slides

LA NUOVA BIOLOGIA
PROSPETTIVE E IMPLICAZIONI ETICHE
Uno sguardo alla nuova biologia
Alessandro Quattrone
Colture cellulari
Affollamento macromolecolare
L’interno delle cellule è un ambiente molto denso ed affollato
Livelli di osservazione nelle cellule
Una visione semplice della cellula
I cromosomi umani
Dai cromosomi al DNA
Il DNA (DeoxyriboNucleic Acid)
Il DNA (DeoxyriboNucleic Acid)
B-type
A-type
Z-type
Le quattro “basi” del DNA
A
G
PURINES
C
PYRIMIDINES
T
Appaiamento obbligato delle basi
Duplicazione del DNA
Le sequenze di DNA
CAACCTTTGGGATGTGTGCATGGTGGCAAGGGGCTGACTGATATGAGATTACTTCTTTTA
AGGGAAATTGTCATTAATGAGTCAAGAAACTGCTCATTTATGATAATTAGCACCATGGAG
CCTCAGGTGTCAAATGGTCCGACATCCAATACAAGCAATGGACCCTCCAGCAACAACAGA
AACTGTCCTTCTCCCATGCAAACAGGGGCAACCACAGATGACAGCAAAACCAACCTCATC
GTCAACTATTTACCCCAGAATATGACCCAAGAAGAATTCAGGAGTCTCTTCGGGAGCATT
GGTGAAATAGAATCCTGCAAACTTGTGAGAGACAAAATTACAGGACAGAGTTTAGGGTAT
GGATTTGTTAACTATATTGATCCAAAGGATGCAGAGAAAGCCATCAACACTTTAAATGGA
CTCAGACTCCAGACCAAAACCATAAAGGTCTCATATGCCCGTCCGAGCTCTGCCTCAATC
AGGGATGCTAACCTCTATGTTAGCGGCCTTCCCAAAACCATGACCCAGAAGGAACTGGAG
CAACTTTTCTCGCAATACGGCCGTATCATCACCTCACGAATCCTGGTTGATCAAGTCACA
GGAGTGTCCAGAGGGGTGGGATTCATCCGCTTTGATAAGAGGATTGAGGCAGAAGAAGCC
ATCAAAGGGCTGAATGGCCAGAAGCCCAGCGGTGCTACGGAACCGATTACTGTGAAGTTT
GCCAACAACCCCAGCCAGAAGTCCAGCCAGGCCCTGCTCTCCCAGCTCTACCAGTCCCCC
AACCGGCGCTACCCAGGTCCACTTCACCACCAGGCTCAGAGGTTCAGGCTGGACAATTTG
CTTAATATGGCCTATGGCGTAAAGAGGTTCTCCCCAATTACCATTGATGGAATGACAAGC
CTTGTGGGAATGAACATCCCTGGTCACACAGGAACTGGGTGGTGCATCTTTGTCTACAAC
CTGTCCCCCGATTCCGATGAGAGTGTCCTCTGGCAGCTCTTTGGCCCCTTTGGAGCAGTG
AACAACGTAAAGGTGATTCGTGACTTCAACACCAACAAGTGCAAGGGATTCGGCTTTGTC
ACCATGACCAACTATGATGAGGCGGCCATGGCCATCGCCAGCCTCAACGGGTACCGCCTG
GGAGACAGAGTGTTGCAAGTTTCCTTTAAAACCAACAAAGCCCACAAGTCCTGAATTTCC
CATTCTTACTTACTAAAATATATATAGAAATATATACGAACAAAACACACGCGCGCACAC
ACACACATACACGAAAGAGAGAGAAACAAACTTTTCAAGGCTTATATTCAACCATGGACT
TTATAAGCCAGTGTTGCCTAAGTATTAAAACATTGGATTATCCTGAGGTGTACCAGGAAA
GGATTTTATAATGCTTAGAAAAAAAGAAAAAAAAA
Flusso dell’informazione: il Dogma Centrale
need a code
Il codice genetico
Una visione moderna del Dogma Centrale
July 25, 2005 Issue of Science
“The great, hard questions that point to critical gaps in our
scientific knowledge”
 What Is the Universe Made Of?
 Can the Laws of Physics be United?
 What Is the Biological Basis of Consciousness?
 Why Do Humans Have So Few Genes?
 What Controls Organ Regeneration?
 How Can a Skin Cell Become a Nerve Cell?
 How Does a Single Somatic Cell Become a Whole Plant?
 What Genetic Changes Made Us Uniquely Human?
Il flusso duale dell’informazione nella vita
development
organism (mortal)
germinal cell line (immortal)
Una curiosa conseguenza: il clonaggio di individui
Il flusso difettivo: malattie
multigenic and multifactorial diseases(“complex”)
single gene diseases (“genetic”)
Geni e malattie
•
malattie a gene singolo 
•
•
una sola lesione molecolare
stessa mutazione
stesso gene ma mutazioni diverse
malattie complesse 
•
più lesioni molecolari copresenti:
in geni differenti
di “peso differente”
in combinationi differenti
La visione dall’alto con dettaglio
21 novembre 1783, Pilâtre de Rozier e marchese d'Arlandes
Diversità biomolecolare
La visione dall’alto con dettaglio
Gli spazi “omici”
metaboloma (piccole molecole)
proteoma (proteine)
trascrittoma (mRNA)
genoma (DNA)
Il genoma umano, alla fine
Nature 431, 931 - 945 (21 October 2004)
Finishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium
The sequence of the human genome encodes the genetic instructions for
human physiology, as well as rich information about human evolution. In 2001,
the International Human Genome Sequencing Consortium reported a draft
sequence of the euchromatic portion of the human genome. Since then, the
international collaboration has worked to convert this draft into a genome
sequence with high accuracy and nearly complete coverage. Here, we report the
result of this finishing process. The current genome sequence (Build 35)
contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers 99% of
the euchromatic genome and is accurate to an error rate of 1 event per 100,000
bases. Many of the remaining euchromatic gaps are associated with segmental
duplications and will require focused work with new methods. The nearcomplete sequence, the first for a vertebrate, greatly improves the precision of
biological analyses of the human genome including studies of gene number,
birth and death. Notably, the human genome seems to encode only
20,000−25,000 protein-coding genes. The genome sequence reported here
should serve as a firm foundation for biomedical research in the decades ahead.
Convergence
Genome Sequencing: read
1995
First bacterial
genome
2001
First metazoan
genome
2003
Human genome
2006
30 vertebrate
genomes
2008
Individual human
genomes
1992
Photolitography
for microarrays
1998
Spotting for microarrays
2000
Mass Spectrometry
for proteins
2005
Microfluidics and
nanobiosensors
DNA manipulation and synthesis: perturb & reproduce
1979
Recombinant DNA
In bacteria
1989
Recombinant DNA
In mice
2005
Synthetic Biology
methods
2008
Synthetic DNA
breakthrough
Mining and Modelling Algorithms: interpret & predict
1940
Models of excitable cell
behaviour
1995
Sequence annotation
algorithms
1998
Ontologies in
Biology
2002
Prediction phenotype
models
new biology
Nanobiotecnology: measure
Convergence
Genome Sequencing: Systems
DNA manipulation and synthesis: Synthetic
Mining and Modelling Algorithms: Semantic
new biology
Nanobiotecnology: Systems/Synthetic
Convergence
Clinical Data Recording
sequence/disease association
Genome Sequencing
Convergence
Clinical Data Recording
Mining and Modelling Algorithms
predictive medicine
Nanobiotecnology
Convergence
Mining and Modelling Algorithms
synthetic biology
DNA manipulation and synthesis
Sequenziatori
Sequenziatore di nuova generazione
Sequenziamento individuale
•
2003: TDG
the “thousand dollar genome”
•
2007: Solexa
sequenziamento massivo
all’1% del costo attuale
L’interattoma umano
I genomi individuali
La visione dall’alto con dettaglio
Un grafico importante
L’immagine d’insieme?
Data Integration
Personal Genetics
Personal Genetics
I business della genomica
farmacogenomica
• Prescrizioni di farmaci
su base individuale,
farmaci meno tossici e
più efficaci
nutrigenomica
• Diete e supplementi su
base individuale
•Identificazione su base
individuale dei composti
pericolosi
• Misure atte ad evitare
sostanze tossiche
nell’ambiente domestico
e di lavoro
• Farmaci più selettivi
• Industria farmaceutica
• Industria biotecnologica
tossicogenomica
• Industria alimentare
• Industria dei diagnostici
• Industria dei diagnostici
• Industria chimica
una vita più lunga e più in salute, invecchiamento rallentato,
decremento del tasso di incidenza di malattie e cure più efficaci
A “synthetic” world
Thomas Knight, Jr: from ARPANET to the new biology through artificial intelligence
3
Biobricks
• Composable set of genetic building blocks (genes, short
pieces of DNA).
– More than 2,000 today
• Consist of sensors, actuators, input and output devices, and
regulatory elements.
• Each BioBrick can send and receive standard biochemical
signals and be cut and pasted into a linear sequence of other
BioBricks
P
S
+
P
P
S
S
Biobricks
Biobrick Assembly
RNA-Related
CMV
UAS mCMV
Kozak
Long ½ life
Kozak
Short ½ life
Stops
Tre mCMV
...
IRES2
FLAG
cMyc
Protein
Targeting
HA
GFP
RFP
NLS
RLuc
GST
...
...
Myri
SV40 pA
...
Done in 5 assemblies!
Your Protein of Interest
3
Biobrick Assembly
3
Adventures in Sinthetic Biology
•
iGEM 2007: more than 600 students at 60+ universities competed using and creating
BioBricks:
-
Biosensors for the detection of arsenic or lead in drinking water.
E. coli robots that freeze, smell, swell and time-keep.
Stem cells to repair infarcted hearts.
Viruses which selectively kill cancer cells.
Implementing memory capabilities in bacterial colonies.