WHO and the G20 have identified the growing threats of Anti-Microbial resistance (AMR) as a major concern that will define the future of global health. Despite these urgent calls, the emergence of AMR in settings of war and distress migration has not been systematically explored. Case reports from Syria, Iraq, Libya, Yemen, and Afghanistan have shown the proliferation of AMR in combatants and civilians injured in these protracted conflicts. With regional conflicts spreading across state borders as well as one of the largest global refugee crises in decades, AMR in the context of conflict has come to pose a serious threat both regionally and internationally. So began penicillin in the Second World War: antibiotics arose in war. Today, in the context of long-running military conflicts we see harbingers of the end of antibiotics. The core question underpinning this proposal is how war, particularly weapons and the industrialised, urbanised context of contemporary conflicts, drives antibiotic resistance by contaminating the environment and the human and non-human organisms that live there. So far, there has been no systematic or holistic consideration of the environmental health impacts of contemporary conflicts conducted in cities. Our program draws together scholars working in the fields of medicine, anthropology, history of science, ethics, epidemiology, microbiology, molecular biology, and environmental sciences to examine the specific intersection of antibiotic resistance and war. Rather than focus on antibiotic resistance as a universal problem afflicting modern societies in general, we focus first on the impact of global conflict on antibiotic resistance more holistically, and second on the case of multi-drug resistant Acinetobacer baumanii (MDRAB), initially reported by American military surgeons under the moniker Iraqibacter, and that has been identified recently by the WHO as a "critical pathogen" for research and the development of new antibiotics. We will focus on a number of specific countries - Iraq, Syria, Palestine, Yemen, and Lebanon-places with history of protracted conflicts and with different, yet overlapping, ecologies of war. The potential global health significance of conflict-related heavy metal mediated antimicrobial resistance is enormous and warrants further study. It will contribute to the field of environmental pathways for antimicrobial resistance more broadly as well as informing the specific intersection of war and antibiotic resistance.

Proteins are the biological machinery of the cell. When this machinery is altered in some way, for instance via modification of a component, addition or removal of one of the units which form this molecular factory, this changes the way in which the cell performs. Such changes are at the root of many diseases. One disease state where changes in amounts and/ or nature of proteins have been implicated is the pregnancy condition pre-eclampsia. In this disease, a poor blood supply to the placenta induces release of factors, at least some of which are proteins, into the mothers' bloodstream. These proteins damage the lining of walls of maternal blood vessels, causing both small and large blood vessels to become leaky. Increased vessel leakiness leads to fluid escaping from vessels, and thus the symptoms of pre-eclampsia, such as high blood pressure, increased protein content in urine, and swelling of the hands and face. Release of these factors from the placenta occurs before any observable clinical symptoms, and currently no screening methods exist. If we can identify these proteins from blood plasma, we can implement screening tests for these within standard prenatal care regimes. Biological fluids such as plasma contain a huge number of different proteins, all of which are present at levels which vary between individuals. More significantly, the levels of different proteins are very different from one another. For instance, albumin is present at very high levels (tens of milligrams per millilitre of plasma (10E-3g/ml) ), whilst interleukin 6, a molecule involved in cell growth, is present at very low levels (just picograms per millilitre (10E-12g/ml)). Methods to identify the nature of proteins within such samples using analytical chemical methods are termed proteomics. The first step in a proteomic workflow is to digest proteins into small pieces, called peptides, using specific enzymes such as trypsin from cow pancreatic extracts. This step converts a mixture of many thousands of proteins into a mixture of many hundreds of thousands of peptides. Peptides are then analysed by spraying them in a stream of solvent under electrical charge into a mass spectrometer. Identity of the peptides is typically established by colliding the charged peptides (ions) with inert gas, which causes them to fall apart in a predictable manner, allowing us to 'read off' peptide sequence. These methods are best-suited to small peptides, as larger peptides are more flexible and do not fragment efficiently. Newer methods of sequencing peptide ions use electrons to induce fragmentation. These methods work best with longer polypeptides. This study will use proteolysis under different conditions, such as different enzymes and using chemicals to block enzyme cutting sites. Enzymatic cleavage will be simulated on a computer and optimal cleavage conditions selected for experimental substantiation. Once a method has been established, this will be used on plasma samples taken from women with pre-eclampsia to identify proteins whose abundance is altered between 'normal' plasma (pregnant, non-pre-eclamptic) and samples taken prior to and after development of disease. This will enable both increased understanding of the causes of pre-eclampsia and establishment of a panel of markers which can be carried forward for establishment of prognostic testing of plasma samples during pregnancy. Eventually, this will allow identification, streaming and appropriate management of women who would otherwise suffer pre-eclampsia. An eventual outcome will be identification of possible targets for drug intervention in this life-threatening illness.

Tuberculosis (TB) is an infection caused by a bacterium, M tuberculosis. It is the biggest infectious killer globally, with a person dying from the disease every twenty seconds. Treatment length urgently needs to be reduced in order to aid compliance to therapy, reducing emergence of antibiotic resistance. Until more can be learnt about the disease pathology and how drugs behave in the lung, however, treatment will remain at six months. New drugs are crucial to permit elimination of the disease, but clinical trials are expensive and long, and not all of the possible new regimens can be evaluated rapidly. This research will use mathematical modelling to assist in the fight against tuberculosis. Model simulations can potentially be used to accelerate the rate of discovery, while reducing the need for expensive lab work and clinical trials. These models are driven by observations and are based on our understanding of the question at hand. They generate specific, explicitly testable predictions that can be proved by experiment. Previous tuberculosis models have quantified treatment response in clinical trials by analysing patients' sputum samples during treatment. A mathematical model that captures disease more accurately will enable better predications to be made. When TB bacteria enter the lungs, the immune system attempts to control the disease, resulting in a localised reaction: a granuloma. When granulomas are unable to contain the bacteria, active disease develops. After diagnosis, patients are given a combination of antibiotics for a minimum of six months. How well the standard treatments penetrate into the granulomas or how well bacteria respond to the mix of antibiotics will define what the outcome of treatment will be. I have developed a model to study tuberculosis disease progression and treatment in the lung. The model describes, using numbers, the movement and interactions of bacteria and immune cells in both time and space. My research plan outlines how I will enhance this model: by completing comprehensive training with collaborating experimentalists, mathematicians and computer scientists, I will develop the skills and knowledge required to consolidate my ability to develop the model. Collaboration with identified key individuals whose research focuses on the penetration of tuberculosis antibiotics into granulomas is the first vital step in our model development. Alongside this, we will incorporate data from a laboratory simulator that mimics changes in drug concentration over time, as they would occur in humans. The system allows multiple combinations of drugs to be integrated into our model. Researchers at the University of Michigan have a well-established model called 'GranSim'. Although they have a different focus to their work, their model simulates granuloma formation in TB infection and both the modelling and the immunology knowledge I would gain from spending time in their research group would be hugely beneficial for this project. Finally, in collaboration with the computer scientists at the University, I plan to extend our mathematical model to 3D. Using various visualization techniques, we will be able to view the model simulations in a more understandable way, and features that were impossible in 2D will be seen. It might be possible to display the model on a 360 degree screen enabling the complex activities going on in the depth of the lung to be seen and the detail understood. My PhD student will develop this work further to create a model which follows the interaction of the granuloma in the wider lung: a key step along the path to a virtual patient. Thus, our proposed model developments will allow us to answer some of the complex questions that underlie poor treatment response and relapse in TB. My innovative research approach integrates clinical and experimental results with mathematical techniques to address the problem of shortening tuberculosis treatment.

DNA, the blueprint of life, is found within 46 chromosomes in every human cell; if stretched out end to end, it would measure two metres in length. In order for these 46 chromosomes to fit into the "control-room" of every cell, known as the nucleus, the DNA must be very tightly packaged. This is achieved by wrapping the DNA around the surface of special proteins, called histones, that are spaced regularly along the DNA like beads on a string. Each DNA-histone bead is known as a nucleosome and each nucleosome is able to pack very closely against its neighbours to form highly compact fibres called chromatin. Although chromatin fibers are very good at compacting DNA into small spaces, they are poor at allowing other proteins access to the DNA. Many normal processes in the cell involve proteins binding to DNA, such as when genes are decoded to make protein, when chromosomes are replicated prior to cell division, and when special repair proteins are called upon to fix sites of DNA damage. Consequently, complicated organisms like humans, with highly packaged DNA, have had to develop specialized machinery for opening chromatin at very specific regions of the chromosome. This machinery includes a large number of specialized proteins. One group of proteins, known as chromatin remodelling complexes (CRCs), help to expose DNA by using energy to slide or remove nucleosomes within chromatin. CRCs are protein machines, much larger than a single nucleosome, and made up of proteins responsible for recruitment to the correct chromosome region, binding to nucleosomes, or helping to generate the force required for nucleosome sliding or removal. Multiple different CRCs exist in human cells, each made up of similar proteins that can interact with chromatin in subtly different ways or target the complex to different regions of the chromosome. The recruitment of a CRC to the start of a gene is an important early step in the process of turning on, or activating, that gene. If the cell makes a mistake, failing to recruit CRCs to their correct sites or instead recruiting those complexes to the wrong set of genes, then a dangerous cascade can result in the loss of control of normal cell events such as cell division and death. This type of gene dysregulation takes place at an early stage in the development of every human cancer. Over the past decade, advances in DNA sequencing technology have allowed scientists to identify mistakes in the DNA code, known as DNA mutations, that are found in many types of human cancer. A surprising finding from these studies was that DNA mutations leading to the loss of protein components from one single CRC, known as the BAF complex, are present in as many as 20% of all human cancers. Further investigations showed that DNA mutations altering the BAF complex cause many normal target genes to be switched off whereas new and inappropriate genes often become active. Although the BAF complex is very often the target of mutations in cancer, surprisingly little is currently known about this important machine, with many questions still unaddressed. For example, how are the different proteins organized in the BAF complex? What roles do the different proteins play in the recruitment of the complex to the correct target genes? How does the BAF complex interact with nucleosomes? How does BAF use energy to bring about nucleosome sliding or eviction? The overarching goal of my future research will be to address these questions using a repertoire of cutting-edge structural biology techniques such as cryo-electron microscopy, protein cross-linking, X-ray crystallography and computational modelling, in order to provide a detailed description of the organization, recruitment and remodelling activity of this important human complex. Such findings will provide a framework for understanding the molecular basis of BAF complex dysregulation, with broad implications for the future treatment of many human cancers.

After fertilization, a single zygote proceeds through a series of cleavage steps to develop into a multicellular embryo, called a blastocyst. The cells of the blastocyst are capable of generating all adult cell types, a phenomenon known as pluripotency. The inner cell mass (ICM) of the blastocyst can moreover be cultured in a dish as pluripotent embryonic stem cells (ESCs). ESCs have become invaluable tools in regenerative medicine and to study development itself. With 1 in 8 couples experiencing infertility in the UK, it is ever more important to understand the factors contributing to healthy embryo development. Transposable elements (TEs) are parts of our DNA that are currently or historically mobile, -i.e. having the capacity to 'paste' themselves into new places in the genome. Many TE sequences used to be thought of as simply 'junk DNA'; however, we are beginning to understand that TEs have evolved to play new and unexpected roles in development and disease. For example, uncontrolled TE activity has been implicated in neurodegeneration and cancer. However, the expression of many TEs is also high in normal development, suggesting that they may also have beneficial roles in cells. This proposal focuses on exploring the function and regulation of a particular TE, called mouse endogenous retrovirus type L, MERVL. MERVL is the earliest expressed TE, and is transiently upregulated in mouse embryos at the 2-cell stage. This stage, conserved in human in 4-8 cell embryos, encompasses an essential process called Zygotic Genome Activation, when the embryo begins to turn on its own genes for the first time. These embryos are also considered "totipotent", meaning that they can not only generate embryonic tissues but also extra-embryonic tissues (like placenta). Interestingly, a small proportion of ESCs transiently become "2C-like" in normal culture, also possessing enhanced developmental potency. Here, we will use mouse ESCs and mouse embryos to investigate how and why MERVL regulation is important in early development. Using these tools, we will identify and characterize key factors required to activate and repress MERVL. In turn, we will investigate how these factors regulate the 2-cell stage, and affect ZGA and totipotency. To understand how MERVL and other TEs are directly regulated, we will combine genome-editing systems, called CRISPR/Cas9, with recent biochemical tools to pull out sets of proteins that bind MERVL. Lastly, we will explore the conservation of MERVL function and regulation in human cells, where a similar TE, HERVL, is known to play a conserved role. We aim to a) understand how HERVL regulates the 4-8 cell stage and human ZGA b) investigate how new HERVL regulators might contribute to specific cases of disease. These studies will significantly increase our understanding of how TEs contribute to early development, and will shed insight on how such processes are perturbed in disease.