This also provides the means for obtaining reduced networks from a given network by excluding the reactions that are not included in the flux configurations with a chosen cut-off value.
It can be shown by computing the corresponding constrained dense and sparse realizations, that excluding the reactions X5 → X3 + X5, X4 → X3 + X4, X2 + X3 → X3 + X5, and X3 + X1 → X3 + X4 is enough to make the reaction structure unique that is identical to the original structure shown in Figure 4.
The other subjects, these subjects did not care the ionization tendency of materials in the pre-test, did not use such category, but they calibrated their answers to exclude the reaction with only high ionization tendency metals.
Based on the flux configuration in Figure 15, we designed a reduced network, which excludes the reactions 6 and 8. From 20 simulations that we performed with this network, two simulations provided flux configurations with identical structures with the cut-off value 0.2 at the time interval 0 to 290 when compared with the flux configurations of the complete network.
Finally, when excluding the transport reactions and focusing on the reactions corresponding to the remaining entry points of the different pathways (44.7%% of all macrophage reactions) we also see an enrichment for the high regulatory load genes (51.6 % of high regulatory load reactions), although with clearly higher p-value (KS-test, p-value = 0.0839).
Appropriate negative controls were performed by incubating the specimens with only secondary antibodies, for excluding the nonspecific reaction.
Interestingly, in both Bref-PKS and Fma-PKS, the extra ketide(s) that form as a result of excluding the TH in the reaction were completely processed by the available reduction domains.
The RNA-degradation reaction mixture was set up in a volume excluding the RNA substrate in the reaction buffer D [22.2 mM Tris.
However, during the developmental stages of germination, all reactions, excluding the Indole-3-acetonitrile nitrilase (Additional file 4: Figure S2A reaction-9) catalyzed reaction (Additional file 4: Figure S2C, 'Other'-aerobic germination study) show induced gene expression.
Genomic DNA (1.5-3 μg) was sheared to 2 4 kb fragments using a Covaris S2 instrument (Covaris, Woburn, MA) and added to a mixture that included all the components of the PCR reaction excluding the primers.
