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