Difference between revisions of "Degradation of C"

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and <math>6.7 \cdot 10^{-6}-6.7 \cdot 10^{-3} s^{-1}</math><ref name="Chatterjee2011"></ref>)
 
and <math>6.7 \cdot 10^{-6}-6.7 \cdot 10^{-3} s^{-1}</math><ref name="Chatterjee2011"></ref>)
 
| Chen et al. empirically calculated the degradation rate of the autoinducer  PAI2 in ''Pseudomonas aeruginosa'' cultures and reported a best-fit degradation constant of <math>0.195 h^{-1} (0.00325 min^{-1})</math>.
 
| Chen et al. empirically calculated the degradation rate of the autoinducer  PAI2 in ''Pseudomonas aeruginosa'' cultures and reported a best-fit degradation constant of <math>0.195 h^{-1} (0.00325 min^{-1})</math>.
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[[Image:DC-text.png|center|thumb|400px|Chen et al. 2005<ref name="Chen2005"></ref>]]
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[[Image:DC-text.png|center|thumb|350px|Chen et al. 2005<ref name="Chen2005"></ref>]]
  
 
Additionally, the degradation rates of the quorum sensing autoinducer AHL have been measured ''in vitro'' by Kaufmann et al. and the reported rates for different AHLs are between <math>4.77 \cdot 10^{-6}-3.07 \cdot 10^{-5} s^{-1} (2.86 \cdot 10^{-4}-1.84 \cdot 10^{-3} min^{-1})</math>. Weber et al. also reported that the degradation rate of AHL ''in vivo'' has been estimated, and is within the range <math>5 \cdot 10^{-3}-2 \cdot 10^{-2} min^{-1}</math>.
 
Additionally, the degradation rates of the quorum sensing autoinducer AHL have been measured ''in vitro'' by Kaufmann et al. and the reported rates for different AHLs are between <math>4.77 \cdot 10^{-6}-3.07 \cdot 10^{-5} s^{-1} (2.86 \cdot 10^{-4}-1.84 \cdot 10^{-3} min^{-1})</math>. Weber et al. also reported that the degradation rate of AHL ''in vivo'' has been estimated, and is within the range <math>5 \cdot 10^{-3}-2 \cdot 10^{-2} min^{-1}</math>.
 
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<li style="display: inline-block;"> [[Image:DC-text2.png|center|thumb|400px|Kaufmann et al. 2005<ref name="Kaufmann2005"></ref>]] </li>
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<li style="display: inline-block;"> [[Image:DC-text2.png|center|thumb|350px|Kaufmann et al. 2005<ref name="Kaufmann2005"></ref>]] </li>
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<li style="display: inline-block;"> [[Image:DC-text3.png|center|thumb|400px|Weber et al. 2011<ref name="Weber2011"></ref>]] </li>
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<li style="display: inline-block;"> [[Image:DC-text3.png|center|thumb|350px|Weber et al. 2011<ref name="Weber2011"></ref>]] </li>
 
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Revision as of 19:09, 17 October 2015

The SCB protein (C) degrades.

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About this image

Chemical equation

C\rightarrow \varnothing

Rate equation

r= d_{C}\cdot[C]

Parameters

The parameter of this reaction is the degradation rate of C (d_{C}).

Name Value Units Value in previous GBL models [1] [2] Remarks-Reference
d_{C} 0-0.001 [3] [4] min^{-1} [5] [6] 6.7 \cdot 10^{-5} s^{-1}[1][2]

(Range tested: 0-2 \cdot 10^{-4} s^{-1})

(Bistability range: 0-0.0085 s^{-1}[1]

and 6.7 \cdot 10^{-6}-6.7 \cdot 10^{-3} s^{-1}[2])

Chen et al. empirically calculated the degradation rate of the autoinducer PAI2 in Pseudomonas aeruginosa cultures and reported a best-fit degradation constant of 0.195 h^{-1} (0.00325 min^{-1}).
Chen et al. 2005[4]

Additionally, the degradation rates of the quorum sensing autoinducer AHL have been measured in vitro by Kaufmann et al. and the reported rates for different AHLs are between 4.77 \cdot 10^{-6}-3.07 \cdot 10^{-5} s^{-1} (2.86 \cdot 10^{-4}-1.84 \cdot 10^{-3} min^{-1}). Weber et al. also reported that the degradation rate of AHL in vivo has been estimated, and is within the range 5 \cdot 10^{-3}-2 \cdot 10^{-2} min^{-1}.

  • Kaufmann et al. 2005[6]
  • Weber et al. 2011[5]
Name Value Units Origin Remarks
d_{C} 0-0.001 [7] min^{-1} Degradation rate of acyl-homoserine lactone (AHL) The assumption that the degradation of SCB1 is slower than

AHL is made, as described in Takano(2006)[3]

Parameters with uncertainty

The most plausible parameter value for the d_{C} is decided to be 0.0002 min^{-1} and the confidence interval 2 . This means that the mode of the PDF is 0.0002 and the range where 95% of the values are found is between 0.0001 and 0.0004 min^{-1}.

The probability distribution for the parameter, adjusted accordingly in order to reflect the above values, is the following:

500px

The location and scale parameters of the distribution are:

Parameter μ σ
d_{C} -8.4046 0.3356

References

  1. ↑ 1.0 1.1 1.2 S. Mehra, S. Charaniya, E. Takano, and W.-S. Hu. A bistable gene switch for antibiotic biosynthesis: The butyrolactone regulon in streptomyces coelicolor. PLoS ONE, 3(7), 2008.
  2. ↑ 2.0 2.1 2.2 A. Chatterjee, L. Drews, S. Mehra, E. Takano, Y.N. Kaznessis, and W.-S. Hu. Convergent transcription in the butyrolactone regulon in streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis. PLoS ONE, 6(7), 2011.
  3. ↑ 3.0 3.1 E. Takano. γ-butyrolactones: Streptomyces signalling molecules regulating antibiotic production and differentiation. Current Opinion in Microbiology, 9(3):287–294, 2006. Cite error: Invalid <ref> tag; name "Takano2006" defined multiple times with different content
  4. ↑ 4.0 4.1 Chen CC., Riadi L., Suh S.J., Ohman D.E., Ju L.K. Degradation and synthesis kinetics of quorum-sensing autoinducer in Pseudomonas aeruginosa cultivation. J Biotechnol. 2005;117(1):1-10.
  5. ↑ 5.0 5.1 Weber M., Buceta J. Noise regulation by quorum sensing in low mRNA copy number systems. BMC Systems Biology 2011, 5:11
  6. ↑ 6.0 6.1 Kaufmann GF, Sartorio R, Lee SH, Rogers CJ, Meijler MM, Moss JA, Clapham B, Brogan AP, Dickerson TJ, Janda KD. Revisiting quorum sensing: Discovery of additional chemical and biological functions for 3-oxo-N-acylhomoserine lactones. Proc Natl Acad Sci U S A. 2005;102(2):309-14.
  7. ↑ S. Basu, Y. Gerchman, C. H. Collins, F. H. Arnold & R. Weiss. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130-1134, 2005
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