Malaria is caused by a parasite that is transmitted exclusively by mosquitoes. The greatest malaria reduction and eradication success stories have been achieved by interrupting transmission. Historically, this has been through mosquito control. Targeting the small population of specialised parasites residing in the human host that are transmitted through mosquitoes would provide a similarly powerful malaria control method but we know too little about this population. Until now, the genes expressed by parasites have been analyzed by combining millions of parasites together. This approach confounds differences between individual parasites that could underlie success in getting into another host or in resisting the drugs we use to kill the parasites. We have recently developed a method to analyse single parasites one at a time. This technological leap has allowed us to understand parasites in the laboratory with more precision than ever before and importantly to understand how one parasite may differ from another during the whole life of the parasite both in the host and in the mosquito. Although the laboratory setting and lab strains of parasites are powerful tools for understanding parasite biology, in the lab we cannot understand the full diversity of parasites that exist in the wild causing devastating consequences for infected individuals. In this project we propose to characterise wild parasites at an individual level in partnership with Malian scientists. Our exploration will allow us to characterise the three main species of malaria parasite in sub-saharan Africa on a single parasite level for the first time. We will integrate the data into an interactive website called the Malaria Cell Atlas. This will become a key resource for the research community. We will then explore the changes from one patient to the other of the deadliest malaria species in both patients that are suffering from malaria symptoms and also from infected carriers who are not suffering from malaria, both of which contribute to the overall reservoir of parasites. Altogether, we will look at more than 300,000 individual parasites and get a very deep understanding of how individual parasites are both similar and different from each other. Understanding this infectious reservoir is pivotal to identifying how parasites efficiently get from one person to the next. Altogether our findings using cutting-edge tools to explore wild parasites will be key to understanding malaria and how to best control it.

We propose to provide state of the art analysis and annotation of the pig genome sequence being generated by the International Pig Genome Sequencing Project. We will make the annotated genome sequence accessible on the Web through the Ensembl site at http://www.ensembl.org . The pig genome is the entire DNA sequence of the pig which defines all the biological molecules that make up a pig. By acquiring, managing and annotating the pig genome sequence one accelerates research for both pig biology and for mammalian biology. Impact on pig biology: Because of the extensive selective breeding which has occurred during domestication, there are a considerable number of breed or line-specific features, from fat/muscle ratios, litter size to skin colour. These features can be mapped genetically into broad regions of the genome, but the final identification of the genes responsible and the causal genetic variation is very complex. The availability of a well-annotated pig genome sequence with links to other data sources, especially those on phenotypes such as growth, carcass composition or responses to infectious disease would provide a dramatic boost to the identification of these causative genes.

Childhood diarrhoea and bacterial bloodstream infections account for a considerable proportion of illnesses and deaths among children under five years of age worldwide. The under-five mortality produced by these infections is disproportionately high in Nigeria and other parts of Africa. This study proposes to examine two causes of these infections, enteroaggregative Escherichia coli and Salmonella, and to identify bacterial lineages that account for a significant proportion of childhood diarrhoeas and invasive infections among Nigerian children. Stool specimens will be obtained from children with diarrhoea and from healthy children attending clinics in Ibadan, Nigeria. E. coli and Salmonella will be isolated from the specimens and characterized at the molecular level to identify disease-causing strains and the disease-causing genes these subtypes carry. Enteroaggregative Escherichia coli and Salmonella isolates will be subjected to further analysis, involving sequencing parts of their genomes. The resulting DNA sequences will be compared to determine inter-relationships among different genetic lineages of bacteria isolated in this study and between these isolates from Nigeria and strains other parts of the world. These analyses will reveal how disease-causing lineages change over time and are transmitted locally and globally. This research will improve our understanding of the epidemiology and evolution of two important but under-addressed bacterial pathogens. The study will determine which subgroups of enteroaggregative Escherichia coli and Salmonella are more likely to cause disease and whether there are subtypes that are associated with life-threatening disease. This is important for the study location, Nigeria, because very little is known about locally-prevalent subtypes within the country or in neighbouring countries. Identification and characterization of predominant subgroups serve as the basis for devising diagnostics to better their detection and surveillance. The findings from this study will also inform vaccine development and vaccine use policy because the most harmful subtypes can be targetted. This research will also determine whether healthy individuals carry these organisms, and if so, to what extent. Understanding healthy carriage is key to determining how these organisms are maintained and transmitted in communities. The study will use molecular methods to characterize the strains in a laboratory to be set up at the University of Ibadan and lead by the African Research Leader Candidate who is co-investigator on this grant. The African Research Leader will additionally build on collaborative links with other regional laboratories and extend some of the expertise built at Ibadan to those labs. The research will therefore build capacity in the area of molecular bacteriology and provide a collaborative link between West African scientists and the Wellcome Trust Sanger Institute, where the principal investigator is located.

During hematopoiesis, the bone marrow microenvironment triggers specific signalling in hematopoietic stem cells (HSCs), inducing their differentiation into multiple immune lineages. A main constraint in the field is the lack of human in vitro models to recapitulate this process and provide mechanistic insights into the early steps of immune cell differentiation. I propose an innovative, multidisciplinary approach to decode the role of the bone marrow microenvironment in shaping cell identity and function. I will define the essential cellular niche driving HSC to B-cell differentiation in the developing human bone marrow by analysing single-cell genomics datasets. This reference will guide the engineering of feeder cells (human bone marrow-like-stromal cells, hBMLSCs) from human induced pluripotent stem cells (hiPSCs) using synthetic biology tools. Finally, I will design novel 3D-cultures to co-culture my engineered feeder cells and HSCs, and induce their differentiation towards the B-cell lineage. My proposal combines single-cell and computational technologies with cell and tissue engineering to provide the first artificial bone marrow model in humans. This model promises to transform the study of hematological disease and pave the way to a new era in immunotherapies. In addition, the experimental and computational framework will guide the future improvement of in vitro models using single-cell genomics data.

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