scholarly journals Modeling and Exploiting Microbial Temperature Response

Processes ◽  
2020 ◽  
Vol 8 (1) ◽  
pp. 121 ◽  
Author(s):  
Philipp Noll ◽  
Lars Lilge ◽  
Rudolf Hausmann ◽  
Marius Henkel
Keyword(s):  
Enzymatic Reaction ◽  
Control Variable ◽  
Temperature Response ◽  
Reaction Rates ◽  
Industrial Biotechnology ◽  
Metabolic Reaction ◽  
Bioprocess Engineering ◽  
Different Temperatures ◽  
Svante Arrhenius ◽  
The 19Th Century

Temperature is an important parameter in bioprocesses, influencing the structure and functionality of almost every biomolecule, as well as affecting metabolic reaction rates. In industrial biotechnology, the temperature is usually tightly controlled at an optimum value. Smart variation of the temperature to optimize the performance of a bioprocess brings about multiple complex and interconnected metabolic changes and is so far only rarely applied. Mathematical descriptions and models facilitate a reduction in complexity, as well as an understanding, of these interconnections. Starting in the 19th century with the “primal” temperature model of Svante Arrhenius, a variety of models have evolved over time to describe growth and enzymatic reaction rates as functions of temperature. Data-driven empirical approaches, as well as complex mechanistic models based on thermodynamic knowledge of biomolecular behavior at different temperatures, have been developed. Even though underlying biological mechanisms and mathematical models have been well-described, temperature as a control variable is only scarcely applied in bioprocess engineering, and as a conclusion, an exploitation strategy merging both in context has not yet been established. In this review, the most important models for physiological, biochemical, and physical properties governed by temperature are presented and discussed, along with application perspectives. As such, this review provides a toolset for future exploitation perspectives of temperature in bioprocess engineering.

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.

Stability of Chemically Degraded Friction Reducers and Their Relationship to Regain Conductivity

2021 ◽  
Author(s):  
Philip Ayazi ◽  
Gabriel Monreal ◽  
Hassan Bleibel ◽  
Frank Zamora ◽  
Larry Watters
Keyword(s):  
Zeta Potential ◽  
Selection Process ◽  
Quantitative Relationship ◽  
Reaction Rates ◽  
Friction Reduction ◽  
Chemical Degradation ◽  
Industry Standard ◽  
Different Temperatures ◽  
Tracking Behavior ◽  
Polymer Dispersions

Abstract Previously, it was shown that zeta potential could be used as a metric to determine friction reducer (FR) performance. Specifically, the extent of and how quickly the FR reaches peak friction reduction in source water. A correlation postulated from the previous work is zeta potentials relationship to an FR's stability during mechanical or chemical degradation. In other words, can zeta potential be used as a metric to determine the extent of polymer breaking and can this relationship be translated to regained conductivity? This paper describes a laboratory study of zeta potential measurements to track breaker reaction rates, stability of broken polymer dispersions, and the relationship between chemical degradation of FRs and regained conductivity. The approach of this investigation involves measuring zeta potential of frac fluids formulated using anionic and cationic FRs with varying types and concentrations of breakers at different temperatures and times. These metrics are then correlated with regain conductivity. A quantitative relationship exists between zeta potential, fluid rheology, and regain conductivity. Zeta potential evaluation of degraded FR's in frac fluids correlate to performance in regain conductivity testing. These measurements can expedite the selection of chemical breakers with respect to performance. Zeta potential measurements of degraded FR are indicative of broken FR dispersion stability which has impact on regain conductivity. Tracking behavior of cationic FR's using zeta potential reveals the materials can become anionic with time and temperature and become susceptible to agglomeration with iron. Zeta potential measurements can be used during a chemical breaker selection process as a viable supplement to industry standard tests for assessing the comparative effectiveness of chemical breakers in frac fluids.

scholarly journals Optimal density of biological cells

2020 ◽  
Author(s):  
Tin Yau Pang ◽  
Martin J. Lercher
Keyword(s):  
Reaction Kinetics ◽  
Mass Density ◽  
Reaction Rates ◽  
Cellular Growth ◽  
Metabolic Reaction ◽  
Optimal Density ◽  
E Coli ◽  
Background Density ◽  
Model Cell ◽  
Metabolic Reactions

AbstractA substantial fraction of the bacterial cytosol is occupied by catalysts and their substrates. While a higher volume density of catalysts and substrates might boost biochemical fluxes, the resulting molecular crowding can slow down diffusion, perturb the reactions’ Gibbs free energies, and reduce the catalytic efficiency of proteins. Due to these tradeoffs, dry mass density likely possesses an optimum that facilitates maximal cellular growth and that is interdependent on the cytosolic molecule size distribution. Here, we analyse the balanced growth of a model cell with metabolic and ribosomal reactions, accounting systematically for crowding effects on reaction kinetics. We find that changes in cytosolic density affect biochemical efficiency more strongly for ribosomal reactions than for metabolic reactions, which involve much smaller catalysts and reactants. Accordingly, optimal cytosolic density depends on cellular resource allocation into ribosomal vs. metabolic reactions. A shift in the relative contributions of these sectors to the cellular economy explains the 10% difference in the cytosolic density between E. coli bacteria growing in nutrient-rich and -poor environments. We conclude that cytosolic density variation in E. coli is consistent with an optimality principle of cellular efficiency.Significance statementThe cellular cytosol harbours diverse molecules, whose crowding slows down diffusion and perturbs the chemical equilibrium of biochemical reactions. Reaction rates thus depend not only on the reactants themselves, but also on the background density of other molecules; consequently, maximal cell growth requires an optimal density. Here, we simulate a model cell with crowding-adjusted metabolic reaction kinetics. Its cytosol accommodates two types of reactions: metabolic reactions involving small molecules, and protein production reactions involving much larger molecules. These two cellular subsystems have distinct optimal densities, and a shift in their relative contribution to the cellular biomass explains the 10% difference in the cytosolic density between E. coli bacteria growing in nutrient-rich and -poor environments.

scholarly journals Phase Separation Can Increase Enzyme Activity by Concentration and Molecular Organization

2020 ◽  
Author(s):  
William Peeples ◽  
Michael K. Rosen
Keyword(s):  
Phase Separation ◽  
Enzymatic Reaction ◽  
Reaction Rates ◽  
Quantitative Model ◽  
Mass Action ◽  
Molecular Organization ◽  
Scaffolding Proteins ◽  
Enzyme Cascade ◽  
Separation Threshold ◽  
Liquid Liquid Phase Separation

AbstractBiomolecular condensates concentrate macromolecules into discrete cellular foci without an encapsulating membrane. Condensates are often presumed to increase enzymatic reaction rates through increased concentrations of enzymes and substrates (mass action), although this idea has not been widely tested and other mechanisms of modulation are possible. Here we describe a synthetic system where the SUMOylation enzyme cascade is recruited into engineered condensates generated by liquid-liquid phase separation of multidomain scaffolding proteins. SUMOylation rates can be increased up to 36-fold in these droplets compared to the surrounding bulk, depending on substrate KM. This dependency produces substantial specificity among different substrates. Analyses of reactions above and below the phase separation threshold lead to a quantitative model in which reactions in condensates are accelerated by mass action and by changes in substrate KM, likely due to scaffold-induced molecular organization. Thus, condensates can modulate reaction rates both by concentrating molecules and by physically organizing them.

scholarly journals Candida albicans phosphate transport, facilitating nucleotide sugar biosynthesis, contributes to cell wall stability.

2021 ◽  
Vol 3 (12) ◽  
Author(s):  
Maikel Acosta-Zaldivar ◽  
Wanjun Qi ◽  
Ning-Ning Liu ◽  
Joann Diray-Arce ◽  
Louise A. Walker ◽  
...  
Keyword(s):  
Cell Wall ◽  
Candida Albicans ◽  
Enzymatic Reaction ◽  
Phosphate Starvation ◽  
Reaction Rates ◽  
Outer Cell ◽  
Cell Wall Polysaccharides ◽  
Nucleotide Sugar ◽  
Structural Cell ◽  
Chitin Synthases

The Candida albicans high-affinity phosphate transporter Pho84 is required for normal Target of Rapamycin signaling, oxidative stress resistance and virulence of this fungal pathogen. It also contributes to C. albicans’ tolerance of two antifungal drug classes, polyenes and echinocandins. Echinocandins inhibit biosynthesis of a major cell wall component, beta-1,3-glucan. Cells lacking Pho84 were hypersensitive to other forms of cell wall stress beyond echinocandin exposure, while their cell wall integrity signaling response was weak. Metabolomics experiments showed that levels of phosphoric intermediates, including nucleotides like ATP and nucleotide sugars, were low in pho84 mutant compared to wild type cells recovering from phosphate starvation. Non-phosphoric precursors like nucleobases and nucleosides were elevated. Outer cell wall phosphomannan biosynthesis requires a nucleotide sugar,GDP-mannose. The nucleotide sugar UDP-glucose is the substrate of enzymes that synthesize two major structural cell wall polysaccharides, beta-1,3- and beta-1,6-glucan. Another nucleotide sugar, UDP-N-acetylglucosamine, is the substrate of chitin synthases which produce a stabilizing component of the intercellular septum and of lateral cell walls. Lack of Pho84 activity, and phosphate starvation, potentiated pharmacological or genetic perturbation of these enzymes. Our model is that low substrate concentrations of beta-D-glucan- and chitin synthases diminish enzymatic reaction rates and potentiate pharmacologic inhibitors to decrease the yield of their cell wall-stabilizing products. Phosphate import is not conserved between fungal and human cells, and humans do not synthesize beta-D-glucans or chitin. Hence inhibiting these processes simultaneously could yield potent antifungal effects with low toxicity to humans.

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.

scholarly journals Bayesian metabolic flux analysis reveals intracellular flux couplings

2019 ◽  
Vol 35 (14) ◽  
pp. i548-i557 ◽  
Author(s):  
Markus Heinonen ◽  
Maria Osmala ◽  
Henrik Mannerström ◽  
Janne Wallenius ◽  
Samuel Kaski ◽  
...  
Keyword(s):  
Steady State ◽  
Metabolic Flux Analysis ◽  
Metabolic Flux ◽  
Reaction Network ◽  
Reaction Rates ◽  
Supplementary Information ◽  
Flux Analysis ◽  
Metabolic Reaction ◽  
Metabolic Systems ◽  
Genome Scale

AbstractMotivationMetabolic flux balance analysis (FBA) is a standard tool in analyzing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place model assumptions on fluxes due to the convenience of formulating the problem as a linear programing model, while many methods do not consider the inherent uncertainty in flux estimates.ResultsWe introduce a novel paradigm of Bayesian metabolic flux analysis that models the reactions of the whole genome-scale cellular system in probabilistic terms, and can infer the full flux vector distribution of genome-scale metabolic systems based on exchange and intracellular (e.g. 13C) flux measurements, steady-state assumptions, and objective function assumptions. The Bayesian model couples all fluxes jointly together in a simple truncated multivariate posterior distribution, which reveals informative flux couplings. Our model is a plug-in replacement to conventional metabolic balance methods, such as FBA. Our experiments indicate that we can characterize the genome-scale flux covariances, reveal flux couplings, and determine more intracellular unobserved fluxes in Clostridium acetobutylicum from 13C data than flux variability analysis.Availability and implementationThe COBRA compatible software is available at github.com/markusheinonen/bamfa.Supplementary informationSupplementary data are available at Bioinformatics online.

Temperature, Dynamics, and Enzyme-Catalyzed Reaction Rates

2020 ◽  
Vol 49 (1) ◽  
pp. 163-180 ◽  
Author(s):  
Vickery L. Arcus ◽  
Adrian J. Mulholland
Keyword(s):  
Molecular Mechanisms ◽  
Activation Parameters ◽  
Reaction Rates ◽  
Rate Theory ◽  
Different Temperatures ◽  
State Ensemble ◽  
Catalyzed Reactions ◽  
Enzyme Catalyzed Reactions ◽  
Transition State Ensemble ◽  
Rate Limiting

We review the adaptations of enzyme activity to different temperatures. Psychrophilic (cold-adapted) enzymes show significantly different activation parameters (lower activation enthalpies and entropies) from their mesophilic counterparts. Furthermore, there is increasing evidence that the temperature dependence of many enzyme-catalyzed reactions is more complex than is widely believed. Many enzymes show curvature in plots of activity versus temperature that is not accounted for by denaturation or unfolding. This is explained by macromolecular rate theory: A negative activation heat capacity for the rate-limiting chemical step leads directly to predictions of temperature optima; both entropy and enthalpy are temperature dependent. Fluctuations in the transition state ensemble are reduced compared to the ground state. We show how investigations combining experiment with molecular simulation are revealing fundamental details of enzyme thermoadaptation that are relevant for understanding aspects of enzyme evolution. Simulations can calculate relevant thermodynamic properties (such as activation enthalpies, entropies, and heat capacities) and reveal the molecular mechanisms underlying experimentally observed behavior.

scholarly journals Synthesis of Thermo-Responsive Block-Graft Copolymer Based on PCL and PEG Analogs, and Preparation of Hydrogel via Click Chemistry

Polymers ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 765 ◽  
Author(s):  
Pei Shang ◽  
Jie Wu ◽  
Xiaoyu Shi ◽  
Zhidan Wang ◽  
Fei Song ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Graft Copolymer ◽  
Self Assembly ◽  
Three Dimensional ◽  
Cycloaddition Reaction ◽  
Temperature Response ◽  
Gel Permeation Chromatography ◽  
Proton Nuclear Magnetic Resonance ◽  
Fluorescence Probes ◽  
Different Temperatures

Thermo-responsive cross-linkable mPEG-b-[PCL-g-(MEO2MA-co-OEGMA)]-b-mPEG was synthesized by ring-opening polymerization (ROP) and atom transfer radical polymerization (ATRP). Then, the cross-linkable block-graft copolymer was used to prepare hydrogel via a copper-catalyzed 1,3-dipolar azide-alkyne cycloaddition reaction. The chemical structure and composition of copolymer were characterized by proton nuclear magnetic resonance (1H NMR), Fourier-transform infrared (FT-IR) and gel permeation chromatography (GPC). The self-assembly behaviors of the copolymer in aqueous solution were studied by UV spectrophotometer, fluorescence probes, the surface tension method, dynamic light scattering, and transmission electron microscopy. The results proved that the copolymer has excellent solubility and better temperature response. The three-dimensional network structure of the gels, observed by scanning electron microscopy at different temperatures, indicated that the gels have temperature response.

Automated Enzymatic Determination of L-Lactate in Serum, with Use of a Miniature Centrifugal Anlyzer

1976 ◽  
Vol 22 (12) ◽  
pp. 2038-2041 ◽  
Author(s):  
T P Hadjiioannou ◽  
S I Hadjiioannou ◽  
S D Brunk ◽  
H V Malmstadt
Keyword(s):  
Lactate Dehydrogenase ◽  
Reaction Rate ◽  
Enzymatic Reaction ◽  
Reaction Rates ◽  
Enzymatic Determination ◽  
Analytical Recovery ◽  
Rate Method ◽  
Relative Errors ◽  
Lithium Lactate

Abstract We describe an automated enzymatic reaction-rate method for spectrophotometric determination of lactate in serum with a miniature centrifugal analyzer. The L(+)-lactate is selectively oxidized in the presence of lactate dehydrogenase (EC 1.1.1.27) and NAD+ to from NADH, whitch is measured from its absorption. Reaction rates are determined automatically, and unknown concentrations are calculated from a computer0generated calibration curve with aqueous lithium lactate standards. Lactte concentrations in the range 0.32-1.6 µg/4 µl (80-400 mg/liter) of sample were determined with relative errors and coefficient of variation of 4.8%. Analytical recovery of lactate added to pooled serum was 89-112% (average, 101%). Comparison with a kit ("Rapid Lactate") method gave a correlation coefficient squared of 0.979 over a concentration range of 39-779 mg/liter.

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