Cover Feature: Superior Proton-Transfer Catalytic Promiscuity of Cytochrome c in Self-Organized Media (7/2021)

Evolutionarily elderly proteins commonly feature greater catalytic promiscuity. Cytochrome c is among the first set of proteins in evolution to have known prospects in electron transport and peroxidative properties. Here, we report that cyt c is also a proficient proton-transfer catalyst and enhances the Kemp elimination (KE; model reaction to show proton transfer catalytic property) by ∼750-fold on self-organized systems like micelles and vesicles. The self-organized systems mimic the mitochondrial environment in vitro for cyt c. Using an array of biophysical and biochemical mutational assays, both acid–base and redox mechanistic pathways have been explored. The histidine moiety close to hemin group (His18) is mainly responsible for proton abstraction to promote the concerted E2 pathway for KE catalysis when cyt c is in its oxidized form; this has also been confirmed by a H18A mutant of cyt c. However, the redox pathway is predominant under reducing conditions in the presence of dithiothreitol over the pH range 6–7.4. Interestingly, we found almost 750-fold enhanced KE catalysis by cyt c compared to aqueous buffer. Overall, in addition to providing mechanistic insights, the data reveal an unprecedented catalytic property of cyt c that could be of high importance in an evolutionary perspective considering its role in delineating the phylogenic tree and also towards generating programmable designer biocatalysts.     

Realization of a temperature sensor using both two- and three-dimensional photonic structures through a machine learning technique

A temperature sensor based on photonic crystal structures with two- and three-dimensional geometries is proposed, and its measurement performance is estimated using a machine learning technique. The temperature characteristics of the photonic crystal structures are studied by mathematical modeling. The physics of the structure is investigated based on the effective electrical permittivity of the substrate (silicon) and column (air) materials for a signal at 1200 nm, whereas the mathematical principle of its operation is studied using the plane-wave expansion method. Moreover, the intrinsic characteristics are investigated based on the absorption and reflection losses as frequently considered for such photonic structures. The output signal (transmitted energy) passing through the structures determines the magnitude of the corresponding temperature variation. Furthermore, the numerical interpretation indicates that the output signal varies nonlinearly with temperature for both the two- and three-dimensional photonic structures. The relation between the transmitted energy and the temperature is found through polynomial-regression-based machine learning techniques. Moreover, rigorous mathematical computations indicate that a second-order polynomial regression could be an appropriate candidate to establish this relation. Polynomial regression is implemented using the Numpy and Scikit-learn library on the Google Colab platform.

     

Suppression of floatability of pyrite in coal processing by carrier microencapsulation

Carrier microencapsulation, CME, is a technique to form a thin layer of metal oxide or hydroxide on pyrite surface using a water soluble organic carrier combined with metal ions. The present study investigated the effect of CME using a tris-catecholato complex of Si⁴⁺, Si(cat)₃²⁻ on pyrite-coal separation by dynamic bubble pick-up experiments and Hallimond tube flotation experiments using coal, pyrite, and a coal-pyrite mixture. The mineral samples were treated in 0-5 mol m^− 3 Si(cat)₃²⁻ solutions at pH 4-9 at treatment times of 1-24 h. Dynamic bubble pick-up experiments showed that CME treatment converted the pyrite surface from hydrophobic to hydrophilic but did not affect coal's hydrophobic surface. The results of the Hallimond tube flotation experiments of a coal-pyrite mixture at pH 7-9 in the presence of kerosene as a collector showed that pyrite floatability was selectively suppressed after 1 h CME treatment with 0.5 mol^− 3 Si(cat)₃²⁻ while both coal and pyrite were floated without the treatment. This indicates that CME treatment is effective in suppressing pyrite floatability in coal-pyrite flotation.     

Bi-objective optimization of the reliability-redundancy allocation problem for series-parallel system

The main objective of this paper is to solve the bi-objective reliability redundancy allocation problem for series-parallel system where reliability of the system and the corresponding designing cost are considered as two different objectives. In their formulation, reliability of each component is considered as a triangular fuzzy number. In order to solve the problem, developed fuzzy model is converted to a crisp model by using expected values of fuzzy numbers and taking into account the preference of decision maker regarding cost and reliability goals. Finally the obtained crisp optimization problem has been solved with particle swarm optimization (PSO) and compared their results with genetic algorithm (GA). Examples are shown to illustrate the method. Finally statistical simulation has been performed for supremacy the approach.     

A numerical study of particle wall-deposition in a turbulent square duct flow

The deposition of dense solid particles in a downward, fully developed turbulent square duct flow at Re_τ = 360, based on the mean friction velocity and the duct width, is studied using large eddy simulations of the fluid flow. The fluid and the particulate phases are treated using Eulerian and Lagrangian approaches, respectively. A finite-volume based, second-order accurate fractional step scheme is used to integrate the incompressible form of the unsteady, three-dimensional, filtered Navier-Stokes equations on an 80 × 80 × 128 grid. A dynamic subgrid kinetic energy model is used to account for the unresolved scales. The Lagrangian particle equation of motion includes the drag, lift, and gravity forces and is integrated using the fourth-order accurate Runge-Kutta scheme. Two values of particle to fluid density ratio (ρ_p/ρ_f = 1000 and 8900) and five values of dimensionless particle diameter (d_p/δ × 10⁶ = 100, 250, 500, 1000 and 2000, δ is the duct width) are studied. Two particle number densities, consisting of 10⁵ and 1.5 × 10⁶ particles initially in the domain, are examined.Variations in the probability distribution function (PDF) of the particle deposition location with dimensionless particle response time, i.e. Stokes number, are presented. The deposition is seen to occur with greater probability near the center of the duct walls, than at the corners. The average streamwise and wall-normal deposition velocities of the particles increase with Stokes number, with their maxima occurring near the center of the duct wall. The computed deposition rates are compared to previously reported results for a circular pipe flow. It is observed that the deposition rates in a square duct are greater than those in a pipe flow, especially for the low Stokes number particles. Also, wall-deposition of the low Stokes number particles increases significantly by including the subgrid velocity fluctuations in computing the fluid forces on the particles. Two-way coupling and, to a greater extent, four-way coupling are seen to increase the deposition rates.     

Crystallization and oxidation resistance properties of boron modified silicon oxycarbides derived from polymeric precursors by sol–gel method

Boron modified silicon oxycarbides (SiBOCs) were prepared from sol–gel derived pre-ceramic polymeric gels followed by pyrolysis at 950 °C under nitrogen. As-prepared SiBOC was found to be amorphous in nature and partially crystallized to SiO₂ at 1500 °C. The effect of boron incorporation on the crystallization of SiBOC was studied and the result revealed that the tendency to crystallization decreased with increasing boron content. This is due to the formation of Si–O–B bridges at higher temperatures, which retards the crystallization of SiO₂, evidenced from FTIR studies. SiBOC also exhibited excellent oxidation resistance ability at high temperature.     

Potentiometric studies of N,N′-Bis(2-dimethylaminoethyl)-N,N′-dimethyl-9,10 anthracenedimethanamine as a chemical sensing material for Zn(II) ions

A liquid membrane based Zn²⁺ ion selective electrode containing N,N′-Bis(2-dimethylaminoethyl)-N,N′-dimethyl-9,10 anthracenedimethanamine (Bis(TMEDA) anthracene) (I) as ionophore has been prepared and characterized. The membrane comprises of PVC, ionophore and plasticizer in the ratio of 33:2:65, respectively. It showed the best response in terms of detection limit (1.5 × 10^− 6 M) and working concentration range (1.0 × 10^− 5 M to 1.0 × 10^− 1 M) with Nernstian response towards Zn²⁺ ions. The electrode responds within 15 s of coming in contact with the solution. The potential response remains almost unchanged over a pH range of 3.0 to 7.5. The electrode can be used for at least 3 months without any considerable alteration in its response behavior. The proposed electrode revealed good selectivity towards Zn²⁺ ions over a number of alkali, alkaline earth, transition metals and some other heavy metal ions. The electrode has been used as an indicator electrode in the potentiometric titration of Zn²⁺ with EDTA. The proposed electrode also detected Zn²⁺ ions from real life samples.     

Lipoxygenase and Tocopherol Profiling of Soybean Genotypes Exposed to Electron Beam Irradiation

Electron beam (EB)-irradiation is increasingly being preferred to radioactive-based gamma irradiation in overcoming the constraints that affect the quality of food material. Soybean seeds of 3 soybean genotypes were exposed to 4 doses viz. 4.8, 9.2, 15.3 and 21.2 kGy of EB-irradiation and assessed for the changes in the contents of lipoxygenase isozymes and tocopherol isomers. Densitometry of protein profile revealed decreasing intensity of lipoxygenase with increasing EB dose. All the 3 lipoxygenase isozymes viz. lipoxygenase-1, -2 and -3 registered significant (P < 0.05) increasing reduction with increasing dose; though genotypic variation was noted for the magnitude of reduction at the same dose. Concomitantly, all the 3 genotypes exhibited significant (P < 0.05) decline in α-, γ- and δ-isomers of tocopherol. δ-Tocopherol was the most sensitive to EB-irradiation. EB dose, which caused minimum and maximum decline in total tocopherol content, was genotype-dependent. Decline in vitamin E activity corresponding to the dose, which induced maximum reduction for total lipoxygenase also varied in 3 genotypes. The study showed the usefulness of EB for significant inactivation of off-flavor generating lipoxygenases in soybean, with a non-significant effect on oil content and varied retention of tocopherol isomers and vitamin E activity depending upon genotype.     

Two-step purification strategy for enhanced recovery of recombinant hepatitis B surface antigen from Pichia pastoris

Univariate screening on factors affecting the purification performance of recombinant hepatitis B surface antigen (HBsAg) on ion exchange chromatography (IEC) and size exclusion chromatography (SEC) and the establishment of a two-step purification strategy were performed. Amongst four IEC adsorbents examined, the use of Q Sepharose XL IEC adsorbent under optimized conditions together with optimized SEC purification was able to efficiently purify HBsAg. An established purification strategy comprising the two techniques further demonstrated adaptability for scale-up operations with a final total purification factor (PF) of 94.82 ± 16.20, HBsAg purity of 95.48% and recovery yield of 78.07%.