes differentially regulated in response to biofilms We will:(1) establish whether GlcNAc is the master metabolic signal controlling QS; (2) determine how QS controls the hut operons; (3) investigate whether HutC regulates motility, T3S and biofilm formation via FlhDC; (4) elucidate whether QS regulates virF and the yop virulon directly or indirectly via the HutC/FlhDC pathway; (5) establish how QS maintains the pYV plasmid; (6) determine the relationship between suspended and C. elegans biofilms; (7) identify the C. elegans ligands that promote biofilm formation; and, (8) investigate how C. elegans responds to Yersina biofilms This research provides a unique opportunity to study the inter-relationship of several important fundamental bacterial processes as well as providing new information in host/invertebrate interactions.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Campylobacter phase variation and its impact on immunity and vaccine development.
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Phase variation (PV) of surface determinants influences both commensal and pathogenic behaviour in many bacterial species. PV in C. jejuni is mediated by mutations in polyC/G tracts. Each genome of C. jejuni contains 16 or more phase variable genes whose products modify capsule, lipo-oligosaccharide and flagella. These surface structures are major targets for host adaptive immunity. We have shown that some phase-variable genes are involved in persistence of C. jejuni in the avian GI-tract suggesting that understanding PV could improve the efficacy of current attempts to limit colonisation. .Reduction of C. jejuni in the poultry food chain would reduce the very high incidence of C. jejuni-associated gasteroenteritis. Colonisation of chickens by C. jejuni induces adaptive immune responses however there is limited evidence for this response promoting clearance. Our published and unpublished data indicates that PV of surface components, including glycosylation of flagella, facilitates colonisation and spread in flocks. There is therefore a strong rationale for investigating the role of PV in immune avoidance and host colonisation. We have already tested the methods required to study PV in vivo and in vitro and shown by analysis of input and output populations from chickens that we can accurately monitor PV in vivo. We will assess PV of 29 genes and the immune responses against C. jejuni following inoculation of chickens with strain 11168. Inoculation of naïve and immunised chickens will permit a thorough assessment of the impact of immune responses on colonisation and selection of phase variants. In silico models will be used to determine whether changes in proportions of phase variants are due to drift, bottlenecks or selection. Outcomes will include an improved understanding of the impact of PV on the course of infections and the variability of vaccine responses. Long-term benefits will comprise identification of novel vaccine strategies.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION