August 31

AUGUST 29TH 2018- Lab

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  • AUGUST 29, 2018
    • PLAQUE ASSAY TEST AFTER NEGATIVE SPOT TEST
    • OBJECTIVE: Conduct a plaque assay with little to no contamination, and as a class also develop an over arching question to investigate this semester 
    • PROCEDURE:  
      • Tables were sanitized and lamps were lit to create an aseptic environment 
      • 4 plates were obtained (one plate was used as control for my group and 3 other groups as seen in figure 5)
      • Next, in a culture tube the following were mixed:
        • .5mL arthro 
        • 10𝝁L of lysate 
      • The lysate and arthro then sat for 15 minutes
      • Then a 50mL tube was filled with:
        • 8.0 mL LB broth
        • 10.0 mL of TA
        • 90𝝁L 1M CaCl2
    • Then 4.5 mL of the TA solution was pipetted into each group member’s culture tube
    • The culture tube was then poured onto a plate, where it sat for 10 minutes to solidify, where it was inverted and put in the incubator 
  • NEXT STEPS: Wait for results from plaques assay and continue to brainstorm a testable question to research 
August 31

AUGUST 27TH 2018- Lab

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  • AUGUST 27, 2018
    • PLATING SPOT TEST + FILTRATION OF DIRECT SAMPLE
    • OBJECTIVE: Be able to a plate spot test without contamination to test for phage presence 
    • PROCEDURE:
      • Tables were sanitized and lamps were lit to create an aseptic environment 
      • 4 plates were obtained, one for each group members as well as the broth TA control 
      • The plates were then labeled
      • Next, a 50mL test tube for the control plate was filled with:
        • .5mL Arthro
        • 4.5mL LB broth
        • 45𝝁L CaCl2 1M
      • Then another 50mL test tube was filled (for the spot test, not control) with:
        • 1.5mL arthro
        • 13.5mL LB broth
        • 15mL 2X TA
        • 135𝝁L CaCl2 1M
      • Then the direct sample was filtered using a syringe:
        • 2mL was taken up into the syringe 
        • A .22𝝁m filter was attached to the end of the syringe 
        • Pressure was applied to the top of the syringe, slowly pushing the solution through the filter and into a micro-centrifuge tube
      • 10mL from the control test tube was pipetted onto the control plate
      • Then 10mL from the mixture for the spot test was then pipetted onto each group members’ plate one at a time 
      • 10 minutes was allowed for the plates to solidify 
      • Each group then took their enriched sample and filtered it:
        • 2mL was taken up into the syringe 
        • A .22𝝁m filter was attached to the end of the syringe 
        • Pressure was applied to the top of the syringe, slowly pushing the solution through the filter and into a micro-centrifuge tube
      • Each group member, one at a time, pipetted 10𝝁L of their direct sample onto the designated spot on their plate
        • The previous step was conducted for the phage buffer and direct sample as well
      • The plates were then left to absorb the samples for 15 minutes before being placed in the incubation cabinet (kept at room temperature)
      • POTENTIAL RESEARCH QUESTIONS:
        • Do phages act as an indicator for wilted oak disease?
        • Do trees suffering from wilted oak lack phages in their soil? If so why?
        • Do trees with wilted oak have less or more phages in their soil?
        • Do trees suffering from wilted oak have greater or lower amounts of phages in the soil compared to healthy oaks?
        • Does having a water source near an oak affect the amount of phages in the soil?
        • Does the amount of phages in different oak species vary?
  • RESULTS: 
    • Plates collected after incubation period were inconclusive due to contamination as seen in figure 3
    • The control came out clear as seen in figure 4
    • This is an indication that there is more than likely no phage presence in the soil sample collected 
    • Further tests will be run in a plaque assay to be fully sure that there are no phages present  
  • NEXT STEPS: 
    • Conduct a plaque assay to test for phage presence again
    • If no phages are found again, then we will go back to soil collection phase
August 31

AUGUST 22ND 2018- Lab

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  • LAB NOTE BOOK INSTRUCTIONS:
    • Date/Title/Rational
    • Description of procedure (what you actually did, NOT what you were told to do)-    storage 
    • Observations/Results/Data
  • AUGUST 22, 2018 
    • CLEANSING AND SEPARATION OF OAK TREE DIRT
    • OBJECTIVE: To clean and separate out the soil sample, into a direct and enriched sample
    • PROCEDURE:
      • The tables were sanitized and lamps were lit to create an aseptic environment
      • A 50mL test tube was filled to the 15mL with soil that was collected 48 hours prior to the lab in section 8, from a healthy oak tree, seen in figure 1
      • Then LB broth was added to the tube util it reached the 35mL mark
      • The tube was then shaken by hand and vortex for 15 minutes 
      • The tubes were then taken to the centrifuge when they centrifuged as a class 
      • The contents of the soil had separated out into supernatant in the top and a solid in the bottom 
      • The supernatant was then pipetted into a filter where pressure was applied to it to force it through the .22 𝝁m and dripped into a 50mL tube as seen in figure 2 (must be conducted in fume hood)
      • The supernatant was filtered until 10mL was filtered out
      • The 10mL of the filtered supernatant had .5mL of Arthro added to it (This became the enriched sample), and the sample was then placed in the fridge 
      • The excess unfiltered supernatant was put into a separate test tube and placed in the fridge 
      • NEXT STEPS: Conduct Spot test with samples + filter out direct sample