Difference between revisions of "Degradation of a"
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and <math>4.1 \cdot 10^{-4}-1.6 \cdot 10^{-2} s^{-1}</math><ref name="Chatterjee2011"></ref>) | and <math>4.1 \cdot 10^{-4}-1.6 \cdot 10^{-2} s^{-1}</math><ref name="Chatterjee2011"></ref>) | ||
| 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 (<math>t_1/2</math>) of mRNA in ''B. cereus'' between <math>1.9-5.6 min </math>, with a median of <math>2.4 min </math>. From these values we calculated the mRNA degradation rate of ''scbA'' as per <math>d_{mA}= /frac{ln(2)}{t_1/2}</math>, which resulted in a degradation rate constant value range <math>0.124-0.365 min^{-1} </math> and a median <math>0.29 min^{-1} </math>. | | 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 (<math>t_1/2</math>) of mRNA in ''B. cereus'' between <math>1.9-5.6 min </math>, with a median of <math>2.4 min </math>. From these values we calculated the mRNA degradation rate of ''scbA'' as per <math>d_{mA}= /frac{ln(2)}{t_1/2}</math>, which resulted in a degradation rate constant value range <math>0.124-0.365 min^{-1} </math> and a median <math>0.29 min^{-1} </math>. | ||
− | [[Image:DmR-text.png|center|thumb| | + | [[Image:DmR-text.png|center|thumb|600px|Kristoffersen et al. 2012<ref name="Kristoffersen2012"></ref>]] |
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 <math>4-22.5 min </math>. By the same calculations, the corresponding mRNA degradation rate constants are in the range <math> 0.031-0.17 min^{-1} </math>. | 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 <math>4-22.5 min </math>. By the same calculations, the corresponding mRNA degradation rate constants are in the range <math> 0.031-0.17 min^{-1} </math>. |
Revision as of 07:05, 16 October 2015
The mRNA of scbA (a) degrades.
Contents
Chemical equation
Rate equation
Parameters
The parameter of this reaction is the degradation rate of a (). The parameter values were derived from calculations of the mRNA half life in gram positive bacteria with low GC content and in Actinomycetes.
Name | Value | Units | Value in previous GBL models [1] [2] | Remarks-Reference |
---|---|---|---|---|
[3] [4] | [1]
(Range tested: ) (Bistability range: [1] and [2]) |
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 () of mRNA in B. cereus between , with a median of . From these values we calculated the mRNA degradation rate of scbA as per , which resulted in a degradation rate constant value range and a median .
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 . By the same calculations, the corresponding mRNA degradation rate constants are in the range . |
Parameters with uncertainty
The most plausible parameter value for the is decided to be and the confidence interval . This means that the mode of the PDF is 0.1785 and the range where 95% of the values are found is between and .
The probability distribution for the parameter, adjusted accordingly in order to reflect the above values, is the following:
The location and scale parameters of the distribution are:
Parameter | μ | σ |
---|---|---|
References
- ↑ 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.
- ↑ 2.0 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.
- ↑ 3.0 3.1 Kristoffersen SM, Haase C, Weil MR, et al. Global mRNA decay analysis at single nucleotide resolution reveals segmental and positional degradation patterns in a Gram-positive bacterium. Genome Biology. 2012;13(4):R30.
- ↑ 4.0 4.1 Ortiz-Ortiz, L. and Bojalil, L.F. and Yakoleff, V. Biological, Biochemical, and Biomedical Aspects of Actinomycetes. Elsevier, 1984