Transcript Chapter 8

Chapter 8 New Research Field in
Molecular Biology
8.1 Bioinformatics
1.
What is bioinformatics?
Bioinformatics and computational biology
involve the use of techniques including applied
mathematics, informatics, statistics, computer
science, artificial intelligence, chemistry, and
biochemistry to solve biological problems
usually on the molecular level.
2. Major research fields
(1) Sequence analysis
(3) Computational evolutionary biology
(4) Measuring biodiversity
(5) Analysis of gene expression
(6) Analysis of regulation
(7) Analysis of protein expression
(8) Analysis of mutations in cancer
(9) Prediction of protein structure
(10) Comparative genomics
(11) Modeling biological systems
(12) High-throughput image analysis
3. Databases
BLAST ACCESS
dbEST / Expressed Sequence Tags database
ceDB databases
 Phenotypic databases
LIMS
BASE
MOLCAS
……..
8.2 Proteome & Proteomics
1. What is Proteome?

Proteome - All the proteins expressed by a
cell , tissue or organism at a particular time
and under specific conditions.
2. What is Proteomics?

Proteomics is the systematic study of all of the
proteins in a cell, tissue, or organism. The
analysis includes the identification, expression,
localizations, functions (physiological and
pathophysiological functions), and interactions
of proteomes.
4. Branches of Proteomics

Expressional Proteomics

Functional Proteomics

Structural Proteomics
Protein Microarrays
蛋白质芯片的意义
用于构建蛋白质表达谱,
 进行抗原-抗体筛选,
 药物靶点筛选,
 蛋白质-蛋白质交互作用筛选等
 是蛋白质组进行功能分析的新技术

一个芯片上可以容纳

一种蛋白质的所有变异体

一个蛋白质家族的所有成员

一条信号通路中的所有蛋白质

一种组织、器官或有机体的所有蛋白质
Different Kinds of Protein Arrays
Antibody Array
Antigen Array
Ligand Array
Detection by: SELDI MS, fluorescence, SPR,
electrochemical, radioactivity, microcantelever
蛋白质芯片检测


无探针标记检测法
探针标记检测法
同位素标记检测
荧光标记检测
化学发光检测
酶免疫标记检测
表面增强激光解吸离子化技术
(Surface enhanced laser
desorption/ionization, SELDI)
表面等离子体共振检测技术
（surface plasmon resonance, SPR）
原子力显微镜检测技术
（atomic force microscope, AFM ）
胶体金标记检测
蛋白质芯片的应用
疾病诊断和预警
药物开发
蛋白质组学
Problems

Expensive

Standard

Specificity

Sensitivity
Functional Proteomics (in vitro)
Multi-well plate readers
 Full automation/robotics
 Fluorescent and/or chemi-luminescent
detection
 Small volumes (mL)
 Up to 1536 wells/plate
 Up to 200,000 tests/day
 Mbytes of data/day

In silico methods (bioinformatics)
 Genome-wide Protein Tagging
 Genome-wide Gene Deletion or Knockouts
 Random Tagged Mutagenisis or Transposon
Insertion
 Yeast two-hybrid Methods
 Protein (Ligand) Chips

Structural Proteomics
High Throughput protein
structure determination via
 X-ray crystallography
 NMR
 spectroscopy
 comparative molecular
modeling
Structural Proteomics: The Goal
Why Structural Proteomics?

Structure
Function

Structure
Mechanism

Structure-based Drug Design

Solving the Protein Folding Problem
Bioinformatics & Proteomics
Agriculture
Medicine
Bioinformatics
Proteomics
Genomics
8.3 Metabonome & Metabonomics
1. What is Metabonome ?
- It refers the complete set of
metabologically regulated
elements in cells.
2. What is Metabonomics
Metabonomics is the branch of science
concerned with the quantitative understandings of
the metabolite complement of integrated living
systems and its dynamic responses to the changes
of both endogenous factors and exogenous factors.
代谢组学的中心任务：
 对内源性代谢物质的整体及其动态变化
 对规律进行检测，量化和编录
 确定此变化规律和生物过程的有机联系
代谢组学的应用
 疾病诊断
 药物的疗效和毒性评价
 植物的细胞代谢组学评价
By the end...
Systems Biology
Final Exam