introduction to the laboratories of bio and soft-matters 陳志強 中央研究院物理研究所...
TRANSCRIPT
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Introduction to the Laboratories of Bio and Soft-matters
陳志強中央研究院物理研究所
中央大學生物物理研究所
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Content
• Overview of Biophysics in Academia Sinica (15 min)
• Laboratory of Soft and Biomatter (30 min)
Effects of Conformations of DNA onsome Physical and Biological Problems
Communications in Excitable Networks
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Institute of PhysicsAcademia Sinica
• Theory / High Energy• Nano/Surface• Complexity
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Research Opportunities in Academia Sinica
• 李世炳 - System Biology• 梁鈞泰 - Flocking• 周家復 - Nano/Bio devices• 林耿慧 - Self-Assembly• 阮文滔 - Single molecule DNA• 陳彥龍 - Single DNA in Microfluidics• 李定國 - Protein folding• 胡進錕 - Protein folding, DNA and etc
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Laboratory of Bio and Softmatters
• Softmatter -- de Gennes in the 90s• Energy comparable to KT, many degree of
freedom (complexity)• Nonlinearity and Cooperativity
• Polymers - proteins, DNA• Networks - polymers, bio-chemical reactions, cells and neurons
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People Involved
陳志強 * 黎璧賢 ( 中大 )
賈魯強 ( 元培 )
• Lab: 519 (NCU)
Lab: 320 (Academia Sinica)
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Nonlinear Phenomena fromSoft-matters
Effects of Conformations of DNA onsome Physical and Biological Problems
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Turbulent Drag Reduction by Polymers
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Passive Drag Reduction Change of B.C.
Drag Reduction = less dissipation by turbulence
Shark Skin Swimming Suit Airplane Skin Coverage
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Trans-Alaska Pipeline (internal flow)
1287 Km5~25ppm Injected every 100Km25%DR up to D=1.2m
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Why DNA ?
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Structure of DNA
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Why DR with DNA ?
1.DNA is very long - can be much longer than
2. DNA processes secondary structure
- elastic properties different from polymers
3. Structure can be changed by pH or temperature
- Good probe for turbulence ?
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Setup
(1) Motor (2) Flexible couple ring (3) Torque sensor(4) Fluid container (5) Rotating disk
(1)
(2) (3)
(5)(4)
Lambda DNA
- Promega Corporation / U.S.A.
- Size: 48,502bp
- Commonly used substrate in
restriction enzyme activity assay.
- Storage: –20℃- Concentration of stock solution: 515
g/ml
Buffer solution
- 10mM tris-HCL (pH 7.8 at 25 ), ℃10mM NaCl and 1mM EDTA.
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Torque Measurement
The Shaft torque measurement for buffer solution and 1.35 wppm solution of lambda DNA in continuous mode rpm sweep at 25℃. (sweep rate;
20rpm/sec)
500 1000 1500 2000 25002,000
3,000
4,000
5,000
6,000
7,000
8,000
9,000
10,000
Date : 2000. 2. 23Sample : -DNA (1.35ppm)Apparatus : 370ml RDA
Temp.: 25oCRPM: 500~2500 RPMSweep rate : 20rpm/secN
RE=250000~1300000
Buffer solution DNA 1.35ppm
To
rqu
e
RPM
Torque Variation
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Only L/2 degradation
The electrophoresis result of lambda DNA after degradation for 1 hour at 1,980 rpm, 25℃.
Electrophoresis
23.1Kp
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Packing of DNA
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What is Spermidine?
J Biol Chem. 2004 Oct 1;279(40):42041-54. Epub 2004 Jul 28.
A,three phosphates adjacent from the samestrand of the major groove.
B, intrastrand across the major groove.
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Physiological role of polyamines
• First discovered in human seminal fluid
• Nucleic acid packaging, DNA replication
• Transcription and translation
• Ubiquitous in many cellular processes
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(N-[3-Aminopropyl]-1,4-butanediamine)
Trihydrochloride
C7H19N3·3HCl FW 254.6
Coil-to-Globule Transition in
duced by Spermidine (SPD)
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)
Poor Drag ReducerGood Drag Reducer
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Summary of DR
• Only a few %DR by improvement of wall properties
• a few ppm of additive of long chain polymers in turbulent flow can produce a max of 80% DR
• Polymers broken (degraded) by turbulence
• NO BASIC UNDERSTANDING YET !
• DNA might provide a good probe for turbulence
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Summary
• Many nonlinear effects induced by the conformation of DNA
• Turbulent Drag Reduction
• Coil-Globule Transition
• Structure and Packing of DNA
• Effect of conformation of the transcription of DNA
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Complexity from Bio-matters
Communications in Excitable Networks
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Life Cycle of Slime Mold
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Aggregation of dicty
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Chemotaxi and cAMP
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Waves of cAMP
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Periodic Motion of Cells
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The Physics of Excitable Systems
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What are excitable systems?
• Unstable state with respect to large perturbations
• Excitatory and Inhibitory states
• Examples:– BZ reactions– Slime molds– Heart muscles– Neurons
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Scaling in Slime Mould ?
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High density
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Low density
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Distribution of Slugs
- Culture with different densities
- Harvest after 36 hour
-Digital pictures
- Population Regulation self-similar shape V = A*L but A = aL
V = bA3/2
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Density dependence of Slug size
Upper critical size
Lower critical size
V ~ Alog(cr)V0
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Exponential Distribution at high density
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Power law distribution in low density?
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Leo Glass, Physics Today , Aug. 1996。
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Spiral Waves
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Spirals in Cardiac cell cultures
Lee et al PRL, 92, 198103, 2005
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Cardiac Cultures
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Early Beatings
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Synchronized Traveling Wave
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Cardiac-Neuron Co-culture
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Cardiac-Neuron Co-culture
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Cardiac-Neuron Co-culture
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Scale-free network
Poisson distribution
Exponential Network
Power-law distribution
Scale-free Network
AirlinesHighway
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Summary
• Biophysics Understanding of Biological Nonlinearity and Complexity in terms of Physical Principles
• Physics of Polymers and Networks of Excitable Systems
• DNA Slime Mould Heart Brains
• Both fundamental and applied problems
• NCU/Academia Sinica Best Combination in Taiwan