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BIOL 239 Experimental Microbiology
with Darcy Blankenhorn

Under continual revision;
Check for updates

Spring Semester 2015, 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 
  • Culturing and identification of organisms from human and environmental sources
  • Synthetic biology and gene regulation
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 requires work on some Fridays.
This is compensated by lab-free date Feb. 13.
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: Slonczewski & Foster (2014) Microbiology: An Evolving Science (Norton, 3E).

Lab reports. Reports are due on Moodle by 11:59 midnight of the date shown. 

  • All reports are submitted electronically using Moodle.
  • Trim photos using Photoshop, and keep size <500kb.
  • 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.
    Each report must be contain Introduction, Methods, Results, Discussion, and References.

Evaluation. Your final grade is based on lab reports and attendance: Labs 1- 6.

Attendance. All missed labs will count against your grade. Lab attendance is 100% absolutely required.
A missed lab results in final grade F for the course.

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

No Withdrawals. Passing this course assumes 100% participation up to and including the final lab.

BIOL 239 Syllabus
Date
Topic
Prep Reading
Due by
11:55pm
Jan
15
16
Lab 1. Microscopy: Observing Protists.
Complete observations as needed.
Lab 1; S&F Ch 2,
Ch 20
1/20
Jan
22
23
Lab 2. Skin Microbiome and Streak plate. Pour plates.
Complete as needed.
Lab 2; S&F Ch 4
Skin1. Skin2.
1/27
Jan

29
30
Lab 3. Growth pH and Multidrug Resistance
Excel practice 1;  Excel practice 2;
Growth rate calc
Lab 3; S&F Ch 5
TolC
2/10
Feb
05
06

Lab 3 (cont). Board instructions.



Feb
12
13

Discussion; observe environmental cyanobacteria.

Discuss Lab 4 & 5.

Feb
19
20

Hospital Field Trip.

S&F Ch 28

Febr
26
Lab 4. Fluorescent gene. Alt: Prep Antarctic DNA
Check plates; store in cold room. Record all data.
Lab 4 or DNA Prep
Desai Arabinose
3/17
SPRING VACATION
Mar
16

Monday or Tuesday: Check Cyanobacterial Growth
No lab Thursday; Bioinformatics due next Tuesday.
SF Ch 18, 21 

Mar
26
27
Lab 6. Soil Antibiotic Producers & Resistance
Check plates.
Lab 5.
4/14
Apr 02
Lab 5 & 6. (cont.)



Apr
09
10
Lab 5. Cyanobacterial Ecology & Bioinformatics
Lab 6. (cont.)
Lab 6. SF Ch 17
 4/28
Apr
16
17
Lab 5. (cont.)


Apr
23
DNA Prep of Producer strains (no report)

-

Apr
30
Water Treatment Plant Field Trip
S&F pp 839-841


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. 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.