The evolution of life science methodologies: From single gene

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
1858
Mycobacterium tuberculosis
Robert Koch
1843 - 1910
Rudolf Virchow
1821 – 1902
“Omnis cellula e cellula ”
Discovery of X-rays, radioactivity, quantum mechanics
Konrad Roentgen
X-rays 1895
Henry Bragg
Linus Pauling
Werner Heisenberg
Established quantum mechanics
1925-1926
1898
Marie & Pierre Curie
Radium, Polonium
Atoms are divisable!!
Lawrence Bragg
X-ray diffraction
Erwin Schroedinger
Understood nature
of chemical bonds,
1932 electronegativity
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
1961 lac operon
Support for
mRNA hypothesis
François Jacob
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
1802 - 1880
Jöns Jacob Berzelius
1779 - 1848
Sequencing, First structures
Frederick Sanger
Bovine insulin sequence
1951
Led to sequence hypothesis
later proposed by Francis Crick
John Kendrew
Myoglobin X-ray structure
1958
Max Perutz
Hemoglobin X-ray structure
1959
myoglobin
hemoglobin
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,
Cause of chronic myelocytic leukemia
Bladder cancer cell karyotype
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
SNP beads
Southern
1980s
Sequencer
RFLP
PCR
1990s
IFOM-IEO-CAMPUS
Since 2009:
1800 samples
16 TB raw data
70 TB elaborated data
Genome draft
2000s
Genome browsers
2010s
RNA seq
The genomic data surge