Bio369 Lecture and Lab Schedule (Spring 2024)
Office Hours Tues 1-2pm, Wed noon-1pm, when my office door is open, and by appointment
No other courses are using blue lab this semester, so it is available to you whenever you need it!
Week 1 (Jan 16-18)
Classes and lab cancelled due to campus closure
Week 2 (Jan 23-25)
Reading/Assignments:
1. Course syllabus,
2. pgs 1-8; 14; 220-222
3. Precourse Survey (please complete by noon Monday Jan 22)
4. Powerpoint Week 2
5. For 1/25: Read Wolpert, 1994 and answer the Wolpert HW questions.
6. Gdoc for in class discussion of Wolpert, 1994.
7. Look at the Developmental Process Analogy Homework due by Feb 29th 1:50pm.
8. Principles of Development List
Topics this week:
1. Course introduction
2. Pattern in organisms and embryos
3. Establishing A-P axis asymmetry
4. Polarity in the oocyte
Movies of Embryonic Development
C. elegans (nematode)
https://www.youtube.com/watch?v= M2ApXHhYbaw
Fruit fly (arthropod)
https://www.youtube.com/watch?v= c5XfGiF0BgI
Sea urchin (echinoderm)
https://www.youtube.com/watch?v=sq-BY- JpPaM
Zebrafish (vertebrate)
https://www.youtube.com/watch?v= ahJjLzyioWM
Frog (vertebrate)
https ://www.youtube.com/watch?v= dXpAbezdOho
Week 2 lab (Jan 25)
Prelab Reading/Assignments:
1. Lab syllabus,
2. Introduction to C. elegans
3. Directions for: Visualizing, chunking, and picking C. elegans
4. Worm picking 101
5. Culturing C. elegans (Section 4)
In lab:
1. Lab powerpoint.
2. Overview of lab organization, logistics, group work, digital notebooks, C. elegans as an experimental system,
3. Culturing C. elegans
4. Recognizing and picking C. elegans adults.
Outside of lab: Grow N2 so that you have unstarved adults laying embryos in lab next week.
Week 3 (Jan 30-Feb 1)
Reading/Assignments:
1. pp. 11-12; 223-224; 265-269;
2. Presentation sign up Feb 1 (For topics see weeks 9-11 below) Directions and scoring rubric for student Presentations on Vertebrate Ectodermal Development (Weeks 9-11)
3. For 1/30: Goldstein & Hird, 1996.pdf
-Human 2 cell embryo asymmetry
4. Article Homework Questions - due 1/30
5. Week 3 Powerpoint
Topics this week:
1. Morphogenesis
2. Fertilization
3. Cleavage
4. Forming epithelia
Week 3 lab (Feb 1 )
Prelab Reading/Assignments:
1. Directions for how to image and score gut/gonad left/right asymmetry in C. elegans adults
2. Read pgs 34-37 of Pohl. 2011 Review of C. elegans L/R asymmetries.
3. Complete the Homework questions for Pohl, 2011.
In lab:
1. The research question: Does cdc-25.1 function in gonad positioning?
2. Gonad positioning in C. elegans.
3. Decide on roles within your lab group.
4. Picking adults onto agar pads.
5. DIC microscopy.
6. Week 3 lab powerpoint.
Outside of lab: Image and score gonad positioning in 80 N2/wild-type adults grown at 20C. See Week 4 lab below for directions for on preparing the table or graph describing your results.
Week 4 (Feb 6-8)
Reading/Assignments:
1. pp. 97-1-1; 320-326
2. For 2/6 read Kostic & Roy, 2002.pdf
3. Article Homework Questions - due 2/6
4. Morphogenesis toolkit.pdf
Topics this week: Morphogenesis
1. Controlling cell number
2. Morphogenesis toolkit
3. Cell shape changes
4. Cell adhesion
5. Gastrulation in C. elegans and sea urchin
Week 4 lab (Feb 8)
Prelab Reading/Assignments:
1. Bring a printed graph or table of gonad position scoring in wild-type (5 pts if on time and complete). Directions and rubric here.
In lab:
1. Discuss data and scoring of intestine-gonad L/R asymmetry in wild type.
2. Receive both cdc-25.1(-) mutants.
3. Week 4 lab presentation.
Outside of lab: Score gonad position in both cdc-25.1(-) mutants at 20C. 80 adults for each strain.
Week 5 (Feb 13-15)
Reading/Assignments:
1. pp. 277-284; 29-38; 45-68; 96; 125-128; 256-273.
2. For 2/13 read : Martin et al., 2009
3. Article Questions - due 2/13
4. You can turn in the Developmental Process Analogy Homework anytime before Feb 29th 1:50pm.
5. Week 5 powerpoint
Topics this week: Morphogenesis:
1. Gastrulation in Drosophila
Patterning:
2. C. elegans gut specification (Asymmetric segregation of transcription factors and cell-cell signaling in the specification of cell fate)
Week 5 lab (Feb 15)
Prelab Reading/Assignments:
1. Graph or table of wild type and cdc-25.1(-) mutant gonad position at 20C with statistical analysis (+5 pts if on time and complete). Directions and rubric here.
In lab:
1. Discuss data and scoring of intestine-gonad L/R asymmetry in wild-type and cdc-25.1(-) mutants.
2. Discuss possible explanations for results in the cdc-25.1(-) mutants
3. Discuss how to test whether cdc-25.1(-) impacts gonad position due to the production of extra gut cells.
4. Week 5 lab powerpoint
Outside of lab: Carry out experiments to address if the cdc-25.1(-) mutants impact gonad position due to the production of extra gut cells.
Week 6 (Feb 20-22)
Reading/Assignments:
1. pp. 38-41; 277-293
2. In Course feedback (optional and anonymous) please submit by Fri Feb 23th
3. Discuss presentations (Weeks 9-12) Directions and scoring rubric for student Presentations on Vertebrate Ectodermal Development
4. For 2/20 read : Zhu et al., 1998
5. Article Questions - due 2/20
6. Week 6 powerpoint
Topics this week: Patterning:
1. C. elegans gut specification (cell-cell signaling in the specification of cell fate)
2. Drosophila A/P cell specification (How morphogens can lead to spatial organization of cell fate)
Week 6 lab (Feb 22)
Prelab Reading/Assignments:
1. Graph or table addressing if the cdc-25.1(-) mutants impact gonad position due to the production of extra gut cells (5 pts).
In lab:
1. Discuss whether cdc-25.1(-) impacts gonad position due to the production of extra gut cells.
2. Plan the timeline and content of micropublication I.
3. Powerpoint
Outside of lab:
1. MicroPublication 1 is due next week.
2. MicroPublication directions.
Week 7 (Feb 27-29)
Reading/Assignments:
1. pp. 294-303
2. For 2/27 read: Spirov et al., 2009
3. Article Questions - due 2/27
4. Developmental Process Analogy Homework due before Feb 29th 1:50pm.
5. Week 7 powerpoint
Topics this week:
Patterning:
1. Drosophila A/P cell specification (Combinatorial transcription regulation of cell fate)
Week 7 lab (Feb 29)
Prelab Reading/Assignments:
1. Submit Micropublication 1 before lab starts today.
-2. Self and peer evaluation of group work (required)
3. Micropublication directions here.
In lab:
-Discuss and design experiment to address experimental question II.
-Project 2 experiment design worksheet (if used make a copy and place in your digital lab notebook)
-Week 7 powerpoint
Outside of lab:
Begin experiments for project II.
Week 8 (Mar 5-7)
Reading/Assignments:
1. Exam I on 3/5
2. No class on 3/7
Week 8 lab (Mar 7)
No Lab this week
Outside of lab:
Continue experiments for project II.
Week 9 (Mar 12-14)
Reading/Assignments:
1. Directions and scoring rubric for student Presentations on Vertebrate Ectodermal Development (Weeks 9-11)
2. Self and peer evaluation of contributions to the presentation. (Required)
2. 3/12 Vertebrate eye development
Brandon A., Bryn R., Will D., Yonas, K.
Textbook: pgs 109-11 (focus on Fig 4.17), 143-146 and 520-527.
Paper: Ksander et al. 2014
Ksander Article HW Questions
3. 3/14 Vertebrate tooth development
Samantha F., Trent N., Caroline M.
Textbook:143-146, 164-166, 529-533.
Paper: Kaukua et al. 2014
Kaukua article HW questions
Week 9 lab (Mar 14)
Prelab Reading/Assignments:
1. Table or graph of data so far.
In lab:
Discuss project II data so far.
Outside of lab:
Continue experiments for project II.
Week 10 (Mar 19-21)
Reading/Assignments:
1. 3/19 Feather development
Abby W., Alexandra G., Nate H.
Textbook: pgs 113, 528-537
Paper: Shyer et al. 2017
Article HW Questions
2. 3/21 Hair follicle development
Imtiyaz W., Kendall F., Amelia M.
Textbook: pgs 128-130, 528-537
Week 10 lab (Mar 21)
Prelab Reading/Assignments:
1. Table or graph of data describing results of project II.
2. Week 10 lab powerpoint
In lab:
Discuss your groups answer to project II question.
Outside of lab:
Prepare micropublication II
Week 11 (Apr 2-4)
Reading/Assignments:
1. 4/2 Development of coat color
Mirabella S., Tomas V., Brynn D.
Textbook: 470-474; 479-480; 533-537
Paper: Kaelin et al. 2021
Article homework questions
2. 4/4 Development of finger prints
Mikah K., Madeline D., Alix A.
Textbook: 631-632, 800-801 and Wertheim 2011
Paper: Glover et al. 2023
Article homework questions
Week 11 lab (Apr 4)
Prelab Reading/Assignments:
1. Micropublication II due before lab today.
2. Fill out self and peer evaluation of group work (required).
3. Micropublication directions here.
4. Lab powerpoint
In lab:
1. Discuss and design an experiment to address experimental question III.
2. Use Hebeisen & Roy, 2008 in designing your experiments.
3. Project III Project Design Worksheet (make a copy and fill it out).
Outside of lab:
Nothing this week.
Week 12 (Apr 9-11)
Reading/Assignments:
1. Directions for reading and discussing Endless Forms Most Beautiful (EFMB).
2. 4/9 We are not meeting as a class:
Watch: What Darwin Never Knew (1hr 50min)
Read EFMB-Preface and Introduction
HW on What Darwin Never Knew and reading in EFMB due by 5pm on 4/9
3. 4/11: EFMB-Chapters 1-2
Reading Questions and
Discussion Questions for 4/11 due before class begins
In class slides Chpt 1-2
Week 12 lab (Apr 11)
Prelab Reading/Assignments:
1. Lab powerpoint
In lab: Prepare for project III.
1. Directions for imaging and scoring ELT-2::GFP using the Zeiss Axio.M2
2. Directions for imaging and scoring ELT-2::GFP using the Zeiss Axio.D2
3. Directions for imaging and scoring ELT-2::GFP using the Zeiss V8 dissecting scope
Outside of lab: Begin project III experiments.
Week 13 (Apr 16-18)
Reading/Assignments:
1. 4/16: EFMB-Chapters 3-4
Reading Questions and
Discussion Questions for 4/16 due before class begins
In class slides Chpt 3-4
2. 4/18: EFMB-Chapters 5-6
Reading Questions and Discussion Questions for 4/18 due before class begins
In class slides Chpt 5-6
Week 13 lab (Apr 18)
Prelab Reading/Assignments:
1. Table or graph of data describing results of project III so far.
In lab:
1. Course and lab evaluations at the start of lab today.
Lab evaluation link here.
2. Discuss your progress so far.
Outside of lab: Continue project III experiments.
Week 14 (Apr 23-25)
Reading/Assignments:
1. 4/23: EFMB-Chapters 7-8
Reading Questions and Discussion Questions for 4/23 due before class begins.
In class slides Chpt 7-8
2. 4/25: EFMB Chapters 9-10
1. Reading Questions and Discussion Questions for 4/25 due before class begins.
In class slides Chpt 9-10
Week 14 lab (Apr 25)
Prelab Reading/Assignments:
1. Table or graph of data describing your results of project III.
In lab:
Discuss your answer to project III question.
Outside of lab:
1. Prepare micropublication III
2. Micropublication directions here.
3. Fill out self and peer evaluation of group work (required).
Micropublication III due before 6pm on Apr 30th.
Week 15: ( Apr 30)
Exam #2 is Tuesday Apr 30 6-9PM
Micropublication III due before 6pm on Apr 30th.