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SUMMARY:Issues in Flux Balance Analysis - Fell\, D (Oxford Brookes Univers
 ity)
DTSTART:20141104T103500Z
DTEND:20141104T105000Z
UID:TALK55930@talks.cam.ac.uk
CONTACT:Mustapha Amrani
DESCRIPTION:Co-authors: Mark Poolman (Oxford Brookes University)\, Hassan 
 Hartman (Oxford Brookes University) \n\nAs the practice of genome scale me
 tabolic modelling by FBA has become more widespread\, certain procedures a
 nd assumptions have been automatically adopted\, almost as a standard\, wh
 ereas their utility and applicability should be assessed for each specific
  model and investigation. In addition\, there are some recurrent biochemic
 al errors that are not always being filtered out.\n \nAmongst the procedur
 es not being given sufficient thought are: 1. Optimisation by maximisation
  or minimisation? Maximisation is generally adopted even though the way th
 at the linear programming algorithm operates results in artefacts in the s
 olutions that are not present on minimisation and that require post-proces
 sing to remove. 2. Expressing the biomass formation as a pseudo-reaction w
 ith non-integer stoichiometry or as part of the constraints in the analysi
 s. Again the former is more general even though it is almost impossible to
  ensure it is correctly stoichiometrically balanced and feasible. 3. Subst
 rate consumption for non-growth associated cell maintenance is for ATP gen
 eration. We have shown that part of this extra substrate consumption in Ar
 abidopsis cells is for NADPH\, presumably to combat oxidative damage\, and
  this has consequences for the predicted fluxes in central carbon metaboli
 sm.\n\nRecurrent errors include: 1. Writing enzyme prosthetic groups as su
 bstrates and products of enzyme reactions. FAD and FADH    are the most fr
 equent culprits. This creates pool metabolites that could generate spuriou
 s redox interactions across the network that will not exist because these 
 groups are contained and recycled entirely within the enzyme reaction. 2. 
 ATP from nothing. There are published models that can generate the ATP to 
 satisfy maintenance requirements without any flows into the metabolic netw
 ork from external material. Needless to say\, all subsequent analysis of s
 uch a model is valueless. Preventing this is an elementary reality check d
 uring model construction.\n
LOCATION:Seminar Room 1\, Newton Institute
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