生命システム解析・構成のための次世代シミュレーション
Hiroki R. Ueda
Center for Developmental Biology
RIKEN @ Kobe, JAPANHiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

1What is LIFE?

Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

2

“Omnis cellula e cellula”(all cells come from cells)[1858]
Experiment which finallydisproved the ancient theory of
spontaneous generation[1862]
Rudolf Virchow

Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

LouisLouis Pasteur
Pasteur3

WHAT is a difference
between LIFE & non-LIFE?

Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

“Understanding of Living Systems”
Laboratory for Systems Biology,
Center for Developmental Biology, RIKEN

How to understand/define LIFE?

Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

Andrew Z. Fire

Craig C. MelloRichard Axel

Linda B. Buck

Günter Blobel

If you were BIOLOGIST…
Especially, Molecular Biologist, Geneticist…
Scientist interested in identification of “components”
of system…

Leland H. Hartwell

R. Timothy
forSystemsBiology, CDB, RIKEN(Tim) HuntHiroki R.
SirUeda,Paul M.Laboratory
NurseSydney
BrennerJohn E. SulstonH. Robert Horvitz

Understand Biological Systems“Understanding of Living Systems”
Laboratory for Systems Biology,
Center for Developmental Biology, RIKEN

1. Identification
To completely identify system components
and their interactions

Identify

Mammalian Clock Circuits
Molecular Biologist’s View

Human Circadian Clock
Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

Francis Harry
Compton Crick

James Dewey
WatsonFrançois Jacob

Jacques Monod

Alan Lloyd Hodgkin

Andrew Fielding
HuxleyIf you were PHYSISIT…
Mathematician, Physiologist,
Systems Biologist, Analytical Chemist…
Scientist interested in design principles of systems…

Erwin Neher

PaulC. Lauterbur
Hiroki R. Allan
Ueda,M.Laboratory
Cormack Godfrey
for SystemsBiology,CDB,
RIKEN
N. Hounsfield
Bert Sakmann

Sir Peter MansfieldUnderstand Biological Systems“Understanding of Living Systems”
Laboratory for Systems Biology,
Center for Developmental Biology, RIKEN

2. Analysis
To quantitatively measure properties of components
and predict the behaviors of biological systems

MeasurePredict

Cellular Circadian Rhythm (Bioluminescence)
Mammalian Clock Circuits
Physicist’s View
Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

Stanley B. Prusiner

Barry J. Marshall

J. Robin Warren

Joseph E. MurrayE. Donnall Thomas

If you were MEDICAL DOCTOER…
Scientist working on disease, Pharmacologist, Chemical Biologist…
Scientist interested in “controlling” systems…

GeorgeH. Hitchings
Laboratory
Biology,
RIKEN
Sir James
W. Blackfor Systems
Gertrude B.
Elion CDB,
Ferid Murad Hiroki R. Ueda,

Understand Biological Systems“Understanding of Living Systems”
Laboratory for Systems Biology,
Center for Developmental Biology, RIKEN

3. Control
To quantitatively perturb properties of components anddirect the behaviors of biological systems
LongPeriodPerturb
NormalPeriodDirect
Short
PeriodCellular Circadian Rhythm (Normal Period)

Medical Doctor’s View
Cellular Circadian Rhythm (Long&ShortPeriod)
Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

Albert von
Szent-GyörgyiNagyrapolt

Sune K. Bergström

Bengt I. Samuelsson

John R. Vane

If you were CHEMIST…
Engineer, Computer Scientist, Synthetic Biologist…
Scientist interested in “designing” systems…

Michael S. Brown

HirokiR. Ueda, Laboratory for Systems
Biology, CDB, RIKEN
JosephL. Goldstein
Arthur Kornberg
Severo Ochoa

Understand Biological Systems“Understanding of Living Systems”
Laboratory for Systems Biology,
Center for Developmental Biology, RIKEN

4. Design
To design and implement artificial circuits with identified
structure and observed dynamics of biological systems

DesignImplement

Artificial Clock Components

Chemist’s View

Artificial Clock Circuit

Cellular Circadian Rhythmwith Artificial Clock Circuit
Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

Understanding of Biological Systems
Analysis of “life as it is”
1. Identification
To completely identify system components
and their interactions

Systems Biology
2. Analysis
To quantitatively measure properties of components andpredict the behaviors of biological systems

3. Control
To quantitatively control properties of components anddirect the behaviors of biological systems

Synthetic Biology

4. Design

To design and implement artificial circuits with identified
structure and observed dynamics of biological systems

Synthesis of “life as it could be”
Hiroki R. Ueda, Laboratory for Systems Biology,EscherCDB,, RIKEN
M.C. (1948) “Drawing hands”

Quantitative Measurement
Perturbation for Design Principles

細胞運命を制御するシグナル伝達ネットワークのモデル化とシミュレーション

数理モデル(理研/畠山・佐甲・黒崎ら、鳥取大/木村、九産大/仲）S = A+BLigand

PIP2PI3KPP

PTEN

PIP3

Grb2Shc
Grb2
PLCg

Src

Receptor ubiquitination

Cbl

PDKSOS

生物パラメータ

AktRasPIP2 IP3 + 1,2DAG

Raf

Bad

PP2A
caspase

MEK
STAT3[Ca2+]

p90RSK ERK

20

MPK3

phospho-ERK(fold change)

PKC

p90RSK ERK

151050Proteins0

STAT3EtsER
CREBSRFFos MycSTAT1/3Elk-1

20

30

40

50

60

70

8090

Time (min)蛍光イメージング 立体構造を元にで直接測定した計算予測

分化10

時系列定量データからの計算予測

増殖

細胞死

細胞運命の定式化

シミュレーションによる分子活性化予測

多細胞システムの形と機能の決定機構(理研/大浪）

形と機能の決定
肝臓

腎臓

乳腺

ヒト受精卵

正常な機能のためには正しい形が必要小腸

生物物理学モデル：
生化学モデル：

脳細胞間に働く力、細胞の変形
遺伝子発現制御ネットワーク、細胞間シグナル伝達

Technology for fabrication
at cellular/tissue resolution
Scale between living cells and atoms

World’s first commercial microprocessor:
2300 transistors fabricated at 10㎛ process rule

1mm

0.2mm

Molecular Biology of the Cell
© 2002 by Bruce Alberts, Alexander Johnson, Julian Lewis,
Martin Raff, Keith Roberts, and Peter Walter.

Intel Museum (http://www.intel.com/museum/index.htm)

Semiconductor technology forcellular resolution
Cell size ~ Transistor size
Fibroblast cell in culture

Density of transistors on a chip

50㎛

Molecular Biology of the Cell
© 2002 by Bruce Alberts, Alexander Johnson, Julian Lewis,Martin Raff, Keith Roberts, and Peter Walter.

Modified from “微細加工の基礎 麻蒔立男 日刊工業新聞社”

Photolithography for micro-structure
Photoresist
spin coatingExposure
UVDevelopment

Dip in PDMS& Degas

100㎛

photoresist
SiPDMSBio-MEMS with fluidics simulation
Detailed flow is unclear because of• Complex cell shape• Physical properties• Micro-scale

VCAD project (RIKEN)• Cell shape• Internal structure• Physical property

What is TIME in us?

Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

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Center of human clock : SCN
Suprachiasmatic nucleus

Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

Bio-MEMS for SCN

Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

What is SPACE in us?

Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

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E9.5 Mouse embryo
Photograph by Kaori Tsujino
at Laboratory for Systems Biology

Neural tube and somites. (Scanningelectron micrograph)
Developmental biology, Scot F. Gilbert -- 6th ed.
SINAUER ASSOCIATES, INC., Publishers

Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

Masamizu et al., PNAS, 2006

Bio-MEMS for Somite

What is INFORMATION in us?

Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

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Pulsatile Secretion of Hormone
Luteinizing
hormone (LH)

InsulinEndocytosis

SignalUbiquitination Degradation
SignalPorksen, Diabetologia, 2002

Guyton & Haul, Textbook of
Medical Physiology, 2005

Cortisol

Ubiquitination

H kkk
R k R*
1

Transcription

timeDegradation

23

Guyton & Haul, Textbook of
Medical Physiology, 2005

Activity-dependent
Inactivation
Hormone Receptors
Hormoneis secretedofpulsatilely

4Expected Response of
Hormone Receptor
Input

Ouputtime

Ueda et al unpublished results

Input
OutputFrequency
Hormone Receptors decode the information encoded in the frequency of signal(i.e. change of signals not strength of the signal)

Quantitative Perturbation by
BIO-MEMS

Computer-controlled
injection of stimulants

System-level Analysis of Cellular Response to the Various Stimulation

Triangle of Technologies
Biological Experiment

Escher , M.C. (1960)“Ascending & Descending ”

Wet

Bio-MEMS

Fluidics Simulation

Penrose’s “Triangle ”

HardSoftHiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

Understanding of Biological Systems
Analysis of “life as it is”
1. Identification
To completely identify system components
and their interactions

Systems Biology
2. Analysis
To quantitatively measure properties of components andpredict the behaviors of biological systems

3. Control
To quantitatively control properties of components anddirect the behaviors of biological systems

Synthetic Biology

4. Design

To design and implement artificial circuits with identified
structure and observed dynamics of biological systems

Synthesis of “life as it could be”
Hiroki R. Ueda, Laboratory for Systems Biology,EscherCDB,, RIKEN
M.C. (1948) “Drawing hands”

世界規模での遺伝子情報の蓄積と共有
世界中の生命科学研究によって得られた分子生物学的知識（遺伝子情報）はデータベースに蓄積され、インターネットを通じて共有されている。

Internet mapDatabase

生命⇒機能⇒物質⇒情報
Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKENCan we design cell?

David S. Goodsell , “E.coli” (1999)

遺伝子情報：ゲノム配列情報
H. sapiens(2001)(2003)

E.coli K12(1997)
E.coli O157:H7(2001)

S. cerevisiae(1997)

S. pombe(2002)

R. norvegicus(2003)
M. musculus(2002)

Oryza sativa L. ssp.
Indica (2002)
Oryza sativa ssp.
japonica (2002)

D. melanogaster(2000)Nature websites

A. thaliana(2000)

2006.11.25
Published 460
Ongoing 998(Bacteria)
Ongoing 631 (Eukaryote)
Ongoing 56 (Archaea)
Total
2,208
Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN
C. elegans(1998)

情報⇒物質⇒機能⇒生命

構造情報:タンパク質の3次元構造

Molecular Structures have been resolved
47,805 structures in Protein Data Bank in 2007

情報⇒物質⇒機能⇒生命
http://www.riken.jp/r-world/research/lab/genome/protein/result.html

情報から物質（遺伝子）へ:遺伝子合成
ゲノム合成は現段階では難しいが複数の遺伝子を人工的に効率よく合成できるようになってきた光によって多種類の短いＤＮＡを人工合成する技術が基盤技術。短いＤＮＡを長いＤＮＡを作るための素材として用いて遺伝子・ゲノムの人工合成を目指す。

Nature 432, 1050-4. (2004)

情報⇒物質⇒機能⇒生命
Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

物質から機能へ：無細胞蛋白質合成系
PURESYSTEM®
Protein synthesis using recombinant elements System

Shimizu Y. et al. (2001) Nature Biotechnology, vol.19, p.751-755.

情報⇒物質⇒機能⇒生命Can we design
memory molecule?

Chromatin fiber model built from
X-ray structure of tetranucleosome

Schalch et.al. Nature 436:138-141, 2005

Can we design
self-replication molecule?

Doublie et.al. Nature 391:251-258, 1998

Can we Design
Protein Synthesis Molecule?

Thermus thermophilus 70S ribosome

Sanbonmatsu et.al. PNAS 102:15854-15859, 2005

Can we Design
Dividing Membrane System?

Growth and division of budding yeast

http://www.marietta.edu/~spilatrs/biol202/budding_yeast.movWhat is LIFE?

Hiroki R. Ueda, Laboratory for Systems Biology, CDB, RIKEN

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