Many studies in the medical sciences involve the measurement of several aspects on each individual on repeated occasions. Often, scientific interest is in studying the inter-relationships, which might be causal, between measurements. Graphical modelling provides a strategy for translating substantive hypotheses about causal relationships into a statistical model. Further, scientifically relevant results from the statistical analysis of the data can be communicated through an intuitively natural graphical representation of the fitted model. The aim of this project is to make use of recent developments in the area of graphical models to advance research in medical contexts, including developmental psychology, neuropsychology and brain ageing. This project will focus on two areas: 1) assessment of decline in the cognitive functions of Alzheimer‘s patients and 2) identification of particular executive and social-cognitive problems associated with focal epilepsy in children. Evaluation of data to study development and deterioration of cognitive performance in individuals requires the consideration of latent variables to represent qualities of individual subjects that cannot be measured directly. Often the directly observed data are qualitative, for example success or failure on a psychometric test. A major goal is to develop a flexible modelling strategy for data of this kind.

Most of the body's energy comes from food which is converted to ATP, the energy currency of the cell. Respiration is the most efficient means of making ATP, a process known as oxidative phosphorylation, and this takes place in a compartment of the cell called mitochondria. Oxidative phosphorylation requires five multisubunit protein complexes. The vast majority of DNA in the cell is contained in the nucleus; however, 13 proteins are produced from DNA in mitochondria, so-called mitochondrial DNA. Unfortunately these 13 proteins are not trivial, but essential to life. They represent key components of the oxidative phosphorylation system. Defects in mitochondrial DNA cause a wide range of diseases in humans and there is growing evidence that they contribute to the natural process of ageing. Mitochondrial DNA, like every other DNA, requires a host of proteins to ensure its faithful reproduction, less obviously it also requires proteins for its organisation, maintenance and segregation. Thus, the depiction of mitochondrial DNA, as an open circle floating free in the mitochondrial matrix without protein, in many textbooks is erroneous. In reality, mitochondrial DNA is organized in multi-genomic nucleoprotein complexes, or nucleoids. The inventory of proteins associated with yeast mitochondrial DNA is closer to completion than that of higher eukaryotes (including humans), however, it is clear that there are substantial differences in the protein composition of animal and yeast mitochondria nucleoids (Chen & Butow 2005). Recently, we have identified a number of new proteins that associate with mitochondrial DNA, using a generic DNA binding protein to capture mitochondrial nucleoprotein complexes. This has opened up a new area of biology and we now plan to characterise these proteins in detail, in order to understand how mammals maintain their mitochondrial DNA and ensure its successful transmission to offspring. Reference: Chen, X.J. and Butow, R.A. (2005) The organization and inheritance of the mitochondrial genome. Nat Rev Genet, 6, 815-25.

Breastfeeding is the best start for a baby's life. The World Health Organisation (WHO) recommends that all women should exclusively breastfeed their babies until six months of age. However not all women have the opportunity to exclusively breastfeed their babies. In the UK it is reported that whilst 81% of mothers start with breast feeding only 17% of infants are exclusively breast-fed until 3 months, and 1% until 6 months of age. This does not have to be the mother's choice, already in the first weeks 13% of the breast feeding mothers get advice to provide the baby with extra feeding. Thus there is a need to design breast-milk alternatives that mimic the nutritional quality of breast milk as closely as possible. Recent evidence suggests that non breast-fed infants have an increased risk of becoming obese and an increased risk of high blood pressure in later life. It is currently unclear why infant feeding practices have such a big impact on health outcomes later in life. However, breastfeeding seems to be metabolised differently by infants than formula milk; our research showed that babies that are breast fed have a significantly different blood lipid (fat) profile compared to bottle fed babies. The aim of this project is to develop novel methods to help us understand the mechanism(s) of the differences in the metabolism of bottle fed babies and breast fed babies. We want to identify specific lipids that can be used as markers that reflect the benefits of breastfeeding. We will do this by exploring changes in the lipid profiles of babies in the UK during their first year of life. By comparing blood markers with patterns of infant growth we will be able to identify markers that can be used to assess the metabolic response to breast-milk alternatives. We will also include mothers and infants from rural and urban sub-Saharan Africa to explore between population differences in the association between mode of feeding, blood lipid levels, and infant health outcomes'. One possible way in which mode of feeding may impact on the baby's metabolism is via bacteria in the gut (the gut microbiome). It is believed that, compounds in food, affect which bacteria live in the gut and that the different combinations of bacteria in the gut leads to different metabolic products that will be taken up into the blood stream. We do not know if these differences in the gut microbiome also affect the lipids in the blood. To explore this potential link, we will also study what the effect is of the gut microbiome of the babies on their metabolism. Recently we developed a method using high resolution mass spectrometry to determine a detailed lipid profile covering over a 100 lipids from one dried blood spot. This is a blood sample obtained from a heel prick and only requires a drop of blood spotted on paper. This is the most suitable method to study the metabolism of babies. We will adapt this dried blood spot based method to captures both lipids and metabolites dependent on gut microbiome. The identified markers, and the methods to measure these, will then be available for use by scientist and industry to study the effect of new formula or new feeding methods for infants who do not have the chance to be exclusively breast fed and give these babies the best possible start in life.

Ischaemia-reperfusion (IR) injury underlies many clinically important conditions, such as heart attack and stroke. Ischaemia occurs when the blood supply to an organ is interrupted, for example by a blood clot. If the blood supply is restored the tissue can recover. However, reperfusion of the ischaemic organ with oxygenated blood leads to extensive tissue damage that worsens the long-term prognosis for the patient. This injury is initiated largely by the production of damaging free radicals from mitochondria during reperfusion that leads to cell death. We have developed a novel mitochondria-targeted drug called MitoSNO that prevents free radical production from mitochondria during IR injury. MitoSNO comprises a lipophilic cation that drives its rapid and extensive uptake into mitochondria within the heart immediately following its intravenous injection during reperfusion of the ischaemic organ. Within mitochondria MitoSNO selectively transfers a nitric oxide moiety onto a particular cysteine on respiratory complex I, thereby preventing the mitochondrial free radical production that normally occurs during reperfusion. This modification is reversed after 5-10 mins allowing the mitochondria to return to full activity. Rodent studies have shown that MitoSNO prevents cardiac IR injury in clinically relevant in vivo models, thereby greatly enhancing the long-term recovery of heart function. MitoSNO is unique as no other protective therapies can be applied to organs at reperfusion to block mitochondrial free radical production. In this study MitoSNO will be assessed to see if it is also protective against IR injury in pigs in preparation for a first-in-man Phase I study. As similar IR injury is found in other situations, such as heart attack and organ transplantation, MitoSNO may also prove a useful therapeutic for a range of indications.

Living cells have genes made of DNA. DNA is a molecule comprising a string of bases of four different types, and the sequence of these bases in a gene directs the synthesis of a particular protein, which consists of a string of amino acids of twenty different types. Three bases encode one amino acid, this code being read by a cellular machine, the ribosome, which makes the protein. Some triplets do not encode amino acids, but act as stop signals. It is possible to engineer cells such that one of these stop triplets instead encodes a synthetic amino acid, which can have novel chemical properties. Genes can be chemically synthesised with any sequence, so by introducing the appropriate triplet proteins can be specified that have novel properties, such as an enzyme that can be turned on by light. Synthetic biology also allows the creation of new kinds of ribosome in bacteria, engineered to translate only particular synthetic genes, which can read four bases at a time instead of three, thus significantly expanding the range of new amino acids that can be encoded. This technology not only makes possible a wide range of experiments to study the functions of cells and organisms, but also allows the production of novel proteins for therapeutic or other use, such as antibodies with drugs attached at specific sites. Ultimately, such engineering could produce entirely new encoded polymers with many potential uses. DNA too can be altered in novel ways. By engineering the enzymes that copy DNA, it is possible to produce, in the test tube, "XNA" molecules that retain the double helical structure of DNA but are made from chemically different precursors, and hence have a different chemical structure that is resistant to natural and chemical degradation, and can have other novel properties. By making billions of variants of a short sequence of bases, one can select molecules that have a desirable property, such as inhibiting an enzyme or catalysing a reaction, copy them into DNA, and identify the particular sequence. These molecules can be chemically synthesised, and used as potential drugs or for many other purposes. The development of these technologies depends on the synthesis of novel DNA sequences and genes, and many sophisticated forms of analysis including mass spectrometry and advanced microscopy to determine the properties of the novel proteins and XNA molecules that result, and their effects on cells and organisms. This award will provide the advanced equipment required to automate gene synthesis, engineer new functions, and test the many different applications of the new technology.