Difference between revisions of "Part:BBa K325909:ArabinosetoLight"
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'''Description'''<br>
 
'''Description'''<br>
 
This page describes the light output of [https://parts.igem.org/Part:BBa_K325909:ArabinosetoLight BBa K325909] as a fucntion of Arabinose concentration in the media. The characterisation has been made in different chassis. TOP 10 cells as well as 2 mutants in which expression of H-NS was repressed.  
 
This page describes the light output of [https://parts.igem.org/Part:BBa_K325909:ArabinosetoLight BBa K325909] as a fucntion of Arabinose concentration in the media. The characterisation has been made in different chassis. TOP 10 cells as well as 2 mutants in which expression of H-NS was repressed.  
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THIS PAGE IS CURRENTLY BEING UPDATED.
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==Data==
 
==Data==
  
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[[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. ''']]
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[[Image:BBa_K325909Aracurve.png|thumb|569px|center|'''Figure 1 - Light output of <partinfo>K325909</partinfo> as a function of Arabinose concentration in the media. The values correspond to the peak intensity within 5 hours of adding Arabinose to the media. Data points and error bars correspond to the mean and the standard deviation of 3 time repeats. ''']]
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[[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. ''']]
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[[Image:BBa_K325909timecourse.png|thumb|569px|center|'''Figure 2 - Evolution of luminescence with time at different Arabinose concentrations for <partinfo>K325909</partinfo>. Measurements were taken every 30 minutes. Data points and error bars correspond to the mean and standard deviation of 3 time repeats. ''']]
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[[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.''']]
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<center>
 
<center>
 
{|{{Table}}
 
{|{{Table}}
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!Date Uploaded
 
!Date Uploaded
 
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|[[Media:BBa_K325219ArabinosetoLight.xls]]
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|[[Media:BBa_K325909ArabinosetoLight.xls]]
 
|Raw data from experiment
 
|Raw data from experiment
 
|21/10/2010
 
|21/10/2010
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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">
 
'''Compatibility'''<br>
 
'''Compatibility'''<br>
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[https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=cell ''Chassis:''] Device has been shown to work in ''Top 10 (Invitrogen)''<br>
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[https://parts.igem.org/cgi/partsdb/pgroup.cgi?pgroup=cell ''Chassis:''] Device has been shown to work in ''Top 10 (Invitrogen)'', [http://www.ecoliwiki.net/colipedia/index.php/BW25113 BW25113 DELTA H-NS::kan] and H-NS mutant JM 230 H-NS -205::tn10.<br>
 
[[Plasmid backbones|''Plasmids:'']] Device has been shown to work on ''<partinfo>pSB1C3</partinfo>'' <br>
 
[[Plasmid backbones|''Plasmids:'']] Device has been shown to work on ''<partinfo>pSB1C3</partinfo>'' <br>
  

Latest revision as of 21:21, 27 October 2010

Input: L-Arabinose
Output: Light

pBad/araC
I0500		PoPS to Light
 Cambridge-Eglowli.png

Part Main Page        Arabinose -> Light        H-NS mutants        Add Data       


Description
This page describes the light output of BBa K325909 as a fucntion of Arabinose concentration in the media. The characterisation has been made in different chassis. TOP 10 cells as well as 2 mutants in which expression of H-NS was repressed.


Data

Figure 1 - Light output of BBa_K325909 as a function of Arabinose concentration in the media. The values correspond to the peak intensity within 5 hours of adding Arabinose to the media. Data points and error bars correspond to the mean and the standard deviation of 3 time repeats.
Figure 2 - Evolution of luminescence with time at different Arabinose concentrations for BBa_K325909. Measurements were taken every 30 minutes. Data points and error bars correspond to the mean and standard deviation of 3 time repeats.
Data Notes Date Uploaded
Media:BBa_K325909ArabinosetoLight.xls Raw data from experiment 21/10/2010


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), [http://www.ecoliwiki.net/colipedia/index.php/BW25113 BW25113 DELTA H-NS::kan] and H-NS mutant JM 230 H-NS -205::tn10.
Plasmids: Device has been shown to work on pSB1C3


References
[http://www.jstor.org/stable/4449975 [1]:] J. Slock, (1995) Transformation Experiments Using Bioluminescence Genes of Vibrio fischeri,The American Biology Teacher, 57, 225-227.

[http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.42.100188.001055 [2]:] E.A. Meighen (1988) Enzymes and genes from the lux operons of bioluminescent bacteria, Annual Reviews in Microbiology 42, 151-176. [http://www.annualreviews.org/doi/pdf/10.1146/annurev.ge.28.120194.001001 [3]:] E.A. Meighen, (1994) Genetics of bacterial bioluminescence, Annual Reviews of Genetics, 28, 117-139.