Microbiology: Bacteria and Viruses

Bio 254

Spring 2007

Instructors:

Dr. Christine White-Ziegler
Office:	Sabin-Reed 457
Office phone:	585-3815
E-mail:	cwhitezi@science.smith.edu
Office hours:	The best times to contact me are immediately after lecture/lab on Monday, Wednesday, or Friday. If these times conflict with your schedule, please contact me for an appointment.

Lecture class:

Course credit:	3 credits
Class times:	MWF 10:00- 10:50 am Th 4:00-4:50 pm
Location:	McConnell 404
Prerequisites:	CHM 111, BIO 111 or equivalent
Co-requisite:	BIO 255 (Microbiology: Bacteria and Viruses Laboratory) must be taken concurrently

Course description and objectives:

This course will focus on the biology of bacteria including prokaryotic cell structure, diversity, metabolism, growth, and genetics. The different environments in which bacteria are found, and the role bacteria play in these environments, is also addressed. Additionally, an introduction to the biology of viruses will be included. A particular emphasis is placed on medical microbiology in which the role of bacteria and viruses in disease is discussed. Special topics covered in this class include antibiotic resistance, evolution of pathogens, virulence factors, emerging infectious diseases, gene regulation, and bacteria in unusual or extreme environments.

In addition to learning important information about the biology of a variety of microorganisms, students will have the opportunity to write a paper on a topic of their interest. Through this assignment, students will experience the research process from the concept stage to a culminating final paper and oral presentation on the topic, giving students the opportunity to practice and improve their written and oral communication skills. The exchange of information learned by individual students will be facilitated by oral presentations and reading of each other’s papers. Also, students will orally present “Microbial Moments” that will allow a more casual exchange of information and discussion of specific microorganisms.

Appointments/contacting us:

As stated above, I can meet with you on Monday, Wednesday, or Friday for appointments. When you want to set an appointment, please let me know a few time slots you are available on those days so we can find a time that matches both of our schedules. Feel free to contact me in class, by email, or by phone. Do, however, make sure that any important information you need to get to me (e.g. appointment times, paper topics, etc) is written down on something and handed to me! I promise you that I will promptly forget anything simply told to me. Also, I do not check email/voicemail on the weekend, in the evening, and (sometimes) not before class, so plan on a lag time in response to emails sent to me at these times.

Lecture text:

The text for the class is Microbiology by Prescott, Harley, and Klein, 6^th edition. It will serve as the primary reference for the course. Additional readings may be assigned and will be available on reserve in the Young Science Library. An extremely helpful resource for the writing assignment in this class is A Short Guide to Writing About Biology by Jan Pechnik, 3^rd edition. It is on reserve for this course at the library.

Evaluation:

Assignment	Points
Microbial Moments (2 x 25 points)	50
Annotated outline	30
Exam 1	100
Exam 2	100
“Near perfect” draft of paper/writing conference	25
Final paper	100
Presentation of paper	50
Exam 3	100
Total	555

Microbial moments

To introduce specific microbes in the class, each student will present 2 “Microbial Moments” during the course of the semester. This will be a short (approximately 3-5 minute talk) about a specific bacterium or virus that will include such information as the unique characteristics of the bacterial genus (or species) and it role in its environment. A handout will be provided as to what information should be covered in these moments. Each class meeting a different person will present. Microbial moments will be started in February.

Exams

Exam 1 and Exam 2 will be self-scheduled exams. In a week in which an exam is given, the exams will be available starting at 1:00 p.m. on the first day until library closing time on the last day. Students can obtain the test in the Young Science Library at the desk. The exam must be completed within two hours and returned to the Science Library desk. Please plan to allocate the full two hours provided to complete the exam. If you have questions pertaining to the exam content, these questions must be asked before the test is made available. Clarifications during the exam can be asked if you take the exam when I am on campus so plan accordingly if you want to have this option.

Exam 3 will cover the content of the last third of the course, primarily student papers. All of the student papers’ will be placed on reserve in the Young Science Library. Each student will be responsible for writing a test question and answer on her individual paper that will be used in formulating the exam. Exam 3 will be on reserve at Science Library desk during final exam week. Material covered in Microbial Moments will be tested on exams.

Annotated outline/Near perfect draft/Final paper

Each student will write a paper on a subject of interest within the field of microbiology (bacteriology or virology). Each student needs to discuss with the instructor and get approval of her topic by the date stated in the lecture outline. This is done primarily to prevent duplication of topics as well as to increase the diversity of special topics. An annotated outline will be written for the paper to delineate the focus of the paper. The majority of references cited should have been written in the past 3 years. The outline is due by the date stated in the schedule, but can be submitted earlier. The paper, limited to 8 pages, should be typed, double-spaced, and include a list of references. The paper should be written from the primary literature and should give the latest information available on the subject.

Each student will hand in a “near perfect” draft a week prior to when the student presents her paper orally. A “near perfect” draft should be as complete a paper as the student can write. Any papers submitted later than this time will be penalized. The student is then responsible for scheduling a writing conference with the instructor, prior to her oral presentation, in which the instructor will offer comments for the writer on ways to improve the paper. Peer review is highly encouraged so students should feel free to exchange drafts and get comments from each other. The final draft of the paper is due one week after the student’s presentation.

Presentations will be held between mid-March and the end of classes; a specific schedule will be determined once class size has stabilized. Each student will give a 10-15 minute presentation of her paper, followed by 5 minutes for questions and discussion. The presentations should be well prepared, concise, and include any visual aids that would enhance the presentation. The presentation time will not be enough to address every point made in the paper. Therefore, students will want to present the most interesting and important points. The purpose of the presentation is to give students a chance to speak in front of others and promote an exchange of information and ideas.

Colloquium:

A colloquium will be given on Monday, February 26 at 4:30 pm in McConnell B05 by Dr. Anna Moscona, Weill-Cornell Medical College, on influenza and pandemic influenza. Extra credit will be given for attendance at this talk along with a brief one-page summary of the talk.

Moodle/Website:

The majority of information for the course will be posted on Moodle. In addition, this course has a web page that is a source for specific and general information. Useful links to immunology and microbiology-related sites, and literature reference databases can be accessed through this page.

www.science.smith.edu/departments/Biology/cwhitezi/default.html

Late policy:

Each assignment is due on the date and at the time stated in the syllabus. An assignment handed in late will be penalized 5 points for each day it is late unless I receive a note from your class dean. Weekend days will be included in this penalty.

Outline of course:

This outline should be viewed as a flowchart of topics in the basic order that they will be covered. It is subject to change.

Class will meet on Thursdays unless noted “NO CLASS”

Week	Lecture	Chapter
M 1/29	Introduction
W 1/31	History of microbiology	1
R 2/1	TBA
F 2/2	Bacterial Diversity I: Gram – and Proteobacteria	21-22
M 2/5	Bacterial Diversity II: Gram +, Low-vs-High G+C	23-24
W 2/7*	Microscopy: Visualizing bacteria and viruses	2
R 2/8	NO CLASS
F 2/9	Prokaryotic cell structure and function	3
M 2/12	Prokaryotic cell wall: Gram + versus Gram -
W 2/14*	Taxonomic classification of bacteria	19, 15
R 2/15	TBA
F 2/16	Archaea	20
	*Submittal of PAPER topic due by 10 am on 2/12
M 2/19	Bacterial nutrition and culture media	5
W 2/21	NO CLASS- Rally Day!	6
R 2/22	TBA
F 2/23*	Measurement of bacterial growth	9
	*Annotated outline of PAPER due at 10 am on 2/23
M 2/26*	Bacterial respiration
W 2/28	Metabolic Diversity I: Fermentation
R 3/1*	TBA
F 3/2	Metabolic Diversity II: Photosynthesis and Chemosynthesis	10
	*Talk by Dr. Anna Moscona, McC B05, Monday, 4:30 pm –EXTRA CREDIT!
	*Self schedule EXAM 1 between 2/26-3/5
M 3/5*	Bacteria and their role in the environment	28-30
W 3/7	Biogeochemical cycles and bioremediation
R 3/8	TBA
F 3/9	Bacterial DNA replication/transcription	11

M 3/12*	Bacterial protein translation
W 3/14	Gene/protein regulation I	12
R 3/15	Meet in lab
F 3/16	Gene/protein regulation II
M-F 3/19- 3/23	NO CLASS- Spring Break!
M 3/26	Genetic mutations	11
W 3/283	DNA repair
R 3/29	TBA
F 3/30	Gene transfer I: Transformation, Conjugation	13
M 4/2	Gene transfer II: Transduction, Transposons
W 4/4	Antibiotics	35
R 4/5	Student presentations
F 4/6	Antibiotic resistance
M 4/9	Viral Structure, function and life cycle	16
W 4/11	Propagation of viruses: Lytic versus lysogenic phages	17
R 4/12	Student presentations
F 4/13	Eukaryotic viruses	18
	*Self schedule EXAM 2 between 4/9-4/16
M 4/16	Viruses and disease	38
W 4/18	Cancer and HIV
R 4/19	Student presentations
F 4/20	Special topics
M 4/23	Special topics
W 4/25	Special topics
R 4/26	Student presentations
F 4/27	Special topics
M 4/30	Special topics
W 5/2	Special topics
R 5/3	Student presentations
F 5/4	Last day of classes
	*EXAM 3 due by 4 pm on 5/10