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BIO 329 (50820) Syllabus Spring 2009
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Course | Prerequisites  | Instructor  | Text | Description
Grading and Test Policy | Tentative Class Schedule | Exam Schedule | Class Notes
For best results in printing, download the PDF version of the syllabus by clicking on the PDF icon to the left. 
Course: BIO 329, 50820, Medical Mycology,
BUR 112, TTH 11:00-12:30 PM 
Prerequisites: Biology 325,325H and 226R with a grade of at least a C in each.  Concurrent or subsequent enrollment in BIO 129L (Medical Mycology Laboratory) is recommended for Medical Technology/Clinical Laboratory Sciences majors.
Instructor:

Dr. Paul J. Szaniszlo: E-mail: pjszaniszlo@mail.utexas.edu
(Office Hours: Mon 11:30 AM-12:30 PM, or by appointment in NMS 2.314)

T.A.:

Samantha Croft: E-mail: sbcroft@hotmail.com
(Office Hour: T from 10-11 AM, or by appointment in MBB 2.424B). Discussion and Test Review Sessions will be held on Tuesday 5-6 PM, Wednesday 4-5 PM (Locations TBA). These sessions are optional, although quizzes may be given and up to 5 bonus points/exam period can be earned during these sessions. If you can not attend either of these sessions, then please let Samantha know your reasons and why you cannot rearrange your schedule, in writing, before the 12th class day (her syllabus for the Discussion Sessions is presented below and she also has a Discussion Section Quiz Website, which is at https://webspace.utexas.edu/sbc/www/ ). She will then try to accommodate you. However, if she can't, and you think you will need those potential points to pass, then you should seriously consider dropping this course.

Text:
(optional)

Dismukes, Pappus and Sobel. 2003. Clinical Mycology, Oxford University Press, N. Y. Unfortunately this text just went out of print, but more than one copy should be available on my reserve shelf in the Life Science Library. Nonetheless assignments will still be made from this text for those who think they need to read in greater depth than is presented in the lectures and/or in the Sz readings (see below). A number of additional reference books will also be available on my reserve book shelf in the Science Library to augment your studies (see below).

Sz Readings:
(required)

As an alternative to the text assignments, or in addition to them, a number of articles will be assigned during the course.  These so-called Sz readings are required and will be available in the Life Sciences Library as one set of uncatalogued articles.  These readings can also be purchased at Speedway Copy and Printing, in Dobie Mall, should you want personal copies. The titles, authors, and sources of these readings are listed below in the general order they will be assigned.

Course Description: This course consists of a basic introduction to medical mycology and a comprehensive study of the yeasts, molds and mycoses (fungal diseases) likely to be encountered in clinical settings by a physician, medical mycologist, or clinical laboratory scientist.  Attention will be distributed as equally as possible between emphasis on the fungal zoopathogen and on its disease.  A general course outline in the form of a Tentative Lecture Schedule (see below) is attached, as well as a short Reserve Book List (see below).  
Grading and Test Policy:

There will be three semester examinations and an optional comprehensive final.  The semester exams will focus on the material covered since the last examination but the second and third exams will all require good knowledge of prior coverage, and particularly the material covered for the first examination.  Each examination will count equally (33.3%), if you opt not to take the comprehensive final.  Should you decide to take the final, it too will count 33.3% and your lowest semester exam grade will be dropped from the calculation for your final average (Note: if you opt to take the final, then it will be one of the three scores used to calculate your final grade). Final averages will generally not be curved, but instead most likely will be assigned as follows:

85-100%                  =               A

70-84%                    =               B

55-69%                    =               C

50-54%                    =               D

and less than 50%     =                F 

PJS's Grading Philosophy: "Students earn grades, they are not given grades."
Examination Schedule: The three semester exams will be scheduled during the regular class period, but in a different room (To be announced).  There will be no make-up exams unless there is a substantial legitimate and documented, significant medical excuse or a documented personal tragedy associated with your absence from an examination.  Failure to take an examination may result in a zero grade for that exam.  The date each exam will be given and the approximate materials to be covered by each are included in the Tentative 2009 Schedule (see below).  Should this schedule not be acceptable then you should consider dropping the course as soon as possible.  
Class Notes Packet: A class notes packet will be available for your purchase at Speedway Copy and Printing, Dobie Mall.  These notes may also be available at this class web site, and in general represent only duplicated and reformatted versions of the computer-generated overheads prepared specifically for Bio 329 from last year's Notes and only a few of the tables, but none of the figures, diagrams or other items to be presented as handouts or possibly at this web-site.  The purchase of these items is totally at your discretion and are provided only for your note-taking convenience, so you don't have to download from the web site, and can more easily take notes, make drawings, or make records of additional materials (information in tables, figures or graphs, for example) related to lecture information that is not included in these notes and which is strongly encouraged to be studied.  
 Class Web Site:

 

To help you keep up with things in BIO 329, there is a class web-site associated with Medical Mycology. Unless you are informed otherwise, the URL for this site will be http://www.sbs.utexas.edu/mycology/bio329/default.htm.
 Discussion Section Syllabus

Discussion sessions are voluntary and will be held twice a week and are designed to allow the students to ask questions about difficult subject matter from the lectures. Quizzes will be given weekly, which thoroughly cover the previous week’s lecture materials. After reviewing the quiz questions, students will be allowed to ask questions and discuss unclear concepts. I will also point out material which students have struggled with in the past and give study tips. The discussions before the exam will be review sessions where I will give an overview of the lecture material covered for that exam and answer questions.

Bonus Points: During the two voluntary discussion sessions, quizzes will be given to allow students to earn up to 5 bonus points per exam.  Each week a quiz worth 5 points will be given and students may take all three quizzes per exam (ONLY one per week), but only the highest quiz score will be applied to their exam.

Attendance: If a student cannot attend either the discussion sessions or the office hours listed below, they must contact me in writing by the twelfth class day with the reason for the scheduling conflict so that other arrangements can be made.  If I am not contacted by this time, I will assume that the student is able to attend one of the allotted times and failure to attend is voluntary. If a scheduling conflict arises mid semester, it is the student’s responsibility to contact me immediately. I will not allow make-up quizzes as there are multiple opportunities per exam for the students to earn points, with exceptions only for serious illness that has caused absence for several weeks.

Discussion sessions: see TA above (site yet to be arranged).

Office Hours: see TA above.

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Tentative Spring 2009 Lecture Schedule - BIO 329
JAN 20 Course Introduction (and start?)
  22 General Introduction to Medical Mycology
  27 Definitions and Fungal Terminology
  29 Fungal Classification , Historical Overview and Chytridiomycota
FEB 3 Zygomycota, Ascomycetes, and Basidiomycetes
   5 Fungi Imperfecti, Conidia and Other Spores
   10 General Aspects of Fungal Immunology and Pathology
   12 Antifungal Therapeutic Agents
  17 Antifungal Therapeutic Agents
  19 The Superficial Mycoses
FEB 24 Exam I-Over information through antifungals
  26 Dermatophytosis and the Dermatophytes
MAR  3 Dermatophytosis and the Dermatophytes   
  5 Introduction to Subcutaneous Mycoses, with emphasis on those caused by dematiaceous (black) fungi
   10 Chromoblastomycosis
   12 Phaeohyphomycosis, Mycetoma, Other Diseases Caused by Black Fungi
MAR 16-20 SPRING BREAK
  24 Sporotrichosis
  26 Introduction to the Pathogenic Yeasts and Candidiasis
  31 Candidiasis and Cryptococcosis
APR  2 Cryptococcosis
APR  7 EXAM II -Coverage through candidiasis
   9 Histoplasmosis
  14 Blastomycosis
  16 Coccidiodomycosis
  21 Coccidiodomycosis  
  23 Aspergillosis
  28 Fungal Allergies and Mushrooms
April  30 EXAM III - Coverage through aspergillosis
MAY  5 Mushrooms and Mushroom Poisonings
   7 Student Evaluations, Mycotoxins and Finishing Up
MAY 14 Optional Comprehensive Final Examination (see grading and test policies above for details).

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Reading List - BIO 329
For best results in printing, download the PDF version of the syllabus by clicking on the PDF icon to the left. 
RESERVE BOOK LIST - Spring 2009- Paul J. Szaniszlo
These books are either on reserve in the Life Science Library or in the stacks there and should be of help if you need supplemental reading on certain topics introduced in Bio 329.
 
Medical Mycology
Clinical Mycology, Dismukes, Papus and Sobel
     QR 245, C566, 2003
Medical Mycology, Kwon-Chung and Bennett

      QR 245, K86, 1992

Atlas of Clinical Mycology, deHoog et al.,

      QR 245, K86, 2000

Microbiology and Microbial Infections, Topley and Wilson’s, 9th ed., Vol. 4.  Medical Mycology

      QR 46, T6, 1998

Molecular Principles of Fungal Pathogenesis, Heitman et al.
       QR 245, M65, 2006
Dimorphic Fungi in Biology and Medicine, Vanden Bossche, Odds and Kerridge (eds)

      QR 245, D55, 1993

Medical Mycology: A Practical Approach, Evans and Richardson

      QR248, M43, 1989

Medical Mycology and Human Mycoses, Beneke and Rogers

      QR245, B46, 1996
Medical Mycology, 3rd ed., Rippon

       RC 117, R5, 1988

Fungal Dimorphism: With Emphasis on Fungi Pathogenic for Humans, Szaniszlo

       QR 245, 1985

Laboratory Handbook of Medical Mycology, McGinnis

       RC 117, E56, 1980

Identifying Filamentous Fungi:  a Clinical Laboratory Handbook, St-Germain and Summerbell

      QR 248, F55

Fungal Pathogenesis: Principles and Clinical Applications, Calderone and Chilar, ed.

     RC117, F864, 2000

 General Mycology

Ainsworth & Bisby's Dictionary of the Fungi, 8th ed., Hawksworth, Krik, Sutton & Pegler

      QK603, A5, 1995

Dictionary of the Fungi,  9th ed., Hawksworth et al.,
      QK 600.35, A5, 2001
The Fifth Kingdom, 3rd ed., Kendrick

      QK 603, K46, 1992

Introductory Mycology, 4th ed., Alexopoulos, Blackwell and Mims

       QK 603, A55, 1996

Fundamentals of the Fungi, 4th ed., Moore-Landecker

       QK 603, M62, 1996

The Fungi, 2nd ed., Watkinson, Carlile and Gooday

   QK 603, C257, 2001    

BIO 329  - RESERVE READING LIST - SPRING 2009- PAUL J. SZANISZLO

(In Life Science Library as a set of articles)

These articles are also available through Speedway Copy and Printing, Dobie Mall, and are required readings.  Although you may not be tested directly on the content of these articles, they will help you to better appreciate the subjects and to write better essay discussions, if requested.

Sz 1  Sternberg, S. 1994.  The emerging fungal threat.  Science 226:1632-1634.
Sz 2

Mitchell, T. G.  1998.  Medical mycological research and training: needs and opportunities. ASM News 64:17-23.

Sz 3 Warnock, D. W. 2006. Fungal diseases: an evolving public health challenge. Med. Mycol.  44:697-705.             
Sz 4 Perfect, J. R. 2005. Weird Fungi. ASM News 71:407-411.
Sz 5 Taylor, J. W. 2006. Evolution of human-pathogenic fungi: phylogenies and species. In: Molecular Principles of Fungal Pathogenesis, ASM Press, pp. 113-131.
Sz 6 Mendoza, L., L. Ajello and J. W. Taylor 2001.  The taxonomic status of Lacazia loboi and Rhinosporidium seeberi has been finally resolved with the use of molecular tools.  Rev. Iberoam. Micol. 18:95-98.
Sz 7

Cushion, M. T. 2004. Pneumocystis: Unraveling the cloak of obscurity. TIM 12:243-249.

Sz 8

O'Goram, C. M., H. B. Fuller and P. S. Dyer. 2008. Discovery of a sexual cycle in the opportunistic pathogen Aspergillus fumigatus. Nature (on line).

Sz 9 Casadevall,  A. 2006. Cards of virulence and the global virulome for humans. Microb, ASM Press, 1:359-364. .
 
Sz 10

Szaniszlo, P. J.  1985.  An introduction to dimorphism among zoopathogenic fungi.  In:  Fungal dimorphism, with emphasis on fungi pathogenic for humans.  Chapter 1, pp. 3-13

Sz 11 Kwon-Chung, K. J. and B. L. Wickes. 2006. The conversion from classical studies in fungal pathogenesis to the molecular era. In: Molecular Principles of Fungal Pathogenesis, ASM Press, pp. 49-70.
Sz 12 Cooney, N. M.and B. S. Klein. 2008. Fungal adaptation to a new world.  Curr. Opin. Microbiol. 11:511-516.
Sz 13a

 

13b

Nicola, A. M., A. Casadevall and  Gueho, E., J. Faergemann, C. Lyman, and E. J. Anaissie.  1994. Malassezia and Trichosporon:  two emerging pathogenic basidiomycetous yeast-like fungi.  J. Med. Vet. Mycol. Suppli. 32:367-378.

van der Veerdonk,  F. L., B. J. Kullberg, J. W. M. van der Meer, N. A. R. Gow and M. G. Netea. 2008. Host-microbe interactions: innate pattern recognition of fungal pathogens. Cutt. Opin. Microbiol. 11:305-317.

Sz 14  Romani, R. 2004. Immunity to fungal infections. Nature Reviews: Immunology. 4:1-12.
Sz 15 Romani, R. 2008. Cell mediated immunity to fungi: a reassessment. Med. Mycol.46: 515-529.
Sz 16 Odds, F. C., A. J. P. Brown, and N. A. R. Gow. 2003. Antifungal agents : mechanisms of action. TIM. 11:272-279.Jacobson, E. S.  (2000)  Pathogenic roles for fungal melanins.  Clin. Microbiol. Rev. 13:708-717
Sz 17 Sable, C. A., K. M. Stromaier and J. A. Chodakeewitz. 2008 Advances in antifungal therapy Annu. Rev. Med. 59:361-379.
Sz 18 Gueho, E., J. Faergemann, C. Lyman and E. J. Anaissie. 1994. Malassezia and Tricosporon: teo emerging pathogenic basidiomycetous yeast-like fungi. J. Med. Vet Mycol. Suppl. 32: 367-375.
Sz 1 9 Weitzman, II. and R. C. Summerbell. 1995. The dermatophytes. Clin. Microbiol. Rev. 8: 240-259.
Sz  20 Kac, G. 2000. Molecular approaches to the study of dermatophytes. Med. Mycol. 38: 329_336.
Sz  21 Nosanchuk, J. D. and A. Casadevall. 2006. Impact of melanin on virulence and clinical resistance to microbial compounds. Antimicrob. Agents Chemother. 50: 3519-3528.
Sz  22 Cooper, C. R., Jr. 2005. Deep phaeohyphomycosis. In Mahey et al. (ed) Topley and Wilson's Microbiology and Microbial Infections. Chapter 35, pp 739-749.
Sz 23 Szaniszlo, P. J. (2002) Molecular genetic studies of the model dematiaceous pathogen Wangiella dermatitidis. Int. J. Med. Microbiol. 292:381-390.
Sz 24 Brandt, M. E. et al.  (2000)  Candida dubliniensis fungemia: the first four cases in North America.  Emerg. Infect. Dis. 6:46-49
Sz 25 Pfaller, M. A., and D. J. Diekema. 2002. Role of sentinal surveiance of candidemia: trends in species distribution and antifungal susceptibility. J. Clin. Microbiol. 40:3551-3557.
Sz 26 Fidel, P. L. 2004. History and new insights into host defenses against vaginal candidiasis. TIM 12: 220-227.
Sz 27 Kumamoto, C. A. 2008. Nitch-specific gene expression during C. albicans infection. Curr. Opin. Microbiol. 11:325-330.
Sz 28 Sudbury, P., N. Gow. and J. Burman. 2004. The distinct morphogenetic states of Candida albicans. TIM, 12:317-324.
Sz 29 Magee, P. T. and B. B. Magee. 2004. Through a glass opaquely: the biological significance of mating in Candida albicans. Curr. Opin. Microbiol. 7:661-665.
Sz 30

Noverr, M. C., D. M. Lindell, G. B. Toews and G. B. Huffnagel. 2006. Fungal interactions with leukocytes. In: Molecular Principles of Fungal Pathogenesis, ASM Press, pp. 555-563.

Sz 31 McClelland, C. M., Y. C. Chang, A. Varma and K.J. Kwon-Chung. 2004. Uniqueness of the mating system in Cryptococcus neoformans. TIM 12:208-212.
Sz 32 Feldmesser, M., S. Tucker and A. Casadevall.  (2001)  Intracellular parasitism of macrophages by Cryptococcus neoformans.  TIM 9:273-278; and related TIM letters 9:417-418..
Sz 33 Holbrook, E. D. and C. A. Rappleye. (2008) Histoplasma capsulatum pathogenesis: making a lifestyle switch. Curr. Opin. Microbiol. 11:318-324.
Sz 34 Brandhorst, T.T., P. J. Rooney, T. D. Sullivan, and B. S. Klien (2002) Molecular genetic analysis of Blastomyces dermatitidis reveals new insights about pathogenic mechanisms. Int. J. Med.Microbiol. 292: 363-371.
Sz 35 Kirkland, T. N., and J. Frierer.  (1996)  Coccidioidomycosis:  a reemerging infectious disease.  Emerg. Infect. Dis. 2:192-199.
Sz 36 Abuodeh, R. O., J. N. Galgiani, and G. M. Scaralone. (2002) Molecular approaches to the study of Coccidioides immitis. Int. J. Med. Microbiol. 292:373-380.
Sz 37 Latgé, J-P.  (2001)  The pathobiology of Aspergillus fumigatus. TIM 9:382-389.
Sz 38 Askew. D. S. (2008) Aspergillus fumigatus: virulence genes in a street-smart mold. Curr. Opin. Microbiol. 11:331-337.
Sz 39 Cooper, C. R., Jr. and N. Vantttahakom. 2008. Insights into the pathogenicity of Penicillium marneffei. Future Microbiol. 343-55.
Sz 40

McGinnis, M. R. 2004. Pathogenesis of indoor fungal diseases. Med. Mycol. 42:107-117.

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