Syllabus

MCB 426 Bacterial Pathogenesis

GENERAL INFORMATION

Office Hours. As of now, I will have office hours in B209 Chemical and Life Sciences Laboratory (CLSL) from 8:30-10:00 a.m. on Mondays and Tuesdays and 4:00-4:30 p.m. on Wednesdays. If you need to speak with me at another time, please email me at bawilson@life.illinois.edu to arrange an appointment. If you would simply like to drop something off and cannot find me, my mailbox is in B128 CLSL. And, of course, I am always available to answer questions via email!

TA. Your TA for this semester will be Carolyn Keeton (ckeeton2@illinois.edu, 333-7289). She will be helping me with grading and is available for questions, if I am not available.

Course Time and Location. 140 Burrill Hall at 3-4 p.m. on Mondays, Wednesdays, and Fridays. Hourly exams will be at 3-5 p.m. in a different location, as indicated on the schedule.

Course Overview. Microbiology 426 is an advanced microbiology course that will cover the mechanisms by which bacterial pathogens cause infections in humans or animal models. This course will not, however, make an attempt to cover every bacterial disease known to man or to describe in great detail the symptoms and treatment of each disease. Instead, the material covered will focus on the general mechanisms of virulence with examples from a select number of well-studied bacterial pathogens and will emphasize the interactions and interplay between these bacteria and their hosts. Also emphasized will be the way in which this information was obtained from a historical point of view, approaches that researchers are currently using to study bacterial pathogenesis, and how that knowledge is currently being applied to the rational design of new vaccines and therapeutic agents. It is hoped that the student will come away with a general knowledge of the various strategies that bacteria use to survive and multiply within their host, and in turn, the strategies used by the host to fend off infections by bacterial pathogens. Current issues on scientific policies and socio-ecological trends in bacterial pathogenesis research will be included as they relate to important aspects of modern molecular microbiology. Although this is a course on bacterial pathogens, considerable time will be devoted to eukaryotic cell biology and immunology in order to fully appreciate how host defenses play a major role in "shaping" strategies used by the bacterial pathogen. In addition, a significant amount of molecular biology and biochemistry will be discussed, so it is imperative that you have had coursework in these areas to keep up. For example, if you do not know the difference between a prokaryote and a eukaryote, Gram-positive and Gram-negative bacteria, transcription and translation, a bacteriophage and a macrophage, a plasmid and a transposon, an enzyme and a protein, an endosome and a lysosome, or a colony and a plaque, then you are going to have difficulty in this course. The majority of the students in this course are seniors, with ~5% advanced-standing juniors and 15-20% 1st and 2nd-year graduate students. If you are an undergraduate student and have not had the prerequisite course MCB 300 (introductory microbiology) and have not had or are not concurrently taking the prerequisite course MCB 354 (biochemistry), you probably will find this course challenging (if you are unsure what is best for you, come see me and we can discuss it). Since a companion laboratory course, MCB 428, covers the identification of bacterial pathogens and the diagnosis of bacterial infections, these topics will not be emphasized in this course.

Companion Course for Graduate Students and Undergraduates Seeking Honors Credit. There is a supplementary primary literature-based discussion course (MCB 526, CRN#54202) offered for graduate students (required for microbiology graduate students) that will meet once a week for ~1hr (at time and location to be arranged after first week of classes). Undergraduates who wish to take MCB 426 for honors credit may do so by attending and participating in this course (but do not enroll in MCB 526, instead register through your honors program for honors credit, e.g. James Scholar honors credit form). Please see me for further details.

Web Resources. This course has a companion MCB 426 webpage. It can be accessed at: www.life.uiuc.edu/mcb/426. On the first day of class, I will provide you with a password for gaining access to the site. On it will be this syllabus, the schedule, lecture outlines/notes, links to previous years' tests, study questions, and a course Q&A page (where your questions will be posted and answered by myself). My lecture notes will also be posted on the web as a downloadable pdf file. I will try to have each of the lectures posted on the web by the evening before the lecture; however, past experience has proven that this is not always possible. In such (hopefully rare) cases, the notes should be posted by the morning of the lecture. In addition to the lecture outlines you will also find links to figures that are used in class, scientific literature that pertains to material presented in class and links to other biology sites, which you might find interesting and useful as supplementary material. Please use my email (bawilson@life.illinois.edu) for asking questions regarding course material or other questions about bacterial pathogenesis that you might have. In addition to emailing you back my answers directly, I will post (anonymously) your question(s) and my answer(s) on the Q&A page. The Q&A page will also have general announcements relevant to the course (e.g. upcoming seminars), as well as any last minute changes, clarifications or corrections to the lecture material or schedule. Maintaining and improving this webpage will be an ongoing project, so please bear with me. Please feel free to make any suggestions that will make the site more interesting or useful to you. Please note that my webnotes and the information on the links that I provide are copyrighted material for your personal, educational use only as a student enrolled in this course. Since I provide them free to you, they are not for sale or transfer!

Textbook. The second edition of the textbook entitled Bacterial Pathogenesis: A Molecular Approach by Drs. Abigail Salyers and Dixie Whitt of this Department will be the primary recommended reference textbook for this course, and you will be responsible for the assigned material in it. However, due to the ever-growing expansion of research in bacterial pathogenesis and a continual shift in focus of research in this area, please keep in mind that there will be many concepts and discussions of materials and topics that are not presented in the textbook, but which will be covered in my lectures and webnotes. (We are currently writing the third edition of the textbook, but it will not be available until next year.) I will provide at the beginning of each lecture a list of additional reading material that might be helpful to you. You will be responsible for all of the assigned material (text chapters, webnotes, lectures), but of course, an emphasis will be placed on the material in my notes and that covered in class.

Examinations:

Number and Timing of Examinations. There will be 4 examinations, each of 100 points, given at the times indicated in the schedule, 3 during the term and 1 during finals week. If there is a problem or conflict, please see me well in advance, if possible.

Review Sessions. At the end of each topic, there are a number of Study Questions, most of which are or are based on past exam questions, which we will go over together in class. Students are encouraged to ask questions at that time. In addition, most of the lecture before each exam will serve as an opportunity for students to ask questions. All of the exams from previous years are available on the webpage and students are strongly encouraged to study them. If you have a question, you can ask me during office hours or during review sessions. However, there will be NO answer key provided, and I will NOT directly go over or give out answers to previous exam questions unless in class or during scheduled review sessions. Please also bear in mind, that the material covered on old exams may not be the same or in the same order as that covered this semester. Students are responsible for being able to discern the relevant material for each exam.

Type of Exam Questions and Material Covered. Each examination will consist of short answer or essay questions, as well as problem-solving questions requiring interpretation of experimental data and design of experiments. Answers are to be written in black or blue INK in exam booklets provided (no pencils or erasable ink!). Questions from previous exams (without answers) will be provided on the webpage to aid in your studies. The questions at the end of each chapter in the textbook are also helpful and are designed to promote critical thinking about the material. Tests will cover primarily (but not limited to) topics and material presented in class or those specifically referred to in class (including study questions and previous exam questions). Note: I will not post answers to the exam questions! We will be going in detail over each exam upon its return. If you miss that session, I expect you to look up the answer yourself or ask a fellow classmate. If you have done so and you are still uncertain about the answer to a question, you may come to me during my office hours.

Grading procedure. Final grades will be based on the top three exam scores. You must take at least three of the four exams. I must be able to average at least three exam grades! All the exams are equally weighted. There will be no makeup exams! If you have an excused absence from an exam and you have talked to me about this, the average of the other three exams will be used. However, you will be permitted only one such absence; subsequent absences will result in a zero for that exam. Except for the final, the first three exams will cover primarily material from after the previous exam. The final will be cumulative and will count as one hourly. The Final Exam will be optional! If you are satisfied with the grade you have going into the final (i.e. after the third exam), then that will be your grade and you do not have to take the final. But, you must tell me by the last day of class if you are going to take the Final. Those who miss one of the hourly exams must take the final (no option). The plus/minus ABCDF grade system will be used, where A=4.0. A grade of "A+" will be given only at my discretion for truly exceptional performance, effort, and participation. Each exam will be graded according to a curve in which the median score will be a B (3.0) and in which the grade cut-offs will be based on the undergraduate scores. Those who do not have a grade of "C-" or better after the third exam must take the final (no option).

Challenging an Exam Grade. You will have one week after an exam is handed back to the class to challenge the grading of the exam. To challenge a grade, you must return the exam plus a clearly written explanation of your reason for challenging the grade to me, and I will seriously consider it. I will NOT re-grade questions that do not have a written explanation/request with justification attached to them. After one week, NO changes will be made! Cautionary Note: It is advisable to use a different color pen for marking on your returned exams, particularly if you think that you might be requesting a regrade.

Extra Credit. To encourage students to broaden their scope of knowledge in microbiology and to gain a "flavor" of current research topics and trends, I will continue this year to allow students to earn extra credit toward their individual final grade: up to 2 points for every bacterial pathogenesis-related seminar or up to 1 point for any microbiology-related seminar (sorry, other types of seminars will NOT count) that they attend during the course of the semester, including seminars in the Department of Microbiology and microbiology-related seminars in other departments, colleges, and institutions, and at meetings (e.g. the Midwest Microbial Pathogenesis Meeting). RULES to receive full credit: The seminar must be a full-length (~1-hr) seminar given by a professor; only half-credit will be given for 30-min seminars. Student seminars do not count! In order to earn credit for a particular seminar, you must submit by the end of the next class period (second class period for long meetings) a summary of each seminar (last acceptable date = December 9), including the title, the speaker's name and affiliation, the time and location of the seminar, and 1-2 page summary (type-written, single-spaced, 10-12 point) of the main points of the seminar and what you learned from it. Do not worry, I understand that the summaries will be less than masterpieces in the beginning, but trust me, as the semester progresses and you learn more, you will find that your summaries will improve greatly. For full credit, all I expect is that you make an obvious, solid effort. And, yes, I do read them!

Academic Integrity. As UIUC students, everyone in this course is expected to be completely familiar with the UIUC Code of Policies and Regulations Applying to All Students Regarding Academic Integrity. Cheating will NOT be tolerated in this course. Any student found cheating will receive a failing "F" grade for the course and could face recommendation for suspension or dismissal from the University.

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