Rapaport, A. | Search bioRxiv

bioRxiv2023

Conic analysis of nonlinear metabolic networks

Polyhedral models of metabolic networks are computationally tractable and can predict some cellular functions. A longstanding challenge is incorporating metabolites without losing tractability. In this paper, we do so using a new second-order cone representation of the Michaelis-Menten kinetics. The resulting model consists of linear stoichiometric constraints alongside second-order cone constraints that couple the reaction fluxes to metabolite concentrations. We formulate several new problems around this model: conic flux balance analysis, which augments flux balance analysis with metabolite concentrations; dynamic conic flux balance analysis; and finding minimal cut sets of networks with both reactions and metabolites. Solving these problems yields information about both fluxes and metabolite concentrations. They are second-order cone or mixed-integer second-order cone programs, which, while not as tractable as their linear counterparts, can nonetheless be solved at practical scales using existing software.

systems biology↗

bioRxiv2020

Bacterial density as an unexpected factor regulating decomposition by soil oligotrophs

Bacterial decomposition of organic matter in soils is generally believed to be mainly controlled by the access bacteria have to their substrate. The influence of bacterial traits on this control has, however, received little attention. Here, we develop a bioreactive transport model to screen the interactive impacts of dispersion and bacterial traits on mineralization. We compare the model results with two sets of previously performed cm-scale soil-core experiments in which the mineralization of the pesticide 2,4-D was measured under well-controlled initial distributions and transport conditions. Bacterial dispersion away from the initial substrate location induced a significant increase in 2,4-D mineralization, revealing the existence of a regulation of mineralization by the bacterial decomposer density, in addition to the dilution of substrate. This regulation of degradation by density becomes dominant for bacteria with an efficient uptake of substrate at low substrate concentrations (a common feature of oligotrophs). The model output suggests that the distance between bacteria adapted to oligotrophic environments is a stronger regulator of degradation than the distance between these bacteria and the substrate initial location. Such oligotrophs, commonly found in soils, compete with each other for substrate even at remarkably low population densities. The ratio-dependent Contois growth model, which includes a density regulation in the expression of the uptake efficiency, provide a more versatile representation than the substrate-dependent Monod model in these conditions. In view of their strong interactions, bioreactive and transport processes cannot be handled independently but should be integrated, in particular when reactive processes of interest are carried out by oligotrophs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/384735v3_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@187f3f4org.highwire.dtl.DTLVardef@a14d46org.highwire.dtl.DTLVardef@1d8362aorg.highwire.dtl.DTLVardef@1cc40f8_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- The impact of spatial distributions on decomposition depends on bacterial traits - Decomposition can be reduced by competition between bacteria even at low densities - Bacterial density regulation counterbalances substrate accessibility regulation - Regulation of decomposition by bacterial density is more acute for oligotrophs

ecology↗