Doctor of Philosophy

dissertationThere is a fundamental connection between growth and nutrient availability. An inbalance between energy intake and energy expenditure can lead to the common diseases of the developed world, including type 2 diabetes, obesity, heart disease and cancer, as well as less common diseases such as anorexia, malnutrition and sarcopenia. The tight link between growth and nutrient availability is extended beyond the whole body level down to a cellular level. There exist cell autonomous signaling mechanisms that allow the cell to detect the environmental conditions and decide to grow, through increase in cell size or cell division. Malfunctions in these signaling pathways are fundamental to many of the diseases related to energetic misregulation. Many of the proteins that are central to these signaling pathways have also become good therapeutic targets. Two well characterized proteins that are central to cellular energy balance are AMPK and TOR. In response to depleted cellular ATP levels AMPK is activated in order to up-regulate ATP generating pathways and downregulate ATP consuming pathways, including growth. However as nutrients become available TOR is rapidly activated in order to efficiently utilize the available nutrients for growth. As our understanding of the function of these two proteins has increased, AMPK and TOR have become effective therapeutic targets. PAS kinase is a newly characterized serine/threonine kinase that can respond to the extracellular conditions in order to regulate nutrient partitioning and provide a progrowth signal. We show here that in budding yeast PAS kinase can respond to environmental cues to phosphorylate the metabolic enzyme Ugp1. P-Ugp1 then nucleates the formation of a unique signaling complex that includes Rom2 and Ssd1. Complex formation is able to activate the small GTPase Rho1, which functions as a progrowth signal. We also show that PASK-/- mice are resistant to the damaging effects of a high fat diet, specifically, obesity, insulin resistance and hepatic steatosis. This protection is likely due to the increased metabolic rate of PASK-/- mice. The hypermetabolic phenotype of the PASK-/- can be recapitulated in cultured cells, which indicates that the increased metabolic rate is due to a cell autonomous change in metabolism. Further characterization of PAS kinase may lead to novel therapeutic strategies to treat the metabolic syndrome

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health