scholarly journals Stochastic simulation platform for visualization and estimation of transcriptional kinetics

2019 ◽  
Author(s):  
Gennady Gorin ◽  
Mengyu Wang ◽  
Ido Golding ◽  
Heng Xu
Keyword(s):  
Rna Synthesis ◽  
Reaction Rates ◽  
Gillespie Algorithm ◽  
Simulation Framework ◽  
Dimensional Parameter ◽  
Turn On ◽  
Optimization Heuristics ◽  
Simulated Gene Expression ◽  
Kinetics Of ◽  
Stochastic Kinetics

AbstractWe present an implementation of the Gillespie algorithm that simulates the stochastic kinetics of nascent and mature RNA. Our model includes two-state gene regulation, RNA synthesis initiation and stepwise elongation, release to the cytoplasm, and stepwise degradation, a granular description currently tractable only by simulation. To facilitate comparison with experimental data, the algorithm predicts fluorescent probe signals measurable by single-cell RNA imaging. We approach the inverse problem of estimating underlying parameters in a five-dimensional parameter space and suggest optimization heuristics that successfully recover known reaction rates from simulated gene expression turn-on data. The simulation framework includes a graphical user interface, available as a MATLAB app at https://data.caltech.edu/records/1287.

scholarly journals Kinetics methods for clinical epidemiology problems

2015 ◽  
Vol 112 (46) ◽  
pp. 14150-14155 ◽  
Author(s):  
Alexandru Dan Corlan ◽  
John Ross
Keyword(s):  
Clinical Epidemiology ◽  
Meta Analysis ◽  
Reaction Rates ◽  
Mass Action ◽  
Reaction Systems ◽  
Disease Epidemiology ◽  
Mass Action Law ◽  
The Individual ◽  
Kinetics Of ◽  
Stochastic Kinetics

Calculating the probability of each possible outcome for a patient at any time in the future is currently possible only in the simplest cases: short-term prediction in acute diseases of otherwise healthy persons. This problem is to some extent analogous to predicting the concentrations of species in a reactor when knowing initial concentrations and after examining reaction rates at the individual molecule level. The existing theoretical framework behind predicting contagion and the immediate outcome of acute diseases in previously healthy individuals is largely analogous to deterministic kinetics of chemical systems consisting of one or a few reactions. We show that current statistical models commonly used in chronic disease epidemiology correspond to simple stochastic treatment of single reaction systems. The general problem corresponds to stochastic kinetics of complex reaction systems. We attempt to formulate epidemiologic problems related to chronic diseases in chemical kinetics terms. We review methods that may be adapted for use in epidemiology. We show that some reactions cannot fit into the mass-action law paradigm and solutions to these systems would frequently exhibit an antiportfolio effect. We provide a complete example application of stochastic kinetics modeling for a deductive meta-analysis of two papers on atrial fibrillation incidence, prevalence, and mortality.

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.

Kinetics of Ion-Pair Effect of Aquation of Bromopentaammine Cobalt(III) Complex in Different Dicarboxylate Media

2011 ◽  
Vol 324 ◽  
pp. 166-169 ◽  
Author(s):  
Farah Zeitouni ◽  
Gehan El-Subruiti ◽  
Ghassan Younes ◽  
Mohammad Amira
Keyword(s):  
Free Energy ◽  
Solvent Effect ◽  
Compensation Effect ◽  
Ion Pairing ◽  
Reaction Rates ◽  
Ion Pair ◽  
Free Energy Of Activation ◽  
Different Types ◽  
Different Temperatures ◽  
Kinetics Of

The rate of aquation of bromopentaammine cobalt(III) ion in the presence of different types of dicarboxylate solutions containing tert-butanol (40% V/V) have been measured spectrophotometrically at different temperatures (30-600°C) in the light of the effects of ion-pairing on reaction rates and mechanism. The thermodynamic and extrathermodynamic parameters of activation have been calculated and discussed in terms of solvent effect on the ion-pair aquation reaction. The free energy of activation ∆Gip* is more or less linearly varied among the studied dicarboxylate ion-pairing ligands indicating the presence of compensation effect between ∆Hip* and ∆Sip*. Comparing the kip values with respect of different buffers at 40% of ter-butanol is introduced.

scholarly journals Changes in J chain and mu chain RNA expression as a function of B cell differentiation.

1984 ◽  
Vol 160 (3) ◽  
pp. 877-892 ◽  
Author(s):  
G Lamson ◽  
M E Koshland
Keyword(s):  
B Cell ◽  
Time Course ◽  
Rna Synthesis ◽  
Rna Expression ◽  
B Cell Differentiation ◽  
Activated Lymphocytes ◽  
J Chain ◽  
Pattern Characteristic ◽  
Kinetics Of ◽  
Lymphoid Cell Lines

The time course of differentiative events in the pentamer IgM response was examined by following the expression of J chain and mu chain RNA and their protein products in mitogen-stimulated lymphocytes. The analyses showed that the shift to mus RNA synthesis begins shortly after stimulation and precedes proliferation of the cells and any increase in mu RNA levels. In contrast, expression of J chain RNA and the amplification of J chain and mus message are late events that coincide with a phase of rapid proliferation and with the secretion of pentamer IgM antibody. The kinetics of J and mu chain RNA expression observed in normal lymphocytes were supported by analyses of lymphoid cell lines. B lymphomas were found to display the RNA pattern characteristic of early-activated lymphocytes, i.e., a partial shift to mus RNA production and no J chain RNA, whereas IgM-secreting lines resembled late-activated lymphocytes in their expression of high levels of both mus and J chain mRNA. Moreover, the kinetics of J and mus chain RNA expression correlates with the sequential action of B cell lymphokines in the induction of the pentamer IgM response. This correlation suggests that the successive differentiative changes are triggered by successive membrane stimuli.

scholarly journals Structure–Function Relations of the First and Fourth Predicted Extracellular Linkers of the Type IIa Na+/Pi Cotransporter

2004 ◽  
Vol 124 (5) ◽  
pp. 475-488 ◽  
Author(s):  
Colin Ehnes ◽  
Ian C. Forster ◽  
Katja Kohler ◽  
Andrea Bacconi ◽  
Gerti Stange ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Reaction Rates ◽  
Transport Pathway ◽  
Extracellular Medium ◽  
Voltage Range ◽  
Substituted Cysteine Accessibility ◽  
Voltage Dependent ◽  
Opposite Behavior ◽  
Rate Limiting ◽  
Kinetics Of

The putative first intracellular and third extracellular linkers are known to play important roles in defining the transport properties of the type IIa Na+-coupled phosphate cotransporter (Kohler, K., I.C. Forster, G. Stange, J. Biber, and H. Murer. 2002b. J. Gen. Physiol. 120:693–705). To investigate whether other stretches that link predicted transmembrane domains are also involved, the substituted cysteine accessibility method (SCAM) was applied to sites in the predicted first and fourth extracellular linkers (ECL-1 and ECL-4). Mutants based on the wild-type (WT) backbone, with substituted novel cysteines, were expressed in Xenopus oocytes, and their function was assayed by isotope uptake and electrophysiology. Functionally important sites were identified in both linkers by exposing cells to membrane permeant and impermeant methanethiosulfonate (MTS) reagents. The cysteine modification reaction rates for sites in ECL-1 were faster than those in ECL-4, which suggested that the latter were less accessible from the extracellular medium. Generally, a finite cotransport activity remained at the end of the modification reaction. The change in activity was due to altered voltage-dependent kinetics of the Pi-dependent current. For example, cys substitution at Gly-134 in ECL-1 resulted in rate-limiting, voltage-independent cotransport activity for V ≤ −80 mV, whereas the WT exhibited a linear voltage dependency. After cys modification, this mutant displayed a supralinear voltage dependency in the same voltage range. The opposite behavior was documented for cys substitution at Met-533 in ECL-4. Modification of cysteines at two other sites in ECL-1 (Ile-136 and Phe-137) also resulted in supralinear voltage dependencies for hyperpolarizing potentials. Taken together, these findings suggest that ECL-1 and ECL-4 may not directly form part of the transport pathway, but specific sites in these linkers can interact directly or indirectly with parts of NaPi-IIa that undergo voltage-dependent conformational changes and thereby influence the voltage dependency of cotransport.

scholarly journals Effect of DNA-interacting drugs on phage T7 RNA polymerase.

1998 ◽  
Vol 45 (1) ◽  
pp. 127-132 ◽  
Author(s):  
M Piestrzeniewicz ◽  
K Studzian ◽  
D Wilmańska ◽  
G Płucienniczak ◽  
M Gniazdowski
Keyword(s):  
Rna Polymerase ◽  
Rna Synthesis ◽  
Actinomycin D ◽  
T7 Rna Polymerase ◽  
Distamycin A ◽  
E Coli ◽  
Phage T7 ◽  
Drug Dependent ◽  
Dna Complex ◽  
Kinetics Of

9-Aminoacridine carboxamide derivatives studied here form with DNA intercalative complexes which differ in the kinetics of dissociation. Inhibition of total RNA synthesis catalyzed by phage T7 and Escherichia coli DNA-dependent RNA polymerases correlates with the formation of slowly dissociating acridine-DNA complex of time constant of 0.4-2.3 s. Their effect on RNA synthesis is compared with other ligands which form with DNA stable complexes of different steric properties. T7 RNA polymerase is more sensitive to distamycin A and netropsin than the E. coli enzyme while less sensitive to actinomycin D. Actinomycin induces terminations in the transcript synthesized by T7 RNA polymerase. Despite low dissociation rates of DNA complexes with acridines and pyrrole antibiotics no drug dependent terminations are observed with these ligands.

scholarly journals Reactivity of Phenol and Aniline towards Quinolinium Chloro Chromate: A Comparative Oxidation Kinetic Study

2015 ◽  
Vol 59 ◽  
pp. 81-92
Author(s):  
Seplapatty Kalimuthu Periyasamy ◽  
H. Satham Hussain ◽  
R. Manikandan
Keyword(s):  
Oxidation Kinetic ◽  
Activation Parameters ◽  
Dipole Interaction ◽  
Reaction Rates ◽  
Hydrogen Ion ◽  
Aqueous Acetic Acid ◽  
Acetic Acid Medium ◽  
First Order ◽  
Different Temperatures ◽  
Kinetics Of

The kinetics of Oxidation of Phenol and aniline by quinolinium Chlorochromate (QCC) in aqueous acetic acid medium leads to the formation of quinone and azobenzene respectively. The reactions are first order with respect to both Phenol and aniline. The reaction is first order with respect to quinolinium chlorochromate (QCC) and is catalyzed by hydrogen ion. The hydrogen-ion dependence has the form: kobs = a+b [H+]. The rate of oxidation decreases with increasing dielectric constant of solvent, indicating the presence of an ion-dipole interaction. The reaction does not induced the polymerization of acrylonitrile. The retardation of the rate by the addition of Mn2+ ions confirms that a two electron transfer process is involved in the reaction. The reaction rates have been determined at different temperatures and the activation parameters have been calculated. From the above observations kinetic results a probable mechanism have been proposed.

Reactions of N-tricyanovinylamines with thiols in aqueous solutions

1990 ◽  
Vol 55 (6) ◽  
pp. 1630-1634 ◽  
Author(s):  
Dušan Podhradský ◽  
Helena Paulíková ◽  
Ján Imrich
Keyword(s):  
Double Bond ◽  
Aqueous Solutions ◽  
Reaction Rates ◽  
Imino Group ◽  
Group A ◽  
Kinetics Of

Kinetics of reactions between N-substituted tricyanovinylamines and thiols, where primarily reduction of the C=C double bond takes place, was investigated under conditions adequate to physiological ones. The reaction rates did not depend either on the type of the reacting thiol, or on the pH of the medium, but they decreased with the increasing pKa value of the imino group. A quantitative conversion of the thiol peptide glutathione to its oxidized form was evidenced.

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