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

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<button class="accordion"> OD600 REFERENCE POINT (CALIBRATION 1)  </button>
 
<button class="accordion"> OD600 REFERENCE POINT (CALIBRATION 1)  </button>
 
<div class="panel">
 
<div class="panel">
−
  <p>
 
 
     <center>
 
     <center>
−
       <table style="width:70%">
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       <table cellspacing="100" style="max-width:70%; width: 72em;">
 
         <tr>
 
         <tr>
 
           <td>
 
           <td>
 
             <i> Materials </i>
 
             <i> Materials </i>
−
             <ol>
+
             <ul style="list-style: none;">
 
               <li>1 ml LUDOX CL-X</li>
 
               <li>1 ml LUDOX CL-X</li>
 
               <li>ddH<sub>2</sub>O</li>
 
               <li>ddH<sub>2</sub>O</li>
 
               <li>96-well plate (black)</li>
 
               <li>96-well plate (black)</li>
−
             </ol>
+
             </ul>
 
             <br>
 
             <br>
−
             <i> Methods </i>
+
             <i> Method </i>
 
             <ol>
 
             <ol>
−
               <li>100 µl of LUDOX was added into wells A1, B1, C1 and D1. </li>
+
               <li style="padding-left: 4em;">100 µl of LUDOX was added into wells A1, B1, C1 and D1. </li>
−
               <li>100 µl of ddH20 was added into wells A2, B2, C2 and D2.</li>
+
               <li style="padding-left: 4em;">100 µl of ddH20 was added into wells A2, B2, C2 and D2.</li>
−
               <li>Abs<sub>600nm</sub> was measured for all samples.</li>
+
               <li style="padding-left: 4em;">Abs<sub>600nm</sub> was measured for all samples.</li>
 
             </ol>
 
             </ol>
 
           </td>
 
           </td>
 
           <td>
 
           <td>
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             <table style="width:25%">
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             <table style="width: auto; font-size:1em;">
 
               <tr>
 
               <tr>
 
                 <td> <i> Results </i> </td>
 
                 <td> <i> Results </i> </td>
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       </table>
 
       </table>
 
     </center>
 
     </center>
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  </p>
 
 
</div>
 
</div>
  
−
<button class="accordion">PARTICLE STANDARD CURVE - MICEOSPHERE PROTOCOL (CALIBRATION 2)</button>
+
<button class="accordion">PARTICLE STANDARD CURVE (CALIBRATION 2)</button>
 
<div class="panel">
 
<div class="panel">
−
  <p>
 
 
     <center>
 
     <center>
−
       <table style="width:70%">
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       <table cellspacing="100" style="max-width:70%; width: 100em;">
−
         <tr>
+
         <tr style="vertical-align:top;">
 
           <td>
 
           <td>
 
             <i> Materials </i>
 
             <i> Materials </i>
−
             <ol>
+
             <ul style="list-style:none;">
 
               <li>300 µl Silica beads (4.7 x 108 microspheres)</li>
 
               <li>300 µl Silica beads (4.7 x 108 microspheres)</li>
 
               <li>ddH<sub>2</sub>O</li>
 
               <li>ddH<sub>2</sub>O</li>
 
               <li>96-well plate (black)</li>
 
               <li>96-well plate (black)</li>
−
             </ol>
+
             </ul>
−
             <br>
+
             <p>&emsp;</p>
 
             <i> Methods </i>
 
             <i> Methods </i>
−
            <br>
 
 
             <i> <u> (A) To prepare the Microsphere Stock Solution </u> </i>
 
             <i> <u> (A) To prepare the Microsphere Stock Solution </u> </i>
 +
            <p>&emsp;</p>
 
             <ol>
 
             <ol>
−
               <li>Tube labelled “Silica Beads” was vortexed vigorously for 30 s.</li>
+
               <li style="padding-left: 4em;">Tube labelled “Silica Beads” was vortexed vigorously for 30 s.</li>
−
               <li>96 µl of microspheres was immediately pipetted into a 1.5 ml eppendorf tube.</li>
+
               <li style="padding-left: 4em;">96 µl of microspheres was immediately pipetted into a 1.5 ml eppendorf tube.</li>
−
               <li>904 µl of ddH<sub>2</sub>0 was added to the microspheres. The eppendorf was vortexed well.</li>
+
               <li style="padding-left: 4em;">904 µl of ddH<sub>2</sub>0 was added to the microspheres. The eppendorf was vortexed well.</li>
 
             </ol>
 
             </ol>
 
             //add picture
 
             //add picture
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           <td>
 
           <td>
 
             <i> <u> (B) To prepare the serial dilution of microsphere </u> </i>
 
             <i> <u> (B) To prepare the serial dilution of microsphere </u> </i>
 +
            <p>&emsp;</p>
 
             <ol>
 
             <ol>
−
               <li>100 µl of ddH20 was added into wells A2, B2, C2, D2...A12, B12, C12, D12.</li>
+
               <li style="padding-left: 4em;">100 µl of ddH20 was added into wells A2, B2, C2, D2...A12, B12, C12, D12.</li>
−
               <li>The microsphere stock solution was vortexed vigorously for 10 s before immediately adding 200 µl of microspheres into A1.</li>
+
               <li style="padding-left: 4em;">The microsphere stock solution was vortexed vigorously for 10 s before immediately adding 200 µl of microspheres into A1.</li>
−
               <li>100 µl of microsphere stock solution was transferred from A1 to A2.</li>
+
               <li style="padding-left: 4em;">100 µl of microsphere stock solution was transferred from A1 to A2.</li>
−
               <li>Mix A2 by pipetting up and down 3 times and transfer 100 µl into A3.</li>
+
               <li style="padding-left: 4em;">Mix A2 by pipetting up and down 3 times and transfer 100 µl into A3.</li>
−
               <li>The subsequent dilutions were prepared as illustrated on Image A (below).</li>
+
               <li style="padding-left: 4em;">The subsequent dilutions were prepared as illustrated on Image A (below).</li>
−
               <li>Samples were re-mixed immediately before putting it in the plate reader. Fluorescence<sub>(Abs600)</sub> all samples were measured. </li>
+
               <li style="padding-left: 4em;">Samples were re-mixed immediately before putting it in the plate reader. Fluorescence<sub>(Abs600)</sub> all samples were measured. </li>
−
               <li> Fluorescence (Abs<sub>600</sub> ) of all samples were measured. Our results are reflected by Fig. 2 and Fig. 3. </li>
+
               <li style="padding-left: 4em;"> Fluorescence (Abs<sub>600</sub> ) of all samples were measured. Our results are reflected by Fig. 2 and Fig. 3. </li>
 
               //add picture
 
               //add picture
 
             </ol>
 
             </ol>
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       </table>
 
       </table>
 
     </center>
 
     </center>
−
  </p>
 
 
</div>
 
</div>
  
 
<button class="accordion"> FLUORESCENCE STANDARD CURVE - FLUORESCEIN PROTOCOL (CALIBRATION 3)</button>
 
<button class="accordion"> FLUORESCENCE STANDARD CURVE - FLUORESCEIN PROTOCOL (CALIBRATION 3)</button>
 
<div class="panel">
 
<div class="panel">
−
  <p>
 
 
     <center>
 
     <center>
−
       <table style="width:70%">
+
       <table cellspacing="100" style="max-width:70%; width: 90em;">
 
         <col width="80">
 
         <col width="80">
 
         <col width="80">
 
         <col width="80">
−
         <tr>
+
         <tr style="vertical-align:top;">
 
           <td>
 
           <td>
 
             <i> Materials </i>
 
             <i> Materials </i>
−
             <ol>
+
             <ul style="list-style:none;">
 
               <li>Fluorescein</li>
 
               <li>Fluorescein</li>
 
               <li>10 ml 1X PBS pH 7.4 - 7.6</li>
 
               <li>10 ml 1X PBS pH 7.4 - 7.6</li>
 
               <li>96-well plate (black)</li>
 
               <li>96-well plate (black)</li>
−
             </ol>
+
             </ul>
 
             <br>
 
             <br>
 
             <i> Methods </i>
 
             <i> Methods </i>
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             <i> <u> (A) To prepare the fluorescein stock solution </u> </i>
 
             <i> <u> (A) To prepare the fluorescein stock solution </u> </i>
 
             <ol>
 
             <ol>
−
               <li>The fluorescein kit tube was spun down to make sure that the pellet was collected at the bottom of the tube. </li>
+
               <li style="padding-left: 4em;">The fluorescein kit tube was spun down to make sure that the pellet was collected at the bottom of the tube. </li>
−
               <li>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.
+
               <li style="padding-left: 4em;">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.
 
                 </li>
 
                 </li>
−
               <li> 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. </li>
+
               <li style="padding-left: 4em;"> 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. </li>
 
             </ol>
 
             </ol>
 
             // add picture
 
             // add picture
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             <i> <u> (B) To prepare the serial dilution of fluorescein </u> </i>
 
             <i> <u> (B) To prepare the serial dilution of fluorescein </u> </i>
 
             <ol>
 
             <ol>
−
               <li>100 µl of PBS was added into wells A2, B2, C2, D2...A12, B12, C12, D12.</li>
+
               <li style="padding-left: 4em;">100 µl of PBS was added into wells A2, B2, C2, D2...A12, B12, C12, D12.</li>
−
               <li>200 µl of 1X fluorescein stock solution was added into A1, B1, C1 and D1. </li>
+
               <li style="padding-left: 4em;">200 µl of 1X fluorescein stock solution was added into A1, B1, C1 and D1. </li>
−
               <li>100 µl of 1X fluorescein stock solution was transferred from A1 to A2. </li>
+
               <li style="padding-left: 4em;">100 µl of 1X fluorescein stock solution was transferred from A1 to A2. </li>
−
               <li>Mix A2 by pipetting up and down 3 times and transfer 100 µl into A3. </li>
+
               <li style="padding-left: 4em;">Mix A2 by pipetting up and down 3 times and transfer 100 µl into A3. </li>
−
               <li>The subsequent dilutions were prepared as illustrated by Fig. 4. </li>
+
               <li style="padding-left: 4em;">The subsequent dilutions were prepared as illustrated by Fig. 4. </li>
−
               <li>Fluorescence of all samples were measured, and our results are reflected by Fig. 5. </li>
+
               <li style="padding-left: 4em;">Fluorescence of all samples were measured, and our results are reflected by Fig. 5. </li>
 
             </ol>
 
             </ol>
 
             // add picture
 
             // add picture
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       </table>
 
       </table>
 
     </center>
 
     </center>
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  </p>
 
 
</div>
 
</div>
  

Revision as of 19:31, 28 June 2018

CONNECT WITH US

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 RECEIVED

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

Abs600 --
  • 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 ml LUDOX CL-X
  • ddH2O
  • 96-well plate (black)

Method
  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
Replicate 1 0.056 0.037
Replicate 2 0.056 0.038
Replicate 3 0.056 0.038
Replicate 4 0.055 0.038
Arth. Mean 0.056 0.038
Corrected Abs600 0.018
Reference OD600 0.063
OD600/Abs600 0.063
Materials
  • 300 µl Silica beads (4.7 x 108 microspheres)
  • ddH2O
  • 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.
//add picture 		(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.
  7. Fluorescence (Abs600 ) of all samples were measured. Our results are reflected by Fig. 2 and Fig. 3.
    8. //add picture
Materials
  • Fluorescein
  • 10 ml 1X PBS pH 7.4 - 7.6
  • 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.
// add picture 		(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 by Fig. 4.
  6. Fluorescence of all samples were measured, and our results are reflected by Fig. 5.
// add picture

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)

Methods Day 1: Transforming 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.

Day 2: Selecting Colonies and Growing Cells Overnight
  1. 2 colonies were selected for being both relatively bigger and more separated from the other colonies.
  2. The selected colonies were then inoculated into 5 ml of LB + Chlor and grown overnight at 37 °C at 220 rpm.
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 for storage, in case there is a need to use them again. To make this stock, 850 µl of culture was added to 350 µl of glycerol.
  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 was covered with tissue paper.
  5. 500 µl of samples of the diluted cultures at 0 h were transferred into 1.5 ml eppendorf tubes labelled A and B. The tubes were placed on ice until they were ready to be laid out according to the plate diagram to measure fluorescence and Abs600. Fluorescence readings at T = 0 h are shown in Fig. 6.
  6. The rest of the cultures were incubated at 37 °C and 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’ fluorescence and Abs600nm were measured again. Fluorescence readings at T = 6 h are shown in Fig. 7.

Part 2: Colony Forming Units per 0.1 OD600 E. coli Cultures
Only Positive Control (BBa_I20270) cultures and Negative Control (BBa_R0040) were involved in this part.
  1. Overnight cultures were diluted 10-fold in LB + Chlor media to ensure they lay in the linear detection range of our plate reader.
  2. The OD600nm of cell cultures were measured. Our results are reflected by Fig. 8.
  3. Overnight cultures were diluted to OD600 = 0.1 in 1 ml of LB + Chlor media. Each culture was done in triplicate.
  4. Diluted overnight cultures were checked to ensure that OD600 = 0.1, excluding the blank measurement
  5. For each starting sample, serial dilutions were prepared as shown in Fig. 9.
  6. 100 µl of Dilutions 3, 4 and 5 were aseptically spread on LB + Chlor agar plates.
  7. The plates were incubated overnight at 37 °C.
  8. Colonies on each plate were counted. Our results are reflected by Fig. 10.

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.

DISCUSSION

Abs600 nm

Rate of growth is inferred from Net Abs 600 nm values; Net Abs 600 nm is a common method of measuring cell concentration. All cells except for cells transformed with Devices 1 and 5 had comparable rates of growth. In cells transformed with Devices 1 and 5, the increase in Net Abs 600 nm was significantly slower than cells transformed with the rest of the devices (see Figure Z). //add pictures

µM Fluorescein per OD

  1. Cells transformed with Devices 1, 4 and 5 had the highest fluorescein readings per OD.
  2. µM fluorescein per OD of cells transformed with Device 3 were very low and at levels comparable to cells transformed with the Negative Control.
  3. Cells transformed with Devices 2 and 6 had similar µM fluorescein per OD to that of cells transformed with the Positive Control.
  4. Similar trends were observed for MEFL/particle.

Derivations/Inferences made about devices
  1. Despite growing at a considerably slower rate, fluorescein readings per OD of cells transformed with Devices 1 and 5 were among the highest. The high GFP production in cells transformed with Devices 1 and 5 might have caused a unhealthy metabolic stress on the cells, which, in turn, could have impeded the growth of the cells.
  2. Cells transformed with Device 4 had a slightly lower fluorescein reading per OD as compared to cells transformed with Devices 1 and 5. Since there was no compromise on the cell growth rate despite the high GFP production, the slightly lower GFP production (as compared to cells transformed with Devices 1 and 5) was inferred to have permitted the cells to grow at normal rates, leading to an overall higher net fluorescein reading.
  3. Cells transformed with Device 3 was observed to produce very little to no GFP. Promoter within Device 3 might have been repressed by a molecule present in the cells, or not activated, to result in minimal GFP expression.
Conclusion about devices

Devices 1 and 5 were inferred to have highest promoter strength upstream of the GFP gene. While they produced the highest fluorescein readings per OD, overexpression of GFP as a result of Devices 1 and 5 do not seem to be healthy for cells: cells were not observed to be able to cope with the overly high expression of GFP. In the same argument, Device 4 seemed to be the most advantageous for the experimenter: there was a high GFP production without a compromise of growth rate. Cells transformed with Device 4 seemed to be able to manage the level of metabolic stress and grow normally.


CFU/mL/OD
Based on the data, NCA, NCB, PCA, PCB averages were computed based on counted CFU units. The percentage errors computed based on the known concentrations of beads against their respective averages showed high error levels.
// Confirm with wiki team

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InterLab

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