2005年度シラバス (Syllabus 2005)

ナノバイオロジー (Nanobiology)

===== Japanese Version =====

(1)科目名：　次世代志向境界領域 I ~ V，　ナノバイオロジー
(2)科目名（英訳）： 
Perspective of Frontiers ｡-･  Nanobiology
(3)単位数：　0.5単位
(4)実施学期：　後期（後半）
(5)曜日：　月曜日
(6)時間：　10:50-12:30
(7)配当年次：1~5 
(8)授業内容と授業計画
（授業内容）
ナノバイオロジーとは、 
生物現象を分子の動きと形として理解する生物学です。
嶋本はその最初の提唱者の一人です。その目標は、ミクロ世界の分子運動が
そのままマクロな生物で働く調節機構となっていることを解明することで、
１分子ダイナミクスを分子生物学と組み合わせて行います。もし、その機構を
バイオテクノロジーとして応用すると、ボトムアップのナノバイオテクノロジー
ともなります。
（授業計画）
日程、講師、テーマ・内容・内容の詳細は英文を参照してください
(9)単位の修得要件、成績評価基準・方法
出席とレポートで評価する
(10)参考書、教材
ナノバイオ入門　（新生命科学ライブラリ）サイエンス社 2005
ナノバイオロジー入門　講談社サイエンテフィク 1994
Biological 
molecules in nanotechnology: The convergence of biotechnology, 
polymer chemistry and material science.  Stephen C. Lee ed. IBC 
Library Series, IBC, 1998 (This is a book on the idea of bottom-up 
nanotechnology.)
(11)講師連絡先
遺伝学専攻　教授　嶋本伸雄　（科目責任者）
（国立遺伝学研究所G309　電話055-981-6843　nshima@lab.nig.ac.jp ） 
質問はe-mail かe-mailで調整した時間の面談を歓迎します。
 (12)履修上の注意等
Web-directed display であるWebLSを用いる予定で、メモ以外のノートを取る
必要はほとんど無く、表示と講義では説明しきれなかった教材がuploadされている。
出席者全員が日本語を主言語とする場合を除き、英語を主言語とする。
ただし、質問は日本語でも受け付ける。
（13）他専攻からの聴講と単位の取得本講義は，総研大のすべての研究科の大学院生
および研究生の聴講を許可する。要件を満たせば所定の単位も取得できる。

===== English Version =====

(1) Course Title (in Japanese): 
 Jisedai Shikougata Kyoukairyouiki I-V, Nanobiology
(2) Course Title (in English): 	Perspective of Frontiers I-V, Nanobiology
(3) Credit: 0.5 
(4) Term:   Winter
(5) Day of the Week:  Monday
(6) Time: 10:50〜12:30
(7) Appropriate Year Level:1st, 2nd, 3rd, 4th, 5th
(8) Contents and Schedule
（Contents）
Nobuo is one of the 
members who first proposed "nanobiology" in 1993. Nanobiology is 
defined as analysis of phenomena where the microscopic movements of 
bio-macromolecules are directly reflected in macroscopic mechanisms 
of gene regulation and other cell physiology.  The main technique 
used is the single-molecule dynamics and analyses combined with 
molecular biology, which is also used in biological nanotechnology. 
Therefore, nanobiology becomes the bottom-up type of biological 
nanotechnology, if applied to create nano-devices.    

（Course Sched） 
1.  Nov 28 
Chapter 1 Nanobiology and nanotechnology: their histories and concepts 
Chapter 2 Nanobiomachines and their differences from artificial machines

2,3.  Dec 5, 12 
Chapter 2 (continue)
Chapter 3 Experimental techniques in nanobiology 

4.Dec 19
Chapter 4 Techniques along time axis 
Chapter 5 Nanostructures and nanomechanics

(9) Grading
Attendance and reports
(10) Textbooks and References
Biological molecules in nanotechnology: The convergence of biotechnology, 
polymer chemistry and material science.  Stephen C. Lee ed. IBC Library Series, IBC, 
1998 (This is a book on the idea of bottom-up nanotechnology.)
(11) 
Contact Address of Lecturers
Nobuo Shimamoto. Professor, Department of Genetics　[Organizer]
（Room G309, 055-981-6843 nshima@lab.nig.ac.jp）
I prefer questions by e-mail or in interviews arranged by e-mail.
(12) Special Notes
A web-directed display, WebLS 
is used in the lecture and thus you may repeat my presentation and 
consult with related materials that I don・t have time to explain in 
my lecture by yourself.  Therefore, you may not need to make a 
detailed notes.  This lecture will be given in English unless all the 
attendants are Japanese.  
(13) Attendance from other Sokendai 
Departments
This lecture is open to graduate students and research 
students of all the Sokendai schools. One can receive the course 
credit upon satisfying the necessary grade conditions.


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Chapter 1 Nanobiology and nanotechnology: their histories and concepts
1 Period of establishing concepts
2 Methodology period
3 The emergence of structural biology
4 The best examples of structural biology
5 Birth of nanobiology
6 Scales and techniques
7 Development of nanobiology
8 Streamlines into biological nanotechnology 
9 Concept of Mode 2 
10 References of Chapter 1

Chapter 2 Nanobiomachines and their differences from artificial machines
1 Thermal motions of nano-biomachines
2 Dilemma of nano-biomachines
3 Hint given by the structure of Tus-ter complex
4 Secret of nano-biomachine 1
5 Hidden energy for determinated motion
6 An enzyme must turn over
7 Turnover and concerted actions of nano-biomachines
8 A secret of nano-biomachine２
9 Deterministic switches in reactions
10 Sigmoid curve generated in multiple-binding
11 Example of cooperative binding: fx174 bacteriophage
12 Positive cooperativity by multiple reaction steps   
13 Single-stranded bacteriophages with no sigmoid
14 Solution of the dilemma of nano-biomachine

Chapter 3 Experimental techniques in nanobiology
1 Planar technology on silicon, glass and resins
1-1 Etching
1-2 Integrated harden process
1-3 Examples of MEMS
2 Scanning probe microscopy
3 Optical techniques
3-1 Principle of Lasers
3-2 Common Lasers
3-3 Laser Trap 
3-4 Comparison between AFM, EM and laser trap
3-5 Abbe’s Law
3-6 Beyond the optical limit
3-7 Detection of light
3-8 comparison of light detectors
4 Electric methods
4-1 Difference between electrophoresis and dielectrophoresis
4-2 Application of electric methods
4-3 Now making analogue circuit is so simple.
5 Molecular imprinting
6 Micro-contact printing
7 DNA techniques
8 RNA techniques
8-1 Functional RNA: Riboswitches
8-2 SELEX Systematic Evolution of Ligands by EXponential enrichment
8-3 Molecular mimicry: a freedom of materials

Chapter 4 Techniques along time axis
1  Temporal changes and their time ranges
1-1 Kinetic hypothesis
2  Local Equilibrium
3  Local equilibrium denies local concentration
4  Crowding effect
5  Transition state theory
6 Single-molecule dynamics
6-1 Studying mechanisms working in cis
6-2 Use of single-molecule dynamics for kinetics?
6-3 Correct use of single-molecule dynamics for kinetics
7 Fluorescent techniques
7-1 Green Fluorescent Protein
7-2 Quantum dots
7-3 Fluorescent anisotropy
7-4 FRETFluorescence resonance energy transfer
7-5 FCS Fluorescence correlation spectroscopy 
7-6 FCCS Fluorescence cross-correlation spectroscopy 
7-7 FLIM Fluorescence lifetime imaging microscopy
7-8 FRAP Fluorescence recovery after photo-bleaching

Chapter 5 Nanostructures and nanomechanics
1 Nano-Gold
2 Carbon nano tube(CNT) and Fullerene 
3 Nanoshells
4 Liposome
5 Cell Surfaces
6 Ribosomes
7 RNA polymerase
7-1 Bridge helix for translocation
7-2 Two models for translocation
8 Loose coupling vs. tight coupling
9 Nanomechanics and force measurement 

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