Variation Of Kinetic Parameters Research Articles

Space-induced bifurcation in repression-based transcriptional circuits.

BackgroundAlbeit the molecular mechanisms of gene expression are well documented, our understanding of their dynamics is much less advanced. Recent experimental evidence has revealed that gene expression might be accurately organized in space, with several molecular actors localized to specific positions in the cell. However, the influence of this spatial localization on the dynamics of gene expression is unclear. This issue is also central in synthetic biology, where one usually considers the spatial localization in the cell of the genes of the inserted synthetic construct as irrelevant for its temporal dynamics.ResultsHere, we assessed the influence of the spatial distribution of the genes on the dynamics of 3-gene transcriptional ring networks regulated by repression, i.e. repressilator circuits, using individual-based modelling to simulate their dynamics in two and three space dimensions. Our simulations suggest that variations of spatial parameters – namely the degree of demixing of the positions of the gene or the spatial range of the mRNA and proteins (i.e. the typical distance they travel before degradation) – have dramatic effects by switching the dynamical regime from spontaneous oscillations to a stationary state where each species fluctuates around a constant value. By analogy with the bifurcations arising from the variation of kinetic parameters, we referred to those transitions as space-induced bifurcations.ConclusionsTaken together, our results strongly support the idea that the spatial organization of the molecular actors of transcriptional networks is crucial for the dynamics of gene expression and suggest that the spatial localization of the synthetic genes in the cell could be used as an additional toggle to control the dynamics of the inserted construct in synthetic biology experiments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-014-0125-z) contains supplementary material, which is available to authorized users.

Quantifying intrinsic and extrinsic noise in gene transcription using the linear noise approximation: An application to single cell data

A central challenge in computational modeling of dynamic biological systems is parameter inference from experimental time course measurements. However, one would not only like to infer kinetic parameters but also study their variability from cell to cell. Here we focus on the case where single-cell fluorescent protein imaging time series data are available for a population of cells. Based on van Kampen's linear noise approximation, we derive a dynamic state space model for molecular populations which is then extended to a hierarchical model. This model has potential to address the sources of variability relevant to single-cell data, namely, intrinsic noise due to the stochastic nature of the birth and death processes involved in reactions and extrinsic noise arising from the cell-to-cell variation of kinetic parameters. In order to infer such a model from experimental data, one must also quantify the measurement process where one has to allow for nonmeasurable molecular species as well as measurement noise of unknown level and variance. The availability of multiple single-cell time series data here provides a unique testbed to fit such a model and quantify these different sources of variation from experimental data.

On photoinduced polymerization of acrylamide

The solution and micellar polymerizations of acrylamide (Aam) initiated by the photoinitiator DAROCUR 2959 (DAR) under UV-light were studied. Variations of kinetic parameters with DAR and AAm concentrations and with the emulsifier type were followed. Furthermore, the kinetics of AAm polymerization under argon and air atmosphere was investigated. Dilatometry was implemented to follow continuously the fast photopolymerization. The polymerization rate vs. conversion curve of the photoinduced polymerization of AAm was described by two and four nonstationary rate intervals. Variation of the rate of polymerization with conversion was discussed in terms of two types of initiating radicals and the gel effect. They are formed by the decomposition of excited DAR* {DAR…AAm}* or {DAR…O2}* exciplexes. The intra- and intermolecular association of polyAAm, the self-assembling of AAm monomers, and the association of PAAm with Aam and cross-linking change the solution polymerization into the dispersion one.

Can phenotypic plasticity in Rubisco performance contribute to photosynthetic acclimation?

Photosynthetic acclimation varies among species, which likely reveals variations at the biochemical level in the pathways that constitute carbon assimilation and energy transfer. Local adaptation and phenotypic plasticity affect the environmental response of photosynthesis. Phenotypic plasticity allows for a wide array of responses from a single individual, encouraging fitness in a broad variety of environments. Rubisco catalyses the first enzymatic step of photosynthesis, and is thus central to life on Earth. The enzyme is well conserved, but there is habitat-dependent variation in kinetic parameters, indicating that local adaptation may occur. Here, we review evidence suggesting that land plants can adjust Rubisco's intrinsic biochemical characteristics during acclimation. We show that this plasticity can theoretically improve CO2 assimilation; the effect is non-trivial, but small relative to other acclimation responses. We conclude by discussing possible mechanisms that could account for biochemical plasticity in land plant Rubisco.

Modeling the effect of cell division on genetic oscillators

Many genetic oscillators (circadian clocks, synthetic oscillators) continue to oscillate across the cell division cycle. Since cell divisions create discontinuities in the dynamics of genetic oscillators the question about the resilience of oscillations and the factors that contribute to the robustness of the oscillations may be raised. We study here, through stochastic simulations, the effect of the cell division cycle on genetic oscillations using the Repressilator—a genetic oscillator developed in the context of synthetic biology. We consider intrinsic noise (molecular noise due to the limited number of molecules) and extrinsic noise (variability in the cell division time and in the partition of the molecules into daughter cells, cell–cell variability in kinetic parameters, etc). Our numerical simulations show that, although noisy, oscillations are quite resilient to cell division and that cell–cell heterogeneity may be the main source of variability observed experimentally. Finally, similar simulations performed with another model, the Goodwin model, show that oscillations may be entrained and synchronized by cell division. This highlights the influence of the clock architecture on the robustness of genetic oscillations. Our approach provides a general framework to study the effect of cell division on dynamical systems and several possible extensions are described.

Optimal aminoglycoside therapy following the sepsis: how much is too much?

Severe sepsis and septic shock are major problems as the result of high rates morbidity and mortality in intensive care units (ICUs). In the presence of septic shock, each hour of delay in the administration of effective antibiotics is associated with a measurable increase in mortality. Aminoglycosides are effective broad-spectrum antibiotics that are commonly used in ICUs for the treatment of life-threatening Gram-negative infections and as a part of empiric therapy for severe sepsis and septic shock. Knowledge of the pharmacokinetic (PK) and pharmacodynamic (PD) properties of the antibiotics used for the management of critically ill patients is essential for selecting the antibiotic dosing regimens and improving patient outcome. Volume of distribution (Vd) and clearance (CL) of aminoglycosides in critically ill patients differs from general population and these parameters change considerably during the therapy. Pathophysiological changes during the sepsis alter the pharmacokinetic and pharmacodynamic profile of many drugs (increase in Vd and variable changes in CL have been reported for aminoglycosides during the sepsis), therefore, dosing regimen optimization is necessary for achieving therapeutic goal, and critically ill patients should receive larger loading doses of aminoglycosides in order to achieve therapeutic blood levels and due to the considerable variation in kinetic parameters, the use of standard doses of aminoglycosides or dosing nomograms is not recommended in these populations.

Crystallization kinetics of Se–Zn–Sb nano composites chalcogenide alloys

Crystallization kinetics could be define the working limits of the material, thereby, this work is described the kinetics of Se96Zn2Sb2 (SZS) chalcogenide alloy and its composites with 0.05% multi walled carbon nano tubes (MWCNT) and 0.05% graphene (GF). The crystallization kinetic parameters have been obtained using the Differential Scanning Calorimetric (DSC) measurement traces at 5, 10, 15 and 20°C/min heating rates, by employing the different approximations at the glass transition, onset crystallization and peak crystallization temperatures. Subsequently, Hruby Hr glass forming ability parameter, thermal stability and nucleation and growth order parameter (n) and dimensional parameter (m) of the materials have also been discussed. Outcomes demonstrate these materials have a variation in kinetic parameters with the incorporation MWCNT and GF in SZS regime. It has been noticed MWCNT composite glass transition activation energy (Eg), onset crystallization temperature (Ec), peak crystallization (Ep) higher than GF composite while lowest for the parent alloy, however, a variation in Hr and thermal stability have been obtained for the composites. The overall two-one dimensional nucleation and growth mechanism have been evaluated for these materials.

Accounting for extrinsic variability in the estimation of stochastic rate constants

SUMMARYSingle‐cell recordings of transcriptional and post‐transcriptional processes reveal the inherent stochasticity of cellular events. However, to a large extent, the observed variability in isogenic cell populations is due to extrinsic factors, such as difference in expression capacity, cell volume and cell cycle stage—to name a few. Thus, such experimental data represents a convolution of effects from stochastic kinetics and extrinsic noise sources. Recent parameter inference schemes for single‐cell data just account for variability because of molecular noise. Here, we present a Bayesian inference scheme that deconvolutes the two sources of variability and enables us to obtain optimal estimates of stochastic rate constants of low copy‐number events and extract statistical information about cell‐to‐cell variability. In contrast to previous attempts, we model extrinsic noise by a variability in the abundance of mass‐conserved species, rather than a variability in kinetic parameters. We apply the scheme to a simple model of the osmostress‐induced transcriptional activation in budding yeast. Copyright © 2012 John Wiley & Sons, Ltd.

Kinetic study of acid-catalyzed cellulose hydrolysis in 1-butyl-3-methylimidazolium chloride

In this paper, the kinetics of acid-catalyzed cellulose hydrolysis in ionic liquids (ILs) was investigated by using 1-butyl-3-methylimidazolium chloride ([Bmim]Cl) as the model IL. General kinetic equations for the formation of glucose as well as cellooligomers were constructed at a molecular level, assuming that cellulose is fully dissolved to form a homogenous solution and that the scission of the glycosidic bond occurs randomly within the cellulose chain. Experimental data were well fitted according to these equations. Variations of kinetic parameters in the presence of different water content indicated that water behaved also as a base to decrease the acidity of the reaction medium. More importantly, it offered a profile of the evolution of cellooligomers. These results provided insights into the detailed mechanisms of cellulose hydrolysis in a non-aqueous, homogenous environment and should be valuable for developing strategies to depolymerize lignocellulosic biomass.

Mutational analysis of allosteric activation and inhibition of glucokinase

GK (glucokinase) is activated by glucose binding to its substrate site, is inhibited by GKRP (GK regulatory protein) and stimulated by GKAs (GK activator drugs). To explore further the mechanisms of these processes we studied pure recombinant human GK (normal enzyme and a selection of 31 mutants) using steady-state kinetics of the enzyme and TF (tryptophan fluorescence). TF studies of the normal binary GK-glucose complex corroborate recent crystallography studies showing that it exists in a closed conformation greatly different from the open conformation of the ligand-free structure, but indistinguishable from the ternary GK-glucose-GKA complex. GKAs did activate and GKRP did inhibit normal GK, whereas its TF was doubled by glucose saturation. However, the enzyme kinetics, GKRP inhibition, TF enhancement by glucose and responsiveness to GKA of the selected mutants varied greatly. Two predominant response patterns were identified accounting for nearly all mutants: (i) GK mutants with a normal or close to normal response to GKA, normally low basal TF (indicating an open conformation), some variability of kinetic parameters (k(cat), glucose S(0.5), h and ATP K(m)), but usually strong GKRP inhibition (13/31); and (ii) GK mutants that are refractory to GKAs, exhibit relatively high basal TF (indicating structural compaction and partial closure), usually show strongly enhanced catalytic activity primarily due to lowering of the glucose S(0.5), but with reduced or no GKRP inhibition in most cases (14/31). These results and those of previous studies are best explained by envisioning a common allosteric regulator region with spatially non-overlapping GKRP- and GKA-binding sites.

Electrochemical Impedance Analysis of a Hierarchical CuO Electrode Composed of Self-Assembled Nanoplates

Although 3d transition metal oxides (TMOs) are well-known as promising anodes for Li ion batteries, little is known about the mechanism of electrode process kinetics. In this work, impedance behavior of the flower-like hierarchical CuO electrode is first investigated to understand the kinetics that influences the performances of TMOs toward lithium. The electrochemical impedance spectra are measured at different discharge and charge states during cycling. A modified two-parallel diffusion path model is set up to account for the Nyquist plots. The kinetic parameters in the model that represent the migration of lithium ions through surface-passivating film, charge transfer on active material/electrolyte interfaces, and diffusion of lithium ions in solid material are discussed in detail. On the basis of the analysis of the variation of kinetic parameters, several promising approaches are proposed to improve the electrochemical performances of copper oxides, which can also be applicable to all the 3d transition metal oxides.

Kinetics of Crystallization of Co-Based Multi-Component Amorphous Alloy

Abstract Crystallization is a thermally activated process in non-crystalline and amorphous solids. The kinetics of the solid state phase transformations can be studied using thermal analysis techniques such as differential scanning calorimetry (DSC). For the kinetic analysis of the crystallization process under non-isothermal conditions, the choice of a reliable method is very important. The methods for the analysis of non-isothermal data are, in general, derived by extending the formalism developed for isothermal conditions. Most methods for the kinetic analysis of crystallization processes rely on the isokinetic hypothesis to separate the kinetics of the transformation from its dependence on temperature. It is assumed that the transformation rate can be described by a differential equation separable in α (transformed fraction) and T (temperature), i.e., for continuous heating regime, (dα/dT)=(1/β)k(T)f(α), where β is the heating rate, k(T) is the rate constant, and f(α) is the kinetic function (reaction model). The crystallization kinetics of glassy Co66Si16B12Fe4Mo2 have been studied with DSC and analyzed using non-isothermal theoretical expressions. The Avrami exponent, (n), frequency factor, (A), and activation energy, (E), of crystallization are evaluated using Matusita and Sakka (MS) and modified Kissinger equations. Besides, isoconversional kinetic analysis has been applied to DSC data for the determination of these different kinetic parameters. The isoconversional methods calculate Eα values at progressive degrees of conversion, α, without modelistic assumptions, and hence, this approach takes care of the variation of kinetic parameters with the fraction crystallized. The activation energy has been determined using both linear integral and differential isoconversional methods and also by the non-linear isoconversional method suggested by Vyazovkin and Wight. These methods are found to give consistent results for E. Furthermore, a comparison has been made among various kinetic parameters obtained using different approaches to investigate the relative applicability and usefulness of the proposed methods.

Relating Dose of Contrast Media Administered to Uptake and Washout of Malignant Lesions on DCEMRI of the Breast

To quantify the relationship between dose of contrast administered and contrast kinetics of malignant breast lesions. A total of 108 patients with 120 malignant lesions were selected for an institutional review board-approved review. Dynamic magnetic resonance protocol: one pre- and three or five post-contrast (at a fixed volume of 20 mL of 0.5 M gadodiamide) images. Patients were stratified into groups based on dose of contrast administered, after calculation of body weight (kg): Dose Group 1, <0.122 mmol/kg; Dose Group 2, 0.123-0.155 mmol/kg; Dose Group, 3 > 0.155 mmol/kg. Analysis of kinetic curve shape was made according to the Breast Imaging Reporting and Data System lexicon. Several quantitative parameters were calculated including initial and peak enhancement percentage (E(1) and E(peak)). Linear regression was used to model the variation of kinetic parameters with dose. There was no difference found in the qualitative Breast Imaging Reporting and Data System descriptors of curve shape between the three dose groups. There was a trend for E(1) and E(peak) to increase from Dose Group 1 to Dose Group 3 in malignant lesions overall, as well as in invasive ductal carcinoma lesions separately. Each decrement/increment of 0.05 mmol/kg in dose yielded a decrease/increase of 78% and 97% in E(1) for in situ and invasive cancers, respectively. Contrast should be administered at fixed dose to achieve comparable levels of lesion uptake in women of different weights. Our results suggest that reducing the contrast administered to 0.05 mmol/kg, as has been suggested for patients at risk of developing nephrogenic systemic fibrosis, could substantially decrease the observed initial enhancement in some cancers.

TH-D-304A-07: Voxel-Based Kinetic Analysis Method Utilizing ROI Fragmentation

UPurpose: Kinetic analysis is important for accurate quantification of PET images. As it is typically done on the region of interest (ROI) level, it does not preserve spatial information of the tracer uptake. We developed a novel method for voxel‐based kinetic analysis on various spatial levels, which overcomes problem of high voxel noise level in dynamic PET images.Methods and materials: The proposed method starts with an ROI‐based kinetic analysis with the standard least‐squares method. Then a series of optimizations on sub‐regions is performed, where estimated parameters from the super‐region are used as initial guesses and a‐priori values for Bayesian parameter estimation procedure on sub‐regions. Procedure is repeated until sub‐regions consist of a single PET image volume element. The method was tested by comparing the model estimated parameters with the true parameters on a mathematical phantom. Several different a‐priori weighting schemes were tested on human cancer patients, dynamically imaged with FLT PET. Tracer kinetics was modeled with a two‐compartment four‐parameter kinetic model.Spatial variation of the kinetic parameters on parametric images was quantified. Results: Adding Bayesian part in the objective function greatly reduces spatial variation of kinetic parameters making images to appear smoother. On the other hand, the accuracy of parameter estimation is not compromised, as shown through phantom simulation studies. The reduction of spatial variation of kinetic parameter was found to be the most distinctive for k 3 parametric images, where variation was reduced approximately 6‐fold and the least evident for k i=k 1 k 3/(k 2+k 3) parametric images, where the reduction was approximately 2‐fold. Conclusion: The proposed method is unique because it does not incorporate population‐based prior knowledge, but develops prior knowledge by kinetic analysis on different spatial levels. It reduces spatial variation in parametric images, which reduces sensitivity to image registration errors, while quantitative accuracy is not decreased as with digital filtration.

Evaluation of a compartmental model for estimating tumor hypoxia via FMISO dynamic PET imaging

This paper systematically evaluates a pharmacokinetic compartmental model for identifying tumor hypoxia using dynamic positron emission tomography (PET) imaging with 18F-fluoromisonidazole (FMISO). A generic irreversible one-plasma two-tissue compartmental model was used. A dynamic PET image dataset was simulated with three tumor regions—normoxic, hypoxic and necrotic—embedded in a normal-tissue background, and with an image-based arterial input function. Each voxelized tissue's time activity curve (TAC) was simulated with typical values of kinetic parameters, as deduced from FMISO-PET data from nine head-and-neck cancer patients. The dynamic dataset was first produced without any statistical noise to ensure that correct kinetic parameters were reproducible. Next, to investigate the stability of kinetic parameter estimation in the presence of noise, 1000 noisy samples of the dynamic dataset were generated, from which 1000 noisy estimates of kinetic parameters were calculated and used to estimate the sample mean and covariance matrix. It is found that a more peaked input function gave less variation in various kinetic parameters, and the variation of kinetic parameters could also be reduced by two region-of-interest averaging techniques. To further investigate how bias in the arterial input function affected the kinetic parameter estimation, a shift error was introduced in the peak amplitude and peak location of the input TAC, and the bias of various kinetic parameters calculated. In summary, mathematical phantom studies have been used to determine the statistical accuracy and precision of model-based kinetic analysis, which helps to validate this analysis and provides guidance in planning clinical dynamic FMISO-PET studies.

Investigation of froth flotation for beneficiation of printed circuit board comminution fines

Froth flotation for beneficiation of printed circuit board comminution fines was investigated in this work, via reverse flotation under a scheme described as natural hydrophobic response. With no reagents, the scheme employed variation of kinetic parameters of airflow rate and impeller speed to optimize metallic enrichment of the sink. The impeller energy and aeration rate required to keep the pulp in suspension and avoid excessive turbulence were found to be much lower compared with conventional mineral flotation. The natural hydrophobic response was found to exist, and stable froth was observed even without the use of any frother. It was submitted that the dynamic froth stability observed is due to fine particle stabilization. Mass pulls obtained were high and cumulative mass pull under the varying kinetic regimes were found to fit very well to the general first order kinetics. The extents of fit, the sink enrichment and the recovery in respect of metallic values were assessed to evaluate the beneficiation performance. Many of the metallic elements were found to concentrate into the sink, while some prefer the froth phase. Notably, gold and palladium were among the best recovered to the sink; with about 64% recovery at enrichment ratio of 3.1 (676 ppm actual assay) for Au. The flotation scheme proved effective for PCB comminution fines, and performance improvement also looks very feasible.

Effect of Concomitant Artesunate Administration and Cytochrome P4502C8 Polymorphisms on the Pharmacokinetics of Amodiaquine in Ghanaian Children with Uncomplicated Malaria

Artesunate (AS) is used in combination with amodiaquine (AQ) as first-line treatment for uncomplicated malaria in many countries. We investigated the effect of concomitant AS administration on the pharmacokinetics of AQ and compared concentrations of desethylamodiaquine (DEAQ), the main metabolite of AQ, in plasma between patients with different variants of the cytochrome P4502C8 (CYP2C8) gene. A two-compartment model was fitted to 169 plasma DEAQ concentrations from 103 Ghanaian children aged 1 to 14 years with uncomplicated malaria treated either with AQ alone (n = 15) or with AS plus AQ (n = 88). The population clearance of DEAQ appeared to increase nonlinearly with body weight, and the central volume of distribution of DEAQ was higher (P < 0.001) in the AS-plus-AQ group than in the AQ-only group. The maximum plasma DEAQ concentration was higher (P < 0.001), and the population distribution half-life was shorter (P < 0.01), in the AQ-only group than in the AS-plus-AQ group. The total areas under the plasma DEAQ concentration-time curves (P = 0.68) and elimination half-lives (P = 0.39) were similar for the two groups. There was a high frequency (0.179) of the non-wild-type allele of CYP2C8, but no differences between CYP2C8 genotypes with regard to AQ efficacy or safety were evident. The sample size, however, was limited, so monitoring of AQ toxicity in the study area is still indicated. The nonlinear clearance of DEAQ and the wide variability in kinetic parameters have safety implications for weight-based dosing of higher-body-weight children with AQ. The pharmacokinetics of artemisinin combination therapies should be studied in malaria patients, because the rapid parasite clearance caused by the artemisinin may affect the kinetics of the partner drug and the combination.

Flow of kinetic parameters in a typical swimming pool type research reactor

Calculations were performed to estimate the variation in kinetic parameters (delayed neutron fraction and prompt neutron generation time) in different core configurations of a typical swimming pool type research reactor. Pakistan research Reactor-1 (PARR-1) was employed for this study. The effect due to burnup of the core was also studied. Calculations were performed with the help of computer codes WIMSD/4 and CITATION. Precursors yield was modified according to the neutron flux averaging only. This is the simple way to calculate the precursor yield for a particular core. The kinetic parameters are different for different core configurations. The β eff decreases with 1.33 × 10 −6/% burnup whereas prompt neutron generation time increases with 6.42 × 10 −8 s/% burnup. The results were compared with safety analysis report and with published values and were found in good agreement. This study provides the confidence to understand the change in the kinetic parameters of research reactors with core change and also with burnup of the core.

Uncertainty in Thermal Process Calculations due to Variability in First‐Order and Weibull Kinetic Parameters

Alternatives to first-order model of death kinetics of microorganisms have been proposed as improvements in the calculation of lethality for a thermal process. Although such models can potentially improve predictions for many situations, this article tries to answer the question of whether the added complexities of these models are a worthwhile investment once we include the effect of uncertainties in various microbiological and process parameters. Monte Carlo technique is used to include variability in kinetic parameters in lethality calculation for a number of heating processes, for both first-order and Weibull kinetics models. It is shown that uncertainties represented by coefficient of variation in kinetic parameters lead to a wide range of final log-reduction prediction. With the same percent variability in kinetic parameters, uncertainty in the final log reduction for Weibull kinetics was smaller or equal to that for first-order kinetics. Due to the large effect of variability in the input parameters on the final log reduction, the effort to move toward more accurate kinetic models needs to be weighed against inclusion of variability.

Modeling Hsp70-Mediated Protein Folding

The Hsp70 chaperone system is the major molecular chaperone system that assists protein-folding processes in all cells. To understand these processes, we analyzed the kinetic characteristics of the Escherichia coli homologs of this chaperone system during folding of a denatured protein using computer simulations and compared the results with in vitro refolding experiments. Rate constants used for the model were derived from recent literature or were determined and scrutinized for their applicability to the refolding reaction. Our simulation results are consistent with reported laboratory experiments, not only simulating the refolding reaction of wild-type proteins but also the behavior of mutant variants. Variation of kinetic parameters and concentrations of components of the Hsp70 system demonstrate the robustness of the chaperone system in assisting protein folding. Furthermore, the importance of the synergistic stimulation of the ATPase activity of Hsp70 is demonstrated. The limitations of our kinetic model indicate sore spots in our understanding of this chaperone system. Our model provides a platform for further research on chaperone action and the mechanism of chaperone-assisted refolding of denatured proteins.