Bio110 Fall 25 Schedule
Class T/Th 1:50-3:20PM
in Blue Lab (Basement of BioPysch)
Office Hours: Mon and Wed 10:30AM-11:30AM, when my office door is open, and by appt. (email to set up a time)
Jump to specific weeks using the links below:
Precourse Survey (please complete by noon Fri Jan 17th)
Slides Week 1 (Sept 2-4)
Sep 2: Introductions to me, to you, and the course, pick groups, and digital lab notebooks
Read before class:
1. Course syllabus
Complete in class today:
1. Pick lab groups and discuss group work
2. Discuss lab notebooks
Sep 4: Experiment 1-Heart rate experiment and graphing with R
Read/complete before class:
1. COVID smell loss and long COVID linked to inflammation
2. Directions for Experiment I
3. BIO110 Handbook (bookmark this!): Your Laboratory Notebook (pgs 11-18) and
Data Analysis and Interpretation (pgs 33-41)
4. Google Quiz
Complete in class today:
1. First experiment!
2. Graph and title placed in your digital lab notebook
3. Rstudio tutorial instructions
Slides Week 2 (Sep 9-11)
Sep 9: Microscopy of Chlamydomonas
Read/complete before class:
1. Directions for using microscopes to visualize Chlamydomonas flagella
2. BIO110 Handbook: Appendix 6-7 (pgs 88-92)
3. Google Quiz
Complete in class today:
1. Drawings and answers to the questions about your slides uploaded to your notebook.
Sep 11 : The Process of "doing" biology
Read/complete before class:
1. Directions for in class work today/facts on Chlamydomonas micro-presentation (2-3 minutes; 3 min max) directions and scoring rubric
2. Carroll: Chpts 1-2, and Appendix: The Scientific Process
3. Google Quiz
Complete in class today:
1. Carroll: Chpts 1-2, and Appendix in class discussion questions
2. Begin preparing (3-4 min) Chlamydomonas micro-presentations
Slides Week 3 (Sep 16-18)
Sep 16: Digital Microscopy of Chlamydomonas
Read/complete before class:
1. Directions for using digital microscopy to study Chlamydomonas this week
2. Complete the GenBio-MAPS Survey (once you have completed it email the instructor to earn +5 bonus pts)
3. Google Quiz
Complete in class today:
1. Acquire images and measurements of flagella.
Sep 18: Chlamydomonas micro-talks, preparing a graph/title/caption
Read/complete before class:
1. Bio110 Handbook: Data Analysis and interpretations (pgs 33-41)
2. Prepare facts on Chlamydomonas (2-3 min; 3min max) micro-presentation directions and scoring rubric
Complete in class today:
1. Micro Presentations on Chlamydomonas!
2. Google sheet template for entering flagella lengths (make a copy and place it in your own Google drive). Do not change the format, labels, or add units to your data.
3. R studio tutorial instructions.
4. As a group create an average flagella length graph with 95% CI of the mean, title, and caption and place it in your lab notebook (+5 pts for completion). Use the class 2 instructions in the directions for using digital microscopy to study Chlamydomonas this week as a guide for creating your graph, title, and and caption.
Slides Week 4 (Sep 23-25)
Sep 23: Chlamydomonas flagella regeneration I
Read/complete before class:
1. There will be a digital notebook check today. Have everything in your notebook before the start of class! See the scoring rubric here.
2. Directions for measurement of Chlamydomonas flagella regeneration
Complete in class today:
1. Make fixed samples from your timepoints
2. Begin measuring flagella lengths
3. Directions for using FIJI on your own computer to measure flagella lengths
Sep 25 Chlamydomonas flagella regeneration II
Read/complete before class:
1. Directions for measurement of Chlamydomonas flagella regeneration
Complete in class today:
1. Complete flagella length measurements and place the data in your digital notebook (all group members)
2. As a group add the measurements to the Google sheet template (make a copy and save it in your Google drive) Do not change the format, labels, or add units to your data.
Slides Week 5 (Sep 30-Oct 2)
Sep 30: Analyze flagella regeneration data and use it in to prepare a figure, title, caption, and results section
Read/complete before class:
1. BIO110 Handbook: Results (pgs 55-58)
2, Create a google sheet with your flagella lengths ( Google sheet template here - make a copy and save it in your own Google drive)
3. Directions for analyzing flagella regeneration data, creating the graph and caption, and writing the results section
Complete in class today:
1. As a group create and share with Greg: Figure, Title, Caption, and Results
Place a copy in your digital lab notebook.
2. Rstudio tutorial instructions
Oct 2 Modeling flagella regeneration
Read/complete before class:
1. Google quiz with videos to watch on DNA to proteins, the axoneme, and microtubules
2. Directions for modeling flagella regeneration
Complete in class today:
1. As a group work on these modeling flagella regeneration questions and make sure each has a copy in your digital notebook after completing it
Slides Week 6 (Oct 7-9)
Oct 7: Modeling flagella regeneration : Designing projects to investigate the the mechanisms underlying flagella regeneration
Read/complete before class:
1. Directions for independent project development and experimental design.
2. Google Quiz
Complete in class today:
1. Place a copy of the independent project proposal and protocol form in your digital lab notebook and fill it out in class. as a group. Share this with the instructor when it has been completed.
2. Microscope practical exam (individual worth 10pts).
Oct 9: No class today Fall Break
Slides Week 7 (Oct 14-16)
Oct 14: Investigating flagella regeneration I
Read/complete before class:
1. Carroll Chapter 18 (The illustrations in this chapter were created by Kate Baldwin, PhD L&C alum class of 2005 www.k8baldwin.com)
2. Google Quiz
3. Directions for carrying out your independent investigations studying the regeneration of Chlamydomonas flagella
Complete in class today:
1. Make a copy and use the treated template and the untreated template spreadsheets to record your data. Do not change the format, labels, or add units to your data.
2. Continue microscope practical exam (individual worth 10pts).
Oct 16: Investigating flagella regeneration II
1. Continue work started on Oct 14th.
Slides Week 8 (Oct 21-23)
Oct 21: Exam I
Read/complete before class:
1. Download any slides/etc. that you want to have access to during the exam to your computer before class today.
Complete in class today:
1. Exam I (open book, open note, open computer, no internet).
Oct 23: The primary literature and analyzing the results of your flagella regeneration experiments
Read/complete before class:
1. Directions for analysis of investigations studying the regeneration of Chlamydomonas flagella
2. Bio110 Handbook pgs 47-62
3. Troemel et al., 1997
4. Bring a hardcopy of this primary literature homework with your answers to class today
Complete in class today:
1. Work on the figure, results (use this results template), and methods (use this methods template) sections
2. Rstudio tutorial instructions
Slides Week 9 (Oct 28-30)
Oct 28: Work on your research manuscripts
Read/complete before class:
1. Bio110 Handbook: Research Manuscripts (Introduction and Discussion sections)
2. Bring 3 printed hard copies of each of your figure, results, and methods sections to class
3. Directions for preparing your manuscripts
4. There will be a digital notebook check today! Have everything in your notebook before class today. Scoring rubric here.
5. Encouraged but optional and anonymous: Midcourse feedback
Complete in class today:
1. Peer review of your figure, results, and methods sections
2. Work on the introduction (use this introduction template) and discussion (use this discussion template) sections.
Oct 30: No class today
Slides Week 10 (Nov 4-6)
Nov 4: Introduction to C. elegans
Read/complete before class:
1. Manuscript due before class today
-Details on what to turn in are described in last weeks "Directions for preparing your manuscripts"
-Share your manuscript as a Google doc that the instructor can edit (so that I can make comments)
-Include cover page with statement of collaboration
-Fill out the self and peer evaluation of group work
-Look at the feedback grading rubric
2. Directions for viewing, washing, and counting C. elegans
3. Watch the introduction to C. elegans video (2min)
4. Google quiz
Complete in class today:
1. New lab groups
2. Using microscopy to study C. elegans
Nov 6: Preparing for the C. elegans chemotaxis assay
Read/complete before class:
1.Watch these two videos: on behavior ( just the 1st 21min ) and C. elegans chemotaxis ( just the first 8 min )
2. Google Quiz
3. Directions for viewing, washing, and counting C. elegans
Complete in class today:
1. Introduction to the chemotaxis assay/washing and counting C. elegans
Slides Week 11 (Nov 11-13)
Nov 11 Can C. elegans smell? research project
Read/complete before class:
1. Roger Tjian video (first 13.5 min)
2. Directions for investigating whether cilia play a role in chemosensation in C. elegans
3. Google Quiz
Complete in class today:
1. Investigating the role of cilia in Chemotaxis part I
2. Manuscripts with comments are returned in class today
Nov 13: Can C. elegans smell? research project
Read/complete before class:
1. Directions for investigating whether cilia play a role in chemosensation in C. elegans
Complete in class today:
1.. Investigating the role of cilia in Chemotaxis part II
2. Google sheet template for entering scoring of your chemotaxis plates (make a copy and then enter your data)
3. R studio tutorial instructions
4. Assign topics for C. elegans presentations
5. Three Google slides -Feedback rubric is here. As a group share your three Google slides with Greg before noon on Tues Nov 25 (work that is on time and complete will earn +5 pts)
Slides Week 12 (Nov 18-20)
Nov 18: Learning about C. elegans
Read/complete before class:
1. Directions for preparing your C. elegans presentations
2. Prepare a 7 minute presentation on the topic assigned to your group last class.
3. Work on your three Google slides -Feedback rubric is here. As a group share your three Google slides with Greg before class on Tues Nov 25 (work that is on time and complete will earn +5 pts) Discuss the results of your daf-19(-) experiments and your Google slides.
Complete in Class today:
1. C. elegans as a model biological research system presentations
Nov 20: Ciliopathies, IntraFlagellar Transport (IFT), Bioinformatics, and gene conservation
Read/complete before class:
1. Revised Manuscripts are due before the start of class today
Include cover page with statement of collaboration here
-Fill out the self and peer evaluation of group work here
-Look at the feedback grading rubric as you prepare your revision here
-Make sure and address all of the comments made on your draft in your revised manuscript
2. Carroll Chapter 6
Preclass video: Bench to Bedside: Ciliopathies (watch the first 15.5 min)
3. Directions for learning about human ciliopathies and studying them in a model system
4. Google Quiz
Complete in class today:
1. IFT homology search and homework template is located here
2. IFT gene pages to be created
Slides Week 13 (Nov 25)
Nov 25: Diversity in the Sciences
Read/complete before class:
1. Directions for preparing a slide describing an underrepresented scientist and preparing for a discussion of diversity in the sciences
2. Example of Diversity in the Sciences slide
3. Carroll Chapter 9
4. How diversity makes us smarter
5. Reflection Questions
Complete in class today:
1. Discussion of Diversity in the Sciences
Slides Week 14 (Dec 2-4)
Dec 2: Chemotaxis project design
Read/complete before class:
1. Look at and think about your answers to the questions on the " Big picture hypothesis worksheet"
Complete in class today:
1. Course evaluations (link here)
1. As a group fill out the big picture hypothesis worksheet
2. Here is a recent review on IFT with information on IFT complex structures (you might find it useful in developing hypotheses)
3. Fill out and turn in the chemotaxis project proposals given to you in class
Dec 4: Analyze chemotaxis data and prepare chemotaxis presentations
Read/complete before class:
1. Directions for Data analysis and preparing your C. elegans chemotaxis presentations
2. There will be a digital notebook check today (covering the last 4 weeks). Have everything in your notebook before class today. (Rubric used to evaluate your notebooks is here).
Complete in class today:
1. Analyze cilia project data
2. Rstudio tutorial instructions
3. Presentation development
Week 15 (Dec 9)
Dec 9: Exam 2
Read/complete before class:
1. Read the results section "ODR-10 Expression in AWB Drives an Avoidance Response" and be prepared to analyze and discuss the data in Figure 3 from: Troemel et al., 1997)
Complete in class today:
1. Exam #2
Dec 15 Final Exam Period (9-11:30AM): Chemotaxis presentations
Read complete before class:
1. Share your presentation slides with Greg
2. Fill out the confidential self and peer evaluation of contributions to your presentation
In class today:
1. Presentations during the final exam period