CE 60370 Advanced Techniques in Environmental Biotechnology

Fall 2008

Course Syllabus

Meeting Time: Monday and Wednesday 10:00 - 11:15 AM

Classroom: B18 Fitzpatrick

Instructor: Robert Nerenberg

E-mail: Nerenberg.1@nd.edu

Office phone: 631-4098

Office location: 163 Fitzpatrick Hall

Office hours: Stop by, or by appointment

Required background: Basic knowledge of environmental chemistry and microbiology

Reading: From literature

Purpose of course: This class will train students in the theory and application of key experimental techniques for environmental biotechnology research. The class will mainly be lab-based, but will involve a significant amount of independent reading and method development on behalf of the students.

Learning objectives: Following this class, the student should be able to design and implement experiments involving one or more advanced techniques for environmental biotechnology research. They also should be able to interpret results.

Class format: Mainly independent research, experiments in lab, lectures/presentations by professor and students.

Summary of Topics covered

Each student will carry out a literature review and develop a protocol for one of the following techniques. Each student will learn to implement each techniques covered in class. Proposed techniques include:

• Identification of mixed microbial communities using PCR-DGGE or cloning and sequencing
• Detection of gene expression via mRNA
• Fabrication and use of liquid ion-exchange microsensors for measurement of ammonium, nitrite, and nitrate in biofilms
• Identification of bacteria with fluorescence in-situ hybridization (FISH)
• Quantitative determination of microbial abundance and gene regulation with real-time PCR.

Grading: The students will be graded based on their written protocol and their presentation to the class.