what physicists can do in biology ?
DESCRIPTION
Pik-Yin Lai 黎璧賢 Graduate Institute of BioPhysics & Center for Complex Systems, National Central University, Chung-Li, Taiwan 320 Email: [email protected]. What Physicists can do in Biology ?. http://www.phy.ncu.edu.tw/~ibp/. Physics is vital in breakthrough in life sciences. - PowerPoint PPT PresentationTRANSCRIPT
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• What Physicists can do in Biology ?
http://www.phy.ncu.edu.tw/~ibp/
Pik-Yin Lai 黎璧賢Graduate Institute of BioPhysics & Center for Complex Systems,
National Central University, Chung-Li, Taiwan 320 Email: [email protected]
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Physics is vital in breakthrough in life sciences
• Breakthrough in physical instrument: optical microscope (Hooke, 1665), amplifier, X-ray, electron microscope, MRI, SPM, mass spectrometer, Single molecule microscopy,….
Nobel laureates in physiology/medicine that were physicists/had physics training:• Georg von Békésy (physical mechanism of the cochlea, 1961)• Francis Crick (DNA, 1962)• Alan Hodgkin (nerve cell ,1963) • Haldan Hartline (visual processes in the eye, 1967)• Max Delbrück (bacteriophage , 1969)• Rosalyn Yalow (radio-immunoassays of peptide hormones, 1977)• Werner Arber (restriction enzymes , 1978)• Erwin Neher (single ion channels in cells ,1991)• Peter Mansfield (NMR, 2003)……
Others: Schroedinger, Cooper,…
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• Why BioPhysics ?• Material Nature of Bio-substances affect Bi
ological properties. (Evolution made use of the physical properties of bio-materials)
• Physical principles & Laws holds from microscopic level macroscopic level
• Traditional Biology is descriptive, non-quantitative
What is Biophysics? Biophysical Society defines as: "that branch of knowledge that applies the principles of physics and chemistry and the methods of mathematical analysis and computer modeling to understand how the mechanisms of biological systems work” .
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Why BioPhysics ?
• Physics is universal. • Rise of molecular biology: DNA, RNA, protein, A
TP… are universal in all living matters• Universality in Central Dogma: DNARNApro
teinBiological functions…• New, interesting, exciting & useful.• Lots of unsolved important problems.• Techniques & Methodology in physics can probe
the fundamental principles in bio-systems of a wide spectrum of scales in a quantitative way.
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Era of modern Biophysics• Length Scales:nm m mm cm m kmDNA,RNA,protein, intracellular, virus, bacteria, Intercellular, collective motion, insects, animals/plants, migration
• Time Scales: fs ps s ms s e transfer,H-bonding,water DNA,RNA,protein rearrangement , protein folding DNA transcription
hr day year Byr cell division Earth organisms , animal migration evolution
• Knowledge: Interdisciplinary 跨越各學科領域 MathematicsPhysicsChemistryBiologyMedical BioPhysics Biology + Physics• Biophysicist is a TRUE Scientist ! Explore to the maximum
freedom for doing science! •需要物理與非物理背景人材加入 !
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Elementary particles of Life
• Universal molecules: DNA, RNA, protein, ATP• Interactions giving rise to bio-process: Central Dog
ma: DNARNAproteinBiological functions…• Nanomachines: molecular motors, FoF1 ATPase..• How physical and chemical interactions lead to co
mplex functions in cells ?• Gene networks, protein networks …….
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Double-stranded biopolymer, 2 sugar-phosphate chains (backbones) twisted around each other forming a RH (B-form) double helix.
CellNucleusChromosomeChromatin
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base pairs: A-T & C-G
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Play (Torture) with DNA
• DNA stretching, elasticity• DNA drag reduction• DNA thermo-phoresis• DNA condensation• DNA under external fields• DNA photolysis• DNA ratchet motion• ……..
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Mechanics/Elasticity of Single Bio-molecules
• To investigate the conformational changes in single bio-molecules, may provide significant insight into how the molecule functions.
• How forces at the molecular level of the order of pN underlie the varied chemistries and molecular biology of genetic materials?
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DNA transcription by RNA polymerase
•effect of template tension polymerase activity•Pausing & arrest during polymerase•Mechanism of polymerization kinetics•Tuning rate of DNA replication with external stresses
T7 DNA polymerase
Bustemante et al, Nature 404, 103 (2000)
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Double helix stabilized by H-bonds (bp interactions)
Polymer of persistence length ~50nm under low force (<10pN):Entropic elasticity. Complicated at high forces: cooperative behavior
Elasticity of dsDNA affect its structure and can influence the biological functions
Physicist’s view of the DNA chain
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Rod-like chain model (twisted stiff chain) Marko et al., Science 256, 506, 1599 (94); Bouchiat et al., PRL 80, 1556 (98)
Can account for some supercoiling properties of DNAPhenomenological model, no description of underlyingmechanism.
|t|=1 inextensible
single strand
Worm-like chain model (stiff chain)
Fitting from expts: A=53nm;
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ZZO model for double-stranded DNAH. Zhou, Z. Yang, Z-.c. Ou-Yang, PRL 82, 4560 (99)
=folding angle
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Force ExperimentsStretching a single end-grafted DNA
S-form
B-form
•Abrupt increase of 1.7 times in contour length of dsDNA near 65pN.•Thermal fluctuations unimportant near onset of transition.
B-form to S-form Transition under a Stretching forceB-form to S-form Transition under a Stretching force
Lai & Zhou, J. Chem. Physics 118, 11189 (2003)
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=0.073 =0.075
First-order elongation:Stretch by untwisting
Untwisting upon stretchingUntwist per contour length from BS,Tw/Lo~-100 deg. /nm;•Almost completely unwound ~ 34deg./bp•Torque ~ 60 pN nm
First order phase transition at First order phase transition at tt
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Untwisting upon stretching
•Untwist per contour length from BS,Tw/Lo~-100 deg. /nm;•Almost completely unwound ~ 34deg./bp•Torque ~ 60 pN nm
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Direct observation of DNA rotation during transcription by Escherichia coli RNA polymerase Harada et al., Nature 409 , 113 (2001)
> 5 pN nm from hydrodynamic drag estimate
•DNA motor: untwisting gives rise to a torque
•BS transition provides a switch for such a motor.
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DNA condensation & packing
Complex competition of DNA elasticity, charge interactions, volume interactions, solvent effects…..
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Single-λ DNA with [SPD]=20mM jamming when entering in 0.7% gel
NH3H3N NH2
NH3H3N N
H2
NH3H3N N
H2
Spermidine (SPD)
NH3H3N NH2
NH3H3N N
H2
NH3H3N N
H2
NH3H3N N
H2
NH3H3N N
H2
NH3H3N N
H2
Spermidine (SPD)
E
DNA condensed by spermidine
0.7% agarose gel
DNA
DNA+SPD
+ +++++ +++
- ----- - --
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DNA under external drive
DNA ratchet motion under AC electric field
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Simple to Complex: emerging properties in bio-systems
Couplings, interactions, nonlinearity, feedback… collective behavior
Coupled oscillator networks of Cardic cells: nonlinear dynamics, spiral waves, spatio-temporal patterns…
(I) cardiac cells Heart
Cardiac myocyte Synchronized beating of myocytes
spiral waves:
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Simple to Complex: emerging properties in bio-systems
Couplings, interactions, nonlinearity, feedback… collective behavior
物種之群體運動理論 : 魚群、昆蟲、細菌之習体運動模式
Dictyostelium discodium
(II) Single cell/organismcollective motion
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emerging properties in bio-systems
(III) Neurons Network Brain
Hodgkin-Huxley Model (1952)
Network connection:synapses
Complex behavior/function determined by neuron connections.Complex neuronal Network: •A single neuron in vertebrate cortex connects ~10000 neurons•Mammalian brain contains > 10**10 interconnected neurons•Signal & information convey via neuronal connections—coding
Neuro/cognitive science
Synchronized Firing
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Neuron & Action Potential
Spike: ~ 1 ms, 100mVPropagates along the axon to the junction of another neuron---synapse
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Hodgkin-Huxley model (1952)Expts. On giant axon of squid: time & voltage dependent Na, K ion channels + leakage current
I(t) = IC(t) + Ik(t)
Ik = gNa m3h (u - ENa) + gK n4 (u - EK) + gL (u - EL).
= (u) (1 - m) - (u) m
= (u) (1 - n) - (u) n
= (u) (1 - h) - (u) h
gating variables:
empirical functions
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Schematic procedures in preparing the sample of neuron cells from celebra
l cortex embryonic rats
Embryos of Wistar ratsE17~E18 breeding days
http://mouse.kribb.re.kr/mousehtml/kistwistar.htm
Experiments
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Growth of axon connection to form a network
Typical confocal microscope pictures of cultures used in our experiments. Red: anti-MAP2 (neuronal marker); Green, anti-GFAP (glia marker). Black &white: phase contrast image; Merge of the three images above.
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Optical recording of fluorescence signals from firing network
Firing of the network is monitored by the changes in intracellular [Ca 2+] which is indicated by the fluorescence probe (Oregon Green).
Non-synchronous Firing in early stage of growth
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Synchronized Firing of Neuronal Network Culture
Spontaneous firing of the cultures are inducedby reducing [Mg2+] in the Buffered salt solution
Synchronized Firing at later stage of growth
Firing the changes in intracellular [Ca 2+] indicated by the fluorescence probe.
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Time dependence of the SF frequency for a growing network
•Critical age for SF, tc
•SF freq. grows with time f=fc+fo log(t/tc)
tc
Phys. Rev. Lett. 93 088101 (2004)PRE (2006)
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Onset time for SF as a function ofcell density
•Critical age for SF
•f=fc+fo log(t/tc)•f increases with the effective connections• fc is indep. of
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Synchronous firing frequency f ~ mean connectivity k
• Well fitted by taking f ~ a + b k, with a small. • f ~ k
Use synchronized firing freq. to probe theGrowth behavior of the network
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Manipulating/attacking the neuronal network
Monitor
CCD雙軸微步進馬達控制器
雙軸微步進馬達
分光鏡
1 : 1 telescope
Infrared Laser1064 nm
He-Ni Laser
分光鏡
Objective
Sample
Microscope
Optical Tweezers
Tailoring network regions by UV lasers
Network attack: random or target attackNetwork robustness Regenerative & Re-routing behavior
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Biological implications
• Active growth in early stage, retarded once goal is achieved.
• Slowing down to maintain a long time span for function: homeostasis
• Continuing fast growth used up energy • Too much connections may exceed
information capacity for a single neuron
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Many Spikes in one pulse: Bursting
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Electrophysiology measurement (whole-cell recording, current-clamp)
0
-60
mV
2 s
Glia and neuron mixed culture (8DIV, 5X105)
Inter-burst synchronized , but intra-burst is NOT synchronized
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• What Physicists can do in Biology ? a lot of interesting and unexplored science
from molecules to collective behavior of organisms
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AcknowlegementsAcknowlegements
Collaborators• C.K. Chan ( 陳志強 ) (Academa Sinica)• L.C. Jia 賈魯強 (Yuanpei Univ.)• Z.C. Zhou 周子聰 (Tamkang U.)• Students: Y.S. Chou, H. H. Chang, C. R. Han, S.F. Hsu• Postdocs: E. Avalos, J. Benoit
SupportNational Science Council, TaiwanBrain Research Center, U. Systems of TaiwanAcademia Sinica, Taiwan