Optimisation of food grade mixed surfactant‐based l‐ascorbic acid nanoemulsions using response surface methodology

Co‐surfactant free l‐ascorbic acid (LAA) nanoemulsions were prepared using mixed surfactants (Soya lecithin and Tween 80). Response surface methodology (RSM) was used to optimise the emulsifying conditions for LAA nanoemulsions. The effects of water proportion (6%–14% w/w), homogenisation pressure (80–160 MPa), surfactant concentrations (4%–12% w/w) and laa concentration (0.5–1.3 w/w) on responses (size of droplets and nanoemulsion stability) were investigated. RSM results showed that the values of responses can be successfully predicted through second‐order polynomial model. The coefficients of determinations for droplet size and nanoemulsion stability were 0.9375 and 0.9027, respectively. The optimum preparation conditions for l‐LAA nanoemulsion were 9.04% water proportion, 114.48 MPa homogenisation pressure, 7.36% surfactant concentration and 1.09% LAA concentration. At the end of one month storage study, the retention of LAA in optimised nanoemulsions stored at 4°C and 25°C were 74.4% and 66.7%, respectively. These results may provide valuable contributions for food and pharmaceutical industry to develop delivery system for food additives and nutraceutical components.     

Tritium-Labeled Compounds VII. Isotope Effects in the Oxidation of d-Mannitols-C14 and d-Mannitols-t to d-Fructoses

d-Mannitols, labeled either with carbon-14 at C1, C2, or C3, or with tritium attached to C1, C2, or C3, were prepared. After oxidation by Acetobacter suboxydans, the distribution of radioactivity in each of the resulting labeled d-fructoses was determined. Labeled d-mannitol is unique among the hexitols in that it may be oxidized by A. suboxydans in either the labeled or the unlabeled part of the molecule. Except in the oxidation of d-mannitol-2-t, the competing reactions result in the formation of a mixture of d-fructoses, each having radioactivity in one of two different positions. Hence, the isotope effect, k*/k, (where k* and k are, respectively, the rate constants for oxidation in the labeled and in the unlabeled part of the labeled d-mannitol molecule) is the ratio of the activities at the two positions of the product, d-fructose.The following isotope effects were found for the bacterial oxidation of labeled d-mannitols: (1) for d-mannitol-2-C¹⁴, k*/k=0.93; (2) for d-mannitol-2-t, k*/k=0.23; and (3) for d-mannitol-3-t, k*/k=0.70. For d-mannitols labeled at other positions, no isotope effect was detected, since k*/k was unity. The large isotope-effect for d-mannitol-2-t is indicative of rupture of the C2–H bond in the rate-determining process. It is suggested that the secondary isotope-effect for tritium at C3 indicates hyperconjugation of the C3 hydrogen atom in the activated enzyme—substrate complex; the lack of such effect for tritium at C1 may be due to unfavorable steric conditions for hyperconjugation of the C1 hydrogen atoms in the complex.The following substances were prepared and their isotopic distributions determined: d-fructose-1,6-C¹⁴ and d-fructose-1,6-t (from 1-labeled d-mannitols); d-fructose-2,5-C¹⁴ and d-fructose-5-t (from 2-labeled d-mannitols); and d-fructose-3,4-C¹⁴ and d-fructose-3,4-t (from 3-labeled d-mannitols). A procedure, employing d-fructose-1,6-C¹⁴ as an internal standard, was devised for the analysis of d-fructose-3,4-t.     

Conformations of the Pyranoid Sugars. II. Infrared Absorption Spectra of Some Aldopyranosides

The conformations of twenty-four aldopyranosides have been studied by analysis of their infrared absorption spectra. The most stable conformations of twelve of the glycosides had previously been assigned by Reeves from a study of their instability factors; these conformations were assumed to apply to the crystalline state, for which the spectra had been recorded. The compounds were classified into (a) configurationally and (b) structurally related groups, and the spectra were intercompared. The analysis revealed groups of absorption bands which showed a concerted shift on change of anomeric disposition.With these groups of absorption bands thus identified, intercomparison with nine of the remaining spectra afforded evidence that the anomeric group (1) is axial in methyl d-glycero-α-l-gluco-heptopyranoside, methyl d-glycero-α-l-manno-heptopyranoside, and methyl d-glycero-α-d-gulo-heptopyranoside; (2) is equatorial in methyl 6-deoxy-β-l-mannopyranoside, methyl d-glycero-β-d-gulo-heptopyranoside, and cyclohexyl d-glycero-β-d-gulo-heptopyrnoside; and (3) either is quasi or occurs as different (or mixed) axial and equatorial forms in methyl α-d-lyxopranoside, methyl β-d-lyxopranoside, and (possibly) α-d-methylgulopyranoside.Three of the glycosides were available as their crystalline complexes with calcium chloride. The spectra of these complexes were also examined, and the effect of co-crystallization with calcium chloride is pointed out.     

Tritium-Labeled Compounds X. Isotope Effects in the Oxidation of Aldoses-1-t With Bromine

Tritium isotope effects have been used in bromine oxidation studies of aldoses to evaluate two reaction paths previously postulated by Isbell and Pigman, namely, direct oxidation and oxidation after anomerization. Because the former path involves a primary isotope effect (k*/k = 0.14, approximately) and the latter a secondary isotope effect (k*/k = 0.80, approximately) it was found possible to evaluate the relative importance of the two reaction paths from the overall isotope effects, which ranged from 0.20 to 0.59.Under the conditions reported, the direct oxidation for the axial anomers ranges from 38 percent for α-d-galactose to 94 percent for α-d-lyxose. Differences in the proportion of the anomer oxidized by each of the two paths are explained by variations in the free energy required for reaching the respective transition states. Aldoses of high conformational stability having an axial C1-hydroxyl group resist the change in conformation necessary for direct oxidation and react in large measure through a change in configuration (anomerization). Aldoses of lower conformational stability having an axial C1-hydroxyl group react largely through a change in conformation, because this path does not have a high energy barrier.The equatorial anomers of d-glucose-1-t and maltose-1-t showed isotope effects of 0.32 and 0.23, respectively in comparison with a value of 0.14 previously found for the oxidation of aldoses-1-t with iodine in alkaline solution. The isotope effect in the oxidation of d-glucose-1-t with d-glucose oxidase at 30 °C was found to be 0.15. These strong isotope effects are in accord with the rupture of the C1 to H bond in the rate-determining step.The following reactions gave the values for k*/k cited in parentheses: d-glucose-1-t +NaCN (0.83); d-glucose-1-C¹⁴ + NaCN (1.00); d-glucose-1-t+NaBH₄ (0.73); d-mannose-1-t + phenylhydrazine (0.83); and d-mannose-1-C¹⁴ + phenylhydrazine (0.95). The values of k*/k are typical of aldose reactions involving rate-determining isomerization of the pyranose structure.The isotope effects were measured by a double-label method and by a newly developed method based on the radioassay of water evolved in the reaction.     

2,3-O-Isopropylidene-α-d-lyxofuranose,the Monoacetone-d-lyxose of Levene and Tipson

A proof of structure is presented for the title compound, previously uncharacterized. In the course of the investigation, the crystalline 2,3-O-isopropylidene acetals of calcium d-lvxonate, d-lyxono-1,4-lactone, d-lyxitol, β-d-erythrofuranose, calcium d-erythronate, and d-erythrono-1,4-lactone were prepared. The diacetate and dibenzoate of 2,3-O-isopropylidene-d-lyxose were also synthesized.     

Describing function‐based approximations of biomolecular systems

Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of analytical and computational approaches, the authors adapt and develop the method of describing functions to represent the input–output responses of biomolecular signalling systems. They approximate representative systems exhibiting various saturating and hysteretic dynamics in a way that is better than the standard linearisation. Furthermore, they develop analytical upper bounds for the computational error estimates. Finally, they use these error estimates to augment the limit cycle analysis with a simple and quick way to bound the predicted oscillation amplitude. These results provide system approximations that can add more insight into the local behaviour of these systems than standard linearisation, compute responses to other periodic inputs and to analyse limit cycles.Inspec keywords: molecular biophysics, physiological models, approximation theoryOther keywords: describing‐function‐based approximations, mathematical methods, computational approaches, biomolecular signalling systems, hysteretic dynamics, saturating dynamics, analytical upper bounds, computational error estimates, oscillation amplitude     

Small RNA‐mediated switch‐like regulation in bacterial quorum sensing

Quorum sensing (QS) is a signalling mechanism by which bacteria produce, release and then detect and respond to changes in their density and biosignals called autoinducers (AIs). There are multiple feedback loops in the QS system of Vibrio harveyi. However, how these feedback loops function to control signal processing remains unclear. In this study, the authors present a computational model for the switch‐like regulation of signal transduction by small regulatory RNA‐mediated QS based on intertwined network involving AIs, LuxO, LuxU, Qrr sRNAs and LuxR. In agreement with experimental observations, the model suggests that different feedbacks play critical roles in the switch‐like regulation. The authors results reveal that V. harveyi uses multiple feedbacks to precisely control signal transduction.Inspec keywords: biocommunications, biocontrol, biology computing, cellular biophysics, physiological models, RNAOther keywords: RNA‐mediated switch‐like regulation, bacterial quorum sensing, signaling mechanism, autoinducers, Vibrio harveyi, feedback loops function, signal processing control, switch‐like regulation     

Conformations of the Pyranoid Sugars. III. Infrared Absorption Spectra of Some Acetylated Aldopyranosides

The infrared absorption spectra of twenty-four acetylated aldopyranosides in the range of 5,000 to 250 cm⁻¹ are reported. The conformation adopted by each of seventeen of the corresponding unacetylated glycosides had previously been assigned by us from a study of their infrared spectra. Analysis of the spectra revealed, for the acetylated glycosides (as for the parent glycosides), groups of absorption bands which showed a concerted shift on change of anomeric disposition. Assignment of conformation by the methods developed earlier led to the conclusion that each acetylated glycoside has the same conformation as its parent glycoside.Intercomparison of the spectra of four of the remaining acetates with those of related acetates, especially in regard to the characteristic groups of absorption bands, afforded evidence that the anomeric methoxyl group is axial in methyl hepta-O-acetyl-4-O-β-d- glucopyranosyl-α-d-mannopyranoside, and equatorial in methyl tetra-O-acetyl-β-d-manno pyranoside, methyl penta-O-acetyl-d-glycero-β-l-manno-heptopyranoside, and methyl hepta- O-acetyl-4-O-β-d-glucopyranosyl-β-d-mannopyranoside. For lack of spectra of related acetylated aldopyranosides, assignments cannot yet be made for methyl hepta-O-acetyl- 6-O-β-d-glucopyranosyl-β-d-glucopyranoside, methyl penta-O-acety-d-glycero-β-d-ido-heptopyranoside, and methyl hepta-O-acetyl-4-O-β-d-galactopyranosyl-β-d-altropyranoside.     

Tritium-Labeled Compounds VI. Alditols-1-t and Alditols-2-t

By reduction of aldoses and aldonic lactones with lithium borohydride-t, the following 1-tritium-labeled alditols were prepared: d-arabinitol-1-t, d-lyxitol-1-t, d-ribitol-1-t, d-xylitol-1-t, d-galaetitol-1-t, d-mannitol-1 (6)-t, d-glucitol-1-t, d-talitol-1-t, l-gulitol-1-t (d-glucitol 6-t), l-rhamnitol-1-t, d-glycero-d-gulo-heptitol-1-t, and 4-O-β-d-galactopyranosyl-d-glucitol-1-t. By reduction of ketoses with lithium borohydride-t, the following epimeric pairs of 2-labeled alditols were prepared and subsequently separated: d-mannitol-2(5)-t and d-glucitol-2-t; l-gulitol-2-t (d-glucitol-5-t) and l-iditol-2-t; d-galactitol-2-t and d-talitol-2-t; d-glycero-d-gulo-heptitol-2-t and d-glycero-d-ido-heptitol-2-t; and d-glycero-B-galacto-heptitol-2-t and d-glycero-d-talo-heptitol-2-t.The yields of the epimeric alditols formed from ketoses were determined by an isotopedilution technique. Stereomeric relationships are discussed for the labeled alditols and for the ketoses derivable from them by oxidation with Acetobacter suboxydans.     

Multi‐scale approach for simulating time‐delay biochemical reaction systems

This study presents a multi‐scale approach for simulating time‐delay biochemical reaction systems when there are wide ranges of molecular numbers. The authors construct a new efficient approach based on partitioning into slow and fast subsets in conjunction with predictor–corrector methods. This multi‐scale approach is shown to be much more efficient than existing methods such as the delay stochastic simulation algorithm and the modified next reaction method. Numerical testing on several important problems in systems biology confirms the accuracy and computational efficiency of this approach.Inspec keywords: biochemistry, delays, biological techniques, predictor‐corrector methodsOther keywords: multiscale approach, time‐delay biochemical reaction systems, predictor–corrector methods, delay stochastic simulation algorithm, modified next reaction method, numerical testing, systems biology, method accuracy, computational efficiency     

Period–amplitude co‐variation in biomolecular oscillators

The period and amplitude of biomolecular oscillators are functionally important properties in multiple contexts. For a biomolecular oscillator, the overall constraints in how tuning of amplitude affects period, and vice versa, are generally unclear. Here, the authors investigate this co‐variation of the period and amplitude in mathematical models of biomolecular oscillators using both simulations and analytical approximations. The authors computed the amplitude–period co‐variation of 11 benchmark biomolecular oscillators as their parameters were individually varied around a nominal value, classifying the various co‐variation patterns such as a simultaneous increase/decrease in period and amplitude. Next, the authors repeated the classification using a power norm‐based amplitude metric, to account for the amplitudes of the many biomolecular species that may be part of the oscillations, finding largely similar trends. Finally, the authors calculate ‘scaling laws’ of period–amplitude co‐variation for a subset of these benchmark oscillators finding that as the approximated period increases, the upper bound of the amplitude increases, or reaches a constant value. Based on these results, the authors discuss the effect of different parameters on the type of period–amplitude co‐variation as well as the difficulty in achieving an oscillation with large amplitude and small period.Inspec keywords: molecular biophysics, oscillations, biology computing, circadian rhythmsOther keywords: period‐amplitude co‐variation, biomolecular oscillators, mathematical models, analytical approximations, co‐variation patterns, power norm‐based amplitude metric, scaling laws     

Parallel implementation of D‐Phylo algorithm for maximum likelihood clusters

This study explains a newly developed parallel algorithm for phylogenetic analysis of DNA sequences. The newly designed D‐Phylo is a more advanced algorithm for phylogenetic analysis using maximum likelihood approach. The D‐Phylo while misusing the seeking capacity of k ‐means keeps away from its real constraint of getting stuck at privately conserved motifs. The authors have tested the behaviour of D‐Phylo on Amazon Linux Amazon Machine Image(Hardware Virtual Machine)i2.4xlarge, six central processing unit, 122 GiB memory, 8 ×  800 Solid‐state drive Elastic Block Store volume, high network performance up to 15 processors for several real‐life datasets. Distributing the clusters evenly on all the processors provides us the capacity to accomplish a near direct speed if there should arise an occurrence of huge number of processors.Inspec keywords: parallel algorithms, Linux, pattern clustering, DNA, molecular biophysics, genetics, biology computingOther keywords: D‐Phylo algorithm parallel implementation, maximum likelihood clusters, DNA sequence phylogenetic analysis, Amazon Linux AMI, HVM, central processing unit, SSD, real‐life datasets, processors, high‐network performance     

Retrieving relevant time‐course experiments: a study on Arabidopsis microarrays

Understanding time‐course regulation of genes in response to a stimulus is a major concern in current systems biology. The problem is usually approached by computational methods to model the gene behaviour or its networked interactions with the others by a set of latent parameters. The model parameters can be estimated through a meta‐analysis of available data obtained from other relevant experiments. The key question here is how to find the relevant experiments which are potentially useful in analysing current data. In this study, the authors address this problem in the context of time‐course gene expression experiments from an information retrieval perspective. To this end, they introduce a computational framework that takes a time‐course experiment as a query and reports a list of relevant experiments retrieved from a given repository. These retrieved experiments can then be used to associate the environmental factors of query experiment with the findings previously reported. The model is tested using a set of time‐course Arabidopsis microarrays. The experimental results show that relevant experiments can be successfully retrieved based on content similarity.Inspec keywords: botany, lab‐on‐a‐chip, genetics, bioinformatics, information retrieval, data mining, data analysis, associative processingOther keywords: relevant time‐course experiment retrieval, time‐course Arabidopsis microarray, time‐course gene regulation, stimulus response, systems biology, computational method, gene behaviour model, gene networked interaction, latent parameter, model parameter estimation, meta‐analysis, data analysis, time‐course gene expression experiment, information retrieval, computational framework, time‐course experiment query, relevant experiment list, repository, environmental factor, query experiment, experimental content similarity     

Modelling the role of catastrophe,crossover and katanin‐mediated severing in the self‐organisation of plant cortical microtubules

Plant cortical microtubules can form ordered arrays through interactions among themselves. When an incident microtubule collides with a barrier microtubule it may entrain if below a certain angle. Else it undergoes collision induced catastrophe (CIC) or crosses over the barrier microtubule. It has been proposed that katanin is necessary to create order by severing these crossover sites. The authors present a three‐state computational model using Arabidopsis thaliana data to show how spontaneous catastrophe, the probability of CIC versus crossover, and katanin‐mediated severing at the crossover sites affect microtubule ordering. The results of the systematic simulations show that (1), the microtubule order is more sensitive to the catastrophe rate than the rescue rate; (2), at 21°C, peak order is observed at 0.3 CIC and order decreases as CIC increases; and (3) at 0.2 CIC, katanin severing acting uniformly at all crossover sites is able to create order within a biologically reasonable time frame, but at lower CICs this becomes unrealistically fast. This would imply that at lower CIC levels preferential crossover site targeting and severing activity regulators would be required for katanin to bring about order.Inspec keywords: cellular biophysics, botany, proteins, molecular biophysicsOther keywords: barrier microtubule crossover, katanin‐mediated severing, self‐organisation, plant cortical microtubules, collision induced catastrophe, three‐state computational model, Arabidopsis thaliana data, microtubule ordering     

Conformations of the Pyranoid Sugars. IV. Infrared Absorption Spectra of Some Fully Acetylated Pyranoses

The infrared absorption spectra of twenty pyranose acetates in the range of 5000 to 250 cm⁻¹ are reported. The conformation adopted by each of fourteen of the corresponding methyl glycopyranosides (or their acetates) had previously been assigned by us from a study of their infrared spectra. Analysis of the spectra revealed, for the pyranose acetates (as for the methyl glycopyranosides and their acetates), groups of absorption bands which showed a concerted shift on change of anomeric disposition. Assignment of conformation by the methods earlier developed indicated that, for most of the compounds examined, the conformation is the same for the pyranose acetate, methyl glycopyranoside, and acetylated methyl glycopyranoside of one anomer of a monosaccharide.The following new assignments of conformation were made: the CA conformation for penta-O-acetyl-α-l-xylo-hexulopyranose and hexa-O-acetyl-α-d-gluco-heptulopyranose; and, possibly, either a non-chair conformation or a mixture of the CA and CE conformations for hexa-O-acetyl-l-glycero-β-d-gluco-heptopyranose and hexa-O-acetyl-d-glycero-β-d-galacto-heptopyranose.     

DOC‐LS,a new liposome for dermal delivery,and its endocytosis by HaCaT and CCC‐ESF‐1 cells

The main objective of this work was to investigate the uptake channels of skin cells through which coumarin 6, transported by deoxycholate‐mediated liposomes (DOC‐LS), was internalised; this was also compared against the action of conventional LS. Coumarin 6‐loaded DOC‐LS and LS were characterised for size distribution, zeta potential, and shape, and analysed in vitro in human epidermal immortal keratinocyte (HaCaT) (epidermal) and human embryonic skin fibroblast (CCC‐ESF‐1) (dermal) cell lines. Various endocytosis inhibitors were incubated with cells treated with the nanocarriers. Flow cytometry results indicated that HaCaT and CCC‐ESF‐1 cells internalise the tested preparations through pinocytotic vesicles, macropinocytosis, clathrin‐mediated endocytic pathways, and via lysosomes, which consume a considerable amount of energy. The endocytosis pathways of DOC‐LS and LS showed no difference. This study provides a basis for the application of LS being combined with a microneedle system for efficient intracellular drug delivery, targeting cutaneous histocyte disorders.Inspec keywords: drugs, nanoparticles, lipid bilayers, nanomedicine, biomedical materials, electrokinetic effects, biomembrane transport, drug delivery systems, skin, organic compoundsOther keywords: dermal delivery, CCC‐ESF‐1 cells, skin cells, deoxycholate‐mediated liposomes, coumarin 6‐loaded DOC‐LS, endocytosis inhibitors, clathrin‐mediated endocytic pathways, endocytosis pathways, HaCaT cell lines, size distribution, zeta potential, nanocarriers, flow cytometry, pinocytotic vesicles, macropinocytosis, microneedle system, efficient intracellular drug delivery, targeting cutaneous histocyte disorders     

Excluded volume effects in on‐ and off‐lattice reaction–diffusion models

Mathematical models are important tools to study the excluded volume effects on reaction–diffusion systems, which are known to play an important role inside living cells. Detailed microscopic simulations with off‐lattice Brownian dynamics become computationally expensive in crowded environments. In this study, the authors therefore investigate to which extent on‐lattice approximations, the so‐called cellular automata models, can be used to simulate reactions and diffusion in the presence of crowding molecules. They show that the diffusion is most severely slowed down in the off‐lattice model, since randomly distributed obstacles effectively exclude more volume than those ordered on an artificial grid. Crowded reaction rates can be both increased and decreased by the grid structure and it proves important to model the molecules with realistic sizes when excluded volume is taken into account. The grid artefacts increase with increasing crowder density and they conclude that the computationally more efficient on‐lattice simulations are accurate approximations only for low crowder densities.Inspec keywords: reaction‐diffusion systems, cellular biophysics, biodiffusion, Brownian motion, cellular automata, molecular biophysics, molecular configurationsOther keywords: crowder density, grid artefacts, grid structure, crowded reaction rates, artificial grid, randomly distributed obstacles, crowding molecules, cellular automata models, on‐lattice approximations, crowded environments, off‐lattice Brownian dynamics, detailed microscopic simulations, living cells, mathematical models, off‐lattice reaction‐diffusion models, on‐lattice reaction‐diffusion models, excluded volume effects