NIHRDataInsights/HRCSData huggingface dataset:
Title: Interactions of the Plasmodium falciparum Erythrocyte Membrane Protein 1 intracellular domain with the erythrocyte cytoskeleton and parasite components.
Funder: Wellcome Trust

Abstract: Adhesion of malarial infected red blood cells to the blood vessel wall is a contributing factor in the severity of malaria caused by the parasite Plasmodium falciparum. Adhesion is caused by the P. falciparum Erythrocyte Membrane Protein 1 (PfEMP1) family, which localises to distinct protein dense protrusions on the red blood cell, referred to as knobs. PfEMP1 family membersspan the red blood cell membrane with a highly divergent extracellular domain,a trans-membrane region and a predominantly conserved, highly disordered intracellular region, referred to as the acidic terminal segment, ATS. The N-terminal region of the ATS has been found to interact with the cytoskeletal protein ?-spectrin, close to the site of actin-spectrin junctions, and the C-terminal region has been found to interact with members of the PHIST family of malarial proteins, which have unknown function. A combination of X-ray crystallography, NMR, electron microscopy and computational approaches will beused to achieve the following key goals: Obtain a structural modle for the ATS-spectrin interaction Obtain a structural model for the ATS-PHIST domain interaction. Build a model of the ATS structural interactiosn within knobs.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Genetics of gene expression in human macrophage response to Salmonella
Funder: Wellcome Trust

Abstract: Understanding how cells sense and respond to their environment, and how these responses are modulated by genetic variation, are fundamental biological problems, particularly for understanding how pathogenic organisms invade and manipulate the cells of the human immune system. Macrophages recognize and respond to many important human pathogens including HIV-1, Mycobacteria tuberculosis and Salmonella. My thesis will focus on the cellular response of human macrophages to Salmonella infection. In addition to being medically relevant, Salmonella is a well-established model system to study host-pathogeninteractions.Understanding host response to Salmonella will also provide insights applicable to other important human pathogens. Previous studies of human macrophage interaction with Salmonella have been hampered by difficulty of obtaining macrophage cells. However, many problems have recentlybeen overcome using in vitro differentiation from induced pluripotent stem (iPS) cells. The goals of my thesis are (i) to establish iPS-derived macrophages as a model system for studying the cellular interaction of the human macrophages with pathogens (ii) to use this model system to systematically map the transcriptional and epigenetic response of macro phages to Salmonella typhimurium and (iii) to identify genetic variants that modulate infection transcriptional response in macrophages, using quantitative trait loci mapping.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Investigating differential phosphorylation of NS5A using super-resolution microscopy.
Funder: Wellcome Trust

Abstract: The aim of this project is to elucidate structural information about the hepathepatitis C virus replication complex using super-resolution microscopy techniques. Our approach is to analyse a critical replication complex component, the non-structural protein 5A. This protein is known to be differentially phosphorylated into basal- and hyper-phosphorylated species, however little information is available on the functions of these distinct witprotein species.s is a global health concern and this project aims to provide The project goals are: o Analysis of the functional roles of NS5A phosphorylation o Use super-resolution imaging to gain insight into the protein organisation within replication complexes Hepatitis C virus is a global health concern and this project aims to provide new information into a crucial part of the virus life cycle.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Biophysical and structural investigations of DNA repair modulation by viruses.
Funder: Wellcome Trust

Abstract: Viral proteins subvert various cellular processes to optimise the propogation or stable sojourn of virus genomes. Viral stealth and replication strategies can be compromised by uracil-DNA glycosylase (UDG) activity, making UDG a kown target of viruses infecting both prokaryotes and eukaryotes. In viruses of prokaryotes, UDG is silenced by the diverse protein inhibitors: a deeper investigation of structural diversity in this realm would benefit methodology in low homology bioinformatics, our understanding of protein evaluation, and inform the development of novel inhibitors of DNA repair enzymes. In human HIV-1 infections, UDG is targeted to the proteosome by association with the viral accessory protein Vpr. As a strategy for dealing with incoming virus genomes, it is possible that the UDG's ancillary role in somatic hyper-mutation may be reprised in combination with the anti-viral deoxycytidine deaminase, APOBEC3g (A3G). The HIV-1 accessory proteins Vif (targeting A3G), and Vpr, are therefore appealing anti-viral targets, and therapeutic molecules could likely be developed through biophysical and structural knowledge to their respective interactions. We aim to develop systems to identify novel viral predictors of UDG and to produce viral proteins using Vpr [and Vif with relevance to A3G] stably for biophysical and structural analyses via NMR and x-ray crystallography.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Structural and Functional characterisation of chlamydial inclusion proteins.
Funder: Wellcome Trust

Abstract: The project aims to study the structure and function of two chlamydial inclusion proteins. Chlamydia is a major human pathogen, causing sexually transmitted disease and trachoma (a form of blindness). To replicate inside host cells, chlamydia build a specialised intracellular compartment called an inclusion, which is segregated from the host endocytic system but selectively engages key host organelles and secretory traffic. To achieve this, Chlamydiae deliver a family of hydrophobic inclusion proteins (Incs) into the inclusion membrane, but very little is kown about their structure and function. Exploiting our ability to purify these membrane proteins, the project aims to fully understand i0 the bases of membrane tubulation by IncC, ii) the nature of the novel endoplasmic reticulum retention signal within IncB, iii) the host targets if IncC and IncB and their roles during bacterial infection. the arising data will allow new insights into the molecular mechanism of this medicallu important pathogen.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Unravelling the in vivo immune response against Schistosoma mansoni eggs
Funder: Wellcome Trust

Abstract: Schistosomiasis is the second-most socioeconomically devastating parasitic disease. After infection, Schistosoma mansoni eggs become trapped in the smallintestine and the liver. These eggs drive a chronic immune response that generates fibrosis, causing a debilitating and eventually fatal loss of organ function. Drugs to reduce this inflammation are not available, and much remains to be learned about this pathogenic immune response against S. mansonieggs in vivo. Here we propose a detailed analysis of the soluble and cellular mediators thatinduce responses to S. mansoni eggs in the small intestine and the liver of mice in vivo. We will use novel tools to generate heretofore-unavailable insights into these mechanisms. These include recently developed flow cytometric analyses of immune cell populations, cell sorting, genetically modified mouse strains, and cutting-edge in vivo techniques. We aim to identify the specific cells that drive pathogenic responses to S. mansoni, andthe precise cellular sources of the soluble mediators that control this response. Our results will not only produce a detailed understanding of the cellular interactions between immune cells that respond to S. mansoni eggs, transferable to other parasitic infections or even allergic responses, but mayalso present targets for the specific immunosuppression of Schistosomiasis.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Characterising mechanisms of macrophage subversion by Leishmania parasites
Funder: Wellcome Trust

Abstract: This project aims to learn how Leishmania parasites can survive and prosper within macrophages. Recent metabolomics experiments have revealed that Leishmania produce and secrete large quantities of citrulline, a metabolic product of arginine deimination. Arginine is a precursor to nitric oxide, a toxic metabolite used as a key part of the antimicrobial reaction cascade within the macrophage. We hypothesise that conversion of arginine to citrulline by Leishmania parasites might be used to limit host-cell access to arginine and thus restrict its ability to create nitric oxide, thus contributing to the parasite's ability to survive. We have identified a gene in the Leishmania genome that is a candidate arginine deiminase, i.e. an enzyme capable of converting arginine to citrulline. We propose to verify thisrole by expressing the gene and assessing activity and also knocking the gene out in Leishmania to determine whether citrulline production is altered and how this affects other phenotypic traits including macrophage infectivity and survival. It is also clear that Leishmania parasites can prevent macrophages entering their activated state. We will therefore also investigate how macrophage metabolism is influenced during activation and how wild type and mutant Leishmania parasites affect these metabolic correlates to macrophage activation.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: The role of Bcl3 in skeletal health and disease
Funder: Wellcome Trust

Abstract: In this project we will develop a microfluidic platform to explore both chemical and biochemical co-evolution for the development and understanding ofchemical and biochemical pathways responsible for antibiotic resistance in bacteria. In embarking on this we will develop a multiplexed droplet based evolutionary 'lab on a chip' device that incorporates digital control of chemical and biochemical input. Genetically engineered systems with increased evolvability will be explored with libraries of peptide-antibiotics produced using solvent-resistant micro-peptide droplet synthesis or available librariessynthesized / purchased. The integration of evolution algorithms controlling the micro-device in synergy with the chemical and bacterial libraries will allow us to explore a range of hypotheses for the development of new mechanisms of antibiotic development. For example, can embodied evolutionary approaches be used to accelerate biological directed evolution? Ultimately theaim will be for the chemical-based evolution of small molecules or biologics as a function of computer controlled algorithms allowing us to develop antibiotic drugs in a fundamentally new way.


Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES;5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Selection activation of Pattern Recognition Receptors to enhance host protective immunity agaisnt infection
Funder: Wellcome Trust

Abstract: The emergence of antibiotic resistance, coupled with the lack of an efficient vaccine means Salmonella infections are still a huge problem the developing world; development of a suitable vaccine would be a significant contribution to disease control. This project aims to identify a modified strain of Salmonella enterica serovar Typhimurium (STm) which utilises host PRRs TLR4 and NLRC4 to initiate a strong Th1 immune response. TLR4 is activated by the binding of the Lipid A component of LPS, initiating asignaling cascade via the Myd88 and TRIF/Tram pathways. It is thought a dephosphorylated form ofLipid A, MPLA, signals exclusively by the TRIF/Tram pathway, reducing the potential foroveractivation of TLR4; engineering a strain to express MPLA would mean it remains immunogenic while reducing harmful side effects. NLRC4 is activated by the binding of bacterial flagellin and components of T3SS. Activation is thought to suppress the Th1 immune response; by mutating components of flagellin to prevent recognition by NLRC4, a maximum Th1 response will be achieved.By coupling activation of TLR4 via the TRIF pathway, and reducing activation of NLRC4, this will induce a strong Th1 immune response while having low toxicity, producing a highly promising vaccine candidate.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;3.4 VACCINES
Health categories: INFECTION
Title: Human cytomegalovirus: investigating the molecular biology of US28 and its potential as a therapeutic target
Funder: Wellcome Trust

Abstract: Human cytomegalovirus (HCMV) establishes latent infection in human myeloid invlineage cells, which isof US28 for therapeutics. We have two objectives regardnecessary for a lifelong persistent infection in a human host. The viral cell surface protein US28 iso understand any changes to the cellular secretome and expressed on latently infected cells. We will be analysing the changes inducedby US28 in global cellntial therapeutic target. Our objectives are to investigsurface protein expression using stable isotope labelling of amino acids. lecuChanges observed in cell surfaceentially in vivo clearance ofthe virus and 4) protein expression may elucidate potential therapeutic drug targets against lllatent cells. We will alson be tested both in vitro and using a humanised mousanalyse changes in the latent cellular secretome, known to be immunosuppressive, using antibody arrays. If US28 induces the secretion of immunosuppressive cytokines, then chemical inhibition of US28 may alleviate immunosuppression and allow T cell-mediated killing. As US28 is currently the only known latent viral protein to be expressed on the cell surface, it may be a potential therapeutic target. We will therefore be testing a highly specific immunotoxin based on the CX(3)C-Chemokine Fractalkine, which binds US28 with very high specificity, for targeted killing of naturally latently infected cells. We also plan to exploit the cell surface expression of US28 to isolate the relatively smallnumber of naturally latently infected cells from a pool of donor monocytes.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Development of a rapid system for diagnosing corneal infections using pathogen-responsive polymers
Funder: Wellcome Trust

Abstract: Infectious diseases of the eye are common causes of ocular damage and blindness in India. Early diagnosis and institution of appropriate therapy are key in reducing both of these negative outcomes. The microbial cause of these infections varies with geographical location (with a marked contrast between India and the UK) and, therefore, identification of the infecting microorganism plays a crucial role in successful treatment. While clinical examination can provide clues, the identifications of the causative organisms typically requires microbiological facilities that are not widely available in India, involve significant cost and yield positive results in only 60% cases. It is not surprising then that many clinicians do not perform microbiological testing and treat patients following empirical observations. This approach not only delays definitive therapy but also can result in failure to arrest the infection or causes corneal damage from toxicity of the various agents used indiscriminately. Therefore, there is a need to develop a rapid and simple diagnostic system that can reliably be used in out-patient clinics to identify the class of micro-organisms involved. The polymer-based technology described here will provide rapid detection of the class of microorganism causing the infection and thereby aid rapid and more targeted treatment to commence.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: Dissecting bacterial interactions with the urothelium using emergent mass al spectrometry techniques
Funder: Wellcome Trust

Abstract: Urinary tract infections (UTI) caused by uropathogenic E. coli (UPEC) cause significant levels of morbidity across a broad spectrum of clinical populations. The urothelium is recognised as an active tissue, with important roles in damage response and sensing within the bladder, including its role asthe primary effector of the immune response to UPEC infection. Previous work in the Southgate group has shown that diffusible mediators, such as ATP, play an important role in urothelial response to damage and healing. Evidence exists that extracellular ATP can also stimulate bacterial biofilm formation, offering protection against the immune response. The effects of UPEC-urothelial interaction and its respective effects on UPEC phenotype ad urothelial homeostasis are poorly understood. We aim to develop state of the art mass spectrometry techniques to enable the analysis of the intracellular metabolome and the extracellular secretome of normal human urothelial (NHU) cells in order to further understand the role that diffusible mediators play in the interaction between the urothelium, UPEC, and the urothelial response to damage and repair.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: The role of the chemokine receptor CCR5 during the infection of macrophages byLeishmania parasites
Funder: Wellcome Trust

Abstract: Infection with Leishmania donovani has been shown to induce CCR5 on the cell surface of human mononuclear phagocytes, and CCR5-/- mice have reduced parasite burden that could reflect reduced intracellular replication and/or decreased parasite uptake. Although these data suggest that CCR5 is important for L. donovani infection, the underlying mechanisms behind it are as yet unknown. In this project, we propose to characterise this interaction in macrophages using an interdisciplinary approach. Within the lab, imaging and biochemical methods will be used to determine expression, functional behaviour, and intracellular trafficking properties of CCR5, comparing infected and non-infected murine and human macrophages. Furthermore, we will characterise the intracellular compartments containing L. donovani and isolatethem for proteomic analysis. Using mathematical modelling, we will then perform comparative proteomics to compare infected and non-infected cells to determine which proteins differ most between datasets. Thus, by better characterising this interaction, we will have an improved understanding of howthe parasite enters macrophages and how it manipulates host cell receptors to its own advantage, which could reveal novel targets for future anti-leishmanial therapies


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Investigation of cross-reactive antibodies against Plasmodium falciparum-infected erythrocytes
Funder: Wellcome Trust

Abstract: The main objectives of the proposed project are twofold; firstly, to identify monoclonal antibodies that broadly react against variant surface antigens on erythrocytes parasitized by diverse Plasmodium falciparum strains, and secondly, to identify the conserved epitopes of the surface antigens that are recognized by these antibodies. Although antibodies against variant surface antigens have been linked to protection against malaria, the prevailing viewpoint is that antibodies against these antigens generated in the course ofinfection are predominantly variant-specific. However, there has been evidencesuggesting some partial cross-reactivity of antibodies, and our preliminary work supports the possibility that broadly cross-reactive antibodies may existin adults who are clinically immune to malaria. This project aims to identify such antibodies by screening large numbers of sera from immune adults against diverse parasite strains. When cross-reactive sera are identified, we will request for blood samples from the individual donors and isolate and transformB cells producing monoclonal antibodies of interest. We will then proceed to identify the corresponding conserved target sites on the antigens, which will be potential targets for vaccine development.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Developing a novel single dose prime-boost vaccine against malaria
Funder: Wellcome Trust

Abstract: The main goal of this project is to develop a new vaccine delivery platform for a single dose prime-boost immunisation regime that would be applicable to current and future vaccines requiring a prime-boost approach. This novel platform is based on the technological advance of the production ofmicrocapsules from biodegradable polymers, which can act as vehicles into which the vaccine can be incorporated and then subsequently released in a delayed time fashion. After achieving the optimal conditions for the microcapsules and the encapsulated vaccine, the aim is to mix the unencapsulated vaccine with the encapsulated booster vaccine dose and then administer both as a single injection. The new methodology will be tested with our current candidate malaria vaccine regime of heterologous immunisation using different viral vectors as a proof of concept. Using this approach, the vaccine delivery efficiency would be optimised by reducing the number of doses required from multiple into a single dose immunisation regime. Reducing the number of repeated injections would mean reduced costs, fewer clinic visits and a higher compliance rate among vaccinees. A successful single dose formulation could provide strong evidence for the initiation of clinical trials of the new technology with considerable benefitsfor future vaccine development


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: The importance of Nef-mediated HLA class I downregulation in HIV-1 and HIV-2 infection
Funder: Wellcome Trust

Abstract: The human immunodeficiency virus (HIV) utilises a number of techniques to evade the immune system and survive in the host. HIV-1 negative factor (Nef) has previously been shown to mediate downregulation of class I human leukocyteantigen (HLA-I) molecules from the surface of cells, which is believed to facilitate evasion of cytotoxic attacks by CD8+ lymphocytes. Furthermore, HLA-B molecules are known to be more resistant to downregulation than HLA-A, whilst HLA-C is not downregulated. Studies so far have primarily used Nef derived from laboratory strains of HIV such as HIV-1SF2, rather than Nef isolated from infected patients. This project aims to explore the role of Nefin a cohort of patients with HIV-1 infection, and correlate the extent of HLA-downregulation with clinical data and progression. Nef from both elite controllers and progressors will be studied. In this cross-sectional investigation, the variability of Nef within the cohort and individual patients will be characterised, and the extent to which the protein mediates HLA-downregulation will be determined using flow cytometry. This phenomenon will also be studied in a well-characterised cohort of patients infected with HIV-2, of which very little is known regarding Nef-mediated HLA-downregulation.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION