Syllabus (download PDF)
To provide a practical experience in the major techniques used in plant genetic analysis at the molecular and bioinformatic levels.
Analysis of genes and genomes. 2004. Richard J. Reece. Ed. Wiley. ISBN 0-470-84380-2.
Required readings will be assigned from this textbook. Please bring your textbook to all lectures. A copy will also be on reserve at the library.
Botany/Zoology 152 or equivalent
Chemistry 104 or equivalent
Professor
Jean-Michel Ané
Office: 348 Plant Sciences
Email: jane@wisc.edu
Phone: 262-6457
MF 1:30-2:30 and by appointment
LEC 11am-12:15 pm T/R 136 Plant Sciences
LAB1 1:20-4:20 pm W 136 Plant Sciences
LAB2 1:20-4:20 pm R 136 Plant Sciences
Mid-term exam 1 8%
Mid-term exam 2 8%
Presentation 8%
Laboratory reports 48% (12 evaluations, 4% per report)
Lectures final exam 8%
Lab final exam 20%
The laboratory evaluations will be based on the manipulations and the laboratory report. The report must be returned to the instructor at the beginning of the next lab course. If the report is not returned on time, no points will be counted for the corresponding lab course.
Each student will make a 10 minutes presentation of a technical article to the class. This presentation will be followed by a 5 minutes discussion with the class. The date and of the article are randomly assigned by the instructor.
Tests will be closed book unless otherwise stated prior to the exam. Tests will generally consist of short answer and essay questions and problems/calculations. Material covered in labs and in assigned readings is considered fair game for tests. Tests outside of regularly-scheduled class period will not be given.
Conversations about how to improve the course or any problems that you may have are welcome anytime.
|
Week |
Topics |
Textbook |
|
1 |
LEC Sept 4: Plant biotechnology Principles and Techniques: what, why, how… LEC Sept 6: From DNA to proteins LAB Sept 5 or 6: Lab safety, notebook, measurements, pipette exercises and basic laboratory sterile techniques (No evaluation of the lab report) |
NONE |
|
2 |
LEC Sept 11: Genes and expression LEC Sept 13: Genes and genomes LAB Sept 12 or 13: Plant genomic DNA isolation and DNA quantification techniques |
Chapter 1 |
|
3 |
LEC Sept 18: Recombinant DNA technology LEC Sept 20: The basics of cloning LAB Sept 19 or 20: Basic bacterial culture techniques (growth, selection, pure culture isolation, cryostorage, inoculation of liquid media and plates). Plasmid DNA isolation |
Chapter 2 |
|
4 |
LEC Sept 25: DNA sequencing and databases LEC Sept 27: Bioinformatics (Midterm exam 1 covers up to here) LAB Sept 26 or 27: DNA restriction analysis, cloning of restriction fragment and transformation of E. coli agarose gel electrophoresis |
Chapter 3 |
|
5 |
LEC Oct 2: Polymerase Chain Reaction (PCR) and applications Oct 4: MIDTERM EXAM 1 ON LECTURES LAB Oct 3 or 4: Designing PCR primers and PCR based screening of colonies and amplification of gene |
Chapter 4 |
|
6 |
LEC Oct 9: Monitoring gene expression LEC Oct 11: Vectors and libraries LAB Oct 10 or 11: Plant RNA extraction, RNA gel and quantification. Reporter gene technology (Green Fluorescent Protein and lacZ) |
Chapter 5 |
|
7 |
LEC Oct 16: Forward genetics (1/2) (Muthusubramanian Venkateshwaran) LEC Oct 18: : Forward genetics (2/2) LAB Oct 17 or 18: Semi-quantitative RT-PCR. Bioinformatic analysis of DNA sequences (sequence alignments, databases, BLAST). Analysis of T-DNA mutants. |
Chapter 6 |
|
8 |
LEC Oct 23: Reverse genetics (1/2) LEC Oct 25: Reverse genetics (2/2) LAB Oct 24 or 25: PCR based Site Directed Mutagenesis |
Chapter 7 |
|
9 |
LEC Oct 30: Information from a cloned gene LEC Nov 1: Protein expression, purification and analysis (1/2) (Midterm exam 2 covers up to here) LAB Oct 31 or Nov 1: Protein extraction, quantification and SDS-PAGE |
Chapter 8 |
|
10 |
LEC Nov 6: Protein expression, purification and analysis (2/2) (Muthusubramanian Venkateshwaran) Nov 8: MIDTERM EXAM 2 ON LECTURES LAB Nov 7 or 8: Western blot and Reverse genetics |
NONE |
|
11 |
LEC Nov 13: Post-translational modifications (Article for presentation assigned) LEC Nov 15: DNA fingerprinting LAB Nov 14 or 15: Genetic maps and RAPD as molecular marker |
Chapter 9 |
|
12 |
LEC Nov 20: Genome mapping NO LAB THANKSGIVING |
Chapter 10 |
|
13
|
LEC Nov 27: Using mutants to clone genes LEC Nov 29: Microarrays LAB Nov 28 or 29: Gene prediction programs. Integration of genetic and physical maps |
Chapter 11 |
|
14
|
LEC Dec 4: Group presentations LEC Dec 6: Group presentations LAB Dec 5 or 6: Bioinformatics, proteomics and genomics tools |
NONE |
|
15 |
LEC Dec 11: Group presentations LEC Dec 13: Group presentations LAB Dec 12 or 13: Molecular phylogenetic techniques (No evaluation of the lab report) |
NONE |
|
16 |
FINAL EXAM ON LECTURES LAB FINAL EXAM |
NONE |
We hope that you will find this site useful. Please send any questions, suggestions or comments to: Jean-Michel Ané