Optimisation of an asymmetric polymerase chain reaction assay for the amplification of single-stranded DNA from Wuchereria bancrofti for electrochemical detection

Single-stranded DNA (ssDNA) is a prerequisite for electrochemical sensor-based detection of parasite DNA and other diagnostic applications. To achieve this detection, an asymmetric polymerase chain reaction method was optimised. This method facilitates amplification of ssDNA from the human lymphatic filarial parasite Wuchereria bancrofti. This procedure produced ssDNA fragments of 188 bp in a single step when primer pairs (forward and reverse) were used at a 100:1 molar ratio in the presence of double-stranded template DNA. The ssDNA thus produced was suitable for immobilisation as probe onto the surface of an Indium tin oxide electrode and hybridisation in a system for sequence-specific electrochemical detection of W. bancrofti. The hybridisation of the ssDNA probe and target ssDNA led to considerable decreases in both the anodic and the cathodic currents of the system's redox couple compared with the unhybridised DNA and could be detected via cyclic voltammetry. This method is reproducible and avoids many of the difficulties encountered by conventional methods of filarial parasite DNA detection; thus, it has potential in xenomonitoring.

Reaction dynamics under confinement: an exact path integral treatment of a two-stage model of stochastic gene expression

Gene expression in living systems is inherently stochastic, and tends to produce varying numbers of proteins over repeated cycles of transcription and translation. In this paper, an expression is derived for the steady-state protein number distribution starting from a two-stage kinetic model of the gene expression process involving p proteins and r mRNAs. The derivation is based on an exact path integral evaluation of the joint distribution, P(p, r, t), of p and r at time t, which can be expressed in terms of the coupled Langevin equations for p and r that represent the two-stage model in continuum form. The steady-state distribution of p alone, P(p), is obtained from P(p, r, t) (a bivariate Gaussian) by integrating out the r degrees of freedom and taking the limit t -> infinity. P(p) is found to be proportional to the product of a Gaussian and a complementary error function. It provides a generally satisfactory fit to simulation data on the same two-stage process when the translational efficiency (a measure of intrinsic noise levels in the system) is relatively low; it is less successful as a model of the data when the translational efficiency (and noise levels) are high.

A catalytic michael/horner-wadsworth-emmons cascade reaction for enantioselective synthesis of thiochromenes

A catalytic enantioselective sulfa-Michael/Horner-Wadsworth-Emmons reaction cascade has been developed, taking advantage of phosphonate as an electrophilic activator and a traceless binding site. Using a chiral bifunctional urea derivative as the catalyst, a variety of aryl and heteroaryl substituted thiochromenes was obtained in excellent yield with a high level of enantioselectivity.

Cross-Hetero-Dehydrogenative Coupling Reaction of Phosphites: A Catalytic Metal-Free Phosphorylation of Amines and Alcohols

Phosphorylation of amines, alcohols, and sulfoximines are accomplished using molecular iodine as a catalyst and H2O2 as the sole oxidant under mild reaction conditions. This method provides an easy route for synthesizing a variety of phosphoramidates, phosphorus triesters and sulfoximine-derived phosphoramidates which are of biological importance.

Production of syngas from steam reforming and CO removal with water gas shift reaction over nanosized Zr0.95Ru0.05O2-delta solid solution

This study presents the synthesis, characterization, and kinetics of steam reforming of methane and water gas shift (WGS) reactions over highly active and coke resistant Zr0.93Ru0.05O2-delta. The catalyst showed high activity at low temperatures for both the reactions. For WGS reaction, 99% conversion of CO with 100% H-2 selectivity was observed below 290 degrees C. The detailed kinetic studies including influence of gas phase product species, effect of temperature and catalyst loading on the reaction rates have been investigated. For the reforming reaction, the rate of reaction is first order in CH4 concentration and independent of CO and H2O concentration. This indicates that the adsorptive dissociation of CH4 is the rate determining step. The catalyst also showed excellent coke resistance even under a stoichiometric steam/carbon ratio. A lack of CO methanation activity is an important finding of present study and this is attributed to the ionic nature of Ru species. The associative mechanism involving the surface formate as an intermediate was used to correlate experimental data. Copyright (C) 2013, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.

Self-assembled multicomponent Pd-6 aggregates showing low-humidity proton conduction

Two Pd-6 molecular aggregates (1 and 2), self-sorted via a template-free three-component self-assembly process, represent new examples of discrete architectures exhibiting very high proton conductivity 0.78 x 10(-3) S cm(-1) (1) and 0.22 X 10(-3) S cm(-1) (2)] at 300 K at low relative humidity (B46%) with low activation energy comparable to that of currently used Nafion in fuel cells.

Template-free multicomponent coordination-driven self-assembly of Pd(II)/Pt(II) molecular cages

Recent years have seen a tremendous increase in the interest for constructing hollowed-out molecular frameworks, for their potential uses. Metal-ligand coordination-driven self-assembly has provided multitudes of opportunities in the formation of molecular architectures of desired shapes and sizes, with the help of the information already coded in the components. This article summarizes the recent developments in the construction of multicomponent molecular cages through this process, with a focus on the decreasing relevance of templates, and use of these systems in catalysis/host-guest chemistry.

Few-Layer Borocarbonitride Nanosheets: Platinum-Free Catalyst for the Oxygen Reduction Reaction

The present study demonstrates the use of few-layer borocarbonitride nanosheets synthesized by a simple method as non-platinum cathode catalysts for the oxygen reduction reaction (ORR) in alkaline medium. Composition-dependent ORR activity is observed and the best performance was found when the composition was carbon-rich. Mechanistic aspects reveal that ORR follows the 4e(-) pathway with kinetic parameters comparable to those of the commercial Pt/C catalyst. Excellent methanol tolerance is observed with the BCN nanosheets unlike with Pt/C.

A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library

With the development of deep sequencing methodologies, it has become important to construct site saturation mutant (SSM) libraries in which every nucleotide/codon in a gene is individually randomized. We describe methodologies for the rapid, efficient, and economical construction of such libraries using inverse polymerase chain reaction (PCR). We show that if the degenerate codon is in the middle of the mutagenic primer, there is an inherent PCR bias due to the thermodynamic mismatch penalty, which decreases the proportion of unique mutants. Introducing a nucleotide bias in the primer can alleviate the problem. Alternatively, if the degenerate codon is placed at the 5' end, there is no PCR bias, which results in a higher proportion of unique mutants. This also facilitates detection of deletion mutants resulting from errors during primer synthesis. This method can be used to rapidly generate SSM libraries for any gene or nucleotide sequence, which can subsequently be screened and analyzed by deep sequencing. (C) 2013 Elsevier Inc. All rights reserved.

A Transition Metal-Free Minisci Reaction: Acylation of Isoquinolines, Quinolines, and Quinoxaline

Transition metal-free acylation of isoquinoline, quinoline, and quinoxaline derivatives has been developed employing a cross dehydrogenative coupling (CDC) reaction with aldehydes using substoichiometric amount of TBAB (tetrabutylammonium bromide, 30 mol %) and K2S2O8 as an oxidant. This intermolecular acylation of electron-deficient heteroarenes provides an easy access and a novel acylation method of heterocyclic compounds. The application of this CDC strategy for acylation strategy has been illustrated in synthesizing isoquinoline-derived natural products.

Mechanistic studies on the diazo transfer reaction

The mechanism of the diazo transfer reaction which converts amines to azides has been studied with labeled amino acids and labeled imidazole-l-sulfonyl azides. Retention of amine nitrogen in the amine, and transfer of the two terminal nitrogen atoms of the imidazole-l-sulfonyl azide to the product, were unambiguously established. (C) 2014 Elsevier Ltd. All rights reserved.

Dynamics of the reaction between the free end of a tethered self-avoiding polymer and a flat penetrable surface: A renormalization group study

The average time tau(r) for one end of a long, self-avoiding polymer to interact for the first time with a flat penetrable surface to which it is attached at the other end is shown here to scale essentially as the square of the chain's contour length N. This result is obtained within the framework of the Wilemski-Fixman approximation to diffusion-limited reactions, in which the reaction time is expressed as a time correlation function of a ``sink'' term. In the present work, this sink-sink correlation function is calculated using perturbation expansions in the excluded volume and the polymer-surface interactions, with renormalization group methods being used to resum the expansion into a power law form. The quadratic dependence of tau(r) on N mirrors the behavior of the average time tau(c) of a free random walk to cyclize, but contrasts with the cyclization time of a free self-avoiding walk (SAW), for which tau(r) similar to N-2.2. A simulation study by Cheng and Makarov J. Phys. Chem. B 114, 3321 (2010)] of the chain-end reaction time of an SAW on a flat impenetrable surface leads to the same N-2.2 behavior, which is surprising given the reduced conformational space a tethered polymer has to explore in order to react. (C) 2014 AIP Publishing LLC.

Nonlinear preconditioning for efficient and accurate interface capturing in simulation of multicomponent compressible flows

Single fluid schemes that rely on an interface function for phase identification in multicomponent compressible flows are widely used to study hydrodynamic flow phenomena in several diverse applications. Simulations based on standard numerical implementation of these schemes suffer from an artificial increase in the width of the interface function owing to the numerical dissipation introduced by an upwind discretization of the governing equations. In addition, monotonicity requirements which ensure that the sharp interface function remains bounded at all times necessitate use of low-order accurate discretization strategies. This results in a significant reduction in accuracy along with a loss of intricate flow features. In this paper we develop a nonlinear transformation based interface capturing method which achieves superior accuracy without compromising the simplicity, computational efficiency and robustness of the original flow solver. A nonlinear map from the signed distance function to the sigmoid type interface function is used to effectively couple a standard single fluid shock and interface capturing scheme with a high-order accurate constrained level set reinitialization method in a way that allows for oscillation-free transport of the sharp material interface. Imposition of a maximum principle, which ensures that the multidimensional preconditioned interface capturing method does not produce new maxima or minima even in the extreme events of interface merger or breakup, allows for an explicit determination of the interface thickness in terms of the grid spacing. A narrow band method is formulated in order to localize computations pertinent to the preconditioned interface capturing method. Numerical tests in one dimension reveal a significant improvement in accuracy and convergence; in stark contrast to the conventional scheme, the proposed method retains its accuracy and convergence characteristics in a shifted reference frame. Results from the test cases in two dimensions show that the nonlinear transformation based interface capturing method outperforms both the conventional method and an interface capturing method without nonlinear transformation in resolving intricate flow features such as sheet jetting in the shock-induced cavity collapse. The ability of the proposed method in accounting for the gravitational and surface tension forces besides compressibility is demonstrated through a model fully three-dimensional problem concerning droplet splash and formation of a crownlike feature. (C) 2014 Elsevier Inc. All rights reserved.

Improved Erlenmeyer Synthesis with 5-Thiazolone and Catalytic Mn(II) Acetate. Crystal Structure Confirmation of the Reaction Stereochemistry

2-Phenylthiazolin-5-one (5, a thioazlactone) condenses with various aldehydes in the presence of the mild base Mn(II) acetate as catalyst in CH2Cl2 solution. This leads to the corresponding Erlenmeyer reaction products (6) in excellent yields in the case of aromatic aldehydes and moderate yields in others. The mildness of the reaction conditions is apparently enabled by the aromaticity of the (putative) intermediate thiazolone anion. The structure and stereochemistry (Z) of the product derived from i-BuCHO was confirmed by single crystal X-ray diffraction. This study overcomes key limitations of the classical Erlenmeyer synthesis and also introduces the relatively nontoxic Mn(II) acetate as a reagent in heterocyclic chemistry.

USEFUL EXTENSIONS OF THE HENRY REACTION: EXPEDITIOUS ROUTES TO NITROALKANES AND NITROALKENES IN AQUEOUS MEDIA

The products of the Henry nitroaldol reaction from nitromethane and several aldehydes were reduced to the corresponding nitroalkanes with (n-Bu)(3)SnH in water under microwave irradiation (80 degrees C/10 min), or dehydrated to the corresponding nitroalkenes with K2CO3 in water (generally 0-5 degrees C/20 min). Both ``one-pot'' reactions occur in excellent yields across a range of aliphatic and aromatic (including heteroaromatic) substrates. It seems likely that the deoxygenation of the nitroaldols occurs via coordination of an oxygen atom of the nitro group with a tin atom, which facilitates hydride delivery in the transition state. The elimination of water from the nitroaldols in mild base is likely driven by the stability of the conjugated nitroalkene products. The elimination required workup with 2N HCl, which likely displaces a nitroalkane-nitroalkene equilibrium towards the latter. These extensions of the Henry reaction lead to products not easily obtained otherwise.