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UCC2: Course Change Transmittal FormDepartment Name and Number
E�ective Term and Year
Current SCNS Course Identi�cation
Course Title
Pre�x Level Course Number Lab Code
Rotating Topic: S/U Only: yes
no
Course Description (50 words or less; if requesting a change, please attach a syllabus)
Prerequisites
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Rev. 10/10
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Change Course Identi�cation to:
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Pre�x Level Course Number Lab Code
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Contact Hours: Base or Headcount From To
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Full Course Title
Fungal Biology PLP 6656C
INSTRUCTOR: Dr. Matthew E. Smith Office: 2517 Fifield Hall Phone: 352-273-2837 Email: <[email protected]> Office Hours: Mondays 9-10 am or by appointment LABORATORY SUPPORT: XXXXXXXX Email: < [email protected]> COURSE(S): PLP 4653C and PLP6656C are taught concurrently. Undergraduates are expected to enroll in PLP 4653C whereas graduate students should enroll in PLP6656C. Students enrolled in the graduate course will be responsible for additional writing assignments, a more extensive fungal collections project, and more rigorous quizzes and exams relative to their undergraduate classmates. PREREQUISITE: BSC 2010 and BSC 2011 or PLP3002C (or consent of instructor) CREDITS: 4 Course Website: https://lss.at.ufl.edu/ (e-Learning in Sakai) CLASS TIMES & LOCATIONS: Lectures: 2306 Fifield Hall, Monday and Friday, 12:50–1:40 am (Period 6) Laboratories: 2306 Fifield Hall, Monday and Friday, 1:55–3:50 pm (Period 7–8) Final Exam: Friday, 13 December 2013 from 12:30-2:30 pm BRIEF DESCRIPTION Mycology is the study of fungal biology. Fungi are extremely diverse in terrestrial and aquatic ecosystems and they serve as the most important decomposers of organic materials. Fungi are also ecologically and economically important as symbionts and pathogens of a wide variety of plants and animals. The main objective of this course is to provide students with a broad overview of this group of organisms. Much of the class will focus on fungal ecology, fungal diversity, and fungal evolution. During the course, students will: 1) learn about fungi, their biology, and the important impacts they have on humans and natural ecosystems, 2) collect and identify a variety of different fungi from local habitats, and 3) use microscopy to examine the morphology of fungi in the laboratory. We will also read, discuss, and critique modern journal articles that address various aspects of fungal biology. COURSE OBJECTIVES By the end of this course, students will be able to:
1. Read, interpret, and critique scientific journal articles focused on fungal biology 2. Locate and use fungal biology resources to interpret fungal nomenclature and systematics 3. Identify major groups of fungi based on morphology (both in the field and in the lab) 4. Understand and explain the ecological roles and trophic modes of major fungal groups 5. Read and interpret a phylogenetic tree 6. Use a dichotomous key to identify local macrofungi to the genus level 7. Perform molecular and computational tasks necessary for DNA barcoding of fungi 8. Give a 10-minute presentation with appropriate visual aids 9. Provide constructive criticism during a peer review
REQUIRED TEXT: Introduction to Fungi. 3rd Edition (2007) Webster & Webster. Cambridge University Press.
ABSENCES AND MAKE-UP WORK: Requirements for class attendance and make-up exams, assignments and other work are consistent with university policies that can be found at: https://catalog.ufl.edu/ugrad/current/regulations/info/attendance.aspx. ATTENDANCE: Attendance is mandatory. This is a highly experiential course - you are expected to participate in every class and laboratory. There will be occasional quizzes and activities that will contribute to your grade in the class. Missed activity grades, tests, and quizzes can be made up for excused absences. Activities in class require that you: 1) have done the readings or other appropriate preparation, 2) show up on time, and 3) actively participate in class. LABORATORY: The laboratory will emphasize principles and concepts of mycology through demonstrations and hands-on exercises using living organisms and prepared specimens as well as short field trips. Labs will typically include an introduction to the exercise, work with demonstration or experimental materials, and sometimes an assignment to be handed in either at the end of the session or the beginning of the subsequent session. It is advised that you keep a lab notebook for all labs. Your lab notebook will not be graded, but a well-kept notebook will be highly beneficial to you in preparing lab assignments and studying for exams. EXAMS AND GRADING: Grading is based on a total of 600 possible points. 100 points will be awarded for student participation in class discussions and laboratory activities. 200 points will be awarded for the completion of two student projects (The Encyclopedia of Fungi Project and the Fungal Collection Project, see below). These projects will be introduced toward the beginning of the term and students will have opportunities to work on their independent projects throughout the semester in lab. 100 points will be awarded based on a series of short quizzes that will be completed in class (students will be allowed to drop their lowest quiz score) and 100 points will be awarded based on the Final Exam. The Final Exam is scheduled for December Xth from X– X pm. Graduate students will also be responsible for three critiques of journal articles on funal biology topics, worth a total of 100 points. Critical due dates for important assignments can be found in the course schedule (see following pages). COURSE PROJECTS: Graduate students will be responsible for completing two course projects worth a total of 200 points. For the Encyclopedia of Fungi Project students will select a target fungus, research the biology of that fungus, and then summarize what is known about the fungus on a webpage for the Encyclopedia of Life (EOL). This project will also involve a peer-review process whereby fellow students will provide constructive feedback to improve the webpage. For the Fungal Collections Project students will collect, identify, and preserve 35 species of local macrofungi. Students will have opportunities to learn basic fungi identification skills to help them with this project during labs and field trips throughout the semester.
Component Points Class & Lab Participation 100 Encyclopedia of Fungi Project 100 3 Journal Article Critiques 100 Fungal Collection Project 100 Quizzes 100 Final Exam 100
Total Number of Possible Points: 600 GRADES AND GRADE POINTS: For information on current UF policies for assigning grade points, see https://catalog.ufl.edu/ugrad/current/regulations/info/grades.aspx Grade points will be assigned as follows.
Letter Grade Percentage A 95 – 100 A- 90 – 94.9 B+ 87 – 89.9 B 83 – 86.9 B- 80 – 82.9 C+ 77 – 79.9 C 73 – 76.9 C- 70 – 72.9 D+ 67 – 69.9 D 63 – 66.9 D- 60.1 – 62.9 E 60 or below WF NA I NA NG NA S-U NA ACADEMIC HONESTY – As a student at the University of Florida, you have committed yourself to uphold the Honor Code, which includes the following pledge: “We, the members of the University of Florida community, pledge to hold ourselves and our peers to the highest standards of honesty and integrity.” You are expected to exhibit behavior consistent with this commitment to the UF academic community, and on all work submitted for credit at the University of Florida, the following pledge is either required or implied: "On my honor, I have neither given nor received unauthorized aid in doing this assignment." It is assumed that you will complete all work independently in each course unless the instructor provides explicit permission for you to collaborate on course tasks (e.g. assignments, papers, quizzes, exams). Furthermore, as part of your obligation to uphold the Honor Code, you should report any condition that facilitates academic misconduct to appropriate personnel. It is your individual responsibility to know and comply with all university policies and procedures regarding academic integrity and the Student Honor Code. Violations of the Honor Code at the University of Florida will not be tolerated. Violations will be reported to the Dean of Students Office for consideration of disciplinary action. For more information regarding the Student Honor Code, please see: http://www.dso.ufl.edu/SCCR/honorcodes/honorcode.php. Students are expected to strictly follow these guidelines:
1. Complete their own independent work (unless the assignment has specifically been defined as a group project) and turn it on time.
2. Cite sources in their written assignments so that the veracity of their statements can be independently verified by the instructor.
3. Use quotations to designate text that was generated by another person. 4. Know the definition of the word “plagiarism” and ensure that their academic work does not plagiarise the
work of others (see www.plagiarism.org/). SOFTWARE USE – All faculty, staff and students of the university are required and expected to obey the laws and legal agreements governing software use. Failure to do so can lead to monetary damages and/or criminal penalties for the individual violator. Because such violations are also against university policies and rules, disciplinary action will be taken as appropriate. CAMPUS HELPING RESOURCES – Students experiencing crises or personal problems that interfere with their general well-being are encouraged to utilize the university’s counseling resources. The Counseling & Wellness Center provides confidential counseling services at no cost for currently enrolled students. Resources are available on campus for students having personal problems or lacking clear career or academic goals, which interfere with their academic performance.
• University Counseling & Wellness Center, 3190 Radio Road, 352-392-1575, www.counseling.ufl.edu/cwc/
Counseling Services Groups and Workshops
Outreach and Consultation Self-Help Library Training Programs Community Provider Database
• Career Resource Center, First Floor JWRU, 392-1601, www.crc.ufl.edu/ SERVICES FOR STUDENTS WITH DISABILITIES – The Disability Resource Center (0001 Reid Hall, 352-392-8565, www.dso.ufl.edu/drc/ )coordinates the needed accommodations of students with disabilities. This includes registering disabilities, recommending academic accommodations within the classroom, accessing special adaptive computer equipment, providing interpretation services and mediating faculty-student disability related issues. Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of Students Office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodation Course Schedule
Lecture Lab
Fri August 23 Intro to Course Microscope Use Mon August 26 Fungi Intro 1 Macrofungi – macromorphology, basics of ID Fri August 30 Paper Discussion 1 [Quiz 1] Field Trip to NATL to collect fungi Mon September 2 Holiday Holiday Fri September 6 Fungi Intro 2 Agarics, Puffballs, and Shelf Fungi Mon September 9 Basidiomycota 1 Dichotomous Key exercise with Basidio fungi Fri September 13 Paper Discussion 2 [Quiz 2] Field Trip to Split Rock to collect fungi Mon September 16 Basidiomycota 2 Molecular Identification & Tree-building Fri September 20 Basidiomycota 3 Field Trip to Newnan’s Lake to collect fungi Mon September 23 Basidiomycota 4 Rusts, Smuts, and Jellies Fri September 27 Paper Discussion 3 [Quiz 3] EOF Peer review exercise Mon September 30 Ascomycota 1 Ascocarp morphology Fri October 4 Ascomycota 2 Asexual states of Ascomycota Mon October 7 Ascomycota 3 EOF Exercise & Student Presentations Due Fri October 11 Paper Discussion 4 [Quiz 4] Fungi Barcoding Lab Mon October 14 Ascomycota 4 Plant Endophyte Lab Fri October 18 Mycorrhizal Symbiosis Mycorrhiza Lab Mon October 21 Lichens Lichen Demography Field Trip Fri October 25 Paper Discussion 5 [Quiz 5] Nematode-Destroying Fungi Mon October 28 Zygomycota 1 Complete Barcode + Nematode Fungi Labs Fri November 1 Zygomycota 2 Zygomycete Morphology Mon November 4 Aquatic Fungi – the chytrids Aquatic Fungi Lab Fri November 8 Holiday Holiday Mon November 11 Holiday Holiday Fri November 15 Oomycota Oomycota Lab Mon November 19 Paper Discussion 6 [Quiz 6] Local Fungi Business Field Trip Fri November 22 Slime molds Slime Mold Lab Mon November 25 Fungi - food & food production Mycophagy Lab Mon November 29 Holiday Holiday Fri December 2 Final Review Fungi Collections Due Fri December 13 Final Exam Final Exam
Outline of major topics to be covered in the course:
- Overview of fungal tree of life - Basics of light microscopy - History of mycology - Macrofungi: basic field identification - Lineage-specific activities for microscopic identification of fungi - Species- and lineage-level diversity based on morphology and evironmental sampling - Basic concepts in molecular phylogenetics - Specimen preservation and herbarium curation - Emerging fungal diseases of plants and animals - Encyclopedia of fungi exercise and peer review - Identifying unknown fungi with DNA barcoding and phylogenetic analysis - Insect and nematode associated fungi – ecology and systematics - Species concepts and cryptic species in fungal biology - Lichen biology and morphology - Mycorrhizal ecology and evolution - Fungi as medicines, toxins, and food products - Fungal sexuality and reproduction - Fungal endophytes of plants, bacterial endophytes of fungi - Aquatic fungi – the biology and diversity of the “chytrids” - Fungi-like organisms: Oomycota and Slime Molds
Assigned readings for Paper Discussions Discussion 1 – Species-level and Deep-level Phylogenetic Diversity
• Blackwell (2011) The Fungi: 1, 2, 3 … 5.1 million species? American Journal of Botany. 98: 426–438 • James et al. (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature.
443: 818 • Jones et al. (2011) Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474:
200 Discussion 2 – Speciation and Species Boundaries
• Taylor et al. (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology. 31: 21–32.
• Henk et al. (2011) Speciation despite globally overlapping distributions in Penicillium chrysogenum: the population genetics of Alexander Fleming’s lucky fungus. Molecular Ecology. 20: 4288–4301
Discussion 3 – Genomics Tools in Fungal Biology
• Ellison et al. (2011) Population genomics and local adaptation in wild isolates of a model microbial eukaryote. PNAS. 108: 2831–2836.
• Ma et al. (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464: 367
Discussion 4 – Fungi as major pathogens of plants and animals
• Warnecke et al. (2012) Inoculation of bats with European Geomyces destructans supports the novel pathogen hypothesis for the origin of white-nose syndrome. PNAS. 109: 6999–7003
• Crawford et al. (2010) Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama. PNAS. 107:13777–13782
Discussion 5 – Fungal Biology and Climate Change
• Gange et al. (2007) Rapid and recent changes in fungal fruiting patterns. Science. 316:71 • Kauserud et al. (2008) Mushroom fruiting and climate change. PNAS. 105: 3811–3814
Discussion 6 – Fungi and Symbioses
• Arnold et al. (2003) Fungal endophytes limit pathogen damage in a tropical tree. PNAS. 100: 15649–15654
• Kiers et al. (2011) Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science 333: 880-882.
Basic Fungal Biology PLP 4653C
INSTRUCTOR: Dr. Matthew E. Smith Office: 2517 Fifield Hall Phone: 352-273-2837 Email: <[email protected]> Office Hours: Mondays 9-10 am or by appointment LABORATORY SUPPORT: XXXXXXXX Email: < [email protected]> COURSE(S): PLP 4653C and PLP6656C are taught concurrently. Undergraduates are expected to enroll in PLP 4653C whereas graduate students should enroll in PLP6656C. Students enrolled in the graduate course will be responsible for additional writing assignments, a more extensive fungal collections project, and more rigorous quizzes and exams relative to their undergraduate classmates. PREREQUISITE: BSC 2010 and BSC 2011 or PLP3002C/PLP5002C (or consent of instructor) CREDITS: 4 Course Website: https://lss.at.ufl.edu/ (e-Learning in Sakai) CLASS TIMES & LOCATIONS: Lectures: 2306 Fifield Hall, Monday and Friday, 12:50–1:40 pm (Period 6) Laboratories: 2306 Fifield Hall, Monday and Friday, 1:55–3:50 pm (Period 7–8) Final Exam: Friday, 13 December 2013 from 12:30-2:30 pm BRIEF DESCRIPTION Mycology is the study of fungal biology. Fungi are extremely diverse in terrestrial and aquatic ecosystems and they serve as the most important decomposers of organic materials. Fungi are also ecologically and economically important as symbionts and pathogens of a wide variety of plants and animals. The main objective of this course is to provide students with a broad overview of this group of organisms. Much of the class will focus on fungal ecology, fungal diversity, and fungal evolution. During the course, students will: 1) learn about fungi, their biology, and the important impacts they have on humans and natural ecosystems, 2) collect and identify a variety of different fungi from local habitats, and 3) use microscopy to examine the morphology of fungi in the laboratory. We will also read, discuss, and critique modern journal articles that address various aspects of fungal biology. COURSE OBJECTIVES By the end of this course, students will be able to:
1. Locate and use fungal biology re sources to interpret fungal nomenclature and systematics 2. Identify major groups of fungi based on morphology (both in the field and in the lab) 3. Understand and explain the ecological roles and trophic modes of major fungal groups 4. Read and interpret a phylogenetic tree 5. Use a dichotomous key to identify local macrofungi to the genus level 6. Give a 10-minute presentation with appropriate visual aids 7. Provide constructive criticism during a peer review
REQUIRED TEXT: Introduction to Fungi. 3rd Edition (2007) Webster & Webster. Cambridge University Press.
ABSENCES AND MAKE-UP WORK: Requirements for class attendance and make-up exams, assignments and other work are consistent with university policies that can be found at: https://catalog.ufl.edu/ugrad/current/regulations/info/attendance.aspx. ATTENDANCE: Attendance is mandatory. This is a highly experiential course - you are expected to participate in every class and laboratory. There will be occasional quizzes and activities that will contribute to your grade in the class. Missed activity grades, tests, and quizzes can be made up for excused absences. Activities in class require that you: 1) have done the readings or other appropriate preparation, 2) show up on time, and 3) actively participate in class. LABORATORY: The laboratory will emphasize principles and concepts of mycology through demonstrations and hands-on exercises using living organisms and prepared specimens as well as short field trips. Labs will typically include an introduction to the exercise, work with demonstration or experimental materials, and sometimes an assignment to be handed in either at the end of the session or the beginning of the subsequent session. It is advised that you keep a lab notebook for all labs. Your lab notebook will not be graded, but a well-kept notebook will be highly beneficial to you in preparing lab assignments and studying for exams. EXAMS AND GRADING: Grading is based on a total of 500 possible points. 100 points will be awarded for student participation in class discussions and laboratory activities. 200 points will be awarded for the completion of two student projects (The Encyclopedia of Fungi Project and the Fungal Collection Project, see below). These projects will be introduced toward the beginning of the term and students will have opportunities to work on their independent projects throughout the semester in lab. 100 points will be awarded based on a series of short quizzes that will be completed in class (students will be allowed to drop their lowest quiz score) and 100 points will be awarded based on the Final Exam. The Final Exam is scheduled for Wednesday, December 12th from 3:00–5:00pm. Critical due dates for important assignments can be found in the course schedule (see following pages). COURSE PROJECTS: Undergraduate students will be responsible for completing two course projects worth a total of 200 points. For the Encyclopedia of Fungi Project students will select a target fungus, research the biology of that fungus, and then summarize what is known about the fungus on a webpage for the Encyclopedia of Life (EOL). This project will also involve a peer-review process whereby fellow students will provide constructive feedback to improve the webpage. For the Fungal Collections Project students will collect, identify, and preserve 20 species of local macrofungi. Students will have opportunities to learn basic fungi identification skills to help them with this project during labs and field trips throughout the semester.
Component Points Class & Lab Participation 100 Encyclopedia of Fungi Project 100 Fungal Collection Project 100 Quizzes 100 Final Exam 100
Total Number of Possible Points: 500 GRADES AND GRADE POINTS: For information on current UF policies for assigning grade points, see https://catalog.ufl.edu/ugrad/current/regulations/info/grades.aspx Grade points will be assigned as follows. Letter Grade Percentage A 95 – 100 A- 90 – 94.9 B+ 87 – 89.9 B 83 – 86.9 B- 80 – 82.9 C+ 77 – 79.9 C 73 – 76.9 C- 70 – 72.9
D+ 67 – 69.9 D 63 – 66.9 D- 60.1 – 62.9 E 60 or below WF NA I NA NG NA S-U NA ACADEMIC HONESTY – As a student at the University of Florida, you have committed yourself to uphold the Honor Code, which includes the following pledge: “We, the members of the University of Florida community, pledge to hold ourselves and our peers to the highest standards of honesty and integrity.” You are expected to exhibit behavior consistent with this commitment to the UF academic community, and on all work submitted for credit at the University of Florida, the following pledge is either required or implied: "On my honor, I have neither given nor received unauthorized aid in doing this assignment." It is assumed that you will complete all work independently in each course unless the instructor provides explicit permission for you to collaborate on course tasks (e.g. assignments, papers, quizzes, exams). Furthermore, as part of your obligation to uphold the Honor Code, you should report any condition that facilitates academic misconduct to appropriate personnel. It is your individual responsibility to know and comply with all university policies and procedures regarding academic integrity and the Student Honor Code. Violations of the Honor Code at the University of Florida will not be tolerated. Violations will be reported to the Dean of Students Office for consideration of disciplinary action. For more information regarding the Student Honor Code, please see: http://www.dso.ufl.edu/SCCR/honorcodes/honorcode.php. Students are expected to strictly follow these guidelines:
1. Complete their own independent work (unless the assignment has specifically been defined as a group project) and turn it on time.
2. Cite sources in their written assignments so that the veracity of their statements can be independently verified by the instructor.
3. Use quotations to designate text that was generated by another person. 4. Know the definition of the word “plagiarism” and ensure that their academic work does not plagiarise the
work of others (see www.plagiarism.org/). SOFTWARE USE – All faculty, staff and students of the university are required and expected to obey the laws and legal agreements governing software use. Failure to do so can lead to monetary damages and/or criminal penalties for the individual violator. Because such violations are also against university policies and rules, disciplinary action will be taken as appropriate. CAMPUS HELPING RESOURCES – Students experiencing crises or personal problems that interfere with their general well-being are encouraged to utilize the university’s counseling resources. The Counseling & Wellness Center provides confidential counseling services at no cost for currently enrolled students. Resources are available on campus for students having personal problems or lacking clear career or academic goals, which interfere with their academic performance.
• University Counseling & Wellness Center, 3190 Radio Road, 352-392-1575, www.counseling.ufl.edu/cwc/
Counseling Services Groups and Workshops Outreach and Consultation Self-Help Library Training Programs Community Provider Database
• Career Resource Center, First Floor JWRU, 392-1601, www.crc.ufl.edu/ SERVICES FOR STUDENTS WITH DISABILITIES – The Disability Resource Center (0001 Reid Hall, 352-392-8565, www.dso.ufl.edu/drc/ )coordinates the needed accommodations of students with disabilities. This includes registering disabilities, recommending academic accommodations within the classroom, accessing special adaptive computer equipment, providing interpretation services and mediating faculty-student disability
related issues. Students requesting classroom accommodation must first register with the Dean of Students Office. The Dean of Students Office will provide documentation to the student who must then provide this documentation to the Instructor when requesting accommodation Course Schedule
Lecture Lab
Fri August 23 Intro to Course Microscope Use Mon August 26 Fungi Intro 1 Macrofungi – macromorphology, basics of ID Fri August 30 Paper Discussion 1 [Quiz 1] Field Trip to NATL to collect fungi Mon September 2 Holiday Holiday Fri September 6 Fungi Intro 2 Agarics, Puffballs, and Shelf Fungi Mon September 9 Basidiomycota 1 Dichotomous Key exercise with Basidio fungi Fri September 13 Paper Discussion 2 [Quiz 2] Field Trip to Split Rock to collect fungi Mon September 16 Basidiomycota 2 Molecular Identification & Tree-building Fri September 20 Basidiomycota 3 Field Trip to Newnan’s Lake to collect fungi Mon September 23 Basidiomycota 4 Rusts, Smuts, and Jellies Fri September 27 Paper Discussion 3 [Quiz 3] EOF Peer review exercise Mon September 30 Ascomycota 1 Ascocarp morphology Fri October 4 Ascomycota 2 Asexual states of Ascomycota Mon October 7 Ascomycota 3 EOF Exercise & Student Presentations Due Fri October 11 Paper Discussion 4 [Quiz 4] Fungi Barcoding Lab Mon October 14 Ascomycota 4 Plant Endophyte Lab Fri October 18 Mycorrhizal Symbiosis Mycorrhiza Lab Mon October 21 Lichens Lichen Demography Field Trip Fri October 25 Paper Discussion 5 [Quiz 5] Nematode-Destroying Fungi Mon October 28 Zygomycota 1 Complete Barcode + Nematode Fungi Labs Fri November 1 Zygomycota 2 Zygomycete Morphology Mon November 4 Aquatic Fungi – the chytrids Aquatic Fungi Lab Fri November 8 Holiday Holiday Mon November 11 Holiday Holiday Fri November 15 Oomycota Oomycota Lab Mon November 19 Paper Discussion 6 [Quiz 6] Local Fungi Business Field Trip Fri November 22 Slime molds Slime Mold Lab Mon November 25 Fungi - food & food production Mycophagy Lab Mon November 29 Holiday Holiday Fri December 2 Final Review Fungi Collections Due Fri December 13 Final Exam Final Exam
Outline of major topics to be covered in the course:
- Overview of fungal tree of life - Basics of light microscopy - History of mycology - Macrofungi: basic field identification - Lineage-specific activities for microscopic identification of fungi - Species- and lineage-level diversity based on morphology and evironmental sampling - Basic concepts in molecular phylogenetics
- Specimen preservation and herbarium curation - Emerging fungal diseases of plants and animals - Encyclopedia of fungi exercise and peer review - Identifying unknown fungi with DNA barcoding and phylogenetic analysis - Insect and nematode associated fungi – ecology and systematics - Species concepts and cryptic species in fungal biology - Lichen biology and morphology - Mycorrhizal ecology and evolution - Fungi as medicines, toxins, and food products - Fungal sexuality and reproduction - Fungal endophytes of plants, bacterial endophytes of fungi - Aquatic fungi – the biology and diversity of the “chytrids” - Fungi-like organisms: Oomycota and Slime Molds
Assigned readings for Paper Discussions Discussion 1 – Species-level and Deep-level Phylogenetic Diversity
• Blackwell (2011) The Fungi: 1, 2, 3 … 5.1 million species? American Journal of Botany. 98: 426–438 • James et al. (2006) Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature.
443: 818 • Jones et al. (2011) Discovery of novel intermediate forms redefines the fungal tree of life. Nature 474:
200 Discussion 2 – Speciation and Species Boundaries
• Taylor et al. (2000) Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology. 31: 21–32.
• Henk et al. (2011) Speciation despite globally overlapping distributions in Penicillium chrysogenum: the population genetics of Alexander Fleming’s lucky fungus. Molecular Ecology. 20: 4288–4301
Discussion 3 – Genomics Tools in Fungal Biology
• Ellison et al. (2011) Population genomics and local adaptation in wild isolates of a model microbial eukaryote. PNAS. 108: 2831–2836.
• Ma et al. (2010) Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464: 367
Discussion 4 – Fungi as major pathogens of plants and animals
• Warnecke et al. (2012) Inoculation of bats with European Geomyces destructans supports the novel pathogen hypothesis for the origin of white-nose syndrome. PNAS. 109: 6999–7003
• Crawford et al. (2010) Epidemic disease decimates amphibian abundance, species diversity, and evolutionary history in the highlands of central Panama. PNAS. 107:13777–13782
Discussion 5 – Fungal Biology and Climate Change
• Gange et al. (2007) Rapid and recent changes in fungal fruiting patterns. Science. 316:71 • Kauserud et al. (2008) Mushroom fruiting and climate change. PNAS. 105: 3811–3814
Discussion 6 – Fungi and Symbioses
• Arnold et al. (2003) Fungal endophytes limit pathogen damage in a tropical tree. PNAS. 100: 15649–15654
• Kiers et al. (2011) Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science 333: 880-882.
7 February 2013 CALS Curriculum Committee 2002 McCarty Hall Dear CALS Curriculum Committee: The Department of Plant Pathology is seeking to revise several aspects of the Fungal Biology curriculum. In November 2011, we hired a new fungal biologist (Dr. Matthew E. Smith) who began teaching our mycology course in Fall 2012. The mycology course is a combined undergraduate-graduate course in which the two different course numbers are taught concurrently (currently PLP 3653C: Introductory Mycology & PLP 5656C: Mycology). The curriculum committee within our department has evaluated the content and scope of the concurrent courses and we are formally requesting the following changes:
• The names of the two courses will be changed from “Introductory Mycology” and “Mycology” to “Basic Fungal Biology” and “Fungal Biology.” This is meant to attract a wider base of undergraduate students who will be more familiar with the term “Fungal Biology” than the older and less common term “Mycology.”
• The courses will be renumbered to better reflect the current information provided
through the course and to bring the courses into compliance with the updated rules governing course numbering. Course PLP 3653C will be changed to PLP 4653C and course PLP 5656C will be changed to PLP 6656C.
• Equalize the number of units so the undergraduate and graduate-level courses
receive equal credit. In the past, graduate students received 5 credits and undergraduates received 4 credits for the same number of contact hours. We intend to make the course a 4-credit course for all students (with 6 contact hours per week divided into two 1-hour lecture periods and two 2-hour lab periods).
• Change the prerequisite courses. The current prerequisite courses are listed as
BOT 2011C (Plant Diversity) or BOT 3303L (Introductory Vascular Plant Morphology) or PLP3002C (General Plant Path) (equivalent to /PLP5002C for graduate students). The General Plant Pathology course provides some background for the course so it is retained as a prerequisite. However, the other two courses provide content that is not relevant for modern fungal biology. Given this information, we suggest that the basic biology series (Integrated Principles of Biology – BSC 2010 and BSC 2011) is a more appropriate and rational
prerequisite. This is appropriate in terms of course content and will also open the course to a wider audience of biology students.
• The course will be offered each fall instead of during odd years. This change
reflects a growing demand for the course as well as our efforts to recruit more undergraduates in the coming years.
We have submitted the syllabi for the two courses so that the committee can assess our changes. The assignments and objectives for the two courses (undergraduate and graduate) are significantly different from one another. Students in the graduate course are required to write three additional “Journal Critique” papers and are also responsible for collecting and identifying 15 additional species of fungi for their fungal collection project. The graduate students also receive more rigorous quizzes and tests than do undergraduate students. Attached is the suggested syllabus for PLP 3653C (under the proposed course name and number Basic Fungal Biology, PLP 4653C). I have also attached the syllabus for the co-listed course (as Fungal Biology PLP 6653) as well as the Syllabus Checklist and the UCC2 form. Either Dr. Matthew Smith or I would be pleased to answer any questions regarding this course proposal. Sincerely, Jeffrey B. Jones, Ph.D. PLP Graduate Coordinator
UCC: External Consultations
Rev. 10/10
External Consultation Results (departments with potential overlap or interest in proposed course, if any)
Department Name and Title
E-mailPhone Number
Comments
Department Name and Title
E-mailPhone Number
Comments
Department Name and Title
E-mailPhone Number
Comments
Matt I have reviewed your course changes and I agree that we are not teaching anything likethat in our department. I see no overlap!Tim!From: Smith,Matthew Sent: Monday, February 18, 2013 3:59 PMTo: White,TimCc: Meldrum,Marie LSubject: changes to mycology curriculum in Plant Pathology Dear Dr. White, I am writing to you because I am a relatively new assistant professor here in PlantPathology and I am trying to make some changes in the Mycology curriculum. Ourmycology class is a grad/undergrad lab course which focuses on morphology,evolution, systematics, and ecology of fungi. We look at fungi across all major lineagesand only briefly touch on forest pathogens. I feel there is no real overlap with the courses in your department but the CALScurriculum committee has asked that I consult with other departments where theremight be some slight possibility of overlap. I have already spoken with Jason Smithand we are in agreement that his Forest Health course does not overlap with my course(see attached letter from Jason). I was hoping that it might be possible for you toquickly review my attached documents and send back some sort of reply that I canattach to my application for changes. If you agree the the statement should just readsomething simple such as: ""
From: "White,Tim" <[email protected]>Subject: RE: changes to mycology curriculum in Plant Pathology
Date: February 19, 2013 7:04:17 AM ESTTo: "Smith,Matthew" <[email protected]>Cc: "Meldrum,Marie L" <[email protected]>, "SMITH,JASON ANDREW" <[email protected]>
9 February 2013 CALS Curriculum Committee 2002 McCarty Hall Dear CALS Curriculum Committee: I am an Associate Professor in the Department of Plant Pathology. I teach the combined course Introduction to Plant Pathogenic Fungi PLP4260C/Fungal Plant Pathogens PLP6262C. This course focuses on the biology of pathogenic fungi and fungal-like organisms with a particular emphasis on lifecycles of pathogenic fungi, disease epidemiology, and applied aspects of fungal plant pathogens.
This letter is to acknowledge that my course does not significantly overlap with Dr. Matthew Smith’s course that is currently being considered for changes by the Committee (Basic Fungal Biology PLP4653C/Fungal Biology PLP6653C). The 4653C/6653C course has a broader focus - it addresses systematic, basic biology, morphology, ecology, and evolutionary biology of all fungi, including non-pathogenic fungi that are not covered in my course (including symbionts, saprobes, and animal associated fungi). I have read and approve of the suggested changes to this course. Sincerely, Jeffrey Rollins, Ph.D. Associate Professor
School of Forest Resources and Conservation University of Florida Gainesville, FL 32611 Tel. (352) 846-0843 Fax (352) 846-1277
9 February 2013 CALS Curriculum Committee 2002 McCarty Hall Dear CALS Curriculum Committee: My name is Dr. Jason Smith and I am an Associate Professor in the Department of Forest Resources and Conservation. I teach a course entitled Forest Health and Management (FOR4624C). This course focuses on the biology of forest pests, including fungal pathogens and insect pests.
This letter is to acknowledge that my course does not significantly overlap with Dr. Matthew Smith’s course that is currently being considered for changes by the CALS Curriculum Committee (Basic Fungal Biology PLP4653C/ Fungal Biology PLP6653C). The 4653C/ 6653C course has a broader focus - it addresses basic biology, morphology, ecology, and evolutionary biology of all fungi whereas the fungal component of my course is strictly focused on forest-associated pathogens of plants. Please feel free to contact me if you have any questions or concerns.
Sincerely,
Jason A. Smith, Ph.D. Associate Professor
School of Forest Resources and Conservation
UCC: Syllabus Checklist
Rev. 10/10
All UCC1 forms and each UCC2 form that proposes a change in the course description or credit hours must include this checklist in addition to a complete syllabus. Check the box if the attached syllabus includes the indicated information.
Instructor contact information (and TA if applicable)
Course objectives and/or goals
Policy related to class attendance
Policy related to make-up exams or other work
Statement related to accommodations for students with disabilities
Information on current UF grading policies for assigning grade points
Syllabus MUST contain the following information:
It is recommended that syllabi contain the following information:
1. Critical dates for exams and other work
2. Class demeanor expected by the professor (e.g., tardiness, cell phone usage)
4. Contact information for university counseling and mental health services
The University’s complete Syllabus Policy can be found at:
3. UF’s honesty policy
http://www.aa.u�.edu/policy/SyllabiPolicy.pdf
A topical outline (at least tentative) of subjects to be covered
Required and recommended textbooks
Methods by which students will be evaluated and their grades determined
