Team:UGA-Georgia/Experiments

Experiments

Transformation via PEG (1.5mL method - Plating and Enrichment)

  1. Check list of items on Day 1
      2. Prepare Minispin and Vortex
      Preheat sandbox
      TB and TB+PEG Buffer
      Recipient strain of OD 0.7-1.0 in a rack (always make at least 2 days ahead)
      Selection markers
      Media and plates
      Latex gloves, tube locks, tips, pipette (1mL), microcentrifuge tubes
      Plasmid concentration determined (0.4-0.6ug per sample)
      100mL beaker (for discarding supernatant)
  2. Day 1 (making plates)
      3. Melt plates (2 plates per sample) by autoclave, let cool down to 65C
      Add Na2S, antibiotics, and additives into plates and let solidify on side way
      Finish check list and prepare chamber (add H2 to 5.0, change catalyst and add CaCl2
  3. Day 2 (transformation and plating)
      4. Wear latex gloves, get 2 1.5mL micro-tubes and place 1.5mL culture (OD 0.7-1.0) into each tube
      Centrifuge at 3,900rpm (Minispin) for 10 minutes
      Discard supernatant, add 75uL of TB, pipetting up and down for 10 times
      Add 0.2-0.3ug of plasmid and 45 uL of TB-PEG, pipetting up and down for 10 times
      Incubate at 37C in sand box for 1 hour
      While waiting, prepare 5mL of broth media plus Na2S in balch tube
      After incubation, combine 2 micro-tubes of cells into 1mL broth (total vol=1.24mL), vortex (strong)
      Take 2 new micro-tubes and add 0.9mL broth to each, now you have -2mL broth left in balch tube
      Do 100, 10-1, and 10-2 serial dilution with cells from the previous step, vortex (strong)
      Plate 0.6mL of cells from 100, and plate 1mL from 10-1 and 10-2. Lay plates sideways overnight before incubating at 37C
      Innoculate remaining cells (~0.6mL) from 10^0 to the balch tube with 2mL broth, record OD and incubate overnight at 37C
  4. Day 3 (enrichment in broth)
      5. Record OD again from the final step in Day 2, inoculate 0.5mL into 2 5mL of selective broth.
      Make frozen stocks of remaining.


Oxygen Exposure Protocol Pt.1 and Pt.2

  1. Check the ODs of the cultures (want ODs to be ~ 0.7)
  2. Relieve pressure inside the tubes.
  3. Remove the foil seal and rubber stopper
  4. Pour the 5mL contents in a 15mL tube with lid.
  5. Place in the rotor adapter and place adapter into rotor.
  6. Secure the rotor.
  7. Run a cycle at 3500rpm, for 20 minutes, at 4oC
  8. Then discard the supernatant of the cultures
  9. Re-suspend the cell pellets in 0.3mL of Pipes.
  10. Take the re-suspended cells to the sonicator.
      11. Microtip – 5(limit)
      Duty cycle – 50%
      Burst – 5sec.
  11. Centrifuge the product
      12. 20000G, 10 minutes, 4C
  12. Collect the supernatant into the 0.5mL centrifuge tubes
      13. Divide the remaining supernatant into ~5 60uL aliquots
      Place the aliquots into the freezer

Making a 1% agarose gel

  1. For 50mL gel: combine 50mL TAE 1X buffer and 0.5g agarose. For a 100mL gel: combine 100mL TAE 1X buffer and 1.0g agarose.
  2. Microwave the contents in a flask, with weighing paper covering the top, for 1.5minutes.
  3. Tape the sides of the gel mold and insert the well mold.
  4. Pour the contents into the gel mold.
  5. Allow to solidify (~20 minutes)

Sequencing Procedure*

  1. Determine which sequences warrant sequencing. The sequences that are sequenced need to have a strong Band around 900BP and a level of fluorescence greater than that of the negative
  2. Give the colonies new labels such as 1-10 that correspond with the a specific colony, For example L1C1A will be 1, L1C2A will be 2 and L1C1B will be 3.
  3. Spin PCR Product down
  4. Get 20ul and 200uL micro pipettes and tips
  5. Retrieve the DNA Clean&Concentrator-25(make sure it is 25 by checking size of columns)
  6. In a 1.5mL microcentrifuge tube, add 5 volumes of DNA binding buffer to 1 volume PCR Product
  7. Transfer Mixture to a provided Zymo-Spin Column in a collection tube
  8. Centrifuge for 30 seconds at 17g Discard Flow-through (set centrifuge timer to 1 minute and end 30 seconds early)
  9. Add 200 uL DNA wash buffer to the column, Centrifuge for 30 seconds at 17G
  10. Repeat previous step
  11. Add 25 uL water directly to column matrix and incubate at room temperature at room temperature for 1 minute,
  12. Transfer column to 1.5 ml microcentrifuge tube and centrifuge for 30 seconds to elute the DNA
  13. Remove Column

*Adpated from Zymo Research

Determining Protein Concentration+

  1. For each sample and one additional sample combine 199uL Quibit buffer and 1 uL Quibet Reagent to create solution; For example if one were testing 1 PCR product they would combine 398uL Buffer and 2 uL Quibet Reagent to create solution
  2. Add 1 uL to DNA to 199 uL solution
  3. Turn on Fluorometer
  4. Choose High Sensitivity, No New Standards DO NOT use first value given
  5. Press calculate sample stock and then change units nanograms/microliter
  6. Record Values in Lab Notebook and microcentrifuge tubes

+Adapted from Qubit HS dsDNA

Making anaerobic formate media for Methanococcus maripaludis (400mL)

  1. Glass-distilled water: 120mL
  2. Glycylglycine buffer, 1M, pH=8.0: 80mL
  3. General Salts Solution: 200mL
  4. K2HPO4 14g/L: 4.0mL
  5. Na acetate-3H2O, 136g/L: 4.0mL
  6. Trace Mineral Solution: 4.0mL
  7. Iron Stock Solution: 2.0mL
  8. Sodium formate (NaCOOH): 10.8g
  9. Sodium Bicarbonate (NaHCO3): 1.5g
  10. Casamino acids: 0.8g
      11. Combine media ingredients and sparge with a stream of N2 gas for >60minutes
      Add 0.05g cysteine-HCl per 100mL and continue sparging for >10minutes.
      Place in the anaerobic chamber overnight
      Dispense media and pressurize to 15psi with N2/CO2 gas

Preparation of Sodium Sulfide

  1. Add 200mL of diH2O to flask and mark water line. Add 2 pellets of NaOH and 20mL more of ddH2O.
  2. Boil the 220mL diH2O while flushing flask with N2 until the water level reaches the original 200mL water line.
  3. Let flask cool while flushing with N2, move the flask to the gassing station in the fume hood. Continue flashing with N2.
  4. While flask is cooling, weigh our slightly moe than 5g Na2S-9H2O. For the following steps, work in the fume hood and wear gloves. Clean the sodium sulfide crystal by briefly rinsing the crystal with diH2O. To do this, swirl the crystal in a small beaker with the water. Dry the crystal by blotting with a paper towel or kimwipe. Reweigh the crytal to insure that the final weight is 90-110% of the desired weight.
  5. Add the clean, weighted sodium sulfide to the cooled flask while flushing with N2 and mix until partially dissolved.
  6. Stopper the flask, discontinue flushing, and transfer to the anaerobic chamber
  7. Dispense into tubes that have been equilibrated in the chamber for at least for one day to allow the O2 to desorb from the glassware. Use the thick butyl stoppers that are ungreased and have been equilibrated in the chamber for one day.
  8. Remove tubes from the chamber and pressure with N2 at 15 psi.
  9. Autoclave on gravity cycle (rapid dry) for 20 minutes.
  10. Store in anaerobic chamber.

Making anaerobic agar plates

  1. Add 0.15g agar to each glass plate bottle and place in chamber for at least overnight.
  2. Make the full volume of media needed and also place in chamber overnight.
  3. Distribute 10mL media to each of the glass plate bottles.
  4. Stopper and seal the bottles.
  5. Pressurize each bottle to 15psi with N2/CO2
  6. Autoclave on gravity cycle with a 30 minutes sterilization.
  7. Remove from autoclave.