Chapter 3 - Genomics, Proteomics, and Related Approaches to Physiology

Chp 3 Genomics, Proteomics, and Related Approaches to Physiology Genomics Genomics: study of the genome of organisms Helps elucidate the evolution of genes and genomes Helps elucidate the current functioning of genes and genomes The case of the Ice Fish Ecological and metabolic points of view Found in Antarctica No hemoglobin in the blood From the point of view of metabolism and survival: How is it possible for these fishes to thrive with a lack of hemoglobin? The case of the Ice Fish Genetic point of view There are about 16 species of Ice Fishes, all in Antarctica So, the following questions: Did they evolve from a single ancestor or did the gene evolved separately? What kind(s) of mutation inactivated the gene? Is the gene non functional? Or is the gene functional but not activated? The case of the Ice Fish Evolutionary point of view Phylogenetic reconstruction: Based on mitochondrial DNA Why is the phylogenetic reconstruction not based on the hemoglobin gene? The loss of hemoglobin is deleterious compared to the ability to synthesize Hb This trait appeared once and was kept. What could be the underlying mechanism? Founder effect? Selection? The case of the Ice Fish Myoglobin Six of the Ice fish species lack myoglobin ? white myocardium Trait appeared several times. The mutations are different The Ice Fish The antifreeze protein The body fluids of bony fishes are more dilute than sea-water ? these body fluids will freeze at higher temperature than sea-water (at 33ppt ? freezing point (-1.9oC) All ice fishes and all red blood fishes in Antarctica have the same antifreeze protein So, when did this trait appear? Prior to or after the appearance of ice fishes? Genomics: Summary The systematic sequencing of animal genome allows for a survey for the presence of genes based on previous knowledge The presence of gens infers a potential function Evolutionary history of the genes can be inferred Top-down order of study: from animal function to tissue function and biochemistry and genes Bottom-up order of study: study from gene to gene expression, then to tissue and to animal function Transcriptomics Study of mRNA expression Use of microarrays Manipulation of gene expression Gene manipulation Gene deletion = gene knockout RNA interference Proteomics and Metabolomics Proteomics: Study of all the proteins present in a cell at a particular time Metabolomics: Study of all organic compounds in a cell Helps to clarify metabolic pathways Helps quantify responses to environmental changes