Redesigning metabolic networks using mathematical programming

Abstract:

:The design of new generation bioprocessing plants is increasingly dependent on the design of process-compatible microorganisms. The latter, whether through genetic or physiological manipulations, can be greatly assisted by metabolic engineering. An emerging powerful tool in metabolic engineering research is computer-assisted cell design using mathematical programming. In this work, the problem of optimizing cellular metabolic networks has been formulated as a Mixed Integer Nonlinear Programming (MINLP) model. The model can assist genetic engineers to identify which cellular enzymes should be modified, and the new levels of activity required to produce an optimal network. Results are presented from the tricarboxylic acid cycle in Dictyostelium discoideum. Copyright 1998 John Wiley & Sons, Inc.

journal_name

Biotechnol Bioeng

authors

Dean JP,Dervakos GA

doi

10.1002/(sici)1097-0290(19980420)58:2/3<267::aid-b

subject

Has Abstract

pub_date

1998-04-05 00:00:00

pages

267-71

issue

2-3

eissn

0006-3592

issn

1097-0290

pii

10.1002/(SICI)1097-0290(19980420)58:2/3<267::AID-B

journal_volume

58

pub_type

杂志文章
  • Lewis cell studies to determine reactor design data for two-liquid-phase bacterial and enzymic reactions.

    abstract::Substrate transfer rates from organic to aqueous phases were measured in the presence and absence of biocatalyst in the reaction medium, using modified Lewis cells. These measurements, in combination with intrinsic aqueous phase biocatalytic reaction kinetics, were used to confirm that benzyl acetate hydrolysis by pig...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260370207

    authors: Woodley JM,Brazier AJ,Lilly MD

    更新日期:1991-01-20 00:00:00

  • Novel non-viral vectors for gene delivery: synthesis of a second-generation library of mono-functionalized poly-(guanidinium)amines and their introduction into cationic lipids.

    abstract::The development of new gene delivery technologies is a prerequisite towards gene therapy clinical trials. Because gene delivery mediated by viral vectors remains of limited scope due to immunological and propagation risks, the development of new non-viral gene delivery systems is of crucial importance. We have synthes...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:

    authors: Byk G,Soto J,Mattler C,Frederic M,Scherman D

    更新日期:1998-04-01 00:00:00

  • On-column refolding of recombinant human interferon-gamma inclusion bodies by expanded bed adsorption chromatography.

    abstract::A refolding strategy was described for on-column refolding of recombinant human interferon-gamma (rhIFN-gamma) inclusion bodies by expanded bed adsorption (EBA) chromatography. After the denatured rhIFN-gamma protein bound onto the cation exchanger of STREAMLINE SP, the refolding process was performed in expanded bed ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20763

    authors: Jin T,Guan YX,Yao SJ,Lin DQ,Cho MG

    更新日期:2006-03-05 00:00:00

  • Morphology of Trichoderma reesei QM 9414 in submerged cultures.

    abstract::The microscopic morphology of Trichoderma reesei QM 9414, growing in submerged culture, was studied by image analysis. The morphology was characterized by the total hyphal length, the total number of tips, the number of actively growing tips, and the length of the main hypha. To describe the growth of a single myceliu...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260470513

    authors: Lejeune R,Nielsen J,Baron GV

    更新日期:1995-09-05 00:00:00

  • Ethene removal from a synthetic waste gas using a dry biobed.

    abstract::A packed granular activated carbon (GAC) biobed, inoculated with the ethane-degrading strain Mycobacterium E3, was used to study ethene removal from a synthetic waste gas. Ethene, for which the dimensionless partition coefficient for an air-water system at 20 degrees C is about 7.6, was used as a model compound for po...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260440511

    authors: De Heyder B,Overmeire A,Van Langenhove H,Verstraete W

    更新日期:1994-08-20 00:00:00

  • Metabolic engineering of acid resistance elements to improve acid resistance and propionic acid production of Propionibacterium jensenii.

    abstract::Propionic acid (PA) and its salts are widely used in the food, pharmaceutical, and chemical industries. Microbial production of PA by propionibacteria is a typical product-inhibited process, and acid resistance is crucial in the improvement of PA titers and productivity. We previously identified two key acid resistanc...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.25902

    authors: Guan N,Li J,Shin HD,Du G,Chen J,Liu L

    更新日期:2016-06-01 00:00:00

  • A cell adhesion peptide from foot-and-mouth disease virus can direct cell targeted delivery of a functional enzyme.

    abstract::The G-H loop of foot-and-mouth disease virus is a disordered protrusion of the VP1 protein exposed on the virion surface. This short stretch includes an arginine-glycine-aspartic acid tripeptide, a recognized integrin-binding motif, which is responsible for cell attachment and infection. Eight copies of a peptide repr...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0290(19980805)59:3<294::aid-bit

    authors: Villaverde A,Feliu JX,Arís A,Harbottle RP,Benito A,Coutelle C

    更新日期:1998-08-05 00:00:00

  • Dynamic tradeoffs in the raft-mediated entry of human immunodeficiency virus type 1 into cells.

    abstract::To initiate an infection human immunodeficiency virus type 1 (HIV-1) particles must first bind to receptors on the surface of their host cells, a process that eventually leads to fusion of viral and cellular membranes and release of the viral genome into the cytoplasm. Understanding the molecular mechanisms of these p...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20680

    authors: Lim KI,Yin J

    更新日期:2006-02-05 00:00:00

  • Efficient production of poly γ-d-glutamic acid from the bloom-forming green macroalgae, Ulva sp., by Bacillus sp. SJ-10.

    abstract::Numerous studies on poly γ-d-glutamicacid (γ-PGA) production have investigated terrestrial renewable sources for reducing production costs, but there are no studies using waste marine resources so far. We aimed to develop a cost-effective production method of γ-d-PGA by Bacillus sp. SJ-10 using green macroalgae (Ulva ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.26966

    authors: Kim JH,Lee JM,Jang WJ,Park HD,Kim YO,Kim CH,Kong IS

    更新日期:2019-07-01 00:00:00

  • Synthesis of 3-tert-butylcatechol by an engineered monooxygenase.

    abstract::Recombinant Escherichia coli JM101 was used for the in vivo biocatalytic synthesis of 3-tert-butyl- catechol. The bacterial strain synthesized the laboratory-evolved variant HbpA(T2) of 2-hydroxybiphenyl 3-monooxygenase (HbpA, EC 1.14.13.44) from Pseudomonas azelaica HBP1. The mutant enzyme HbpA(T2) is able to hydroxy...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10487

    authors: Meyer A,Held M,Schmid A,Kohler HP,Witholt B

    更新日期:2003-03-05 00:00:00

  • A novel population balance model to investigate the kinetics of in vitro cell proliferation: part I. Model development.

    abstract::In biotechnology and biomedicine reliable models of cell proliferation kinetics need to capture the relevant phenomena taking place during the mitotic cycle. To this aim, a novel mathematical model helpful to investigate the intrinsic kinetics of in vitro culture of adherent cells up to confluence is proposed in this ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.24351

    authors: Fadda S,Cincotti A,Cao G

    更新日期:2012-03-01 00:00:00

  • Physiological, biochemical, and mathematical studies of micro-aerobic continuous ethanol fermentation by Saccharomyces cerevisiae. II: intracellular metabolite and enzyme assays at steady state chemostat cultures.

    abstract::Intracellular metabolite concentration and enzyme activity measurements were made to explain the new metabolic and growth phenomena seen in the micro-aerobic, continuous yeast cultures described in Part I. The results of these assays suggested mechanisms for the observed maximum in the specific ethanol productivity as...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260361007

    authors: Grosz R,Stephanopoulos G

    更新日期:1990-12-05 00:00:00

  • Surface transformation of bioactive glass in bioreactors simulating microgravity conditions. Part I: experimental study.

    abstract::Surface modified bioactive glass with surface properties akin to those of the bone mineral phase is an attractive candidate for use as a microcarrier material for 3-D growth of bone-like tissue in rotating wall vessel bioreactors (RWVs). The critical surface properties of this material are the result of reaction in so...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10023

    authors: Radin S,Ducheyne P,Ayyaswamy PS,Gao H

    更新日期:2001-11-05 00:00:00

  • H2 production by photofermentation in an innovative plate-type photobioreactor with meandering channels.

    abstract::Hydrogen production by Rhodobacter capsulatus is an anaerobic, photobiological process requiring specific mixing conditions. In this study, an innovative design of a photobioreactor is proposed. The design is based on a plate-type photobioreactor with an interconnected meandering channel to allow culture mixing and H2...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.27656

    authors: Turon V,Ollivier S,Cwicklinski G,Willison JC,Anxionnaz-Minvielle Z

    更新日期:2020-12-15 00:00:00

  • Algal autoflocculation--verification and proposed mechanism.

    abstract::Biomass autoflocculation in outdoor algal cultures was found to be associated with increases of culture pH levels, due to CO(2) consumption by the algal photosynthetic activity. Under these alkaline conditions, some medium chemical ions precipitated together with the algal biomass. The chemical substances involved wit...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260260206

    authors: Sukenik A,Shelef G

    更新日期:1984-02-01 00:00:00

  • Fluid mechanics of a spinner-flask bioreactor.

    abstract::Spinner-flask bioreactors have been used for the production of articular cartilage in vitro. The dynamic environment within bioreactors is known to significantly affect the growth and development of the tissue. The present research focuses on the experimental and numerical characterization of the flow field within a s...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10788

    authors: Sucosky P,Osorio DF,Brown JB,Neitzel GP

    更新日期:2004-01-05 00:00:00

  • Electric field control of lipase membrane activity.

    abstract::Lipase (EC 3.1.1.3., from Pseudomonas sp.) was entrapped in collagen membrane containing liquid crystal (4-methoxybenzilidene-4'-n-butylaniline). The activity of the lipase-liquid crystal membrane at an applied voltage of 4 V was 3.4 compared to a membrane tested without imposition of an external electric field. A lin...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260191007

    authors: Karube I,Yugeta Y,Suzuki S

    更新日期:1977-10-01 00:00:00

  • Suggestions for the operation of radial flow cells in cell adhesion and biofouling studies.

    abstract::An analysis of the radial flow cell is presented to show that the assumption of creeping laminar flow should be used cautiously. Simple models which account for the influence of fluid inertial forces over most of the width of the plate are reviewed. A modified Reynolds number is introduced which may be used to test th...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260270407

    authors: Fryer PJ,Slater NK,Duddridge JE

    更新日期:1985-04-01 00:00:00

  • Introduction of glycine synthase enables uptake of exogenous formate and strongly impacts the metabolism in Clostridium pasteurianum.

    abstract::Autotrophic or mixotrophic use of one-carbon (C1) compounds is gaining importance for sustainable bioproduction. In an effort to integrate the reductive glycine pathway (rGP) as a highly promising pathway for the assimilation of CO2 and formate, genes coding for glycine synthase system from Gottschalkia acidurici were...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.27658

    authors: Hong Y,Arbter P,Wang W,Rojas LN,Zeng AP

    更新日期:2020-12-17 00:00:00

  • Shikimic acid production by a modified strain of E. coli (W3110.shik1) under phosphate-limited and carbon-limited conditions.

    abstract::Shikimic acid is one of several industrially interesting chiral starting materials formed in the aromatic amino acid pathway of plants and microorganisms. In this study, the physiology of a shikimic acid producing strain of Escherichia coli (derived from W3110) deleted in aroL (shikimic acid kinase II gene), was compa...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20546

    authors: Johansson L,Lindskog A,Silfversparre G,Cimander C,Nielsen KF,Lidén G

    更新日期:2005-12-05 00:00:00

  • Fractionating recalcitrant lignocellulose at modest reaction conditions.

    abstract::Effectively releasing the locked polysaccharides from recalcitrant lignocellulose to fermentable sugars is among the greatest technical and economic barriers to the realization of lignocellulose biorefineries because leading lignocellulose pre-treatment technologies suffer from low sugar yields, and/or severe reaction...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.21386

    authors: Zhang YH,Ding SY,Mielenz JR,Cui JB,Elander RT,Laser M,Himmel ME,McMillan JR,Lynd LR

    更新日期:2007-06-01 00:00:00

  • Effects of heat shock on the production of human erythropoietin from recombinant CHO cells.

    abstract::The production of recombinant proteins by mammalian cells demands a highly controlled environment for cell cultivation. Temperature stress represents a commonly encountered disturbance in both research and process environments. In this study, we examined the effects of heat shock on the expression of recombinant human...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260401008

    authors: Tsao EI,Bohn MA,Omstead DR,Munster MJ,Numsuwan V

    更新日期:1992-12-05 00:00:00

  • Increased curvature of hollow fiber membranes could up-regulate differential functions of renal tubular cell layers.

    abstract::Tissue engineering devices as in vitro cell culture systems in scaffolds has encountered the bottleneck due to their much lower cell functions than real tissues/organs in vivo. Such situation has been improved in some extent by mimicking the cell microenvironments in vivo from either chemical or physical ways. However...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.24874

    authors: Shen C,Meng Q,Zhang G

    更新日期:2013-08-01 00:00:00

  • Measuring kLa with randomly pulsed dynamic method.

    abstract::This reports on the determination of the overall oxygen transfer coefficient in a mechanically agitated vessel using a randomly pulsed dynamic method. This method consists in exciting the system by randomly switching the inlet gas stream with air or nitrogen with an identical volumetric flow rate. A pseudo-random bina...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260370914

    authors: Gauthier L,Thibault J,LeDuy A

    更新日期:1991-04-15 00:00:00

  • Controlled regioselectivity of fatty acid oxidation by whole cells producing cytochrome P450BM-3 monooxygenase under varied dissolved oxygen concentrations.

    abstract::Utilising whole cells of recombinant Escherichia coli K27 (pCYP102, pGEc47) containing active cytochrome P450BM-3 monooxygenase [E.C. 1. 14.14.1], multiple oxidations of saturated and unsaturated fatty acids were performed by the enzyme under conditions of excess oxygen. The amount of oxygen dissolved in the culture m...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0290(19990805)64:3<333::aid-bit

    authors: Schneider S,Wubbolts MG,Oesterhelt G,Sanglard D,Witholt B

    更新日期:1999-08-05 00:00:00

  • Continuous propionic acid fermentation by immobilized Propionibacterium acidipropionici in a novel packed-bed bioreactor.

    abstract::Continuous propionic acid fermentations of lactate by Propionibacterium acidipropionici were studied in spiral wound fibrous bed bioreactors. Cells were imobilized by natural attachment to fiber surfaces and entrapment in the void volume within the fibrous matrix. A high cell density of approximately 37 g/L was attain...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260400404

    authors: Lewis VP,Yang ST

    更新日期:1992-08-05 00:00:00

  • A process for microbial hydrocarbon synthesis: Overproduction of fatty acids in Escherichia coli and catalytic conversion to alkanes.

    abstract::The development of renewable alternatives to diesel and jet fuels is highly desirable for the heavy transportation sector, and would offer benefits over the production and use of short-chain alcohols for personal transportation. Here, we report the development of a metabolically engineered strain of Escherichia coli t...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22660

    authors: Lennen RM,Braden DJ,West RA,Dumesic JA,Pfleger BF

    更新日期:2010-06-01 00:00:00

  • Live reporting for hypoxia: Hypoxia sensor-modified mesenchymal stem cells as in vitro reporters.

    abstract::Natural oxygen gradients occur in tissues of biological organisms and also in the context of three-dimensional (3D) in vitro cultivation. Oxygen diffusion limitation and metabolic oxygen consumption by embedded cells produce areas of hypoxia in the tissue/matrix. However, reliable systems to detect oxygen gradients an...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.27503

    authors: Schmitz C,Pepelanova I,Seliktar D,Potekhina E,Belousov VV,Scheper T,Lavrentieva A

    更新日期:2020-07-15 00:00:00

  • Flotation of Streptomyces pilosus after lead accumulation.

    abstract::The flotation of Streptomyces pilosus was studied in the absence and presence of adsorbed Pb(II) ions on the cell walls and with and without using sodium dodecylsulfate (SDS) as collector. Adsorption of SDS onto the organism in the absence and presence of Pb(II) ions was also investigated. It was found that in the abs...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260371009

    authors: Sadowski Z,Golab Z,Smith RW

    更新日期:1991-04-25 00:00:00

  • Self-renaturing enzymes: design of an enzyme-chaperone chimera as a new approach to enzyme stabilization.

    abstract::Molecular chaperones in aqueous-organic mixtures can broaden the utility of biocatalysis by stabilizing enzymes in denaturing conditions. We have designed a self-renaturing enzyme-chaperone chimera consisting of penicillin amidase and a thermophilic chaperonin that functions in aqueous-organic mixtures. The flexible l...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22254

    authors: Bergeron LM,Gomez L,Whitehead TA,Clark DS

    更新日期:2009-04-01 00:00:00