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Biosc 1999 Medical Microbiology Syllabus 03-1

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Biological Sciences 1999

Medical MicrobiologyFall Term 2001 (01-2)

Instructor: Dr. Susan Godfrey

A359 Langley Hall

624-4254

e [email protected]

Office hours Monday 10:00-11:00 amWednesday 5:00-6:00 pmThursday 5:30-6:30 pm

web sites http://www.pitt.edu/~ssg1/http://www.pitt.edu/~biohome/Dept/Frame/Faculty/godfrey.htm

Teaching

methods:

The class, scheduled for M, W, F 9:00-9:50 am A214 Langley Hall, will consist primarily oflectures but include a variety of other classroom activities when suitable for specifictopics.

Textbook

(Required):

Bacterial Pathogenesis, a molecular approach, 2nd edition, A.A. Salyers and D.D. Whitt, ASMPress, 2002.. A copy of the book will be on reserve in Langley Library (no overnight). For afew topics alternate resources will be recommended, in particular the on-line textbook Microbiology & Immunology On-line, http://www.med.sc.edu:85/book/welcome.htm,where materials will be assigned to support lectures on viral, protozoan, and fungalpathogens.

Other course

materials &

study

supports:

• Course handouts, lecture illustrations, exam preparation materials, and other studymaterials will be provided via the BlackBoard website. When you log into Courseweb athttp://courseweb.pitt.edu/ you will be presented with a list of the BlackBoard sites inwhich you are registered. This site will be the main way that course materials aredistributed to the class: if you have problems getting access to the site, please let me know.

• Additional print materials have been placed on reserve in Langley Library. These areprovided for your interest, and relate principally to social, economic, and political factorsthat influence public health measures relevant to the diseases discussed in this course.When I use material from these sources in a lecture, for examinations you will beresponsible only for the information provided in the lecture, and are not for other

information to be found in these sources.• Lecture illustrations will be posted on the course web site at least 24 hours prior to eachlecture. Students are encouraged to bring these to class, to keep up with the text readingassignments for each lecture, and to complete the questions for thought and review at theend of each text chapter.

• I welcome office hours visits, phone or e-mail questions, or visits by individualappointment, whether to answer questions about the course materials, look over yourpractice work to give you feedback, or to get to know you individually.

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Course

rationale:

Students who have successfully completed the prerequisite course Microbiology (Biosci1850) will be familiar with the basic types of ways that microorganisms earn a living. Inthe present course we will explore the pathogenic life style in greater detail, particularlyfor bacterial pathogens, from the host as well as the pathogen perspective.

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Course Goals: This course aims to familiarize students with the basic biology of pathogenesis, and thebasic biology of host response to pathogenic attack. We will consider also ways and meansof preventing and treating various types of infections, issues surrounding bacterialresistance to antibiotics, epidemiology and public health measures, and the use of

microbes as bioweapons.

Grading: • There will be two hour exams during the term, given during regularly scheduled classperiods (see attached schedule). Each of these exams is mandatory. In addition, there willbe a 2 hour final examination given during the final examination period, as set by theregistrar: Wednesday December 11 from 10:00 to 11:50 am in A214 Langley Hall. The firsthour of the final exam will cover material appearing on the syllabus after Hour Exam 2,and the second hour of the final exam will be cumulative over the whole course. Thescheduled examinations will consist of short essays and short answer questions. If youmust request a make-up examination and your request is granted, the make-upexamination will be in oral format.

• There will be one paper, assignment details as given below.

• Your final grade will be based on the two hour exams, your final exam scores, and thepaper, as shown below. Your final grade will be based on the total points earned duringthe semester (500 points available). The course will be graded on a curve and letter gradeswill not be assigned until the end of term.

Distribution of points for final grade

Hour exams 1 & 2 40% (100 points each)

Final exam 40% (100 points for final third ofcourse, 100 points cumulative)

Paper 20% (100 points)

Special

arrangements:If you have a disability or other difficulty that requires special testing accommodations or other classroom modifications, you need to notify both the instructor and the Office ofDisability Resources and Services. To notify Disability Resources and Services, call 648-7890 (Voice and TDD) to schedule an appointment.

Missed Examinations: If you must miss any exam due to an emergency (illness, seriousinjury or death in your immediate family) you must submit, in writing, yourdocumentation to obtain an excused absence for that exam and request a makeup

examination. If your request for a make-up exam is granted, the make-up exam will be

in oral format. If you must miss the final exam you must also fulfill the conditions required for

the awarding of a G grade (please see below). A car breakdown is not an accepted excuse formissing an examination: please make sure you have reliable transportation. Please use thefollowing guidelines when preparing your request:

1. Your written request MUST indicate your name, the nature of the emergency, andappropriate documentation. At a minimum, medical emergencies require a letter fromyour physician.

2. Your request must be detailed, typed and signed by you. A copy of this requestmust be given directly to each instructor no later than one week after the missed exam,or before grades are due, whichever is sooner.

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If you miss the final exam and have a valid excuse, you may be awarded a G grade, butonly after the excuse has been documented and verified and arrangements to finish the coursework in a timely fashion have been made with the Instructor s.

G Grades:G grades, as outlined in the CAS guidelines, are to be given ONLY when students whohave been attending a course and making regular progress are prevented bycircumstances beyond their control from completing the course after it is too late towithdraw (see the University of Pittsburgh Undergraduate Bulletin). To petition theinstructor for a G grade, you must submit a written request for this grade, and you mustdocument your reason(s) as described above. You will be required to sign an agreementoutlining the specific tasks which must be completed in order to remove the G grade, andthe date by which these tasks must be completed. Failure to complete the work by theagreed upon date could result in a zero recorded for the work not done, and your finalgrade will be calculated with this score.

AcademicIntegrity:

Students in this course are expected to comply with the University of Pittsburgh’s Policyon Academic Integrity: Student Obligations. Any student suspected of violating thisobligation for any reason during the semester at a minimum will be assigned a “0” for theaffected exam or paper. Offenses include, but are not limited to, copying from anotherstudent, copying from unauthorized materials brought into the examination, orplagiarism of any sort. Further consequences may ensue, as outlined in the UniversityGuidelines on Academic Integrity.

Please note that no student may bring any unauthorized materials to an examination,including texts, notes, dictionaries, pagers/beepers, telephones, PDAs, and calculators.Such materials should be left at home, or zipped into book-bags and left under chairs or atthe back of the room. When sources of information are used in writing papers, you must

acknowledge those sources in conventional format. Please see the paper assignmentinstructions for further details.

Please see also my separate page on academic integrity policies in my courses (availablefrom http://www.pitt.edu/~ssg1/).

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Schedule# Biosc 1999 Medical Microbiology Fall 2002

Lecture#

Date Topic Reading**

Principles: the role of Public Health agencies1 8.26.02 Medical microbiology & public health agencies Chapter 1 +h

A disease that points up public health issues

2 8.28.02 Cholera (Part 1) See note 1

Virulence factors: bacterial exotoxins

3 8.30.02 Bacterial exotoxins Ch. 9 to p. 138

9.2.02 LABOR DAY— no classes

4 9.4.02 Bacterial exotoxins (continued) Ch. 9 p. 138 to end

5 9.6.02 Cholera (Part 2) See note 2

Principles: disease detection, description, & diagnosis

6 9.9.02 Methods for establishing causes of diseases, measuring diseases Chapter 2

7 9.11.02 Molecular approaches to diagnosis & characterization Ch. 3 to p. 41

8 9.13.02 Molecular approaches (continued). Ch. 3 p. 41 to end

Issues of detection, description, & diagnosis

9 9.16.02 Evolution of bacterial pathogens tba ‡

10 9.18.02 Sniffing out & defending against bioterrorism agents tba

Principles: physical defenses of the body

11 9.20.02 Defenses of the body: Prevention & phagocytosis Chapter 4

Opportunistic infections when physical defenses fail

12 9.23.02 Insect bites: Lyme disease Chapter 12

13 9.25.02 Review for hour exam 1

F 9.27.02 HOUR EXAM 1←

14 9.30.02 Burns, opportunistic infections, & Pseudomonas Chapter 16

15 10.2.02 Legionnaire’s disease Chapter 20

16 10.4.02 Listeriosis Chapter 27

Principles: chemical defenses of the body

17 10.7.02 Defenses of the body: complement, chemokines, & cytokines Chapter 5

Diseases that subvert chemical defenses of the body18 10.9.02 Staphylococcal diseases Chapter 14

19 10.11.02 Streptococci & enterococci Chapter 15

Principles: immune defenses of the body

20 10.14.02 Antibodies & cytotoxic T cells Chapter 6

Diseases that point up immunity issues

21 10.16.02 Herpes viruses tba

22 10.18.02 A closer look at the herpes viruses tba

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23 10.21.02 The common cold tba

24 10.23.02 AIDS tba

Principles: fighting back with vaccination

25 10.25.02 Vaccination Chapter 7

26 10.28.02 Review for hour exam 2 (none) W 10.30.02 HOUR EXAM 2←

Diseases that point up vaccination issues

27 11.1.02 Pertussis (whooping cough) Chapter 17

Principles: bacterial evasion of our body defenses

28 11.4.02 Bacterial evasion strategies Chapter 8

Diseases that point up bacterial evasion tactics

29 11.6.02 Salmonella species Chapter 26

30 11.8.02 Neisserial diseases Chapter 30

31 11.11.02 A closer look at the gonococcus tba

More diseases that illustrate bacterial exotoxins

32 11.13.02 E. coli– 1 Chapter 28

33 11.15.02 E. coli– 2 Chapter 29

34 11.18.02 A closer look at bacterial toxins tba

11.20.02 THANKSGIVING HOLIDAY— no classes

11.22.02 THANKSGIVING HOLIDAY— no classes

Principles: antimicrobial compounds

35 11.25.02 Antimicrobial compounds Chapter 10

Not all antimicrobial compounds are “antibiotics”

36 11.27.02 Malaria tbaPrinciples: antibiotic resistance

37 11.29.02 Antibiotic resistance Chapter 11

A disease that points up problems of antibiotic resistance

38 12.2.02 Tuberculosis Chapter 19

39 12.4.02 A closer look at TB

40 12.6.02 Course summary & review for final exam

# Guest lecturers have been invited for a few lectures and there may be some adjustments of the lectureschedule to suit their convenience. ** Text is Bacterial Pathogenesis: A Molecular Approach, 2nd edition, A. Salyers & D.D. Whitt, ASM Press, 2002.

+h indicates a handout will be supplied in class

‡ tba = to be announced. This indicates that coverage in the Salyers and Whitt book is not sufficient for thelecture and an additional recommendation of reading from either web-based or print sources will be provided.

Note 1: Lecture 2 reading is Chapter 25 to middle of p. 368, p. 376 to the end of the chapter, and handoutmaterial provided.

Note 2: Chapter 4 lecture is p. 368 to p. 376. You should review from your microbiology course material onregulation of gene expression in bacteria (Biosc 1850 Lecture 25 in 2002).

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FINAL EXAMINATION: as scheduled by the Registrar last spring, this examination will be held on WednesdayDecember 11 from 10:00 to 11:50 am.

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Assigned paper: Biosc 1999 Medical Microbiology Fall 2002You will write an 8 page paper on one of the bacterial disease lecture topics listed among the above lectures.There are 14 such topics and at most two students may choose any particular one of those.

Bacterial disease topics (in lecture order):

Cholera, Lyme disease, Pseudomonas aeruginosa infections, Legionnaire’s disease, Listeriosis, Staphylococcusaureus diseases, Streptococcus diseases (GAS or non-GAS), pertussis, Salmonella diseases, Neisserial diseases, E.coli diseases (HUS or non-HUS), & tuberculosis.

Paper content:

Your paper should either take one aspect of a bacterial disease that is covered in the text chapter/lecture onthat specific pathogen to develop that in more depth than is covered in those sources, or pursue an aspect ofthe pathogenesis of the organism you have chosen that is not covered in the text. In either case pleaseincorporate into your discussion how the aspect on which you focus relates to each of the other major diseaseissues, such as habitat and ecology of the organism, relevant defenses of the victim and how they are breached,virulence factors of the pathogen, technical methods for diagnosis or epidemiological tracking of the disease,other epidemiological considerations, and containment, control, & treatment of the disease.

To support your discussion of new material you must use at least one review article pertinent to your topic

and at least 2 technical articles about the specific aspect on which your focus, citing these sources in correctformat. You may also use additional materials of this type or web sources (when correctly cited) if you choose.

The assignment includes three elements, as follows:

(i) Submit a brief request for topic listing the specific disease you want to be the focus of yourpaper (If two of your classmates have chosen that topic already I will let you know so thatyou can choose another. If > two of you simultaneously request the same topic we’llnegotiate). List a review article you have identified that will give you access to the primaryliterature (in technical journals), and suggest what the main theme of your paper will be.

Due: any tbefore or uto 9.18.02, am in class

(ii) Submit a draft of your paper, at least 5 pages, and containing, at least in brief, all the typesof arguments and subtopics you intend to include in the final paper. Your paper mustconform to the specifications given above and below, with citations.

Due: 10.23at 9 am inclass.

(iii) Submit a final draft of your paper, pursuing new ideas you got in writing the first draft,incorporating any new materials and responding to the comments I make in returningyour first draft.

Due: 12.6.0at 9 am inclass.

Your writing:

Your paper will be a kind of review article, so inclusion of figures or tables would not be usual, except insofaras you choose to create new arrangements of data published elsewhere because by so doing you can make apoint not made by the persons who published the data originally, or to collate data previously published inmore than one source. In this case of course you carefully document the original publications in which youfound the data. As is conventional for papers of this kind, you will use standard prose text in grammaticallycorrect English and using technical language as it is used by others in this field. The paper must be entirelyyour own writing. This means that you may not collaborate with classmates or others on the writing of yourpaper, or use direct quotes from any of your sources. You must take notes in such a way that any languagequoted from your source in your notes is in quotation marks, so that you rephrase in your own words beforeincorporating those ideas into your paper. Ideas not your own must be credited to the appropriate source.

Typography, etc.:

Please write your drafts in Microsoft Word and submit them to me electronically (by email) as attached files. Itshouldn’t matter whether you are using a PC or a Mac as Word is cross-platform. I will submit your paperselectronically to the website Turnitin, which scans the text for inappropriately copied (plagiarized) materials.

Your paper should be written in a serif typeface (such as Palatino) in a font size between 10 and 12, and withmargins between 0.5 and 1 inch on each side. You may format the paper otherwise as you wish.

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