Stable isotope-free quantitative shotgun proteomics combined with sample pattern recognition for rapid diagnostics

Mass spectrometry (MS) has become a powerful tool for the quantitative analysis of complex protein samples. A high-throughput strategy for the comparative analysis of multiple protein samples with high complexity becomes more and more important. Two strategies, spectral count and peak intensity, for label-free MS analysis of prefractionated complex mixtures have been described recently to be useful for quantitation. Here we compare both strategies for rapid and quantitative 1-D shotgun LC/MS/MS analyses of highly complex protein mixtures using silica-based monolithic columns. First, we validated linearity and sensitivity of these methods by spiking varying amounts of an internal standard protein in a complex plant protein extract. Secondly, quantitative data of proteins of Medicago truncatula nodules were visualized with independent components analysis using data either obtained from spectral count or peak integration performed with commercial software. Spectral count showed apparent advantages over peak integration because several peptides per protein are automatically averaged, the linear dynamic range of quantitation increases in complex matrices and the number of quantified proteins surpasses the number of proteins using peak integration. Thus, for the need of rapid comparative analysis of highly complex protein samples, spectral count enables sample pattern recognition and identification of biomarkers in nongel based proteomic studies.     

Comparison of Benzyl Celluloses Synthesized in Aqueous NaOH and Dimethyl Sulfoxide/Tetrabutylammonium Fluoride

Cellulose was benzylated starting from the dissolved polymer in dimethyl sulfoxide (DMSO)/tetrabutylammonium fluoride trihydrate (TBAF) and heterogeneously in aqueous NaOH as reaction media. Differences in the distribution of benzyl moieties within the anhydroglucose unit in dependence on the synthesis pathway couldn't be found. However, as revealed by means of ¹H-NMR spectroscopy, significant differences in the distribution of substituents along the cellulose chains occurred. Conventionally synthesized samples (in aqueous NaOH), even in the presence of a phase transfer catalyst, possess a block-wise distribution of substituents, while a dissolution of cellulose in DMSO/TBAF prior to the reaction gives products that are uniformly substituted along the cellulose chains.     

Influence of polymer molecular weight on the chemical modifications induced by UV laser ablation

This paper investigates the influence of polymer molecular weight (M(W)) on the chemical modifications of poly(methyl methacrylate), PMMA, and polystyrene, PS, films doped with iodonaphthalene (NapI) and iodophenanthrene (PhenI), following irradiation at 248 nm (KrF excimer laser, 20 ns fwhm and hybrid excimer-dye laser, 500 fs fwhm) and at 308 nm (XeCl excimer laser, 30 ns fwhm). The changes of intensity and position of the polymer Raman bands upon irradiation provide information on cleavage of the polymer bonds. Degradation of PMMA, which is a weak absorbing system at 248 nm, occurs to a higher extent in the case of a larger M(W), giving rise to the creation of unsaturation centers and to degradation products. For highly absorbing PS, no degradation is observed upon irradiation with a KrF laser. Consistently irradiating doped PS at 308 nm, where the absorption is low, induces degradation of the polymer. Results provide direct support for the bulk photothermal model, according to which ejection requires a critical number of broken bonds. In the case of irradiation of doped PMMA with pulses of 248 nm and 500 fs, neither degradation nor dependence with polymer M(W) are observed, indicating that mechanisms involved in the femtosecond laser ablation differ from those operating in the case of nanosecond laser ablation. Participation of multiphoton/avalanche processes is proposed.     

Chemical and photochemical reactivity of 6‐hydroxymethyl‐7,8‐dihydropterin in aqueous solutions

6‐Hydroxymethyl‐7,8‐dihydropterin (H₂Hmp) is an intermediate in the biosynthesis of folate, a precursor of coenzymes involved in the metabolism of nucleotides and amino acids. In this work, we have investigated the reactions undergone by H₂Hmp in aqueous solutions at physiological pH, in the absence and in the presence of UV‐A radiation (320–400 nm). In air‐equilibrated solutions, H₂Hmp undergoes slow thermal oxidation (half‐life 37 h) to yield 7,8‐dihydroxanthopterin (H₂Xap) as the main product. The reaction of H₂Hmp with hydrogen peroxide also yields H₂Xap as a main product. In contrast, UV‐A excitation of H₂Hmp leads to the formation of a dimer identified by electrospray ionization mass spectrometry. The corresponding quantum yield of H₂Hmp consumption (Φ_?R) was independent of O₂ and reactant concentration and has a value of 0.10 (±0.02), more than twice higher than that measured for other 6‐subtituted 7,8‐dihydropterins. Copyright © 2012 John Wiley & Sons, Ltd.     

Center,Centroid, Extended Centroid,and Quotients of Jordan Systems

In this article we prove that the extended centroid of a nondegenerate Jordan system is isomorphic to the centroid (and to the center in the case of Jordan algebras) of its maximal Martindale-like system of quotients with respect to the filter of all essential ideals.     

Chalcogen–chalcogen-bond activation by an ambiphilic,doubly reduced organoborane

The 9,10-dimethyl-9,10-dihydro-9,10-diboraanthracene dianion salt Li₂[1] instantaneously reacts with the dichalcogens O₂(tBu)₂, S₂Me₂, S₂(pTol)₂, Se₂Ph₂, and Te₂Ph₂ under reductive cleavage of the chalcogen–chalcogen bonds to give lithium chalcogenides and neutral 1. In solution, the products are involved in rapid association/dissociation equilibria. In the crystalline state, 1 and Li[O(tBu)] form a diadduct, whereas Li[SMe] gives a B?B-bridged monoadduct. In the three remaining cases, the crystal lattices contain monoadducts of 1 with one tri- and one tetracoordinate boron atom.     

Halichonic acid,a new rearranged bisabolene-type sesquiterpene from a marine sponge Halichondria sp.

A new compound, halichonic acid (1), was isolated from a marine sponge Halichondria sp., together with (6R,7S)-7-amino-7,8-dihydro-α-bisabolene (2). The structure of 1 was elucidated by spectroscopic analysis and ECD spectrum calculation to be a rearranged bisabolene-type sesquiterpene having a 3-azabicyclo[3.3.1]nonene moiety. Compound 2 was cytotoxic against HeLa cells with an IC₅₀ value of 50?μM, whereas 1 did not show cytotoxicity even at 50?μM. It is possible that 1 is biosynthesized from farnesyl pyrophosphate and glycine, with rearrangement.     

3D-Printed Phenacrylate Decarboxylase Flow Reactors for the Chemoenzymatic Synthesis of 4-Hydroxystilbene

Continuous flow systems for chemical synthesis are becoming a major focus in organic chemistry and there is a growing interest in the integration of biocatalysts due to their high regio- and stereoselectivity. Methods established for 3D bioprinting enable the fast and simple production of agarose-based modules for biocatalytic reactors if thermally stable enzymes are available. We report here on the characterization of four different cofactor-free phenacrylate decarboxylase enzymes suitable for the production of 4-vinylphenol and test their applicability for the encapsulation and direct 3D printing of disk-shaped agarose-based modules that can be used for compartmentalized flow microreactors. Using the most active and stable phenacrylate decarboxylase from Enterobacter spec. in a setup with four parallel reactors and a subsequent palladium(II) acetate-catalysed Heck reaction, 4-hydroxystilbene was synthesized from p-coumaric acid with a total yield of 14.7 % on a milligram scale. We believe that, due to the convenient direct immobilization of any thermostable enzyme and straightforward tuning of the reaction sequence by stacking of modules with different catalytic activities, this simple process will facilitate the establishment and use of cascade reactions and will therefore be of great advantage for many research approaches.