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| | ==Data== | | ==Data== |
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| − | [[Image: Arabinose_activation.png|thumb|569px|center|'''Figure 1 - Transfer function of <partinfo>K325219</partinfo>. The data points represent the mean of 11 values obtained for light output at 30 min interval from 450 min to 750 min after injection of D-Luciferin. These values are the mean of 3 readings as shown in Figure 3. The corresponding error bars represent an interval of twice the standard deviation across the 11 data points centred around the mean value. ''']] | + | [[Image: IntegratedactiPP+LRE.png|thumb|569px|center|'''Figure 1 - Transfer function of <partinfo>K325219</partinfo>. The data points represent the mean of 11 values obtained for light output at 30 min interval from 450 min to 750 min after injection of D-Luciferin. These values are the mean of 3 readings as shown in Figure 3. The corresponding error bars represent an interval of twice the standard deviation across the 33 data points centred around the mean value. ''']] |
| − | [[Image:MaximumlumPP+LRE.png|thumb|569px|center|'''Figure 2 - Growth curves of cultures of [[Part:BBa_V1000|MG1655]] bearing <partinfo> BBa_T9002</partinfo> from the transfer function experiment under zero input and an input of 1E-4 M [[3OC6HSL|3OC<sub>6</sub>HSL]]. The data points represent the mean of three identical samples; the error bars represent the 95% confidence interval in the estimate of the mean. The growth curves approximate straight lines on a log-ordinate axis, suggesting that exponential growth continues for the course of the experiment.''']] | + | [[Image:MaximumlumPP+LRE.png|thumb|569px|center|'''Figure 2 - Maximum luminescence output of <partinfo> K325219</partinfo> as a function of Arabinose concentration. These values are the mean of 3 readings as shown in Figure 3. The corresponding error bars represent an interval of twice the standard deviation across the 3 data points centred around the mean value. ''']] |
| − | [[Image:BBa F2620TransferFunctionSurfaceForSI.png|thumb|569px|center|'''Figure 3 - Time and dose response measurements of GFP synthesis rate per cell following addition of [[3OC6HSL|3OC<sub>6</sub>HSL]]. The surface shown is the average of six or nine independent measurements at each datapoint. The heavy black line is the 60 min time-slice that defines the transfer function shown in Figure 1.''']] | + | [[Image:TimePP+LRE.png|thumb|569px|center|'''Figure 3 - Evolution of luminescence with time at different Arabinose concentrations. The interval between measurements is 30 min. Mean values and error bars are based on 3 time repeats.''']] |
| | <center> | | <center> |
| | {|{{Table}} | | {|{{Table}} |
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| | !Date Uploaded | | !Date Uploaded |
| | |- | | |- |
| − | |[[Image:BBa F2620-Variability-3-P2.txt]] | + | |[[Media:BBa_K325219ArabinosetoLight.xls]] |
| − | |Raw data for colonies 1-3 | + | |Raw data from experiment |
| − | |12/11/2006 | + | |21/10/2010 |
| − | |-
| + | |
| − | |[[Image:BBa F2620-Variability-4-P1.txt]]
| + | |
| − | |Raw data for colonies 4-6
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| − | |1/4/2007
| + | |
| − | |-
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| − | |[[Image:BBa F2620-Variability-5-P1.txt]]
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| − | |Raw data for colonies 7-9
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| − | |1/5/2007
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| | |} | | |} |
| | </center> | | </center> |
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| − | ==Protocol==
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| − | #Three 5 ml cultures of [http://openwetware.org/wiki/Endy:M9_media/supplemented supplemented M9 medium] and antibiotic (kanamycin, 20 µg/ml) were inoculated with single colonies (~2mm ø) from a freshly streaked plate of [[Part:BBa_V1000|MG1655]] containing <partinfo>BBa_T9002</partinfo>. One 5 ml culture was inoculated with a single colony from a freshly streaked plate of [[Part:BBa_V1000|MG1655]] containing a <partinfo>BBa_T9002</partinfo> mutant (T9002m) lacking a GFP expression device described in the [[Part:BBa_F2620:Stability|stability section]].
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| − | #Cultures were grown in 17 mm test tubes for 15 hrs at 37°C with shaking at 70 rpm.
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| − | #Cultures were diluted 1:1000 into 5.5 ml of fresh medium and grown to an OD600 of 0.15 under the same conditions as before. This growth took on average 4.5 hrs.
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| − | #Twenty-four 200 µl aliquots of each of the cultures were transferred into a flat-bottomed 96 well plate (Cellstar Uclear bottom, cat. # T-3026-16, Greiner).
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| − | #2 µl of the stock concentrations of the cognate AHL, 3-oxohexanoyl-homoserine lactone ([[3OC6HSL|3OC<sub>6</sub>HSL]]), was added to each well to yield 8 different final concentrations (0, 1E-10, 1E-9, 1E-8, 1E-7, 1E-6, 1E-5 and 1E-4 M). Three replicate wells were measured for each concentration of [[3OC6HSL|3OC<sub>6</sub>HSL]]. Three wells were each filled with 200 µl of medium to measure the absorbance background. Three further wells were each filled with 200 µl of the <partinfo>BBa_T9002</partinfo> mutant culture to measure fluorescent background.
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| − | #The plate was incubated in a [http://openwetware.org/wiki/Endy:Victor3_plate_reader Wallac Victor3 multi-well fluorimeter] (Perkin Elmer) at 37°C and assayed with an automatically repeating protocol of absorbance measurements (600 nm absorbance filter, 0.1 second counting time through 5 mm of fluid), fluorescence measurements (488 nm excitation filter, 525 nm emission filter, 0.5 seconds, CW lamp energy 12901 units), and shaking (1 mm, linear, normal speed, 5 seconds). Time between repeated measurements was 2 min and 21 s. Approximately 6 min elapsed between beginning addition of [[3OC6HSL|3OC<sub>6</sub>HSL]] to the wells and the first plate reader measurement. [[3OC6HSL|3OC<sub>6</sub>HSL]] was added in order of increasing concentration to minimize GFP synthesis during plate loading. Cells appear to grow exponentially for the duration of the plate reader measurement protocol (see Figure 2 for representative growth curves).
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| − | #We repeated steps 1 through 6 on three separate days to obtain data for nine colonies from a single plate.
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| − | #We processed the data to compute the PoPS output from <partinfo>BBa_F2620</partinfo> as described on the [[Part:BBa_F2620:Experience/Endy/Data analysis|Data analysis page]]. The data for each colony tested was averaged across the three replicate wells. The mean for each colony was then averaged to obtain a population mean. The time and dose dependent input-output surface is shown above in Figure 3. Following an initial transient response, device output reached an approximate steady state.
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| − | #The snapshot transfer function in Figure 1 is the 60 min time-slice from the surface shown in Figure 3 (highlighted as a heavy black line). Error bars in Figure 1 representing the 95% confidence interval in the population for the nine independent samples. The cyan shaded region represents the range of the nine independent samples.
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| − | #To estimate parameters that characterize the measured transfer function, we used least squares estimation to fit a simple model to the data. A Hill equation derived from simple biochemical equations describes the data well (R<sup>2</sup>=0.99). In the equation (shown below), P<sub>out</sub> is the PoPS per cell output of <partinfo>BBa_F2620</partinfo>, P<sub>max</sub> is the maximum output level, K is the switch point, and n is the hill coefficient describing the steepness of the transition from low output to high output.
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| − | #To gain further information about the transition region of the transfer function, measurements were subsequently taken at two intermediate [[3OC6HSL|3OC<sub>6</sub>HSL]] concentrations (3.3E-09 M and 3.3E-08 M) using the same protocol defined above. Measurements were simultaneously taken at a subset of the original concentrations to ensure the new data was consistent with the earlier data. The new data was processed simultaneously with the original data, with the exception that only six independent colonies were measured for the intermediate [[3OC6HSL|3OC<sub>6</sub>HSL]] concentrations.
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| | | | |
| − | <math>
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| − | P_{out} = \frac{P_{max}[3OC_6HSL]^n}{K^n+[3OC_6HSL]^n}
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| − | </math>
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| − | </div>
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| − | </center>
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| − | <sup>1</sup>
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| | </div>Measured by the [http://2010.igem.org/Team:Cambridge Cambridge iGEM team 2010] | | </div>Measured by the [http://2010.igem.org/Team:Cambridge Cambridge iGEM team 2010] |
| | <div style="padding: 00px; width: 680px"> | | <div style="padding: 00px; width: 680px"> |
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| | '''References'''<br> | | '''References'''<br> |
| | [http://www.ncbi.nlm.nih.gov/pubmed/18949818 '''[1]:'''] S.M. Marques and J.C.G. Esteves da Silva, (2009) Firefly Bioluminescence: A Mechanistic Approach of Luciferase Catalyzed Reactions,''Life'' '''61''', 6-17. | | [http://www.ncbi.nlm.nih.gov/pubmed/18949818 '''[1]:'''] S.M. Marques and J.C.G. Esteves da Silva, (2009) Firefly Bioluminescence: A Mechanistic Approach of Luciferase Catalyzed Reactions,''Life'' '''61''', 6-17. |
| − | </div>
| + | |
| | + | |
| | [http://www.nature.com/nature/journal/v440/n7082/abs/nature04542.html '''[2]:'''] T. Nakatsu ''et al.'' (2006) Structural Basis for the spectral difference in luciferase bioluminescence, ''Nature'' '''440'''(16), 372-376. | | [http://www.nature.com/nature/journal/v440/n7082/abs/nature04542.html '''[2]:'''] T. Nakatsu ''et al.'' (2006) Structural Basis for the spectral difference in luciferase bioluminescence, ''Nature'' '''440'''(16), 372-376. |
| − | </div>
| + | |
| | + | |
| | [http://www.ncbi.nlm.nih.gov/pubmed/11457857 '''[3]:'''] K. Gomi and N. Kajiyama, (2001) Oxyluciferin, a Luminescence Product of Firefly Luciferase, Is Enzymatically Regenerated into Luciferin, ''The Journal of Biological Chemistry'', '''276'''(39), 36508-36513. | | [http://www.ncbi.nlm.nih.gov/pubmed/11457857 '''[3]:'''] K. Gomi and N. Kajiyama, (2001) Oxyluciferin, a Luminescence Product of Firefly Luciferase, Is Enzymatically Regenerated into Luciferin, ''The Journal of Biological Chemistry'', '''276'''(39), 36508-36513. |
Description
This page describes the relationship between Arabinose concentration in the medium with light output. We used a [http://www.bmglabtech.com/products/microplate-reader/instruments.cfm?product_id=2 FLUOstar OPTIMA] microplate reader to quantify the light output. Protocol and plate reader settings used are given below.
Data
Figure 1 - Transfer function of BBa_K325219. The data points represent the mean of 11 values obtained for light output at 30 min interval from 450 min to 750 min after injection of D-Luciferin. These values are the mean of 3 readings as shown in Figure 3. The corresponding error bars represent an interval of twice the standard deviation across the 33 data points centred around the mean value. 
Figure 2 - Maximum luminescence output of BBa_K325219 as a function of Arabinose concentration. These values are the mean of 3 readings as shown in Figure 3. The corresponding error bars represent an interval of twice the standard deviation across the 3 data points centred around the mean value. 
Figure 3 - Evolution of luminescence with time at different Arabinose concentrations. The interval between measurements is 30 min. Mean values and error bars are based on 3 time repeats.
Measured by the [http://2010.igem.org/Team:Cambridge Cambridge iGEM team 2010]
Compatibility
Chassis: Device has been shown to work in Top 10 (Invitrogen)
Plasmids: Device has been shown to work on pSB1C3
References
[http://www.ncbi.nlm.nih.gov/pubmed/18949818 [1]:] S.M. Marques and J.C.G. Esteves da Silva, (2009) Firefly Bioluminescence: A Mechanistic Approach of Luciferase Catalyzed Reactions,Life 61, 6-17.
[http://www.nature.com/nature/journal/v440/n7082/abs/nature04542.html [2]:] T. Nakatsu et al. (2006) Structural Basis for the spectral difference in luciferase bioluminescence, Nature 440(16), 372-376.
[http://www.ncbi.nlm.nih.gov/pubmed/11457857
[3]:] K. Gomi and N. Kajiyama, (2001) Oxyluciferin, a Luminescence Product of Firefly Luciferase, Is Enzymatically Regenerated into Luciferin,
The Journal of Biological Chemistry,
276(39), 36508-36513.
