bio361-fa25-schedule

Week 1 lab (Sep 3)

Prelab Reading/Assignment:
1. Lab syllabus,
2. A primer on  C. elegans;  
3. Directions for: Visualizing, chunking, and picking C. elegans
4. Culturing C. elegans (Just read Section 4-Culturing C. elegans on petri plates)

Due before lab:
Google quiz  

In lab:
1. Powerpoint (here).
2. Overview of lab organization, logistics, group work, digital notebooks
2. C. elegans as an experimental system
3. Culturing C. elegans
4. Recognizing
different C. elegans life stages with a dissecting scope.
5. Worm picking.

Outside of lab: Grow N2 so that you have non-starved adults in lab next week.

Week 2 lab (Sep 10)
Prelab Reading/Assignment:
1. Lysosome-Related Organelles (Sections 1, 3, and 4 only)
2. Gut granules are autofluorescent in adults (read  Clokey & Jacobson, 1986) Read pages 79-80 and 83-90.
3. Directions for how to add adults to agar pads and how to image and score autofluorescent organelle numbers and size in adults
4. Directions and feedback rubric for how to create a table presenting your scoring of autofluorescent organelle numbers and size

Due before lab on Sep 10:
1. Google quiz on readings

In lab:
1. The research question: Does R144.6/TMEM-144 function to regulate lysosome-related organelle (LRO) size or number?
2. LROs and gut granules.
3. Decide on roles within your lab group.
4. Picking adults onto agar pads. 
5. Using fluorescence microscopy to  image and score autofluorescent organelle number and size.
6. Week 2 lab powerpoint.

Outside of lab:
1. Score autofluorescent organelle number and size in 40 N2 and 40 GH1704 R144.6/TMEM-144(gk464716) adults.  Create two tables summarizing your results. Capture images that show the take home message from your quantification.
Directions and feedback rubric for how to create tables presenting your scoring of autofluorescent organelle numbers and size. 

Week 3 lab (Sep 17) 

Prelab Reading/Assignment:
1. Read "Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity" focusing on pages 3-4 and 16-17

Due by Sep 17th (before lab):
1. Google quiz on the reading.
2. Prepare and bring a table summarizing your scoring of autofluorescent organelle number and size. Directions here.

In lab:
Week 3 powerpoint . 
1. Discuss your results by looking at your tables in  lab (bring a hardcopy). Directions and feedback rubric for how to create tables presenting your scoring of autofluorescent organelle numbers and size.
2. Discuss if there are any changes in autofluorescent organelle number or size in GH1704.  If yes, are they caused by R144.6/TMEM-144(gk464716)?

Outside of lab:
1. Score autofluorescent organelle number and size in 40 adults of the new GH1663 strain.
2. Create an adult autofluorescent organelle figure for next week.  Figure directions and rubric here.
Adding scale bar directions here.
3. Create revised tables (hard copy) including any new data acquired over the past week.

Week 4 lab (Sept 24)

Prelab Reading/Assignment:
1. Create revised tables including any new data acquired over the past week (bring a hard copy to lab, will be scored worth 5pts).
2. Create a figure of images of autofluorescent organelles in adults that show the results of your experiments so far and place it in your digital lab notebook before 1pm on the day of lab (5 pts for completion, feedback in class). Figure directions and rubric here.
Adding scale bar directions here.

In lab:
1. Discuss your figures and results in class. Todays lab powerpoint.
2. Are changes in adult autofluorescent organelles size or numbers caused by R144.6/TMEM-144(-) mutations?
3. Discuss how to be more quantitative in documenting autofluorescent organelle size.

Outside of lab:
1. Image and measure autofluorescent organelle size in your N2, GH1704, and GH1663 strains using the measuring protocol here. Bring a complete data set of autofluorescent organelle diameters input in a copy of the sample Google sheet to lab next week.
2. Create a revised adult autofluorescence figure and place it in your digital lab notebook prior to next lab (will be scored, worth 5 pts). Figure directions and scoring rubric here. 

Week 5 lab (Oct 1) 

Prelab Reading/Assignment:
1. Create a revised adult autofluorescence figure and place it in your digital lab notebook prior to lab (it will be scored, worth 5 pts). Figure directions and scoring rubric here.
2. Have a complete data set of autofluorescent organelle diameters input in a copy of the sample Google sheet.  

In lab:
1. Use the SuperPlotsofData website to graph and analyze your autofluorescent organelle size data.
2. Sample Google sheet to copy and use for creating your graph. 
3. SuperPlots of Data Article.
4. Prepare a graph and legend of your results using SuperPlotsofData graph directions and scoring rubric here and place a copy of it in your digital lab notebook.  This is worth 5 pts.
5. Discuss localization experiments using the R144.6/TMEM-144::mNeonGreen tagged form of R144.6 presented in Fig 8J of Yu et al. (2024) eLife.
6. Slides shown in lab.

Outside of lab:
1. Analyze whether the R144.6/TMEM-144::mNeonGreen tagged form of R144.6/TMEM-144 is functional. Create a figure and graph showing these results and bring them to lab next week.
2. If you have not already, prepare a graph and legend of your results using SuperPlotsofData graph directions and scoring rubric here and place a copy of it in your digital lab notebook.  This is worth 5 pts.

Week 6 lab (Oct 8)
Prelab Reading/Assignment: 

Due before lab:
1. Have a figure and graph showing your results of your experiments assessing R144.6/TMEM-144::mNG function in your digital lab notebook.

In lab:
1. Discuss your results of experiments assessing R114.6/TMEM-144::mNG function. 
2. Analyze your data and plan the timeline and content of Micropublication I using the preparation worksheet located here.
3. Slides presented in lab here.

Outside of lab: 
1. Prepare Micropublication 1 to submit before lab next week.
2. MicroPublication directions here.
3. Example micropublication with Greg's comments here.

Week 7 lab (Oct 15)

Groups 1, 3, 5, 7  meet 1:50-3:15pm
Groups 2, 4, 6, 8  meet 3:25-4:50pm

Prelab Reading/Assignment:
1. Instructions for developing your independent project and proposal

Due before lab:
1. Micropublication 1
2. 2ndary author feedback
3.  Self and peer evaluation of group work (required)

In lab: 
Project Planning I
1. Article identifying R144.6/TMEM-144.
2. Folder with articles on gut granules, LROs, and TMEM-144 proteins
3. In lab powerpoint slides

Outside of lab:
Begin drafting your sections of the proposal.

Week 8 lab (Oct 22)

Groups 2, 4, 6, 8  meet 1:50-3:15pm
Groups 1, 3, 5, 7  meet 3:25-4:50pm 

Prelab Reading/Assignment: 

In lab: 
Project Planning II
1. Project Design Worksheet (make a copy and place it in your digital lab notebook)
2. Powerpoint slides today

Outside of lab:
1. Prepare proposal for submission due before 10am on Monday Oct 27: Four hardcopies of the proposal due  at this time, only include author names on the coversheet.  Include the proposal title at the top of the body of the proposal.
2. Instructions for developing your independent project and proposal
3. Submit a self and peer evaluation of proposal development by 10am on Oct 27

Week 9 lab (Oct 29)
Prelab Reading/Assignment:
WE ARE MEETING IN ALBANY 220 TODAY
1, Proposals are due in the box outside of Greg's office on  Monday Oct 27 before 10am.  Turn in four hardcopies of the proposal.  Only include author names on the coversheet.  Include the proposal title at the top of the body of the proposal.  Share an editable Google doc of the proposal with the instructor.
2. Proposals to review will be available for pickup outside Greg's office after noon on Monday Oct 27.  Review sheet due in lab on Oct 29.  Proposal critique due in lab today.
3. Instructions for reviewing the proposal and information on the review session.
4. Submit a self and peer evaluation of proposal development by 10am on Oct 27.

In lab:
-Proposal review and feedback session 

Week 10 lab (Nov 5)
Prelab Reading/Assignment:
1. Review Greg's and peer feedback on your proposal -are there any changes to your experiments?
2. Make a timeline for your experiments.

In lab: Independent Investigations I
1. Individual 20min group meetings with Greg to discuss your independent research projects.

Outside of lab: Independent investigations begin

Week 11 lab (Nov 12)
Prelab Reading/Assignment:

In lab: Independent Investigations II

Outside of lab: Independent investigations.