RESUMEN

The recognition and characterization of gene-encoded nitric oxide synthase (NOS) from Exiguobacterium profundum are reported in this study. A new gene was sequenced and cloned from E. profundum and heterologously expressed in E. coli for functional identification, followed by protein purification using the His-tag. The stability and activity characteristics of the recombinant NOS were evaluated using different concentrations of IPTG at various time points. A band of approximately 42 kDa was observed by SDS-PAGE. The Km value of NOS, calculated based on the Michaelis-Menten equation, was 0.59 µmol/L. Additionally, homologous sequence alignment analysis indicated that the new NOS shared 80.48% similarity with the same protein from Bacillus subtilis and Umezawaea. The construction of the NOS expression vector and the purification of the recombinant protein provide a foundation for further functional research and inhibitor development.

RESUMEN

Depending on the chemical energy from ATP hydrolysis, myosin V can drive the multistep and continuous coupled cycling process to transport cellular cargo to targeted regions. However, it is still obscure how the molecular memory induced by the multistep coupled transported process could regulate the dynamic behavior of the motor state of myosin V. Here, we propose a novel non-Markovian polymorphic mechanochemical model to investigate the effect of the molecular memory on the mechanic of noise attenuation of myosin V system. We first define an effective transition rate for a multistep coupled reaction process which is the function of memory and system states to transform equivalently the non-Markovian process into the classical Markov process. By noise decomposition technology, it is observed that both the intrinsic and extrinsic noises of the ADP-myosin V bound state (AM ⋅ ADP) exhibit a monotonically decreasing trend with lengthening the molecular memory. Molecular memory as a regulation factor can amplify the contribution of intrinsic noise to the overall noise while reducing the influence of extrinsic noise on the AM ⋅ ADP. Moreover, the modulation of molecular memory could induce stochastic focusing. These results indicate that the role of molecular memory in the myosin V state transition can not only offer a handle to maintain the robustness of the motion system but also serve as a paradigm for studying more complex molecular motors.

Asunto(s)

RESUMEN

BACKGROUND: Standard pediatric growth curves cannot be used to impute missing height or weight measurements in individual children. The Michaelis-Menten equation, used for characterizing substrate-enzyme saturation curves, has been shown to model growth in many organisms including nonhuman vertebrates. We investigated whether this equation could be used to interpolate missing growth data in children in the first three years of life and compared this interpolation to several common interpolation methods and pediatric growth models. METHODS: We developed a modified Michaelis-Menten equation and compared expected to actual growth, first in a local birth cohort (N = 97) then in a large, outpatient, pediatric sample (N = 14,695). RESULTS: The modified Michaelis-Menten equation showed excellent fit for both infant weight (median RMSE: boys: 0.22 kg [IQR:0.19; 90% < 0.43]; girls: 0.20 kg [IQR:0.17; 90% < 0.39]) and height (median RMSE: boys: 0.93 cm [IQR:0.53; 90% < 1.0]; girls: 0.91 cm [IQR:0.50;90% < 1.0]). Growth data were modeled accurately with as few as four values from routine well-baby visits in year 1 and seven values in years 1-3; birth weight or length was essential for best fit. Interpolation with this equation had comparable (for weight) or lower (for height) mean RMSE compared to the best performing alternative models. CONCLUSIONS: A modified Michaelis-Menten equation accurately describes growth in healthy babies aged 0-36 months, allowing interpolation of missing weight and height values in individual longitudinal measurement series. The growth pattern in healthy babies in resource-rich environments mirrors an enzymatic saturation curve.

Asunto(s)

RESUMEN

Foodborne pathogenic bacteria are widespread in various foods, whose cross-contamination and re-contamination are critical influences on food safety. Rapid, accurate, and sensitive detection of foodborne pathogenic bacteria remains a topic of concern. CRISPR/Cas12a can recognize double-stranded DNA directly, showing great potential in nucleic acid detection. However, few studies have investigated the cleavage properties of CRISPR/Cas12a. In this study, the trans-cleavage properties of LbCas12a and AsCas12a were investigated to construct the detection methods for foodborne pathogenic bacteria. The highly sensitive fluorescent strategies for foodborne pathogens were constructed by analyzing the cleavage rates and properties of substrates at different substrate concentrations. Cas12a was activated in the presence of foodborne pathogenic target sequence was present, resulting in the cleavage of a single-stranded reporter ssDNA co-labelled by fluorescein quencher and fluorescein. The sensitivity and specificity of the Cas12a fluorescent strategy was investigated with Salmonella and Staphylococcus aureus as examples. The results showed that AsCas12a was slightly more capable of trans-cleavage than LbCas12a. The detection limits of AsCas12a for Salmonella and Staphylococcus aureus were 24.9 CFU mL-1 and 1.50 CFU mL-1, respectively. In all the seven bacteria, Staphylococcus aureus and Salmonella were accurately discriminated. The study provided a basis for constructing and improving the CRISPR/Cas12a fluorescence strategies. The AsCas12a-based detection strategy is expected to be a promising method for field detection.

Asunto(s)

RESUMEN

Maud Menten was born and raised in remote regions of Canada. She obtained her MB/MD at the University of Toronto (1907/1911) and her PhD in biochemistry at the University of Chicago (1916). From 1907 to 1916, she trained at the Rockefeller Institute for Medical Research, the New York Infirmary for Women and Children, Western Reserve University in Cleveland, the Berlin Municipal Hospital in Germany, and the Barnard Free Skin and Cancer Hospital in St Louis. In 1916, she was appointed as pathologist at the Elizabeth Steel Magee Hospital, a charitable maternity hospital in Pittsburgh. She received a faculty appointment at the University of Pittsburgh (1918) and was appointed pathologist at Pittsburgh Children's Hospital (1926). In addition to being one of the first woman academic pathologists, she was likely the first perinatal, the second pediatric-perinatal, and the fourth pediatric pathologist to practice in North America. The importance of Menten's overall scientific contributions place her in the very upper echelon of 20th century pathologists. Her enzyme kinetic work resulted in the Michaelis-Menten equation, and her work in George Crile's laboratory in Cleveland provided a physiological basis for improved surgical outcomes. Her work in Pittsburgh was equally innovative, including initiating the field of enzyme histochemistry.

Asunto(s)

RESUMEN

The natural pigment of monascus is favored by human for its special coloring and physiological activity, and its development and application have attracted much attention. In this study, a novel corn oil-based nanoemulsion encapsulated with Yellow Monascus Pigment crude extract (CO-YMPN) was successfully prepared via the phase inversion composition method. The fabrication and stable conditions of the CO-YMPN including Yellow Monascus pigment crude extract (YMPCE) concentration, emulsifier ratio, pH, temperature, ionic strength, monochromatic light and storage time were investigated systemically. The optimized fabrication conditions were the emulsifier ratio (5:3 ratio of Tween 60 to Tween 80) and the YMPCE concentration (20.00% wt%)). Additionally, the DPPH radical scavenging capability of the CO-YMPN (19.47 ± 0.52%) was more excellent than each YMPCE or corn oil. Moreover, the kinetic analysis results based on Michaelis-Menten equation and constant revealed that CO-YMPN could improve lipase hydrolysis capacity. Therefore, the CO-YMPN complex had excellent storage stability and water solubility in the final water system, and the YMPCE showed brilliant stability.

Asunto(s)

RESUMEN

Background and Objectives: Standard pediatric growth curves cannot be used to impute missing height or weight measurements in individual children. The Michaelis-Menten equation, used for characterizing substrate-enzyme saturation curves, has been shown to model growth in many organisms including nonhuman vertebrates. We investigated this equation could be used to interpolate missing growth data in children in the first three years of life. Methods: We developed a modified Michaelis-Menten equation and compared expected to actual growth, first in a local birth cohort (N=97) then in a large, outpatient, pediatric sample (N=14,695). Results: The modified Michaelis-Menten equation showed excellent fit for both infant weight (median RMSE: boys: 0.22kg [IQR:0.19; 90%<0.43]; girls: 0.20kg [IQR:0.17; 90%<0.39]) and height (median RMSE: boys: 0.93cm [IQR:0.53; 90%<1.0]; girls: 0.91cm [IQR:0.50;90%<1.0]). Growth data were modeled accurately with as few as four values from routine well-baby visits in year 1 and seven values in years 1-3; birth weight or length was essential for best fit. Conclusions: A modified Michaelis-Menten equation accurately describes growth in healthy babies aged 0-36 months, allowing interpolation of missing weight and height values in individual longitudinal measurement series. The growth pattern in healthy babies in resource-rich environments mirrors an enzymatic saturation curve.

RESUMEN

Kinetic modeling has relied on using a tedious number of mathematical equations to describe molecular kinetics in interacting reactions. The long list of differential equations with associated abstract variables and parameters inevitably hinders readers' easy understanding of the models. However, the mathematical equations describing the kinetics of biochemical reactions can be exactly mapped to the dynamics of voltages and currents in simple electronic circuits wherein voltages represent molecular concentrations and currents represent molecular fluxes. For example, we theoretically derive and experimentally verify accurate circuit models for Michaelis-Menten kinetics. Then, we show that such circuit models can be scaled via simple wiring among circuit motifs to represent more and arbitrarily complex reactions. Hence, we can directly map reaction networks to equivalent circuit schematics in a rapid, quantitatively accurate, and intuitive fashion without needing mathematical equations. We verify experimentally that these circuit models are quantitatively accurate. Examples include 1) different mechanisms of competitive, noncompetitive, uncompetitive, and mixed enzyme inhibition, important for understanding pharmacokinetics; 2) product-feedback inhibition, common in biochemistry; 3) reversible reactions; 4) multi-substrate enzymatic reactions, both important in many metabolic pathways; and 5) translation and transcription dynamics in a cell-free system, which brings insight into the functioning of all gene-protein networks. We envision that circuit modeling and simulation could become a powerful scientific communication language and tool for quantitative studies of kinetics in biology and related fields.

RESUMEN

A colorimetric assay based on an enzyme-inhibition strategy is promising for the on-site detection of pesticide residues. However, very few works of pesticide detection were reported based on the inhibition toward nanozymes although nanozymes have demonstrated many advantages in sensing various targets. Herein, a facile colorimetric detection for Glyp was developed based on ß-CD@DNA-CuNCs enzyme mimics. The ß-CD@DNA-CuNCs with high peroxidase-like activity was synthesized using random DNA double strands as template and ß-CD as surface ligand. ß-CD@DNA-CuNCs could catalyze the H2O2-3,3',5,5'-tetramethylbenzidine (TMB) system. The oxidation product OxTMB with a blue color and presented a large absorption signal at 652 nm. However, Glyp could destroy the synergic effect between redox doublet (Cu2+/Cu+) on the ß-CD@DNA-CuNCs surface, resulting in the inhibition of the peroxidase-like activity. Colorimetric detection for Glyp could be established by detecting the changes of absorption signal at 652 nm. The linear range was 0.02-2 µg/mL and the detection limit was 0.85 ng/mL (3δ/s). The method was applied in measuring Glyp spiked in lake water and various food samples. This method had rapidness, high sensitivity, and selectivity advantages, indicating the high application potential in monitoring Glyp residue in food.

Asunto(s)

RESUMEN

The increasing interest in natural health-promoting compounds, which are mostly plant secondary metabolites, inspired attempts to stimulate mechanisms strengthening their bioaccumulation in crop plants via abiotic stress while maintaining the yield potential. This study investigates the long-term effects of limiting nitrogen (N) supply on the concentration of total phenolics, free radical activity of natural antioxidants, betacyanin content, biomass production, net photosynthetic rate, total chlorophyll content, and plant water relations in red beetroot plants (Beta vulgaris L.) grown hydroponically. Depending on fertilization, the range of N supply for evaporative demand comprises two contrasted nutrient zones, in which N is limiting (zone-1) or non-limiting (zone-2). Based on the carbon-nutrient-balance hypothesis, at the transition from 1st-zone to 2nd-zone, there is a narrow transition zone in which the plant nutrient status is considered 'critical'. Herein, to determine the 'critical' zone, a modified Michaelis-Menten (M-M) model was used using a piecewise linear regression on two indexes: net photosynthetic rates and free radical-scavenging capacity of phenolic antioxidants. The model showed that the 'critical' transition points of net photosynthetic rate and phenolic free radical content are located in a narrow zone ranging between 196.70 ± 8.75 and 271.54 ± 75.50 ppm NO3-, while the cropping season appears to affect slightly the range of 'critical' (transition) zone. Thus, supplying N to red beetroot plants to levels ranging within this 'critical' zone may be an efficient, profitable and sustainable way to increase the accumulation of health-promoting plant bioactive compounds (total phenolic compounds with radical activity and betacyanins) in hydroponically cultivated reed beetroot plants.

Asunto(s)

RESUMEN

The area where progress curve exhibits maximum curvature contains the most information about kinetic parameters. To determine these parameters more accurately from progress curves, we propose an iterative approach that calculates the area of maximum curvature based on an estimate of kinetic parameters and then recalculates the parameters based on time-concentration data points within this area. Based on this algorithm, we developed a computer script called iFIT as a free web application at http://www.i-fit.si. The benefits of working with iFIT are that it decreases the importance of initial substrate concentration and the impact of certain side reactions on the final calculated kinetic parameters.

Asunto(s)

RESUMEN

Soil nutrient cycling can be best studied by supplementing the soil with N and P fertilizers. Soil enzyme kinetic parameters (Vmax and Km) can be used to reflect the maximum reaction rates and affinities of soil enzymes. However, how N and P fertilizers affect the temperature sensitivity of soil enzyme kinetics is poorly understood. Therefore, our study investigated the response of soil enzyme kinetic temperature sensitivity relevant to C, N, and P cycles based on a 9-year fertilization (N and P) experiment performed in an alpine grassland on the Qinghai-Tibetan Plateau in China. Our results showed the following: N and P addition positively affected the Km of ß-glucosidase (BG); P and NP interaction significantly increased the Km of phosphatase (AP), indicating that N and P addition significantly negatively affected the substrate affinity of soil enzymes. The temperature sensitivity of Michaelis-Menten kinetics was different for different enzymes. N and P fertilization decreased the temperature sensitivity of Km of BG but increased the temperature sensitivity of the Km of N-acetyl-glucosaminidase (NAG) and AP. In our study, P and NP fertilization increased the temperature sensitivity and activation energy of the Vmax of BG, indicating that P elements promoted the secretion of more extracellular enzymes by soil microbes to cope with temperature changes. The enzymes involved in the soil N and P cycle responded to the exogenous N and P through increases and decreases in the temperature sensitivity of the Km and Vmax, respectively. This study is crucial for investigating the impact of nutrient input on soil ecosystem functions under future climate warming conditions.

Asunto(s)

RESUMEN

Several approaches for determining an enzyme's kinetic parameter Km (Michaelis constant) from progress curves have been developed in recent decades. In the present article, we compare different approaches on a set of experimental measurements of lactonase activity of paraoxonase 1 (PON1): (1) a differential-equation-based Michaelis-Menten (MM) reaction model in the program Dynafit; (2) an integrated MM rate equation, based on an approximation of the Lambert W function, in the program GraphPad Prism; (3) various techniques based on initial rates; and (4) the novel program "iFIT", based on a method that removes data points outside the area of maximum curvature from the progress curve, before analysis with the integrated MM rate equation. We concluded that the integrated MM rate equation alone does not determine kinetic parameters precisely enough; however, when coupled with a method that removes data points (e.g., iFIT), it is highly precise. The results of iFIT are comparable to the results of Dynafit and outperform those of the approach with initial rates or with fitting the entire progress curve in GraphPad Prism; however, iFIT is simpler to use and does not require inputting a reaction mechanism. Removing unnecessary points from progress curves and focusing on the area around the maximum curvature is highly advised for all researchers determining Km values from progress curves.

Asunto(s)

RESUMEN

BACKGROUND: Pharmacokinetics (PK) is the process of absorption, distribution, metabolism and elimination (ADME) of drugs. Some drugs undergo zero-order kinetics (ethyl alcohol), first order kinetics (piroxicam) and mixed order kinetics (ascorbic acid). Drugs that undergo Michaelis-Menten metabolism are characterized by either increased or decreased metabolism constant (Km) and maximum velocity (Vmax) of enzyme reaction. Hence literatures were searched with a view to translating in vitro-in vivo enzyme kinetics to pharmacokinetic/pharmacodynamic parameters for determination of enzyme inducing and inhibiting drugs, in order to achieve optimal clinical efficacy and safety. METHODS: A narrative review of retrospective secondary data on drugs, their metabolites, Vmax and Km, generated in the laboratory and clinical environments was adopted, using inclusion and exclusion criteria. Key word search strategy was applied, to assess databases of published articles on enzyme inducing and inhibiting drugs, that obey Michaelis-Menten kinetics. In vitro and in vivo kinetic parameters, such as concentration of substrate, rate of endogenous substrate production, cellular metabolic rate, initial velocity of metabolism, intrinsic clearance, percent saturation and unsaturation of the enzyme substrate, were calculated using original and modified formulas. Years and numbers of searched publications, types of equations and their applications were recorded. RESULTS: A total of fifty-six formulas both established and modified were applied in the present study. Findings have shown that theophylline, voriconazole, phenytoin, thiopental, fluorouracil, thyamine and thymidine are enzyme inducers whereas, mibefradil, metronidazole, isoniazid and puromicin are enzyme inhibitors. They are metabolized and eliminated according to Michaelis-Menten principle. The order could be mixed but may change to zero or first order, depending on drug concentration, frequency and route of drug administration. CONCLUSION: Hence, pharmacokinetic-pharmacodynamic translation can be optimally achieved by incorporating, newly modified Michaelis-Menten equations into pharmacokinetic formulas for clinical efficacy and safety of the enzyme inducing and inhibiting therapeutic agents used in laboratory and clinical settings.

Asunto(s)

RESUMEN

This chapter will provide a general introduction to the kinetics of enzyme-catalyzed reactions, including a general discussion of catalysts, reaction rates, and binding constants. This section will be followed by a discussion of various types of enzyme kinetics observed in drug metabolism reactions. A large number of enzymatic reactions can be adequately described by Michaelis-Menten kinetics. The Michaelis-Menten equation represents a rectangular hyperbola, with a y-asymptote at the Vmax value. However, in other cases, more complex kinetic models are required to explain the observed data. Atypical kinetic profiles are believed to arise from the simultaneous binding of multiple molecules within the active site of the enzyme (Tracy and Hummel, Drug Metab Rev 36:231-242, 2004). Several cytochromes P450 (CYPs) have large active sites that enable binding of multiple molecules (Yano et al., J Biol Chem 279:38091-38094, 2004; Wester et al., J Biol Chem 279:35630-35637, 2004). Thus, atypical kinetics are not uncommon in in vitro drug metabolism studies.

Asunto(s)

RESUMEN

An electrical conductivity (EC)-based closed-loop soilless culture system is practical for in-field deployment. Literature on the closed-loop soilless culture nutrient management premise the limitations in managing recycled nutrients under dynamic changes in individual nutrient uptake concentrations. However, recent systems analysis studies predicting solutions for nutrient fluctuation stabilization in EC-based closed-loop soilless culture systems suggest that the system may have a deterministic side in nutrient variation. This study aims to derive a nutrient control principle in an EC-based nutrient recycling soilless culture system by theoretical and experimental analyses. An integrated model of solutes such as K+, Ca2+, and Mg2+ and water transport in growing media, automated nutrient solution preparation, and nutrient uptake was designed. In the simulation, the intrinsic characteristics of nutrient changes among open-, semi- closed-, and closed-loop soilless cultures were compared, and stochastic simulations for nutrient control were performed in the closed-loop system. Four automated irrigation modules for comparing nutrient changes among the soilless culture systems were constructed in the greenhouse. Sweet pepper plants were used in the experiment. In the experimental analysis, nutrient concentration conversion to the proportion between nutrients revealed distinctive trends of nutrient changes according to the treatment level of drainage recycling. Theoretical and experimental analyses exhibited that nutrient variations in open-, semi- closed-, and closed-loop soilless culture systems can be integrated as a function of nutrient supply to the system's boundary areas. Furthermore, stochastic simulation analysis indicated that the nutrient ratio in the soilless culture system reveals the nutrient uptake parameter-based deterministic patterns. Thus, the nutrient ratio in the closed-loop soilless culture could be controlled by the long-term feedback of this ratio. We expect that these findings provide theoretical frameworks for systemizing nutrient management techniques in EC-based closed-loop soilless culture systems.

RESUMEN

Hydrodynamics has received considerable attention for application in improving microbial fuel cell (MFC) performance. In this study, a method is proposed to calculate the effect of fluid flow on MFC current production from sewage wastewater. First, the effect of flow velocity in an up-flow channel was evaluated, where an air-core MFC was polarized with external resistance (Rext). When tested at a flow velocity ranging from 0 to 20 cm s-1, the MFC with the higher flow velocity produced more current. In sewage wastewater with a chemical oxygen demand (COD) of 76 mg L-1, the MFC polarized with 3 Ω of Rext, and a flow velocity of 20 cm s-1 had 5.4 times more current than the MFC operating in a no-flow environment. This magnitude decreased with higher Rext and COD values. The Michaelis-Menten equation, modified herein by integrating COD and flow velocity, demonstrated the production of current by MFC operating under different conditions of flow. Calculation of current by MFC in a virtual fluid suggested that the flow surrounding the MFC varied with the configuration and affected the current production.

Asunto(s)

RESUMEN

Objective: To quantify metabolism, a physiologically based pharmacokinetic (PBPK) model for a volatile compound can be calibrated with the closed chamber (i.e. vapor uptake) inhalation data. Here, we introduce global optimization as a novel component of the predictive process and use it to illustrate a procedure for metabolic parameter estimation.Materials and methods: Male F344 rats were exposed in vapor uptake chambers to initial concentrations of 100, 500, 1000, and 3000 ppm chloroform. Chamber time-course data from these experiments, in combination with optimization using a chemical-specific PBPK model, were used to estimate Michaelis-Menten metabolic constants. Matlab® simulation software was used to integrate the mass balance equations and to perform the global optimizations using MEIGO (MEtaheuristics for systems biology and bIoinformatics Global Optimization - Version 64 bit, R2016A), a toolbox written for Matlab®. The cost function used the chamber time-course data and least squares to minimize the difference between data and simulation values.Results and discussion: The final values estimated for Vmax (maximum metabolic rate) and Km (affinity constant) were 1.2 mg/h and a range between 0.0005 and 0.6 mg/L, respectively. Also, cost function plots were used to analyze the dose-dependent capacity to estimate Vmax and Km within the experimental range used. Sensitivity analysis was used to assess identifiability for both parameters and show these kinetic data may not be sufficient to identify Km.Conclusion: In summary, this work should help toxicologists interested in optimization techniques understand the overall process employed when calibrating metabolic parameters in a PBPK model with inhalation data.

Asunto(s)

RESUMEN

This study describes the development of a new methodology based on a new integrated equation which allows the determination of the kinetic parameters for two mutually non-exclusive inhibitors when one of which is produced during the time-course reaction. Alkaline phosphatase simultaneously inhibited by phosphate and urea is used to illustrate this methodology, including the evaluation of interaction effects between them. Data analyses were carried out using two integrated velocity equations: exclusive linear mixed inhibition (EMI) and non-exclusive linear mixed inhibition (NEMI). Kinetic parameters are estimated using non-linear regression and results show that (i) the interaction between enzyme and the inhibitors urea and phosphate exhibit a mutually non-exclusive behavior; (ii) more specifically, these inhibitors are non-exclusive only in free enzyme (E) species; (iii) the inhibitors also show an interaction with enzyme classified as facilitation; (iv) phosphate is a competitive inhibitor and urea a mixed inhibitor; (v) the inhibition constant for phosphate is much lower than that determined for urea. In addition, a functional Excel Spreadsheet which can be adapted to any kinetic study is also included as a supplement.

Asunto(s)

RESUMEN

Measurement of steady-state rates (vSS) is straightforward in standard enzymology with soluble substrate, and it has been instrumental for comparative biochemical analyses within this area. For insoluble substrate, however, experimental values of vss remain controversial, and this has strongly limited the amount and quality of comparative analyses for cellulases and other enzymes that act on the surface of an insoluble substrate. In the current work, we have measured progress curves over a wide range of conditions for two cellulases, TrCel6A and TrCel7A from Trichoderma reesei, acting on their natural, insoluble substrate, cellulose. Based on this, we consider practical compromises for the determination of experimental vSS values, and propose a basic protocol that provides representative reaction rates and is experimentally simple so that larger groups of enzymes and conditions can be readily assayed with standard laboratory equipment. We surmise that the suggested experimental approach can be useful in comparative biochemical studies of cellulases; an area that remains poorly developed.

Asunto(s)