To further curate the models, we performed additional BLAST OSI-027 datasheet searches [40] among the corresponding buy BTSA1 strain of Blattabacterium, other flavobacteria and E. coli K-12 available in GenBank (e-values below e-11), to incorporate reactions either absent in E. coli or undetected due to the divergence among strains. In addition, we identified functional domains by means of the interface SMART (Simple Modular Architecture Research Tool) (http://smart.emblheidelberg.de/help/smart_about.shtml) [41, 42]. Flux balance analysis (FBA) was performed using the COBRA toolbox [43], a freely available Matlab toolbox and the models were described using the Systems Biology Markup Language (SBML) [44]
(Additional Files 5 and 6). We used the biomass equation derived from the iJR904 E. coli model [37] with a few adaptations derived on updated network of such microorganism, i.e. iAF1260 [33]. In particular
we added the cofactors thiamine selleck products diphosphate and tetrahydrofolate. Additionally, we adjusted the amounts of the four different deoxynucleotide triphosphates in the biomass equation to reflect the GC content of the Blattabacterium strains (Bge, 27 mol%; Pam, 28 mol%). Furthermore, since Blattabacterium strains are unable to completely synthesize cardiolipin, glycogen, lipopolysaccharide, and spermidine, we removed these components from the biomass equation. Robustness analysis The study of network robustness was performed with the function robustnessAnalysis of the COBRA toolbox [43]. In addition, we evaluated the effect of a gene deletion experiment on cellular growth
of aminophylline the resultant mutant using the option singleGeneDeletion of the COBRA toolbox. We set to zero the upper and lower flux bounds for the reaction(s) corresponding to the simulated deleted gene. If a single gene is associated with multiple reactions, the deletion of that gene will result in the removal of all associated reactions. On the contrary, a reaction that can be catalyzed by multiple non-interacting gene products will not be removed in a single gene deletion. The possible results of a single deletion are unchanged maximal growth (non-lethal), reduced maximal growth or no growth (lethal). We simulated growth and subsequent fragility analysis with all the different sources which enhance/support biomass formation. Authors’ information CMGD: postdoctoral specialist in Microbiology and Systems Biology; EB: postdoctoral specialist in Bioinformatics, Evolutionary Genomics and Systems Biology; RPN: PhD student specialist in Genetics, ‘omics’ Sciences and Bioinformatics; AM: Full Professor of Genetics; JP: Associate Professor of Biochemistry and Molecular Biology; AL: Full Professor of Genetics. Acknowledgements Financial support was provided by grants BFU2009-12895-C02-01/BMC (Ministerio de Ciencia e Innovación, Spain) to AL and Prometeo Program (Generalitat Valenciana) to AM. Dr.
Related posts:
- A two level full factorial is performed with a model equation des
- Section 2 3 is devoted to exploring the distribution of essential
- An additional vital consideration was the availability with the P
- Both alleles were cloned into the R6K-origin
based suicid - Real-time PCR primers are listed in Additional file 1: Table S4