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.     

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...     

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.     

Robust half-metallicity at the zincblende CrTe(0 0 1) surfaces and its interface with ZnTe(0 0 1)

All electron full potential calculations based on spin density functional theory are performed to study cubic zincblende (ZB) and hexagonal NiAs structures of bulk CrTe, free (0 0 1) surfaces of ZB CrTe, and interface of ZB CrTe with ZnTe(0 0 1). The ferromagnetic NiAs structure is reported to be about 0.26 eV more stable than the ferromagnetic ZB phase while ZB CrTe is found to be a half-metallic ferromagnet with a half-metallic gap of about 2.90 eV. Thermodynamic stability of CrTe(0 0 1) surfaces are studied in the framework of ab-initio thermodynamic. The obtained phase diagram evidences more stability of the Te terminated surface compared with the Cr termination. We discuss that both Te and Cr ideal terminations of CrTe(0 0 1) retain bulk-like half-metallic property but with a reduced half-metallic gap compared with bulk value. The structural, electronic, magnetic, and band alignment properties of the ZB CrTe/ZnTe(0 0 1) interface are computed and a rather large minority valence band offset of about 1.09 eV is observed in this heterojunction.     

Nonlinear forced vibration of strain gradient microbeams

In this paper, the strain gradient theory, a non-classical continuum theory able to capture the size effect happening in micro-scale structures, is employed in order to investigate the size-dependent nonlinear forced vibration of Euler–Bernoulli microbeams. The nonlinearities are caused by mid-plane stretching and nonlinear external forces such as van-der-Waals force. The nonlinear governing equations of the microbeams are solved analytically utilizing the perturbation techniques. The primary, super-harmonic and sub-harmonic resonances of a microbeam are studied and the size-dependency of the frequency responses is assessed. The results indicate that the nonlinear forced vibration behavior of microbeams is size-dependent and the ratio of the microbeam thickness to the material length scale parameter, an additional material property appearing in the strain gradient theory, plays an important role.     

Flat sheet direct contact membrane distillation desalination system using temperature-dependent correlations: thermal efficiency via a multi-parameter sensitivity analysis based on Monte Carlo method

Journal of Thermal Analysis and Calorimetry - In this paper, a 1D model of direct contact membrane distillation is presented in which all fluid properties are temperature-dependent. In addition, a...