BIOLOGY
Dept.

DePauw
University

Fall 2011

Instructor:
Chet Fornari

BIO 250 Laboratory

Lab: R from 1:40-3:30, AND as arranged in the M-W-F lecture periods, Olin 224

Prof. Fornari's Office: 232 Olin
phone: 658-4781
email: cfornari@depauw.edu

Lab Supervisor: Betsy Bowlin
Office: Olin 229; phone: 658-4774


Lab Manual: Customized Microbiolgoy Laboratory Manual,
Barnett/Harley/Prescott/Benson, Wm. C. Brown Publishers

This particular series of introductory microbiology lab exercises emphasizes the basic techniques and fundamental principles of experimental microbiology, and is not intended to be an exhaustive or comprehensive treatment of this discipline. After thoroughly familiarizing yourself during the first few weeks of the semester with the theory and practice of the 4 basic techniques of microbiology, you will be able to perform almost any introductory-level experiment found in any standard laboratory manual.

The lab exercises in the latter half of the semester demonstrate the scientific process through an investigative, discovery-driven project. This project is often centered around the Winogradsky Column (WC), which shows how physiological, biochemical, genetic and evolutionary processes give rise to complex ecological interactions and population dynamics in a "mini" or portable microbial community that grows and develops over time. Other semesters involve a research project centered around identifying bacterial species from complex mixtures of unknowns retrieved from naturally occurring sources in the environment (instead of the WC). You will learn and apply molecular and biochemical techniques to identify bacterial species. Therefore the emphasis of the lab combines basic techniques with general, fundamental biological concepts, and uses microbial organisms in an investigative project to demonstrate and integrate these concepts.

Attendance and Participation in all laboratories is required. Your performance in the lab will be evaluated by a variety of criteria, including:
(1) my observations of your laboratory technique, laboratory notebook, and approaches to organizing and executing particular experiments.
(2) your understanding of the genetic and biochemical basis of each lab exercise and lab test, as reflected in the answers to the questions and problems at the ends of each lab exercise.
(3) your final written lab report and presentation of your research project.
(4) in addition, I will include questions on the hourly exams from the lab exercises.

Lab Exercise Schedule

A25

Lab #1

 Lab Orientation:
 --choose lab bench partners and sign seating chart and index cards.
--microscope assignments; hall-locker assignments.
--description of lab supplies and equipment; check supplies against list.
--safety rules and procedures; sign safety sheet.
--introduction to the Custom Lab Manual (CLM)

S1

Lab #2

 Exercise #1 in CLM (Custom Lab Manual): The Compound Microscope
Exercise #3 in CLM: Aseptic Transfer Techniques, p.11-23

S8

Lab #3

 Explanation of the Research Project (handout provided)
Ex. #7 in CLM: Preparing a Smear and simple stain
Ex. #8 in CLM: Gram-staining
S15 Lab #4 Ex. #12 in CLM: Pour plate techniques
Ex. #13 in CLM: Streak plate and spread plate techniques; assignment and processing  of unknown bacterial samples.
S22 Lab #5 Gram-staining of all assigned unknowns; Group discussions with instructor; see Biochemical Tests (and more Biochemical tests) for excellent reviews with diagnostic pictures for some of your biochemical tests
Research Project handout
Ex. #21 in CLM: Selected Microbial enzymes and Biochemical tests
Start Enterotube experiments
S29 Lab #6 Continue Enterotube; relate theoretically (and by class presentations of assigned enzymes) to exercises below:
Ex. #23 in CLM: Carbohydrate fermentation
Ex. #24 in CLM: the IMViC biochemical tests
Ex. # in CLM: antibiotics disk test
O6 Lab #7

EXAM #1 - Oct. 6th
O13 Lab #8

Ex. # in CLM: Ames Test for enviornmental mutagens, based on reverse mutation.
Antibiotics Research Project and Presentations; see handout for assignments

Begin Molecular Analyses of all Unknowns: Preparation of Known and Unknown template DNA samples; PCR of Known and Unknown Microbial DNA template DNA samples.
O20 No lab Fall Break
O27 Lab#9 Gel Electrophoresis of PCR fragments from Lab #8; estimation of fragment sizes against DNA standards.
N3 Lab#10 ExoSAP treatment of all PCR products in preparation for DNA sequencing
N10 Lab#11 DNA Sequencing on the CEQ 8000 Automated Genetic Analysis Instrument
N17 Lab#12 Genomic and Bioinformatic Analyses of Bacterial genomes and rRNA genes (and see: Ribosomal Database Project hosted by MSU)
N24 No lab Thanksgiving Break
D1 Lab#13 Discussion, Analysis, and Presentation of Cumulated Morphological, Physiological, Biochemical, and Genetic (sequnce) data to identify your unknown and place it into a Phylogenetic context (tree).
D8 Lab#14 EXAM #2 - Dec. 8th
  Lecture Lab Check-out: clean drawers, remove tubes and slants, check microscope
D16   Final Project due - Dec. 16th (final exam period)

Top of Page