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.     

(−)-Daucic acid: Proof of -lyxo configuration, synthesis of its -ribo, -xylo, -arabino and -lyxo analogs, and biosynthetic implications

The dimethyl esters of the 2,6-anhydro-3-deoxy-hept-2-enaric acids with -xylo, -lyxo, -arabino, -lyxo- and -ribo-configuration were synthesized from -galactose and -mannose, respectively, and further characterized by their di-O-acetyl and di-O-benzoyl derivatives. Comparison of their physical data with those of Daucus carota derived products revealed (−)-daucic acid to have -lyxo-configuration 46 rather than the previously assigned -xylo stereochemistry 1. Dimethyl daucate 43 could be converted by acid-induced ring contraction and dehydration into naturally occurring (+)-osbeckic acid 47, thereby proving its (S)-configuration. Configurational identity in the pyranoid rings of (−)-daucic acid and KDO, together with available biosynthetic evidence on chelidonic acid 4, a leaf closing factor, suggests a joint, KDO 8-P-based pathway for their biosynthesis in plants.     

Deuterium substitution effect on proton relaxation times as a direct means for elucidating molecular interaction in solution. An application to 2′,3′-isopropylideneadenosine

Proton T₁ measurement with the Fourier transform method combined with quenching of dipolar coupling through selective deuterium substitution is shown to be a useful method for elucidating intra- and intermolecular interactions in solution, with 2′,3′-isopropylideneadenosine as an example. Average distances between H-8 and ribose protons are determine in combination with carbon-13 T₁ measurement. The method is compared with the nuclear Overhauser effect.     

Identification of Shiga toxins in Shiga toxin-producing Escherichia coli using immunoprecipitation and high-performance liquid chromatography-electrospray ionization mass spectrometry

We developed a rapid and reliable identification method for Shiga toxins in Shiga toxin-producing Escherichia coli (STEC) using immunoprecipitation and high-performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-ESI-MS). Polyclonal antisera specific for Shiga toxin 1 (Stx1) and Shiga toxin 2 (Stx2) were raised in rabbits so as to be used for the immunoprecipitation. The immunoprecipitaion was carried out by mixing sample solutions with 50 microl each of the antisera to Stx1 and Stx2 followed by allowing the mixed solutions to stand for 30 min. The quantity required to obtain the immunoprecipitate was more than 0.5 microg of Shiga toxins. HPLC-ESI-MS analysis of the resulting immunoprecipitates provided accurate molecular weight information on Shiga toxins, leading to direct evidence for the presence of these toxins. It requires at most two days to perform our procedure from toxin extraction to measurement of HPLC-ESI-MS whereas the previous method using isolation procedures required about two weeks to complete. The usefulness of the present method has been demonstrated by identifying Stx1, Stx2 and a variant of Stx2 (Stx2e) in the immunoprecipitates prepared from STEC strains.     

Dynamic stability of carbonyl ylides

The non- and fluorine-substituted singlet carbonyl ylides are studied by using ab initio MCSCF calculations. The thermodynamic stability of the carbonyl ylides and the intramolecular stability to isomerization or fragmentation reaction coordinates is demonstrated in terms of the topological structure of the ab initio potential energy surfaces. The allylic resonance is found to be dynamically unstable, considering out-of-plane vibrational mode. The instability is studied by the symmetries of the low-lying excitations out of the MCSCF wave function.     

A new route to 3-alkyl-2,5-di-t-butyl-2,4-cyclopentadienones from 4-alkyl-2,6-di-t-butylphenols

Base-catalyzed reaction of 5-acylmethyl-2,5-di-$\text{t}$-butyl-4-oxa-2-cyclopentenones selectively derived from 4-alkyl-2,6-di-$\text{t}$-butylphenols $\text{via}$ three steps involving oxygenation, acetylation, and acid-treatment gave 3-alkyl-2,5-di-$\text{t}$-butyl-2,4-cyclopentadienones in excellent yield.     

Base-labile tert-butoxycarbonyl (Boc) group on phenols

Phenols are deprotected with weak bases from their tert-butoxycarbonyl (Boc) derivatives. Boc deprotection with bases can avoid side reactions during the deprotection with acids. We note the lability of the Boc to bases and are able to utilize it as a new cleavage condition for synthetic studies.     

Ultraweak Luminescence Generated by Sweet Potato and Fusarium oxysporum Interactions Associated with a Defense Response

Abstract— Ultraweak luminescence generated by sweet potato and nonpathogenic Fusarium oxysporum interactions associated with a defense response was detected by a photoncounting method using ultrahigh-sensitive photodetectors. The time-dependent intensity variation, the spectrum and the two-dimensional imaging of the ultraweak luminescence are indicative of the defense response of the sweet potato to F. oxysporum. The production of ipomeamarone as a phytoalexin means that F. oxysporum induced the defense response in the sweet potato.     

Synthesis of 3-epi-6,7-dideoxyxestobergsterol A

3-Epi-6,7-dideoxyxestobergsterol A (2), an analogue of xestobergsterol A, has been synthesized from dehydroepiandrosterone (3) in 15 steps. The key synthetic intermediate, 15beta,16alpha-dioxypregn-17(20)E-ene derivative 8, was prepared from the corresponding 15beta,16beta-epoxide 6 by treating with acetic acid and titanium tetraisopropoxide. The 23-oxo side chain was constructed stereoselectively by orthoester Claisen rearrangement of 8 followed by introduction of an isobutyl group. Basic treatment of the 15,23-diketone 12 followed by deprotection gave the title compound 2.     

Synthesis and antiallergic activity of N-[4-(4-diphenylmethyl-1-piperazinyl)butyl]-1,4-dihydro-4-oxopyridine-3 - carboxamides

A new series of oxopyridinecarboxamide derivatives 3a--g and 5a were synthesized and evaluated for their antiallergic activity. 1,4-Dihydro-7-methyl-4-oxo-1,8-naphthyridine-3-carboxamides 3a and 5a exhibited potent antiallergic activity (inhibitory rates of 80.7 and 88.3%, respectively, at 20 mg/kg, p.o.) in the rat passive cutaneous anaphylaxis (PCA) test and also exhibited much more potent in vitro inhibitory activity than caffeic acid against the enzyme 5-lipoxygenase (5-LO). Their in vitro antihistamine activity, however, was weaker than that of ketotifen. Compounds 3a and 5a are viewed as promising candidates for antiallergic agents.