一、課程簡介:
To introduce graduate students with techniques being utilized to study functional genomics. Let graduate students have a simple appreciation on what functional genomics is and how to utilize the techniques in animal research and current development of biotechnology. The class will emphasize on the basic threory behind each of the techniques and the application of the techniques in animal research.
課程大綱：
1. Functional genomics: approaches and methodologies
1). Introduction: functional genomics
2). Current methods in functional genomics
3). Future developments in functional genomics

2. Construction of a EST library as a functional genome establishment
甲、 Total RNA extraction and mRNA purification
乙、 Reverse transcription
丙、 Double strand DNA
丁、 Ligation
戊、 Transformation
3. Construction and screening of a subtractive cDNA library
1). Introduction
2). Deoxyribonuclease-free and ribonuclease-free conditions
3). Preparation of nucleic acid probes for subtractive hybridization
4). Subtractive hybridization
5). Construction of subtractive cDNA library

4. Identification of differentially expressed genes by suppression subtractive hybridization
1). Introduction
2). The principle of SSH
3). Preparation of the subtractive cDNA library
4). Differential screening of the subtracted cDNA library
5). Conclusions
5. Differential display analysis of alteration in gene expression
1). Introduction: Differential display
2). Principle of Differential display
3). Methods
4). Practical considerations for Differential display
6. Representational difference analysis of cDNA
1). Introduction
2). Principles of cDNA RDA
3). Experimental design
4). Application of cDNA RDA
5). Modifications to cDNA RDA
7. Gene expression analysis by cDNA microarrays
1). Introduction to cDNA microarray technology
2). Preparation and printing of target DNA
3). Labelling and hybridization of complex cDNA probes to arrayed targets
4). Generation and analysis of image data
5). Future directions
8. SADE: a microassay for serial analysis of gene expression
1). Introduction and overview
2). Tissue sampling and mRNA isolation
3). First and second strand synthesis
4). Linker design, preparation, and ligation
5). Data analysis

9. Analysis of gene expression by two-dimensional gel electrophoresis
1). Introduction
2). Basic methods for running 2-D gels
3). Special techniques for detection of differential gene expression
4). Pattern analysis and spot assignment
5). Troubleshootings

10. Proteome research: methods for protein characterization
1). Introduction
2). Western blotting
3). Edman protein microsequencing
4). Proteinase cleavage, clean-up, and preparation for mass spectrometry
5). Mass spectrometry

11. Data sorting
1). On line data base
2). Blast analysis
3). Fast local alignment for gigabases (FLAT)

The course is designed to familiarize students with techniques that are used in functional genomics research. We will base the course on a real research project. In this course, each student will be assigned to a research project that will start with a technique called suppression subtractive hybridization to study the genes that are differentially expressed in two experimental treatments. You will get the chance to practice techniques that associate with this type of research. For instance, RNA extraction, mRNA purification, reverse-transcriptase reaction, PCR, suppression subtractive hybridization, and if you are lucky, you might have a chance to practice cDNA library construction and full length cDNA cloning. Of course some of the basic techniques, e.g., northern analysis and gene transformation will be necessary. Beside the techniques that you can practice, we will discuss your projects on a timely basis. Therefore the discussion in class is essential for the class and will be a big part of the course evaluation. You will be assigned to present one of the techniques and host a discussion session for the class. The course will have many short or long lectures with real working hours in the lab. The lecture length depends on the need of in-lab experiment. Everyone is required to attend the class and the lab period, so think about it before you take the course. There will be at least 3 hours of time including the discussion and the lab session. Your time in the lab will depend greatly on your planning and execution of the techniques, so think ahead.
Ideally, two people will work as a group and you will choose a project for this semester’s technique learning and a technique to discuss.
You will be evaluated based on your involvement in class discussion (30 %), your presentation and discussion session (30 %), and your final results for your project. And yes you are right there is no exam in this course. Hope we all learn well.

二、先修課程:Biochemistry, Molecular biology

三、參考書目:1. Hunt, S. P. and R. Livesey, 2000. Functional genomics. Oxford University Press. New York.
2. Starkey, M. P. and R. Elaswarapu, 2001. Genomics Protocols. Humana Press. New Jersey.
3. Innis, M. A., D. H. Gelfand, and J. J. Sninsky, 1999. PCR application. Protocols for functional genomics. Academic Press. San Diego.