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Mycology Syllabus Biology 5425 Fall 2018 Mycology Syllabus Instructor: Bryn Dentinger Office: LS 207 & NHMU Office: 801-585-1506 Lab: 801-587-5729 Email: [email protected] Office hours: by appointment Teaching Assistant: Alex Bradshaw Office: LS 207 Phone: Email: Office hours: by appointment Text: there is no officially assigned text for the class. However, these are recommended for general reference and some readings will be assigned from them (made available through Canvas): Webster, J. & Weber, R.W.S. 2007. Introduction to Fungi. 3rd Edition, J. Webster & R.W.S. Weber. Cambridge University Press. Alexopolous CJ, Mims CW, & Blackwell MM. 1996. Introductory Mycology. 4th Edition. Wiley Press. + updated chapters Esser, K. The mycota: a comprehensive treatise on fungi as experimental systems for basic and applied research. Multiple volume series. Springer Press. Course Web site: Canvas (https://utah.instructure.com/courses/517082) Class meets: Tu, Th 9:10-10:30 am, CSC 25 (lecture) Fr 12:55-5:00 pm, BIOL 140 (lab) Grading: 3 Lecture exams (100 points each) 2 Lab practical exams (25 points each) 5 Quizzes (10 points each) 1 Class presentation (50 points) 1 Lab report (100 points) 1 Fungus collection (50 points) TOTAL: 600 points 1 Biology 5425 Fall 2018 % of total % of total Grade Grade points points 100-93 A 77.9-73 C 92.9-90 A- 72.9-70 C- 89.9-88 B+ 69.9-68 D+ 87.9-83 B 67.9-60 D 82.9-80 B- 59.9- 0 F 79.9-78 C+ Final Exam: none Exams: Lecture exams will be based on lecture material and assigned reading. The best study guide for the exams is your own lecture and discussion notes. Exams may include short essay questions. Exams will be graded as quickly as possible and returned to you in class. There will be no makeup exams. In the event of a true emergency (e.g., you are hit by a car on the way to the exam and are in the process of a blood transfusion during the scheduled exam period), OBTAIN WRITTEN DOCUMENTATION of the emergency and contact me as soon as you are able and I will try to work something out with you. You can arrange to take an exam early if you have a legitimate scheduling conflict, but you cannot take an exam after it is given to the class. Quizzes and practical exams will be based on the lab and lecture material and will test practical knowledge of fungus manipulation and identification. The class presentation will be on a taxon assigned to you during a class. The lab report will be a formal document written in the form of a scientific manuscript and will be based on an analysis of samples collected during the required field trip. This will include a data analysis component which will be completed as a practical lab session. Every student will make a fungus collection using 5 samples collected during the field trip augmented where needed by independently collected specimens. Evaluation of each collection will be based on accuracy and completeness of collection information entered into a database (5 points/specimen), the number of correctly identified specimens (2 points/genus), and proper preparation and organization of the specimens (3 points). Regrade policy: Lecture and laboratory exams are graded with care against a predetermined key, which will be presented in class at the time exams are returned to you. We will correct any addition errors on exams, but we will NOT regrade exams. Course Drop Policy: The course withdrawal policy is the same as the University of Utah policy described in the Class Schedule. September 4 is the last day to drop with no tuition and no notation on the transcript, or elect the CR/NC or audit option. October 19 is the last day students 2 Biology 5425 Fall 2018 can withdraw from classes, but tuition will be assessed. November 30 is the last day to reverse a CR/NC option. Withdrawal from the course after October 19 requires special permission from the instructor. It will NOT be allowed except in cases of significant medical or personal emergency that must be documented by a medical professional or other relevant person. Americans with Disabilities Act (ADA): The University of Utah Department of Biology seeks to provide equal access to its programs, services and activities for people with disabilities. If you will need accommodations in this class, reasonable prior notice needs to be given to the instructor and to the Center for Disability Services, http://disability.utah.edu/, 162 Olpin Union Bldg, 581-5020 (V/TDD) to make arrangements for accommodations. This information is available in alternative format with prior notification. 3 Biology 5425 Fall 2018 Expected Learning Outcomes Students in Mycology should have the following Expected Learning Outcomes (ELOs). 1. Learn how to collect fungi from the environment and how to preserve, process and curate specimens in a fungus collection. 2. Learn how to isolate and manipulate fungal cultures on/in agar and liquid media using aseptic technique. 3. Learn how to interpret and discuss phylogenetic relationships of major groups within Fungi and of Fungi to other clades in the Tree of Life. 4. Learn how to identify fungi using a combination of morphological and molecular (DNA- based) techniques, including light microscopy, BLAST and basic phylogenetic analysis. 5. Learn the ecological roles of fungi and how these relate to ecosystem health and global carbon cycles. 6. Learn to use critical reading and thinking skills to interpret and critique research papers from the primary mycological literature. 7. Learn how to discuss the coevolutionary interactions between fungi and other organisms, both mutualistic and antagonistic. 8. Demonstrate an appreciation of the diversity and importance of fungi to human well- being. 4 Biology 5425 Fall 2018 Mycology Lecture & Lab Schedule Date Topic Reading Assignment Other Readings Lab Introduction Aug 21 Tu Taxonomy and Systematics 23 Th McLaughlin et al. 2009 Adl et al. 2012 24 F Field Trip Fungal-like organisms (slime molds, water molds) 28 Tu Stephenson 2014 Yoshida et al. 2013 Basidiomycota I. Introduction to Basidiomycota 30 Th Alexopolous et al. 1996, Chapter 16 Bennett 2015 31 F Field Trip Basidiomycota II. Form and function of basidiomata Webster & Weber, Chapter 18 - QUIZ 1 (http://lib.myilibrary.com/Open.aspx? Money 1998, Fischer et Sep 4 Tu id=95622) al. 2010 Basidiomycota III. Sexual reproduction, life cycles Banuett 2015, James 6 Th Heitman 2015 2015 7 F Field Trip - PRACTICAL 1 Basidiomycota IV. Litter and wood decomposition 11 Tu Floudas et al. 2012, Riley et al. 2014 Basidiomycota V. Coevolution: Plant and animal 13 Th relationships Plett et al. 2012 14 F Field Trip 18 Tu Basidiomycota : Agaricomycetes I. Hibbett et al. 2014 20 Th Basidiomycota : Agaricomycetes II. 21 F Field Trip 25 Tu Basidiomycota : Agaricomycetes III. - QUIZ 2 Gould 1992 Basidiomycota : Jellies (Dacrymycetes & 27 Th Tremellomycetes) 28 F Field Trip Basidiomycota : Ustilaginomycotina, & Pucciniomycotina Oct 2 Tu Begerow et al. 2014 Weiss et al. 2014 1ST EXAM 4 Th 5 Fr Field Trip fall break 7-14 FALL BREAK Webster & Weber, Chapter 8 Ascomycota I. Introduction to Ascomycota (http://lib.myilibrary.co 16 Tu Alexopolous et al. 1996, Chapter 7 m/Open.aspx?id=9562 Ascomycota II: Sexual & asexual reproduction; life cycles 18 Th LeTacon et al. 2016 19 F PCR & DNA Sequencing Ascomycota III. Coevolution: Plant and animal 23 Tu relationships - QUIZ 3 de Bekker et al. 2014 Ascomycota : Saccharomycotina & Taphrinomycotina 25 Th Kurtzman & Sugiyama 2015 26 F DNA sequence analysis, phylogenetics 30 Tu Ascomycota : Pezizomycotina I - Presentations Pfister 2015, Zhang & Wang 2015 1 Th Ascomycota : Pezizomycotina II - Presentations Gueidan et al. 2015 Nov 2 F isolating fungi from environmental samples 6 Tu Ascomycota : Pezizomycotina III - Presentations Geiser et al. 2015 8 Th Ascomycota : Pezizomycotina IV - Presentations Schoch & Grube 2015 9 F microscopy of ascos & zygos - PRACTICAL 2 13 Tu 2ND EXAM 15 Th "Zygomycota" & "Glomeromycota" Spatafora et al. 2016 Benny et al. 2015, 16 F Curate collections - NHMU 20 Tu Early diverging fungi (chytrids et al.) - QUIZ 4 Powell & Letcher 2015 James et al. 2015, Thanksgiving 22-25 Thanksgiving 27 Tu Guest Lecture: TBA TBD 29 Th Guest Lecture: TBA 30 F Food Lab - Lab repot due Dec 4 Tu Fungi & Society - QUIZ 5 TBD 6 Th 3RD EXAM 5 .
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