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BIOL 239 Experimental Microbiology
with Darcy Blankenhorn

Spring Semester 2009, HIG 322
Thurs. 1:10-4:00; Fridays as needed

Microbiology is the study of organisms too small to be seen by the naked eye. In this experimental lab course, we observe bacteria, protists, and archaea. Our experimental approaches include:
  • Microscopy of live and stained organisms from human and environmental sources
  • Culturing and biochemistry, using state-of-the-art digital instrumentation
  • PCR molecular genetic analysis and bioinformatic taxonomy
  • Clinical methods to identify potential pathogens from food
Prerequisite courses. BIOL 109 is required. BIOL 238 must be taken concurrently or previously.

Lab hours. Lab starts in HIG 322 Thursday at 1:10. Followup for microbial growth requires work on Fridays.
All lab procedures must be read before the day the exercise is performed. All lab exercises must be turned in on the date indicated.

Lab Procedures are linked on line for each lab. Always check the blackboard for modifications.

Text: Leboffe, M. J., and Burton E. Pierce, Microbiology Laboratory Theory and Applications, 2E, Morton, 2006. The text provides background reading.

Readings: Slonczewski & Foster (2008) Microbiology: A Genomic Approach (Norton, 1E). In most cases appropriate material will have been covered already in BIOL 238, but some additional readings are assigned.

Lab reports. Reports are due on the date and time shown on syllabus.

  • All pages must be stapled. Lack of staple subtracts 1/3 grade point.
  • Do not redraw sketches; use pencil on un-lined paper.
  • Each lab report must show all results, including those of your lab partner(s). Always cite the names of all your lab partners. You are encouraged to discuss results with your fellow students, and cite their assistance (as professional scientists do) but the text and graphics of your report must be your own work.

Evaluation. Your final grade is based on lab reports:
Labs 1-6, 8 (70% total); Lab 7 (30%).
Each report must be word-processed and proof-read, with Introduction, Methods, Results, and Discussion.

Attendance. All missed labs will count against your grade. Lab attendance is 100% absolutely required. If you have a sports conflict, you must inform the instructor in writing a week before the lab date. In some cases, a lab partner may be able to help complete the procedures. No labs can be "made up." A missed lab results in final grade F for the course.

Special needs. The Coordinator of Disability Services must be consulted for special arrangements.

Withdrawals. Passing this course assumes 100 % participation up to and including the final lab.
The instructor of this course does NOT sign forms for Withdrawal Passing (WP) or Withdrawal Late (WL). Make sure you intend to complete the course.


BIOL 239 Syllabus
Date
Topic
Prep Reading
Date/Time
Due
Jan
15
16
Lab 1. Visualizing eukaryotes. Pour plates.
Complete observations as needed.
Lab 1; Ex 1-1, 3-1, 3-3
1/20 8am
Jan
22
23
Lab 2. Throat Culture: streak plate & Gram Stain
Complete as needed. Throat Slides
Lab 2; Ex 1-3, 2-2
1/27 8am

Jan
29
30
Lab 3. Growth and temperature.
Growth calculations.
Lab 3; S&F pp 134-138
2/3 8am
Feb
5
6

Lab 4. Metabolism.
Observe tubes and plates.

 Lab 4; cited pages 2/10 8am
Feb
12
13

Lab 5. Virus plaque assay.
Continue Lab 5

 Lab 5; Ex 6-4
2/17 8am
Feb
19
20
Lab 6. UV radiation damage.
--
 Lab 6; Ex 9-2; S&F pp 326-332
2/26 1pm
Feb
26
Hospital Field Trip. 4:15 Dan Wozniak, Bio Seminar
Extra Credit: Thursday 5:30 Middle School Science Fair
S&F pp 1063-1072
-
SPRING VACATION
Mar
21
22
Lab 7. Isolate and Identify Environmental Bacteria. Restreak colonies & stab cultures.
 Lab 7; Peterson
4/30
Mar
25
26

Wednesday: Inoculate 15 tubes from isolated colonies.
DNA preparation.

 DNA prep

Apr

1
2
Wednesday: PCR amplification.
Thursday AM: DNA gel. Thursday PM: Purify PCR.
Send out DNA for sequencing
PCR prep  
Apr
9
10
 Physiology tests; Enterotube; ENTERIC program -  
Apr
16
17
 Lab 8. Pathogen test: Antibody agglutination test.
Followup physiology tests. 		Lab 8; Ex 10-4
4/21 8am
Apr
23
 DNA analysis--BLAST. Followup physiology tests.

 

Apr
30
Lab 7 Presentations. Water Treatment Plant Field Trip
Lab 7 due;
S&F pp 839-841
4/30 1pm

Laboratory Safety Rules

The purpose of these rules is to keep you and your fellow students safe and healthy.Remember that in a microbiology lab, any microorganism is considered a potential pathogen.Observance of safety rules will be a factor in your lab grade.

Know the location of the fire extinguisher, emergency shower and first aid kit.

Remember to assume that any microbe is a potential pathogen. There is no mouth pipetting in microbiology lab; use the pipettors.Smoking, eating, drinking and chewing gum are not allowed in the lab.

Read the day’s procedure for the lab exercise and the appropriate report pages before you come to class.

Before the lab period begins, check the lab blackboard for any modification of your procedure.Wait for the instructor to arrive before beginning work.

Protect your microscope.Always carry with both hands; grasp the arm with one hand, and support the base with the other hand.Keep your microscope covered when not in use. Never remove or exchange eyepieces with other microscopes.

Avoid excess immersion oil. Always clean oil off lenses and slides when you are finished. Use only lens paper with 70% ethanol to clean lenses; blot, not rub.

Do not pour liquefied agar medium down the sink drain, as it will cool and gel in the pipes. Do not pour any contaminated media down the drain; instead, leave it in the prep room for autoclaving and safe disposal.

Your lab area must be left clear and disinfected with ethanol before you leave the lab. Hang up your lab coat before you leave the lab.

Always bring a friend when working in the lab after 5:00 pm or on weekends.