Talk:Knight:Beta-galactosidase assay/96 well format

This is an outline of various control experiments that I need to do. It is a work in progress and has not been done.

A₆₀₀ versus cell density

1. Grow an overnight culture to saturation in EZ Rich Media
2. Pellet the cells
3. Resuspend in 1/4 of the original volume with EZ Rich Media
4. Add 350 μL of cell suspension to the first well
5. Add 175 μL of previous well to next well.
6. Add 175 μL of EZ Rich Media to that well.
7. Repeat dilution series until the well's solution looks totally clear.
8. Add an additional well of 175 μL EZ Rich Media.
9. Measure A₆₀₀ of each well in the plate reader.
10. Plot A₄₂₀ versus dilution factor. This relationship should be linear.

Effect of evaporation on absorbance readings

This experiment was designed to assess the impact of evaporation upon the absorbance reading at 600nm of a culture sample in the Victor3 plate reader. A master culture of both MG1655 or pSB4K5-R2000.E0433 in TOP10 was grown. Either 50μL or 100 μL of culture was aliquoted into each well of a row in a 96 well plate. Two rows were left empty. To each well, between 0 and 140 μL of H₂O was added to the sample and the absorbance at 600nm was measured. This setup was intended to mimic the situation in which there is a sample with a constant amount of absorbing material (i.e. cells) in the well, and there is evaporation of water over time from the well thereby changing both the concentration of material and volume of liquid (path length) in the well. Thus, the variability in absorbance due to different amounts of H₂O added should reflect the variability in absorbance due to evaporation in experiments. This graph also shows replicates of the samples with 50 μL of culture and increasing amounts of H₂O to provide an indication of the variability between identical samples. Click to view the larger image.

Effect of evaporation on A₆₀₀ readings

1. Aliquot 50 μL of culture into an entire row of wells.
   • Do duplicates rows to assess measurement variability in duplicate samples.
2. Aliquot 100 μL of a of culture into a second row of wells.
3. Add increasing volumes of water to each well (by 10 μL increments).
4. Measure the A₆₀₀ of the plate.

Effect of evaporation on A₄₂₀ readings

1. Aliquot 50 μL of a set concentration of ONP into an entire row of wells.
   • Could add different concentrations of ONP to different rows.
2. Add increasing volumes of water to each well (by 10 μL increments).
3. Measure the A₄₂₀ of the plate.

β-galactosidase activity versus number of cells

1. Do parallel β-galactosidase assays with a variable volumes of cells from the same grown culture.
   • 1 = 1 μL of cells
   • 2 = 2 μL of cells
   • 3 = 3 μL of cells
   • 4 = 4 μL of cells
   • 5 = 5 μL of cells
   • 6 = 5 μL of media

β-galactosidase activity versus growth phase of culture

1. Grow an overnight culture of several constructs
   • A = MG1655
   • B = MG1655+IPTG
   • C = P20060+IPTG+AHL
   • D = P20060.E0433+IPTG
   • E = P20060.E0433+IPTG+AHL
   • F = R2000.E0433+IPTG+AHL
   • G =
   • H = Media+IPTG+AHL
2. In the morning, dilute back samples into EZ Rich Media to an A₆₀₀ of 0.001 (via a Nanodrop reading) in a 96 well plate. (Each well in a row should be identical with 175 μL of culture according to the list above.)
3. Let grow 1 hour.
4. Add IPTG and/or AHL to rows as appropriate.
5. Prepare the permeabilization buffer and aliquot 80 &muL into each well of a 96 well plate.
   • Using a larger volume for permeabilization step because the samples are sitting for a while.
6. Measure the A₆₀₀ of the plate every 30-60 minutes or grow the plate in the plate reader and pause it every 30-60 mins.
   • Use a gas permeable plate cover. Leave this on for absorbance measurements?
7. At each hour point, take 20 μL of the next column of culture and add it to the corresponding columns of the permeabilization plate.
8. Once each time point has been taken, move 25 μL of each well from the permeabilized culture to a new plate.
9. Add 150 μL of substrate solution to each well.
10. Place plate in the plate reader to measure change in A₄₂₀ as a function of time.
11. Plot the β-galactosidase activity in Miller Units as a function of the A₆₀₀ of the culture.

A₄₂₀ versus o-nitrophenol concentration

1. Make up a solution of 14 mL to control for background absorbance in β-galactosidase assays
   • 1600 μL permeabilization solution
   • 12 mL substrate solution without ONPG
   • 400 μL EZ rich media supplemented with kanamycin and AHL
2. Make up 1mL of 1 mg/mL ONP.
3. Add 350 μL of 1mg/mL solution to the first well.
4. Move 175 μL of previous well to next well.
5. Add 175 μL of background solution to that well.
6. Repeat dilution series until the well's solution looks totally clear.
7. Add an addditional well of 175 μL background solution.
8. Measure A₄₂₀ of each well in the plate reader.
9. Plot A₄₂₀ versus ONP concentration. This relationship should be linear.

Concentration series:

1mg/mL -> 0.5 mg/mL -> 0.25 mg/mL -> 0.125 mg/mL -> 62.5 μg/mL -> 31.25 μg/mL -> 15.625 μg/mL

-> 7.8125 μg/mL -> 3.90625 μg/mL -> 1.953125 μg/mL -> 0.9765625 μg/mL