NIHRDataInsights/HRCSData huggingface dataset:
Title: Cellular dissection of Plasmodium falciparum erythrocyte invasion
Funder: Wellcome Trust

Abstract: Plasmodium falciparum parasites still cause nearly half a million deaths each year. The repeated emergence of antimalarial drug resistance and the lack of a highly effective vaccine mean that there is an urgent need to identify new intervention targets. Erythrocyte invasion is an excellent target as it is essential for both parasite survival and for malaria pathology. Invasion involves multiple parasite ligands, but little is known about their function at the cellular level and even less about how they fit into the broader network of invasion proteins. This proposal will revolutionise our understanding of the function of two families of P. falciparum invasion ligands, the EBLs and the RHs, that are together responsible for the key decision point in the invasion process. The key goals are to: 1. Systematically dissect functional equivalence between EBLs and RHs 2. Establish the roles that EBLs and RHs play in discriminating between erythrocyte variants within and between humans 3. Use innovative combinatorial approaches to move from a gene to a network understanding of EBL and RH function. The proposal will provide a step change for the field, both biologically and technically, and will identify new candidates for testing in a rationally designed, multi-component invasion-blocking vaccine.

Lay abstract: Malaria parasites cause disease by invading and multiplying inside human red blood cells. Red blood cell invasion is a possible vaccine target because if it is prevented, the parasite is unable to grow and divide. Invasion is a complex process that involves multiple interactions between parasite and red blood cell proteins, but we currently know little about the function of the parasite proteins involved. We aim to understand invasion in a much more comprehensive way. We will focus on understanding the function of two specific families of parasite invasion proteins, the EBLs and RHs. We will establish how these proteins interact with each other and with other invasion proteins, and explore their role in allowing malaria parasites to distinguish between different types of red blood cell. This work will significantly change our understanding of the essential process of invasion, and help prioritise components for future vaccine development.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: The Type II and Tad Secretion Systems in Bacterial Pathogenesis
Funder: Wellcome Trust

Abstract: Bacterial secretion systems release effectors into the extra-cellular milieu or directly into foreign cells. They represent fundamental mechanisms by which bacteria modulate their environment and induce human infection. Here we study two related and complementary secretion systems, the bacterial type II secretion system (T2SS) and the Tad secretion system (TdSS). The T2SS secretes effectors and toxins involved in cell adherence, biofilm formation and host cell death. The TdSS drives cell adherence and colonization through extra-cellular pilus formation. Both secretion systems constitute multi-component complexes with many shared components that span the cell envelope of Gram-Negative bacteria. The overall goal is to determine the molecular mechanism underlying T2SS and TdSS operation. Key aims for the T2SS include showing how substrate is recruited, how inner membrane components are organised, and how pseudo-pilus assembly is coordinated. The repertoire of K. pneumoniae T2SS virulence factors will also be expanded. For the TdSS, key aims include structure-function studies on the outer membrane secretin with its associated pilotin and pilus. Comparison of T2SS and TdSS structures will reveal common mechanistic and evolutionary principles. By understanding how the T2SS and TdSS function and promote pathogenesis, this research has the potential to facilitate drug development and combat anti-microbial resistance.

Lay abstract: Some bacteria cause infections in humans that kill millions of people annually. To trigger the infection, the bacteria contain nanomachines within their cell surface that act like miniature pumps. These are secretion systems. One role of secretion systems is to deliver harmful proteins from inside the bacteria to outside environments like your cells. These harmful proteins act as molecular weaponry in many ways. They can form grappling hooks to help the bacteria attach to environments like your intestine or as molecular malware that maliciously reprogram your cells. We use a powerful technique called cryo-electron microscopy, which allows us to visualize the precise position of the atoms within the secretion systems. In this way we can learn the 3D structure and chemistry of the secretion systems. By understanding how the secretion systems work we have a much greater chance of developing medicines that stop the secretion systems from causing human illness.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Molecular basis of the escalation of insecticide resistance in malaria vectors and its impact on malaria control
Funder: Wellcome Trust

Abstract: Malaria prevention relies heavily on insecticide-based interventions including Long Lasting Insecticidal Nets (LLINs). Unfortunately, insecticide resistance threatens these tools. Worryingly, an escalation of resistance in Anopheles funestus, major malaria vector, is inducing an extensive loss of efficacy of all pyrethroid-LLINs including the newly introduced PBO-pyrethroid nets. If such super-resistance spreads Africa-wide, insecticide-based interventions could be compromised with catastrophic consequences. This super-resistance is likely driven by a dramatic increase in metabolic resistance and/or the development of a reduced penetration in super-resistant mosquitoes allowing them to now survive exposure to even PBO-pyrethroid nets and potentially conferring cross-resistance to other insecticide classes. Unfortunately, the molecular drivers of this super-resistance remain unknown preventing the design of diagnostic assays to track it and assess its impact on malaria control. Therefore, to help mitigate the impact of super-resistance, I will pursue the following aims: Aim 1: detecting molecular markers of the increased metabolic resistance driving the resistance escalation to insecticides in An. funestus; Aim 2: detecting genetic variants of the reduced penetration mechanism contributing to super-resistance, cross-resistance and design DNA-based assays to track it; Aim 3: establishing the impact of the escalation of resistance on the effectiveness of insecticide-based interventions and malaria transmission using molecular markers.

Lay abstract: Malaria prevention relies extensively on mosquito control using insecticides. However, insecticide resistance in major transmitting-mosquitoes threatens malaria control in Africa. Worryingly, recent evidences show that resistance is getting worse leading to extensive loss of protection from most bed nets. It is of urgent importance to understand how mosquitoes become super-resistant to help prevent such resistance spreading Africa-wide. The possibility that super-resistance is caused by mosquitoes producing greater amount of enzymes able to breakdown insecticides faster and/or more efficiently will be investigated and DNA markers associated with this trait identified. Evidence that mosquitoes are hardening their body armor (cuticle) to reduce insecticide uptake will be investigated and tools designed to track such super-resistance. Furthermore, this project will establish the extent to which this super-resistance is reducing the efficacy of insecticide-treated nets and thereby contributing to the increase in malaria cases being reported in Africa.

Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: INFECTION
Title: Expansion and support of SARS-CoV-2 sequencing in West and Central Africa to support the COVID-19 pandemic response
Funder: Wellcome Trust

Abstract: The recently emerged SARS-CoV-2 variants of concern (VOC) have altered transmissibility, virulence and susceptibility to neutralising antibodies, leading to concern over the potential for new variants to emerge that have increased resistance to vaccine-induced immunity. This has led to a renewed focus on the deployment of whole-genome sequencing surveillance to detect variants early, to stop or slow their spread, and to enable vaccine programmes to adapt. However, despite increased genome sequencing, disparity in access to laboratory support and genomic sequencing across the globe has become increasingly evident: to date West and Central Africa produced ~2,000 sequences (<0.002% of all sequences available) vs >400,000 from the UK. The VOCs such as P.1 in Brazil and B.1.351 in South Africa can emerge anywhere, further highlighting the urgent unmet need to develop sustainable solutions for COVID-19 sequencing in this underserved region. This proposal builds on the experience of the ARTIC network and regional collaborators to support SARS-CoV-2 sequencing in West and Central Africa. The key goals of this proposal are to: 1. Develop a hub and spoke network of SARS-CoV-2 sequencing labs in West and Central Africa. 2. Develop a suite of COVID-19 focused training materials and tools for whole-genome sequencing and subsequent data analysis.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY);4.5 RESOURCES AND INFRASTRUCTURE (DETECTION)
Health categories: INFECTION
Title: Structural basis of use of ion flow across the bacterial inner membrane to power secretion and motility
Funder: Wellcome Trust

Abstract: Bacteria need to control import/export of charged molecules across their relatively impermeable membrane(s) which also house many nano-machines critical for motility and hence infection. These processes are often driven by harvesting the energy stored in ion gradients across the inner-membrane by ion flow through inner-membrane resident channels. Unpublished work from my group has demonstrated that bacterial inner-membrane ion channels which couple ion flow to protein secretion, nutrient import and bacterial motility unexpectedly share a common architecture within their membrane domains. The architecture revealed unexpectedly suggests rotation between components may be mechanistically important and this application seeks to test this hypothesis. The question will be assessed by a series of structural and mechanistic studies that will seek to determine what commonalities in mechanism underlie this shared architecture and how this is adapted to perform the very different biologies achieved. Specifically, what adaptations allow coupling of uni-directional ion flow to achieve work on both sides of the inner-membrane. Using structural and functional tools developed in my group we will study the ion channels in more native contexts both in terms of the membrane bilayer and in terms of the protein interactions that couple ion flow to work to tease out molecular mechanisms.

Lay abstract: Bacteria are separated from their environment by a relatively impermeable barrier. Survival requires control of import/export across this barrier. Many pathogenic bacteria also contain nano-machines embedded within it that enable motility to drive infection. Import/export and motility use energy harvested by protein complexes embedded in the barrier from the chemical gradient across it. Work from my group has demonstrated that systems previously thought to achieve this function via very different molecular mechanisms actually share a common structural architecture. I will test the hypothesis that there is a single molecular mechanism by which bacteria harvest chemical energy for these roles and determine how each system is specialised for its specific task. This will add to our basic knowledge of how bacteria achieve these critical functions, and the evolutionary relationships between the systems. The importance of these processes for bacterial survival and pathogenicity mean such knowledge will likely inform future therapeutic approaches.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFECTION
Title: Defining the molecular determinants required for Leishmania life cycle progression and virulence
Funder: Wellcome Trust

Abstract: Leishmania parasites cause a neglected disease on the WHO priority list. During their life cycle, these single-celled parasites must migrate through the sandfly (promastigotes), pre-adapt for mammalian infectivity (metacyclic promastigotes) and proliferate inside macrophages (amastigotes) while withstanding host immune defences. Adaptation to these radically different environments involves many changes, including metabolic and cell structure specialisations, ensuring survival and transmission. However, current understanding of these processes is disjointed and biased towards predicted/expected pathways. Half of Leishmania’s protein-coding genes, including most unique to Leishmania, have no known or predicted function, (the “dark genome”), leaving potentially exploitable parasite biochemistry untapped in the search for new therapeutics. We aim to identify all major parasite pathogenicity factors. We will determine a) the subcellular localisation of all proteins with poorly predicted function (~50% of the genome) and b) the fitness cost of gene deletion in each life cycle stage (100% of the genome). Integrative analysis of this deep dataset will identify key pathways in 1) organelle adaptation for an intracellular parasitic lifestyle and 2) host interaction, which we will then functionally dissect. This will identify virulence factors on a genome scale, determine the most important pathways required for parasitism and illuminate the ‘dark genome’.

Lay abstract: Leishmania are parasites that cause diseases affecting the poorest communities globally. 15 years ago we sequenced all the genes in this parasite but have made limited progress in connecting these genes to parasite infectivity, due to our limited ability to perform genome-wide experiments. However, using CRISPR genome modification tools we have developed approaches for genome-wide functional analysis. We will delete each gene individually generating 9000 Leishmania mutants which we will use to infect mice to determine if that gene is important for causing disease. In parallel we will tag 3000 proteins with a fluorescent marker enabling us to work out where in the cell this protein is found, helping to define its function. By combining this positional and functional information we will discover the most important pathways for parasite infectivity and then will dissect their specific functions in more detail, which will identify new ways to treat these diseases.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Elucidation of host-pathogen interactions during Orientia tsutsugamushi infection and translation into new diagnostics
Funder: Wellcome Trust

Abstract: Orientia tsutsugamushi (Ot) is an obligate intracellular Rickettsiales bacterium that causes the mite-borne human disease scrub typhus, a leading cause of severe febrile illness in Asia and an emerging public health challenge in other parts of the world. Scrub typhus is the most significant rickettsial disease in severity and prevalence. Its fundamental biology is not well understood, limiting advances in the development of urgently needed vaccines, diagnostics, and treatments. My lab has spent the past eight years working in the USA and Thailand to develop Ot into a robust and experimentally tractable system. We are now poised to gain a deep understanding of the cellular microbiology of this organism. We recently identified Ot subpopulations with distinct physical properties. This project will characterize the mechanism whereby these Ot forms enter cells and escape detection by the endolysosomal pathway. We will also investigate how Ot exploits the host cellular machinery to grow and develop; budding-off mechanisms preceding bacterial dissemination also will be explored. Our knowledge of Ot heterogeneity will provide essential insights for development of improved diagnostic tools. Our physical presence in Thailand and our local partners who can rapidly apply laboratory findings to the clinic will benefit at-risk populations the most.

Lay abstract: Scrub typhus is a life-threatening human disease caused by a bacterium transmitted from mites. It is widespread in Asia but has recently been found in other parts of the world. Changes in climate and land-use patterns raise concerns that it may spread further. It is technically challenging to work with Orientia tsutsugamushi (Ot), the bacterium that causes scrub typhus. For this reason, Ot has not been well studied compared with other bacterial pathogens. Limited efforts to understand the biology of Ot have prevented significant progress in the development of urgently needed vaccines, diagnostic tools, and new treatments. To address the knowledge gap, we must uncover fundamental aspects of Ot biology, including how these bacteria infect, exploit the host machinery, and exit human cells before spreading throughout the body. We will then take advantage of these insights to improve diagnostic tests for scrub typhus, and develop human vaccines and effective treatments.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Malaria exposure, emergency care and severe disease phenotypes in African children
Funder: Wellcome Trust

Abstract: Malaria continues to pose a huge burden on African communities and hospitals. Despite scaled mosquito vector control coverage, many children across the central belt of Africa continue to be infected with the malaria parasite every year. Despite improved access to effective malaria medicines and diagnostics, malaria remains the leading cause of admission to paediatric wards at many hospitals, with children often admitted with life-threatening illness. New evidence is required to understand the relationship between rates of infection exposure and severe malaria in childhood and how these children reach emergency services. I propose to use a network of hospitals in Africa, to answer two related questions: a) how does the incidence and phenotype of severe malaria vary between malaria ecologies, at a time of increased control coverage? and b) what are the pathways to hospitalization with severe malaria? This work is intended to improve our ability to predict impacts of current and new tools aimed at reducing parasite exposure, identify points of improved referral care and demonstrate how upgraded hospital data can be used as epidemiological surveillance instruments to measure impacts of community-based control.

Lay abstract: Malaria continues to pose a huge burden on African communities and hospitals. Despite scaled mosquito vector control coverage, many children across the central belt of Africa continue to be infected with the malaria parasite every year. Despite improved access to effective malaria medicines and diagnostics, malaria remains the leading cause of admission to paediatric wards at many hospitals, with children often admitted with life-threatening illness. Work will take place at 16 hospitals in Kenya and Uganda and 20 additional hospitals in the Africa region, to define the relationship between how often a child is infected with the malaria parasite and the chances of being hospitalized with different forms of severe malaria; how children with severe malaria reach hospital; and how these surveillance data might lead to a best-practice model for future surveillance of severe disease, allowing countries to measure control impact.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Refining the Drug Discovery Paradigm for Schistosomiasis
Funder: Wellcome Trust

Abstract: “Schistosomiasis is a neglected tropical disease, caused by parasitic worms that live in the blood vessels around the intestines or bladder. Approximately 230-440 million people are currently infected and the disease causes approximately 300,000 deaths per year, either directly or indirectly, and many other health related problems due to chronic infection, including cognitive development issues with children and exacerbation of the effects of other infectious diseases. There is only one drug, praziquantel, registered to tackle this disease, creating an urgent need for the development of new drugs to treat this disease, to improve the efficacy and also in case of resistance developing to praziquantel. Furthermore, there is little known about drug discovery for this parasite. In this Project the University of Dundee, Aberystwyth University and Cardiff University are developing new assays and optimising existing assays to facilitate the drug discovery process. The team has discovered a series of chemical start points through previous work which will be progressed through the improved pathway with the eventual aim of discovering a late lead, a molecule that has the potential to be developed for treatment of schistosomiasis.”

Lay abstract: Schistosomiasis is neglected tropical disease, caused by parasitic worms that live in the blood vessels around the intestines or bladder. Approximately 230-440 million people are currently infected. The disease causes approximately 300,000 deaths per year, either directly or indirectly and many other health related problems due to chronic infection, including cognitive development issues with children and exacerbation of the effects of other infectious diseases. There is only one drug, praziquantel, registered to tackle this disease. There is urgent need for the development of new drugs to treat this disease, to improve the efficacy and also incase of resistance developing to praziquantel. There is little known about drug discovery for this parasite. In this project we propose to develop some new assays and optimise existing assays to facilitate the drug discovery process. We have discovered a series of chemical start points through previous work and we will exemplify our revised drug discovery pathway through taking these compounds forwards. Our eventual aim is to discover a late lead, a molecule that has the potential to be developed for treatment of schistosomiasis, following extensive safety testing.

Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION