Syllabus for: PLB 571-4 Genomics of Eukaryotes (Same as PSGA 570-4)

Fall 2004

4 CREDIT HOURS 

Prerequisites: 400 course in genetics, biotechnology, biochemistry or consent of instructor. 

Instructors: David A. Lightfoot, PPI 113 & Guest Lecturers 

       Genomics, Proteomics and Bioinformatics are rapidly making important contributions to the Life Sciences through biotechnology. An appreciation of the genomic tools is important to all in agriculture and biology. The relationships between plant molecular biology and the biotechnology industry will be explored. Short independent practical projects in genomics, proteomics or bioinformatics will be pursued.  

Objectives:

1. Gain an understanding of genomics, proteomics or bioinformatics.
2. Study the relationship between genomics and biotechnology.
3. Understand the gains attainable through genomics, proteomics or bioinformatics.
4. Appreciate the nature of  social concerns over Genomics. 

Required Text: “Statistical Genomics” Ben Hui Liu,
CRC Press $60. ISBN 0-8493-3166-8 

Selected Readings from:
A, Original References.
B, "Bioinformatics" by D. Mount, CSHP $60 ISBN 0-87969-608-7   

Basis for Grading:
Lectures total                            - 70% of grade
Test after 5 weeks                    - 20%.
Test after 10 weeks                  - 20%.
Final Exam                               - 60%. 

Laboratories total                     - 30% of grade
Experimental Design                 - 30%
Practical Project                       - 40%
Laboratory Notes                     - 30% 

Grading Scale:            100-91% A

                                     90-81% B

                                     80-71% C

                         70-69% D
 

   % OF    
   TIME        TOPICAL OUTLINES
 

5                 INTRODUCTION
                   Historical Perspective
                   Genomics.
                   Protemics
                   Bioinformatics.  

5                 BIOLOGY IN GENOMICS
                   Mendelian Genetics and Cytogenetics
                   Population Genetics
                   Quantitative Genetics
                   Molecular Genetics 

10                INTRODUCTION TO GENOMICS
                    Genomes
                    Biological Techniques in Genomics
                    Mapping Populations
                    Genetic Markers           

10                              GENETIC MAPPING
                   Family Studies
                   Complex Traits
                   Genetic Maps
                   Identification of DNA polymorphism
                   The importance of SNPs
                   DNA typing; Pharmacogenomics.

5                 PHYSICAL MAPPING
                   Cytogenetics
                   Chromosome painting and FISH
                   Micro-dissection and Flow sorting.

15               PHYSICAL MAPPING
                   Gene Isolation
                   Long Range and Global Physical Mapping
                   Integration of Genetic and Physical Maps
                   Isolation of genes  from genomic DNA; by cDNA; exon traps; gene prediction.
                   Transient expression of Transgenes
                   DGGE  in mutation detection 

10               DNA SEQUENCING
                   Sequencing Strategies
                   Templates
                   Chemistries
                   Labelling and Detection
                   Future Methods. 

10               FUNCTIONAL ANALYSIS with cDNA
             DNA Chips
             Expression Analysis
             Bionformatics for large data sets 

10                 MODEL SYSTEMS
              Mouse
              Human
              Drosphila
              Nematodes
              Arabidopsis
              Rice
              Soybean 

10                PROTEOMICS
              2-D Gels
              ES and MALDI-TOF MS
              Antibody applications
              Future Prospects 

10                BIOINFORMATICS- INTERNET RESOURCES
              Databases and Genome Resource Centers
              Self Instructional Courses.