当前位置： SCI文献检索 > MATHEMATICAL BIOSCIENCES期刊下所有文献 > Strategies for representing metabolic pathways within biochemical systems theory: reversible pathways.

Strategies for representing metabolic pathways within biochemical systems theory: reversible pathways.

Abstract：

:The search for systematic methods to deal with the integrated behavior of complex biochemical systems has over the past two decades led to the proposal of several theories of biochemical systems. Among the most promising is biochemical systems theory (BST). Recent comparisons of this theory with several others that have recently been proposed have demonstrated that all are variants of BST and share a common underlying formalism. Hence, the different variants can be precisely related and ranked according to their completeness and operational utility. The original and most fruitful variant within BST is based on a particular representation, called an S-system (for synergistic and saturable systems), that exhibits many advantages not found among alternative representations. Even within the preferred S-system representation there are options, depending on the method of aggregating fluxes, that become especially apparent when one considers reversible pathways. In this paper we focus on the paradigm situation and clearly distinguish the two most common strategies for generating an S-system representation. The first is called the "reversible" strategy because it involves aggregating incoming fluxes separately from outgoing fluxes for each metabolite to define a net flux that can be positive, negative, or zero. The second is the "irreversible" strategy, which involves aggregating forward and reverse fluxes through each reaction to define a net flux that is always positive. This second strategy has been used almost exclusively in all variants of BST. The principal results of detailed analyses are the following: (1) All S-system representations predict the same changes in dependent concentrations for a given change in an independent concentration. (2) The reversible strategy is superior to the irreversible on the basis of several criteria, including accuracy in predicting steady-state flux, accuracy in predicting transient responses, and robustness of representation. (3) Only the reversible strategy yields a representation that is able to capture the characteristic feature of amphibolic pathways, namely, the reversal of nets flux under physiological conditions. Finally, the results document the wide range of variation over which the S-system representation can accurately predict the behavior of intact biochemical systems and confirm similar results of earlier studies [Voit and Savageau, Biochemistry 26: 6869-6880 (1987)].

journal_name

Math Biosci

journal_title

Mathematical biosciences

authors

Sorribas A,Savageau MA

doi

10.1016/0025-5564(89)90066-7

subject

Has Abstract

pub_date

1989-06-01 00:00:00

pages

239-69

issue

2

eissn

0025-5564

issn

1879-3134

pii

0025-5564(89)90066-7

journal_volume

94

pub_type

杂志文章,评审

相关文献

MATHEMATICAL BIOSCIENCES文献大全
  • A competition model for viral inhibition of host cell proliferation.

    abstract：:Some viruses encode proteins that promote cell proliferation while others, such as the human immunodeficiency virus (HIV), encode proteins that prevent cell division. It has been hypothesized that the selective advantage determining which strategy evolves depends on the ability of the virus to induce a cellular enviro...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/s0025-5564(00)00020-1

    authors： Holtea S,Emerman M

    更新日期：2000-07-01 00:00:00

  • Evolution of natal dispersal in spatially heterogenous environments.

    abstract：:Understanding the evolution of dispersal is an important issue in evolutionary ecology. For continuous time models in which individuals disperse throughout their lifetime, it has been shown that a balanced dispersal strategy, which results in an ideal free distribution, is evolutionary stable in spatially varying but ...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2016.11.003

    authors： Cantrell RS,Cosner C,Lou Y,Schreiber SJ

    更新日期：2017-01-01 00:00:00

  • Some exact solutions of a generalized Fisher equation related to the problem of biological invasion.

    abstract：:The problem of biological invasion in a model single-species community is considered, the spatiotemporal dynamics of the system being described by a modified Fisher equation. For a special case, we obtain an exact solution describing self-similar growth of the initially inhabited domain. By comparison with numerical s...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/s0025-5564(01)00068-2

    authors： Petrovskii S,Shigesada N

    更新日期：2001-08-01 00:00:00

  • A new five-parameter Birnbaum-Saunders distribution for modeling bicoid gene expression data.

    abstract：:An extended version of Birnbaum-Saunders distribution with five parameters is introduced. Theoretical aspects of five-parameter Birnbaum-Saunders distribution and the maximum likelihood estimation of parameters are presented. The reliability and applicability of the proposed distribution is evaluated using both simula...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2019.108275

    authors： Hassani H,Kalantari M,Entezarian MR

    更新日期：2020-01-01 00:00:00

  • Using the EM algorithm to weight data sets of unknown precision when modelling fish stocks.

    abstract：:Stocks of commercial fish are often modelled using sampling data of various types, of unknown precision, and from various sources assumed independent. We want each set to contribute to estimates of the parameters in relation to its precision and goodness of fit with the model. Iterative re-weighting of the sets is pro...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2004.03.001

    authors： Cotter AJ,Buckland ST

    更新日期：2004-07-01 00:00:00

  • Evaluating spread of invaders from gravity scores--a way of using gravity models in ecology.

    abstract：:This study is a theoretical excursion into gravity models and their usability in evaluating importance of spatial structure and population development for the spread of colonizing organisms. A so called "gravity score" for sites is deduced, and such a score could be used for predicting risk of colonization once one si...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2009.08.008

    authors： Järemo J

    更新日期：2009-11-01 00:00:00

  • Comparing methods to quantify experimental transmission of infectious agents.

    abstract：:Transmission of an infectious agent can be quantified from experimental data using the transient-state (TS) algorithm. The TS algorithm is based on the stochastic SIR model and provides a time-dependent probability distribution over the number of infected individuals during an epidemic, with no need for the experiment...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2007.04.009

    authors： Velthuis AG,De Jong MC,De Bree J

    更新日期：2007-11-01 00:00:00

  • Stochastic models for the spread of HIV in a mobile heterosexual population.

    abstract：:An important factor in the dynamic transmission of HIV is the mobility of the population. We formulate various stochastic models for the spread of HIV in a heterosexual mobile population, under the assumptions of constant and varying population sizes. We also derive deterministic and diffusion analogues for these mode...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2006.09.024

    authors： Sani A,Kroese DP,Pollett PK

    更新日期：2007-07-01 00:00:00

  • The basic reproduction number and the probability of extinction for a dynamic epidemic model.

    abstract：:We consider the spread of an epidemic through a population divided into n sub-populations, in which individuals move between populations according to a Markov transition matrix Σ and infectives can only make infectious contacts with members of their current population. Expressions for the basic reproduction number, R₀...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2012.01.002

    authors： Neal P

    更新日期：2012-03-01 00:00:00

  • On global and local critical points of extended contact process on homogeneous trees.

    abstract：:We study spatial stochastic epidemic models called households models. The households models have more than two states at each vertex of a graph in contrast to the contact process. We show that, in the households models on trees, two thresholds of infection rates characterize epidemics. The global critical infection ra...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2008.02.004

    authors： Sugimine N,Masuda N,Konno N,Aihara K

    更新日期：2008-05-01 00:00:00

  • Evaluating treatment of hepatitis C for hemolytic anemia management.

    abstract：:The combination therapy of antiviral peg-interferon and ribavirin has evolved as one of the better treatments for hepatitis C. In spite of its success in controlling hepatitis C infection, it has also been associated with treatment-related adverse side effects. The most common and life threatening among them is hemoly...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2010.02.005

    authors： DebRoy S,Kribs-Zaleta C,Mubayi A,Cardona-Meléndez GM,Medina-Rios L,Kang M,Diaz E

    更新日期：2010-06-01 00:00:00

  • An epidemic model with fatal risk.

    abstract：:A new epidemic model is developed that describes the spread of an infectious disease with fatal risk. The model includes as extreme cases the standard general epidemic process (for diseases that confer immunity after infection) and the fatal epidemic process (for diseases that lead inevitably to death). Both determini...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/0025-5564(93)90019-7

    authors： Lefèvre C,Picard P

    更新日期：1993-09-01 00:00:00

  • Multi-gene-loci inheritance in resistance modeling.

    abstract：:The ability of an organism to degrade harmful substances to less toxic compounds is referred to as metabolic resistance. The biochemical processes result in a shift of dose-response curves associated with the toxic substances. Hence, the development of metabolic resistance may cause great problems of managing pests an...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2012.11.010

    authors： Langemann D,Richter O,Vollrath A

    更新日期：2013-03-01 00:00:00

  • Closed-loop stability of pharmacokinetic-pharmacodynamic models.

    abstract：:In automatic feedback control of intravenous drug infusions, convergence to the setpoint is an important objective. This paper examines the stability of pharmacokinetic-pharmacodynamic models of patient response regulated with proportional integral feedback. The model consists of three components: linear compartmental...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/s0025-5564(97)00076-x

    authors： Wada DR

    更新日期：1997-12-01 00:00:00

  • Growth of necrotic tumors in the presence and absence of inhibitors.

    abstract：:A mathematical model is presented for the growth of a multicellular spheroid that comprises a central core of necrotic cells surrounded by an outer annulus of proliferating cells. The model distinguishes two mechanisms for cell loss: apoptosis and necrosis. Cell loss due to apoptosis is defined to be programmed cell d...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/0025-5564(96)00023-5

    authors： Byrne HM,Chaplin MA

    更新日期：1996-07-15 00:00:00

  • The influence of soluble fragments of extracellular matrix (ECM) on tumor growth and morphology.

    abstract：:A major challenge in matrix-metalloproteinase (MMP) target validation and MMP-inhibitor-drug development for anti-cancer clinical trials is to better understand their complex roles (often competing with each other) in tumor progression. While there is extensive research on the growth-promoting effects of MMPs, the gro...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2017.11.014

    authors： Nargis NN,Aldredge RC,Guy RD

    更新日期：2018-02-01 00:00:00

  • A geometrical model for diffusion of hydrophilic compounds in human stratum corneum.

    abstract：:A three-dimensional diffusion model with either hexagonal or cylindrical symmetry has been constructed to simulate desorption profiles of hydrophilic chemicals from the topmost layer of human skin (the stratum corneum) as measured in ex vivo studies. The tissue is pierced by skin appendages - sweat glands and hair fol...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2018.03.010

    authors： Yu F,Kasting GB

    更新日期：2018-06-01 00:00:00

  • Habitat destruction, habitat restoration and eigenvector-eigenvalue relations.

    abstract：:According to metapopulation theory, the capacity of a habitat patch network to support the persistence of a species is measured by the metapopulation capacity of the patch network. Mathematically, metapopulation capacity is given by the leading eigenvalue lambda(M) of an appropriately constructed non-negative n x n ma...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/s0025-5564(02)00150-5

    authors： Ovaskainen O

    更新日期：2003-02-01 00:00:00

  • The optimal strategy for brood-parasitism: how many eggs should be laid in the host's nest?

    abstract：:We consider the optimal strategy for intra-specific brood-parasitism, especially with respect to the number of eggs laid by the parasitic individual in the nest of non-parasitic individual, in particular, a host that does not reject the parasite's eggs. With a fundamental mathematical model, assuming that the survival...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/s0025-5564(99)00037-1

    authors： Maruyama J,Seno H

    更新日期：1999-10-01 00:00:00

  • Mean and quasideterministic equivalence for linear stochastic dynamics.

    abstract：:In linear, stochastic dynamics it is shown that the quasideterministic population size is equivalent to the mean population size. The quasideterministic dynamics are defined by the conditional infinitesimal mean of the process. The stochastic component of the dynamics includes both Gaussian and Poisson white noise, wi...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/0025-5564(89)90010-2

    authors： Hanson FB,Ryan D

    更新日期：1989-03-01 00:00:00

  • Stability and backward bifurcation in a malaria transmission model with applications to the control of malaria in China.

    abstract：:In this paper, we consider a deterministic malaria transmission model with standard incidence rate and treatment. Human population is divided into susceptible, infectious and recovered subclasses, and mosquito population is split into susceptible and infectious classes. It is assumed that, among individuals with malar...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2015.05.005

    authors： Feng X,Ruan S,Teng Z,Wang K

    更新日期：2015-08-01 00:00:00

  • Heterogeneity in dynamic species abundance models: the selective effect of extinction processes.

    abstract：:There is often large variation in traits across the species of a community. In particular, variation in life history traits affecting population dynamics is likely to affect the species abundance distribution. Applying a dynamic and heterogeneous species abundance model we study how differences in extinction time for ...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2007.06.002

    authors： Engen S

    更新日期：2007-12-01 00:00:00

  • Spread of excitation in 3-D models of the anisotropic cardiac tissue. III. Effects of ventricular geometry and fiber structure on the potential distribution.

    abstract：:In a previous paper we studied the spread of excitation in a simplified model of the left ventricle, affected by fiber structure and obliqueness, curvature of the wall and Purkinje network. In the present paper we investigate the extracellular potential distribution u in the same ventricular model. Given the transmemb...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/s0025-5564(98)10004-4

    authors： Colli Franzone P,Guerri L,Pennacchio M,Taccardi B

    更新日期：1998-07-01 00:00:00

  • Strain driven transport for bone modeling at the periosteal surface.

    abstract：:Bone modeling and remodeling has been the subject of extensive experimental studies. There have been several mathematical models proposed to explain the observed behavior, as well. A different approach is taken here in which the bone is treated from a macroscopic view point. In this investigation, a one-dimensional an...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2010.12.008

    authors： Banks-Sills L,Ståhle P,Svensson I,Eliaz N

    更新日期：2011-03-01 00:00:00

  • Closure operations in phylogenetics.

    abstract：:Closure operations are a useful device in both the theory and practice of tree reconstruction in biology and other areas of classification. These operations take a collection of trees (rooted or unrooted) that classify overlapping sets of objects at their leaves, and infer further tree-like relationships. In this pape...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2006.11.005

    authors： Grünewald S,Steel M,Swenson MS

    更新日期：2007-08-01 00:00:00

  • Yule-generated trees constrained by node imbalance.

    abstract：:The Yule process generates a class of binary trees which is fundamental to population genetic models and other applications in evolutionary biology. In this paper, we introduce a family of sub-classes of ranked trees, called Ω-trees, which are characterized by imbalance of internal nodes. The degree of imbalance is de...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2013.08.008

    authors： Disanto F,Schlizio A,Wiehe T

    更新日期：2013-11-01 00:00:00

  • Analysis of a compartmental model of amyloid beta production, irreversible loss and exchange in humans.

    abstract：:Amyloid beta (Aβ) peptides, and in particular Aβ42, are found in senile plaques associated with Alzheimer's disease. A compartmental model of Aβ production, exchange and irreversible loss was recently developed to explain the kinetics of isotope-labeling of Aβ peptides collected in cerebrospinal fluid (CSF) following ...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2014.11.004

    authors： Elbert DL,Patterson BW,Bateman RJ

    更新日期：2015-03-01 00:00:00

  • Effect of non-well-mixed compartment and bulk flow on diffusion through a pore.

    abstract：:The assumptions of well-mixed and zero bulk flow in compartmental analysis are reexamined. Using Poiseuille flow inside and radial flow outside a pore, the mass-transfer equations are solved by perturbations on simple diffusion. Formulas are obtained for solute distribution, total mass transfer, and apparent permeabil...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/0025-5564(89)90054-0

    authors： Wang CY

    更新日期：1989-07-01 00:00:00

  • Material modeling of biofilm mechanical properties.

    abstract：:A biofilm material model and a procedure for numerical integration are developed in this article. They enable calculation of a composite Young's modulus that varies in the biofilm and evolves with deformation. The biofilm-material model makes it possible to introduce a modeling example, produced by the Unified Multi-C...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2014.02.007

    authors： Laspidou CS,Spyrou LA,Aravas N,Rittmann BE

    更新日期：2014-05-01 00:00:00

  • Crossover in spreading behavior due to memory in population dynamics.

    abstract：:The reaction-diffusion equation is one of the possible ways for modeling animal movement, where the reactive part stands for the population growth and the diffusive part for random dispersal of the population. However, a reaction-diffusion model may not represent all aspects of the spatial dynamics, because of the exi...

    journal_title：Mathematical biosciences

    pub_type： 杂志文章

    doi：10.1016/j.mbs.2020.108346

    authors： Oliveira KA,Berbert JM

    更新日期：2020-06-01 00:00:00