scholarly journals Estimating Network Kinetics of the MAPK/ERK Pathway Using Biochemical Data

2012 ◽  
Vol 2012 ◽  
pp. 1-34 ◽  
Author(s):  
Vilda Purutçuoğlu ◽  
Ernst Wit
Keyword(s):  
Rate Constants ◽  
Dynamic Models ◽  
Growth Control ◽  
Biological Response ◽  
Biological Knowledge ◽  
Erk Pathway ◽  
Signal Transduction System ◽  
Activation Kinetics ◽  
Cellular Processes ◽  
Kinetics Of

The MAPK/ERK pathway is a major signal transduction system which regulates many fundamental cellular processes including the growth control and the cell death. As a result of these roles, it has a crucial importance in cancer as well as normal developmental processes. Therefore, it has been intensively studied resulting in a wealth of knowledge about its activation. It is also well documented that the activation kinetics of the pathway is crucial to determine the nature of the biological response. However, while individual biochemical steps are well characterized, it is still difficult to predict or even understand how the activation kinetics works. The aim of this paper is to estimate the stochastic rate constants of the MAPK/ERK network dynamics. Accordingly, taking a Bayesian approach, we combined underlying qualitative biological knowledge in several competing dynamic models via sets of quasireactions and estimated the stochastic rate constants of these reactions. Comparing the resulting estimates via the BIC and DIC criteria, we chose a biological model which includes EGFR degradation—Raf-MEK-ERK cascade without the involvement of RKIPs.

Submerged upflow biotower operation and computer simulation

1994 ◽  
Vol 30 (11) ◽  
pp. 143-146
Author(s):  
Ronald D. Neufeld ◽  
Christopher A. Badali ◽  
Dennis Powers ◽  
Christopher Carson
Keyword(s):  
Computer Simulation ◽  
Benzoic Acid ◽  
Computer Model ◽  
Rate Constants ◽  
Batch Mode ◽  
Operational Conditions ◽  
First Order ◽  
Low Concentrations ◽  
Biological Transformation ◽  
Kinetics Of

A two step operation is proposed for the biodegradation of low concentrations (< 10 mg/L) of BETX substances in an up flow submerged biotower configuration. Step 1 involves growth of a lush biofilm using benzoic acid in a batch mode. Step 2 involves a longer term biological transformation of BETX. Kinetics of biotransformations are modeled using first order assumptions, with rate constants being a function of benzoic acid dosages used in Step 1. A calibrated computer model is developed and presented to predict the degree of transformation and biomass level throughout the tower under a variety of inlet and design operational conditions.

Kinetics of hydrolysis of peroxodisulphate ions in acidic medium to peroxomonosulphuric acid

1981 ◽  
Vol 46 (5) ◽  
pp. 1229-1236 ◽  
Author(s):  
Jan Balej ◽  
Milada Thumová
Keyword(s):  
Ionic Strength ◽  
Rate Constants ◽  
Acidic Medium ◽  
Measured Data ◽  
Molar Ratios ◽  
Starting Solution ◽  
Kinetics Of Hydrolysis ◽  
Rate Of Hydrolysis ◽  
Kinetics Of ◽  
Hydrolysis Of

The rate of hydrolysis of S2O82- ions in acidic medium to peroxomonosulphuric acid was measured at 20 and 30 °C. The composition of the starting solution corresponded to the anolyte flowing out from an electrolyser for production of this acid or its ammonium salt at various degrees of conversion and starting molar ratios of sulphuric acid to ammonium sulphate. The measured data served to calculate the rate constants at both temperatures on the basis of the earlier proposed mechanism of the hydrolysis, and their dependence on the ionic strength was studied.

Kinetics of the reaction between hexamethylenediisocyanate and 1-pentanol

1983 ◽  
Vol 48 (11) ◽  
pp. 3279-3286
Author(s):  
Slavko Hudeček ◽  
Miloslav Bohdanecký ◽  
Ivana Hudečková ◽  
Pavel Špaček ◽  
Pavel Čefelín
Keyword(s):  
Liquid Chromatography ◽  
Rate Constants ◽  
Reversed Phase ◽  
Order Reaction ◽  
Second Order ◽  
Second Order Reaction ◽  
Reversed Phase Liquid Chromatography ◽  
Consecutive Reactions ◽  
Phase Liquid ◽  
Kinetics Of

The reaction between hexamethylenediisocyanate and 1-pentanol in toluene was studied by means of reversed-phase liquid chromatography. By employing this method, it was possible to determine all components of the reaction mixture including both products, i.e. N-(6-isocyanate hexyl)pentylcarbamate and N,N'-bis(pentyloxycarbonyl)hexamethylenediamine. Relations for the calculation of kinetic constants were derived assuming a competitive consecutive second-order reaction. It was demonstrated that the reaction involved in this case is indeed a second-order reaction, and the rate constants of the first and second consecutive reactions were determined.

Kinetics of esterification of monoisopropylphenols with phosphoryl trichloride

1989 ◽  
Vol 54 (5) ◽  
pp. 1311-1317
Author(s):  
Miroslav Magura ◽  
Ján Vojtko ◽  
Ján Ilavský
Keyword(s):  
Liquid Phase ◽  
Rate Constants ◽  
Reaction Rates ◽  
Activation Energies ◽  
The Individual ◽  
Kinetics Of

The kinetics of liquid-phase isothermal esterification of POCl3 with 2-isopropylphenol and 4-isopropylphenol have been studied within the temperature intervals of 110 to 130 and 90 to 110 °C, respectively. The rate constants and activation energies of the individual steps of this three-step reaction have been calculated from the values measured. The reaction rates of the two isomers markedly differ: at 110 °C 4-isopropylphenol reacts faster by the factors of about 7 and 20 for k1 and k3, respectively. This finding can be utilized in preparation of mixed triaryl phosphates, since the alkylation mixture after reaction of phenol with propene contains an excess of 2-isopropylphenol over 4-isopropylphenol.

Determination of the Nucleophilicity of Tricarbonyliron Coordinated Cyclohepta-1,3,5-triene

1999 ◽  
Vol 64 (11) ◽  
pp. 1770-1779 ◽  
Author(s):  
Herbert Mayr ◽  
Karl-Heinz Müller
Keyword(s):  
Gibbs Energy ◽  
Ambient Temperature ◽  
Rate Constants ◽  
Second Order ◽  
Order Rate ◽  
Electrophilic Additions ◽  
Kinetics Of

The kinetics of the electrophilic additions of four diarylcarbenium ions (4a-4d) to tricarbonyl(η4-cyclohepta-1,3,5-triene)iron (1) have been studied photometrically. The second-order rate constants match the linear Gibbs energy relationship log k20 °C = s(E + N) and yield the nucleophilicity parameter N(1) = 3.69. It is concluded that electrophiles with E ≥ -9 will react with complex 1 at ambient temperature.

scholarly journals Kinetics of tau aggregation reveals patient specific tau characteristics among Alzheimer's cases

2021 ◽  
Author(s):  
Tarun V Kamath ◽  
Naomi Klickstein ◽  
Caitlin Commins ◽  
Analiese R Fernandes ◽  
Derek H Oakley ◽  
...  
Keyword(s):  
Growth Phase ◽  
Tau Proteins ◽  
Patient Specific ◽  
Lag Phase ◽  
Plateau Phase ◽  
Kinetic Assay ◽  
Cellular Processes ◽  
Morphological Differences ◽  
Tau Aggregation ◽  
Kinetics Of

Abstract The accumulation of tau aggregates throughout the human brain is the hallmark of a number of neurodegenerative conditions classified as tauopathies. Increasing evidence shows that tau aggregation occurs in a “prion-like” manner, in which a small amount of misfolded tau protein can induce other, naïve tau proteins to aggregate. Tau aggregates have been found to differ structurally among different tauopathies. Recently, however, we have suggested that tau oligomeric species may differ biochemically among individual patients with sporadic Alzheimer disease, and have also showed that the bioactivity of the tau species, measured using a cell-based bioassay, also varied among individuals. Here, we adopted a live-cell imaging approach to the standard cell-based bioassay to explore further whether the kinetics of aggregation also differentiated these patients. We found that aggregation can be observed to follow a consistent pattern in all cases, with a lag phase, a growth phase, and a plateau phase, which each provide quantitative parameters by which we characterize aggregation kinetics. The length of the lag phase and magnitude of the plateau phase are both dependent upon the concentration of seeding-competent tau, the relative enrichment of which differs among patients. The slope of the growth phase correlates with morphological differences in the tau aggregates, which may be reflective of underlying structural differences. This kinetic assay confirms and refines the concept of heterogeneity in the characteristics of tau proteopathic seeds among individuals with Alzheimer’s disease and is a method by which future studies may characterize longitudinal changes in tau aggregation and the cellular processes which may influence these changes.

scholarly journals Mixing state and compositional effects on CCN activity and droplet growth kinetics of size-resolved CCN in an urban environment

2012 ◽  
Vol 12 (21) ◽  
pp. 10239-10255 ◽  
Author(s):  
L. T. Padró ◽  
R. H. Moore ◽  
X. Zhang ◽  
N. Rastogi ◽  
R. J. Weber ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Water Soluble ◽  
Anthropogenic Sources ◽  
Droplet Growth ◽  
Mixing State ◽  
Aerosol Composition ◽  
Activation Kinetics ◽  
Aerosol Mixing State ◽  
Kinetics Of ◽  
Ccn Activity

Abstract. Aerosol composition and mixing state near anthropogenic sources can be highly variable and can challenge predictions of cloud condensation nuclei (CCN). The impacts of chemical composition on CCN activation kinetics is also an important, but largely unknown, aspect of cloud droplet formation. Towards this, we present in-situ size-resolved CCN measurements carried out during the 2008 summertime August Mini Intensive Gas and Aerosol Study (AMIGAS) campaign in Atlanta, GA. Aerosol chemical composition was measured by two particle-into-liquid samplers measuring water-soluble inorganic ions and total water-soluble organic carbon. Size-resolved CCN data were collected using the Scanning Mobility CCN Analysis (SMCA) method and were used to obtain characteristic aerosol hygroscopicity distributions, whose breadth reflects the aerosol compositional variability and mixing state. Knowledge of aerosol mixing state is important for accurate predictions of CCN concentrations and that the influence of an externally-mixed, CCN-active aerosol fraction varies with size from 31% for particle diameters less than 40 nm to 93% for accumulation mode aerosol during the day. Assuming size-dependent aerosol mixing state and size-invariant chemical composition decreases the average CCN concentration overprediction (for all but one mixing state and chemical composition scenario considered) from over 190–240% to less than 20%. CCN activity is parameterized using a single hygroscopicity parameter, κ, which averages to 0.16 ± 0.07 for 80 nm particles and exhibits considerable variability (from 0.03 to 0.48) throughout the study period. Particles in the 60–100 nm range exhibited similar hygroscopicity, with a κ range for 60 nm between 0.06–0.076 (mean of 0.18 ± 0.09). Smaller particles (40 nm) had on average greater κ, with a range of 0.20–0.92 (mean of 0.3 ± 0.12). Analysis of the droplet activation kinetics of the aerosol sampled suggests that most of the CCN activate as rapidly as calibration aerosol, suggesting that aerosol composition exhibits a minor (if any) impact on CCN activation kinetics.

scholarly journals Determination of the steady-state turnover rates of the metabolically active pools of phosphatidylinositol 4-phosphate and phosphatidylinositol 4,5-bisphosphate in human erythrocytes

1989 ◽  
Vol 259 (3) ◽  
pp. 893-896 ◽  
Author(s):  
C E King ◽  
P T Hawkins ◽  
L R Stephens ◽  
R H Michell
Keyword(s):  
Steady State ◽  
Rate Constants ◽  
Human Erythrocytes ◽  
Turnover Rates ◽  
Metabolic Fluxes ◽  
Metabolic Pool ◽  
Phosphatidylinositol 4 ◽  
Kinetics Of ◽  
Phosphate Groups

When intact human erythrocytes are incubated at metabolic steady state in a chloride-free medium containing [32P]Pi, there is rapid labelling of the gamma-phosphate of ATP, followed by a slower labelling of the monoester phosphate groups of phosphatidylinositol 4-phosphate (PtdIns4P) and phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P2] [King, Stephens, Hawkins, Guy & Michell (1987) Biochem. J. 244, 209-217]. We have analysed the early kinetics of the labelling of these phosphate groups, in order to determine: (a) the steady-state rates of the interconversions of phosphatidylinositol, PtdIns4P and PtdIns(4,5)P2; and (b) the fractions of the total cellular complement of PtdIns4P and PtdIns(4,5)P2 that participate in this steady-state turnover. The experimental data most closely fit a pattern of PtdIns4P and PtdIns(4,5)P2 turnover in which one-quarter of the total cellular complement of each lipid is in the metabolic pool that participates in rapid metabolic turnover, with rate constants of 0.028 min-1 for the interconversion of PtdIns and PtdIns4P, and of 0.010 min-1 for the PtdIns4P/PtdIns(4,5)P2 cycle. These rate constants represent metabolic fluxes of approx. 2.1 nmol of lipid/h per ml of packed erythrocytes between PtdIns and PtdIns4P and of approx. 5.7 nmol/h per ml of cells between PtdIns4P and PtdIns(4,5)P2.

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