MALDI analysis of proteins after extraction from dissolvable ethylene glycol diacrylate cross‐linked polyacrylamide gels

Although the extraction of intact proteins from polyacrylamide gels followed by mass spectrometric molecular mass determination has been shown to be efficient, there is room for alternative approaches. Our study evaluates ethylene glycol diacrylate, a cleavable cross‐linking agent used for a new type of dissolvable gels. It attains an ester linkage that can be hydrolyzed in alkali conditions. The separation performance of the new gel system was tested by 1D and 2D SDS‐PAGE using the outer chloroplast envelope of Pisum sativum as well as a soluble protein fraction of human lymphocytes, respectively. Gel spot staining (CBB), dissolving, and extracting were conducted using a custom‐developed workflow. It includes protein extraction with an ammonia–SDS buffer followed by methanol treatment to remove acrylamide filaments. Necessary purification for MALDI‐TOF analysis was implemented using methanol–chloroform precipitation and perfusion HPLC. Both cleaning procedures were applied to several standard proteins of different molecular weight as well as ‘real’ biological samples (8–75 kDa). The protein amounts, which had to be loaded on the gel to detect a peak in MALDI‐TOF MS, were in the range of 0.1 to 5 μg, and the required amount increased with increasing mass.     

Synthesis of Nanocomposites from Pd0 and a Hyper‐Cross‐Linked Functional Resin Obtained from a Conventional Gel‐Type Precursor

Hyper‐cross‐linked resins stemming from a gel‐type poly‐chloromethylated poly(styrene‐co‐divinylbenzene) resin (GT) have been investigated by a multi‐methodological approach based on elemental analysis, scanning electron microscopy, X‐ray microanalysis, and solvent absorption. The hyper‐cross‐linking of the parent resin was accomplished by Friedel–Crafts alkylation of the phenyl rings of the resins with the chloromethyl groups. This produced a permanent pore system comprising both micropores (<2.0 nm in diameter) and mesopores (2.2 nm). The chloromethyl groups that did not react in the hyper‐cross‐linking step were transformed into methylmercaptan groups and the latter were then converted into sulfonic groups by oxidation with hydrogen peroxide. By this procedure the extensive permanent porosity of the parent unsulfonated hyper‐cross‐linked polymer (HGT) was retained by the sulfonated polymer (HGTS). The final exchange capacity of HGTS was determined to be 0.36 mmol g^?1. HGTS was easily metalated with Pd^II and the subsequent reduction of the metal centers with either aqueous sodium borohydride, formaldehyde, or dihydrogen produced three Pd⁰/HGTS nanocomposites. The metal nanoparticles had diameters in the 1–6 nm range for all the nanocomposites, as determined by TEM, but with somewhat different distributions. When formaldehyde was used, more than 90 % of the nanoparticles were less than 3 nm and their radial distribution throughout the polymer beads was quite homogeneous. These findings show that with this reducing agent the metal nanoparticles are generated within the pore system of the polymer matrix, hence their size is controlled by the dimensions of the pores of the polymeric support.     

Assessment of reproducibility and uncertainty of food microbiology methods: statistical approach of a multi-site laboratory

The validation of food microbiology methods and assessment of measurement uncertainty are required for laboratories operating EN ISO/IEC 17025 accreditation systems. This paper aims to describes the statistical approach adopted by a multi-site laboratory to satisfy these requirements and to routinely check the performance of the methods. A validation protocol was performed, reflecting a great variability of experimental conditions, represented by the period of time during which determinations were made, the different laboratories concerned, the large number of technicians involved, the differences in the level of contamination of the matrix analyzed and the operating conditions (equipment, reagents, culture media, environmental conditions, etc.). Despite the very high variability of the experimental conditions, the values of repeatability and reproducibility obtained for the methods were lower than those stated in the respective regulations. In addition, the top-down approach adopted in this study is to be considered effective overtime and allows to randomize all variable factors, including the effects of sensitivity and specificity, in order to simulate the conditions of real reproducibility. A specific Excel spreadsheet was also developed for the routine expression of analytical results. This spreadsheet represents a very useful tool for operators to calculate and routinely check the results, as well as to assess the uncertainty of measurement. This particular quality assessment system is enabling the multi-site laboratory to implement the accuracy, reliability and comparability of the analytical results and to ensure the analytical control of data output.     

Synthesis of Porphyrin‐Anthraquinone Conjugates as Photosensitizing Agents

A series of 5,10,15,20‐tetraarylporphyrins covalently linked to anthraquinones belonging to the class of emodin were synthesized following two different pathways. The first method exploits the functionalization of the methyl group in position 6 of O‐protected emodins, which can be converted either into a carboxylic acid or into a bromo‐methyl derivative. The modified emodins were then bound through amido or ether bonds to one of the tetraarylporphyrins meso phenyl rings bearing an amino or hydroxyl group, respectively. An alternative synthesis exploits the mixed condensation of triacetoxy‐emodinaldehyde (or trimethoxy‐emodinaldehyde) with pyrrole in the presence of variable amounts of benzaldehyde, thus affording two similar 5‐emodin‐10,15,20‐triphenylporphyrins differing from one another in the emodin hydroxyl group protection. These compounds are characterized by direct conjugation of the emodin moiety to the tetrapyrrolic ring. Preliminary experiments were performed in vitro on the human colon adenocarcinoma cell line HCT116 to evaluate the photocytotoxicity of the new compounds.     

Rigidity results in diffusion Markov triples

We consider stable solutions of semilinear equations in a very general setting. The equation is set on a Polish topological space endowed with a measure and the linear operator is induced by a carré du champs (equivalently, the equation is set in a diffusion Markov triple).Under suitable curvature dimension conditions, we establish that stable solutions with integrable carré du champs are necessarily constant (weaker conditions characterize the structure of the carré du champs and carré du champ itéré).The proofs are based on a geometric Poincaré formula in this setting. From the general theorems established, several previous results are obtained as particular cases and new ones are provided as well.     

Measurement of S-methylcysteine and S-methyl-mercapturic acid in human urine by alkyl-chloroformate extractive derivatization and isotope-dilution gas chromatography-mass spectrometry

S‐methylcysteine (SMC) is a minor amino acid naturally excreted in human urine, a protective agent against oxidative stress and a biotransformation product of the fumigant biocide methyl bromide and of nicotine. A metabolic source of SMC is catabolism of the repair catalytic protein MGMT (EC 2.1.1.37), which specifically removes the methyl group from the modified DNA nucleotide O‐6‐methyl‐guanine to revert the normal GC base pairing. To assess the value of SMC and of S‐methylmercapturic acid (SMMA) as candidate biomarkers of proliferative phenomena, a sensitive analytical method by GC‐MS was applied in a pilot study of healthy subjects to assess their urinary elimination and the intra‐ and inter‐individual variability. Extractive alkylation with butylchloroformate‐n‐butanol‐pyridine (Husek technique) was employed for sample derivatization and isotope dilution GC‐MS with S‐[CD₃]‐SMC and ‐SMMA was applied for specific and sensitive detection. To resolve the target analytes from the main coeluting interferents in the derivatized urine extract a medium‐polarity stationary phase was employed. SMMA was not detected in the morning urine of three healthy fertile‐age women followed for one month above the minimum detectable level of approx. 500 µg/L while SMC concentrations were in the 0.02–0.7 µg/mL range (n = 61) with large inter‐day and inter‐individual variations. In a young healthy male urine samples taken throughout a few days yielded concentrations in the same 90–810 µg/L range (n = 11). These preliminary results points at SMC as a candidate biomarker for the study of methylation turnover in several biochemical processes. Copyright © 2010 John Wiley & Sons, Ltd.     

X-Ray absorption spectroscopy investigation of 1-alkyl-3-methylimidazolium bromide salts

X-ray absorption spectroscopy (XAS) has been used to unveil the bromide ion local coordination structure in 1-alkyl-3-methylimidazolium bromide [C(n)mim]Br ionic liquids (ILs) with different alkyl chains. The XAS spectrum of 1-ethyl-3-methylimidazolium bromide has been found to be different from those of the other members of the series, from the butyl to the decyl derivatives, that have all identical XAS spectra. This result indicates that starting from 1-buthyl-3-methylimidazolium bromide the local molecular arrangement around the bromide anion is the same independently from the length of the alkyl chain, and that the imidazolium head groups in the liquid ILs with long alkyl chains assume locally the same orientation as in the [C(4)mim]Br crystal. With this study we show that the XAS technique is an effective direct tool for unveiling the local structural arrangements around selected atoms in ILs.     

Energy and density analysis on the H2 molecule from the united atom to dissociation: The Σ, Π, Δ, ϕ, and Γ manifolds

We present 140 accurate potential energy curves, PECs, for the Σ, Π, Δ, ?, and Γ manifolds for the H₂ molecule, mapping all the states with energy below the H ground state. The full configuration interaction, nonrelativistic Born–Oppenheimer computations are performed with large and optimized basis sets of Slater‐type and spherical Gaussian functions; these new basis sets are somewhat larger than those used in recent published studies on the 60 Σ state PECs. The full CI computations are performed twice, with Hartree–Fock and with Heitler–London‐type functions, allowing the identification of the ionic component in the total energy. The computed energies are within 10^?5 hartree from the most accurate PECs in literature. We aim (a) at the evaluation of the PECs starting at very short and unexplored internuclear distances (0.01 bohrs) and ending at full dissociation, (b) at the systematic prediction of high excited state PECs dissociating as 1s + 4l and 1s + 5l, and (c) at the characterization of the evolution of the 140 PEC electronic densities from united atom to dissociation. With this work we fill a gap in today literature, which has dealt mainly with low excited states, generally excluding short internuclear distances. The electronic configuration at the united atom persists as dominant configuration well beyond the equilibrium separation, and it switches to that at dissociation often with energy patterns seemingly irregular, in particular when the values of the principal quantum number at dissociation and at the united atom differ by one or more unit. The Hund's singlet‐triplet splitting, which propagates from the united atom to the molecule, is discussed. The singlet and triplet states are rather close in energy in the Π manifolds, and approach degeneracy in the Δ and ? manifolds, to become fully degenerate in the Γ manifolds. Discussions on the correlation energy correction, adiabatic correction, spectroscopic constants and on general features of the H₂ excited states are presented. The H₂ molecule is a system, which—to be understood—needs consideration of both the very short internuclear distances in approaching the united atom and of the very high excited states below H. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Au nanoparticle monolayers covered with sol-gel oxide thin films: optical and morphological study

In this work, we provide a detailed study of the influence of thermal annealing on submonolayer Au nanoparticle deposited on functionalized surfaces as standalone films and those that are coated with sol-gel NiO and TiO(2) thin films. The systems are characterized through the use of UV-vis absorption, X-ray diffraction (XRD), atomic force microscopy (AFM), scanning electron microscopy (SEM), and spectroscopic ellipsometry. The surface plasmon resonance peak of the Au nanoparticles was found to red-shift and increase in intensity with increasing surface coverage, an observation that is directly correlated to the complex refractive index properties of Au nanoparticle layers. The standalone Au nanoparticles sinter at 200 °C, and a relationship between the optical properties and the annealing temperature is presented. When overcoated with sol-gel metal oxide films (NiO, TiO(2)), the optical properties of the Au nanoparticles are strongly affected by the metal oxide, resulting in an intense red shift and broadening of the plasmon band; moreover, the temperature-driven sintering is strongly limited by the metal oxide layer. Optical sensing tests for ethanol vapor are presented as one possible application, showing reversible sensing dynamics and confirming the effect of Au nanoparticles in increasing the sensitivity and in providing a wavelength dependent response, thus confirming the potential use of such materials as optical probes.     

SrP3N5O: a highly condensed layer phosphate structure solved from a nanocrystal by automated electron diffraction tomography

The oxonitridophosphate SrP₃N₅O has been synthesized by heating a multicomponent reactant mixture that consisted of phosphoryl triamide OP(NH₂)₃, thiophosphoryl triamide SP(NH₂)₃, SrS, and NH₄Cl enclosed in evacuated and sealed silica‐glass ampoules up to 750 °C. The compound was obtained as nanocrystalline powder with needle‐shaped crystallites. The crystal structure was solved ab initio on the basis of electron diffraction data by means of automated electron diffraction tomography (ADT) and verified by Rietveld refinement with X‐ray powder diffraction data. SrP₃N₅O crystallizes in the orthorhombic space group Pnma (no. 62) with unit‐cell data of a=18.331(2), b=8.086(1), c=13.851(1) Å and Z=16. The compound is a highly condensed layer phosphate with a degree of condensation κ=1/2. The corrugated layers ${{{\hfill 2\atop \hfill \infty }}}The oxonitridophosphate SrP(3)N(5)O has been synthesized by heating a multicomponent reactant mixture that consisted of phosphoryl triamide OP(NH(2))(3), thiophosphoryl triamide SP(NH(2))(3), SrS, and NH(4)Cl enclosed in evacuated and sealed silica-glass ampoules up to 750 °C. The compound was obtained as nanocrystalline powder with needle-shaped crystallites. The crystal structure was solved ab initio on the basis of electron diffraction data by means of automated electron diffraction tomography (ADT) and verified by Rietveld refinement with X-ray powder diffraction data. SrP(3)N(5)O crystallizes in the orthorhombic space group Pnma (no. 62) with unit-cell data of a=18.331(2), b=8.086(1), c=13.851(1) ? and Z=16. The compound is a highly condensed layer phosphate with a degree of condensation κ=?. The corrugated layers (∞)(2){(P(3)N(5)O)(2-)} consist of linked, triangular columns built up from P(O,N)(4) tetrahedra with 3-rings and triply binding nitrogen atoms. The Sr(2+) ions are located between the layers and exhibit six-, eight-, and ninefold coordination. FTIR and solid-state NMR spectra of SrP(3)N(5)O are discussed as well.