NIHRDataInsights/HRCSData huggingface dataset:
Title: Exploring the function and regulation of surface molecules in the reaction to predation by Gram-negative bacteria during predation by the predatory bacterium Bdellovibrio bacteriovorus in host-appropriate settings.
Funder: Wellcome Trust

Abstract: The number of infections caused by bacteria that are resistant to antibiotic treatment is increasing, potentially threating the treatment of infectious disease and other illnesses. New treatment approaches are therefore desperately needed, one of which involves the application of the predatory bacteria Bdellovibrio bacteriovorus. B. bacteriovorus is a bacterium that is able to prey upon a wide range of these antibiotic resistant organisms, potentially providing an alternative treatment for infections. This work builds on previous work with other clinically relevant bacteria to further characterise the mechanisms behind the prey recognition and invasion of bacteria by B. bacteriovorus predators and how this interaction is affected by components of the host immune system (1, 2) and prey surface factors (3). By looking at the factors that may prevent or decrease predation and experimentally removing them, we can characterise the mechanisms behind this interaction further and aid the potential application of B. bacteriovorus as a novel antimicrobial therapy in the future.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Structural and functional analysis of a minor pilin playing a key role in the type IV pilus biology of the opportunistic pathogen Streptococcus sanguinis
Funder: Wellcome Trust

Abstract: Long and flexible hair-like filaments, called type IV pili (Tfp), decorate the surface of many bacteria. Tfp confer an impressive variety of properties upon bacteria, ranging from adhesion and motility to electric conductance. Importantly, Tfp play a key role in the development of diseases, caused by many prominent bacterial pathogens. My research focuses on the opportunistic Gram-positive pathogen Streptococcus sanguinis which causes infective endocarditis. S. sanguinis represents a convenient model for studying poorly defined aspects of Tfp biology due to the simplicity of its Tfp machinery. Tfp are composed of small protein subunits, called major and minor (less abundant) pilins which share sequence and structural features. S. sanguinis has two major pilins (PilE1 and PilE2) and three minor pilins (PilA, PilB and PilC). The minor pilin PilA, essential for S. sanguinis piliation, has an unusual sequence and an uncharacteristic structure. Using a combination of molecular genetics, protein biochemistry and structural biology techniques, I aim to characterise how PilA is assembled into pili and what role it plays in Tfp biology. A better understanding of Tfp assembly mechanisms and their disease-associated functions can help design anti-bacterial drugs that suppress the ability of bacteria to cause disease.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Investigating the interplay between the Plasmodium oocyst and mosquito vector towards identification of new targets for malaria transmission blocking interventions
Funder: Wellcome Trust

Abstract: Malaria is a significant global health burden, causing over 200 million new infections and 400,000 deaths every year. It is caused by Plasmodium parasites that are transmitted between people by Anopheles mosquitoes. Conventional antimalarial therapies aim to clear parasites in already infected humans, but elimination of the disease can only be achieved by blocking parasite transmission through the mosquito vector. Rising insecticide resistance among mosquitoes and increasing drug resistance among Plasmodium parasites have led to a stall in progress towards malaria control and elimination, respectively. It is therefore of vital importance to identify new therapeutic targets and to develop novel intervention strategies to achieve further progress. This project will focus on the interplay between the mosquito and the Plasmodium oocyst, the longest stage of parasite development that results in an explosion in parasite numbers. A high-throughput screen will aim to identify transporters and other key molecules on the oocyst surface required for normal development. Follow-up experiments will genetically and functionally characterise promising candidate genes and assess their potential as transmission blocking targets. This work will therefore help us to further understand the biology of malaria transmission and inform future interventions towards disease elimination.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Developing de-novo assembly tools to predict gene transcriptional markers of severe malaria disease and ways to prevent it
Funder: Wellcome Trust

Abstract: 219 million cases of malaria occurred globally in 2017. Vaccine development is considered the most cost-effective tool to combat malaria, however identifying suitable vaccine targets is problematic. Malaria disease can have many different symptoms and overall severity. Differences in disease severity have been associated with the parasite gene expression, polymorphisms within a gene and splicesome variation. However, quantifying transcript abundance of highly polymorphic genes is extremely difficult. This research aims to produce a pipeline that assemblies and quantify the abundance of these highly polymorphic genes. I will then investigate the degree of polymorphism for genes expressed in the mosquito stages of Malaria, as this is thought to be the most promising stage for identifying vaccine targets.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Testing the roles of polyamines in predator-prey interactions of B. bacteriovorus
Funder: Wellcome Trust

Abstract: Antibiotic resistance is one of the greatest threats to human health faced today. Infections previously treatable with antibiotics no longer respond, and bacteria have emerged that are resistant to all currently available antibiotics (O’Neill, 2016). As such, it is imperative to find novel treatment options including new antibiotics but also to develop alternative methods. One such method is to use other bacteria for our own benefit. Bdellovibrio bacteriovorus is a small, highly motile bacterium with an interesting food - it preys upon other bacteria, eating them from the inside out, including many bacteria that cause harmful infections in humans. However more must be known about the predatory behaviour of Bdellovibrio before it can used in the clinic. This project focuses on chemical signals (polyamines) produced by Bdellovibrio, its prey, and its potential patient hosts. It asks how these signals alter the predatory ability of Bdellovibrio. This will increase our understanding of how Bdellovibrio senses its prey in host and natural environments and the signals it needs to continue the hunt. More detailed knowledge of this predatory behaviour in vitro will allow us to better predict how Bdellovibrio may behave in vivo inside a patient during future potential therapeutic uses.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Understanding the role of circadian and hypoxic signalling pathways in HIV infection
Funder: Wellcome Trust

Abstract: Rhythmicity is fundamental for the existence of life and 24 h circadian rhythms regulate every cell of the body. Synchronizing biological processes to certain times of the day optimizes the host response to invading pathogens and asynchrony can increase the severity of infection. Another basis of human life is oxygen and following infection, viruses can experience environments with variable oxygen tension that can influence their replication and persistence. Previous studies from our laboratory have shown that the circadian system and oxygen signalling pathways can independently influence viral infection. My project will study the interplay between these pathways to understand their role in human immunodeficiency virus (HIV) infection. I will use laboratory models of active or latent HIV replication along with genetic and pharmacological agents that modulate hypoxia and circadian pathways to study their role in the viral life cycle. Our goal is to uncover new therapeutic approaches.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFECTION
Title: Prevention is better than a cure: Novel biomaterials to stop biofilms formation on blood contacting catheters
Funder: Wellcome Trust

Abstract: Antimicrobial-resistant pathogens are of increasing concern, and the O’Neill report [https://amr-review.org] predicts that, by 2050, more deaths globally will be caused by antimicrobial-resistant infections than cancer. One solution is reducing antimicrobial dependence. Our approach is preventing formation of biofilms (communities of microbes attached to surfaces) on blood-contacting catheters. The immune system is then able to deal with the infection, preventing antimicrobial treatment (Jeffery and Mundy 2020). Hook et al (Hook et al. 2012) identified polymers that resist biofilm formation in the absence of blood, now used to coat urinary catheters (Jeffery et al. 2019) with Wellcome Trust funding. In vitro testing of candidate co-polymer coatings in bacterial culture in blood and the analysis of the adsorption of blood components on their surface will allow optimisation of biofilm resistance and haemocompatibility of the coating. Co-polymerising with protein biofouling resistant monomers will be conducted, leading to materials that perform both anti-protein biofouling and anti-biofilm functions. Determination of mechanical properties will ensure integrity of the coating during mechanical deformation. Once optimised, the coating will be tested in an in vivo foreign body infection model. This technology has the potential for patients with blood-contacting catheters to experience fewer infections and associated risks.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Obtaining macrophages from induced pluripotent stem cells to investigate the influence of the host genetic background on the outcome of HIV-1 infection
Funder: Wellcome Trust

Abstract: The influence of host genetic factors upon HIV-1 infection is still not fully elucidated. As the virus relies on the host cell machinery and proteins to replicate, host genetics are a key determinant not only of the proteins expressed but also of their functional capabilities – therefore dictating the outcome of virus infection. This research aims to link the natural occurring genetic variation found in the human population with the inherent variability in the capacity of cells from different individuals to support HIV-1 growth. The work will employ well characterised cells from a bank of human induced pluripotent stem cells to obtain macrophages, which are natural targets of HIV-1 infection. Experimental procedures will include characterising how the virus infects and replicates in macrophages, and employing a bespoke bioinformatics pipeline to compare the genome sequences and transcriptomes of cells showing extreme infection phenotypes. With this approach, we aim to identify novel host factors that can regulate viral replication. These results will add new insights into the understanding of HIV-1 infection and disease (AIDS) and suggest avenues to explore as potential novel therapeutic strategies to treat and control HIV-1.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Characterising the effect of seasonality on the spatiotemporal transmission dynamics of dengue virus.
Funder: Wellcome Trust

Abstract: Dengue virus (DENV) transmission is dependent on the vector capacity of mosquito populations (their ability to carry and transmit DENV), which is influenced by seasonally varying traits such as mosquito lifespan. Novel and effective DENV control measures include the release of mosquitoes infected with Wolbachia bacteria, which confers reduced vector capacity, and vaccination. The high global economic and health burden of DENV is increasing with growing urbanisation and climate change. To target control measures to areas with the greatest burden of DENV, accurate estimates of where DENV is spreading the most are necessary.We will develop DENV transmission models which integrate mosquito traits fitted to data describing the number of reported DENV cases over time in South East Asia and South America. The models will be further developed (addition of spatial structure) to explore the impact of population movement on the spread of DENV. In addition, the potential impact of novel control measures will be evaluated, including the release of Wolbachia infected mosquitoes, to explore their impact on DENV transmission. This research is therefore of high relevance to public health and to the DENV research field.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Understanding biotin mediated metformin resistance within Pseudomonas aeruginosa
Funder: Wellcome Trust

Abstract: Biotin synthesis deficient mutants of Pseudomonas aeruginosa can be killed by the diabetes drug metformin. I previously hypothesised that metformin disrupts metabolism and energy production, but not enough to kill Pseudomonas. This loss in energy may be compensated for by biotin mediated energy production, and therefore when this is also lost metformin has antimicrobial activity. I aim to understand the mechanism of action of metformin, the resistance mechanism of biotin and to try produce a novel combination therapy using metformin and a biotin production inhibitor. I will test P. aeruginosa growth in different carbon source medias +/- metformin to validate if metformin mechanism of action is metabolism linked. I will also try to elucidate the target of metformin via a suppressor screen and the use of TRADIS. Alternatively, I propose 2D-TPP. To validate if biotin resistance is related to bio-energetic compensation I propose an extracellular ATP accumulation assay. Next, the biotin synthesis enzyme BioA would be purified and an existing drug library will be used to screen for inhibitors. Should time permit, I will elucidate the structure of BioA using x-ray crystallography. These studies will help produce or inform the production of a novel combination therapy for P. aeruginosa infection.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: The evaluation of azoreductases as infection specific targets for antimicrobial delivery
Funder: Wellcome Trust

Abstract: Bacterial biofilms pose a major threat to global health, due to their ability to evade antibiotics and host defence systems; therefore, leading to the development of chronic infections. The process of biofilm development is regulated by a series of molecular pathways, including cell-to-cell quorum sensing (QS) signalling. The disruption of this QS signalling pathway, through the use of QS inhibitors, shows great potential for the treatment of biofilm infections, while minimizing the selection pressure exerted on the bacteria. The incorporation of nanoparticle drug delivery systems enables the enhancement of antimicrobials delivery, including an increase in drug solubility and prolonged systemic circulation. Furthermore, these materials can be equipped with stimuli-responsive switches enabling a targeted drug delivery. Of particular interest is the use of poly(b-amino esters) (PBAEs) reported to selectively target and accumulate within bacterial biofilms. We hypothesize azoreductase enzymes, released by bacteria, can induce the opening of PBAE nanoparticles equipped with azobenzene moieties. This targeted cleavage of the azo bond would result in the release of encapsulated QS inhibitors, leading to the prevention of biofilm maturation. This delivery pathway has the potential of significantly enhancing the efficiency of antimicrobial delivery to biofilms, enabling the prevention of highly challenging chronic infections.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Development of artificial oligonucleotide catalysts (XNAzymes) for specific targeting of disease-associated RNA.
Funder: Wellcome Trust

Abstract: Nucleic acids (DNA & RNA) are commonly known for their ability to store genetic information. However, when single-stranded, nucleic acids can also fold into sophisticated 3D structures including catalysts capable of speeding up chemical transformations. RNA-cutting catalysts can be programmed to target specific RNA sequences in order to turn off harmful mutant genes or destroy viruses. However, catalysts composed of natural DNA and RNA, among other limitations, are rapidly degraded in the blood, hampering their clinical applications. Recently, it has become possible to evolve such catalysts in the test tube using robust, artificial alternatives to DNA known as “xeno nucleic acids” (XNAs). Our aim, therefore, is to explore the use of biologically stable XNA chemistries to evolve novel enzymes (“XNAzymes”) capable of degrading disease-associated RNA (aberrant mRNA, microRNA and viral RNA). We will establish systems for engineering XNAzymes using chemistries resistant to degradation and which (unlike protein enzymes) do not trigger unwanted immune responses. Currently, there are few clinically-suitable molecular tools for manipulation of cellular RNAs and they often lack precision, XNAzymes are thus promising alternatives.


Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: INFECTION
Title: Characterising HIV-1 infections in East African epidemics: an interdisciplinary approach to analysing network dynamics and transmission clusters using viral phylodynamics and agent-based modelling.
Funder: Wellcome Trust

Abstract: With a yearly 1.7 million new people infected with HIV, the HIV/AIDS epidemic remains a major global health threat. Characterising HIV transmissions using phylogenetic tools like phylogeography and phylodynamics aids our understanding of HIV infections, both evolutionarily and epidemiologically, shaping epidemic control measures through increased knowledge on transmission events and thus, their prevention. Sub-Saharan Africa (SSA) constitutes 59% of all new HIV infections, and phylogenetic studies highlighting HIV transmission dynamics have historically been less common in this region due to limited sequence availability. However, the recent sequencing upscale in SSA will inform the poorly understood structure of transmission networks and HIV epidemic dynamics in the region. I aim to use viral phylogenetics, epidemiology and mathematical modelling to investigate the evolutionary dynamics of HIV-1 transmission networks in East African epidemics: firstly, using HIV-1 sequences from a trial in rural Uganda and Kenya, I will characterise HIV-1 infections and analyse HIV-1 transmission networks and cluster dynamics; secondly, I will undertake a comparative analysis of HIV-1 phylodynamics amongst different East African study populations; finally, I will model local transmission dynamics and intervention effects in these populations. Altogether this will ultimately inform the design and evaluation of HIV prevention interventions.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Determining the role of ubiquitin in transmission stage Plasmodium
Funder: Wellcome Trust

Abstract: Approximately half of the global population is currently at risk of malaria infection, with an estimated 0.5 million deaths annually. Malaria is caused by Plasmodium parasites, which have a complex life cycle involving a vertebrate host and mosquito vector. Blood stage parasites cause the symptoms of malaria in humans, and are therefore the target of most current therapies. In order to reduce the incidence of malaria, and therefore global disease burden, a drug to block transmission between the host and vector is needed. The complex regulation required in transmission stage parasites remains poorly understood. Ubiquitylation is a well-researched post-translational modification which is commonly associated with protein degradation, but also has a range of effects from protein re-localisation to induction or arrest of cell signalling events. The role of ubiquitin in transmission stage parasite development is unknown. We aim firstly to identify the ‘ubiquitome’ of Plasmodium bergheiparasites during transmission stage development using ubiquitin capture systems and mass spectrometry. We subsequently aim to investigate the role of these ubiquitylated proteins during transmission using genetic engineering. These results will improve our understanding of the role ubiquitin may play in the regulation of transmission stage parasite development, and inform future drug discovery efforts.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Defining the role of RND efflux pumps in antibiotic resistance
Funder: Wellcome Trust

Abstract: I will investigate the role of efflux pumps in antibiotic resistance by researching two themes. Firstly, by looking at the function, prevalence and impact of plasmid encoded efflux pumps. There have been increasing reports of plasmid encoded RND efflux genes. To our knowledge no one has collated the incidence of RND pumps found on plasmids, their spread or potential roles in antibiotic resistance via the efflux of antibiotics. Using a clinical Acinetobacter pittii isolate, I will define the functional role of RND efflux pump genes in the laboratory for example by using efflux assays to measure export and minimum inhibitory concentration experiments to define the substrate profile.The second theme will explore two Acinetobacter species: A. baumannii and A. lwoffii. Both species inhabit the same niche (hospitals) and cause high numbers of infections in immunocompromised patients. We wish to understand why A. baumannii is drug resistant and A. lwoffii is drug susceptible. To do this we will look at the variations in the resistance and efflux pump genes in clinical isolates of both species and hypothesise why A. lwoffii has not yet developed drug resistance and if there are any indications that it might in the future.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Mechanisms of CD4+ T Cell Dysfunction During HTLV-1 Infection
Funder: Wellcome Trust

Abstract: Human T-cell Lymphotropic Virus type-1 (HTLV-1) infects 5-10 million people worldwide. The majority of people infected remain asymptomatic carriers (ACs), while 2-6% of those infected develop adult T-cell leukaemia and another 2-3% go on to develop chronic inflammatory diseases including HTLV-1 associated myelopathy (HAM). CD4+ T cells carry 95% of the HTLV-1 proviral burden. While CD4+ T cell dysfunction has been implicated in HAM pathogenesis, the mechanism of tissue damage is still unclear. Limited research has been done on the HTLV-1-specific CD4+ T cell immune response and little is known about CD4+ T cell dysfunction during chronic viral infections. The overall aim of this project is the identification and deep phenotypical and functional characterisation of live HTLV-1 specific CD4+ T cells in healthy individuals, ACs and HAM patients. We have optimised an ex vivo assay to identify and isolate live HTLV-1-specific CD4+ T cells. The results obtained in this project will have implications for vaccination approaches against HTLV-1 and for the development of strategies that could reduce inflammation and control disease, as well as providing mechanistic insights into HAM immunopathology.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION