Genomic Computing, DEIB, 4-7 March 2013 The evolution of life science methodologies: From single gene discovery to the ENCODE project and beyond Heiko Muller Computational Research IIT@SEMM [email protected] Trepanation and humorism Out of 120 prehistoric skulls found at one burial site in France dated to 6500 BC, 40 had trepanation holes, used to allow bad ghosts to leave the body Ancient doctors strived to find rational explanations for diseases: Health = equilibrium of 4 fluids (humorism): black bile, yellow bile, phlegm, blood Formed the basis of treatments like bloodletting, fire cupping, laxatives etc. Hippocrat 460-370 bc Paracelsus 1493-1541 critique Galen of Pergamon 129-200 ad Renaissance Renaissance doctors tried to drill deeper doing autopsies and using microscopy 1628 “De Motu Cordis” Blood circulation William Harvey 1578 – 1657 Antonie van Leeuwenhoek, “Father of Microbiology“, 1676 observed microorganisms Built about 200 microscopes by hand, best quality at the time. 1632 – 1723 Microscopy and cellular pathology 19th century saw cellular pathology sweeping away humorism Mycobacterium tuberculosis 1858 Robert Koch 1843 - 1910 Rudolf Virchow 1821 – 1902 “Omnis cellula e cellula ” Discovery of X-rays, radioactivity, quantum mechanics Konrad Roentgen Henry Bragg Linus Pauling X-rays 1895 Werner Heisenberg Understood nature of chemical bonds, 1932 electronegativity Established quantum mechanics 1925-1926 1898 Marie & Pierre Curie Lawrence Bragg Radium, Polonium Atoms are divisable!! X-ray diffraction Erwin Schroedinger Significance and structure of DNA Oswald Avery 1944, nucleic acid is transforming (causing heredity) Rosalind Franklin, James Watson, Francis Crick 1953: DNA double helix Cracking the genetic code (1960s) Marshall Nirenberg Poly-U experiment Jacques Monod François Jacob 1961 lac operon Support for mRNA hypothesis Gobind Khorana oligosynthesis Robert Holley 1964 Ala-tRNA sequence Linking DNA-RNA-protein Central dogma of Molecular Biology (Francis Crick) Protein RNA DNA Discovery of proteins Described proteins distinguished by ability to coagulate or flocculate under treatments with heat or acid. e.g. albumin from egg whites, blood serum albumin Antoine François, comte de Fourcroy 1755 - 1809 1838: On the composition of some animal substances First use of term protein (the “leader”). Gerardus Johannes Mulder Jöns Jacob Berzelius 1802 - 1880 1779 - 1848 Sequencing, First structures Frederick Sanger Bovine insulin sequence myoglobin 1951 John Kendrew Led to sequence hypothesis Myoglobin X-ray structure later proposed by Francis Crick 1958 hemoglobin Max Perutz Hemoglobin X-ray structure 1959 Western blot Protein profiling: 2D gels, mass spectrometry 2D gel electrophoresis Protein and peptide mass spectrometry Monoclonal antibodies (1975) César Milstein Discovery of DNA, RNA Discovered 1869 by Friedrich Miescher in the kitchen of castle Tuebingen, “nuclein” Phoebus Levene 1909: ribose 1919: nucleic acid = base + sugar + phosphate, “nucleotide” 1929: deoxyribose Semiconservative replication of DNA Meselson-Stahl 1958, semi-conservative DNA replication Manipulating DNA Werner Arber, Hamilton Smith, 1970, restriction enzymes Stanley Cohen, 1972, Molecular cloning Sequencing DNA Frederick Sanger 1977, dideoxy sequencing or chain-termination sequencing φX174 Identification of specific DNA fragments by hybridization, Southern blot Sir Edwin Mellor Southern, Southern blot http://science.bard.edu/biology/ferguson/course/bio310/student_presentations/Southern_1975.pdf Amplification of DNA Kary Mullis 1983, polymerase chain reaction, amplification of genetic material Quantitative PCR (Taqman PCR), molecular beacons The human genome project (1990) Spotted microarrays (1995) Patrick O. Brown Oligonucleotide microarrays (1996) DNA and disease karyotype Spectral karyotyping 1960, Philadelphia chromosome, Bladder cancer cell karyotype Cause of chronic myelocytic leukemia By Robert Sanders, Media Relations | July 26, 2011 ChIP-chip, ChIP-seq, copy number variation, SNPs (single nucleotide polymorphisms) Discovery of RNA 1900 - 1950 Phoebus Levene 1909: ribose 1919: nucleic acid = base + sugar + phosphate, “nucleotide” 1929: deoxyribose differences in base composition and chemical stability 1950s microsome (ribosome) observation by electron microscopy and centrifugation, radiactive aminoacids are incorporated into microsomes rapidly and microsomes have an RNA component (rRNA) radiactive aminoacids bind to tRNA polysomes ->mRNA concept 1960s cracking the genetic code, tRNA sequence Reverse transcription of RNA Isolation of reverse transcriptase, 1970 David Baltimore Howard Temin Northern blot, identification of specific RNA molecules by hybridization RNA processing Late 70 s Louise Chow and Sue Berget Phil Sharp, Rich Roberts mRNA splicing, exons, introns RNA as a regulator: microRNA, RNA interference RNA-induced silencing complex (RISC) RNA profiling: differential display Identify differentially expressed bands, Clone and sequence them, validate RNA profiling: SAGE, microarrays, RNA-seq Spotted microarray Probes = cDNA oligonucleotide microarray Probes = oligonucleotides RNA-seq Macrobiomolecules and disease The genomic data surge Northern Differential Display SAGE Expression chips SNP chips Sequencer SNP beads Southern RFLP IFOM-IEO-CAMPUS Since 2009: 1800 samples 16 TB raw data 70 TB elaborated data PCR Genome draft 1980s 1990s 2000s 2010s Genome browsers RNA seq The genomic data surge .