mcb 229

Syllabus for Spring 2003

Prof. Thomas Terry
Last revised: Tuesday, January 21, 2003

A. General Information


Welcome to "Fundamentals of Microbiology", MCB 229. This course is a comprehensive, one-semester introduction to the world of microbes, emphasizing mainly bacteria and viruses, with a little material on fungi. The world of microbes is, by definition, composed of those creatures too small to be seen with the naked eye. We tend to ignore what cannot see, but as we learn how how to study them, we will learn that microbes are the most abundant, the most ancient, the most diverse, and the most successful of earth's creatures. There are far more microbes than macrobes (visible organisms), not only in numbers but even in biomass. New methods for the study of microbes have radically changed the study of this invisible world. Microbes provide many benefits, but also include many pathogens that cause a wide range of diseases. Our study will include a significant focus on pathogenesis, including the mechanics of host defenses provided by fixed and learned immune mechanisms.

Microbiology is a laboratory science, and the laboratory is an integral and important part of this course. We will be training you in the basic skills needed to work with bacteria: proper use of the microscope, how to prepare stained slides, aseptic technique for transfer and inoculation of bacteria, use of various media to select, isolate, and characterize bacteria. We will challenge you with a number of learning tasks: isolating and identifying unknowns, an "antimicrobial olympics" where you will have to isolate specific organisms that produce antibiotics, then vie for the honor of finding the most potent antibiotic producer, surveying the distribution of microbes on your body, as well in water, meat, and soil samples, and much more.

What preparation do you need to take this course? I recommend that you have had at least one prior course in biology, preferably Biology 107 or a comparable course that introduces the structure and function of cells and the genetic code. If you don't have this, don't worry -- you may find certain things a bit more challenging, but you can pick it up. In addition, you should have some background in chemistry, preferably a semester of organic chemistry, which can be taken concurrently. The machinery of microbes is chemical, and the only way to understand how many microbial processes work is to examine some of the details of this machinery. I will often use diagrams that show organic molecules, and expect you to understand what I am talking about without my having to go back and explain what these diagrams mean. Your textbook also uses chemical diagrams where needed.

If you are unsure whether your background is sufficient to take this course at this time, I urge you to spend a few minutes skimming the textbook and perusing lecture notes online. If you find these materials incomprehensible in substantial part, you should probably wait until your background preparation is better. Feel free to visit my office to discuss this.

B. Course Logistics

Lectures: meet Tuesday and Thursday from 8:00 - 9:15 a.m. in TLS 154.
Laboratories: meet on scheduled dates Monday, Tuesday, or Wednesday in TLS 207. You must attend the section for which you are registered. There are usually a few drops as the semester progresses, so there may be a few openings in other sections -- if you want to switch to a section that is currently filled, check PeopleSoft registration every few days to see if a space opens up. If you must miss your scheduled lab, ask me as soon as possible if it is possible for you to attend a different lab section that week -- if space permits, I will write you a lab pass to allow for this.

On some occasions, you may need to visit the lab briefly within 1-3 days to record data or transfer cultures, and you will need to plan the timing for such visits carefully in order not to interfere with other classes being held in TLS 207. Here are the ground rules for access outside of your regular lab time:
  1. If laboratory instructors are giving a talk, or administering a quiz, you are not allowed to enter TLS 207 at that time. You must wait or come back later. Please observe this rule at all times!
  2. If another lab is in session in TLS 207, and students are actively at work (i.e., situation "1" above is not in effect), you should not use bench space in TLS 207. However, you can access your incubator boxes and take materials to the adjacent room TLS 203, which is available at all times except for a scheduled class Wed 3:30-5:30.
  3. If there is no scheduled class in TLS 207, you may use that room, up until 15 minutes before the next scheduled class. At that time, you must either move to TLS 203 (if available) or leave.
  4. If any room becomes too crowded, you may be asked to leave or denied entry by a lab instructor or supervisor. In such cases, please be flexible and return later. We must enforce safety and fire regulations regarding crowding.
  5. Security regulations require us to close the labs when there is no supervisor available nearby. Labs are normally open shortly after 8 a.m. (please wait until the morning cleanup crew has swabbed down all benches before using them) and closed at 4 p.m., unless a scheduled class is in later session. Labs are not open on weekends.
Course instructor: Prof. Thomas Terry
Office location: Biology/Physics 402B
Office hours: Mon 2-3 p.m., Tues 9:30-10:30 a.m., Wed 9-10 a.m., or by appointment
Phone: 486-4255. If you leave a message, pronounce your name and phone number slowly and clearly! About 10% of student calls are partially unintelligible and I cannot respond because I don't get your name, your number is not pronounced clearly, or you fail to leave a number.
e-mail: thomas.terry@uconn.edu

C. Materials needed. Available at the UConn Coop

1. Required Text: Microbial Life by Perry, Staley, and Lory. Available at UConn Coop. This is a new text, with more current information than many texts. You should consider keeping it as a reference.
2. Required Text: Fundamentals of Microbiology Laboratory Manual, May 2001 version. (Note: this is different than the manual used last fall.)
3. Required for Laboratory: wax marking pencil (dark color) or felt-tipped indelible marking pen (not water soluble). Available in supply dept.
4. Required for Laboratory: disposable (not cloth) lab coat. State and federal regulations make lab coats a requirement when working with certain bacteria, including some of those we use regularly. Once potentially contaminated by use, coats may not be removed from the lab without being sterilized -- hence we cannot allow use of cloth coats that you take away after lab. Bring your coat to the first lab, with your name marked on the coat. Store coats in drawers under your lab bench, or as indicated by lab instructor. Lab coats are assumed to be contaminated and are not to leave the lab after initial use. At the end of the semester, all lab coats will be autoclaved and disposed of.
5. Strongly Recommended: 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. Note: when sending me e-mail, please list "MCB 229" plus a brief topic in the subject field. All my e-mail is sorted, and your failure to include this subject may cause your message to be delayed or ignored.
6. Password access to protected images. Certain images must be kept behind a password barrier in order to comply with licensing and copyright provisions. Record the userID and password in the space below so you can find it when you need it.
UserID   Password


D. Reading Assignments and Study Guides

Reading assignments in the text are listed on a separate Lecture Outline index page. 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. I will hand out weekly study guides with goals and questions to focus your study. You should use these when reading to make sure you do not skip over important concepts. Study guides are available from the Study Guide index page.

You should plan on reading approximately 20-40 pages in the text per class. 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. Reading a text is not like reading a novel. Keep a pad of paper next to your text while reading and use it to sketch diagrams, make outlines or concept maps, jot down unfamiliar terms, and make other notes to yourself. Stop frequently to ask yourself "What did I just read"? Work with practice questions to see what you don't understand.

E. Laboratory

The lab will count for 30% of your course grade. Lab grades will be based on satisfactory completion of exercises, on keeping clear and accurate records, on demonstrated mastery of critical lab skills such as the use of a microscope, pure colony isolations, identification of microorganisms, and ability to correctly interpret diagnostic test results, on quizzes, and on quality of work and reports. Lab grades will be determined by your Teaching Assistants (TAs).

The separate Laboratory Schedule lists exercises to be done. You should come to lab having read the lab exercise beforehand! The lab will generally take 2 to 2 1/2 hours. There is usually no opportunity to make up labs missed -- different cultures and materials are prepared for each lab, and these are not available otherwise. You should make every effort to attend all labs. If for some reason you miss a lab, you are responsible for the material you missed, and should make every effort to get your lab partner to show you what was done. On rare occasions, there may be a seat available in a different lab section that you may be allowed to attend after receiving a permission slip from the instructor -- ask by e-mail or in class if you miss a lab.

Note that section 007L, originally scheduled for Wednesday evening, was dropped because of enrollments. The 3 students registered for this section were notified at their UConn e-mail account and asked to register for a different section. If you were one of the students affected, we apologize for the inconvenience.

F. Exams and Grades

Two 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. Exams will cover topics discussed in class as well as any questions from study guides and posted lecture notes, whether discussed extensively in class or not. The average of the 3 exam scores will count for 70% of your course grade. Your laboratory grade will count for the remaining 30% of the course grade.
Exam #1: Tuesday, Feb. 25
Exam #2: Tuesday, April 8
Final Exam: Monday, May 12, 1-3 p.m.
(scheduled by registrar)

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.

If you work with the center for students with disabilities (CSD) and cannot work effectively in the classroom setting, make arrangements with me prior to each exam. I can arrange for you to take the exam at the CSD with their proctors. Note that the group exam feature is only available to students who take the exam at the regulary scheduled room and time, and will not be available to students taking the exam at CSD or taking a makeup exam.

If English is not your native language, you may bring a translation dictionary. You don't have to have any certified disability or difficulty to take advantage of this offer. Once you have begun the exam, I ask that you not leave until the exam is complete, so please use the rest rooms before starting.


Note: on exam days, you are welcome to arrive early if you want to have extra time and not feel stressed. I will be here at 7:40 a.m. on exam days, so you can have up to 20 minutes extra. If you experience exam anxiety, I strongly recommend taking advantage of this! (This does not apply to the final exam, which is scheduled for a 2-hour period long enough to allow for extra time.) Consider this one of the few advantages of having the first class of the day!

G. Class Groups

In the "real world", much work is done in groups. Learning improves when students work together in groups -- the act of verbalizing your thoughts significantly enhances learning, and groups can promote this. Every employer I've talked to tells me that the one failing of college is that we don't adequately train students to work together -- this is standard procedure in the working world! I encourage you to form groups and to work together wherever possible, and have structured certain activities to encourage this.

H. Academic Integrity

A fundamental tenet of all educational institutions is academic honesty; academic work depends upon respect for and acknowledgement of the research and ideas of others. Misrepresenting someone else's work as ones own is a serious offense in any academic setting and it will not be condoned.

Academic misconduct includes, but is not limited to, providing or receiving assistance in a manner not authorized by the instructor in the creation of work to be submitted for academic evaluation (e.g. papers, projects, and examinations); any attempt to influence improperly (e.g. bribery, threats) any member of the faculty, staff, or administration of the University in any matter pertaining to academics or research; presenting, as one's own, the ideas or words of another for academic evaluation; doing unauthorized academic work for which another person will receive credit or be evaluated; and presenting the same or substantially the same papers or projects in two or more courses without the explicit permission of the instructors involved.

A student who knowingly assists another student in committing an act of academic misconduct shall be equally accountable for the violation, and shall be subject to the sanctions and other remedies described in The Student Code.

I. Makeup Policy

Makeup exams are available only to students who have a legitimate excuse for missing an exam, such as illness, sanctioned athletic team event out of town, or death in the immediate family.

If you miss an exam, or know in advance that you will have to miss an exam, fill out the Petition for Makeup Exam form and return with appropriate documentation. Until I have your completed form, I do not have the information needed to decide whether you are entitled to a makeup, so please don't bother leaving voice messages on my phone or e-mails -- just fill out the form and get it to me as soon as possible.

Makeup exams will be given on the following days for those students who missed the scheduled exam and who have received permission to make up the exam. Makeups may include short-answer, short essay, and/or multiple-choice questions. Note: if you have Monday lab, try to leave lab by 3 p.m. -- if that is not possible, just come as soon as you can but not later than 3:30 p.m.
Exam # Date Time Room
Makeup for Exam #1 Monday, March 3 3 p.m. TLS 153
Makeup for Exam #2 Monday, April 14 3 p.m. TLS 153

J. Extra credit option

Students wishing to improve their course grade can write up to three short essays. Topics on specific microbiological issues will be posted at different stages of the course on our Web site, with appropriate due dates. Each paper submitted on time may earn one of 3 grades: The total of these grades will be added to the final course grade (out of 100 points), after any scaling and determination of letter grades has been done. Any evidence of plagiarism will result in zero points for all students involved and denial of any extra credit points otherwise earned. Essays must include at least two reference citations using formats indicated in the extra credit index page. Failure to include references will automatically result in a grade of 0 for that essay.

K. How to succeed in this course

In order to succeed in this course, you should plan to attend all lectures and labs, take careful notes, and allow ample time to read and study the assigned material. You will get more out of lectures if you can read the assigned chapter before the lecture, then read relevant material carefully as soon after the lecture as convenient. You should plan on spending at least two hours of study time for each hour of lecture. 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 an exam.

Some of you may find that attending lectures and reading the text is all the support you need. Others will have problems with some of the material. I offer several forms of support to help you with difficulties you may experience. Different students have different optimum learning stratagems; experiment with the options listed, and find what best helps you.
  1. Handouts will be given from time to time in lecture; these may include suggestions for specific material and/or study problems. Spend some time with these materials as soon as you can review them -- don't just put them aside and wait till the night before an exam to look at them.
  2. I will be posting certain materials for your use on our class website:
    http://www.sp.uconn.edu/~terry/229sp03/index.html (case sensitive -- be sure all is lower case). If you are using your own computer, bookmark this page once you set it up. These materials will include:
    1. lecture outlines, including access to most graphic materials
    2. an announcement page which lists any information relevant to the course.
    3. study guides which list terms and ideas you are responsible for, specific page and figure references to important material in the text, and questions to help focus your study.
    4. interactive practice quizzes to help you prepare for exams
    5. links to interesting microbiology sites on the Web. These will be interspersed in lecture outlines.
  3. I will offer review sessions every few weeks, especially shortly before exams. These sessions offer you an opportunity to ask questions about any of the material you wish to have explained.
  4. I am available for individual consultation regarding any aspect of the course. If you have unanswered questions or concerns, or are in serious academic trouble, contact me!
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