MCB 426 Bacterial Pathogenesis

GENERAL INFORMATION

Course rubric: MCB 426 (3 credit hours, CRN#30515)

Moodle Website: https://learn.illinois.edu/course/view.php?id=7171

Class Time: Mondays, Wednesdays, and Fridays at 11:00-11:50 am

Class Location: 106B1 Engineering Hall (1EH), 1308 West Green Street. 

Note: Hourly exams will be held at the times and locations indicated on the course schedule.

Course Instructor: Brenda A. Wilson, Ph.D., Professor of Microbiology

Contact Information:

Office: B209 Chemical & Life Sciences Laboratory

Email: bawilson@life.illinois.edu

URL: http://mcb.illinois.edu/faculty/profile/wilson7

Office hours: Wednesdays 3:30pm-5:00pm or by appointment, B124 CLSL (note: this is not my regular office). If you need to speak with me at another time, please email me to arrange an appointment. If you would simply like to drop something off and cannot find me, my departmental mailbox is in B124 CLSL or you can leave it in the folder on my office door, which is B209 CLSL. And, of course, I am ALWAYS available to answer questions via email! Just be sure to include "MCB 426" in the subject line, so that I know it is "high priority".

Course TA: Your TA for this semester will be Mr. Nathan Clemons, Email: nclemons@illinois.edu. He will be helping me with grading and is available for questions, especially if I am not available, via email or during his office hours: Fridays 4:00pm-5:00pm in the MCB Learning Center, 101 Burrill Hall

Course Objectives:

Microbiology 426 is an advanced microbiology course that will cover the mechanisms by which bacterial pathogens cause infections in humans and/or animals. 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 understanding virulence mechanisms and disease transmission, combatting infectious diseases through antibiotics and the rational design of new drugs, 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 interact with each other and their host, to survive and multiply within their host and to cause disease, 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 and infection biology.

Note:  This is a course on bacterial pathogenesis, which means that time will be devoted to host-pathogen interactions, and so this will entail a working knowledge of eukaryotic cell biology and immunology in order to fully appreciate how host environment and defenses play a major role in "shaping" strategies used by the bacterial pathogen to overcome those defenses and cause infection. 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% 1st and 2nd-year graduate students. If you are an undergraduate student and have not had or are not concurrently taking the prerequisite course MCB 300 (introductory microbiology) and the courses MCB 354 (biochemistry) or MCB 408 (immunology), you probably will find this course a bit 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 diagnostic aspects of bacterial infections, these topics will not be emphasized in this course.

Companion Course for Graduate Students and Undergraduate Students 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 a 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.

Course Website & Moodle Resources. This course has a companion MCB 426 Moodle webpage, accessed at: https://learn.illinois.edu/course/view.php?id=7171. If you are enrolled in the class, then you will have access to the course website using your own UIUC Active Directory password. On the Moodle website will be this syllabus, the schedule, lecture outlines/notes, links to previous years' tests, study questions, a course Blog page (where you may post any questions and I will answer them - discussions from others are encouraged!), and other course material. My lecture notes will be posted on the web as a downloadable pdf file. 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 third edition of the textbook, entitled Bacterial Pathogenesis: A Molecular Approach by Drs. Brenda A. Wilson, Abigail A. Salyers, Dixie D. Whitt, and Malcolm E. Winkler (also available as an eBook) will be the primary recommended reference textbook for this course, and you will be responsible for the assigned material in it. Note: this edition was published in 2011. 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 may be concepts and discussions of materials and topics that are not presented in the textbook, but which will be covered in my lectures. I will provide for each lecture any additional reading material that might be helpful to you. You will be responsible for ALL of the assigned material, with an emphasis on corresponding text chapters, relevant study questions and example questions from previous exams, and class lecture notes.

Examinations:

Number and Timing of Examinations. There will be 4 examinations, each worth 100 points, given at the times and locations indicated in the schedule, 3 hourly exams during the term and 1 exam during finals week. You will have at least 2 hours to complete the hourly exams and up to 3 hours to complete the final exam. 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 and review material. 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 lectures, office hours or review sessions. However, there will be NO answer key posted, and I will NOT 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 (if uncertain, you may ask me during class, review session or office hours).

Type of Exam Questions and Material Covered. Each examination will consist of short answer or essay-style questions, with emphasis on problem-solving questions requiring interpretation of experimental data and/or 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 – students are strongly encouraged to do this. Note: the 3rd edition of the textbook also has many of my old exam questions incorporated at the end of relevant chapters. The study 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), but it is expected that students should be able to extrapolate material that they have learned and to apply that information to new but similar scenarios. Note: I will NOT post answers to the exam questions! We will be going over each exam in detail upon its return. If you miss that class 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. I expect students to come to class and ask questions while we go over the exam, so I will not go over an entire exam with a single student during an individual appointment outside of normal office hours.

Grading procedure for exams. 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 score of "0" for that exam. Except for the final, the first three exams will cover primarily material from after the previous exam. The final exam will be cumulative, but 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., your grade 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 Reading Day (i.e., the day after the last day of classes), if you are going to take the Final Exam. 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 1 standard deviation from the mean and on the undergraduate student scores. Those who miss one of the hourly exams must take the final (no option). 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 to me the exam plus (on a separate sheet of paper) a clearly written explanation of your reason for challenging the grade (specifically state which questions you want me to regrade), and I will seriously consider it. Except for simple score calculation errors, I will NOT re-grade questions that do not have a written explanation/request with justification attached to them. After one week, NO changes to grades will be made! Cautionary Note: It is strongly 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 enhance the students' learning experience by gaining 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 Annual Midwest Microbial Pathogenesis Meeting). RULES to receive full extra 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 extra credit for a particular seminar, you must submit within 1 week of the seminar a summary of that seminar (last acceptable submission date = December 12), including the title, the speaker's name and affiliation, the time and location of the seminar, and a 2-page summary (type-written, single-spaced, 10-12 point, 1" margins) of the main points of the seminar, including a paragraph about any connections to material covered in class and pointing out what you learned from the seminar. Submit your summaries to the Moodle site. In some cases, you may find the material covered difficult to understand. In such cases, it may be necessary for you to look up information that was not clear during the seminar (perhaps by reading some recent papers by the speaker) - this is acceptable so long as you provide a citation of the source you used. 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 (it thrills me to see this progression in students!). 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 Student Code, Article 1. Part 4. Academic Integrity (sections 401-406). Cheating will NOT be tolerated in this course. Any student found cheating could face receiving a failing "F" grade for the course and recommendation for suspension or dismissal from the University.