AGRO/HORT/BOTA 339:

Plant biotechnology principles and techniques I

 

Syllabus (download PDF)

 

Course Objective

To provide a practical experience in the major techniques used in plant genetic analysis at the molecular and bioinformatic levels.

 

Textbook

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.

 

Prerequisites

Botany/Zoology 152 or equivalent

Chemistry 104 or equivalent

Credits: 4cr

Instructors

Professor                                                     

Jean-Michel Ané                                      

Office: 348 Plant Sciences             

Email: jane@wisc.edu  

Phone: 262-6457   

 

Office hours

MF 1:30-2:30 and by appointment

Schedule

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

Supplies needed: textbook only

How Your Grade Will Be Determined?

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%

 

Laboratory evaluation

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.

 

Group presentations

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.

 

Policies on Testing

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.

 

Feedback on the Course

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 

 

 Pictures of the 2005 course

Pictures of the 2006 course

 

 

We hope that you will find this site useful. Please send any questions, suggestions or comments to: Jean-Michel Ané