bio361-fa24-schedule

Week 1 lab (Sep 5)

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

Due before lab Sep 5th:
Google quiz (due before lab).

In lab:
In lab powerpoint (here). Overview of lab organization, logistics, group work, digital notebooks, C. elegans as an experimental system, culturing C. elegans, recognizing and picking different C. elegans life stages.

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

Week 2 lab (Sep 12)
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 12:
1. Google quiz on readings

In lab:
1. The research question: Does ACP-5 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: Score autofluorescent organelle number and size in 40 N2 and 40 GH1195 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 19) 

Prelab Reading/Assignment:
1. Read "Single-tissue proteomics in Caenorhabditis elegans reveals proteins resident in intestinal lysosome-related organelles" focusing on the data in Figures 1 ,5 and Table 1.

Due by Sep 19th (before lab):
1.. Google quiz on the reading.
2. Prepare and bring tables summarizing your scoring of autofluorescent organelle size and number. Directions here.

In lab:
Week 3 powerpoint (here). 
1. Discuss your results by looking at your two tables in  lab (bring hardcopies). 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 GH1195.  If yes, are they caused by acp-5(gk529425))? 

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

Week 4 lab (Sep 26) 

Prelab Reading/Assignment:
1. Create revised tables including any new data acquired over the past week (place them in your digital lab notebook, will be scored worth 5pts).
2. Create a figure using images of autofluorescent organelles in adults that show the results of your experiments and place it in your digital lab notebook (5 pts for completion, feedback in class). Figure directions and rubric 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 acp-5(-)?
3. Discuss how to be more quantitative in documenting autofluorescent organelle size.

Outside of lab:
1. Images and measure autofluroescent organelle size in your N2, GH1195, and VCXXXXX strains using the measuring protocol here.
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 3) 

Prelab Reading/Assignment:
1. Have a full set of diameter measurements placed in a copy of the sample Google sheet linked below created using the measuring protocol here.

Due before lab Oct 3rd:
1. Create a  revised figure showing autofluorescent organelles in adults that show the result of your experiments and place it in your digital lab notebook (will be scored, worth 5 pts). 

In lab:
1. Use the SuperPlotsofData website to graph and analyze your autofluorescent organelle size data.
2. Sample Google sheet to copy and use in lab today. 
3. Graphing directions here.  SuperPlots of Data Article.
4. Prepare a graph and legend of your results in lab today using SuperPlotsofData graph directions and scoring rubric here and place a copy of it in your digital lab notebook.
5. Analyze your data and plan the timeline and content of Micropublication I using the worksheet located here.
6. Slides presented in lab here.
7. Does ACP-5 regulate gut granule size or number?
.
Outside of lab:  MicroPublication 1 is due Oct 17 by 1pm (no lab next week b/c of fall break).
-microPublication directions.

Week 6 lab (Oct 10)

Fall Break no lab Oct 10 

Prelab Reading/Assignment:
1. We will not meet in lab this week.
2. Submit Micropublication 1 before 1pm Oct 17th .
-Self and peer evaluation of group work (required)
-MicroPublication directions here. 

Week 7 lab (Oct 17)

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

Due before lab Oct 17th:
1. Micropublication 1
2. 2ndary author feedback
3.  Self and peer evaluation of group work (required)

In lab: 
Project Planning I
1. Proteomic paper identifying  putative gut granule proteins in C. elegans including ACP-5
2. Folder with articles on gut granules, LROs, and acp-5
3. In lab powerpoint slides

Outside of lab:
Proposal primary author begin writing introductory sections of the proposal.

Week 8 lab (Oct 24)

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 in class on Oct 29th: Four hardcopies of the proposal due  in class 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 5pm Oct 29th.

Week 9 lab (Oct 31)

Prelab Reading/Assignment:
WE ARE MEETING IN ALBANY207  TODAY
1. Proposal due in class on Oct 29th. Pick up proposal to review after 3pm on Oct 29th outside of Greg's office.  2. Proposal critique due in lab today.
2. Instructions for reviewing the proposal and information on the review session.
3. Submit a self and peer evaluation of proposal development by 5pm Oct 29th.

In lab:
-Proposal review and feedback session WE ARE MEETING IN ALBANY207  TODAY

Outside of lab:  

Week 10 lab (Nov 7)
Prelab Reading/Assignment:
1. Review Greg's and peer feedback on your proposal

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

Outside of lab: Independent investigations begin

Week 11 lab (Nov 14)
Prelab Reading/Assignment:

In lab: Independent Investigations II

Outside of lab: Independent investigations.

Week 13 lab (Nov 28)

No lab Thanksgiving Break.

Week 14 lab (Dec 5)
Prelab Reading/Assignment:
Directions for Project Presentations

In lab: 
Independent Investigations IV
1. Course evaluations at the start of lab.
2. Lab evaluation here
3. Copy and fill this out in your digital lab notebook: Presentation Worksheet

Due on Dec 17th:
1. MicroPublication II is due by 6pm on Dec 17th.
2. Project presentations are 6pm on Dec 17th..