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MYCOLOGY

Utah Valley University

Since we are back in a face-to-face setting, we will be running this course as a course-based undergraduate research experience. This web page is still a very good resource for learning about fungi, but consider it “enrichment material” rather than a map of the course. It was built with a remote learning model in mind for when we were unable to do lab work in-person.

This webpage will host links to all resources and videos, and serves as a roadmap for the semester, listing readings, assignments, etc.

Course overview:

The course consists of several components:

  • Required readings
    • Textbook: Webster and Weber, Introduction to Fungi - 3rd ed. (specific sections)
    • Scientific papers: Usually weekly, linked below
  • Weekly quizzes on reading material (on Canvas)
  • Assorted “home mycology” lab, research, and field exercises (on Canvas)
  • Exams (3 of these, on Canvas, open-note)

The course is broken into 4 rough sections:

1. Getting to know fungal biology and major groups (get ready for a bunch of mycological terminology)

2. Fungi as the enemy (human and plant pathogens, fungal distribution, secondary compounds)

3. Fungi as a friend (mutualistic symbioses)

4. Molecular mycology (intro to modern methods and fungal bioinformatics)

Course assumptions (about you):

  • You know how to read a phylogeny and argue whether a trait is ancestral or derived
  • You know how to find and read a scientific journal article
  • You can write intelligibly
  • You understand the following terms and concepts:
    • monophyletic, taxon, clade, outgroup
    • central dogma of biology
    • chromosome, locus, gene, variant, phenotype
    • niche, dispersal, genetic drift, diploid/haploid
    • respiration, oxidation/reduction
  • In other words, you’ve had (and paid attention to) the material from BIOL1610 and BIOL1620

Course Syllabus

Course Text Book

My Hillbilly Mycology resource page

Good web resources

21st Century Guidebook to Fungi (This is pretty useful for this class!) Full download link for older edition (zipped).

“The Fifth Kingdom” website

Cornell’s Virtual Fungal Library (Extensive links to resources!)

Fungal Gene Database (Exactly what it sounds like.)

Emerging fungal diseases CDC resource page for those with a medical bent

Nice YouTube Channel with videos featuring do-it-at-home mycology

Weekly content:

Week 1

Topics:

  • What are fungi? | Chytrids and divergence from metazoa | Fungal phylogeny

Readings and Assignments

  • Study the lesson slides (link below)
  • Read James, et al., 2006
  • Read Webster & Weber: 1.1 | 1.5 | 6.1
  • Canvas quiz on readings (due before class Wednesday)
  • Watch this video on how fungi changed the world. Watch it before next week.
  • Find and grow zygomycete fungi (Canvas assignment; video walkthrough below)
  • Buy this cool pocket microscope Amazon link (this is in lieu of your textbook fee)
  • Teams discussion on readings (Wednesday 1pm)

Resources

Videos

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Week 2

Topics

  • The “hyphal lifestyle” | Fungal physiology | Zygomycetes | Reproduction in fungi

Readings and Assignments

  • No class Monday (Washington and Lincoln Day) … We will have class Friday instead!
  • Read Fisher, et al., 2018 (Have a phylogeny of Zygomycetes at the ready while you read this)
  • Read Webster & Weber: 1.2 | 1.3 | 1.4 | 7.1 | 7.2 | 7.3.1 | 7.3.2
  • Canvas quiz on readings (due before class Friday)
  • Teams discussion on readings (Friday 1pm)
  • Turn in your Zygomycete microscopy photos (Canvas)

Resources

Videos

  • Generic Zygomycete life cycle video
  • Another life cycle video
  • Zygospore formation video
  • Hyphal types video (though she mispronounces “coenocytic” … it’s like “see - no - sit - ic”)
  • Mucor as a human pathogen video
  • Mucor as a model of Zygomycete anatomy video (ridiculous music warning)
  • Cool time-lapse video of growing hyphae
  • Hyphal morphology video

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Week 3

Topics

  • Ascomycetes | Species concept in fungi | Anamorphs and Teleomorphs | Dikaryotism

Readings and Assignments

  • Read Webster & Weber: 8 | 10.2 | 12.1 | 12.2.1 | 17.2.6
  • Canvas quiz on readings (due before class Wednesday)
  • Teams discussion on readings (Wednesday 1pm)
  • How many Ascomycete species exist? (Canvas assignment)

Resources

Videos

  • Good overview of Ascomycete characteristcs
  • Sordaria crossing over
  • How fungi helped us solve the central dogma of biology:
    • Part 1 (Why Neruospora crassa was the perfect model organism)
    • Part 2 (The famous Beadle and Tatum experiment)

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Week 4

Topics

  • Basidiomycetes

Readings and Assignments

  • Read Webster & Weber: 18 | 19.1 | 19.4.5 | 20.1 | 20.3 | 21.1 | 21.5
  • Canvas quiz on readings (due before class Wednesday)
  • Teams discussion on readings (Wednesday 1pm)

Resources

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Week 5

Topics

  • Fungal development | Mushroom mechanics | Active dispersal | Mushroom ID

Readings and Assignments

  • Read Kiss, et al., 2019
  • Canvas quiz on readings (due before class Wednesday)
  • Teams discussion on readings (Wednesday 1pm)
  • Exam 1 (Covers material from weeks 1-4 … Due Friday 11:59pm)
  • Fungal collections (5 types of macrofungi) and IDs (Turned in on Canvas next week)
    • Photo of fungus in its habitat
    • Photo of spore print and/or micrograph of spores
    • Description of each fungus according to the mushroom characters cheat sheet (below)
    • Tentative genus identification if you are feeling bold
  • LINK to an example for one collection.

Resources

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Week 6

Topics

  • Medical mycology

Readings and Assignments

  • No class Monday (Washington and Lincoln Day) … We will have class Friday instead!
  • Read Huffnagle & Noverr, 2013
  • Canvas quiz on readings (due before class Friday)
  • Teams discussion on readings (Friday 1pm)

Resources

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Week 7

Topics

  • Plant pathogens

Readings and Assignments

  • Read Roy, 1993
  • Canvas quiz on readings (due before class Wednesday)
  • Teams discussion on readings (Wednesday 1pm)
  • Keep working on lab assignments!

Resources

Videos

  • Life cycle of wheat stem rust video
  • Plant-Pathogen interactions video

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Week 8

Topics

  • Distribution and dispersal | Population ecology

Readings and Assignments

  • Read Bacigalupe, et al., 2017
  • Canvas quiz on readings (due before class Wednesday)
  • Teams discussion on readings (Wednesday 1pm)

Resources

Videos

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Week 9

SPRING BREAK

Go find some mushrooms if you haven’t already!







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Week 10

Topics

  • Symbioses: Endophytes

Readings and Assignments

Resources

  • Major Topics
  • Leson slides
  • Lesson video (Part 1 - Discuss Bacigalupe paper; Endophyte lesson)
  • Lesson video (Part 2 - Discuss Christian et al, 2017 paper)

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Week 11

Topics

  • Symbioses: Mycorrhizae

Readings and Assignments

Resources

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Week 12

Topics

  • Symbioses: Lichens

Readings and Assignments

  • Read Spribille, et al., 2016
  • Canvas quiz on readings (due before class Wednesday)
  • Teams discussion on readings (Wednesday 1pm)

Resources

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Week 13

Topics

  • Fungi and ecosystems

Readings and Assignments

  • Read Halvorson, et al., 2019
  • Listen to Halvorson, et al. podcast (~ 15 min)
  • Canvas quiz on readings (due before class Wednesday)
  • Teams discussion on readings (Wednesday 1pm)

Resources

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Week 14

Topics

  • Ethnomycology

Readings and Assignments

  • Read Dugan, 2008
  • Exam 3 (Covers material from weeks 9-12 and Dugan, 2008)
    • Symbioses
    • Ecology

Resources

Week 15

Topics

  • Molecular mycology | Intro to fungal bioinformatics

Readings and Assignments

  • Read Raja, et al., 2017
  • Canvas quiz on readings (due before class Wednesday)
  • Teams discussion on readings (Wednesday 1pm)

Resources

Videos

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Week 16

Topics

  • Wrap-up

Readings and Assignments

  • Start on Final Exam

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Final Exam

For the Final Exam schedule, click here