BIO540 – Mycology
Course Information – Fall 2016
FFSC 1244, Tuesday/ Thursday 8:30AM-11:30AM
Students will gain the skills necessary to:
- Understand basic fungal biology
- Be familiar with major fungal lineages
- Collect and identify fresh fungi
- Culture and barcode fungi using PCR
- Create and interpret phylogenetic trees using molecular sequence data
- Understand how fungi are utilized and encountered every day
- Describe various fungal ecological strategies
- Analyze and explain methods and results from primary scientific research literature
Classes will meet on Tuesday and Thursday from 8:30-11:30AM in French 1244, including both lecture and lab. Unless otherwise noted, classes will begin with lectures about topics indicated on the schedule. The lab portion of each class will consist of a discussion about the assigned readings, and allotted time for specific lab activities introducing methods, concepts, and protocols. Papers will include both recent and seminal manuscripts from scientific journals.
|Date||Lecture Topic||Lab Activity||Quiz/Due date|
|30-Aug||Introduction to fungi, collections, & ID||Reading, EOL, & flash phyla signup, fungal isolation set up, field trip|
|1-Sep||Fungal Tree of Life||Media preparation, culture methods||flash fungal phyla presentations|
|6-Sep||Basidiomycetes I: Agaricomycete families & poisonous fungi||Field trip|
|13-Sep||Basidiomycetes II: Agaricomycete families cntd.||sterile technique & field trip|
|15-Sep||Environmental culture ID & microscopy photography||cultures, microscopy|
|20-Sep||Fungal toxins||Discussion 1: fungal toxins papers||Quiz 1|
|22-Sep||Medical mycology||Discussion 2: medical mycology papers||First blog post due on Sunday (9/25)|
|27-Sep||Basal basidiomyetes, mating compatibility, population biology|
|29-Sep||Wood rotting fungi||Discussion 3: rust papers|
|4-Oct||Plant Pathogenic Fungi||Plant Pathogens labDiscussion 4: wood rot papers||Quiz 2|
|11-Oct||FALL BREAK (no class)|
|13-Oct||Molecular Systematics, species, speciation, & barcoding||PCRs for pure cultures|
|18-Oct||Mycorrhizal Ecology||PCR gel analysis & field trip|
|20-Oct||Mushroom cultivation||BLASTing & mushroom kit making|
|25-Oct||Industrial mycology/ Biotechnology||Field trip to Mystery Brewing|
|27-Oct||Ethnomycology||Discussion 5: ethnmycology papers|
|1-Nov||Mycorrhizal community ecology||Mycorrhizal community ecology lab||Quiz 3|
|3-Nov||Lichenized fungi||Lichens lab|
|8-Nov||Chytridiomycota and other aquatic fungi||Chytrids lab|
|10-Nov||Zygomycetes||Discussion 6: zygomycete papers|
|15-Nov||Oomycete biology & slime molds||Discussion 7: slime & water molds|
|17-Nov||Plant Fungal Interaction Genomics||Discussion 8: interaction genomics papers|
|24-Nov||thanksgiving week (no class)||EOL pages due|
|29-Nov||open lab for special topics|
|1-Dec||open lab for special topics|
|6/8 Dec||Symposium: class presentations & banquet|
Assignments and Grading:
|Item||points||total points||% grade|
|flash talks (2)||50||100||10%|
|blog post/specimens (8)||50||400||25%|
|EOL page aka quiz 4 (1)||50||50||5%|
|Discussion leader (1)||200||200||15%|
|term paper & blog post||300||300||25%|
- Quizzes: Quizzes will be administered bi-weekly and will cover materials presented in the previous two classes and labs.
- Encyclopedia of Life (EOL) Page: Each student will create and contribute a page for the Encyclopedia of Life (EOL) website. The topic will be a zygomcete fungal species of the students choosing. Relevant information can include macro- and microscopic photos, taxonomic information, links to publications, and genome statistics if available.
- Specimen collection & blog: A representative, well-documented and preserved collection of 12 field-collected specimens will be required of each student (that’s one species per wk). Collections should reflect diversity of fungi you encounter along with information about the species, identified to genus and species, with photos and notes on fresh and microscopic characteristics, spore prints, and other data used in their identification. Descriptions and photos of your specimens will be published in the class blog.
- Class discussion & presentations: Each student shall help lead a weekly discussion on a particular subject area within mycology. The papers will be posted on our blog site. Everyone reads the papers and participates in discussion- discussion leaders should be prepared to lead discussion with questions.
- Individual project: Each student will write a term paper on a selected topic in Mycology, and give a presentation at the end of the class. Previous research topics have included: Fungal communities on wood and litter, Strategies for spore dispersal, Unusual fungal niches: aquatic, marine, deserts, polar regions, Mycology of food, brewing and baking, Evolution of truffles and other hypogeous fungi, Interesting fungal diseases, Mycorrhizal ecology, Orchid and their mycorrhizae, Fungal decomposition on wood or litter, or other substrate, Mushroom cultivation, Population biology, clonality and individualism in fungi, Pathogenic chytrids & global amphibian decline, Nutrient cycling by fungi, Fungal pharmacology, Ethnomycology, Fungi on/in plants (endophytes), and Fungi on/in insects.
- Keep cell phone usage minimal, no cell phones or lap tops during quizzes.
- No cheating. Plagiarism reports will go to the Dean’s office.
- Turn in your work on time.
- Communicate about foreseeable absences.
- Come on time and be respectful to your peers and instructor.
Resources for students regarding academic problems:
Academic Resource Center (ARC), which contains 3 relevant programs:
- Peer Tutoring Program (PTP), a free service where students meet once a week with previous student in course, but only available for some courses.
- Program for Students with Disabilities (PSD), which provides support for students diagnosed with learning disabilities.
- Students Academic Skills Instructional Program (ASIP), which offers individual appointments to help you develop effective and efficient academic skills and strategies.
Other relevant resources:
The Writing Studio, where students can attend workshops and individual appointments to improve brainstorming, formatting, and writing skills.
The Academic Advising Center (AAC), which offers students advising in field specific aspects such as choosing a major, utilizing resources within Duke’s scientific community, making progress toward career goals, and maximizing your experience at Duke.