NIHRDataInsights/HRCSData huggingface dataset:
Title: Understanding unconventional kinetoplastid kinetochores in Trypanosoma brucei
Funder: Wellcome Trust

Abstract: I am interested in understanding the mechanism of how eukaryotic cells inherit their genetic material at each round of cell division. I have been studying the kinetochore, the macromolecular protein complex that drives chromosome segregation. Although it was widely believed that the structural core of kinetochores would be composed of proteins that are conserved in all eukaryotes, I discovered an unconventional class of kinetochore proteins (KKT1–20) in Trypanosoma brucei, an evolutionarily-divergent kinetoplastid parasite. My current goal is to understand how they carry out conserved kinetochore functions such as binding to DNA and microtubules. Based on preliminary data, I propose that two homologous protein kinases KKT2 and KKT3 lie at the base of the kinetoplastid kinetochore. I will aim to understand how these proteins localize specifically at the centromeric DNA using a variety of approaches. I will also characterize the KKT4 protein to reveal the mechanism of microtubule interaction. To understand the design principle of kinetoplastid kinetochores, I will reconstitute and characterize kinetochore subcomplexes. Finally, I will examine how the evolutionarily-conserved Aurora B kinase regulates the function of unconventional kinetoplastid kinetochores.

Lay abstract: All cells must transmit their genetic material accurately to offspring. Errors in this process lead to various diseases such as cancer and birth defects in humans. Revealing the mechanism of how cells inherit their genetic material (chromosomes) is a fundamental question in biology and also important for understanding the molecular basis of diseases. I am studying trypanosomes because they are divergent from popular model organisms such as yeast and human. I discovered that trypanosomes use a different set of proteins to separate chromosomes. By characterizing these proteins, I will try to gain deeper understanding of how cells accurately transmit their genetic material. Our work is also medically important because trypanosomes cause sleeping sickness that affects a number of people in Africa. Understanding how trypanosomes uniquely inherit their genetic material will facilitate the development of drugs that specifically kill the parasite and cure sleeping sickness.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Decoding riboregulation in complex cellular behaviour of bacteria
Funder: Wellcome Trust

Abstract: In cells from every domain of life, RNA acts to communicate hereditary information, to regulate gene expression, and to support network control. Therefore, the fates of diverse RNA molecules, their biogenesis and lifetime, play a critical role in determining complex cellular behaviour. We propose to investigate the processes that govern RNA fate in bacteria. We hypothesise that defined ribonucleoprotein complexes act in key steps of cellular control, including co-transcriptional ribonucleoprotein folding and surveillance of transcripts during translation. We will test this experimentally and will also seek to understand how such complexes might be linked to sensing and responding to cellular status, including metabolic remodelling. To this end, we will study the structure and function of key RNA-processing complexes in model bacterial species. Our targets include both stable protein-RNA complexes, which will be isolated and examined by high-resolution structural and functional analysis, and more transient assemblies, which will need to be investigated inside the cells to capture their information-rich physiological states. Our work will help to elaborate rules that define the lifetime and biological impact of RNA and its contribution to complex cellular phenotypes, including infectious virulence and antibiotic resistance of various bacterial species.

Lay abstract: The behaviour of cells is dependent on the expression of genetic information and can be especially important in responses to stress and other environmental signals. In particular, rapid adaptations to constantly changing environments enable bacteria to withstand harmful conditions, to use available resources efficiently, and to launch complex programs during host infection. Regulatory RNA molecules, together with dedicated partner proteins, are often involved in controlling this adaptive process. We will study regulatory RNA-protein complexes by determining their structures and functions, moving from individual molecules to large flexible assemblies within cells. We will investigate both established model bacteria and pathogenic species, including those that are highly antibiotic-resistant organisms and for which new drugs are urgently needed. Understanding how bacteria employ RNA-protein complexes to control nutrient utilisation and virulence would not only aid the general understanding of cellular adaption to changing environments but could also lead to new antibacterial treatments.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Whipworm infection – defining and exploiting the niche biology of a parasitic intestinal nematode
Funder: Wellcome Trust

Abstract: Little is known about the mechanisms underpinning chronic infection by intestinal dwelling nematode parasites. If we are to develop novel and effective ways to control these infections and exploit their immune evasion strategies, we require a much deeper understanding of the parasite itself, how it interfaces with its environment and how it survives immune attack during long-term infection. We will address this bottleneck using the Trichuris muris mouse model of human whipworm infection. We will: 1. Define the biology of the major secreted protein produced by whipworm during chronic infection, which we have shown binds interleukin 13 and tethers to glycosaminoglycans and matrix. We will precisely map binding sites, define function in vitro and in vivo and the activity of the human parasite homologue (T. trichiura). 2. Define the tripartite interaction between parasite, host and intestinal microbiota which we have demonstrated is critical to both establishment and survival of the parasite. We will re-colonise germ free mice with Bacteroides thetaiotamicron which effectively supports whipworm infection and plays a major role in scavenging intestinal glycosaminoglycans to identify the key genes of each partner that underpins chronic infection and will test them functionally in vivo to identify novel pathways for intervention.

Lay abstract: Parasitic roundworms that live in the intestine infect hundreds of millions of people across the globe causing ill health to the poorest communities. Current drugs to remove worms require repeated treatments and for some parasites such as whipworm are ineffective. Our immune systems respond but cannot effectively remove these parasites. We urgently require a greater understanding of how these parasites survive attack by our immune system and how they have adapted to thrive in our intestines alongside our commensal bacteria, which profoundly influences our overall health. We have discovered that whipworm changes our intestinal bacterial communities to their own advantage and produces a protein that neutralizes a key immune molecule that the body uses to expel parasites. We will precisely define how the parasite changes our intestinal bacteria and how the parasite protein works so that we can intervene in these processes to develop new effective methods of parasite control.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: A collaborative platform and network for responsive infectious diseases bioethics research
Funder: Wellcome Trust

Abstract: We seek to establish a research network and collaborative platform for rapidly identifying and analysing ethical and policy issues arising in infectious disease treatment, research, response, and preparedness, and engaging in research on the profound ethical challenges presented by infectious diseases across the globe. The platform and network will provide real-time ethics and policy support, create a mechanism for collaborative responsive research as well as forward-looking projects with longer timeframes and engaging with crucial stakeholders from across high-resource and LMICs, all focusing on the critically important area of infectious disease and global health bioethics. In addition to being responsive to the needs as identified by the network, we expect the platform and network to be available to respond to needs identified by the WHO Public Health Emergency Ethics Preparedness and Response (PHEEPR) Network and other global bioethics efforts. The Platform and Network will be structured into two related and overlapping sets of activities, which will complement and build on each other. These will comprise: an Infectious Disease Ethics Forum for discussion of emerging ethical issues, a Collaborative Network to identify important issues for policy response and research; and, a programme of global health ethics research focusing on infectious disease.


Research activity codes: 8.3 POLICY, ETHICS AND RESEARCH GOVERNANCE
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Mechanisms and Regulation of RNAP transcription
Funder: Wellcome Trust

Abstract: This grant focuses on four lines of scientific enquiry converging on RNAP function 1. Characterisation of the molecular mechanisms underlying RNA polymerase and basal factors that facilitate transcription initiation, elongation and termination by using multidisciplinary approaches in vivo and in vitro. This includes using bespoke transcription assays, structure elucidation and a global characterization of the occupancy and transcriptomes. 2. Identification of novel gene-specific factors and characterization of the proteomes of transcription preinitiation- and elongation complexes in vivo. Identification and characterization of RNAP-associated proteinaceous- and RNA regulators. 3. Characterisation of the structure and function of archaeal chromatin formed by A3 and 1647 histone variants. A biophysical characterization of protein-DNA interactions and a whole-genome view of histone occupancy. Focus on the impact of chromatin on RNAP as it progresses through the transcription cycle, and the role of elongation factors to overcome the inhibitory effect of chromatin. 4. Characterisation of factors that modulate RNAP during virus-host interactions. Virus (RIP)- and host (TFS4)-encoded RNAP-binding factors function as global inhibitors of transcription and their mechanism is reminiscent of antibiotics. Using two virus libraries of we want to screen for novel RNAP-binding regulators and use them as molecular probes to dissect RNAP function.

Lay abstract: The first step in gene expression (transcription) is carried out by molecular machines that engage with the DNA and produce an RNA copy. The mechanisms are poorly understood and we are proposing four lines of investigation to deepen our understanding of this process 1. Transcription is carried out by RNA polymerase (RNAP) enzymes and aided by general transcription factors; we want to investigate how they function. 2. The action of RNAP is orchestrated by many specific regulatory factors, some are known, most are not; we want to identify novel factors and characterize their function with the aim to explain how transcription is regulated in the cell. 3. The DNA is packed into more or less compact protein-DNA complexes (chromatin) and is not always readily available for RNAP; we want to characterize how different types of chromatin allow or prevent transcription. 4. When viruses infect cells they can radically change host transcription. Virus encoded regulators take over the host RNAP for their own purpose, and the host responds in kind to counter the infection. We want to investigate the molecular mechanisms by which both virus and host factors alter transcription in the context of this arms race.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Decoding mechanisms of gene regulation in African trypanosomes
Funder: Wellcome Trust

Abstract: Trypanosomes are divergent eukaryotic parasites and excellent models for investigating the diversity of gene regulatory mechanisms, including allelic exclusion, histone modification and post-transcriptional control. The variant surface glycoproteins (VSGs) are major virulence determinants and have provided starting-points for decoding regulatory mechanisms. I propose to build upon the following discoveries from my laboratory; • A VSG allelic exclusion machinery that associates with the single active VSG and silences all other alleles. I propose a detailed dissection of the exclusion mechanism. • Characterisation of the histone acetyltransferases and deacetylases. I propose detailed characterisation of the essential nuclear enzymes, factors they associate with, histone residues they modify and impact on gene regulation. • Hundreds of post-transcriptional regulatory 3’-untranslated regions have been identified using a high-throughput genetic screen. I propose identification of regulatory RNA-binding proteins, the genes they regulate and the underpinning regulatory mechanisms. The proposed studies will fill major gaps in understanding, illuminating mechanisms of VSG allelic exclusion, chromatin-based control and post-transcriptional regulons. How eukaryotic cells express only one gene from the largest gene families, in particular, remains a major unresolved question. Potentially druggable targets that emerge will also present opportunities for further collaboration with colleagues in the Wellcome Trust Centre for Anti-Infectives Research.

Lay abstract: Single-celled parasites, known as trypanosomes, are transmitted by African tsetse flies and cause deadly diseases in humans and animals. One prominent feature, antigenic variation, allows these persistent parasites to thwart host adaptive immunity. Another notable feature, that allows the parasites to use sugar in human blood, for example, is major remodeling during the transmission cycle. These features require sophisticated gene expression controls. For experimentalists, trypanosomes are highly tractable; we can even precision edit parasite DNA sequences. I propose studies designed to determine exactly how the above controls work. With powerful technologies in hand, and key regulatory proteins and hundreds of regulatory sequences already identified, we can now determine how the parasites activate specific proteins and shut down others. Our studies will yield insights into mechanisms that also operate in other parasites. Since we work closely with drug-discovery teams in Dundee, we can also readily exploit opportunities to develop new therapies.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: The Science of Rabies Elimination
Funder: Wellcome Trust

Abstract: Rabies is a horrific, but vaccine-preventable disease that kills thousands of people every year in low-income countries. International agencies now advocate investment in rabies control and have set a 2030 target for global elimination. With regional programmes underway, the major research questions are now how to optimize rollout and impact, addressing challenges as elimination is approached. My fellowship aims to address these questions through synergistic research embedded within large-scale rabies control programmes around the world. Through a large-scale vaccination intervention in Tanzania I will test the hypothesis that rabies circulates at low incidence with spatial correlations in transmission curtailing outbreaks through localized susceptible depletion, and permitting co-circulation of genetically divergent lineages. I will pilot surveillance approaches to increase case detection, improve patient care, track the spread of infection and inform elimination programmes. The resulting data will be used to formulate and parametrize models to investigate strategies to rapidly control rabies, minimize incursion risks, and maintain disease freedom. A global network of scientists, policy-makers, and practitioners provides an enabling environment for my intervention-based research across intercontinental settings. Findings will therefore translate directly into policy at the highest level, delivering impact through timely transferrable insights to guide elimination efforts.

Lay abstract: Rabies is a horrific, but vaccine-preventable disease that kills thousands of people every year in low-income countries. International agencies now advocate investment in rabies control and have set a 2030 target for global elimination. The major research questions are now how to ensure the effective rollout and implementation of control programmes and address challenges during the endgame when incidence has been reduced to low levels and may circulate undetected. My fellowship aims to address these questions through synergistic research embedded within rabies control programmes around the world. I will pilot approaches for the surveillance of rabies to increase case detection, improve treatment of people bitten by rabid animals and track in real-time the spread of infection. Capitalizing on large-scale dog vaccination programmes will enable me to address questions about how long it takes to control rabies and what impedes progress towards elimination. My aim is to build an operational toolbox underpinned by a fundamental understanding of rabies dynamics to guide policy and practice. Working with policy-makers, and practitioners to integrate my research into ongoing rabies control programmes will bring immediate benefits to their implementation and success, and transferrable insights to guide elimination efforts and policy around the world.

Research activity codes: 8.3 POLICY, ETHICS AND RESEARCH GOVERNANCE
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: State of the art cryo electron microscope for molecular and cellular biology
Funder: Wellcome Trust

Abstract: Dramatic advances in the power of cryo electron microscopy (EM) to resolve macromolecular and cellular machinery have greatly expanded the field and our need for access to state-of-the-art microscopes. With its internationally renowned research programme on macromolecular machines, the ISMB EM lab is ideally placed to benefit from recent instrumental developments. Although the eBIC facility at Diamond helps by providing intermittent access to state of the art 300 kV systems, this cannot sustain our large research programmes and expanding user base without substantial in-house facilities. Our ever-increasing number of structural and cell biology users are now waiting 3-5 weeks for access to high-end microscopes. Our recent equipment award contributes to an intermediate, 200 kV system, suitable for single-particle work but sub-optimal for tomography and cell biology, limiting its wider impact. In contrast, a 300 kV machine, with cutting-edge performance for single particles, unique assemblies, and cellular sections, would have a transformative impact, enabling new research from a wider community including outstanding local cell biologists. Therefore, we request a Cryo-EM Equipment Grant to upgrade from the 200 kV system to a high-end 300 kV system to be accommodated by an expansion and reorganisation of our EM laboratory.

Lay abstract: The field of cryo-electron microscopy is currently in a major phase of advancement and expansion, with great impact on molecular and cellular biology. The tools for determining the structures of biological machines, both in isolation and in situ as they perform their functions, have greatly progressed in the last few years. This progress, in both equipment and software, has enhanced the range of structures that can be detected and resolved to a level of detail that reveals their functions and provides the basis for new approaches to therapeutics. At Birkbeck and UCL, we already have very substantial expertise and activity in this area, but continuing funding is urgently required to keep pace with the formidable, rapid technological progress currently taking place in biological electron microscopy. This application is for the additional funding needed to provide us with a state-of-the-art system that will enable us to determine high-resolution molecular and cellular structures at an internationally competitive level. The upgrade from a 200 to a 300 kV microscope is particularly important for electron tomography work that enables structural cell biology and the study of intact biological systems, and will bring in new cell biology users.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: GENERIC HEALTH RELEVANCE;INFECTION
Title: Defining the biological basis of Staphylococcus aureus carriage
Funder: Wellcome Trust

Abstract: Staphylococcus aureus is major cause of infection worldwide. This bacterium persistently colonises the nose (its natural niche) in around 20% of the population, which increases their risk of S. aureus infection. Why some people carry S. aureus while others never do is not understood, but is likely to reflect a complex trait influenced by multiple factors. This may include the human genome, host immunity, the nasal microbiota, bacterial-nasal epithelial cell interactions and lifestyle choices. We propose that key determinants for S. aureus carriage can be defined in a powered cohort study in which these parameters are established. Our study will capitalise on existing cohorts (INTERVAL & COMPARE) of healthy volunteers who have been extensively characterised through human genome sequencing and phenotypic profiling. We will screen 25,000 INTERVAL participants for S. aureus carriage, and using sequencing methods define their nasal microbiota composition. We will use existing as well as generate additional data on lifestyle. These datasets will be mined during a series of genome-wide and phenotypic association studies to identify factors that influence the nasal microbiota and S. aureus carrier status. Selected phenotypic and genetic variants of interest will then be tested in relevant experimental systems.

Lay abstract: Around 20% of healthy humans persistently carry a bacterium called Staphylococcus aureus. Although carriage alone is harmless, carriers are at greater risk of developing of S. aureus infection. This is particularly important when people are undergoing medical treatment, since S. aureus is the most common cause of healthcare-related infection. Our research will seek to discover why some people carry S. aureus, while others do not. This knowledge would inform the future development of treatments that control carriage and so prevent S. aureus infection. We will screen 25,000 healthy people to determine who are carrying the bacterium (or not) and then look at their genetic code and related biological markers (e.g. blood groups, iron levels, etc) to detect differences that could explain carriage. We will also consider lifestyle factors, and identify the pattern of other bacteria present in the nose (where S. aureus is most commonly found).

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: GENERIC HEALTH RELEVANCE;INFECTION