NIHRDataInsights/HRCSData huggingface dataset:
Title: Structural studies of lipid-enveloped viruses by cryo-EM
Funder: Wellcome Trust

Abstract: Lipid-enveloped viruses such as orthomyxoviruses and retroviruses include major human pathogens. Influenza viruses, from the Orthomyxoviridae family, are the causative agent of seasonal flu epidemics and can lead to severe illness or even death. Infection of the host cells by the virus is possible thanks to a spike protein named hemagglutinin (HA) located in the outermost layer of the virus: the viral envelope. HA binds its receptor on the target cell surface and later mediates entry of the virus into the host cell by a process termed membrane fusion. I aim to further study the detailed mechanism by which HA mediates membrane fusion. I will use the high-resolution structural techniques cryo-EM and cryo-ET to understand how structural changes in HA enable viral entry, including how the protein interacts with cell and viral membranes. The analysis of HA-mediated membrane fusion at a structural level will provide a better understanding of this process, which may help in identifying steps that may be therapeutically blocked. This detailed understanding may also be applicable to the infection process by other lipid-enveloped viruses, as well as to other membrane fusion processes in biology.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Understanding the effects of MKRN1 in HIV-1 infection
Funder: Wellcome Trust

Abstract: The human immunodeficiency virus type 1 (HIV-1) is the causative agent of acquired immune deficiency syndrome (AIDS). In 2018 the World Health Organisation estimated 37.9 million people worldwide are living with AIDS, for which we have no cure. My project aims to establish some of the mechanisms underlying the interaction between HIV-1 and human cells. The impact of this research will further our understanding of HIV-1 and may enable the production of targeted therapies. HIV-1 has a complex lifecycle and relies on host RNA-binding proteins (RBPs) to replicate and spread. The Castello lab identified a group of host RBPs that are present inside HIV-1 particles, holding great potential as HIV-1 regulators. One of these RBPs, makorin-1 (MKRN1), is a ubiquitin ligase, an enzyme that modifies other proteins by adding protein tag called ubiquitin. The ubiquitin tag signals to the cell to destroy the tagged protein. I hypothesise that MKRN1-driven ubiquitination is critical to control HIV-1 infection. Throughout my PhD I aim to assess if MKRN1 supports or restricts infection, determine how MKRN1 is recruited into HIV-1 particles and discover how MKRN1 controls HIV-1.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: The role of RNA Methylation (m6A) in Chikungunya virus replication
Funder: Wellcome Trust

Abstract: Chikungunya virus (CHIKV) is an emerging human pathogen, which is transmitted by mosquitos. CHIKV has a widening distribution due to the impact of globalization, including changing land use and international travel and trade. Viruses manipulate host cells in a variety of ways, including through gene expression. Genome modifications have been shown to play a role in a range of other viruses’ lifecycles, including the closely related Zika virus (ZIKV). We seek to build a more comprehensive understanding of CHIKV biology in both their insect and mammal hosts, from the point of RNA modifications which has been shown to regulate replication of related viruses. We aim to dissect the extent and function of virus and host-cell genome modificationson CHIKV replication, to better understand the basic biology of the virus in its varied host environments and identify potential therapeutic targets.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Evaluating the potential of antivirulence strategies to treat bacterial infection
Funder: Wellcome Trust

Abstract: Untreatable bacterial infections due antibiotic resistance is a major threat to human health with devastating future implications. Potent alternative therapeutics are desperately needed. Antivirulence therapy (AVT) is an alternative strategy which aims to disarm bacterial pathogens by inhibiting the virulence factors (VFs) they require to cause disease. Research suggests AVT may be effective when administered prophylactically, however it is unknown to what extent inhibiting VFs can resolve established infections. We will develop a platform to comprehensively validate putative VF targets and address pre-existing concerns. An antibody mimetic (affimer) will be employed to inhibit VFs during established bacterial infection in an insect model. If inhibition of a specific VF increases insect survival in the infection model, the candidate may be an attractive therapeutic target. Unlike previous research that has examined AVT, our work will examine the effectiveness of inhibiting VF targets after a bacterial infection is underway. In addition, the platform developed will be employed to address previous concerns regarding AVT such as resistance development. This project could produce reagents that could be further optimised for companion diagnostics in the future. Additionally, the platform could be utilised by researchers to thoroughly examine candidate VFs of interest prior to expensive therapeutic development.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: The structure, function and essentiality of Trypanosoma cruzi mitochondrial fucosyltransferase
Funder: Wellcome Trust

Abstract: The protozoan parasites Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. are the causative agents of neglected tropical diseases. They rely on surface glycans, chains of sugar units attached to proteins and lipids, for their survival and infectivity. These surface glycans are synthesized by enzymes called glycosyltransferases located in the secretory pathway. However, contrary to this canonical model of glycan synthesis and surface expression, our group has recently described the presence of an essential glycosyltransferase, a fucosyltransferase, in the mitochondrion of T. brucei. A similar putative fucosyltransferase gene, called TcFUT1, has been found in the genome of T. cruzi, the causative agent of Chagas’ disease, endemic in the Americas. We aim to obtain recombinant, active TcFUT1 protein in order to analyse its enzymatic activity, define its preferred substrate(s) in vitro, design assays for compound screening and to raise antibodies against it for immuno-localisation. In parallel, we also aim to define its essentiality and characterise its endogenous substrates. This work will provide an opportunity to uncover the function(s) of this novel mitochondrial fucosyltransferase and provide a much-needed drug target for Chagas’ disease.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Investigating the emerging pathogen Shigella sonnei
Funder: Wellcome Trust

Abstract: Bacterial dysentery is a major cause of infant morbidity and mortality. Shigella flexneri and sonnei are responsible for 90% of these cases. Interestingly these bacteria are distributed differently and S. sonneiis the dominant serotype in transitional and high-income countries. Recent work has highlighted key differences between these Shigellaspecies including higher lethality of S. sonneiin an infection model, different interaction with immune cells and an increased ability to survive and persist under low nutrient conditions compared to S. flexneri. I aim to identify and understand the underlying molecular mechanisms behind these differences using a multi-disciplinary approach. I will use a combination of targeted and untargeted metabolite profiling (mass spectrometry, NMR spectroscopy and LC-MS) as analytic platforms in addition to the development of novel assays (to dissect polysaccharide biosynthesis pathways and nucleotide biosynthesis) to test specific hypotheses about nutrient flux in S. sonnei. Results here would better inform our understanding of Shigella persistence and how this could be mitigated in public health and infrastructure settings. In addition, any new techniques developed could be used to study other bacterial pathogens as polysaccharide biosynthesis is an important aspect of pathogen biology.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Characterising the regulators of trypanosome development and virulence in selected and natural parasite isolates
Funder: Wellcome Trust

Abstract: Trypanosoma brucei, the causative agent of human and animal trypanosomiasis, has two distinct life stages. The proliferative ‘slender’ bloodstream-form morphs into a transmissible ‘stumpy’ form, which is adapted to surviving in its vector’s (Glossina spp.) midgut. The transition occurs in a density-dependent quorum sensing (QS) like process which is initiated by a ‘stumpy induction factor’ (SIF). I propose to use a wide diversity of pleomorphic (capable of morphing from slender to stumpy) field and laboratory strains of T. brucei to generate, via multiple passages, monomorphic cells (unable to become stumpy). I will create genomic, transcriptomic and epigenetic data from these cells at the beginning and end of the selection in an attempt to determine the cause of monomorphism, and therefore, the integral components of the QS process. By performing the study on diverse T. brucei cell lines, it will be possible to establish if the monomorphic phenotype can arise via convergent evolution. Alongside the genomes produced during this project, publicly available trypanosomatid genomes will be collated to identify conserved genes associated with increased virulence and monomorphism.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Structural Characterization of the Human Endogenous Retrovirus K (HERV-K)
Funder: Wellcome Trust

Abstract: Approximately 8% of the human genome consists of Human Endogenous Retroviruses (HERVs) which have been found to be active in several diseases such as cancer and HIV infections. This raises several questions as to why these sequences were retained in the genome and why they become active in such a broad range of diseases. We have decided to study HERV-K (HML-2) as a representative of this class as it is the most recently acquired retrovirus, the most transcriptionally active and encodes all structural and enzymatic proteins to form virus-like particles (VLPs). We start by studying one polypeptide of the virus which is sufficient to form non-infectious VLPs. We will then include the other proteins step-by-step until we have the structure of the fully formed virus. This gives us the possibility to work up to the more complicated virus on the basis of the earlier results. VLPs can be seen in cryo-electron tomography easily and sub-tomogram averaging of the highly symmetric lattice gives the opportunity to achieve a sub-nanometre structure of HERV-K. These findings lay the basis to find the mechanism of how HERV-K acts and will be tested by in vivo assays to develop compounds for blocking HERV-K.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Mycobacterial drug target deconvolution using Genetic, Phenotypic and Proteomic approaches
Funder: Wellcome Trust

Abstract: Mycobacterium tuberculosis is the causative agent of tuberculosis (TB) and leads to 1.8 million deaths per year. Resistance to the currently used anti-TB drugs is growing, which will increase death rates in the future if unchecked, hence there is a high demand for new drugs. My project aims to identify how novel anti-TB molecules work, to increase our understanding of their targets and how they can be improved to increase their activity and selectivity. The protein targets will be produced and then purified, allowing the drug-protein interactions to be studied. Specific interactions will be identified, providing evidence for alterations to these drugs to increase their potency. Another section will be the identification of new drug targets, which could be taken forward for targeting by studying the protein-protein interactions occurring in the outer membrane and wall of M. tuberculosis. The main output of my work would be increased knowledge of protein-molecule interactions of novel anti-TB drugs and will allow them to be altered to increase their selectivity and activity. This would hopefully lead to these novel drugs being taken forward as potential drugs for the treatment of TB, expanding treatment options against multi-drug resistant M. tuberculosis strains.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Investigating the impacts of nutrition on gastrointestinal helminth infection and immunity in a wild mouse model
Funder: Wellcome Trust

Abstract: Gastrointestinal (GI) parasitic helminths, pose a significant threat to the health of humans and animals worldwide. Those affected are continuously exposed and rapidly re-infected post-treatment, however, the level of infection (worm burden) varies among individuals. The underlying drivers of such individual differences are multifaceted; however, host immune and nutritional status influence exposure and susceptibility to helminths. Much of our understanding of GI helminth infections in mammals has derived from lab mouse models that may not reflect real-life scenarios. Instead, using wild hosts and their coevolved wild parasites may provide a more ecologically relevant model of GI helminths for humans and wildlife. Currently, limited research has investigated the relationship between nutrition and immunity in natural host-helminth systems. We aim to determine the role nutrition plays in immunity and infection within a natural host-helminth system; wood mice (Apodemus sylvaticus) and wild isolates of Heligmosomoides polygyrus. By conducting parallel experiments in the lab and wild, with the same host-parasite system, we can control for variation in parasite exposure and nutritional status to determine the key drivers of susceptibility to infection. We will combine both ecological and immunological data to gain a greater understanding of the interplay between nutrition, immune response and helminth infections.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Investigating the female sexual life-cycle of Cryptosporidium, a diarrhoeal pathogen of global significance
Funder: Wellcome Trust

Abstract: Cryptosporidiosis is a diarrhoeal disease of global significance caused by the intracellular parasite, Cryptosporidium spp. Infections can cause malnutrition, growth stunting and be fatal in children. Unlike other causes of diarrhoea, cryptosporidiosis lacks effective treatment or vaccine. Shortcomings in the clinic persist due to the lack of a continuous in vitro culture system. This year, we established and infected mouse intestinal organoids (miniaturized, self organized organs) in our laboratory. Combining these in vitro culture abilities with gene-editing tools, we can now study the complete life-cycle of Cryptosporidium and stages which precede transmission that were not readily observed previously. I aim to better define the female life cycle stage of Cryptosporidium. It is important to understand how female parasites regulate building environmentally resilient cyst walls, and sporulate new parasites inside this cyst. I aim to generate a female stage-reporter strain of C. parvum and validate Cryptosporidium-organoid co-culture in the first 6 months. Furthermore, isolated females may be further characterized by single cell RNA-sequencing and proteomics. This research will better define the formation of the transmissible stage of Cryptosporidium and provide a basic understanding on which to develop vaccine and drug discovery.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Characterisation of a host receptor for Plasmodium falciparum-infected erythrocyte rosette formation
Funder: Wellcome Trust

Abstract: Rosetting, the binding of two or more uninfected erythrocytes to an infected erythrocyte, is associated with severe P. falciparum malaria. Therefore, anti-rosetting therapies that reduce microvascular obstruction may be beneficial as adjunctive therapy to reduce severe malaria deaths. Rosettes are formed by an interaction between parasite-derived Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) and host erythrocyte membrane receptors. PfEMP1 is highly polymorphic and therefore a challenging target for vaccines. Recent work by the Rowe lab suggests that PfEMP1 mediates rosetting by an interaction with the Wrightb antigen formed by Band 3 and Glycophorin A. An antibody targeting Wrightb has disrupted rosettes in all P. falciparum strains tested to date, suggesting that this small antibody fragment (BRIC14) has therapeutic potential. I propose to test BRIC14 across a panel of rosetting P. falciparum strains to determine the efficacy of BRIC14 in severe disease states. I aim to characterise the interaction between PfEMP 1 and Wrightb to determine if BRIC14 reduces rosetting by direct inhibition of a ligand-receptor interaction or by altering erythrocyte deformability. The present study aims to characterise a key receptor-ligand interaction implicated in rosetting and determine if a rosette-disrupting antibody has potential as a therapy against disease-causing P. falciparum strains.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: A multifaceted exploration of the dynamics of acute respiratory infections in Denmark using deep learning approaches
Funder: Wellcome Trust

Abstract: Acute respiratory infections (ARIs) including bronchitis and pneumonia are common illnesses in children in high-income countries [1]. Childhood adversaries such as death, illness or unemployment in the family, alongside environmental factors such as pollution are thought to increase the chances of someone developing an ARI [2]. Previous studies measured the impact of risk factors for ARIs but focused on a single associated risk and did not factor comorbidities including stroke, cancer, diabetes or mental illness. To our knowledge no study has looked at a multifaceted view of the causes and associations of ARIs. I aim to look at a variety of sociodemographic, environmental and individual specific factors and evaluate the landscape of ARI disease risk. I will use a unique dataset collated from Danish Registers for people born after 1980 [3]. This dataset contains unparalleled information on longitudinal health outcomes and childhood adversaries and, unlike single timepoint surveys, allows the study of risk trajectories for the entire susceptible population. I will study the spatial and temporal influence of risk factors on ARI incidence and develop a modelling framework for predicting disease progression and could be used as an early warning system to identify high risk populations and inform intervention strategies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: A global model for the evolutionary dynamics of seasonal influenza
Funder: Wellcome Trust

Abstract: Influenza epidemics infect between 10% and 20% of the global population each year. Infection typically infers a lifetime immunity on an individual, but due to the gradual accumulation of mutations new strains can emerge that evade the host’s immunity and allow repeat infection. This ‘antigenic drift’ of influenza has been well characterised, but the origins of the observations are not well understood. A limited number of models have attempted to explain the observed effects. However, none of the models has included a realistic spatial component or realistic population sizes. The aim of this project will be to develop a computational model of influenza evolution that incorporates realistic population sizes and spatial spread at a global scale. The model will be based on individuals and allow spatially dependent transmission. The model will include a probability of mutation of a strain upon infection of an individual. By tracking each individual’s immune status based on previous infections evolution will naturally occur in the model to evade population immunity. This model will lead to a greater understanding on the complex relationship between human ecology and the evolutionary dynamics of influenza. It is possible it may also inform future surveillance and vaccine protocol.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Understanding behavioral clustering in epidemics
Funder: Wellcome Trust

Abstract: An increasingly interconnected world provides a greater opportunity for the emergence of epidemics. In the last decade alone, the World Health Organization (WHO) has announced five Public Health Emergencies of International Concern. Additionally, there has recently been a resurgence in vaccine-preventable diseases. The increasing risk of epidemics necessitates a greater ability to understand how they spread. Current outbreak models have struggled to reproduce outbreak data across a number of diseases, from Ebola Virus disease in West Africa, to a measles outbreak in Brazil. One reason for this is that current models do not consider how the behavior of individuals in contact with each other is clustered. For example, people who are hesitant to vaccination are more likely to be in contact with each other, and less likely to be in contact with vaccine adherents. This clustering increases the susceptibility of the unvaccinated population to disease. This PhD will use explore how clustering of individuals affects the spread of outbreaks. I will develop a mathematical model which simulates disease outbreaks through a network of individuals with clustering based on behavior. The work could be applied in a number of disease contexts from Ebola in West Africa to Measles in Latam.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: INFECTION
Title: Understanding the dynamics of agr expression in vivo and the efficacy of agr pathway inhibitors
Funder: Wellcome Trust

Abstract: Staphylococcus aureus is a common cause of hospital acquired infections. Infections caused by S. aureus are difficult to treat due to the emergence of drug resistant strains and growth in biofilms which limits the efficacy of antibiotic drugs. Due to emergence of antibiotic resistant bacteria there is a need for drugs which do not succumb to conventional methods of antibiotic resistance. One method is through attenuation of the virulence of the bacteria. This will reduce the infection with less pressure for resistance to emerge. One promising anti-virulence target is cell-cell communication known as quorum sensing. This PhD will involve investigation of the agr quorum sensing system in S. aureuswhich is known to control virulence. This is temporally expressed during infection and a model using bacteria with NanoLuc/GLuc luminescent reporters linked to the agr system will be developed and used to determine when and where this system is activated in vivo. This model can then be used to screen for inhibitors of the agr system and their efficacy determined in in vivo models.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION