NIHRDataInsights/HRCSData huggingface dataset:
Title: The host innate immunity limits the zoonotic potential of animal viruses.
Funder: Wellcome Trust

Abstract: Mammalian cells possess a variety of sophisticated antiviral mechanisms that sense an incoming virus and trigger secretion of type I interferon (IFN-? and IFN-?) and type III interferon (IFN- ). The IFN response is the keystone of the host "innate" immunity against virus infections and results in the rapid expression of hundreds of IFN-stimulated genes (ISGs). Viruses have developed several strategies to cope with the host innate immunity. Interestingly, the vast majority of viruses that circulate in human populations originate from animals. However, crossing the species barrier is a significant hurdle for viruses to overcome. We hypothesise that in many cases the "jump" of an animalvirus to the human population is halted by human ISGs. In this project, we will investigate the anti-viral properties of a library of human ISGs against bluetongue virus (BTV) and African horse sickness virus (AHSV). We will selectthe human ISGs that have a major effect on BTV replication and obtain their sheep orthologs. Subsequently, we will compare the effect of human and sheep ISGs on BTV and AHSV replication. Our hypothesis is that human ISGs strongly inhibit replication of BTV and AHSV while sheep ISGs will be more effective in limiting AHSV than BTV.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: The role of mucosal-associated invariant T cells during dengue infection
Funder: Wellcome Trust

Abstract: Dengue virus is a mosquito-borne virus that causes dengue fever or severe dengue. Dengue virus infections are now one of the biggest threats to public health in a number of developing countries. It has been observed that haemorrhagic and shock manifestations arenot directly driven by the virus, but by an aberrant immune response and that CD8+ T cell plays a key role in the immunopathogenesis of dengue. However, not much is known about the roleof the different CD8+ T cell subset during dengue infection. MAIT cell, a subset of CD8+ T cells, has recently been shown to play a role in hepatitis C viral infection, which belongs to the same family of viruses. The key goals of the project will be: (1) To study whether MAIT cells do play a role in dengue infection. This will be achieved by investigating the frequency and the cell stage of MAIT cells in peripheral blood of dengue infected patients using flow cytometry. (2) To investigate how MAIT cells are activated using an in vitro setting with dengue infected cell lines.(3) To investigate in an in vivo setting, the role of MAIT cells in different organs in dengue infected mice.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Transcriptional Regulation of Collagenase Gene Expression in Tuberculosis
Funder: Wellcome Trust

Abstract: This project investigates the hypothesis that hypoxia in tuberculosis is a keyfactor modulating collagenase gene expression and hence inflammatory tissue destruction in patients. Specific aims are first to investigate the effect of hypoxia on gene expression of MMP-1/8 in primary human respiratory epithelial cells and neutrophils exposed to direct TB infection and TBdependent cellular networks. Functional MMP activity is measured by DQ collagen degradation assay. Next the MicroRNA signature regulating MMP-1 gene expression in TB willbe examined before determining the effect of hypoxia. This project builds on workperformed by KF investigating hypoxia and neutrophi MMP-8 gene expression. A genome wide analysis of miRNA expression will be performed in Mtb-infected and control cells (MiltenyiBio-tech system). RT-PCR will be performed for miRNAs found to be over- or under-expressed. miRNA expression quantification will use a miRNA specific qRT-PCR approach called miR-Q. The effect of activating or inhibiting a single miRNA on MMP-1 gene expression will be determined using transfection experiments with either specific miRNA molecules or their antagomir (miRNA specific antagonist)/siRNA. Cultures will then be studied in different degreesof hypoxia. This project will generate novel data and provide KF with a broad training in TB immunobiology.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: The role of chromatin structure in expression and persistence of HTLV-1
Funder: Wellcome Trust

Abstract: Human T lymphotropic virus Type 1 (HTLV-1) is a retrovirus that is widely endemic in the tropics and subtropics, where it imposes a significant burden of morbidity and mortality. The virus is thought to achieve persistence within its host primarily via latency, but the mechanisms by which this latency is regulated remain poorly understood. It has recently beendiscovered in the host laboratory that the virus sequence contains a motif that binds CTCF, a protein of central importance in controlling chromatin structure and gene expression in higher eukaryotes, The host group has also shown that clones of infected cells with a proviral integration site in the acrocentric (nucleolus-associated) chromosomes have preferential survival in vivo. We hypothesize that integration of the HTLV-1 provirus can disrupt the normal organisation and structure of host chromatin, and that higher-order chromatin structure plays akey role in the regulation of proviral expression. We will investigate this hypothesis using circular chromosome conformation capture (4C), 3D-fluorescence in situ hybridisation (3D-FISH) andqRT-PCR.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Investigating patterns of Pyrethroids and DDT resistance in Anopheles funestus populations in Benin: study of the distribution, resistance mechanisms and investigation on novel resistance management strategies.
Funder: Wellcome Trust

Abstract: Malaria remains a major public health burden in Africa Malaria control relies heavily on insecticides-based vector control strategies. Unfortunately, the emergence of resistance to main insecticides is threatening the success of these strategies. In Benin, and its neighbouring west African countries, resistance to pyrethroids and DDT was mainly reported in An. gambiae while An. funestus, the other major malaria vector, was always considered to be susceptible and of less interest and attention to NMCP. However, our recent studies conducted in the southern Benin revealed the presence of pyrethroids and DDT resistance in populations of An. funestus. This recent discovery is prompting set of unanswered questions on


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: INFECTION
Title: Cellular and molecular understanding of the multifunctional Shigella virulencefactor IcsA
Funder: Wellcome Trust

Abstract: Shigella flexneri is a human pathogen transmitted by the fecal-oral route, establishing infection once it reaches the large intestine. It is responsible for approximately 1 million deaths each year and emergent antibiotic resistant strains have been reported. After replication in the cytoplasm of epithelial cells, S.flexneri moves by hijacking host cytoskeletal machinery, spreading to adjacent epithelial cells. Understanding Shigella movement within host cells will provide insight into processes of actin-based motility in other pathogens and into the development of more effective therapies. lcsA, a key virulence factor of S. flexneri, is crucial for the cell-to-cell spreading process. This protein is able to bind and activate the host actin regulator N-WASP, which once active recruits and activates the Arp213 complex. The complex in tum nucleates actin polymerization, forming F-actin comet tails that propel the bacterium through the cytoplasm. The aim of this project is to understand the role of lcsA in Shigella infection. To achieve this, I intend to map the lcsA - N-WASP interface and determine the structure of lcsA alone and in complex with NWASP. This work will be the complemented by functional studies consisting of actin polymerization and bacterial motility assavs.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Pathogenomics of Staphylococcus aureus: identification of novel virulence traits.
Funder: Wellcome Trust

Abstract: Staphylococcus aureus (S. aureus) is a bacterium (germ) capable of causing a variety of infections. These range from mild skin infections treated by a General Practitioner, to severe bloodstream infections that can be very difficult to treat such as methicillin-resistant S. aureus (MRSA). Patients can become infected with this organism whilst in hospital for an unrelated condition and preventing this is a high priority in the NHS. Research has shown that aspects of the genetic makeup of these germs can explain why some cause more severe disease compared to others, but the knowledge is far from complete. A new way of looking at this has emerged by using a fish model that allows us to examine a high number of different germs in a short time period. Combining this with new technology that presents the entire genetic makeup of S. aureus, we can focus on targets that may be responsible for causing severe infections. To rationalize animal use in research, fish are extremely useful to guid e our future experiments. Ultimately, we hope to find improved ways of treating S. aureus infections by understanding why this germ can outwit us, despite our current best efforts.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: INTRAHOST DYNAMICS IN TREATED AND UNTREATED MALARIA PATIENTS.
Funder: Wellcome Trust

Abstract: Malaria is a parasitic disease that is transmitted to human beings through mosquito bites, and kills millions of children in Africa annually. Unlike in regions of low malaria transmission in South East Asia and South America, malaria infections in high transmission areas of sub-Saharan Africa are often complex, and contain several genetically distinct malaria parasites in the same patient. Infection by more than one parasite genotype may influence the severity of malaria disease, malaria transmi ssion and the spread of antimalarial drug resistance. However, our knowledge about these complex infections is still quite limited because we currently dont have suitable tools needed to isolate individual parasite genotypes on a large scale. The major goal of this proposal is to develop and apply novel approaches for rapid dissection of multiple-genotype infections to improve our understanding of malaria parasite biology, and to examine their impact on malaria disease. The second goal of this p roposal is to assess the effect of multiple-genotype infections on our ability to detect emerging drug resistance in the field. Developing suitable tools will help prepare for the surveillance and management of resistance, and is critical given the emergence of resistance to the key antimalarial drug, artemisinin, in SE Asia.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Interrogating genomic and transcriptomic data sets to reveal the genetic basis of insecticide resistance in malaria vectors.
Funder: Wellcome Trust

Abstract: Mosquito-borne diseases kill more than one million people and debilitate hundreds of thousands every year. Most deaths in sub-Saharan Africa are attributable to malaria where the mosquito Anopheles gambiae is the major vector. The use of insecticides targeting mosquito populations has been fundamental in reducing the burden of Malaria. However, genetic information allows mosquitoes to survive insecticides compromising the effectiveness of control campaigns. Thus, the ability to correctly iden tify the genes and gene interactions involved in insecticide resistance is fundamental for the development of malaria control policies. In order to increase our understanding of the mechanisms of insecticide resistance the key goals of this research are: 1. Create realistic models of vector demography to verify the statistical performance of methods to detect genes under selection caused by insecticides. Developed new methods if necessary. 2. Apply these statistical methods to detect sel ection in a very large datasets to find genes involved in insecticide resistance. 3. Do comparative studies of the expression of genes, by analysing RNA expression data from mosquitoes subjected to insecticide treatment and try to find genes that, cooperatively, allow mosquitoes to survive insecticides. Also find those signals in the genome.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Dissecting a bacterial secretion system: recruitment and secretion of diverse effectors.
Funder: Wellcome Trust

Abstract: The Type VI secretion system (T6SS) is the most recently identified secretion system in Gram-negative bacteria and it is found in many pathogens. It has been demonstrated that bacteria can use the T6SS to target either eukaryotic cells or competitor bacteria, making it a key direct or indirect virulence factor. Serratia marcescens is an opportunistic human pathogen that uses its T6SS to efficiently kill competitor bacteria. However, the molecular mechanismof the T6SS is still poorly understood. Diverse proteins secreted by the T6SS of S. marcescens and other bacteria ('effectors') have recently been identified. However no obvious secretion signal defining proteins as substrates for the system has been identified and the mechanism of effector selection and secretion is unknown. The aim of this project is to use the S. marcescens T6SS as a model:(1) to identify and characterise the signal that targets proteins for secretion via the T6SS; and (2) to establish the role of the Valine-Glycine Repeat Protein G (VgrG) and other core components in the recruitment and secretion of effectors by the T6SS. This work will provide important new insight into how S. marcescens and other pathogens utilise the T6SS to attack other cells in order to outcompete rival bacteria and mount a successful infection.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: System wide characterisation of Trypanosoma brucei protein complexes utilising chromatography and proteomics.
Funder: Wellcome Trust

Abstract: The work proposed here aims to characterise the composition of protein complexes in the protozoan parasite Trypanosoma brucei, the etiological agent of African sleeping sickness. We will attempt to describe T. brucei protein complexes in a system-wide manner, through combining chromatographic separation and mass-spectrometry based proteomics of trypanosome lysates. The initial work will utilise the clinically relevant blood-stream form of the parasite, where methodology will be developed to optimise production of lysates, chromatographic separation and proteomic analysis. This will produce a large data set of putative protein interactions that will be a highly valuable resource to understand protein function in trypanosomes. We will alsoextend our analysis to aspects of trypanosome biology, characterising complexes of the procyclic form of the parasite, found in the mid gut of the tsetse fly vector, enhancing our knowledge of how T. brucei adapts it's proteome to enable survival in a new environment. Furthermore, as trypanosomesare a highly divergent eukaryote we can further our understanding of the evolution of protein complexes by comparison with previously produced data sets from human cells, potentially identifying core conserved components of complexes.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Advancing human and veterinary vaccinology.
Funder: Wellcome Trust

Abstract: New vaccines are needed to combat major infectious disease of humans and livestock. The Jenner Institute has provided core facilities to support its vaccine researchers leading to substantial progress in new vaccine development against important global diseases which are recognised as difficult targets for vaccine design, such as tuberculosis, malaria, HIV and foot and mouth disease. A viral vector core facility has been key to the development of many new vaccine candidates. We propose here t o develop a new core facility that will analyse the changes in RNA in samples from vaccinees. This 'transcriptomics' approach allows changes in the expression of thousands of genes to be measured cost effectively. This provides information on the early innate response to vaccines and also on the acquired immune response that provides durable protection. In preliminary studies we find differences between weak and strong responders to vaccines and evidence that such patterns may predict the effica cy of vaccination in different individuals. We plan to extend these studies to a wide range of investigational and established vaccines for humans and livestock, aiming to find better biomarkers of vaccine performance and to define molecular pathways that will allow improved vaccine design.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Identification of T-cell epitopes for vaccine targets against melioidosis in North East Thailand.
Funder: Wellcome Trust

Abstract: People continue to die around the world from infections for which there is no vaccine. Infections caused by bacteria, viruses and parasites which hide inside the body's cells, such as TB, HIV and malaria are especially difficult to develop powerful lasting vaccines against. An example of a pathogen that hides inside cells is melioidosis. Melioidosis is a common cause of illness and death in North East Thailand, and neighbouring regions. It is caused by a bacterium called Burkholderia pseudomalle i which is identified as a potential bioterrorism weapon. Understanding how human immune systems fight melioidosis naturally is a key step in developing a vaccine. Blood will be taken from 280 patients admitted to hospital unwell with melioidosis, both with and without diabetes. Blood from people with diabetes in the region who are currently well, and from unexposed healthy subjects will be used as negative controls in the studies. A number of state of the art studies will be performed on the samples in Thailand and internationally through collaborations. This study will be a major step forward in our understanding of response to pathogens that live inside cells and will advance the field of tropical immunology and vaccine design.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Investigating the role of oxygen tolerance in a [NiFe]-hydrogenase in bacterial competition.
Funder: Wellcome Trust

Abstract: The oxygen tolerance of [NiFe]-hydrogenases is proposed to have a key role in bacterial virulence. Single site mutants of oxygen-tolerant Escherichia coli Hyd-1 will be generated and tested for key properties such as tolerance to oxidative and acidic stress using protein film electrochemistry. In addition to a Hyd-1 deletion strain of E. coli from the Keio collection, E. coli containing these variants of Hyd-1 shall be placed in competition experiments against the wild type strain to determine if those lacking, or with a mutated,Hyd-1 are at a competitive disadvantage. The competition experiments will be conducted in a chemostat in order to strictly control conditions such as pH, percentage of atmospheric hydrogen and percentage of atmospheric oxygen. Macrophage studies will be conducted on the mutant and wild type E. coli in order to determine how bacterial survival is impacted by the mutations created. Given success in these trials, the relevance of this work to human gut flora will be explored using in vivo experiments on a novel invertebrate animal model.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Investigation of the pro and anti-inflammatory effects of neutrophils in response to RSV infection.
Funder: Wellcome Trust

Abstract: Bronchiolitis is a lower respiratory tract infection, especially common in babies and often caused by Respiratory Syncytial Virus (RSV). Symptoms of infection can be mild but RSV can also cause airways to become swollen and blocked, making it difficult to breath. In the UK, 3% of all infants are hospitalised with this condition. The immune response to RSV infection in the airways includes an invasion of white blood cells called neutrophils. Neutrophils fight infection by ingesting microbes, and releasing chemical messengers; as a result, inflammation occurs in the airways. Neutrophils are capable of both producing and preventing further inflammation but we don't know the balance of these two responses in RSV infection. In other conditions, infant neutrophils act in a different way to adult neutrophils. I want to investigate how neutrophils in young babies behave when exposed to RSV compared to adult neutrophils, and whether their behaviour could explain why young children get more severe disease. Key goals 1. Establish how neutrophils respond to RSV and RSV-infected lung cells. 2. Explore the mechanisms behind the neutrophil response. 3. Compare the responses between infant neutrophils and adult neutrophils to better understand the cause of severe disease in infants.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: An investigation of cell dynamics, migration and differentiation resulting in the generation of a CD8+ T-cell memory response following vaccination with anti-malarial viral vectors.
Funder: Wellcome Trust

Abstract: In this research project, the immunological response to viral vector vaccines will be investigated; specifically to adenovirus and poxvirus vectors currently being developed at Jenner Institute against pre-erythocytic malaria.A comparison between the two viral vectors, and a heterogeneous prime-boost regime will be performed. By using a wide range of imaging techniques such as confocal and two-photo microscopy, multi-channel flow-cytometry and histo-cytometry, the subsets of antigen presenting cells involved in the priming of effector CD8+ T-cells will be studied, along with the subsequent cell activation, differentiation and migration to various tissues. The techniques chosen will allow for both a statistically quantifiable, temporal, and visual study of the cellular interactions involved in their physiological state. These cellular interactions will be observed particularly in the liver,but also in the relevant draining lymph nodes and intra-muscular vaccine administration site. The goal is to understand in greater depth how a protective CD8+ T-cell immune response is generated, so as to improve future


Research activity codes: 3.4 VACCINES
Health categories: INFECTION