The silicon trypanosome (SilicoTryp)

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In this proposal we intend to set the foundation for a description of the cellular workings of parasitic protozoa called trypanosomes. Trypanosomes are responsible for the disease sleeping sickness in sub-Saharan Africa. The parasites are transmitted between people by biting tsetse flies. Once injected into the bloodstream they begin to proliferate and eventually invade the brain and central nervous system. Once inside the brain the presence of parasites leads to decreasing neurological function. Patients become depressed and cognitive function breaks down. They eventually become mad, fall into a coma and die. In recent years it has become possible to dissect trypanosomes at the molecular level. We have determined the sequence of their genetic code. We can measure the abundance of the individual proteins that are assembled within the trypanosome's structure. We can also measure the manner by which chemicals are transformed from one to another within the parasite. In short, we have at our disposal the parts list that comprises a trypanosome. We would like to exploit this information to assist in designing drugs that can perturb the parasite's inner workings. However, in order to achieve this, it is not enough to have a simple parts-list of the parasite. We need to understand how those parts assemble and how they interact with one another in order to create this living system, the trypanosome. Systems Biology is a recently emerged discipline that combines high throughput measurements of cellular parts, along with measurements of the dynamics of interactions between those parts and then employs high capacity computational modelling in efforts to describe how cellular constituents combine to create recognisable biological function. An ambition of systems biology is to reconstruct biological systems from descriptions of their component pieces with mathematical descriptions that describe how those pieces interact. Increasingly, models are emerging that describe biological function emerging from combined components of the cell. For several model organisms, including yeast and the bacterium Escherichia coli, models of cellular function are being combined into a project termed 'The silicon cell' which ultimately aims to include all component pieces of a cellular system and to describe the dynamics of the connectivity between them in order to predict how the system behaves as a whole. Profiting from the availability of the full genome sequence and methods to determine how genes are turned on to produce RNA transcripts that are then translated into proteins which ultimately control the flow of life through these cells we propose to generate a 'silicon trypanosome', i.e. we propose to build fully descriptive mathemical models of the flow of information that defines a trypanosome. We will take a bottom up approach, starting with a biochemical pathway, the so-called trypanothione pathway that dictates how well trypanosomes can deal when exposed to oxidative stresses. We have chosen this pathway because a great deal is already known about biochemical parameters of the component proteins, or enzymes, of this pathway. Furthermore the trypanothione pathway links directly through the NADPH generating pentose phosphate pathway to the glycolytic pathway, which consumes the parasite's major energy supply, glucose. A comprehensive mathematical model describing the glycolytic pathway in trypanosomes already exists, hence in a bottom up manner, extending into an adjacent pathway, offers a rational way towards a comprehensive model of the trypanosome. In addition to collecting data on the component pieces of the trypanosome we will alsoimplement a range of novel mathematical techniques to ensure the models we build are testable and robust. Ultimately we aim to use the models to predict the best ways to perturb the parasite's biological make up with the hope of generating new drugs.