Survival and apoptotic pathways initiated by TNF-alpha: modeling and predictions.


:We present a mathematical model which includes TNF-alpha initiated survival and apoptotic cascades, as well as nuclear transcription of IkappaB. These pathways play a crucial role in deciding cell fate in response to inflammation and infection. Our model incorporates known specific protein-protein interactions as identified by experiments. Using these biochemical interactions, we develop a mathematical model of the NF-kappaB-mediated survival and caspase-mediated apoptosis pathways. Using mass action kinetics, we follow the formation of the survival and late complexes as well as the dynamics of DNA fragmentation. The effect of TNF-alpha concentration on DNA fragmentation is modeled and compares well with experiment. Nuclear transcription is also modeled phenomenologically by means of time lagged cytosolic concentrations. This results in transcription related concentrations undergoing under-damped oscillations, in qualitative and quantitative agreement with experiment. Using a tumor cell as a hypothetical model, we explore the interplay between the components of the survival and apoptotic pathways. Results are presented which make predictions on the limits of cellular oscillations in terms of time delay, initial concentration ratios and other features of the model. The model also makes clear predictions on cell viability in terms of DNA damage within the framework of TNF-alpha stimulus duration.


Biotechnol Bioeng


Rangamani P,Sirovich L




Has Abstract


2007-08-01 00:00:00












  • A non-chromatographic method for the removal of endotoxins from bacteriophages.

    abstract::The Ff filamentous bacteriophages show potential as a new class of therapeutics, displaying utility in materials science as well as pharmaceutical applications. These phages are produced by the infection of E. coli, a Gram-negative bacterium which unavoidably sheds endotoxins into the extracellular space during growth...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Branston SD,Wright J,Keshavarz-Moore E

    更新日期:2015-08-01 00:00:00

  • Modeling of a foamed emulsion bioreactor: II. model parametric sensitivity.

    abstract::The sensitivity of a conceptual model of a foam emulsion bioreactor (FEBR) used for the control of toluene vapors in air was examined. Model parametric sensitivity studies showed which parameters affect the removal of toluene (as model pollutant) in the FEBR the most significantly, and enabled definition of the limits...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Kan E,Deshusses MA

    更新日期:2009-02-15 00:00:00

  • Partitioning of low molecular combination peptides in aqueous two-phase systems of poly(ethylene glycol) and dextran in the presence of small amounts of K2HPO4/KH2PO4 buffer at 293 K: experimental results and predictions.

    abstract::Buffered aqueous two-phase systems are effective extraction systems for separating amphoteric hydrocarbons like, for example, polypeptides from aqueous phases. The design and basic engineering of such processes requires the knowledge of the liquid-liquid equilibrium. The study presented here aims to contribute to the ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Grossmann C,Tintinger R,Zhu J,Maurer G

    更新日期:1998-12-20 00:00:00

  • Maximizing interferon-gamma production by Chinese hamster ovary cells through temperature shift optimization: experimental and modeling.

    abstract::The Chinese hamster ovary (CHO) cell line producing interferon-gamma (IFN-gamma) exhibits a 2-fold increase in specific productivity when grown at 32 degrees C compared to 37 degrees C. Low temperature also causes growth arrest, meaning that the cell density is significantly lower at 32 degrees C, nutrients are consum...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Fox SR,Patel UA,Yap MG,Wang DI

    更新日期:2004-01-20 00:00:00

  • Sustained and constitutive high levels of protein production in continuous cultures of bacillus subtilis.

    abstract::The feasibility of continuous production of proteins in chemostat cultures of Bacillus subtilis was investigated. An expression system consisting of the bacterium B. subtilis BR151 carrying plasmid p602/19 was used. The plasmid contains the cat (chioramphenicol acetyltrans-ferase) gene downstream of a strong vegetativ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Vierheller C,Goel A,Peterson M,Domach MM,Ataai MM

    更新日期:1995-09-05 00:00:00

  • Combinatorial approaches as a component of high-throughput experimentation (HTE) in catalysis research.

    abstract::We consider the application of high-throughput experimentation (HTE), including combinatorial methods, to catalyst discovery and early-phase optimization. While combinatorial- and parallel-testing methods have an already substantial history in catalysis, recent work by several groups promises significant efficiency ga...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Newsam JM,Schüth F

    更新日期:1998-01-01 00:00:00

  • Biomass evolution in porous media and its effects on permeability under starvation conditions.

    abstract::The purpose of this study was to understand bacteria profile modification and its applications in subsurface biological operations such as biobarrier formation, in situ bioremediation, and microbial-enhanced oil recovery. Biomass accumulation and evolution in porous media were investigated both experimentally and theo...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Kim DS,Fogler HS

    更新日期:2000-07-05 00:00:00

  • Resting cells of recombinant E. coli show high epoxidation yields on energy source and high sensitivity to product inhibition.

    abstract::Metabolically active resting (i.e., nongrowing) bacterial cells have a high potential in cofactor-dependent redox biotransformations. Where growing cells require carbon and energy for biomass production, resting cells can potentially exploit their metabolism more efficiently for redox biocatalysis allowing higher spec...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Julsing MK,Kuhn D,Schmid A,Bühler B

    更新日期:2012-05-01 00:00:00

  • Production of micronic particles of biocompatible polymer using supercritical carbon dioxide.

    abstract::Three micronization techniques, based on the use of supercritical carbon dioxide, were investigated to produce microspheres of a natural biocompatible polysaccharide. Particles smaller than 20 mum were obtained by means of the rapid expansion of a supercritical solution method (RESS), both with and without cosolvents....

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Benedetti L,Bertucco A,Pallado P

    更新日期:1997-01-20 00:00:00

  • Influence of cytoskeleton organization on recombinant protein expression by CHO cells.

    abstract::In this study, we assessed the importance of cytoskeleton organization in the mammalian cells used to produce therapeutic proteins. Two cytoskeletal genes, Actin alpha cardiac muscle 1 (ACTC1) and a guanosine triphosphate GTPase-activating protein (TAGAP), were found to be upregulated in highly productive therapeutic ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Pourcel L,Buron F,Arib G,Le Fourn V,Regamey A,Bodenmann I,Girod PA,Mermod N

    更新日期:2020-04-01 00:00:00

  • Enzyme engineering: Reshaping the biocatalytic functions.

    abstract::Enzyme engineering is a powerful tool to fine-tune the enzymes. It is a technique by which the stability, activity, and specificity of the enzymes can be altered. The characteristic properties of an enzyme can be amended by immobilization and protein engineering. Among them, protein engineering is the most promising, ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章,评审


    authors: Ali M,Ishqi HM,Husain Q

    更新日期:2020-06-01 00:00:00

  • Microbial synthesis of polyhydroxybutyrate from glycerol: gluconeogenesis, molecular weight and material properties of biopolyester.

    abstract::Glycerol is considered as an ideal feedstock for producing bioplastics via bacterial fermentation due to its ubiquity, low price, and high degree of reduction substrate. In this work, we study the yield and cause of limitation in poly(3-hydroxybutyrate) (PHB) production from glycerol. Compared to glucose-based PHB pro...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Tanadchangsaeng N,Yu J

    更新日期:2012-11-01 00:00:00

  • 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


    authors: Woodley JM,Brazier AJ,Lilly MD

    更新日期:1991-01-20 00:00:00

  • The design of controllers for batch bioreactors.

    abstract::The implementation of control algorithms to batch bioreactors is often complicated by variations in process dynamics that occur during the course of fermentation. Such a wide operating range often renders the performance of fixed gain proportional-integral-differential (PID) controllers unsatisfactory. In this work, d...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Cardello RJ,San KY

    更新日期:1988-08-05 00:00:00

  • Enhanced d-lactic acid production by recombinant Saccharomyces cerevisiae following optimization of the global metabolic pathway.

    abstract::Utilization of renewable feedstocks for the production of bio-based chemicals such as d-lactic acid by engineering metabolic pathways in the yeast Saccharomyces cerevisiae has recently become an attractive option. In this study, to realize efficient d-lactic acid production by S. cerevisiae, the expression of 12 glyco...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Yamada R,Wakita K,Mitsui R,Ogino H

    更新日期:2017-09-01 00:00:00

  • Lipase activity in vesicular systems: characterization of candida cylindracea lipase and its activity in polymerizable dialkylammonium surfactant vesicles.

    abstract::Lipase from Candida cylindracea (CCL) was incorporated into polymerizable positively charged dialkylammonium bromide surfactant vesicles. The enzyme was incorporated by the use of the dehydration-rehydration method or by incubation. In the latter case, trapping efficiencies of up to 100% could be obtained. Activities ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Mosmuller EW,Franssen MC,Engbersen JF

    更新日期:1993-06-20 00:00:00

  • Hydrophobic salts markedly diminish viscosity of concentrated protein solutions.

    abstract::Reducing viscosities of concentrated solutions of therapeutic proteins is important for their subcutaneous and intravenous delivery. Although inorganic salts and optimizing the pH were previously reported to dramatically lower the viscosity of a monoclonal antibody solution, herein we have determined these effects not...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Du W,Klibanov AM

    更新日期:2011-03-01 00:00:00

  • Polymer surfaces derivatized with poly(vinyl-N-hexylpyridinium) kill airborne and waterborne bacteria.

    abstract::A facile methodology has been developed for covalently derivatizing the surfaces of common materials with a designed antibacterial polycation, poly(vinyl-N-pyridinium bromide), wherein the first, key step involves surface coating with a nanolayer of silica. Various commercial synthetic polymers derivatized in this man...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Tiller JC,Lee SB,Lewis K,Klibanov AM

    更新日期:2002-08-20 00:00:00

  • Analysis of continuous cultures of recombinant methylotrophs.

    abstract::Static and dynamic characteristics of continuous cultures of recombinant methylotrophs, which are designed to improve the selectivity of plasmid-bearing cells and the plasmid stability, are investigated in detail. Operational regions in which coexistence (survival of plasmid-bearing and plasmid-free cells) operation i...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Parulekar SJ,Chang YK,Modak JM,Lim HC

    更新日期:1987-06-01 00:00:00

  • Methodological analysis for determination of enzymatic digestibility of cellulosic materials.

    abstract::Accurate measurement of enzymatic cellulose digestibility (X) is important in evaluating the efficiency of lignocellulose pretreatment technologies, assessing the performance of reconstituted cellulase mixtures, and conducting economic analysis for biorefinery processes. We analyzed the effect of sugars contained in e...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Zhang YH,Schell DJ,McMillan JD

    更新日期:2007-01-01 00:00:00

  • Identification of a novel repressor encoded by the putative gene ctf1 for cellulase biosynthesis in Trichoderma reesei through artificial zinc finger engineering.

    abstract::Strains from Trichoderma reesei have been used for cellulase production with a long history. It has been well known that cellulase biosynthesis by the fungal species is controlled through regulators, and elucidation of their regulation network is of great importance for engineering T. reesei with robust cellulase prod...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Meng QS,Zhang F,Liu CG,Zhao XQ,Bai FW

    更新日期:2020-06-01 00:00:00

  • Substrate inhibition kinetics for toluene and benzene degrading pure cultures and a method for collection and analysis of respirometric data for strongly inhibited cultures.

    abstract::We present an evaluation of the qualitative and quantitative effects that high concentrations of benzene and toluene have on the growth rate of several pure cultures that use these compounds as their sole carbon and energy source. The cultures employed were five widely studied environmental isolates: Pseudomonas putid...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Alagappan G,Cowan R

    更新日期:2003-09-30 00:00:00

  • On-line estimation of the biomass activity during animal-cell cultivations.

    abstract::A software sensor was developed to determine the volumetric biomass activity of animal cell cultivations on-line. It was based on the on-line estimation of the ATP-production rate from the oxygen uptake and the lactic-acid production rate. The sensor was verified for a batch culture of Vero cells, and a batch and a co...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Dorresteijn RC,Numan KH,de Gooijer CD,Tramper J,Beuvery EC

    更新日期:1996-07-20 00:00:00

  • Comparison of microbial community composition and activity in sulfate-reducing batch systems remediating mine drainage.

    abstract::Five microbial inocula were evaluated in batch tests for the ability to remediate mine drainage (MD). Dairy manure (DM), anaerobic digester sludge, substrate from the Luttrell (LUTR) and Peerless Jenny King (PJK) sulfate-reducing permeable reactive zones (SR-PRZs) and material from an MD-treatment column that had been...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Pereyra LP,Hiibel SR,Pruden A,Reardon KF

    更新日期:2008-11-01 00:00:00

  • Escherichia coli "TatExpress" strains super-secrete human growth hormone into the bacterial periplasm by the Tat pathway.

    abstract::Numerous high-value proteins are secreted into the Escherichia coli periplasm by the General Secretory (Sec) pathway, but Sec-based production chassis cannot handle many potential target proteins. The Tat pathway offers a promising alternative because it transports fully folded proteins; however, yields have been too ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Browning DF,Richards KL,Peswani AR,Roobol J,Busby SJW,Robinson C

    更新日期:2017-12-01 00:00:00

  • Dynamic simulator for anaerobic digestion processes.

    abstract::A transient, two-culture model simulating methane production from biomass has been developed. The simulator, based partially on the work by Andrews and McCarty, is capable of calculating the hydrolysis products of several common organic materials, accommodating various substrate feeding modes, and simulating the trans...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Kleinstreuer C,Poweigha T

    更新日期:1982-09-01 00:00:00

  • Cellulase production by a solid state culture system.

    abstract::Production of cellulase using solid culture systems of Trichoderma reesei QM9414 and Sporotrichum cellulophilum on wheat bran was studied. By using moisture-controlled solid culture equipment, the effect of water content of wheat bran on cell growth and cellulase production was investigated. Cellular biomass grown on ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Kim JH,Hosobuchi M,Kishimoto M,Seki T,Yoshida T,Taguchi H,Ryu DD

    更新日期:1985-10-01 00:00:00

  • On the estimation of average shear rate in bubble columns.

    abstract::Development of bioengineering using such biomaterials as plant tissues or genetically produced microorganisms makes it important to accurately estimate the prevailing shear rate in bioreactors because they are generally sensitive to shear. Various authors have discussed ways to estimate the average shear rate in a bub...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Nishikawa M

    更新日期:1991-03-25 00:00:00

  • Cell cycle model to describe animal cell size variation and lag between cell number and biomass dynamics.

    abstract::The use of cell numbers rather than mass to quantify the size of the biotic phase in animal cell cultures causes several problems. First, the cell size varies with growth conditions, thus yields expressed in terms of cell numbers cannot be used in the normal mass balance sense. Second, experience from microbial system...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Nielsen LK,Reid S,Greenfield PF

    更新日期:1997-11-20 00:00:00

  • Adsorption of BSA on strongly basic chitosan: Equilibria.

    abstract::Equilibrium isotherms for adsorption of bovine serum albumin (BSA) on a new adsorbent, a strongly basic crosslinked chitosan (Chitopearl 2503), which is hard and is not compressed by pressure in a column, have been presented and compared with diethylaminoethyl (DEAE) Sepharose Fast Flow (hard gel). In Chitopearl 2503,...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章


    authors: Yoshida H,Nishihara H,Kataoka T

    更新日期:1994-05-01 00:00:00