Escherichia coli single-stranded DNA-binding protein,a molecular tool for improved sequence quality in pyrosequencing

Pyrosequencing is a four-enzyme bioluminometric DNA sequencing technique based on a DNA sequencing by synthesis principle. Currently, the technique is limited to analysis of short DNA sequences exemplified by single-nucleotide polymorphism analysis. In order to expand the field for pyrosequencing, the read length needs to be improved and efforts have been made to purify reaction components as well as add single-stranded DNA-binding protein (SSB) to the pyrosequencing reaction. In this study, we have performed a systematic effort to analyze the effects of SSB by comparing the pyrosequencing result of 103 independent complementary DNA (cDNA) clones. More detailed information about the cause of low quality sequences on templates with different characteristics was achieved by thorough analysis of the pyrograms. Also, real-time biosensor analysis was performed on individual cDNA clones for investigation of primer annealing and SSB binding on these templates. Results from these studies indicate that templates with high performance in pyrosequencing without SSB possess efficient primer annealing and low SSB affinity. Alternative strategies to improve the performance in pyrosequencing by increasing the primer-annealing efficiency have also been evaluated.     

Superb catalytic properties of nickel cobalt bimetallic nanoparticles immobilized on 3D nitrogen-doped graphene for thermal decomposition of ammonium perchlorate

Research on Chemical Intermediates - Nickel cobalt bimetallic nanoparticles (NiCo NPs) with different molar ratios were stabilized over three-dimensional nitrogen-doped graphene [3D-(N)G] by a...     

A Modified Peng–Robinson Equation of State for Heavy Hydrocarbons

Russian Journal of Physical Chemistry A - A new simple and accurate functional form for an attractive parameter α is introduced for Peng–Robinson equation of state. The modified...     

Nonlinear dynamics of a flexible rotor on tilting pad journal bearings experiencing rub–impact

Nonlinear Dynamics - Rub–impact phenomenon occurring in hydrodynamic journal bearings is one of the main malfunctions in rotating machines and causes undesirable dynamic behavior. In order to...     

A nonnormal look at polychoric correlations: modeling the change in correlations before and after discretization

Two algorithms for establishing a connection between correlations before and after ordinalization under a wide spectrum of nonnormal underlying bivariate distributions are developed by extending the iteratively found normal-based results via the power polynomials. These algorithms are designed to compute the polychoric correlation when the ordinal correlation is specified, and vice versa, along with the distributional properties of latent, continuous variables that are subsequently ordinalized through thresholds dictated by the marginal proportions. The method has broad applicability in the simulation and random number generation world where modeling the relationships between these correlation types is of interest.     

Efficient model order reduction for dynamic systems with local nonlinearities

In the nonlinear structural analysis, the nonlinear effects are commonly localized and the rest of the structure behaves in a linear manner. Considering this fact, this research work proposes a harmonic balance solution in order to determine the nonlinear response of the structures. The solution is simplified by using an exact dynamic reduction along with the modal expansion technique. This novel approach, which is applicable to both discrete and continuous systems, converts the system equations of motion in each harmonic to a small set of nonlinear algebraic equations. The full set of system equations is reduced to a discrete system with a few generalized degrees of freedom (DOFs) confined to the localized nonlinear regions. The resultant reduced order model is shown to be accurate enough for determining the periodic response. To demonstrate the capability of the proposed method, numerical case studies for continuous and discrete systems, including systems with internal resonance, have been studied and the outcomes are validated with benchmark studies. In addition, the method is applied in the identification process of an experimental test setup with unknown frictional support parameters, and the results are presented and discussed.     

Per Aqueous Liquid Chromatography (PALC) as a Simple Method for Native Separation of Protein A

Staphylococcal protein A (protein A) is an important protein frequently used in research studies within the fields of biomedicine and biotechnology. Due to some limitations in available protein purification methods which can hold the native structure of the protein A without changing the folding or adding histidine to structure of this protein, its separation in the native form is difficult. In this study, a new cost-effective and powerful technique was introduced for separation of the full-length and truncated forms of recombinant protein A, without any alteration in their 3D structures. Per aqueous liquid chromatography with bare silica gel stationary phase and water:acetonitrile as the mobile phase was proved to be an attractive choice among the range of separation methods. Similar to hydrophilic liquid chromatography, this method employs high percentage of water in mobile phase. The effects of mobile phase composition, pH, and salt concentration on the retention behavior of protein A on bare silica gel stationary phases were investigated. In this method, applying high amounts of aqueous solvent accompanied by a minimum percentage of organic solvent could successfully separate protein A with preservation of folding, and any affinity-tagged group such as histidine has not occurred on its structure. Purity of the fractions obtained by the proposed method was confirmed using SDS-PAGE, western blotting, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry. According to the results of ELISA, separated proteins retained their ability of binding to antibody.     

An efficient chemoselective synthesis of O-vinylaryl systems using acetylenic esters and dihydroxybenzenes in the presence of triphenylphosphine or alkyl isocyanides

<正>The addition of 2,4-dihydroxyaceto(and benzo)phenone to propiolic ester is catalyzed by triphenylphosphine or tert-butyl isocyanide to form O-vinyl aryl derivatives in fairly good yields.     

Negative echo in the density evolution of ultracold fermionic gases

We predict a nonequilibrium critical phenomenon in the space-time density evolution of a fermionic gas above the temperature of transition into the superfluid phase. On the BCS side of the Bose-Einstein condensation-BCS crossover, the evolution of a localized density disturbance exhibits a negative echo at the point of the initial inhomogeneity. Approaching the Bose-Einstein condensation side, this effect competes with the slow spreading of the density of bosonic molecules. However, even here the echo dominates for large enough times. This effect may be used as an experimental tool to locate the position of the transition.