A. General information

B. Course logistics

C. Materials

D. Reading assignments

E. Tests and grades

F. Class groups

G. Students requiring accommodations

H. Make up policy

I. Extra credit

J. How to succeed

K. Lecture outline and readings

Welcome to "Biology of Bacteria", BIO397B. This course is being offered for the first time as an experimental course to gauge student interest. Students who have completed BIO208, "Microbiology" and have been turned on to the invisible world of microbes, who may be considering microbiology as a career option, this course is for you!!! The Biology department at Central Michigan University offers several advanced courses in microbiology, in addition, many of our students decide to pursue graduate training in the field of microbiology. This course is being designed to prepare students for further studies in microbiology at the advanced undergraduate and graduate levels.

In "Biology of Bacteria" we will be focusing only on the Domain Bacteria (remember that from 208?). We will be delving into important topics to a much deeper depth than was possible in "Microbiology" and will be introducing entirely new topics as well. Despite devoting an entire semester to the study of Bacteria, we still cannot possibly do justice to all topics in microbiology in this short time, so I have had to make choices about what to exclude as well as what to include. Still, the content of this course should provide greater appreciation for the subjects covered in our advanced courses such as "Microbial Diversity", "Applied and Environmental Microbiology", and "Medical Microbiology", as well as prepare you for taking microbiology courses in graduate programs at CMU or at other institutions.

What preparation do you need to take this course? Of course "Microbiology" is a prerequisite. I will assume that you are familiar with the material covered in an introductory microbiology course and will not spend valuable class time reviewing basic information. If you need a refresher in basic microbiology you may want to review the notes from BIO208, spring 1999 or even to sit in on specific lectures in Bio208, fall 1999. In addition to basic microbiology, you will need a decent background in chemistry. Microbes are "chemists". The machinery of microbes is chemical, after you remove the cell membrane you are left with chemical pathways and the only way to understand how microbial processes work is to examine some of the details of this machinery. I will regularly use diagrams that show organic molecules and will expect that you understand what I am talking about, without my having to go back and explain what these mean. If you felt that your chemistry background was deficient at the 208 level, then you should not be taking BIO397 at this time. If you are seriously considering a career in microbiology, then a firm foundation in chemistry will be critical to your success.

Lectures meet Tues. and Thurs. from 11:00 - 12:20 a.m. in BR 201.

Course instructor: Dr. Elizabeth Alm

Office hours: Tues. 12:30-5:30, or by appointment (there will be some Tues. that office hours will be abbreviated due to faculty meetings). I will have a sign-up sheet outside my door and if you sign up for time it is certain that 1) I will be there, and 2) you will not be waiting on other students.

e-mail: elizabeth.w.alm@cmich.edu (Note: this is the easiest way to reach me). Important: If you have a BIO397 question, put "BIO397" as the beginning of the subject line of your e-mail message. I group these for reading at one time a day. If you fail to include this header I may miss your question.

Example:

To: Elizabeth W. Alm <elizabeth.w.alm@cmich.edu>

From: Susan B. Student <susan90001@cmich.edu>

Subject: BIO397: questions on today’s lecture

Phone: 774-2503. This is really not the best way to reach me, even if you call during office hours there is a good chance that I will already be with a student and will not be able to take your call. If you leave a message on the answering machine, please speak slowly and clearly so I don't have to replay a half a dozen times to figure out who it is, and leave a phone number if you would like me to return your call.

Textbook: You have a choice. I have not ordered a text for the bookstore and will be providing photocopies of sections from whichever text listed below I feel gives the most complete coverage of whatever the topic is we are discussing. Readings from both texts are listed in the lecture schedule. Despite the fact that I am not requiring a text for this course, as a budding microbiologist, you should purchase and keep one of the two texts described below.

Madigan, Martinko, and Parker. 1997. Brock Biology of Microorganisms. 8th Ed. Prentice Hall. Hardcover ISBN 0-13-520875-0.

This text is probably used more widely than any other. It is used in most of the microbiology departments that I can think of (incl. MSU) and almost all microbiologists have a copy of this text on their reference shelf. It contains a wealth of information. It probably contains the best treatment of environmental microbiology of any text and is the text I use when I teach "Applied and Environmental Microbiology". On the downside... it may take some getting used to as far as readability. A 9th ed. is either available now or will be available soon but I haven't seen this yet.

From the Publisher

KEY BENEFIT: For nearly 30 years and seven editions, the newly retitled Brock Biology of Microorganisms has been the bible for microbiology with a focus on microbes as organisms in their own right. The book offers balanced, in-depth treatment of basic microbiological principles, including molecular biology, medical microbiology, genetics, immunology, and other topics. KEY TOPICS: Contains an early and solid chemistry chapter (Ch. 2), which readers need to understand the metabolism of microorganisms and its applications in industry, ecology and medicine. Enhancements to the Eighth Edition include new chapters on Regulation of Gene Expression (Ch. 7).

Prescott, Harley, and Klein. 1999. Microbiology. 4th Ed. WCB McGraw-Hill. Hardcover ISBN 0-697-35439-3

The second most popular microbiology text, I find this to be a very readable text. Its coverage of environmental microbiology is not as complete as the Madigan text but its medical coverage may be more complete (but I use a different text when I teach Medical Microbiology). This text has the advantage of covering microbial diversity in a phylogenetic organization, which is the "very latest".

From the Publisher

FEATURES: Comprehensive general microbiology, but written at a level that is appropriate for both majors and non-majors. Updated coverage of Microbial Ecology. Outstanding pedagogical system including outlines, concepts, key terms, cross-referencing, and readings. Complete updating of classification system, especially in chapters 19-24, 36, 37, 38. Text most closely reflects updates to Bergey's Manual of Bacteriology.

Amazon.com

Textbook search site

Access to the World Wide Web and an e-mail account. I will be posting many class materials on the Web, and expect every student to check the Web site for announcements at least once a week. I can be reached more easily by e-mail than by any other method, and will reply to any concern or question you raise if you have an e-mail account. Go to the computer center help desk to find out how to obtain and use e-mail (available free to all students).

Reading assignments in the text are listed on the tentative lecture schedule. Readings and lectures will complement each other — I cannot cover every detail in lecture, and will expect you to obtain certain information from reading the text rather than from lecture. Don't fall behind! Try to read the assignment before each class, but at the very latest read it on the same day as the class.

Subjective - attendance, attentiveness, attitude - 5% (no reason you shouldn't all get full credit here!)

Quizzes - A short quiz will be given each Tues. at the beginning of class, except for Tues. when an Exam is scheduled. The quizzes will be worth a total of 20%.

Two hour exams will be given during scheduled class times; each will cover approximately 1/3 of the course material. The final exam will cover the final third of material. Grades will be determined as follows:

Exam #1 - 25%

Exam #2 - 25%

Final Exam - 25% - Note the University policy on scheduling of final exams "Students scheduled for more than three examinations on the same day may arrange to have the examination in excess of three [that means the 4th one] rescheduled for another time during the examination week." Therefore, I do not anticipate rescheduling a final for anyone.

Hour exams may include a mixture of different types of questions, such as short-answer, multiple-choice, true-false, and/or short essay. Each exam will include both an individual and a group exam component. The final exam will contain only multiple choice questions.

Learning improves when students work together. All students will be asked to form a class group of 4 students by the end of the second week of the semester. I prefer that you form groups of your own choosing, but if necessary, I will assign you to a group. Group members are asked to sit together in every lecture. Occasionally, groups will be asked to work together during class on a problem designed to reinforce lecture material. In addition, class groups will be allowed to work together at each exam, in the following way. For the first part (40 minutes) of the exam, students will work individually, and turn in individual answer sheets. After that time, students will assemble by groups and go over the exam together, turning in one group answer sheet. No student will lose points if the group score is lower than his/her individual score. If the group score is higher than the best individual score from the group, then each student in the group will earn bonus points (maximum limit 5 points out of 100 added to exam score). This format does not apply to the final exam, nor to make-up exams.

Groups are also encouraged to spend time studying together. You should exchange phone numbers with members of your class group early on, and schedule occasional meetings outside of class to review course material and quiz each other. After the first exam, you will have a chance to join a different group if you are unhappy with your existing group.

G. Students requiring accommodations

CMU provides individuals with disabilities reasonable accommodations to participate in educational programs, activities and services. Students with disabilities requiring accommodations for participation in class activities or meet course requirements should contact me as early as possible.

Makeup exams are available only to students who have a legitimate excuse for missing an exam, such as personal illness or injury, sanctioned athletic team event out of town, or death in the immediate family. If you know in advance that you must miss an exam, see me in advance and bring documentation to support your anticipated absence. If you miss an exam unexpectedly because of last-minute illness or accident, contact me when you return to campus (or by phone if you will be away for some time) with documentation of your situation. In accordance with University policy, makeups for the final exam will be scheduled for Friday Dec. 17.

Students wishing to make up for poorer than expected exams, or to boost scores, can write up to three short essays, attend a microbiology seminar, or attend a microbiology conference for a maximum of 3 points extra credit.

Essays - Essay topics will be posted on the course web page with appropriate due dates. You may write up to three short (2-3 pages, double-spaced) essays on suggested topics during the semester, if you meet the appropriate deadlines. Each paper submitted on time will earn up to 1 point added to the course grade, as follows:

• 1 point - good work, appropriate references,
• 1/2 point - basically acceptable content but marred by mechanical problems such as incorrect spelling or grammar, or lack of clarity in explaining the topic, lack of or inappropriate references,
• 0 point - unacceptable or plagiarized.

**Any evidence of plagiarism will result in zero points for all students involved and denial of any extra credit points otherwise earned in the course. Essays should include at least two citations to primary literature, not textbooks or internet sources.

Fun tips

Seminar - "Ethanol from Sugar Beets - A Sweet Idea" Dr. Joy Doran, CMU. Thursday, October 14. BR 176, 4pm.

• 1 point - 1 page summary of the seminar

Meeting - "Microbial Ecology and Infectious Disease: Exploring the Connections" Michigan Branch of the American Society for Microbiology at Lansing Community College. Saturday, October 9. Registration for this meeting costs $10, ($7 for members). If you pre-register by Sept. 25, you get lunch too. Students who wish to attend this meeting should see me as soon as possible about arranging transportation to Lansing. Attendance at this meeting may result in the addition of 3 points to the course grade. Points will be added as follows:

• 3 points - attendance and a written 1 paragraph summary of each of the primary talks,
• 1 1/2 points - attendance only,
• 0 point - display of behavior unbecoming to a professional microbiologist (and/or embarrassing to your instructor!).

As you proceed upward in course level difficulty from 100 to 200 to 300, and so on, you need to develop greater responsibility for your own learning. The ultimate goal of college is to develop independent learners and critical thinkers. Therefore, you will find that less structured learning assistance is provided for you in this course than was provided, for instance, in BIO208. This does not mean that I am not still happy to help you with any material during my office hours.

In order to succeed in this course you should plan to attend all lectures, take careful notes, allow ample time to read and study assigned material and turn assignments in on time. You will get more out of lectures if you read (or at least skim) the assigned readings before lecture and then reread relevant material carefully soon after lecture.

You should plan on spending a minimum of two hours of study time for each hour of lecture. This is standard academic advice you will find in any book on how to study. This is a minimum requirement for most students to perform satisfactorily (C level). If you desire an A, you will probably need to put in more time than this minimum recommendation. If you begin to fall behind, make every effort to catch up quickly, otherwise you may find yourself swamped with too much material to assimilate before a test. Tips for scheduling your time.

Many of you will find attending lectures and reading the text is all the support you will need to do well in the course. Some of you may have problems with some of the material. I offer several forms of assistance to help you with difficulties you may experience.