chp 3 genomics, proteomics, and related approaches to physiology
Post on 21-Dec-2015
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Chp 3Genomics, 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 FishEcological 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 FishGenetic 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 FishEvolutionary 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 FishMyoglobin
• Six of the Ice fish species lack myoglobin white myocardium
• Trait appeared several times.
• The mutations are different
The Ice FishThe 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