PMB/IB 110 Biology of the Fungi, 4 units, Fall 2020 Lectures: Mon (#2 6355, # 27151) , Wed 1-2; Currently in 5 6 - Social Sciences Building Lab/discussion sections Mon/Wed 10-12 # 26356;# 27152) ; Mon/Wed 3-5 (# 26357;Class # 27153); all lab in 209 GPBB (above Pat Brown’s) Synopsis: T his course surveys the biology of fungi and selected fungal-like eukaryotes through lectures, lab/discussions and student projects. Our goal is to help students develop a broad understanding of the diversity of fungi, their basic biology, and the major roles fungi play in our natural ecosystems, agriculture, medicine, and biotechnology. Lectures w ill be back to live, in-person lectures this year - hallelujah! Lectures will start promptly at 1:10 and end at 2:00. Please plan to arrive on time. Most of the material on tests will come straight from these lectures. Lab sections A PDF handout for each lab will be available for download on the Bcourses site in the Lab folder prior to the scheduled lab. This will outline the goals of each lab and list the fungi that we expect to see. Please download it for use prior to coming to the lab. Labs will start promptly at 9:10 AM and 2:10 PM. Sign in the attendance register at the front when you arrive, as attendance is required. With the exception of days when you are presenting a discussion paper, you may miss a maximum of 2 labs without penalty or excuse, Labs will start with a s hort show and tell period, where students and instructors can share fungal observations with the class. This is a great time to bring in material or images of fungi to share, especially if you need help with identifying them. For smaller fungi come with photos that can be projected for the class to see. For almost all labs there will be live or preserved material to see. The purpose of this material is to allow you to see these organisms and structures in person and to reinforce the information in lecture and discussions. We will not generally test you on identification with a “lab practical” format, but key structures and common organisms that you see in lab, lecture, or both are fair game for quizzes and tests. The lab participation grade (5%) will be based on: 1) your attendance; 2) uploading of labeled images or videos from lab to a shared photo site that we will provide; 3) signing up for 2 labs during the semester to extract DNA from the demonstration cultures in lab and to sort through the uploaded photos and select those to be posted on B-courses. Requirement 2, uploading of lab images/videos (1), is a chore we hope everyone will do frequently, however it is not necessary or expected for each student to upload an image from every lab. Requirement 3, extracting DNA from the cultures and sorting through the images from a lab to select the ones to post, will be a small-group effort because more than one student will normally be signed up for each lab. Coordinating with others signed up for the same day is encouraged and will make this easier. A major focus of the lab this year is the c ulture/observations project (see PDF on Bcourses). This project involves each student finding a diverse set of fungi in their local environment, and posting them to I naturalist.org. All class posts will be assembled so that everyone can see each other’s observations, and collectively view the diversity of fungi in our environments. At least three pure culture isolates must be made as part of this project. You should set aside some time in each lab to work on obtaining these three cultures and photographing them. On days with a paper discussion we try to start the discussion at 10:30 and 3:30 after the viewing the lab materials. These discussions will be based on assigned readings that are posted on bcourses. The topics we have selected are a mixture of current and classic issues in fungal biology, and we have set up the format to maximize participation and discussion (s ee group presentation project handout ). Textbook No textbook is required for the course. However, there will be assigned readings that are part of the lab discussions. These are posted on bcourses, and we will likely post other unassigned readings to provide backgrounds in particular topics. Field trips Field trips have always been a part of this course. We will try to carry on that tradition this year with two half-day field trips and one overnight/weekend field trip. The dates are listed on the schedule below. Transportation will be provided. The half-day field trips are free. The weekend field trip has an estimated cost of $48 to cover two meals and overnight accommodations. If you cannot afford this, but want to go, contact Prof. Bruns. All field trips are optional. Grades This course has usually been ranked as difficult by students because of the amount of material covered. Nevertheless, roughly 2/3rds of the students usually receive As and Bs. To be in that subset our advice is for you to a ttend lecture and lab discussions, take notes, stay current, and ask questions in class or office hours if you don’t understand the material. Without a textbook, it is really important to attend lectures and remain engaged during them. We will try to keep the grade book on bCourses reasonably current. But totals may not be precisely accurate because things like quizzes and participation grades may have different nominal points that will get scaled to the correct percentage later. Grade breakdown % pts Midterm 20 100 Final 40% 200 Midterm 20% 100 Best five quizzes (of 7) 10% 50 paper/discussion (lab) group presentation 8% 40 participation 2% 10 Personal observation project 15% 75 Lab participation 5% 25 Total 100% 500 The midterm and final will be biased toward material presented in lecture, but may also include information from all other parts of the course. Material that shows up in lecture and is repeated in labs or discussions has the highest probability of being tested. The f inal is cumulative, but weighted toward material given after the midterm. 7 Quizzes will be short (10-15 min) and given at the start of the lab period in which they are scheduled. They will cover material from lecture, lab, and discussions that were presented after the previous quiz. Th e lowest two quizzes are dropped. Thus you can skip up to two quizzes without penalty. Office hours w ill all be on zoom this year. Please feel free to stop in and say hi. If the times listed are inconvenient you can email us and set up an alternative. W e have an excellent student/instructor ratio - take advantage of it! Instructors: Prof. Rachel Brem Office hours: Thursday 3-4; Zoom: https://berkeley.zoom.us/j/93465472022?pwd=SmI3ZjV0V1JSNXNCTFp5aHB2TWFLQT09. Email r [email protected] Prof. Tom Bruns Office hours: Friday 10:30-11:30; Zoom: https://berkeley.zoom.us/j/91570768866?pwd=VkJHdXpKVzkyOHBVTU5naFJpT01NUT09 Or by appointment at 1012 Valley Life Science Building Email p [email protected] Prof. Louise Glass Office hours: Fridays 10-11 AM; Zoom: https://berkeley.zoom.us/j/97323796751?pwd=cExmejZxT2tKRk8wcHFEUytRd1ZPdz09 Meeting ID: 973 2379 6751 Passcode: 587260 Email l [email protected] Will Horner (G SI) General office hours Tuesdays from 9-10 AM; Zoom: https://berkeley.zoom.us/j/2850469838 Email h [email protected] Grace (Frances) Stark ( GSI) Office hours Tuesdays 4-5 PM: https://berkeley.zoom.us/j/5360603928 Email f [email protected] day date topic lecturer Wed 8/25/21 Lec Introduction to Fungi and Course Glass Kohler illumination and microscope use, Lab making wet mounts, cell phone Wed 8/25/21 photomicroscopy How do we tell one fungal species from Lec Mon 8/30/21 another? Brem Mon 8/30/21 Lab Isolation methods, simple DNA extraction, Wed 9/1/21 Lec Myxogastria: Acellular slime molds Glass Wed 9/1/21 Lab Myxogastria: acellular slime molds Mon 9/6/21 Labor Day Holiday Mon 9/6/21 Labor Day Holiday Wed 9/8/21 Lec Dictyostelia: Cellular slime molds Glass Quiz 1 R eading: Myxo mazes (GSI lead); Lab Dictyoselia and relatives; start water mold Reading Wed 9/8/21 baiting Deadline to sign up for an Inaturalist assign Fri 9/10/21 account class Mon 9/13/21 Lec Oomycota - Peronosporales Brem Phytophthora and other Lab Peronosporomycetes c heck and transfer Mon 9/13/21 watermold isolations from 9/8 Molecular evolution of Oomycota Lec Wed 9/15/21 pathogens Brem Pythium - c heck and transfer watermold Lab isolations from 9/8; d eadline to join Inat class assign Wed 9/15/21 project; Deadline to make your first Inaturalist assign Fri 9/17 post Mon 9/20/21 Lec Oomycota - Saprolegniales Brem Mon 9/20/21 Lab Saprolegnia & Achlya - pick up dung jars Early Diverging Fungi and Lec Wed 9/22/21 Chytridiomycota Brem Quiz 2; B lastocladiomycota; baiting for Lab chytrids BD:paper Reading https://royalsocietypublishing.org/doi/10.1098 Wed 9/22/21 /rspb.2019.0833 Sat 9/25/21 Fieldtrip Far West Fungi tour 1/2 day (Tentitive) Emerging Chytrid pathogens of Lec Mon 9/27/21 amphibians Brem Mon 9/27/21 Lab Chytridiomycota; Wed 9/29/21 Lec Mucoromycota Glass Mucorales - mating structures, and light Lab responsive dung fungi R eading: Massospora Reading Wed 9/29/21 and cicadas: Boyce et al.