BIOLOGY
Dept.

DePauw
University

Fall 2017

Instructor:
Chet Fornari

BIO 250 Laboratory

Lab: T from 1:00-3:30 (and as needed in the MWF lecture periods), Olin 224

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

Lab Supervisor: Wendy Tomamichael
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 of your research project.
(4) in addition, I will include questions on the hourly exams from the lab exercises.

Lab Exercise Schedule

8/29

Lab #1

 Lab Orientation:
 --choose lab bench partners and sign seating chart and index cards.
--microscope 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)

9/5

Lab #2

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

9/12

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
9/19 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.
9/26 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
10/3 Lab #6 EXAM #1
10/10 Lab #7

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. #20 in CLM: antibiotics disk test

10/17 No lab

Fall Break: 10/14-22
10/24 Lab #8

Experiment: Ames Test for enviornmental mutagens, based on reverse mutation.

Begin Molecular Analyses of all Unknowns: Preparation of Known and Unknown template DNA samples; PCR of Known and Unknown Microbial DNA template DNA samples.
10/31 Lab#9 Gel Electrophoresis of PCR fragments from Lab #8; estimation of fragment sizes against DNA standards. ExoSAP treatment of all PCR products in preparation for DNA sequencing
11/7 Lab#10 DNA Sequencing on the CEQ 8000 Automated Genetic Analysis Instrument
11/14 Lab#11 EXAM #2
11/21 Lab#12

Genomic and Bioinformatic Analyses of Bacterial genomes and rRNA genes (and see: Ribosomal Database Project hosted by MSU); also see the new EZbioCloud; Also see: ABIS online
11/28 Lab#13 Discussion, Analysis, and brief Summary/Presentation of Cumulated Morphological, Physiological, Biochemical, and Genetic (sequnce) data to identify your unknown and place it into a Phylogenetic context (tree).
12/6 Lab#14 EXAM #3
12/8 Lecture Lab Check-out: clean drawers, remove tubes and slants, check microscope
12/15   Final Project due - (during Finals Week)
     

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