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ChE 450-A/550-A

Engineering and Molecular Biology Techniques

SPRING 2004

Instructor.  Lars Angenent, Ph. D.

Environmental Engineering Science Program and Department of Chemical Engineering

phone: 314-935-5663 ; e-mail: angenent@seas.wustl.edu

Location of class: Whitaker Hall, 216.

Time of class: Tuesdays and Thursdays from 10:00 am – 11:30 am.

Office Hours: Wednesdays: 2:00 – 4:00 pm.  Please contact me via e-mail if you need to see me at a different time.  I want to discourage you to walk in at anytime, because I plan my days to work on specific tasks.

Pre-requisite.  A biology or microbiology course, or equivalent, or permission of instructor.

Course Description. Molecular techniques that target cellular compounds, such as DNA, RNA, proteins, etc., are now not only used by scientists in the field of life sciences, but also by scientists in the field of engineering.  These techniques (e.g., polymerase chain reaction [PCR], restriction fragment length polymorphism [RFLP], membrane or slot-blot hybridization) have shown to be helpful for the research of engineers to unravel mechanistic problems in biological systems.  This course will first tackle basic (micro)biology knowledge that is needed to understand the mechanisms of molecular techniques.  Next, the course will teach an in-depth techniques-based assessment of the molecular techniques that are currently being used.  In addition, a group-based approach will be encountered in the lab to perform fluorescence in-situ hybridization (FISH) tests on a biological sample of choice.  After taking this course you should be able to critically read and evaluate scientific papers that show results obtained with molecular techniques from biological engineered systems.  More specifically, you should be able to know the limitations of the utilized techniques and be able to give other techniques that may complement or improve the knowledge gained from the study.

Required Text.  Analysis of Genes and Genomes, John Wiley and Sons, Ltd, Chichester, West Sussex, England.

In addition to the textbook, several handouts and papers will be used as reading assignments or study material.  Such materials will be posted on the web and will be password protected.  The password will be given to you at the beginning of the course.  The following books will be available in Kim Coleman’s office in Cupples II, 208:

  • Brock Biology of Microorganisms, tenth edition, Madigan, Martinko, and Parker, Prentice Hall, Pearson Education, Inc. Upper Saddle River, NJ.
  • Environmental Molecular Microbiology: Protocols and Applications. Edited by Paul A. Rochelle, Horizon Press, Norfolk, England.
  • Molecular Biotechnology: Principles and Applications of Recombinant DNA, third edition.  Glick and Pasternack, ASM Press, Washington, DC.
  • Microbial Genetics, David Freifelder, Jones and Bartlett Publishers, Boston, MA (1987).

Homework Projects.  Homework projects will be performed individually.  Homework projects will generally be due 2 weeks after it is assigned.  The homework is due before class on the due date.  If the homework cannot be turned in before class on the due date, permission from the instructor to change the due date is necessary.  Without this permission, the homework will not be graded.

Some homework assignments will include material that has not been covered in class yet at the time of the assignment, but requires reading of papers or books available in Kim Coleman’s office.

Writing assignments are required to be typed with 1.5 line spacing, 1" margins, and font 12 points Times or Times New Roman.  Writing assignments are primarily evaluated for content, but writing effectiveness is also important (e.g., organization, style, grammar, punctuation, spelling, and neatness).

Examples of references that can be consulted for writing effectiveness are:

•    W. Strunk Jr. and E. B. White. 1979. The Elements of Style. 3rd Ed. MacMillan Publishing Co., Inc., New York.

•    J. G. Smith and P. A. Vesilind.  1996. Report Writing for Environmental Engineers and Scientists. Lakeshore Press, Woodsville, NH.

Laboratory Project.  The Laboratory project entails spending 2-3 consecutive afternoons or evenings in the molecular biotechnology lab (Urbauer 108).  Groups of 2-3 students will be composed by the instructor.  These groups have to find a microbial environmental sample, and this sample will be examined with fluorescent in-situ hybridization (FISH).  The students need to hand in a lab journal describing this technique on an individual basis.  The grade will be given based on the team effort and the individual lab journal grade (students evaluate the group effort and the individual worker).

Phylogeny Project.  A phylogeny project will be performed with the same group of students who worked together during the laboratory project.  The result will be a phylogenetic (evolutionary relationships) tree (one for each group) with additional text describing how the tree was obtained (approximately 1-page description).  This description will be performed in a format that is similar to a materials and methods section of a peer-reviewed paper.

Teaching of a Molecular Technique + Term Paper.  Students (individually) will teach a lecture about a Molecular Technique for 40-45 minutes.  First the basic mechanisms of the technique need to be taught and subsequently a peer-reviewed paper will be discussed.  The student is expected to choose a paper that uses the lectured molecular technique to solve an engineering-related problem.  The instructor may be consulted to choose a topic and a paper.  A 5-page, single space term paper needs to be handed in before the lecture starts.  This term paper needs to summarize, discuss, and critically evaluate the chosen peer-reviewed research paper.  For example, the limitations of the utilized molecular technique needs to be assessed and other techniques that may complement or improve the knowledge gained from the study may be discussed.

Exams:  All exams will be “open book” exams.  Permission for a make-up exam needs to be obtained before the exam. You will be prepared in class on what type of exams you can expect.

Grading:          

Homework Projects (4)                                 20% (5% of grade per project part)

 Laboratory Project + Phylogeny Project:           20% (10% of grade per project part)

Mid-term Exam:                                          15%

Teaching of Molecular Technique + Term Paper:   20%

Final Exam:                                               20%

Class Participation and Professional Evaluation  5%