bio361-fa23-schedule

Week 1 lab (Sep7)

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

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 laying embryos in lab next week.

Week 2 lab (Sep 14)
Prelab Reading/Assignment:
1. Lysosome-Related Organelles (Sections 1, 3, and 4 only)
2. Gut granules are autofluorescent in embryos (read  pgs 317-320 of Bossinger & Schierenberg, 1992)
3. Google quiz on both readings.
4. Directions for how to add embryos and adults to agar pads.
5.  Directions for how to image and score autofluorescent organelle diameters in embryos

In lab:
1. The research question: Does LAAT-1 regulate gut granule size?
2. LROs and gut granules.
3. Decide on roles within your lab group.
4. Picking embryos and adults onto agar pads. 
5. Using fluorescence microscopy to  image and measure autofluorescent organelle size.
6. Week 2 lab powerpoint.

Outside of lab: Image and measure the diameter of 25 autofluorescent organelles from six N2 and six GH1708 pretzel stage embryos.

Week 3 lab (Sep 21) 

Prelab Reading/Assignment:
1. Read "LAAT-1 is the lysosomal lysine/arginine transporter that maintains amino acid homeostasis" focusing on the data in Figures 1-2.
2. Google quiz on the reading. 

In lab: In lab Week 3 powerpoint (here). 
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.  
5. Discuss your results in class. Are any changes in autofluorescent organelles size caused by laat-1(-)? 

Outside of lab: Experiments as discussed in lab today.

Week 4 lab (Sep 28) 

Prelab Reading/Assignment:
1. Create a SuperPlotsofData graph + legend of three strains that have been scored and place it in your digital lab notebook.
2. Create a figure using images of autofluorescent organelles in embryos that show the result of your experiments and place it in your digital lab notebook. 

In lab:
1. Turn in autofluorescence figure by placing it in your digital lab notebook prior to lab. Figure directions and scoring rubric here.
2. Discuss new autofluorescent organelle size data in class. 
3. Discuss whether gut granules are enlarged as a result of laat-1(-).
4. Directions-Polarization microscopy training and scoring the colocalization of autofluorescent and birefringent material.
5. Slides presented in lab here.

Outside of lab: Next experiments as discussed in lab today.

Week 5 lab (Oct 5) 

Prelab Reading/Assignment: 

In lab:
1. Have SuperPlotsofData of colocalization graph and figure showing colocalization result in your digital lab notebook. 
2. Use your data so far to discuss your groups answer to the experimental question: Does LAAT-1 regulate gut granule size?  
3. Plan the  timeline and content of  your micropublication I.

Outside of lab:  MicroPublication 1 is due next week.
-microPublication directions.

Week 6 lab (Oct 12)

Prelab Reading/Assignment:
1. We will not meet in lab this week.
2. Submit Micropublication 1 before 5pm Oct 12th .
-Self and peer evaluation of group work (required)
-Micropublication directions here. 

Week 7 lab (Oct 19)

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

In lab: 
Project Planning I
LAAT-1 in C. elegans article
Folder with articles on gut granules and LROs

Outside of lab:

Week 8 lab (Oct 26)

Prelab Reading/Assignment: 

In lab: 
Project Design Worksheet (make a copy)
Project Planning II

Outside of lab: 

Week 9 lab (Nov 2)

Prelab Reading/Assignment:
WE ARE MEETING IN ALBANY 207 TODAY
Proposal due in class on Oct 31st. Pick up proposal to review after 3pm on Oct 31st.  Proposal critique due in lab today.
-Instructions for reviewing the proposal and information on the review session
-Submit a self and peer evaluation of proposal development by 5pm Oct 31st.

In lab:  Albany 207 today!
-Proposal review and feedback session

Outside of lab:  

Week 10 lab (Nov 9)
Prelab Reading/Assignment:
-Review peer feedback on the proposal

In lab: Individual group meetings with Greg to discuss your independent research projects.

Outside of lab: Independent investigations

Week 11 lab (Nov 16)
Prelab Reading/Assignment:

In lab: Independent Investigations I

Outside of lab: Independent investigations.

Week 13 lab (Nov 30)

Prelab Reading/Assignment:

In lab: Independent Investigations II

Outside of lab: Independent investigations.

Week 14 lab (Dec 7)
Prelab Reading/Assignment:

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

Directions for Project Presentations

Outside of lab: Independent investigations.