Optimization of in-gel protein digestion system in combination with thin-gel separation and negative staining in 96-well plate format

Improvement of in-gel digestion efficiency is highly desirable for one- or two-dimensional gel electrophoretic separation and mass spectrometric (MS) analysis in proteomics, because the resultant increases in sequence coverage and MS signal intensity lead to higher confidence in protein identification. Here an optimized in-gel digestion system, in combination with thin-gel separation and negative staining in a high-throughput format using 96-well plates, is described. The combination of negative staining and protein separation on a 0.9 mm thick gel showed a clear improvement in in-gel digestion efficiency in comparison with the more typical protocols such as the combination of silver staining and a 1.0 mm gel. In addition, the use of 96-well plates to increase throughput did not decrease the efficiency of this strategy when the stirring of the gel pieces in processes such as destaining, washing, gel-shrinking and peptide extraction was performed by sonication instead of shaking the plates. This procedure was optimized and applied to identify proteins of the postsynaptic density fraction; 105 proteins were identified after SDS-PAGE separation.     

Post-oxidative conversion of thiol residue to sulfonic acid in the binding sites of molecularly imprinted polymers: disulfide based covalent molecular imprinting for basic compounds

An imprinted polymer using a disulfide derivative as a template was treated with NaBH4 to yield the polymer with thiol groups in the binding sites. The thiol groups were then oxidized with H2O2/AcOH to yield the molecularly imprinted polymer with sulfo groups in the binding sites. This site conversion can provide amine-imprinted polymers, in which amine is retained to the imprinted polymer by the strong electrostatic interaction between the amino group and the sulfo group in the binding sites.     

Radiation-induced heterogeneous polymerization of acrylamide in acetone and acetone–water mixtures

The effects of temperature, dose rate, and monomer concentration on the heterogeneous polymerization of acrylamide in acetone–water mixtures have been studied. Heterogeneous polymerization takes place in mixtures containing less than 60 vol-% water. The polymerization is steady in acetone and nonsteady in acetone an nonsteady in mixtures containing 10–50 vol-% water. The average rate of polymerization is highest in mixtures with about 20 vol-% water. Polymer molecular weight increases with the increasing water content in range 0–10 vol-% and does not change in the range of 30–70 vol-% water. For the polymerization in acetone and an acetone–water 60/40 mixture the activation energies are 2.3 and ?1.8 kcal/mole, the dose rate exponents of rate are 0.78 and 0.52, and the monomer concentration exponents of rate are 0.5 and 1.6, respectively. The polymer molecular weight increases with decreasing dose rate, decreasing temperature, and increasing monomer concentration. These results are discussed in connection with the mechanism of heterogeneous polymerization and the solvent effect.     

A long-range-corrected time-dependent density functional theory

We apply the long-range correction (LC) scheme for exchange functionals of density functional theory to time-dependent density functional theory (TDDFT) and examine its efficiency in dealing with the serious problems of TDDFT, i.e., the underestimations of Rydberg excitation energies, oscillator strengths, and charge-transfer excitation energies. By calculating vertical excitation energies of typical molecules, it was found that LC-TDDFT gives accurate excitation energies, within an error of 0.5 eV, and reasonable oscillator strengths, while TDDFT employing a pure functional provides 1.5 eV lower excitation energies and two orders of magnitude lower oscillator strengths for the Rydberg excitations. It was also found that LC-TDDFT clearly reproduces the correct asymptotic behavior of the charge-transfer excitation energy of ethylene-tetrafluoroethylene dimer for the long intramolecular distance, unlike a conventional far-nucleus asymptotic correction scheme. It is, therefore, presumed that poor TDDFT results for pure functionals may be due to their lack of a long-range orbital-orbital interaction.     

Effects of a Single Exposure to UVB Radiation on the Activities and Protein Levels of Copper-Zinc and Manganese Superoxide Dismutase in Cultured Human Keratinocytes

Abstract— Ultraviolet B irradiation has been believed to decrease or impair the activity of reactive oxygen species (ROS) scavenging enzymes such as superoxide dismutase (SOD) in the skin. It has been recently reported that two isozymes of SOD, namely copper-zinc SOD (Cu-Zn SOD) and manganese SOD (Mn SOD), exist in mammalian cells and that the two enzymes play different roles in living systems. The aim of this study was to investigate changes in SOD activities and protein levels in cultured human keratinocytes after acute UVB irradiation. In addition, the protein levels of Cu-Zn SOD and Mn SOD were quantified separately. A single exposure to UVB irradiation produced an increase in SOD activity and protein level that peaked immediately after UVB irradiation, after which a decline was observed, with subsequent recovery to baseline levels 24 h after irradiation. In individual assays of Mn SOD and Cu-Zn SOD, the amount of Mn SOD protein decreased and then gradually recovered 24 h after irradiation. In contrast, the amount of Cu-Zn SOD protein increased immediately after UVB irradiation, and then gradually declined. To evaluate the mechanisms of these changes, we examined the effects of the cytokines, interleukin-1α (IL-1α) and tumor necrosis factor-α (TNF-α), which can be secreted from keratinocytes after UVB irradiation, on the SOD activity and protein levels in keratinocytes. Interleukin-la and TNF-α enhanced both the SOD activity and protein level of Mn SOD, while these cytokines had no effect on Cu-Zn SOD protein levels in cultured human keratinocytes after incubation for 24 h. Furthermore, when neutralizing antibodies against IL-1α and TNF-α were added separately or together to the culture medium before UVB irradiation, the recovery of total SOD activity and Mn SOD protein level were markedly inhibited 24 h after irradiation. Our results suggest that significant increases in SOD activity and protein level occur as a cutaneous antioxidant defense mechanism that protects against the cytotoxicity as a result of UVB irradiation, and that this increase in SOD is attributed to Cu-Zn SOD. The Cu-Zn SOD and Mn SOD protein levels changed in a different manner after UVB irradiation. The former may participate in an early phase and the latter in a late phase defense mechanism directed against oxidant cytotoxicity through UVB irradiation. In addition, the recovery of Mn SOD to baseline levels 24 h after UVB irradiation seems to be mediated through cytokines such as IL-1α and TNF-α, which are secreted from keratinocytes.     

Isolation, characterization, and theoretical study of La2@C78

A new metallofullerene, La2@C78, has been synthesized by DC arc discharge method, isolated by high-performance liquid chromatography, and characterized by laser desorption time-of-flight mass spectrometry, UV-vis-NIR absorption, differential pulse voltammetry, 13C NMR spectroscopy, and theoretical calculations. The La2@C78/CS2 solution is dark violet and presents several characteristic absorption features at 647, 561, 533, and 386 nm, with an onset around 1000 nm. With respect to empty D3-C78, the capability of La2@C78 as an electron acceptor or donor is stronger. Addition of 1,1,2,2-tetrakis(2,4,6-trimethylphenyl)-1,2-disirane to La2@C78 photochemically, as well as thermally, affords bis- and mono-adducts. Theoretical studies and 13C NMR spectroscopic analysis of La2@C78 indicate that it possesses a D3h-C78 cage (78:5).     

Synthesis of porphyrin-introduced silica gels by sol-gel process

Using a hydroxyl group appended free base porphyrin derivative (HP), porphyrin-introduced silica gels were synthesized by a sol-gel process. The HP content in the materials linearly increased with increasing the HP concentration. Meanwhile, free base tetraphenylporphyrin (TPP) with no hydroxyl groups were almost not incorporated into the silica gels. These facts suggested that the interaction between hydroxyl groups of the HP molecules and silica network is considerably strong. The UV-vis characters of HP-introduced materials were almost the same as pure HP molecules. The Beer's plot indicated that the HP molecules in the materials are dispersed.     

Smectic layer structure of ferroelectric liquid crystal formed between fine polymer fibres

This paper describes the alignment of ferroelectric liquid crystal (FLC) structures formed between aligned polymer fibres, where the FLC smectic layers are determined by polarising microscopy and X-ray diffraction. The FLC/polymer composite films were formed from a nematic phase FLC/monomer solution using a photopolymerisation-induced phase separation method. It was found that bending of the FLC smectic layers was induced in both the film plane and the cross-sectional plane at the phase transition from smectic A to chiral smectic C of the FLC material. The light transmittance properties of the composite film between crossed polarizers was analysed by light propagation simulation in several optical anisotropic media, based on the evaluated smectic layer model.     

Michael addition reactions between chiral equivalents of a nucleophilic glycine and (S)- or (R)-3-[(E)-enoyl]-4-phenyl-1,3-oxazolidin-2-ones as a general method for efficient preparation of beta-substituted pyroglutamic acids. Case of topographically controlled stereoselectivity

This paper describes a systematic study of addition reactions between the chiral Ni(II) complex of the Schiff base of glycine with (S)-o-[N-(N-benzylprolyl)amino]benzophenone and (S)- or (R)-3-[(E)-enoyl]-4-phenyl-1,3-oxazolidin-2-ones as a general and synthetically efficient approach to beta-substituted pyroglutamic acids and relevant compounds. These reactions were shown to occur at room temperature in the presence of nonchelating organic bases and, most notably, with very high (>98% diastereomeric excess (de)) stereoselectivity at both newly formed stereogenic centers. The stereochemical outcome of the reactions was found to be overwhelmingly controlled by the stereochemical preferences of the Michael acceptors, and the chirality of the glycine complex influenced only the reaction rate. Thus, in the reactions of both the (S)-configured Ni(II) complex and the Michael acceptors, the reaction rates were exceptionally high, allowing preparation of the corresponding products with virtually quantitative (>98%) chemical and stereochemical yields. In contrast, reactions of the (S)-configured Ni(II) complex and (R)-configured Michael acceptors proceeded at noticeably lower rates, but the addition products were obtained in high diastereo- and enantiomeric purity. To rationalize the remarkably high and robust stereoselectivity observed in these reactions, we consider an enzyme-substrate-like mode of interaction involving a topographical match or mismatch of two geometric figures. Excellent chemical and stereochemical yields, combined with the simplicity and operational convenience of the experimental procedures, render the present method of immediate use for preparing various beta-substituted pyroglutamic acids and related compounds.