Direct Blue 71 staining as a destaining‐free alternative loading control method for Western blotting

In Western blotting, a suitable loading control is indispensable for correcting errors in the total amount of loaded protein. Immunodetection of housekeeping proteins and total protein staining have traditionally been used as loading control methods. Direct Blue 71 (DB71) staining—a novel, sensitive, dye‐binding staining method compatible with immunodetection—may offer advantages over these traditional loading control methods. Three common neuroscientific samples (human plasma, human oligodendrocytes, and rat brain) were employed to assess DB71 staining as a loading control method for Western blotting. DB71, CBB, one traditional housekeeping protein, and one protein of interest were comparatively assessed for reliability and repeatability and linear dynamic range over 2.5–40 μg of protein loaded. DB71's effect on the reliability and repeatability and linear dynamic range of immunoreaction were also assessed. Across all three sample types, DB71 was either equivalent or superior to CBB and housekeeping protein‐based methods in terms of reliability and repeatability and linear dynamic range. Across all three sample types, DB71 staining did not impair the reliability and repeatability or linear dynamic range of immunoreaction. Our results demonstrate that the DB71 staining can be used as a destaining‐free alternative loading control method for Western blotting.     

Fluorescent staining of protein in SDS polyacrylamide gels by salicylaldehyde azine

As a noncovalent fluorescence probe, in this study, salicylaldehyde azine (SA) was introduced as a sensitive fluorescence‐based dye for detecting proteins both in 1D and 2D polyacrylamide electrophoresis gels. Down to 0.2 ng of single protein band could be detected within 1 h, which is similar to that of glutaraldehyde‐silver stain, but approximately four times higher than that of SYPRO Ruby fluorescent stain. Furthermore, comparative analysis of the MS compatibility of SA stain with SYPRO Ruby stain indicated that SA stain is compatible with the downstream of protein identification by LC‐MS/MS. Additionally, the probable mechanism of the SA stain was investigated by molecular docking. The results demonstrated that the interaction between SA and protein was mainly contributed by hydrogen bonding and hydrophobic forces.     

Computational gibberellin‐binding channel discovery unraveling the unexpected perception mechanism of hormone signal by gibberellin receptor

Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. In this work, fundamental mechanism of hormone perception by receptor GID1 has been studied by performing computational simulations, revealing a new GA‐binding channel of GID1 and a novel hormone perception mechanism involving only one conformational state of GID1. The novel hormone perception mechanism demonstrated here is remarkably different from the previously proposed/speculated mechanism [Murase et al., Nature 2008 , 456, 459] involving two conformational states (“OPEN” and “CLOSED”) of GID1. According to the new perception mechanism, GA acts as a “conformational stabilizer,” rather than the previously speculated “allosteric inducer,” to induce the recognition of protein DELLA by GID1. The novel mechanistic insights obtained in this study provide a new starting point for further studies on the detailed molecular mechanisms of GID1 interacting with DELLA and various hormones and for mechanism‐based rational design of novel, potent growth regulators that target crops and ornamental plants. © 2013 Wiley Periodicals, Inc.     

Multiscale geometric modeling of macromolecules II: Lagrangian representation

Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics, and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as that from X‐ray, NMR, and cryo‐electron microscopy, and theoretical/mathematical models, such as molecular dynamics, the Poisson–Boltzmann equation, and the Nernst–Planck equation. In this work, we present a family of variational multiscale geometric models for macromolecular systems. Our models are able to combine multiresolution geometric modeling with multiscale electrostatic modeling in a unified variational framework. We discuss a suite of techniques for molecular surface generation, molecular surface meshing, molecular volumetric meshing, and the estimation of Hadwiger's functionals. Emphasis is given to the multiresolution representations of biomolecules and the associated multiscale electrostatic analyses as well as multiresolution curvature characterizations. The resulting fine resolution representations of a biomolecular system enable the detailed analysis of solvent–solute interaction, and ion channel dynamics, whereas our coarse resolution representations highlight the compatibility of protein‐ligand bindings and possibility of protein–protein interactions. © 2013 Wiley Periodicals, Inc.     

Investigation on the Stability of the Dispersion System of Cross-Linked Polyacrylamide Microspheres

The salt resistance, temperature resistance, and shear stability of a cross-linked polyacrylamide microsphere system are studied by microfiltration, light diffraction analysis, and optical microscopy. The results show that other conditions being equal, the particle diameter of cross-linked polyacrylamide microspheres decreases with increased NaCl concentration. When NaCl concentration is lower than 10,000 mg/L, its effect on the plugging performance of a cross-linked polyacrylamide microsphere system in regard to the nuclear pore membrane is weak in comparison with a linked polymer solution, but the former system has better salt tolerance. Particle diameter decreases with increased swelling temperature. When the swelling temperature is below 90°C, its effect on the plugging performance of the cross-linked polyacrylamide microsphere system in regard to nuclear pore membrane is weak in comparison with the linked polymer solution, but has better temperature tolerance. Particle size shows little change, with shearing rate being increased, while the shape remains about the same and the effect of shearing on the plugging performance of the cross-linked polyacrylamide microsphere dispersion system in regard to the nuclear pore membrane is weak in comparison with the linked polymer solution, but has better shear stability. The salt tolerance, temperature tolerance, and shear stability of microspheres are associated with a particular cross-linked structure.     

The Effects of Alcohol with Different Chain Length on the Phase Equilibria of Nonionic Surfactant System

Addition of alcohol with longer chain length (C₆H₁₃OH, C₈H₁₇OH, and C₁₂H₂₁OH) caused a reduction the cloud point of a commercial nonionic surfactant, Tesgitol (T_15-s-9). The formation of lamellar liquid crystal (LLC) was favored so that isotropic liquid (L₁)-LLC two-phase region became wider with increasing temperature at an appropriate weight ratio of surfactant to alcohol. The isotropic liquid phase/liquid two phase transformation was replaced by a two-phase transformation to isotropic liquid/lamellar liquid crystal at the cloud point for the system without alcohol.     

Determination of the Diffusion Coefficient for SDS Micelle with Different Shape and the Effects of Ethanol by Cyclic Voltammetry Without Probes

Micelle diffusion coefficient of SDS with different micelle shape in aqueous and water-ethanol solutions are determined by cyclic voltammetry without any probe. The diffusion coefficient decreases with as increasing SDS concentration. The first critical micellar concentration is 8.0xl0³, mol 1¹.corresponding to the transformation from premicelle to spherical micelle. The second critical micellar concentration is 5.60x10²and corresponding to transformation from spherical micelle to rod-like micelle. The less the weight ratio of SDS to ethanol is, the larger the diffusion coefficient is. The influence of added water to the micelle solution is almost the same for SDS-ethanol-HaO system with different micelle shape. Mechanism of electrochemical reaction for SDS at platinum electrode is discussed as well.     

Relationship Between the Polymer Structures and Destabilization of Polymer‐Containing Water‐in‐Oil Emulsions

The viscous properties, scanning electronic microscopy (SEM), and water/oil interfacial tension (IFT) of partially hydrolyzed polyacryamide (HPAM) and hydrophobically associating hydrolyzed polyacryamides modified with N‐dodecylacrylamide were studied with the objective of investigating the influence on destabilization of emulsions. As expected, the copolymers exhibit significant viscosity enhancing capacity and three‐dimensional network structures due to intermolecular hydrophobic associations, and also present high interfacial activities as the IFT decrease with increasing polymer concentration. As a result, the existences of copolymers increased both the viscosity of emulsions and the intensity of interfacial film, in which case slow down the diffusion of demulsifier molecules and enhance the stability of emulsions, finally, the separation of water from oil becomes more difficult.     

Swelling of Water/Nonionic Surfactant Lamellar Liquid Crystals: A Model

A model is presented to provide quantitative measures to estimate the trends of the change in the penetration of the added component into the polar part of the amphiphile layer in lamellar liquid crystals of water and ethoxylated surfactants with added water (or polar solvents). The total thickness of the bi‐layer is treated as composed of an aqueous layer, of a layer of the polar groups from the surfactant and of the hydrocarbon chains of the latter. A fraction α of the added water is assumed penetrating the polar group layer leading to its expansion. The evaluation is built on the fact that experimental determinations of the interlayer spacing in the overwhelming majority of cases show a first order linear dependence on the ratio of added water. In the model this linearity is obtained by variation of the degree of penetration of water. The model indicated a reduction in the degree of penetration with added water, which is a rational trend. The model demonstrates the earlier interpretation of a structure, whose interlayer spacing is invariant with water contents as nonswelling; for example, in which all added water penetrates the amhiphile layer, is not appropriate. The model demonstrates the constancy of the interlayer spacing to be a consequence of a balance between the expansion of the amphiphile layer and the increase of a “free water” layer.     

Synthesis and Characterization of Multi‐Walled Carbon Nanotube/Polythiophene Composites

Multi‐walled carbon nanotube (MWCNT)/polythiophene (PTh) composites have been prepared by in situ chemical oxidative polymerization. PTh is synthesized onto the sidewalls of the MWCNTs, which play a role as hard templates for PTh to produce one‐dimensional nanostructures. The morphology and structures of the MWCNT/PTh composites are characterized by High‐resolution transmission electron microscopy, x‐ray diffraction, and Fourier transform infrared spectrometry. Their electrical property and thermal stability are determined using vector network analyzer and thermal gravimetric analyzer. Moreover, the mechanism of MWCNT/PTh nanowire formation is described. The studies show that the composites are nanowires with core‐shell structure, in which the outer shells and inner cores are formed by PTh and MWCNTs, respectively. The addition of MWCNTs does not change the backbone structure of PTh and affect the amorphous condition of PTh very slightly, however, it improves the electrical conductivity and thermal stability of PTh.