Spot overlapping in two-dimensional polyacrylamide gel electrophoresis separations: a statistical study of complex protein maps

A statistical approach able to extract the information contained in a two-dimenisional polyacrylamide gel electrophoresis (2-D PAGE) separation is here reported. The method is based on the quantitative theory of peak overlapping, a procedure previously developed by the authors and here extended to 2-D separations. The whole map is divided into many strips in order to obtain 1-D separations on which the statistic procedure is applied: the developed algorithms, on the basis of spot experimental data (intensity and spatial coordinates) permit to estimate the intrinsic number of components and to single out the specific order present in spot positions. The procedure was validated on computer-simulated maps. Its applicability to real samples was tested on maps obtained from literature sources. The following important information on protein mixtures can be extracted: (i) the number of proteins can be accurately estimated, on the basis of the spatial coordinates and intensities of spots detected in the 2-D PAGE map; (ii) the model describing distribution of interdistance between adjacent spots can be identified in both the separation dimensions; (iii) the presence of repeated interdistances in spot positions in the maps can be easily singled out: these regularities suggest specific protein modifications.     

The Physico-Chemical Properties of Glipizide: New Findings

The present work is a concrete example of how physico-chemical studies, if performed in depth, are crucial to understand the behavior of pharmaceutical solids and constitute a solid basis for the control of the reproducibility of the industrial batches. In particular, a deep study of the thermal behavior of glipizide, a hypoglycemic drug, was carried out with the aim of clarifying whether the recognition of its polymorphic forms can really be done on the basis of the endothermic peak that the literature studies attribute to the melting of the compound. A number of analytical techniques were used: thermal techniques (DSC, TGA), X-ray powder diffraction (XRPD), FT-IR spectroscopy and scanning electron microscopy (SEM). Great attention was paid to the experimental design and to the interpretation of the combined results obtained by all these techniques. We proved that the attribution of the endothermic peak shown by glipizide to its melting was actually wrong. The DSC peak is no doubt triggered by a decomposition process that involves gas evolution (cyclohexanamine and carbon dioxide) and formation of 5-methyl-N-[2-(4-sulphamoylphenyl) ethyl] pyrazine-2-carboxamide, which remains as decomposition residue. Thermal treatments properly designed and the combined use of DSC with FT-IR and XRPD led to identifying a new polymorphic form of 5-methyl-N-[2-(4-sulphamoylphenyl) ethyl] pyrazine-2-carboxamide, which is obtained by crystallization from the melt. Hence, our results put into evidence that the check of the polymorphic form of glipizide cannot be based on the temperature values of the DSC peak, since such a peak is due to a decomposition process whose Tonset value is strongly affected by the particle size. Kinetic studies of the decomposition process show the high stability of solid glipizide at room temperature.     

Chiral Nano-Liquid Chromatography and Dispersive Liquid-Liquid Microextraction Applied to the Analysis of Antifungal Drugs in Milk

A novel chromatographic application in chiral separation by using the nano-LC technique is here reported. The chiral recognition of 12 antifungal drugs was obtained through a 75 µm I.D. fused-silica capillary, which was packed with a CSP-cellulose 3,5-dichlorophenylcarbamate (CDCPC), by means of a lab-made slurry packing procedure. The mobile phase composition and the experimental conditions were optimized in order to find the optimum chiral separation for some selected racemic mixtures of imidazole and triazole derivatives. Some important parameters, such as retention faction, enantioresolution, peak efficiency, and peak shape, were investigated as a function of the mobile phase (pH, water content, type and concentration of both the buffer and the organic modifier, and solvent dilution composition). Within one run lasting 25 min, at a flow rate of approximately 400 nL min⁻¹, eight couples of enantiomers were baseline-resolved and four of them were separated in less than 25 min. The method was then applied to milk samples, which were pretreated using a classical dispersive liquid–liquid microextraction technique preceded by protein precipitation. Finally, the DLLME-nano-LC–UV method was validated in a matrix following the main FDA guidelines for bioanalytical methods.     

Molecular evaluation of soil organic matter characteristics in three agricultural soils by improved off-line thermochemolysis: The effect of hydrofluoric acid demineralisation treatment

The molecular composition of soil organic matter (SOM) in three agricultural fields under different managements, was evaluated by off-line thermochemolysis followed by gas chromatography mass spectrometry analysis (THM-GC-MS). While this technique enabled the characterization of SOM components in coarse textured soil, its efficiency in heavy textured soils was seriously affected by the interference of clay minerals, which catalyzed the formation of secondary artifacts in pyrolysates. Soil demineralization with hydrofluoric acid (HF) solutions effectively improved the reliable characterization of organic compounds in clayey soils by thermochemolysis, while did not alter significantly the results of coarse textured soil. A wide range of lignin monomers and lipids molecules, of plant and microbial origin, were identified in the pyrograms of HF treated soils, thereby revealing interesting molecular differences between SOM management practices. Our results indicated that clay removal provided by HF pretreatment enhanced the capacity of thermochemolysis to be a valuable and accurate technique to study the SOM dynamics also in heavy-textured and OC-depleted cultivated soils.     

Shotgun proteomic analytical approach for studying proteins adsorbed onto liposome surface

The knowledge about the interaction between plasma proteins and nanocarriers employed for in vivo delivery is fundamental to understand their biodistribution. Protein adsorption onto nanoparticle surface (protein corona) is strongly affected by vector surface characteristics. In general, the primary interaction is thought to be electrostatic, thus surface charge of carrier is supposed to play a central role in protein adsorption. Because protein corona composition can be critical in modifying the interactive surface that is recognized by cells, characterizing its formation onto lipid particles may serve as a fundamental predictive model for the in vivo efficiency of a lipidic vector. In the present work, protein coronas adsorbed onto three differently charged cationic liposome formulations were compared by a shotgun proteomic approach based on nano-liquid chromatography–high-resolution mass spectrometry. About 130 proteins were identified in each corona, with only small differences between the different cationic liposome formulations. However, this study could be useful for the future controlled design of colloidal drug carriers and possibly in the controlled creation of biocompatible surfaces of other devices that come into contact with proteins into body fluids.     

Experimental study of the pH influence on the transport mechanisms of phenols in soil

The study of the transport mechanisms connected to solid-liquid interactions is fundamental in the determination of the extension of the pollution of a site and in the evaluation of the best remediation process to be applied. The sorption of hydrophobic ionizable organic contaminants from the groundwaters is supervised not only by the physico-chemical properties of soil and pollutants, but also by the groundwaters pH, which deeply influences their solubility in the aqueous media, and consequently their transport mechanisms in the aquifer. In this work an experimental study of the sorption of phenol and 2-nitrophenol on two soils, different in particle-size distribution, CEC and organic carbon content, was realized. The sorption potential of the soils was evaluated by means of a physical, mineralogical and chemical characterization. The experimental data coming from some batch tests, performed at pH values equal to 4, 7 and 10 were fitted by means of linear, Freundlich and Langmuir isotherms models. The soil-contaminants interaction mechanisms that influence the isotherms shapes were then analyzed and discussed, and a comparison between the theoretical and experimental values of the partitioning coefficient KD was performed.     

A simple geometrical model for emulsifier free polymer colloid formation

In this paper we propose a simple model for the formation of monodisperse polymer colloids, which provides a convenient set of synthetic parameters for given bead diameters. We provide experimental data in support of this model.     

Synthesis of 4H-3,1-benzoxazines, quinazolin-2-ones, and quinoline-4-ones by palladium-catalyzed oxidative carbonylation of 2-ethynylaniline derivatives

An effective and straightforward approach to the synthesis of 4H-3,1-benzoxazines 3 and 4, quinazolin-2-ones 5, and quinoline-4-one derivatives 6 and 7 is provided by palladium-catalyzed cyclization-alkoxycarbonylation of variously substituted 2-(trimethylsilanyl)ethynylaniline amide or urea derivatives 2. Reactions are carried out in 7:1 MeCN/MeOH at 65 or 75 degrees C in the presence of catalytic amounts of 10% Pd/C in conjunction with Bu(4)NI and KF and under 2.4 MPa of a 3:1 mixture of CO and air. Anti and syn 6-exo-dig cyclization modes account for the formation of the two stereoisomers. Isomerization of the vinylpalladium intermediate may occur as well. Formation of a double carbonylation product 7r and of a gem-dimethoxycarbonylation product 6s, whose structures have been determined by X-ray diffraction analysis, is justified through an unusual type of rearrangement.     

Thermodynamics of binding of 2-methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine to the major urinary protein

In the present study we examine the thermodynamics of binding of two related pyrazine-derived ligands to the major urinary protein, MUP-I, using a combination of isothermal titration calorimetry (ITC), X-ray crystallography, and NMR backbone (15)N and methyl side-chain (2)H relaxation measurements. Global thermodynamics data derived from ITC indicate that binding is driven by favorable enthalpic contributions, rather than the classical entropy-driven hydrophobic effect. Unfavorable entropic contributions from the protein backbone and side-chain residues in the vicinity of the binding pocket are partially offset by favorable entropic contributions at adjacent positions, suggesting a "conformational relay" mechanism whereby increased rigidity of residues on ligand binding are accompanied by increased conformational freedom of side chains in adjacent positions. The principal driving force governing ligand affinity and specificity can be attributed to solvent-driven enthalpic effects from desolvation of the protein binding pocket.