pen marneffei
In vivo yeast phase of Penicillium marneffei (courtesy of www.doctorfungus.org)
Medical Mycology
Summer 2011 Semester
Second 6-Week Session (CRN 30224)

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Modified/Posted: August 12, 2011 (9:45 AM)
  -   current date       The current time is 
chromo P. ver
Chromoblastomycosis of a foot due to Phialophora verrucosa (courtesy of www.doctorfungus.org)

Course Instructor: Dr. Chet Cooper, Professor
Biological Sciences, Youngstown State University

Office Location:
3016 Ward Beecher Hall
Office Hours:
Mondays and Wednesdays, 10:15 AM - 11:45 AM
Telephone/Voice:
330.941.1361   Email: crcooper01@ysu.edu

Lecture Day/Time: Mondays, Wednesdays, and Fridays, 8:00 AM - 10:15 AM
Location: Ward Beecher Science Hall, Room 4045


Quick Links to Scheduled Course Days

July 6     July 8     July 11     July 13     July 15     July 18     July 20     July 22     July 25     July 27     July 29

August 1     August 3     August 5     August 8     August 10     August 12



"Welcome to Medical Mycology"

dr cI am Dr. Chet Cooper, your course instructor for BIOL 4849,
Medical Mycology.  BIOL 4849 is three semester-hour upper-division course at Youngstown State University (YSU)  intended for undergraduate students majoring in biology, but students in other majors may also find this course quite beneficial. 

As your instructor, I am wholly committed to providing you a sound education in the foundations of fungal diseases, which are also known by the scientific term "mycoses".  With the same commitment on your part, I guarantee that your experiences in this course will give you a different and accurate perspective of the role that fungi play in causing disease in humans and animals.


I very much look forward to an exceptional enjoyable semester as your  instructor.  Should you have any questions or comments about anything related to this, please be sure to contact me.

Best Wishes for a Great Semester in Medical Mycology!

                                                                                     dr c. sig

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Course Description:


(as published in the 2010-2011 YSU Undergraduate Bulletin)

BIOL 4849.  Medical Mycology.  Survey of infectious diseases caused by fungi including their etiology, epidemiology, histopathology, diagnosis, and treatment.  Host-parasite interactions and the environmental and molecular factors that contribute to establishment of fungal disease in humans and animals.  Prereq.: BIOL 3702.   3 s.h.

Note:  The pre-requisite for this course has been changed to BIOL 2602.  The current description has yet to be ammended.



Course Goals and Objectives:

The goal of BIOL 4849 is to prepare students for professional careers that employ the principles of medical mycology.  This will be accomplished through the mastery of the following specific objectives:

  • Discover how other disciplines contributed to the study of mycotic diseases;
  • Recognize the etiology of different mycoses;
  • Learn the fundamental basis for diagnosing fungal infections;
  • Differentiate the different pathologies of the mycoses;
  • Identify environmental and host factors that promote fungal infections;
  • Comprehend the various treatment regimens for the mycoses;
  • Appreciate the role of fungi in human affairs;
  • Recognize the importance of proper public dissemination of information; and
  • Understand the contributions of fungi to current concepts in infectious disease



Course Materials:

There is no standard textbook for this course.  However, the following is a RECOMMENDED text:

Clinical Mycology, 2nd ed.  2009.  Elias J. Anaissie, Michael R. McGinnis, Michael A. Pfaller, eds. Churchill Livingstone.

Located in the Maag Library Reserves (ask at the Circulation Desk, Main Floor) under the following call number: QR245 .A53 2009x

Plese note the following:

i) The above text is NOT REQUIRED.  It will help (if you read it), but if you have good study habits, you won't necessarily need it.

ii) I will use material from the recommended text, but my exams will come 99% or greater from my notes (or yours, as the case will be), as well as the presentations you and your peers make to the class. 


In addition, much of Dr. Cooper's lecture material will come from a variety of sources including the following:
  • Atlas of Fungal Infections, 2nd ed.  2007.  Carol A. Kauffman, ed.  Springer.
Located in the Maag Library Reserves (ask at the Circulation Desk, Main Floor) under the following call number:
RC117 .A86 2007 [textbook]
RC117 .A86 2006x CD-ROM [CD-ROM version of textbook]
  • Clinical Mycology.  2003.  Elias J. Anaissie, Michael R. McGinnis, Michael A. Pfaller, eds. Churchill Livingstone.
Located in the Maag Library Reserves (ask at the Circulation Desk, Main Floor) under the following call number: QR245 .C565 2003

  • Clinical Mycology, 2nd ed.  2009.  Elias J. Anaissie, Michael R. McGinnis, Michael A. Pfaller, eds. Churchill Livingstone.
Located in the Maag Library Reserves (ask at the Circulation Desk, Main Floor) under the following call number: QR245 .A53 2009x
  • Clinical Mycology.  2003.  William E. Dismukes, Peter G. Pappas, Jack D. Sobel, eds.  Oxford University Press.
Located in the Maag Library Reserves (ask at the Circulation Desk, Main Floor) under the following call number: QR245 .C566 2003 
  • Topley & Wilson's Microbiology & Microbial Infections, 10th ed.  2005.  Vol. 3.  Medical Mycology.  Hodder Arnold.
Located in the Maag Library Reserves (ask at the Circulation Desk, Main Floor) under the following call number: QR46 .T6 2005x [be sure to request volume 3 of this series]
  • Medical Mycology. 1992. K.J. Kwon-Chung and John E. Bennett.  Lea & Febiger.
Maag Library does not own this book.  However, limited numbers of this book available via OhioLink (interlibrary loan) by clicking here.


In addition, the following items have been placed on reserve in the Maag Library (3-hour in-library use):
  • Identifying Filamentous Fungi. A Clinical Laboratory Handbook. 1996. St-Germain, G. and Summerbell, R. Star Publishing.
  • Pathologic Diagnosis of Fungal Infections. 1987.  Chandler, F. W. and Watts, J. C. ASCP Press.
  • Medical Mycology and Human Mycoses. 1996.  Beneke, E. S. and Rogers, A. L. Star Publishing.
Please note that some of the above books are the personal property of Dr. Cooper.  As with any library book, please handle them with great care and respect.

Also, some additional electronic resources you should consider using during this course:

  • Immunology of fungal infections [electronic resource] / edited by Gordon D. Brown and Mihai G. Netea. Dordrecht : Springer, 2007.   Persitent Link

  • Diagnosis and treatment of human Mycoses [electronic resource] / edited by Duane R. Hospenthal, Micheal G. Rinaldi.  Totowa, N.J. : Humana Press, 2008.  Persistent Link

  • Pathogenic yeasts [electronic resource] / edited by Ruth Ashbee, Elaine M.  Bignell.  Berlin; London : Springer,  2010.  Persistent Link

  • New insights in medical mycology [electronic resource] / edited by Kevin Kavanagh.  Dordrecht : Springer,  2007.  Persistent Link

  • Medical Mycology (journal) [electronic resource] Available on EBSCOhost. Full text available 2/1/2003 - . (Due to publisher restrictions, the most recent 12 months are not available.).  Persistent Link
  • SPECIAL NOTE: If you need an article dated 2010-2011 from this journal, contact Dr. Cooper for assistance.

In lieu of a textbook and in addition to the above reserve materials, students are encouraged to refer to qualified web resources.  Use caution!  There are a number of web sites that discuss fungi and the infections they cause.  Listed below are some excellent web sites endorsed for use in this course:





Other web site links may be added in the near future, so check back periodically.

Finally, Dr. Cooper and your peers may make available a number of electronic versions of journal articles for you to read.  These will be available for downloading directly from this web page or from the Electronic Journal Center of OhioLink.



Grade Components:

A student's final grade in BIOL 4849 will be based upon scores earned in four lecture examinations and three group presentations.  Each examination is worth 100 points, whereas each presentation is worth 100 points, of which students will make two.  Attendance will be taken, beginning on the second day of the course, and will be worth 150 points (5 points for each session) towards a student's final grade.  For a student to receive a full day's attendance points, he/she must be present for the entire period.  Hence, there are a total of 650 points in this course.

The format of the examinations may vary to include short essay, multiple-choice, true-false, and matching questions.

Students who are absent from an examination will have a score of "0" recorded.  No exemptions to taking the examination on the scheduled date will be given except in cases of extreme circumstances.  The decision of whether or not to grant an exemption is entirely at the discretion of the instructor and is not subject to further appeal.

Student presentations will be small group projects and will be both peer and instructor graded according to a rubric that will be described prior to the assignment of topics.

No opportunities will be granted for earning extra credit.  Student initiated requests for extra credit opportunities will not be entertained and may be acidly received. 


Grading Scale.  The following scale will be used to assign final grades for this course:

Final Grade Total Points
A (90% or greater) 585 points or more
B (80 to 89 %) 520 to 584 points
C (70 to 79%) 455 to 519 points
D (60 to 69%) 390 to 454 points
F (59% or less) 389 points or less

This grading scale is absolute.  This is no "curving" of grades.     
      



Resources Used By The Course Instructor:


Unless otherwise noted by Dr. Cooper, all material presented to students in this course represents either i) selected portions of information contained within the noted textbook(s) or supplementary material, ii) information published in the scientific literature, iii) current issues reported by the news media, or iv) knowledge otherwise commonly known to professional microbiologists or mycologists.  Dr. Cooper makes no claim of "ownership" of facts and/or ideas presented in this course unless specifically noted.  All facts and/or ideas are used solely for educational purposes.  Dr. Cooper makes every effort to appropriately attribute facts and/or ideas to their proper sources.




Academic Dishonesty:

Academic dishonesty, in any form, will not be tolerated in this course.

Students are urged to read the section on "Academic Honesty" as 
printed in the YSU Undergraduate Bulletin, 2010-2011.  Students should also be aware of pertinent sections in The Code (the latter  is a PDF document).

Any student enrolled in BIOL 4849 shown to have committed academic dishonesty in this course is deemed solely accountable for his/her actions and will receive a final course grade of "F".   Additional sanctions may also be sought, i.e., a recommendation by the instructor for dismissal of the student from the University.

Be aware that this policy includes unauthorized access of computer files associated with this course.  The web site files associated with BIOL 4849 are monitored for unauthorized access.  Entering these files even by "accident"  will be considered a violation of academic integrity.



Disability Statement:

In accordance with University procedures, students who have a documented disability and require accommodations to obtain equal acess in this course must contact Dr. Cooper privately to discuss the individual's specific needs.  Persons enrolled in this course and currently having a documented disability must notify Dr. Cooper of their needs no later than July 8, 2011.  In addition, students having a disability must be properly registered with the Disability Services Office (275 Fifth Avenue; telephone 330.941.1372).  Also, to be properly registered, a letter of accommodations verifying the student's eligibilty must be provided.  Individuals who develop a disability during the semester must notify Dr. Cooper within one week after being properly registered with the Disability Services Office.  Students with disabilities are reminded that in addition to certain rights and privileges covered by law and University policy, they also have obligations and responsibilities that must be met.  Students are strongly encouraged to review these rights and responsibilities as outlined on the Disability Services Office web page.


Other Responsibilities/Expected Behavior:

Electronic Communication/Data Storage Devices.  During lecture, all cellular telephones, pagers, or other electronic communication devices must be turned off or set in the quiet/vibration mode of operation.  Data storage devices (e.g., personal desk assistants, lap top computers, etc.) may be used during lectures and only if they do not cause distraction to other students or the course instructor.  Students failing to meet this expectation will be invited to leave the classroom until such time that they comply with this policy.

During examinations and quizzes, all electronic devices (including personal desktop assistants, computers, etc.) are strictly prohibited.  Students violating this policy will be suspected to have committed academic dishonesty.

Recording of Lectures.  Students are reminded that Dr. Cooper's lectures are copyright protected (see Copyright Restrictions).  However, students are permitted to electronically record lectures in the classroom provided that: i) such activity is not disruptive to the instructor or fellow students; ii) the recording is used solely for the personal study of the student making the recording; iii) the recording is not sold or transmitted to others in any form without the expressed written permission of Dr. Cooper; and iv) the recording does not serve as a substitute for attending class or actively participating in the lecture.

Examinations.  Examinations are to be taken without assistance from other students.  If you are aware of any student cheating or having a copy of the current exam, please contact the instructor.  Academic dishonesty in any form will not be tolerated in this course.  Penalties for such action will be enforced.

Decorum.  At all times, students are expected to exhibit behavior appropriate for young (or even older) adults.  Such behavior is delimited by University policy.  Inappropriate behavior, including disrespect for Dr. Cooper, is subject to expulsion from one or more lecture sessions without the opportunity to begin or complete the assigned exercises.  In cases of extremely inappropriate behavior, Dr. Cooper will recommend more severe sanctions (including dismissal from the University).

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Pm conidia

Moldt phase of Penicillium marneffei.  Lactophenol cotton blue
stain from a slide culture (C. R. Cooper, Jr.)



Posting of Grades/Scores:

Student grades/scores are periodically posted via this web page.  However, students must provide their approval to have their individual grades/scores posted via the downloadable Grade Posting Permission Form.  [click  on the button below to download this form]
gppf

Wtihout this form, individual student scores/grades will not be posted.  A student may withdraw this permission at anytime by written notice to the course instructor.


current gradres
[Posted August 12, 2011] (PDF file)
FINAL SCORES/GRADES

Have a great break!  See you soon!

saf
[required by July 8th]

gppf
[required for posting of your scores/grades]


Links to Important Student Presentation Documents

Presentation Guidelnes
   
Student Peer Scoring Rubric
      TeamWork Scoring Rubric

Dr. Cooper's Student Presentation Scoring Rubric

(All of the above are PDF documents)


PowerPoint Presentation Template  (PPT document)

PowerPoint Presentation Template  (PDF document)





Course Calendar


NOTE: Each scheduled course day is broken into two halves.  The first half begins promptly at 8:00 AM an last until approximately 9:00 AM.  This session will always meet in the scheduled classroom.  The second half of each scheduled course day begins promptly at 9:15 AM (unless otherwise noted or changed by Dr. Cooper) and ends at 10:15 AM.  Most of these sessions will meet on the fourth floor of Maag Library.  Dr. Cooper will provide additional instructions regarding these second sessions.


Wednesday, July 6th

1st Session: Course Introduction
Introduction Memo (PDF)

Background Reading: History of Medical Mycology in the United States.  ANA ESPINEL-INGROFF.  CLINICAL MICROBIOLOGY REVIEWS 9: 235–272, 1996.  [PDF Document - Click HERE]

2nd Session:  Library Orientation/Database Search

     Maag Library, 4th Floor Instruction Laboratory
Ms. Cynthia Harrison, Science Librarian

ISI Handout (PDF)    Search Strategies (PDF)

 EJC (PDF)   PubMed (PDF)

Friday, July 8th

Syllabus Acknowledgment Form Due

1st Session:  Lecture - What are Fungi?
Lecture Slides (PDF)

Background Reading: The Fifth Kingdom (on line) - free digitial textbook on the fungal kingdom.  This on line version of the book contains almost all the material found int he printed version.  The introductory chapters address the question "What are Fungi?"

2nd Session: Library Research

Use this time to work as a group on the research for your presentations.

During these sessions, Dr. Cooper who will be in the library on the 4th floor near the Tech Desk unitl about 10:15 AM.


Topic
Team Members
Candida and Candidiasis
Adamson, Bees, Bischoff, and Candle

Cryptococcus and Cryptococcosis
Carlozzi, Forte, and Galioto


Malassezia Infections
Gupta, Lileas, and Madden

Aspergillosis
Mohney, Olenick, and Omair

Zygomycosis
Mariani, Rose, Runyon, and Russell

Dermatophyte Infections
Seman, Speerstra, and Thurston

Monday, July 11h

1st Session: 
Lecture - What are Fungi? (cont.)

2nd Session: Library Research (cont.)

Tuesday, July 12th

Last Day to Add Classes or
Change Grading Option
Wednesday, July 13th

1st Session:  Lecture - Epidemiology of Fungal Infections

2nd Session: Library Research (cont.)
 
Friday, July 15th

1st Session:  Lecture - Epidemiology of Fungal Infections (cont.)
Special Reading Assignment: Bat White-Nose Syndrome in North America (PDF from Microbe)

Lecture Slides (PDF)

2nd Session: Student Presentations I

Candida and Candidiasis [PDF]

Cryptococcus and Cryptococcosis
[PDF]

Malassezia Infections
[PDF]

Monday, July 18th

 Student Presentations II - Beginning at 8:30 AM


Wednesday, July 20th

1st Session:  Lecture - Fungal Pathogenesis

2nd Session: Library Research


Topic
Team Members
Hyalohyphomycosis

Candle, Mohney, and Seman

Phaeohyphomycosis Carlozzi, Madden, and Russell

Chromoblastomycois Forte, Mariani, Runyon, and Thurston

Histoplasmosis
Bischoff, Lileas, and Rose

Blastomycosis Bees, Gupta, Omair, and Speerstra

Coccidioidomycosis Adamson, Galioto, and Olenick
Friday, July 22nd

1st Session:  Lecture - Immunology of Fungal Infections
In Class Assignment

2nd Session: Library Research

Monday, July 25th

1st Session:  Exam I

2nd Session: Library Research

Wednesday, July 27th

1st Session:  Lecture - Immunology of Fungal Infections (cont.)
Lecture Outline (PDF) REVISED/REPOSTED
Special Reading Assignment: The Last Vaccine Frontier (Full Text from The ScientistNote: This article is a shortened version of a more comprehensive article located at Facutly of 1000

2nd Session: Student Presentations III

Thursday, July 28th

Last Day for Withdrawing with a Grade of 'W'
Friday, July 29th

1st Session: Lecture -  Histopathology of Fungal Infections

2nd Session: Student Presentations IV


Monday, August 1st

1st Session: Lecture - Antifungal Agents
2nd Session: Library Research


Topic
Team Members
Penicillium marneffei Infections
Bees, Thurston, and Speerstra


Sporotrichosis Galioto, Lileas, Mariani, and Olenick

Paracoccidioidomycosis Adamson, Carlozzi, and Runyon

Lacaziosis
Bischoff, Mohney, and Omair

Pythiosis Forte, Gupta, and Rose

Rhinosporidiosis Madden, Russell, and
Seman
Wednesday, August 3rd

 NO CLASS MEETING TODAY

Library Research - ON YOUR OWN!!!!

You have your assignments, so work in your groups.  I will be available in my office until 8:20 AM, then, if time permits, I will come by the 4th floor of the library to answer questions

Friday, August 5th  

1st Session:  Lecture -  Antifungal Agents (cont.)

2nd Session: Library Research
Monday, August 8th

1st Session:  Videos: Specimen Collection and Global Warming-Emerging Fungal Diseases
Specimen Collection Video - Part 1 (YouTube)
Specimen Collection Video - Part 2 (YouTube)
Global Warming-Emerging Mycoses  (YouTube)
Accompanying Article: Global Warming Will Bring New Fungal Diseases for Mammals by Garcia-Solache and Casadevall [FullText]

2nd Session: Student Presentations V

Penicillium marneffei Infections [PDF]
Version 1
Version 2

Sporotrichosis [PDF]

Paracoccidioidomycosis [PDF]

Wednesday, August 10th

NOTE: Class will begin at 8:30 AM

 Student Presentations VI

Friday, August 12th

Exam II

The exam will begin promptly at 8:00 AM

Exam results/final grades will be posted to this web page no later than Sunday, August 14th.


cocci

Multiple skin lesions due to disseminated infection
of Coccidioides immitis (courtesy of www.doctorfungus.org)



Attendance:

A record of attendance will be kept beginning on the second day of the course.  Attendance is worth 150 points towards a student's final grade.  Each lecture day, is worth 10 points (5 points per session).  For a student to receive a full day's attendance points, he/she must be present for the entire period. 

Please note, the lecture for this course begins promptly at 8:00 AM throughout the semester.   Also, be aware that this course operates on "Ward Beecher Time", which may or may not correlate to the time that exists at other places on campus.  Students are strongly encouraged to synchronize their timepieces as well as to arrive early enough to find a suitable parking place.

On those dates for which an examination is scheduled, students who are late may not be permitted to take the examination.  This is entirely at Dr. Cooper's discretion.

Moreover, except for extenuating circumstances, it is generally unacceptable for a student to request to take an examination at a time other than the scheduled date.  Having a second examination the day before, the day after, or on the same day is absolutely certain not to evoke any sympathy from Dr. Cooper.  Please do not even ask for special dispensation for such a reason.  However, Dr. Cooper is willing to listen (and perhaps chuckle to himself) other reasons that a student may deem to be extenuating (please note - havng in excess of two grandmothers die during the semester will be considered suspicously gratuitous).  The decision regarding the student's reasoned argument/request for a change in the examination date/time is solely at Dr. Cooper's discretion and, once rendered, is final.



scytalidium

Darkly pigmented hyphae of Scytalidium dimidiatum
in tissue (courtesy of www.doctorfungus.org)




Distribution of Course Material:

All original material on the BIOL 4849 course web site, as well as all original material presented in either the classroom or laboratory, including orally-transmitted lectures, is considered protected by a copyright held by Dr. Cooper.  In general, students enrolled in BIOL 4849 have permission to download, print, and distribute materials copyrighted by Dr. Cooper without his expressed written permission so long as such materials are not used for activities i) associated with the commission of academic dishonesty, ii) intended to circumvent course policies, iii) which result in monetary profit by either the student or others, and iv) that do not violate copyright protections.  For further information, please see Copyright Restrictions.


       peteysu

Required YSU Email Account:

All electronic communications with students enrolled in BIOL 4849 will only be made using the University's myYSU email system.  Students should activate their myYSU accounts if they have not done so already.  To activate your free myYSU account, go to the web page located at the following URL: http://helpdesk.ysu.eduPlease note that a myYSU account does not have to supplant your current  email service.  A feature of the myYSU system is that all incoming messages can be forwarded to another email account.  Hence, you can retain your present services and still receive all communications from Dr. Cooper.



Syllabus Acknowledgement Form:

All students enrolled in this course must read this electronic  syllabus and  verify  that they have done so by submitting  a  completed  Syllabus Acknowledgement  Form by July 7th.   [click  on the button below to download this form]

No grades will be given until this form is received.

saf
Due by July 8th!!!


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