CE 742 Advanced Topics in Environmental Engineering: Molecular Methods Applications for
Environmental Engineers – Course Outline
Meeting Times: Monday: Readings and Discussion, 2:10 – 3:50 PM, B101 ENG
Wednesday: Lab, 2:10 -5:00 PM, B12 ENG
Instructor: Amy Pruden
apruden@engr.colostate.edu
http://www.engr.colostate.edu/ce/homepages/pruden/index.shtml
Office phone: 491-6670 (campus), 491-8814 (ERC, voicemail)
Office: A207D ENG, 307B ERC
Office Hours: Set appointment by email or phone.
TA: Anurita, anurita@engr.colostate.edu.
Text: No required text for this course. You will be required to purchase a lab notebook/journal and
you are recommended to purchase a 3” binder to organize course materials. Lab protocols will be
provided and readings will be assigned.
Course Format:
Mondays will be dedicated to a short lecture followed by class discussion. Readings will be assigned
each Monday due by the following Monday. You are expected to complete the readings prior to the
next class period and to be prepared with any questions for discussion. In addition to the readings
provided by the instructor- students will also be assigned to bring readings on given topics. Alsoeach week you will be expected to write a journal entry in which you discuss your thoughts and
reflections on the material covered that week.
Wednesdays are your opportunity to learn the methods “hands-on.” You will be assigned a lab group
for the semester. Each group will choose a sample of environmental engineering relevance to work
on for the semester. You will be provided with the protocol for Wednesday lab the previous
Monday. Make sure you are familiar with the protocol before the lab meeting time. Be sure to keep
a detailed lab notebook recording what is done in the lab. You may combine this with your journal if
you wish. Lab books and journals will be collected periodically for evaluation.
There will be three short quizzes, a final exam and one group lab report. The lab report should
summarize your findings in the format of a journal manuscript (Abstract, Introduction, Materials and
Methods, Results and Discussion, Conclusion, References, and Figures). The total report should not
be more than 20 pages double-spaced, and should represent a “team effort”.
Grading:
Class Discussion/Participation:
Lab Book/ Journal:
Lab Report:
Quizes (3):
Final Exam:
Percent Total Grade:
25%
25%
25%
15%
10%
100%
Summary of Topics to be covered:
Schedule:
DATE
TOPIC
Weds. Jan. 21
Course Introduction, 1st reading Assignment, pre-test.
Mon. Jan. 26
Discussion- Nucleic Acid Extraction
Weds. Jan. 28
Lab- DNA Extraction and Quantification
Mon. Feb. 2
Discussion- Polymerase Chain Reaction (PCR)
Weds. Feb. 4
Lab- PCR I (for clones and DGGE)
Mon. Feb. 9
Discussion- Community Profiling Techniques Part I
Weds. Feb. 11
Lab- PCR II
Mon. Feb. 16
Discussion- Community Profiling Techniques Part II
Weds. Feb. 18
Denaturing Gradient Gel Electrophoresis (DGGE)- making the gel
Mon. Feb. 23
Discussion- Community Profiling Techniques Part III
Weds. Feb. 25
DGGE II- Imaging and cutting the gel.
Mon. Mar. 1
Discussion- Quantitative Techniques Part I (Quiz #1)
Weds. Mar. 3
Cloning I
Mon. Mar. 8
Discussion- Quantitative Techniques Part II
Weds. Mar. 10
Screening clones- Make up day
Mon. Mar. 15
Spring Break March 15-19
Weds. Mar. 17
Spring Break March 15-19
Mon. Mar. 22
Discussion- Sequence analysis
Weds. Mar. 24
Screening Clones – sequence preparation
Mon. Mar. 29
Functional Genes and Genomics I
Weds. Mar. 31
Sequence analysis
Mon. April 5
Functional Genes and Genomics II (Quiz #2)
Weds. April 7
Phospholipids I
Mon. April 12
Alternative Analyses (PLFA, FAME)
Weds. April 14
Phospholipids II
Mon. April 19
Microbial Proteomics
Weds. April 21
Real-Time PCR I
Mon. April 26
Engineering Applications I (Quiz #3)
Weds. April 28
Real-Time PCR II
Mon. May 3
Engineering Applications II
Weds. May 5
Make-up Day
Mon. May 10
Final Exam 7-9 AM