theme 5(2)

• Transcriptome


  The entire complement of RNA produced under a given set of conditions
• Hybridization


  To measure gene expression
• Microarrays


  • Small solid-state supports to which genes or portions of genes are fixed and arrayed spatially in a known pattern
• What can we learn from microarrays

  • Global gene expression
  • Expression of specific groups of genes under different conditions
  • Expression of genes with unknown function- help with genome/annotation
  • Compare gene content with closely related organism
  • Identify specific organisms
• RNA sequence analysis


  • Measures amount of expressed mRNA and non-coding RNA (advantage over microarrays)
  • With DNA sequence you can determine which genes ARE transcribed and how many copies of each RNA are made
• Proteomics


  Genome-wide study of the structure, function, and regulation of an organism's proteins

  
• Proteomics terms


  • Proteome: all proteins encoded in the genome/ those present at a given time
  • Translatome: proteins translated under specific conditions
  • Secretome: secreted proteins
• Methods in proteomics


  • Mass spectrometry determines molecular formula, identified using peptides
  • High pressure liquid chromatography used to separate proteins by difference in chemical properties
  • Matrix-assisted laser desorption ionization: advanced MS, sample is fixed to matrix, ionized, vaporized and molecular formula determined
• Interactome


  Set of interactions between molecules, data expressed in network diagrams (can also be transcription regulators)
• Metabolomics


  Complete set of metabolic intermediates and other small molecules produced in an organism
• Metabolomics methods


  • NIMS (Nanostructure initiator MS) can directly analyze samples without special preparation
  • NMR (nuclear magnetic resonance)
  • MALDI (matrix assisted laser desorption ionization)
  • TOF (time of flight)
• Plants produce several thousand metabolites
• Secondary metabolites

  Scents, flavours, pigments, alkaloids
• Metabolomics is used to study microbial cultures and communities, and to characterize the human microbiome and metabolites produced by humans and microbes