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Reference books: Molecular Biology of the Cell, 4th edition, by B. Alberts et al., 2002. Molecular Cell Biology, 5th ed

Reference books: Molecular Biology of the Cell, 4th edition, by B. Alberts et al., 2002. Molecular Cell Biology, 5th edition, by H. Lodish et al., 2004. Molecular Biology of the gene, 5th edition, J. Watson et al, 2004. Planches à voir Tazi 1. PPT METHODOLOGIE.PDF.

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Reference books: Molecular Biology of the Cell, 4th edition, by B. Alberts et al., 2002. Molecular Cell Biology, 5th ed

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  1. Reference books: Molecular Biology of the Cell, 4th edition, by B. Alberts et al., 2002. Molecular Cell Biology, 5th edition, by H. Lodish et al., 2004. Molecular Biology of the gene, 5th edition, J. Watson et al, 2004 Planches à voir Tazi 1. PPT METHODOLOGIE.PDF

  2. Watson & Crick with DNA model Rosalind Franklin with X-ray image of DNA Watson & Crick – “…the secret of life” • Watson: a zoologist, Crick: a physicist • “In 1947 Crick knew no biology and practically no organic chemistry or crystallography..” – www.nobel.se • Applying Chagraff’s rules and the X-ray image from Rosalind Franklin, they constructed a “tinkertoy” model showing the double helix • Their 1953 Nature paper: “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”

  3. DNA pol fidelity Replication DNA Error rate of ~ 10-9 to 10-12. RNA pol fidelity Transcription Error rate of ~ 10-4 to 10-5. RNA Translation Post-transcriptional regulation Protein

  4. GENOMICS TRANSCRIPTOMICS Discovering PROTEOMICS BIOINFORMATICS

  5. (Genome) DNA Pre-mRNA mRNA mRNA (Transcriptome) Proteins (Proteome) Metabolites (Metabolome)

  6. Steps in DNA Sequencing and Genotyping • Selecting part of genome to sequence or genotype • Amplifying nucleic acid • Determine sequence of one or a succession of nucleic acids: • Chemical reaction format • Read out format • Resequencing vs de novo sequencing

  7. Sequence Tagget sites (STSs) Short segments of unique DNA sequence along every chromosome

  8. Dideoxynucleoside Sequencing

  9. Dideoxynucleoside Sequencing

  10. Dideoxynucleoside Sequencing

  11. Séquençage par des ddNTP Fluorescents

  12. Genome Sequencing Approaches

  13. https://www.roche-applied-science.com/sis/sequencing/flx/ Multimedia presentation

  14. Pyrosequencing Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001

  15. Pyrosequencing - Solid Phase Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001

  16. Pyrosequencing - Liquid Phase Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001

  17. Pyrogram Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res 2001

  18. 454 LifeSciences Sequencer

  19. 454 LifeSciences Sequencer - Process Overview

  20. 454 LifeSciences Sequencer - Process Overview

  21. 454 LifeSciences Sequencer

  22. 454 LifeSciences Sequencer

  23. 454 LifeSciences Sequencer

  24. Applications of Ultra-Low-Cost Sequencing • Sequencing individual human genomes as component of preventive care. • Genotype-phenotype associations • Comprehensive gene expression profiling in vitro and in situ at all stages of development of a multicellular organism • Comprehensive analysis of mutations present in cancer clones. • Mitochondrial heteroplasmy • Microbial diversity (metagenomic studies) Shendure N. Advanced sequencing technology: methods and goals. Nat Rev Gen 2004

  25. 3 billion bases 20,000 – 30,000 genes 3000 nucleotide/gene (on average) 99,9% nucleotide similarity to each other 99% nucleotide similarity to chimpanzees Less than 2 % codes for proteins Chromosome 1 has the most genes Chromosome Y has the fewest genes

  26. Variations in human genome Microsatelitte sequences and variation "Microsatellites" are defined as loci (or regions within DNA sequences) where short sequences of DNA are repeated in tandem arrays.  This means that the sequences are repeated one right after the other.  The lengths of sequences used most often are di-, tri-, or tetra-nucleotides. Single Nucleotide polymorphisms

  27. * Protein Coding sequences represent less than 2% of human genome * More than 50% of human genome sequences are repetitive sequences

  28. CpG islands density on each chromosome

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