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.     

Trimesic acid is a suitable building block in triple four-component Ugi reaction: access to unique trivalent compounds

Monatshefte für Chemie - Chemical Monthly - A triple four-component Ugi reaction of isocyanide, amine, aldehyde, and trimesic acid as the acid component with three acidic functional groups in...     

Magnetic‐based picolinaldehyde–melamine copper complex for the one‐pot synthesis of hexahydroquinolines via Hantzsch four‐component reactions

A picolinaldehyde–melamine copper complex was loaded on a magnetic Fe₃O₄ core, so that it contained 0.33 mmol of Cu per gram, and was used as an efficient catalyst. The as‐synthesized catalyst was characterized using various techniques, including Fourier transform infrared spectroscopy, X‐ray diffraction, energy‐dispersive X‐ray spectroscopy, field emission scanning electron microscopy, transmission electron microscopy, vibrating sample magnetometry and thermogravimetric analysis. The catalyst was used to activate the raw materials in the synthesis of hexahydroquinoline derivatives in one‐pot four‐component reactions. Low reaction time (minutes versus half an hour), solvent‐free condition and magnetically separable catalyst are some salient features of the developed catalyst. Also, the optimum amount of catalyst and temperature were determined as 0.07 g and 87.6 °C, respectively, which were obtained using response surface methodology and optimization techniques.     

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.     

Enhancing endothelial differentiation of human mesenchymal stem cells by culture on a nanofibrous polycaprolactone/(poly-glycerol sebacate)/gelatin scaffold

Cardiovascular diseases have always been one of the main causes of death worldwide and eventually one of the major medical concerns. Tissue engineering is promising strategies of treating cardiovascular, which can be an effective approach with the design of appropriate scaffold. In this study, to develop engineering basement membrane for endothelial differentiation with good cell attachment, we produced polycaprolactone (PCL)/poly (glycerol sebacate) (PGS)/gelatin nanofibrous scaffold via electrospinning. Attenuated total reflectance-Fourier transform infrared and the proton nuclear magnetic resonance results confirmed the chemical structure of synthesized PGS. Scanning electron microscope images of the electrospun scaffold revealed that the nanofibers are smooth, continues and uniform. Moreover, due to the presence of hydrophilic functional groups in the scaffold, the contact angle is in the appropriate range for cell adhesion especially endothelial cells. The elastic modulus and ultimate tensile stress of electrospun scaffold were calculated 1.32 ± 0.27 MPa and 1.23 ± 0.18 MPa respectively. Quantitative polymerase chain reaction was performed for evaluation of endothelial differentiation of mesenchymal stem cells cultured on standard plate and fibrous scaffold under chemical stimulation with growth factor. Specific endothelial gene expression results postulated that our modified scaffold could support and significantly promote endothelial differentiation of MSCs.     

Dispersive solid phase extraction of lead(II) using a silica nanoparticle-based ionic liquid ferrofluid

We demonstrate the application of an ionic liquid-based ferrofluid to the dispersive solid phase extraction of lead(II) using PAN as the chelator. The ionic liquid contains silica nanoparticles with a magnetic core as the dispersion medium, and its use results in improved stability of the colloidal dispersion and a complete extraction of lead(II) within a few seconds. In addition, there is no need for centrifugation. Specifically, the effect of different variables on the extraction of lead(II) was studied using an experimental design. Lead(II) was quantified by AAS. Under optimized conditions, the calibration graph for lead(II) is linear in the range from 5 to 372 μg L⁻¹, the relative standard deviation is 1.34 % (for n = 7), the limit of detection is 1.66 μg L⁻¹, and the enrichment factor is 200. The maximum adsorption capacity of sorbent was calculated to be 10.7 mg g⁻¹, and adsorption follows a Langmuir isotherm.

A schematic view of D-SPE experimental set up. We demonstrate the application of an ionic liquid-based ferrofluid to the dispersive solid phase extraction of lead(II) using PAN as the chelator. The ionic liquid contains silica nanoparticles with a magnetic core as the dispersion medium

     

A New Quantum Gray-Scale Image Encoding Scheme

In this paper, a new quantum images encoding scheme is proposed. The proposed scheme mainly consists of four different encoding algorithms. The idea behind of the scheme is a binary key generated randomly for each pixel of the original image. Afterwards, the employed encoding algorithm is selected corresponding to the qubit pair of the generated randomized binary key. The security analysis of the proposed scheme proved its enhancement through both randomization of the generated binary image key and altering the gray-scale value of the image pixels using the qubits of randomized binary key. The simulation of the proposed scheme assures that the final encoded image could not be recognized visually. Moreover, the histogram diagram of encoded image is flatter than the original one. The Shannon entropies of the final encoded images are significantly higher than the original one, which indicates that the attacker can not gain any information about the encoded images.     

A detailed study of metallic surface-relief grating

This paper presents a more detailed interaction of an electromagnetics light with a metallic surface-relief subwavelength grating utilizing the rigorous coupled-wave analysis. The focus of this work is the accurate modeling of undetermined aspects of diffraction patterns produced by binary metallic grating structures, specially gold grating. First-order diffraction efficiency for rectangular-groove gold grating with equal groove and ridge widths are presented for various wavelengths as a function of period, groove depth, polarization and angle of incidence. We also studied diffraction efficiency of both of TE and TM polarization modes against increasing of incident angle as well as TE polarization against increment of grating period. As a result, very low reflectivity at zero-order was found out for TE and TM polarizations at the pitch of Λ = 2λ. Having been studied diffraction efficiency of metallic surface-relief gratings, we also examined polarization-dependent efficiency of diffraction orders, for different groove depths. Simulation results have been completely presented.