Chp 3 Genomics, Proteomics, and Related Approaches to Physiology

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Chp 3Genomics, Proteomics, and Related
Approaches to Physiology
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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

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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?

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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?

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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?

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The case of the Ice FishMyoglobin

• Six of the Ice fish species lack myoglobin ?
  white myocardium
• Trait appeared several times.
• The mutations are different

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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?

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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

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• 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

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Transcriptomics

• Study of mRNA expression
• Use of microarrays
• Manipulation of gene expression

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Gene manipulation

• Gene deletion gene knockout
• RNA interference

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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

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