Substrate Kinetics Research Articles

Inhibition and Mechanism of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase.

Plasmodium falciparum hypoxanthine-guanine-xanthine phosphoribosyltransferase (PfHGXPRT) is essential for purine salvage of hypoxanthine into parasite purine nucleotides. Transition state analogue inhibitors of PfHGXPRT are characterized by kinetic analysis, thermodynamic parameters, and X-ray crystal structures. Compound 1, 9-deazaguanine linked to an acyclic ribocation phosphonate mimic, shows a kinetic Ki of 0.5 nM. Isothermal titration calorimetry (ITC) experiments of 1 binding to PfHGXPRT reveal enthalpically driven binding with negative cooperativity for the binding of two inhibitor molecules in the tetrameric enzyme. Crystal structures of 1 bound to PfHGXPRT define the hydrogen bond and ionic contacts to complement binding thermodynamics. Dynamics of ribosyl transfer from 5-phospho-α-d-ribosyl 1-pyrophosphate (PRPP) to hypoxanthine were examined by 18O isotope exchange at the bridging phosphoryl oxygen of PRPP pyrophosphate. Rotational constraints or short transition state lifetimes prevent torsional rotation and positional isotope exchange of bridging to nonbridging oxygen in the α-pyrophosphoryl group. Thermodynamic analysis of the transition state analogue and magnesium pyrophosphate binding reveal random and cooperative binding to PfHGXPRT, unlike the obligatory ordered reaction kinetics reported earlier for substrate kinetics.

Substrate Specificity and Kinetics of RNA Hydrolysis by SARS-CoV-2 NSP10/14 Exonuclease.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the virus that causes COVID-19, continues to evolve resistance to vaccines and existing antiviral therapies at an alarming rate, increasing the need for new direct-acting antiviral drugs. Despite significant advances in our fundamental understanding of the kinetics and mechanism of viral RNA replication, there are still open questions regarding how the proofreading exonuclease (NSP10/NSP14 complex) contributes to replication fidelity and resistance to nucleoside analogs. Through single turnover kinetic analysis, we show that the preferred substrate for the exonuclease is double-stranded RNA without any mismatches. Double-stranded RNA containing a 3'-terminal remdesivir was hydrolyzed at a rate similar to a correctly base-paired cognate nucleotide. Surprisingly, single-stranded RNA or duplex RNA containing a 3'-terminal mismatch was hydrolyzed at rates 125- and 45-fold slower, respectively, compared to the correctly base-paired double-stranded RNA. These results define the substrate specificity and rate of removal of remdesivir for the exonuclease and outline rigorous kinetic assays that could help in finding next-generation exonuclease inhibitors or nucleoside analogs that are able to evade excision. These results also raise important questions about the role of the polymerase/exonuclease complex in proofreading during viral replication. Addressing these questions through rigorous kinetic analysis will facilitate the search for desperately needed antiviral drugs to combat COVID-19.

An assay procedure to investigate the transformation of toxic heme into inert hemozoin via plasmodial heme detoxification protein

Most antimalarial therapeutics, including chloroquine and artemisinin, induce free heme-mediated toxicity in Plasmodium. This cytotoxic heme is produced as a by-product during the large-scale digestion of host hemoglobin. Conversion of this host-derived heme into inert crystalline hemozoin is the only defense mechanism in Plasmodium against heme-induced cytotoxicity. Heme detoxification protein (HDP), a highly conserved plasmodial protein, is reported to be the most efficient biological mediator for heme to hemozoin transformation. Despite its significance, HDP has never been extensively studied for heme transformation into hemozoin. Therefore, we wish to develop a method to study the HDP-mediated transformation of heme into hemozoin. We have adopted, modified, and optimized the pyridine hemochrome assay to study HDP catalysis and use substrate and time kinetics to study the HDP-mediated transformation of heme into hemozoin. In contrast to the previously reported assay for HDP, we found that the new assay is more precise, accurate, and handy, making it more suitable for kinetic studies. HDP-mediated transformation of heme into hemozoin is not a single-step process, and involves a transient intermediate, most likely a cyclic heme dimer. The kinetics and the manner of HDP-mediated hemozoin production are dependent on the substrate concentration, and a small fraction of substrate remains untransformed to hemozoin irrespective of reaction time. Combining HDP as a catalyst and the pyridine hemochrome assay will facilitate the efficient screening of future antimalarials.

DECOMPOSITION OF ENZYME KINETICS SYSTEM WITH FAST AND SLOW VARIABLES IN SUICIDE SUBSTRATE PROBLEM

In this paper an example of cooperative phenomenon, in which the substrate is known as suicide substrate, because it binds to the active enzyme as a substrate, inactivates because enzyme turns it into an inhibitor and provides an irreversible reaction is considered. In this case the substrate commits suicide. The aim of the work is to apply the method of integral manifolds to the reduction of the system of kinetics of suicide substrate. Work describes in detail the rationale for the decomposition algorithm of the enzyme kinetics problem for dynamical systems with fast and slow variables and the construction of integral manifolds for such systems, this article presents the results of applying the above methods to systems of the suicide substrate kinetics and compares solutions for four equations graphically. Comparisons of solutions for four equations are given graphically, the graphs are created using Microsoft Excel.

Nitrogen and Phosphorus Removal Efficiency and Denitrification Kinetics of Different Substrates in Constructed Wetland

Constructed wetlands (CWs) are generally used for wastewater treatment and removing nitrogen and phosphorus. However, the treatment efficiency of CWs is limited due to the poor performance of various substrates. To find appropriate substrates of CWs for micro-polluted water treatment, zeolite, quartz sand, bio-ceramsite, porous filter, and palygorskite self-assembled composite material (PSM) were used as filtering media to treat slightly polluted water with the aid of autotrophic denitrifying bacteria. PSM exhibited the most remarkable nitrogen and phosphorus removal performance among these substrates. The average removal efficiencies of ammonia nitrogen, total nitrogen, and total phosphorus of PSM were 66.4%, 58.1%, and 85%, respectively. First-order continuous stirred-tank reactor (first-order-CSTR) and Monod continuous stirred-tank reactor (Monod-CSTR) models were established to investigate the kinetic behavior of denitrification nitrogen removal processes using different substrates. Monod-CSTR model was proven to be an accurate model that could simulate nitrate nitrogen removal performance in vertical flow constructed wetland (VFCWs). Moreover, PSM demonstrated significant pollutant removal capacity with the kinetics coefficient of 2.0021 g/m2 d. Hence, PSM can be considered as a promising new type of substrate for micro-polluted wastewater treatment, and Monod-CSTR model can be employed to simulate denitrification processes.

Transport and kinetics in an electroenzymatic process incurred in PPO-based rotating disk bioelectrodes

• A nonlinear system of equation arising in PPO-based rotating disc electrodes is studied. • The reliable and closed-form of expression of concentrations and current are obtained. • The effect of rotation rate on sensitivity and amplification factors is discussed. • Numerical and analytical results are compared for experimental values of parameters. The motivation for this work was to develop a theoretical analysis corresponding to the transport and kinetics of substrate and product in PPO-based rotating disk bioelectrodes. This model is based on a nonlinear reaction–diffusion system containing the nonlinear term related to the CEC' mechanism. The hyperbolic function approach was used to solve the nonlinear coupled system of reaction–diffusion equations. The approximate analytical expressions concentrations of phenol, catechol and o-quinone and current response for all possible diffusion and kinetic parameters values are reported. The bioelectrode's sensitivity and amplification factor towards phenol substrate were also presented in terms of rotation rate and enzyme layer thickness. The numerical solution of this problem is also reported using Scilab/Matlab program. Also, a satisfactory agreement is noted between the analytical and numerical results upon comparison.

Nanoarrays-propped in situ photoelectrochemical system for microRNA detection

The exploitation of accurate and robust photoelectrochemical (PEC) approaches in whole biosensing community counts on the smooth electrons transport and delicate biological design. An aptasensor using depositional rutile titanium dioxide/bismuth vanadate nanoarrays (TiO2/BiVO4 NAs) as photoanode generator and strand-displacement model as nucleic acid frame was developed for microRNA-155 (miRNA-155) detection root in original idea. Photoanode was fabricated via a three-step overlayer deposition procedure including hydrothermal method, electrodeposition and ion beam sputtering. With a sufficient dense of oriented arrays, it provided a solid substrate and fast electronic kinetics reaction during host−guest recognition. In situ yielding electron donors were integrated into the PEC system to provide the most accurate quantitative analysis. The nanoarrays-triggered PEC platform opens another potential perspective in biosensing.

Response of substrate kinetics and biological mechanisms to various pH constrains for cultured Nitrobacter and Nitrospira in nitrifying bioreactor

Nitrite (NO2−) oxidation is an essential step of biological nitrogen cycling in natural ecosystems, and is performed by chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Although Nitrobacter and Nitrospira are regarded as representative NOB in nitrification systems, little attention has focused on kinetic characterisation of the coexistence of Nitrobacter and Nitrospira at various pH values. Here, we evaluate the substrate kinetics, biological mechanism and microbial community dynamics of an enrichment culture including Nitrobacter (17.5 ± 0.9%) and Nitrospira (7.2 ± 0.6%) in response to various pH constrains. Evaluation of the Monod equation at pH 6.0, 6.5, 7.0, 7.5, 8.0 and 8.5 showed that the enrichment had maximum rate (rmax) and maximum substrate affinity (KS) for NO2− oxidation at pH 7.0, which was also supported by the largest absolute abundance of Nitrobacter nxrA (5.26 × 107 copies per g wet sludge) and Nitrospira nxrB (1.975 × 109 copies per g wet sludge) genes. Moreover, the predominant species for the Nitrobacter-like nxrA were N. vulgaris and N. winogradskyi, while for the Nitrospira-like nxrB, the predominant species were N. japonica, N. calida and Ca. N. bockiana. Furthermore, the rmax was strongly and positively correlated with the abundance of the Nitrobacter nxrA or Nitrospira nxrB genes, or N. winogradsk, whereas KS was positively correlated with the abundance of Nitrobacter nxrA or Nitrospira nxrB genes or Ca. N. bockiana. Overall, this study could improve basis kinetic parameters and biological mechanism of NO2− oxidation in WWTPs.

Characterization of Lipases from <i>Geobacillus stearothermophilus</i> and <i>Anoxybacillus flavithermus</i>cell Lysates

The aim of this study was to characterize lipases from two thermophilic bacteria, Geobacillus stearothermophilus (GS) and Anoxybacillus flavithermus (AF) in heat treated cell lysates. The pH optimum, pH stability, temperature stability and substrate kinetics and specificity of the lipases were determined. Optimum activity of the lipase from GS (LGS) was observed at pH 7.5, and the optimum activity of the lipase from AF (LAF) was at pH 8.0. LGS was stable up to 70°C after 12 hrs while LAF was stable up to 90°C after 12 hrs. Both enzymes were stable at a pH range of 6 to 8 over 12 h at 4°C. LGS had a highest Vmax value of 22 mM·min-1·mg-1 with p-nitrophenyl acetate while the lowest Km was 0.8 mM with p-nitrophenyl laurate. The highest Vmax of LAF was 2.5 mM·min-1·mg-1 with p-nitrophenyl myristate, and the lowest Km was 0.4 mM with p-nitrophenyl octanoate. LGS preferentially hydrolyzed p-nitrophenyl acetate and p-nitrophenyl octanoate while LAF preferentially hydrolyzed p-nitrophenyl myristate and p-nitrophenyldodecanoate. Lipases from both GS and AF showed characteristics that would be beneficial in food processing.

Impact of the diffusion coefficient calculation on predicting Fe2B boride layer thickness

Abstract In this study, a single-phase boride layer thickness Fe2B is predicted on two different substrates (Armco iron and XC38 steel) by following the integral method. This method is a mathematical model based on a system of differential algebraic equations that help to deduce the diffusion coefficient, which is the key factor on predicting the layer thickness. Literatures cover different diffusion coefficients for each substrate, albeit researchers usually extract from experimental data, variations of growth rate constants within only one time treatment and deduce the diffusion coefficient from them. This deduction is done via an estimation of a frequency factor and an activation energy from the growth rate constants. Therefore, our main aim is to illustrate the impact of the deduction of the diffusion coefficient on predicting the boride layer thickness. Lastly, the impact with and without incubation time on the boriding kinetics of both substrates was also examined.

Radiotracer stereochemistry affects substrate affinity and kinetics for improved imaging of system xC- in tumors.

Amino acid utilization is perturbed in cancer cells, which rewire their metabolism to support cell survival and proliferation. This metabolic reprogramming can be exploited for diagnostic purposes through positron emission tomography imaging of fluorine-18 labeled amino acids. Despite its promise, little is known regarding transporter-recognition of non-natural amino acid stereoisomers or their utility for cancer imaging. We report here the synthesis and in vivo characterization of a radiolabeled amino acid (R)-4-(3-18F-fluoropropyl)-ʟ-glutamate ([18F]FRPG) and compared its tumor imaging properties to the 4S-isomer, [18F]FSPG.Methods: [18F]FRPG and [18F]FSPG uptake was assessed in H460 lung cancer cells, with efflux measured 30 min after removal of exogenous activity. Specificity of [18F]FRPG for system xC- was further examined following transporter inhibition and blocking studies with system xC- substrates. [18F]FRPG and [18F]FSPG pharmacokinetics was next quantified in mice bearing subcutaneous A549, H460, VCAP and PC3 tumors, with mice bearing A549 tumors imaged by PET/CT. To better-understand differential tumor retention, radiometabolite analysis was performed on tissue and blood samples after imaging. Next, [18F]FRPG and [18F]FSPG retention in lipopolysaccharide-treated lungs were compared to an orthotopic H460 lung cancer model. Finally, the sensitivity of [18F]FRPG to manipulation of the redox environment was examined in cell and in vivo models.Results: [18F]FRPG was specifically transported across the plasma membrane by the cystine/glutamate antiporter system xC- and retained at high levels in multiple tumor models. Conversely, [18F]FRPG was rapidly extracted from the blood and cleared from tissues with low system xC- expression. Due to its favorable imaging properties, tumor-to-blood ratios ≥10 were achieved with [18F]FRPG, which were either equal to or greater than [18F]FSPG. In addition, [18F]FRPG retention in orthotopic lung tumors with high system xC- expression was 2.5-fold higher than inflamed tissue, allowing for clear tumor visualization. In vivo, [18F]FRPG and [18F]FSPG were metabolized to a single species, with [18F]FRPG showing a higher percentage of parent radiotracer in tumors compared to [18F]FSPG. [18F]FRPG was sensitive to redox manipulations and tumor retention was reduced following treatment with liposomal doxorubicin in mice bearing ovarian tumors.Conclusions: Given the fast clearance and low background retention of [18F]FRPG throughout the body, this radiotracer holds promise for the imaging of system xC- activity and treatment response monitoring in tumors of the thorax, abdomen, and head and neck. [18F]FRPG PET imaging provides a sensitive noninvasive measure of system xC- and excellent properties for cancer imaging.

In Vitro Histone Demethylase Assays.

Dynamic histone methylation regulates gene activation and repression. It is involved in proliferation, differentiation, lineage specification, and development. Histone demethylase assays are invaluable in studying histone demethylation substrate recognition, kinetics, regulation, and inhibition by small molecules, many of which are potential therapeutics. Here we describe general procedures to purify recombinant enzymes from different expression hosts, and to prepare a broad range of substrates, as well as to set up a variety of in vitro histone demethylase assays. These assays provide useful tools for discoveries from enzymes to drugs.

Purification and Characterization of Thermostable Alkaline Xylanase by Aspergillus terreus from Elephant Dung

Aims: Purification and characterization of xylanase by Aspergillus terreus isolated from elephant dung.
 Study Design: Xylanase enzyme produced by A. terreus was extracted from the fermented solid medium using solid state fermentation and purified using chromatographic techniques. The purified enzyme was characterized for physio-chemical and kinetic properties.
 Place and Duration of Study: Experiments were performed at the School of Biotechnology, Devi Ahilya University, Indore, INDIA and Maharaja Ranjit Singh College of Professional Sciences, Indore, INDIA, between June, 2019 and September, 2021.
 Methodology: The enzyme was extracted and purified using ammonium sulphate precipitation, ion exchange chromatography using DEAE cellulose and gel filtration chromatography (GFC) using Sephadex G-200. The molecular weight of the purified enzyme was determined using native poly acrylamide gel electrophoresis (Native PAGE) and sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). The purified enzyme was characterized to determine pH and temperature optima. Thermostability, pH stability and substrate kinetics were studied for purified xylanase. Effect of several metal ions and detergents were also studied.
 Results: The alkali-thermo xylanase of Aspergillus terreus was purified to 14.6-fold with a 39.48% recovery through IEC on DEAE-cellulose and GFC using Sephadex G-200. The purified enzyme had a specific activity, 111.6 U/mg. The SDS-PAGE revealed that the enzyme was monomeric with a molecular weight of 87 kDa. The optimum pH and temperature were 8 and 60⁰C, respectively. The Km and Vmax values of the partially purified xylanase were found to be 0.016 mg/l and 102.64 U/mg protein, respectively with birch wood xylan as substrate.
 Conclusion: The enzyme was active over a wide pH range of 6-11 and temperature range of 40⁰C to 80ºC, indicating its alkali tolerant and thermostable characteristics which is the requirement of different industries. Several ions namely Zn2+ enhanced xylanase activity by 187% followed by Ca2+ (129%), Mg2+ (123%), NH4+ (146%) and Fe3+ (118%) at 10 mM concentration. However, Cu2+ and Hg2+ completely inhibited xylanase activity. This research provides the basis for application of xylanase and improves its biotechnological potential in mainly in paper pulp industry, biofuel generation and in bread baking.

Albumin and fibrinogen kinetics in sepsis: a prospective observational study

BackgroundThe measurement of circulating substrate concentrations does not provide information about substrate kinetics. It, therefore, remains unclear if a decrease in plasma concentration of albumin, as seen during critical illness, is a consequence of suppressed production in the liver or increased peripheral clearance. In this study, using stable isotope tracer infusions, we measured albumin and fibrinogen kinetics in septic patients and in a control group of non-septic subjects.MethodsWith the approval from the institutional Research Ethics Board and after obtaining written informed consent from patients or their substitute decision maker, mechanically ventilated patients with sepsis and patients scheduled for elective coronary artery bypass grafting were enrolled. Patients in the non-sepsis group were studied on the day before surgery. The stable isotope L-[ring-2H5]phenylalanine was used to measure absolute synthesis rates (ASR) of albumin and fibrinogen. A priming dose of L-[ring-2H5]phenylalanine (4 µmol/kg) was given followed by a six-hour infusion at a rate of 0.15 µmol/kg/min. At baseline and hourly thereafter, blood was drawn to measure isotope enrichments by gas chromatography/mass spectrometry. Very low density lipoprotein apolipoprotein-B 100 isotopic enrichment was used to represent the isotopic enrichment of the phenylalanine precursor pool from which the liver synthesizes proteins. Plasma albumin and fibrinogen concentrations were also measured.ResultsMean plasma albumin in septic patients was decreased when compared to non-septic patients, while synthesis rates were comparable. Mean plasma fibrinogen and ASR in septic patients was increased when compared to non-septic patients. In non-septic patients, no statistically significant correlation between plasma albumin and ASR was observed but plasma fibrinogen significantly correlated with ASR. In septic patients, plasma albumin and fibrinogen significantly correlated with ASR.ConclusionsWhile septic patients showed lower plasma albumin levels than non-septic patients, albumin synthesis was similar in the two groups suggesting that hypoalbuminemia during sepsis was not caused by suppressed hepatic production but a result of enhanced clearance from the circulation. Hyperfibrinogenemia in septic patients was a consequence of increased fibrinogen production.Trial registration: ClinicalTrials.gov: NCT02865408 (registered on August 12, 2016) and ClinicalTrials.gov: NCT02549443 (registered on September 15, 2015).

Quantifying Carbohydrate-Active Enzyme Activity with Glycoprotein Substrates Using Electrospray Ionization Mass Spectrometry and Center-of-Mass Monitoring

Carbohydrate-active enzymes (CAZymes) play critical roles in diverse physiological and pathophysiological processes and are important for a wide range of biotechnology applications. Kinetic measurements offer insight into the activity and substrate specificity of CAZymes, information that is of fundamental interest and supports diverse applications. However, robust and versatile kinetic assays for monitoring the kinetics of intact glycoprotein and glycolipid substrates are lacking. Here, we introduce a simple but quantitative electrospray ionization mass spectrometry (ESI-MS) method for measuring the kinetics of CAZyme reactions involving glycoprotein substrates. The assay, referred to as center-of-mass (CoM) monitoring (CoMMon), relies on continuous (real-time) monitoring of the CoM of an ensemble of glycoprotein substrates and their corresponding CAZyme products. Notably, there is no requirement for calibration curves, internal standards, labeling, or mass spectrum deconvolution. To demonstrate the reliability of CoMMon, we applied the method to the neuraminidase-catalyzed cleavage of N-acetylneuraminic acid (Neu5Ac) residues from a series of glycoproteins of varying molecular weights and degrees of glycosylation. Reaction progress curves and initial rates determined with CoMMon are in good agreement (initial rates within ≤5%) with results obtained, simultaneously, using an isotopically labeled Neu5Ac internal standard, which enabled the time-dependent concentration of released Neu5Ac to be precisely measured. To illustrate the applicability of CoMMon to glycosyltransferase reactions, the assay was used to measure the kinetics of sialylation of a series of asialo-glycoproteins by a human sialyltransferase. Finally, we show how combining CoMMon and the competitive universal proxy receptor assay enables the relative reactivity of glycoprotein substrates to be quantitatively established.

Human variability in polymorphic CYP2D6 metabolism: Implications for the risk assessment of chemicals in food and emerging designer drugs

The major human cytochrome P450 CYP2D6 isoform enzyme plays important roles in the liver and in the brain with regards to xenobiotic metabolism. Xenobiotics as CYP2D6 substrates include a whole range of pharmaceuticals, pesticides and plant alkaloids to cite but a few. In addition, a number of endogenous compounds have been shown to be substrates of CYP2D6 including trace amines in the brain such as tyramine and 5-methoxytryptamine as well as anandamide and progesterone. Because of the polymorphic nature of CYP2D6, considerable inter-phenotypic and inter-ethnic differences in the pharmaco/toxicokinetics (PK/TK) and metabolism of CYP2D6 substrates exist with potential consequences on the pharmacology and toxicity of chemicals. Here, large extensive literature searches have been performed to collect PK data from published human studies for a wide range of pharmaceutical probe substrates and investigate human variability in CYP2D6 metabolism. The computed kinetic parameters resulted in the largest open source database, quantifying inter-phenotypic differences for the kinetics of CYP2D6 probe substrates in Caucasian and Asian populations, to date. The database is available in supplementary material (CYPD6 DB) and EFSA knowledge junction (DOI to added). Subsequently, meta-analyses using a hierarchical Bayesian model for markers of chronic oral exposure (oral clearance, area under the plasma concentration time curve) and acute oral exposure (maximum plasma concentration (Cmax) provided estimates of inter-phenotypic differences and CYP2D6-related uncertainty factors (UFs) for chemical risk assessment in Caucasian and Asian populations classified as ultra-rapid (UM), extensive (EMs), intermediate (IMs) and poor metabolisers (PMs). The model allowed the integration of inter-individual (i.e. inter-phenotypic and inter-ethnic), inter-compound and inter-study variability together with uncertainty in each PK parameter. Key findings include 1. Higher frequencies of PMs in Caucasian populations compared to Asian populations (>8% vs 1-2%) for which EM and IM were the most frequent phenotype. 2. Large inter-phenotypic differences in PK parameters for Caucasian EMs (coefficients of variation (CV)>50%) compared with Caucasian PMs and Asian EMs and IMs (i.e CV<40%). 3. Inter-phenotypic PK differences between EMs and PMs in Caucasian populations increase with the quantitative contribution of CYP2D6 for the metabolism (fm) for a range of substrates (fmCYP2D6 range: 20-95% of dose) (range: 1-54) to a much larger extent than those for Asian populations (range: 1-4). 4. Exponential meta-regressions between FmCYP2D6 in EMs and inter-phenotypic differences were also shown to differ between Caucasian and Asian populations as well as CYP2D6-related UFs. Finally, implications of these results for the risk assessment of food chemicals and emerging designer drugs of public health concern, as CYP2D6 substrates, are highlighted and include the integration of in vitro metabolism data and CYP2D6-variability distributions for the development of quantitative in vitro in vivo extrapolation models.

Conceptualizing Biogeochemical Reactions With an Ohm's Law Analogy

AbstractIn studying problems like plant‐soil‐microbe interactions in environmental biogeochemistry and ecology, one usually has to quantify and model how substrates control the growth of, and interaction among, biological organisms (and abiotic factors, e.g., adsorptive mineral soil surfaces). To address these substrate‐consumer relationships, many substrate kinetics and growth rules have been developed, including the famous Monod kinetics for single‐substrate‐based growth and Liebig's law of the minimum for multiple‐nutrient‐colimited growth. However, the mechanistic basis that leads to these various concepts and mathematical formulations and the implications of their parameters are often quite uncertain. Here, we show that an analogy based on Ohm's law in electric circuit theory is able to unify many of these different concepts and mathematical formulations. In this Ohm's law analogy, a resistor is defined by a combination of consumers’ and substrates’ kinetic traits. In particular, the resistance is equal to the mean first passage time that has been used to derive the Michaelis‐Menten kinetics under substrate replete conditions for a single substrate as well as the predation rate of individual organisms. We further show that this analogy leads to important insights on various biogeochemical problems, such as (a) multiple‐nutrient‐colimited biological growth, (b) denitrification, (c) fermentation under aerobic conditions, (d) metabolic temperature sensitivity, and (e) the legitimacy of Monod kinetics for describing bacterial growth. We expect that our approach will help both modelers and nonmodelers to better understand and formulate hypotheses when studying certain aspects of environmental biogeochemistry and ecology.

Dual Active and Kinetically Inter-Promoting Li3VO4/Graphene Anode Enabling Printable High Energy Density Lithium Ion Micro Capacitors

Planar micro-supercapacitors (MSCs) with high energy/power densities and long cycle life are expected to expedite the development of the future wearable miniaturized electronics. However, its low energy density issue always falls short in ever-increasing demands of specific energy consumption. Herein, a dual active and kinetically inter-promoting Li3VO4 (LVO)/graphene composite is designed as the anode for high energy density lithium ion micro capacitors (LIMCs). The LVO nanoparticles are evenly confined on graphene nanosheets through an atomic layer pre-deposition (ALD) technique, which substantially disperses the nucleation site and impedes the coarse grain growth in the successive solid-state formation of LVO. The much-promoted reaction kinetics of LVO and graphene substrate with sufficient diffusion space in the interdigital electrodes of LIMCs synergistically boost the three-dimensional and efficiently lithium ion storage behavior. The LVO/graphene exhibits extraordinary rate capability (98.5 mAh g−1 at 40 A g−1 (100 C)) and long-term stability. All the current collectors and asymmetric interdigital electrodes are spray printed, opening a facile and delicate technique for a large-scale production of LIMCs. The LIMCs deliver a superior volumetric energy density of 51.4 mWh cm−3, excellent flexible and cyclic stability, demonstrating a great potential for the future miniaturized, flexible, and high-performance energy storage devices.

Structure and hydrogen bonds of hydrophobic deep eutectic solvent‐aqueous liquid–liquid interfaces

AbstractHydrophobic deep eutectic solvents (DESs) emerge as candidates to extract organic substrates from aqueous solutions. The DES‐aqueous liquid–liquid interface plays a vital role in the extraction ability of DESs because the nonbulk structure of interfacial molecules could cause thermodynamic and kinetic barriers. One question is how the DES compositions affect the structural features of the interface. We investigate the density profile, dipole moment, and hydrogen bonds of eight hydrophobic DES‐aqueous interfaces using molecular dynamics simulations. The eight DESs are composed of four organic compounds: decanoic acid, menthol, thymol, and lidocaine. The results show the variations of dipole moment and hydrogen bond structure and dynamics at the interfaces. These variations could influence the extraction ability of DES through adjusting the partition and kinetics of organic substrates in the DES‐aqueous biphasic systems. We also analyze the relationship between the variation of these interfacial features and the size and hydrophobicity of DES components.

Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities

Nitrification, the oxidation of ammonia to nitrate, is an essential process in the biogeochemical nitrogen cycle. The first step of nitrification, ammonia oxidation, is performed by three, often co-occurring guilds of chemolithoautotrophs: ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox). Substrate kinetics are considered to be a major niche-differentiating factor between these guilds, but few AOA strains have been kinetically characterized. Here, the ammonia oxidation kinetic properties of 12 AOA representing all major cultivated phylogenetic lineages were determined using microrespirometry. Members of the genus Nitrosocosmicus have the lowest affinity for both ammonia and total ammonium of any characterized AOA, and these values are similar to previously determined ammonia and total ammonium affinities of AOB. This contrasts previous assumptions that all AOA possess much higher substrate affinities than their comammox or AOB counterparts. The substrate affinity of ammonia oxidizers correlated with their cell surface area to volume ratios. In addition, kinetic measurements across a range of pH values supports the hypothesis that—like for AOB—ammonia and not ammonium is the substrate for the ammonia monooxygenase enzyme of AOA and comammox. Together, these data will facilitate predictions and interpretation of ammonia oxidizer community structures and provide a robust basis for establishing testable hypotheses on competition between AOB, AOA, and comammox.