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.     

Swelling-shrinking behavior of a polyampholyte gel composed of positively charged networks with immobilized polyanions

Polyampholyte gels were prepared by free radical polymerization of aqueous monomer solutions with the following composition: 69% N-isopropylacrylamide (thermosensitive neutral monomer), 1% N,N'-methylenebisacrylamide (cross-linker), 15% 1-vinylimidazole (cationic monomer), and either 15% acrylic acid (AAc, anionic monomer) or poly(acrylic acid) (PAAc, polyanion). We thus obtained two sorts of polyampholyte gels; that is, G1 with immobilized PAAc and G2 with randomly copolymerized AAc. The equilibrium swelling ratio (Qe) was studied as a function of the pH, NaCl concentration, and temperature. Also studied was the kinetics of swelling and shrinking in response to a sudden pH change. The significant results obtained were as follows: (i) A fully collapsed state was observed at pH 4.5-9.0 for G1 and at pH 4.5-7.0 for G2. (ii) Below and above these pH ranges, both gels were in a swollen state; therefore, an isoelectric point (pI) appeared in a wide pH range. (iii) At alkaline pH regions where a hysteresis was observed in the Qe versus pH curves of G1 and G2 as the pH was first increased then decreased, G1 exhibited very slow swelling-shrinking kinetics. (iv) An increase in the NaCl concentration allowed the gel to swell at pH approximately pI (antipolyelectrolyte behavior) but to shrink at pHs below and above the pI range (polyelectrolyte behavior). (v) The magnitude of the salt-induced shrinking of G1 is smaller than that of G2 at pH 10 and at NaCl concentrations > 0.01 M. (vi) At pH 10, an increase in the temperature from 35 to 50 degrees C led to a shrinking change of G1 but not of G2. These results were found to be explicable in terms of a different distribution of negative charges within the polyampholyte gel network.     

Synthesis and physiological activity of novel tocopheryl glycosides

Vitamin E glycosides were synthesized and enzymatic hydrolysis was examined for use as potential pro-drugs, however, the glycoside bond was found to be stable. On the other hand, among the glycosides synthesized, dl-alpha-tocopherylglucoside (6b) and dl-alpha-tocopherylmannoside (6c) showed strong inhibitory action on histamine release from mast cells. In addition, 6c also showed a suppressive action on IgE antibody formation. Thus, tocopheryl glycoside showed new properties compared to tocopherol (vitamin E). In particular, 6c was shown to be a novel lead compound with excellent manifold anti-allergic activity and anti-inflammatory activity.     

Excited states of phosphorescent platinum(II) complexes containing N wedge C wedge N-coordinating tridentate ligands: spectroscopic investigations and time-dependent density functional theory calculations

The absorption and emission spectra of the Pt(II) complexes containing N wedge C wedge N-coordinating tridentate ligands, platinum(II) 1,3-di(2-pyridyl)benzene chloride [Pt(dpb)Cl] and platinum(II) 3,5-di(2-pyridyl)toluene chloride [Pt(dpt)Cl], together with their corresponding free ligands, 1,3-di(2-pyridyl)benzene (dpbH) and 3,5-di(2-pyridyl)toluene (dptH), have been analyzed by density functional theory (DFT) for the ground state and time-dependent DFT (TDDFT) for the excited states. T(1)(A(1)) and S(1)(B(2)) of the complexes (in C(2)(v) symmetry) were assigned on the basis of the calculated excitation energies as well as comparison of the experimental spectroscopic properties and the calculated states' characteristics. The calculated excitation energies for T(1) and S(1) of the complexes as well as those for T(1) of the free ligands were in good agreement with their observed values within 600 cm(-1). The d-pi* characters of the excited states were evaluated from the change in electron densities between the ground and excited states by Mulliken population analysis; values of 25% for T(1) and 32% for S(1) were obtained for both complexes. The calculated values of d-pi* character were found to be consistent with the reported emission lifetimes as well as the observed emission energy shifts from the corresponding free ligands. Most spectroscopic properties of the complexes and the free ligands, which include solvatochromic shift, Stokes shifts, methyl substitution shifts, and emission spectra profiles, were well explained from the calculation results.     

Effects of adrenergic blockers or bicuculline on diazepam induced changes in rat pineal melatonin synthesis in vivo and in vitro.

The effect of propranolol (PPL), phenoxybenzamine (PBZ) or bicuculline (BCL) on the diazepam (DZP)-induced changes of pineal melatonin synthesis in male rats was examined in vivo and in vitro. Administration of PBZ did not affect the inhibitory action of DZP on pineal melatonin synthesis in vivo. A single injection of PPL inhibited the pineal melatonin synthesis similarly to the administration of DZP alone, but the two drugs together did not exhibit additive or synergistic effects on the melatonin synthesis. Significant decreases in the N-acetyltransferase (NAT) activity and the N-acetylserotonin (NAS) and melatonin contents were observed in the BCL-injected group, being greater than those in the DZP-treated group. Unexpectedly, however, the combination treatment of DZP and BCL causes an increase in the NAT activity and melatonin content compared with the BCL-alone group. Incubation with DZP at higher concentrations resulted in an increase of pineal NAT activity in vitro, but this increase was inhibited by preincubation with PPL, PBZ or BCL. DZP treatment thus appeared to have different effects on pineal NAT activity in vivo and in vitro. These results suggest that both a GABAergic mechanism and peripheral benzodiazepine (BZP) receptors in rat pineal gland may be involved in the modulation of melatonin synthesis by DZP.     

Stereospecific living radical polymerization for simultaneous control of molecular weight and tacticity

The simultaneous control of the molecular weights and the tacticity was attained even during radical polymerization by the judicious combinations of the living/controlled radical polymerizations based on the fast interconversion between the dormant and active species, and the stereospecific radical polymerizations mediated by the added Lewis acids or polar solvents via the coordination to the monomer/polymer terminal substituents. This can be useful for various monomers including not only conjugated monomers, such as acrylamides and methacrylates, but also nonconjugated ones such as vinyl acetate and N‐vinylpyrrolidone. Stereoblock polymers were easily obtained by the addition of the Lewis acids or by change of the solvents during the living radical polymerizations. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 6147–6158, 2006     

Total synthesis of (+/-)-stemodinone via an efficient ring-exchange strategy

A total synthesis of (+/-)-stemodinone, a tetracyclic stemodane diterpene, from the known tricyclic methyl olefin 11 is described. The key steps involve an efficient ring-exchange reaction and palladium(0)-catalyzed lactone migration. The ring-exchange strategy for controlling the stereochemistry was based on an initial Diels-Alder reaction to form a new ring followed by cleavage of the original ring. Cleavage of the original ring of the Diels-Alder adduct 9 was achieved by an initial regio- and chemoselective Baeyer-Villiger oxidation followed by the Pd(0)-catalyzed lactone-migration reaction reported by us.     

Midgap levels of photoexcited conductive polymers. I. A simple description of the midgap levels based on molecular orbital interaction

We studied the midgap levels appearing in the photoexcited conductive polymers such as trans- and cis-polyacetylenes, poly(p-phenylene), polypyrrole, and polyacene based on the molecular orbital analysis. The midgap levels are constructed from the transformation of the highest occupied molecular orbital and the lowest unoccupied molecular orbital of the ground state. As the result of the localization of the wave functions associated with these midgap levels, large polarization is induced between adjacent carbon atoms. Based on the examination of the energy gap between the two midgap levels, the polymers with a nondegenerate ground state such as cis-polyacetylene, poly(p-phenylene), and polypyrrole would show no sizable photoconductivities.     

Two-dimensional Monte Carlo simulations of a polydisperse colloidal dispersion composed of ferromagnetic particles for the case of no external magnetic field

We have investigated the aggregation phenomena in a polydisperse colloidal dispersion composed of ferromagnetic particles by means of the cluster-moving Monte Carlo method. The results have been compared with those for a monodisperse system. The internal structures of aggregates have been analyzed in terms of the radial distribution function in order to clarify the quantitative differences in the internal structures of clusters. In addition, the cluster size distribution and angular distribution function have been investigated. The results obtained in the present study are summarized as follows. In a monodisperse system, open necklacelike clusters are formed and they extend with increasing strength of the magnetic particle-particle interaction. In a polydisperse system with a small standard deviation in the particle size distribution, sigma=0.2, larger necklacelike clusters are formed and some looplike clusters can also be observed. In a polydisperse system with a larger standard deviation, sigma=0.35, clumplike clusters are formed for a weak magnetic particle-particle interaction. For a stronger magnetic interaction, larger size clusters that exhibit a complicated network structure are formed. These complicated cluster formations found in a polydisperse system are mainly due to the effect of the presence of larger particles.     

Quinolone analogues 6 [1‐5]. Synthesis of 3‐halogeno‐1‐methylpyridazino[3,4‐b]quinoxalin‐4(1H)‐ones

The reaction of the quinoxaline N‐oxides 7a,b with diethyl ethoxymethylenemalonate gave the 1‐methylpyridazino[3,4‐b]quinoxaline‐4,4‐dicarboxylates 8a,b , whose reaction with N‐bromosuccinimide or N‐chlorosuccinimide afforded the 3‐halogeno‐1‐methylpyridazino[3,4‐b]quinoxaline‐4,4‐dicarboxylates 9a‐d. The reaction of compounds 9a‐d with hydrazine hydrate resulted in hydrolysis and decarboxylation to provide the 3‐halogeno‐1‐methylpyridazino[3,4‐b]quinoxaline‐4‐carboxylates 10a‐d , whose reaction with nitrous acid effected oxidation to furnish the 3‐halogeno‐4‐hydroxy‐1‐methylpyridazino[3,4‐b]quinoxaline‐4‐carboxylates 11a‐d , respectively. The reaction of compounds 11a‐d with hydrazine hydrate afforded the 3‐halogeno‐1‐methylpyridazino[3,4‐b]quinoxalin‐4‐ols 12a‐d , whose oxidation provided the 3‐halogeno‐1‐methylpyridazino[3,4‐b]quinoxalin‐4(1H)‐ones 6a‐d , respectively. Compounds 6a‐d had antifungal activities in vitro.