Syllabus – Bio 321W – Microbiology

Spring 2011

Instructor: Jeffrey D. Newman Room: Heim 110 Phone: 570-321-4386 email: newman@lycoming.edu office hours: Mon 3:30-4:30 PM Tues 3:30-4:30 PM

Lecture meets MWF 10:15 – 11:05 in Heim G-11 Lab meets Tues & Thurs 9:45 - 11:35 or 1:00 – 2:50 in Heim 106 Course web page: on moodle and iGoogle (login: lycomicro, pw: 16srrna1

Catalog Description of Course: A study of microorganisms. Emphasis is given to the identification and physiology of microorganisms as well as to their role in disease, their economic importance, and industrial applications. Three hours of lecture and two two-hour laboratory periods per week. Prerequisite:Bio110-111.

Text: Willey, Sherwood, & Woolverton. Prescott, Harley, Klein’s, Microbiology,
7^th ed. 2008, McGraw Hill

Grades will be determined based on the following assessments:

5 exams (lowest dropped) 4 x 100 pts = 400 pts

Prep papers 33 x 3 pts + 1 = 100 pts

Lab Data Reports 6 x 5 pts = 30 pts

Unknown Microbe Lab Report 200 pts

Lab Practical 100 pts

Lab Report Peer Reviews 30 pts

Other homework/problem sets up to 40 pts

Total 900 pts

	B+ = 86.7 - 89.9%	C+ = 76.7 – 79.9%	D+ = 66.7 - 69.9%
A = 93.3 – 100%	B = 83.3 – 86.6%	C = 73.3 – 76.6%	D = 63.3 – 66.6%	F= below 60%
A- = 90.0 – 93.2%	B- = 80.0 – 83.2%	C- = 70.0 – 73.2%	D- = 60.0 – 63.2%

• Exams will be taken in class and will consist of multiple choice, short answer, experimental design, data interpretation and/or essays.
• For the Microbial Genome Report, each student will choose a different Bacterium or Archaeon, read the original paper describing the organism’s genome, and write a 4-5 page report describing unique characteristics and what was learned from the genome. Specific guidelines to follow.
• Unknown microbe lab report will be in the form of a research paper and will describe the analysis and identification of a microbe from stream sediments. Specific guidelines to follow.
• Lab practical will assess students’ abilities to use the microscope, perform differential stains, perform aseptic technique, streak for single colonies, interpret the results of biochemical tests, and perform dilutions.
• Lab report critique will be a peer-review of another student’s lab report.
• Lab quiz will assess understanding of the Unknown microbe identification lab, prior to beginning the lab report.

This is a writing intensive course that satisfies the guidelines specified by the College’s Writing Across the Curriculum Committee. As a “W” course, we will spend class/lab time on the process and goals of writing, reviewing and revising formal written work. Note that a draft of the unknown microbe lab report will be submitted, undergo peer review and be returned to you so that you may revise the lab report before submission for a final grade

In addition, to encourage the use of writing to organize your thoughts about the course material, we will do “prep papers” for this class.

Daily “Prep Papers” are due at the beginning of each class (except for exam or lab days). Any instances of academic dishonesty with prep papers (e.g. turning in the same prep paper on multiple days or two people turning in identical, or obviously copied & edited prep papers) WILL result in a loss of ALL prep paper points for the semester.

Prep papers may be submitted for excused absences with proper documentation.

Guidelines:

• Name and date should be indicated on top of page
• 1 paragraph summarizing key points from previous class and asking questions in bold.
• 1 paragraph summarizing key points from reading assignment and asking questions in bold.
• 0.5 – 1 page typed, Arial or Times Roman 12 pt font
• 2.5 cm (1 inch) margins
• Each paper that meets guidelines earns 3 points
• 100 points are built into the grading scale
• If you do 33 prep papers, you score 100% on 100 point part of your grade
• If you do 36 prep papers, you score 100% on 100 point part of your grade and get 9 bonus points
• If you do 28 prep papers, you score 85% on 100 point part of your grade
• If prep papers are not done, a sign-in sheet will be available to confirm attendance
• Prep papers may be submitted for missed classes only when accompanied by a documented excuse (Note from Health Care Provider or coach).
• If a class is missed, the prep paper that is submitted upon return to class should summarize the last class attended and the reading assignment given on that day.

Tentative Course Schedule

	Lecture Topics (chapter)	Tuesday Lab	Thursday Lab
Week 1 1/10 – 1/14	Introduction, History (1), Prokaryotic Cell Structure (3)	#1 Lab Safety, Aseptic Technique, Inoculation, streak plate technique, choose known and unknown organisms.	#1 Collect colony morphology results, photograph. Prepare pure cultures for stains, permanents. Discuss documentation on iGoogle page and data management.
Week 2 1/17 – 1/21	Microbial nutrition, growth Microbial Growth Control (5-7)	#2 Wet mount, gram stain, spore stain, microscopy, permanents.	#3 Media Preparation
Week 3 1/24 – 1/28	Microbial Growth Control - Antibiotics (34) 1/28 Exam 1	#4 Control of microbial growth by oxygen, temperature, ionic strength and antibiotics.	#4 Control of Microbial Growth – Data collection.
Week 4 1/31 – 2/4	Energy Metabolism (8-10)	#5 Inoculate carbohydrate and nitrogen metabolism biochemical tests.	#5 Collect carbohydrate & nitrogen metabolism test results
Week 5 2/7 – 2/11	Microbial Genetics (11-13)	#6 Inoculate exoenzyme tests, differential and selective medium	#6 collect results from exoenzyme tests, differential and select medium
Week 6 2/14 – 2/18	Biotech & Genomics (13-15)	#7 Introduction to Bergey's Manuals. #8 PCR amplification of rRNA gene	W #9 Inoculate BUG + Blood plates for Biolog, TSA plates for MIDI. Th - Inoculate Biolog GenIII plate. #8 Run gel, quantify PCR products
Week 7 2/21 – 2/25	2/21 Exam 2 Microbial Phylogeny (19-20)	#10 – Extract fatty acids – run MIDI Unknown hypothesis, biochem results due	Review MIDI, Biolog results
Week 8 2/28 – 3/4	Microbial Diversity (21-24)	Discuss lab report, Microbiology literature, the Process of Scientific Publication,	#11 Analyze sequence data to ID unknown, compare to other organisms, construct tree.
Week 9 3/7 – 3/11	Microbial Ecology (27-30) 3/11 Exam 3	Redo tests as needed. Work on lab report	Collect data from repeated tests. Work on lab report
Week 10 3/21 – 3/25	Viruses (16-18)	#12 Phage titering, host specificity	complete #12 Phage titering, host specificity Unknown microbe lab report draft due 3/24
Week 11 3/28 – 4/1	The Immune Response (31-32)	#13 Clinical Micro – API test strips	#13 Clinical Micro – API test strip results #14 Water/Milk Analysis
Week 12 4/4 – 4/8	Unknown lab report reviews due 4/4 Pathogenicity (33) 4/8 Exam 4	#14 Water/Milk Analysis	#14 Water/Milk Analysis
Week 13 4/11 – 4/15	Clinical Microbiology, Epidemiology (35-36)	Lab Skills Practical	Field Trip: Clinical Microbiology Lab
Week 14 4/18 – 4/22	Microbial Diseases (Ch 37-39)	Field Trip-Tour of the Bullfrog Brewery	Field Trip: Wastewater Microbiology Unknown lab report Final Paper due 4/22