THEME 5(1)

• Genomics


  Discipline of sequencing, analysing, annotation and comparing genomes
• Gene knockouts / mutations


  Sequencing techniques
• Sequencing techniques


  1. Determining the precise order of nucleotides in DNA/RNA

  2. Sanger dideoxy method (1st generation)

  3. Massively parallel methods (2nd generation)

  4. Sequence single DNA molecules (3rd generation)

  5. Oxford Nanopore Technologies system, Ion torrent semiconductor sequencing (4th generation)

  
• 1st generation sequencing


  • Sanger dideoxy method

  
• 2nd generation sequencing


  • 100x faster than 1st, Massively parallel methods (large # sequenced together), Using increased computer power and miniaturization
• 3rd generation sequencing


  • Sequence single DNA molecules, HeliScope Single Molecule Sequencer, Pacific Biosciences SMRT (single molecules real time sequencing) – carried out in nanocontainers

  
• 4th generation sequencing


  • Oxford Nanopore Technologies system, Ion torrent semiconductor sequencing, Don't use optical detection
• Genome


  Genes, regulatory seq, and noncoding DNA
• Comparative genomics


  Sequence similarity to genes in other organisms
• Functional genomics


  Predict pathogenicity, virulence factors and transport systems
• As genome size increases, gene content does
• Smaller genomes = parasitic/endosymbiotic (totally host dependent for nutrients)
• Metagenome

  Total gene content of the organisms in an environment (eg. In a deep sea sediment). Metagenomics: total gene content of microbial community

  
• Metatranscriptomics


  Gene expression profiles within a microbial community

  
• Metaproteomics


  Protein expression patterns within a microbial communities