BISC219/F12: RNAi Lab 10

Lab 10: Series 3 Investigation of Gene Regulation Using RNAi

Preparation of the Na+ gradient in the Chemotaxis Assay media
The day before lab your instructor will add the chemicals needed to prepare the chemotaxis assay plates.

1. 10 μL of 2.5M NaCl is added to the Na dot you drew on your plate. Once the NaCl is absorbed the Na+ ions will disperse in a gradient away from the dot. The Cl₂ is not in a gradient due to the addition of MgCl₂ to the media during initial preparation.
2. 10 μL of sterile water is added to the W dot you drew to serve as a negative control.

Harvesting the C. elegans
Thoroughly washing the worms to remove any residual food and media is critical for the chemotaxis assay to work properly.

1. Label 2 15 ml conical tubes with wild type - treated
2. Label 2 15 ml conical tubes with rrf-3- treated
3. Label 1 15 ml conical tubes with wild type - control
4. Label 1 15 ml conical tubes with rrf-3 - control
5. Label 2 15 ml conical tubes with lsy-2 mutant
6. Wash the worms off of each RNAi feeding plate 3x with 5 ml ice cold sterile water (kept in your ice buckets)- putting each wash in the correct labeled 15 ml tube - store the tubes with worms in them on ice.
7. Once all the worms are collected, put the caps on the tubes and invert a few times to mix the worms.
8. Let the worms settle to the bottom of the tubes - about 10 minutes
9. Remove all but 1 ml of the water with a disposable Pasteur pipette.
10. Add sterile water to 15 ml and cap the tube again. Invert and let the worms settle.
11. Remove all but 1 ml of the water with a disposable Pasteur pipette.
12. Transfer the remaining 1 ml of water + worms to a sterile 1.5 ml microfuge tube.
13. Spin the worms at 10,000 rpm for 1 minute to pellet.
14. Remove all but approximately 50 ul of worms and water at the bottom of the tube.
15. Using a razor blade, cut the end off of a micropipette tip (this will prevent the pellet of worms from being damaged).
16. Pipette the entire pellet of worms to the appropriate assay plate on the central 2 cm circle.
17. Wick away any extra water with the corner of a Kimwipe

While the C. elegans are settling: Add 3 μL of 0.25M sodium azide on the Na and W dots on your chemotaxis assay plates. The sodium azide will immobilize the worms close to the dots

The Assay:

1. The worms are allowed to move around each plate for 1 hour
2. Take a photograph of each of the plates (rrf-3 from RNAi Feeder and HT115(DE) control plates; N2 from RNAi Feeder and HT115(DE) control plates; and lsy-2 mutants) at the end of the hour using one of the lab digital cameras or your own camera held to the eye piece of the microscope. Make sure you carefully organize each plate so that the photos have the quadrants in the same comparative position.
3. At the end of the hour (after photographing the plates), the worms in the two quandrants nearest the Na dot are counted and compared to the number in the two quandrants near the W dot. Counting is best done by inverting the plates. Use your dissecting scope and a Sharpie to make a dot on the plastic surface of the plate where every worm you see is located. Then count the dots/quandrant and record the numbers of worms on each quandrant in the google doc data spread sheet in the Project 3 folder in Resources in Sakai. Your instructor will have that spreadsheet open on a computer in the back of the lab. Add the numbers of worms in quandrants 1&2 (Na) and compare that total to the number in quandrants 3&4 (Water). Make conclusions about general trends in the worm distribution and record those notes in your lab notebook.
4. With a different color sharpie for each strain circle the area of the plate containing the greatest concentration of worms - generally this shape will be a circle or oval. If there is no particular area with a greater concentration do not make any mark.
5. Take a second set of photographs (one per strain of worm: N2, rrf-3 or mutant) using the BIORAD imager (Directions below). Arrange the plates for each strain so that the position of the control plates vs. RNAi treated plates is the same among the photos and that the quandrants are positioned the same in all plates.