Difference between revisions of "Team:NUS Singapore-A/InterLab"

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Revision as of 08:59, 26 June 2018

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Interlab Study

OVERVIEW

A challenge of synthetic biology is repeating measurements in different laboratories. For example, fluorescence data is difficult to compare either because it is reported in different units, or because different groups handle raw data differently. iGEM’s Measurement Committee thus aims to use the InterLab Study to eventually develop absolute units for measurements of green fluorescent protein (GFP) in a plate reader. This will improve the measurement tools of synthetic biologists.

This year, the Committee aims to discover if it is possible to reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of optical density (OD). For this, we were required to measure the cell density of Escherichia coli ( E.Coli ) DH5⍺ cells using the methods below.

Method 1: Converting between absorbance of cells to absorbance of a known concentration of beads

In the first method, silica beads are used to estimate the actual amount of cells during fluorescence measurement. These beads are modeled after a typical E. coli cell and are thus expected to scatter light in a similar way to E. Coli cells. As a sample of these silica beads gives a consistent and known absorbance measurement at 600 nm, absorbance measurements from a sample’s cell density can be converted into an “equivalent concentration of beads” measurement that should be more universal and comparable between different labs.

Method 2: Counting colony-forming units (CFUs) from the sample

In the second method, cell concentration is approximated is by plating a known volume of the sample and letting bacterial colonies grow. As each bacterial colony is assumed to represent a single cell (for cells that do not stick together), the cell concentration in the sample is then directly proportional to the number of CFUs. Using a scaling factor computed from negative and positive control CFUs, a conversion factor from absorbance to CFU can be computed.

PARTS RECEVIED

Device Part Number Usage
Negative control BBa_R0040 TetR repressible promoter, medium strength promoter
Positive Control BBa_I20270 Promoter MeasKit (J23151)
Test Device 1 BBa_J364000 GFP expressing constitutive device
Test Device 2 BBa_J364001 GFP expressing constitutive device
Test Device 3 BBa_J364002 GFP expressing constitutive device
Test Device 4 BBa_J364007 Expresses GFP under the control of a constitutive promoter
Test Device 5 BBa_J364008 Expresses GFP under the control of a constitutive promoter
Test Device 6 BBa_J364009 Expresses GFP under the control of a constitutive promoter

MATERIALS & METHODS

Plate Reader
BioTek Synergy H1

Abs 600
  • Wavelength: 600nm
  • Read Speed: Normal
  • Delay: 100 msec
Fluorescence
  • Excitation: 485
  • Emission: 525
  • Optics: Top
  • Gain: 50
  • Light Source: Xenon Flash
  • Lamp Energy: High
  • Read Speed: Normal
  • Delay: 100 msec
  • Read Height: 7 mm

Materials
  1. 1 ml LUDOX CL-X
  2. ddH2O
  3. 96-well plate (black)

Methods
  1. 100 µl of LUDOX was added into wells A1, B1, C1 and D1.
  2. 100 µl of ddH20 was added into wells A2, B2, C2 and D2.
  3. Abs600nm was measured for all samples.
Results LUDOX CL-X H2O

Click here to see results for Calibration 1.

Materials
  1. 300 µl Silica beads (4.7 x 108 microspheres)
  2. ddH2O
  3. 96-well plate (black)
 Methods
(A) To prepare the Microsphere Stock Solution
  1. Tube labelled “Silica Beads” was vortexed vigorously for 30 s.
  2. 96 µl of microspheres was immediately pipetted into a 1.5 ml eppendorf tube.
  3. 904 µl of ddH20 was added to the microspheres. The eppendorf was vortexed well.

(B) To prepare the serial dilution of microsphere
  1. 100 µl of ddH20 was added into wells A2, B2, C2, D2...A12, B12, C12, D12.
  2. The microsphere stock solution was vortexed vigorously for 10 s before immediately adding 200 µl of microspheres into A1.
  3. 100 µl of microsphere stock solution was transferred from A1 to A2.
  4. Mix A2 by pipetting up and down 3 times and transfer 100 µl into A3.
  5. The subsequent dilutions were prepared as illustrated on Image A (below).
  6. Samples were re-mixed immediately before putting it in the plate reader. Fluorescence(Abs600) all samples were measured.

Click here to see results for Calibration 2.

Materials
  1. Fluorescein
  2. 10 ml 1X PBS pH 7.4 - 7.6
  3. 96-well plate (black)
 Methods
(A) To prepare the fluorescein stock solution
  1. The fluorescein kit tube was spun down to make sure that the pellet was collected at the bottom of the tube.
  2. 10X fluorescein stock solution (100 µM) was prepared by resuspending fluorescein in 1 ml of 1X PBS. Fluorescein was checked to be properly dissolved in PBS by checking for no more visible particulates in the pipette tip when resuspending.
  3. 10X fluorescein stock solution was diluted with 1X PBS to make a 1X fluorescein solution (10 µM): 100 µl of 10X fluorescein stock solution was mixed with 900 µl of 1X PBS.

(B) To prepare the serial dilution of fluorescein
  1. 100 µl of PBS was added into wells A2, B2, C2, D2...A12, B12, C12, D12.
  2. 200 µl of 1X fluorescein stock solution was added into A1, B1, C1 and D1.
  3. 100 µl of 1X fluorescein stock solution was transferred from A1 to A2.
  4. Mix A2 by pipetting up and down 3 times and transfer 100 µl into A3.
  5. The subsequent dilutions were prepared as illustrated on Image B (below). .
  6. Fluorescence of all samples are measured.

Click here to see results for Calibration 3.

Materials
  1. Competent cells (Escherichia coli strain DH5α)
  2. Luria Bertani (LB) media
  3. Chloramphenicol (stock concentration 25 mg/ml dissolved in ethanol)
  4. 50 ml Falcon tube (wrapped with a thick layer of paper towel to block light)
  5. 1.5 ml eppendorf tubes
  6. Incubator at 37 °C
  7. Ice bucket with ice
  8. 96-well plate (black)
Device Part Number Plate Location
Negative control BBa_R0040 Kit Plate 7 Well 2d
Positive Control BBa_I20270 Kit Plate 7 Well 2B
Test Device 1 BBa_J364000 Kit Plate 7 Well 2F
Test Device 2 BBa_J364001 Kit Plate 7 Well 2H
Test Device 3 BBa_J364002 Kit Plate 7 Well 2J
Test Device 4 BBa_J364007 Kit Plate 7 Well 2L
Test Device 5 BBa_J364008 Kit Plate 7 Well 2N
Test Device 6 BBa_J364009 Kit Plate 7 Well 2P
Methods
(A) Day 1: Transform Escherichia coli strain DH5α with devices provided in the Distribution Kit.
  1. Each device (powder form) was resuspended in 10 µl of ddH2O.
  2. 1 µl of each respective plasmid was transformed into 50 µl E. coli DH5α via electroporation.
  3. 500 µl of LB was immediately added into each tube for recovery of the transformed cells.
  4. Each sample tube was incubated with shaking at 37 °C for 30 mins before 100 µl of each sample was plated onto LB + Chlor agar plates and grown overnight at 37 °C.

(B) Day 2: Selecting Colonies and Growing Cells Overnight.
  1. Two colonies were selected according to their size (bigger colonies were preferably selected) and to their proximity to one another (those more sparsely separated from other colonies were preferred).
  2. Selected colonies were inoculated into 5 ml of LB + Chlor and grown overnight at 37 °C, at 220 rpm.
  3. 100 µl of 1X fluorescein stock solution was transferred from A1 to A2.

(C) Day 3: Cell Growth, Sampling and Assay. Part 1: Abs600nm and Fluorescence Measurement
  1. A cell stock of each overnight culture was made in glycerol (850 µl of culture + 350 µl of glycerol for storage, in case there is a need to use them again).
  2. A 1:10 dilution of each overnight culture was made in LB + Chlor (0.5 mL culture + 4.5 mL media).
  3. Abs600nm of the 1:10 diluted cultures were measured.
  4. Cultures were diluted further to a target Abs600nm of 0.02 in a final volume of 12 ml LB + Chlor in a 50 ml falcon tube that is covered in tissue paper
  5. 500 µl of samples of the diluted cultures at 0 h were transferred into 1.5 ml eppendorf tubes (A and B each). Eppendorf tubes were placed on ice until ready to be laid out according to the plate diagram to be measured for fluorescence and Abs600nm. Click here to see fluorescence readings at T = 0 h
  6. The remainder of the cultures were incubated at 37 °C, 220 rpm for 6 hours.
  7. After the 6-hour-incubation, 500 µl of these cultures were transferred into 1.5 ml eppendorf tubes before being laid out according to the plate diagram below. The samples were measured again for its fluorescence and Abs600nm. Click here to see fluorescence readings at T = 6 h.

Part 2: Colony Forming Units per 0.1 OD600 E. coli Cultures (only Positive Control (BBa_I20270) cultures and Negative Control (BBa_R0040) was involved in this experiment)
  1. Overnight cultures were diluted 10-fold in LB + Chlor media to make sure it lies in the linear detection range of our plate reader.
  2. OD600nm of cell cultures were measured. Click here to see results.
  3. Overnight cultures were diluted to OD600 = 0.1 in 1 ml of LB + Chlor media. Each culture was done in tripliFor each starting sample, serial dilutions were prepared as shown in the illustration below. cates.
  4. Diluted overnight cultures were checked to ensure that OD600 = 0.1 (minus the blank measurement).
  5. 100 µl of Dilutions 3, 4 and 5 were aseptically spread on LB + Chlor agar plates. Plates were incubated overnight at 37 °C

Colonies on each plate were counted. Click here to see results.

Materials
  1. SpheroTech Rainbow calibration beads, type RCP-30-5A (Lot Number: AAF02)
  2. Flow cytometer set to collect 10,000 events per well or a read time of 1 min per well
 Methods
  1. A sample of SpheroTech beads was prepared according to the manufacturer instructions
  2. Plate setup was as shown below.

Results

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InterLab

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