Research Question:

To find out how the presence of bacteriophages in the soil around red or white oak trees has a correlation with the health condition of oak trees.

Rationale:

From the pellet collected the DNA could be extracted via DNA extraction protocols, which could help determine the concentration of the DNA and further tests such as PCR and electrophoresis could be run in the future.

Plaque Assay for Sample (Gabe):

Materials:

• Pellet
• Sterile Water
• DNA Clean-Up Resin at 37 degrees Celcius
• 80% Isoproponal
• Column
• Vacuum
• Elution Buffer at 80 degrees Celcius

Procedure:

1. Added 0.5 ml sterile water to resuspend the pellet after returning to room temp
2. Added 2 ml of DNA Clean-Up Resin at 37 degrees Celcius to the resuspended pellet. mixed the resin before adding and the pellet solution after adding the resin
3. Distribute the pellet to two separate microcentrifuge tubes
4. Spin at 12.5 x 1000 g for 3 min
5. Removed the supernatant from the tubes without disturbing the cloudy precipitant and add 1 ml 80% Isoproponal to the tubes each
6. Repeated step 4 and 5 for 2 times
7. Removed the supernatant from the tubes without disturbing the cloudy precipitant and add 1 ml 80% Isoproponal to the tubes each
8. Transfer the solution to two columns and allow the vacuum to pull the liquid through the filter
9. Centrifuge the columns at 120000 g for 5 min
10. Added 100 ul of elution Buffer at 80 degrees Celcius to each column and set still for 1 min
11. Centrifuge the columns at 120000g g for 1 min
12. Combined the two tubes of DNA sample collected and Quantify the concentration using the nanodrop machine

Observations, Results & Data:

There were large amounts of resin observed through the steps of the experiment

Interpretations & Conclusions:

The low g spin setting while precipitating the pellet seemed to not affect the DNA count on the sample.

Next Step:

The next step would be to run a PCR on the DNA sample and run a gel to test the cluster.