scholarly journals The calculation of transcript flux ratios reveals single regulatory mechanisms capable of activation and repression

2018 ◽  
Vol 115 (50) ◽  
pp. E11604-E11613 ◽  
Author(s):  
Eric A. Galburt
Keyword(s):  
Rate Constants ◽  
Flux Ratio ◽  
Stringent Response ◽  
Kinetic Mechanism ◽  
Regulation Of Transcription ◽  
Sequence Motifs ◽  
Response Factors ◽  
Initiation Rate ◽  
Dna Sequence Motifs ◽  
Kinetics Of

The regulation of transcription allows cells to adjust the rate of RNA polymerases (RNAPs) initiated in a promoter-specific manner. Classically, transcription factors are directed to a subset of promoters via the recognition of DNA sequence motifs. However, a unique class of regulators is recruited directly through interactions with RNAP. Surprisingly, these factors may still possess promoter specificity, and it has been postulated that the same kinetic mechanism leads to different regulatory outcomes depending on a promoter’s basal rate constants. However, mechanistic studies of regulation typically report factor activity in terms of changes in the thermodynamics or kinetics of individual steps or states while qualitatively linking these observations to measured changes in transcript production. Here, I present online calculators that allow for the direct testing of mechanistic hypotheses by calculating the steady-state transcript flux in the presence and absence of a factor as a function of initiation rate constants. By evaluating how the flux ratio of a single kinetic mechanism varies across promoter space, quantitative insights into the potential of a mechanism to generate promoter-specific regulatory outcomes are obtained. Using these calculations, I predict that the mycobacterial transcription factor CarD is capable of repression in addition to its known role as an activator of ribosomal genes. In addition, a modification of the mechanism of the stringent response factors DksA/guanosine 5′-diphosphate 3′-diphosphate (ppGpp) is proposed based on their ability to differentially regulate transcription across promoter space. Overall, I conclude that a multifaceted kinetic mechanism is a requirement for differential regulation by this class of factors.

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 Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ting-Ying Wu ◽  
Marlen Müller ◽  
Wilhelm Gruissem ◽  
Navreet K. Bhullar
Keyword(s):  
Gene Expression ◽  
Dna Sequence ◽  
Expression Patterns ◽  
Grain Filling ◽  
Aleurone Layer ◽  
Rice Grain ◽  
Sequence Motifs ◽  
Grain Development ◽  
Spatio Temporal ◽  
Dna Sequence Motifs

Abstract Background Rice is an important food source for humans worldwide. Because of its nutritional and agricultural significance, a number of studies addressed various aspects of rice grain development and grain filling. Nevertheless, the molecular processes underlying grain filling and development, and in particular the contributions of different grain tissues to these processes, are not understood. Main Text Using RNA-sequencing, we profiled gene expression activity in grain tissues comprised of cross cells (CC), the nucellar epidermis (NE), ovular vascular trace (OVT), endosperm (EN) and the aleurone layer (AL). These tissues were dissected using laser capture microdissection (LCM) at three distinct grain development stages. The mRNA expression datasets offer comprehensive and new insights into the gene expression patterns in different rice grain tissues and their contributions to grain development. Comparative analysis of the different tissues revealed their similar and/or unique functions, as well as the spatio-temporal regulation of common and tissue-specific genes. The expression patterns of genes encoding hormones and transporters indicate an important role of the OVT tissue in metabolite transport during grain development. Gene co-expression network prediction on OVT-specific genes identified several distinct and common development-specific transcription factors. Further analysis of enriched DNA sequence motifs proximal to OVT-specific genes revealed known and novel DNA sequence motifs relevant to rice grain development. Conclusion Together, the dataset of gene expression in rice grain tissues is a novel and useful resource for further work to dissect the molecular and metabolic processes during rice grain development.

Oxidation of Olefins Representing Some Structural Units of GR-S

1952 ◽  
Vol 25 (1) ◽  
pp. 21-32 ◽  
Author(s):  
W. C. Warner ◽  
J. Reid Shelton
Keyword(s):  
Phenyl Group ◽  
Kinetic Mechanism ◽  
Oxidation Reactions ◽  
Chain Reaction ◽  
Instantaneous Rate ◽  
Initial Oxygen ◽  
Oxidation Of Olefins ◽  
A Minor ◽  
The Relationship ◽  
Kinetics Of

Abstract Three olefins were oxidized in the liquid phase with molecular oxygen to determine the kinetics of the oxidation reactions and the relationship to oxidation of rubber. The instantaneous rate of oxidation was found to be related to the analytically determined olefin and peroxide concentrations by the equation : Rate=k (unreacted olefin)(peroxide), where rate equals moles of oxygen per mole of original olefin per hour and the parentheses represent molarities. Presence of a phenyl group was found to affect k, but only in a minor way, indicating that the same fundamental kinetic mechanism applies in both aromatic and aliphatic olefins. The data are consistent with the general kinetic mechanism of Bolland involving oxygen attack at the alpha-methylenic group. However, it appears probable that initial oxygen attack can also occur at the double bond, resulting in the formation of a peroxide biradical, which may then react with other olefin molecules, initiating the usual chain reaction mechanism.

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.

Sign in / Sign up

Export Citation Format

Share Document