Optimization of protein sample preparation for two-dimensional electrophoresis

Optimized 2DE sample preparation protocols that maximize total protein recovery are fundamental to improving proteome capture and increasing the utility of 2DE, which is in part limited by inadequate recovery of proteins with diverse physicochemical properties. Maintaining protein solubility is an important factor for protein recovery, but the multitude of solubility-enhancing agents and the relatively low-throughput nature of 2DE limit the systematic study of sample preparation. In this work, design of experiment (DOE) approaches are used to optimize protein recovery by altering the levels of four solubility-enhancing agents (urea, DTT, CHAPS, and SDS) in the initial suspension solution. Protein recovery is quantified by a total protein concentration assay, which is demonstrated to be representative of SDS-PAGE and 2DE recovery. DOE methodologies are presented as relatively high-throughput procedures for optimizing 2DE sample preparation parameters for a variety of sample types. Optimal suspension solution compositions are shown to vary across a model protein solution (no urea or DTT), Chinese hamster ovary (CHO) cell lysate (8 M urea, ≥2% CHAPS, ≥32.5 mM DTT), and Escherichia coli cell lysate (8 M urea, 4% CHAPS, 65 mM DTT), with optimized conditions increasing 2DE protein recovery at least 50% compared to suboptimal conditions.     

Synthesis and Nonlinear Optical Properties of Novel Polyurethane Containing Cyanovinylnitroresorcinoxy Group

Novel X-type polyurethane 5 containing 4-(2′-carbomethoxy-2′-cyano)vinyl-6-nitroresorcinoxy groups as nonlinear optical (NLO) chromophores, which constitute part of the polymer backbone, was prepared and characterized. Polyurethane 5 is soluble in common organic solvents such as acetone and N,N-dimethylformamide. It shows thermal stabilities up to 260°C from thermogravimetric analysis with glass transition temperature obtained from differential scanning calorimetry near 108°C. The second harmonic generation (SHG) coefficient (d₃₃) of poled polymer film at 1064 nm fundamental wavelength is 9.83 × 10^?9 esu. Polymer 5 exhibits a high thermal stability even at 2°C higher than T_g, and no significant SHG decay is observed below 110°C, which is acceptable for nonlinear optical device applications.     

Unimolecular dissociation of aniline molecular ion: A theoretical study

The potential energy surface (PES) for dissociation of aniline ion was determined using density functional theory molecular orbital calculations at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) level. On the basis of the PES obtained, kinetic analysis was performed by Rice–Ramsperger–Kassel–Marcus (RRKM) calculations. The RRKM dissociation rate constants agreed well with previous experimental data. The most favorable channel was formation of the cyclopentadiene ion by loss of HNC, occurring through consecutive ring opening and re-closure to a five-membered ring. Loss of H could compete with the HNC loss at high energy, which occurred by direct cleavage of an N–H bond or through ring expansion.     

Dictyostelium cells bind a secreted autocrine factor that represses cell proliferation

Background  

Mycobacterium tuberculosis, an intracellular pathogen encounters redox stress throughout its life inside the host. In order to protect itself from the redox onslaughts of host immune system, M. tuberculosis appears to have developed accessory thioredoxin-like proteins which are represented by ORFs encoding WhiB-like proteins. We have earlier reported that WhiB1/Rv3219 is a thioredoxin like protein of M. tuberculosis and functions as a protein disulfide reductase. Generally thioredoxins have many substrate proteins. The current study aims to identify the substrate protein(s) of M. tuberculosis WhiB1.     

Sequential self-assembly in metal-organic frameworks

This perspective discusses the use of sequential self-assembly in the construction of metal-organic frameworks through the systematic insertion, replacement, and removal of organic structural building units. We review previous works that can be classified as such sequential self-assembly in multidimensional MOFs.     

Syringaresinol causes vasorelaxation by elevating nitric oxide production through the phosphorylation and dimerization of endothelial nitric oxide synthase

Nitric oxide (NO) produced by endothelial NO synthase (eNOS) plays an important role in vascular functions, including vasorelaxation. We here investigated the pharmacological effect of the natural product syringaresinol on vascular relaxation and eNOS-mediated NO production as well as its underlying biochemical mechanism in endothelial cells. Treatment of aortic rings from wild type, but not eNOS(-/-) mice, with syringaresinol induced endothelium-dependent relaxation, which was abolished by addition of the NOS inhibitor N(G)-monomethyl-L-arginine. Treatment of human endothelial cells and mouse aortic rings with syringaresinol increased NO production, which was correlated with eNOS phosphorylation via the activation of Akt and AMP kinase (AMPK) as well as elevation of intracellular Ca(2+) levels. A phospholipase C (PLC) inhibitor blocked the increases in intracellular Ca(2+) levels, AMPK-dependent eNOS phosphorylation, and NO production, but not Akt activation, in syringaresinol- treated endothelial cells. Syringaresinol-induced AMPK activation was inhibited by co-treatment with PLC inhibitor, Ca(2+) chelator, calmodulin antagonist, and CaMKKβ siRNA. This compound also increased eNOS dimerization, which was inhibited by a PLC inhibitor and a Ca(2+)-chelator. The chemicals that inhibit eNOS phosphorylation and dimerization attenuated vasorelaxation and cGMP production. These results suggest that syringaresinol induces vasorelaxation by enhancing NO production in endothelial cells via two distinct mechanisms, phosphatidylinositol 3-kinase/Akt- and PLC/Ca(2+)/CaMKKβ-dependent eNOS phosphorylation and Ca(2+)-dependent eNOS dimerization.     

Structural studies on the yttrium-doped cobalt ferrite powders synthesized by sol–gel combustion method

Y_0.2CoFe_1.8O₄ nanopowders were prepared using a sol–gel combustion method. Metal nitrates, such as yttrium nitrate, cobalt nitrate and ferric nitrate, were used as the source materials. Citric acid and polyvinyl alcohol were used as the burning agent and agglomeration reducing agent, respectively. The pH of the precursor was maintained at 7. The mean crystallite size of the prepared ferrite was in the range of ∼20–70 nm. The inverse spinel structure, cubic morphology, and the identification of functional groups of the yttrium-doped cobalt ferrite were analyzed systematically using several analytical tools.     

Synthesis of highly monodisperse polystyrene microspheres via dispersion polymerization using an amphoteric initiator

The highly monodisperse polystyrene (PS) microspheres were produced by dispersion polymerization using an amphoteric initiator, 2,2'-azobis [N-(2-carboxyethyl)-2-2-methylpropionamidine] (VA-057). The polymerization characteristics were investigated and compared with conventional initiators, 2,2-azobis(isobutyronitrile) (AIBN) and benzoyl peroxide (BPO). The monodisperse PS microspheres having the coefficient of variation (C(v)) of diameter all less than 4% are obtained at very low stabilizer, poly(vinyl pyrrolidone) (PVP) concentrations of 1 and 2 wt%. It is found that the size dependence of the VA-057 system, D(n) proportional, variant [VA-057](0.267), is less sensitive than a conventional initiator system. When the same amount, 2 wt%, of AIBN, BPO, and VA-057 is used under the identical PVP concentration of 2 wt%, the D(n)/C(v)'s are 1.95/11.57, 1.47/22.44, and 2.08 microm/2.50%, respectively. The uniformity of particles was characterized employing an optical analyzer, Turbiscan. For the VA-057 system, the back scattering intensity is linearly reduced with time having a constant sedimentation rate of 48.98 microm/min throughout the settling process. The uniformity of PS particles in the VA-057 system stems from (1) the higher rate of polymerization in early stage of polymerization, followed by significantly faster reduction of the rate, and (2) good dispersion stability of primary particles. Therefore, it is found that the use of an amphoteric initiator, VA-057, is promising for producing monodisperse particles in dispersion polymerization.     

Chow group of 1-cycles on the moduli space of vector bundles of rank 2 over a curve

Let X be a non-singular complex projective curve of genus ≥3. Choose a point x ∈ X. Let M_x be the moduli space of stable bundles of rank 2 with determinant We prove that the Chow group CH^Q₁(M_x) of 1-cycles on M_x with rational coefficients is isomorphic to CH^Q₀(X). By studying the rational curves on M_x, it is not difficult to see that there exits a natural homomorphism CH₀(J)→CH₁(M_x) where J denotes the Jacobian of X. The crucial point is to show that this homomorphism induces a homomorphism CH₀(X)→CH₁(M_x), namely, to go from the infinite dimensional object CH₀(J) to the finite dimensional object CH₀(X). This is proved by relating the degeneration of Hecke curves on M_x to the second term I^*2 of Bloch's filtration on CH₀(J). Insong Choe was supported by KOSEF (R01-2003-000-11634-0).