Degradation of C

The SCB protein (C) degrades.

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	Remarks-Reference
$d_{C}$	$0-0.001$	$min^{-1}$	$6.7 \cdot 10^{-5} s^{-1}$ (Range tested: $0-2 \cdot 10^{-4} s^{-1}$) (Bistability range: $0-0.0085 s^{-1}$ and $6.7 \cdot 10^{-6}-6.7 \cdot 10^{-3} s^{-1}$)	In a study on global analysis of mRNA decay in gram positive bacteria by RNA-Seq, Kristoffersen et al. reported a range of values for the half-life ($t_{1/2}$) of mRNA in B. cereus between $1.9-5.6 min$, with a median of $2.4 min$. From these values we calculated the mRNA degradation rate of scbR as per $d_{mR}= \frac{ln(2)}{t_{1/2}}$, which resulted in a degradation rate constant value range $0.124-0.365 min^{-1}$ and a median $0.29 min^{-1}$. Kristoffersen et al. 2012 Additionally, in a book on biological and biochemical aspects of Actinomycetes, Ortiz-Ortiz et al. reported a range of mRNA degradation rates for Streptomyces antibioticus spores between $4-22.5 min$. By the same calculations, the corresponding mRNA degradation rate constants are in the range $0.031-0.17 min^{-1}$. Ortiz-Ortiz et al. 1984

Name	Value	Units	Origin	Remarks
$d_{C}$	$0-0.001$	$min^{-1}$	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)

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:

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The location and scale parameters of the distribution are:

Parameter	μ	σ
$d_{C}$	$-8.4046$	$0.3356$