Improved protein identification efficiency by mass spectrometry using N-terminal chemical derivatization of peptides from Angiostrongylus costaricensis, a nematode with unknown genome

Matrix-assisted laser desorption ionization (MALDI), Peptide Mass Fingerprinting (PMF) and MALDI-MS/MS ion search (using MASCOT) have become the preferred methods for high-throughput identification of proteins. Unfortunately, PMF can be ambiguous, mainly when the genome of the organism under investigation is unknown and the quality of spectra generated is poor and does not allow confident identification. The post-source decay (PSD) fragmentation of singly charged tryptic peptide ions generated by MALDI-TOF/TOF typically results in low fragmentation efficiency and/or complex spectra, including backbone fragmentation ions (series b and y), internal fragmentation etc. Interpreting these data either manually and/or using de novo sequencing software can frequently be a challenge. To overcome this limitation when studying the proteome of adult Angiostrongylus costaricensis, a nematode with unknown genome, we have used chemical N-terminal derivatization of the tryptic peptides with 4-sulfophenyl isothiocyanate (SPITC) prior to MALDI-TOF/TOF MS. This methodology has recently been reported to enhance the quality of MALDI-TOF/TOF-PSD data, allowing the obtainment of complete sequence of most of the peptides and thus facilitating de novo peptide sequencing. Our approach, consisting of SPITC derivatization along with manual spectra interpretation and Blast analysis, was able to positively identify 76% of analyzed samples, whereas MASCOT analysis of derivatized samples, MASCOT analysis of nonderivatized samples and PMF of nonderivatized samples yielded only 35, 41 and 12% positive identifications, respectively. Moreover, de novo sequencing of SPITC modified peptides resulted in protein sequences not available in NCBInr database paving the way to the discovery of new protein molecules.     

A highly efficient dioxo(mu-oxo)molybdenum(VI) dimer catalyst for olefin epoxidation

The oxo-bridged dimer [Mo(2)O(4)(mu(2)-O)Cl(2)(pzH)(4)] (1; pzH = pyrazole) exhibits unusually high activity in the liquid-phase catalytic epoxidation of the cyclic olefins cyclooctene and (R)-(+)-limonene under mild conditions and in the absence of additional organic solvents, using tert-butyl hydroperoxide as the oxidant. The complex is stable under the reaction conditions and can be used in further catalytic runs without significant loss of performance. An X-ray crystallographic investigation reveals that 1 has an unprecedented and extremely rare all-cis configuration at each of the MoO(2)-(mu(2)-O)Cl(pzH)(2) cores, which can be understood by considering supramolecular contacts and geometric factors.     

Effect of terbium(III) chloride on the micellization properties of sodium decyl- and dodecyl-sulfate solutions

The effect of TbCl3 on the aggregation processes of the anionic surfactants sodium decyl sulfate (SDeS) and sodium dodecyl sulfate (SDS) has been investigated. Electrical conductivity data, combined with Tb(III) luminescence measurements suggest that the formation of micelles involving TbCl3 and SDS occurs at concentrations below the critical micelle concentration (cmc) of the pure surfactants; the formation of these mixed aggregates was also monitored by light scattering, which indicates that the addition of TbCl3 to surfactant concentration at values below the pure surfactant cmc results in a much greater light scattering than that found with pure sodium alkylsulfate surfactant micelles. This phenomenon is dependent upon the alkyl chain length of the surfactant. With Tb(III)/DS-, complexes are formed with a cation/anion binding ratio varying from 3 to 6, which depends upon the initial concentration of Tb(III). This suggests that the majority of the cation hydration water molecules can be exchanged by the anionic surfactant. When the carbon chain length decreases, interactions between surfactant and Tb(III) also decrease, alterations in conductivity and fluorescence data are not so significant and, consequently, no binding ratio can be detected even if existing. The surfactant micellization is dependent on the presence of electrolyte in solution with apparent cmc being lower than the corresponding cmc value of pure SDS.     

Precise mass measurement of a double-stranded 500 base-pair (309 kDa) polymerase chain reaction product by negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICRMS) has been used to determine the mass of a double-stranded 500 base-pair (bp) polymerase chain reaction (PCR) product with an average theoretical mass of the blunt-ended (i.e. unadenylated) species of 308 859.35 Da. The PCR product was generated from the linearized bacteriophage Lambda genome which is a double-stranded template. Utilization of ethanol precipitation in tandem with a rapid microdialysis step to purify and desalt the PCR product was crucial to obtain a precise mass measurement. The PCR product (0.8 pmol/μL) was electrosprayed from a solution containing 75% acetonitrile, 25 mM piperidine, and 25 mM imidazole and was infused at a rate of 200 nL/min. The average molecular mass and the corresponding precision were determined using the charge-states ranging from 172 to 235 net negative charges. The experimental mass and corresponding precision (reported as the 95% confidence interval of the mean) was 309 406 +/- 27 Da (87 ppm). The mass accuracy was compromised due to the fact that the PCR generates multiple products when using Taq polymerase due to the non-template directed 3'-adenylation. This results in a mixture of three PCR products with nearly identical mass (i.e. blunt-ended, mono-adenylated and di-adenylated) with unknown relative abundances that were not resolved in the spectrum. Thus, the experimental mass will be a weighted average of the three species which, under our experimental conditions, reflects a nearly equal concentration of the mono- and di-adenylated species. This report demonstrates that precise mass measurements of PCR products up to 309 kDa (500 bp) can be routinely obtained by ESI-FTICR requiring low femtomole amounts. Copyright 1999 John Wiley & Sons, Ltd.     

Catalytic Transfer Hydrogenation and Acid Reactions of Furfural and 5-(Hydroxymethyl)furfural over Hf-TUD-1 Type Catalysts

Heterogeneous catalysis, which has served well the petrochemical industry, may valuably contribute towards a bio-based economy by sustainably enabling selective reactions to renewable chemicals. Carbohydrate-containing matter may be obtained from various widespread sources and selectively converted to furanic platform chemicals: furfural (Fur) and 5-(hydroxymethyl)furfural (Hmf). Valuable bioproducts may be obtained from these aldehydes via catalytic transfer hydrogenation (CTH) using alcohols as H-donors under relatively moderate reaction conditions. Hafnium-containing TUD-1 type catalysts were the first of ordered mesoporous silicates explored for the conversion of Fur and Hmf via CTH/alcohol strategies. The materials promoted CTH and acid reactions leading to the furanic ethers. The bioproducts spectrum was broader for the reaction of Fur than of Hmf. A Fur reaction mechanism based on literature data was discussed and supported by kinetic modelling. The influence of the Hf loading and reaction conditions (catalyst load, type of alcohol H-donor, temperature, initial substrate concentration) on the reaction kinetics was studied. The reaction conditions were optimized to maximize the yields of 2-(alkoxymethyl)furan ethers formed from Fur; up to 63% yield was reached at 88% Fur conversion, 4 h/150 °C, using Hf-TUD-1(75), which was a stable catalyst. The Hf-TUD-1(x) catalysts promoted the selective conversion of Hmf to bis(2-alkoxymethyl)furan; e.g., 96% selectivity at 98% Hmf conversion, 3 h/170 °C for Hf-TUD-1(50).     

Optimizing ICA in fMRI using information on spatial regularities of the sources

Spatial independent component analysis (ICA) is a well-established technique for multivariate analysis of functional magnetic resonance imaging (fMRI) data. It blindly extracts spatiotemporal patterns of neural activity from functional measurements by seeking for sources that are maximally independent. Additional information on one or more sources (e.g., spatial regularity) is often available; however, it is not considered while looking for independent components. In the present work, we propose a new ICA algorithm based on the optimization of an objective function that accounts for both independence and other information on the sources or on the mixing model in a very general fashion. In particular, we apply this approach to fMRI data analysis and illustrate, by means of simulations, how inclusion of a spatial regularity term helps to recover the sources more effectively than with conventional ICA. The improvement is especially evident in high noise situations. Furthermore we employ the same approach on data sets from a complex mental imagery experiment, showing that consistency and physiological plausibility of relatively weak components are improved.     

Structural properties and electrical behaviour in the polycrystalline lanthanum-deficiency La1−x□xMnO3 manganites

Electrical conductance and X-ray diffraction (XRD) measurements of lanthanum-deficiency La_1−x□_xMnO₃ (x=0.05, 0.10 and 0.20) polycrystalline samples were performed to examine the effect of the internal pressure at B-site on the conduction mechanism. The structural study reveals that all samples crystallize in the rhombohedral system. The electronic conduction appears to be thermally activated at high temperature, which indicates the presence of semiconductor behaviour. The increase of the x content converts 3x Mn³⁺ to 3x Mn⁴⁺ ions with smaller ionic radius, which reduces the internal pressure and leads to the increase of the one-electron bandwidth W. This increase causes the appearance of metallic behaviour at low temperature for x=0.10 and 0.20 content.     

X-ray photoelectron spectroscopy and magnetism of Mn1−xAlxNi alloys

X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), magnetization and magnetic susceptibility of Mn_1−xAl_xNi alloys are reported. A change in the crystallographic structure takes place around x=0.4 from CuAuI to CsCl (B2) structure type. For x0.5 a mixed B2+L2₁ state exists which incorporates antiferromagnetic (B2) and ferromagnetic (L2₁) parts. A direct evidence for the existence of local moments on Mn sites in Mn_1-xAl_xNi alloys is given by the exchange splitting of XPS Mn 3s and Mn 2p3/2 core levels. The gradual filling of the Ni 3d band as the Al concentration increases can be explained by the hybridization of the Ni 3d band and Al 3sp states.     

Construction of novel spiroisoxazolines via intramolecular cyclization/methylation

Improved yields for the syntheses of a variety of spiroisoxazolines were achieved through intramolecular cyclization/methylation reactions of functionalized 5,5-disubstituted isoxazolines in one reaction vessel. Aromatic ring containing nitrile oxides and disubstituted geminal alkenes reacted in a 1,3-dipolar fashion to afford the corresponding 5,5-isoxazoline. A comparison of the relative location of the nucleophile and electrophile on the isoxazoline and two different ester functional groups was performed in order to determine the best isoxazoline system for the intramolecular cyclization/methylation reaction.     

Improved Molecular Weight Control in Ring‐Opening Metathesis Polymerization (ROMP) Reactions with Ru‐Based Olefin Metathesis Catalysts Using N Donors and Acid: A Kinetic and Mechanistic Investigation

The effect of the addition of H₃PO₄ on the ROMP activity of cyclooctene (COE) with first‐ [Cl₂(PCy₃)₂Ru?CHPh] and second‐generation [(H₂IMes)Cl₂(PCy₃)Ru?CHPh] Grubbs’ catalysts 1 and 4 (Cy=cyclohexyl, Ph=phenyl, Mes=2,4,6‐trimethylphenyl (mesityl)), their inhibited mixtures with 1‐methylimidazole (MIM), as well as their isolated bis‐N,N′‐dimethylaminopyridine (DMAP) derivatives [Cl₂(PCy₃)(DMAP)₂Ru?CHPh)] ( 5 b ) and [Cl₂(H₂IMes)(DMAP)₂Ru?CHPh] ( 7 b ) (DMAP=dimethylaminopyridine), a novel catalyst, has been investigated. The studies include the determination of their initiation rates, as well as a determination of the molecular weights and molecular weight distributions of the polymers obtained with these catalysts and catalyst mixtures from the exo‐7‐oxanorbornene derivative 11 . The structure of catalyst 7 b was confirmed by means of X‐ray diffraction. All N‐donor‐bearing catalysts or N‐donor‐containing catalyst mixtures not only exhibited elevated activity in the presence of acid, but also increased initiation rates. Using the reversible inhibition/activation protocol with MIM and H₃PO₄ enabled us to conduct controlled ROMP with catalyst 4 producing the isolated exo‐7‐oxanorbornene‐based polymer 12 with predetermined molecular weights and narrow molecular weight distributions. This effect was based on fast and efficient catalyst initiation in contrast to the parent catalyst 4 . Hexacoordinate complex 5 b also experienced a dramatic increase in initiation rates upon acid‐addition and the ROMP reactions became well‐controlled in contrast to the acid‐free reaction. In contrast, complex 7 b performs well‐controlled ROMP in the absence of acid, whereas the polymerization of the same monomer becomes less controlled in the presence of H₃PO₄. The closer evaluation of catalysts 5 b and 7 b demonstrated that their initiation rates exhibit a linear dependency on the substrate concentration in contrast to catalysts 1 and 4 . As a consequence, their initiation rates are determined by an associative step, not a dissociative step as seen for catalysts 1 and 4 . A feasible associative metathesis initiation mechanism is proposed.