User:Daniela A. Garcia S./Notebook/Modeling 2011 UNAM Genomics-Mexico/2011/04/01

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Supplementary Appendix 1: FBA Primer
Metabolic Network Reconstruction
 * In the absence of kinetic information it is still possible to accurately assess the theoretical capabilities and operative modes of metabolic systems using metabolic flux balance analysis (FBA.
 * FBA only requires information regarding the stoichiometry of metabolic pathways and the metabolic demands; furthermore, FBA can incorporate additional information when it is available. FBA is particularly applicable for post-genomic analysis, because the stoichiometric parameters can be defined from the annotated genome sequence).
 * First step toward reconstructing the metabolic network is to identify the coding regions or open reading frames (ORFs) within a genomic sequence.
 * |E. coli reactions

Matlab Bibliography
It was needed to install a different solver glpx, but initCobraToolbox still shows warnings. However once downloading the |Core E.coli Model it is possible to follow the Tutorial: What is flux balance analysis?, Supplementary Tutorial
 * COBRAToolbox

Tutorial
| COBRAToolbox |COBRAToolbox_Palsson


 * Calculating growth rates

model = changeRxnBounds(model,'EX_glc(e)',-18.5,'l');

model = changeRxnBounds(model,'EX_o2(e)',-1000,'l');

model = changeObjective(model,'Biomass_Ecoli_core_w_GAM');

FBAsolution = optimizeCbModel(model,'max');

.f, solution of the objetive function

.x, steady state vector

changeRxnBounds Change upper or lower bounds of a reaction or a set of

Exchange reactions are written as export reactions

changeObjetive Changes the objective function of a constraint-based model

optimizeCbModel Solve a flux balance analysis problem

Flux maps were drawn using SimPheny

FBA can predict if it is possible for the organism to grown under a specific set of constrains depending in the bounds fixed. ''The maximum amount of ATP that can be produced from this amount of succinate is less than the minimum bound of 8.39 mmol gDW-1 hr-1 of the ATP maintenance reaction, ATPM, there is no feasible solution...The growth rates are all much lower anaerobically (0 hr-1 in most cases) because the electron transport chain cannot be used to fully oxidize the substrates and generate as much ATP. ''
 * Growth on alternate substrates

model = changeRxnBounds(model,'EX_glc(e)',-1,'b');
 * Production of cofactors and biomass precursors

model = changeObjective(model,'ATPM');

model = changeRxnBounds(model,'ATPM',0,'l');

FBAsolution = optimizeCbModel(model,'max');

''ATPM is a stoichiometrically balanced reaction that hydrolyzes ATP (atp[c])and produces ADP (adp[c]), inorganic phosphate (pi[c]), and a proton (h[c]). It works as an objective for maximizing ATP production'''

Other

 * Rhizobium etli Genetically Engineered for the Heterologous Expression of Vitreoscilla sp. Hemoglobin: Effects on Free-Living and Symbiosis
 * Construction plasmid pMR4


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