Studies on nitroenamines. Part III. Synthesis and spectral properties of 4-Acyl-1-arylimidazoles

The catalytic (C/Pd) hydrogenation of 3-arylamino-2-nitro-2-enones ( 1 ) in the presence of carboxylic ortho esters ( 2 ) affords 4-acyl-1-arylimidazoles ( 3 ) in yields (20–70%) which depend on the degree of substitution of the imidazole ring. The spectral properties of compounds 3 , and particularly the ¹³C-nmr spectra, reflect both the electronic and steric effects of the substituents on the π-electron delocalization and planarity of the bicyclic system.     

Evaluation of the efficiency of extraction of PAHs from diesel particulate matter with pressurized solvents

Pressurized Fluid Extraction (PFE) was evaluated for the extraction of polycyclic aromatic hydrocarbons (PAHs) and nitro-derivatives from diesel particulate matter. Extraction conditions were set up by performing several tests in which temperature, solvent strength, pressure, and static time were gradually increased. The results obtained on a laboratory test material made of a "lean" (low content of soluble fraction) Diesel particulate matter indicate that very severe conditions were needed in order to obtain better recoveries of the higher molecular weight molecules. Moreover, extraction efficiency seems to be influenced by the amount of soluble matter in the particulate, so that a "lean" particulate appears more difficult to extract. Recoveries of the deuterated standards of certain PAHs (i.e. indeno[1,2,3- cd]pyrene) were incomplete even with the toughest conditions tested. Experiments carried out on a certified material (SRM 1650 from NIST) also indicate that PFE can perform a better extraction of some of the PAHs than the method used for certification, but still incomplete. Comparison of results obtained on the SRM with different extraction techniques suggests that the composition of the extract varies considerably with the extraction technique and conditions. It is relevant to notice that recent Diesel engines produce leaner particulate: for future materials more drastic extraction conditions will be required.     

Application of recombinant phage display antibody system in study of Codakia orbicularis gill proteins

We used the recombinant phage display antibody system (RPAS) to obtain chimeric single-chain fragment variable (ScFv) antibodies to gill proteins of the white clam Codakia orbicularis (Linné, 1758). After three rounds of selection on immunotubes loaded with total gill protein extract, recombinant phages exhibiting antibodies to gill proteins were isolated and tested by enzyme-linked immunosorbent assay (ELISA). Clones exhibiting a high affinity for the mollusk proteins were selected for production of soluble ScFv antibodies, which were purified for subsequent analysis. ScFv antibodies exhibited a reaction specific for a protein whose molecular mass was about 15,000 Daltons and that was detected by the antigen capture technique followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis and Western blotting.     

A comparison between different techniques for the isolation of rosemary essential oil

Traditional hydrodistillation (HD), supercritical fluid extraction (SFE), organic solvent extraction (SE), and water microwave assisted hydrodistillation (MAHD) techniques were compared and evaluated for their effectiveness in the isolation of rosemary essential oil. The microwave assisted hydrodistillation technique was optimized in terms of both delivered power and time duration. The extracts/distillates were analyzed by GC and GC-MS. Microwave distillation, which exploits the physical action of microwaves on plants, showed a series of advantages over the other approaches: low cost, use of water in sample pre-treatment step, greatly reduced isolation time, and attainment of high quality essential oil distillate. Moreover, the absence of environmental impact of this innovative technique was also emphasized.     

Synthesis, Structure, and Antimicrobial Activity of Complexes of Pt(II), Pd(II), and Ni(II) with the Condensation Product of 2-(Diphenylphosphino)benzaldehyde and Semioxamazide

Complexes of Pt(II), Pd(II), and Ni(II) with the condensation derivative of 2-(diphenylphosphino)benzaldehyde and semioxamazide were synthesized, characterized, and their antimicrobial activity was evaluated. The ligand and the complexes were characterized by spectroscopic methods with the particular accent on NMR spectral analysis. For the palladium(II) complex, the crystal structure was determined by X-ray analysis. In all the complexes the ligand is coordinated as a tridentate via a P, N, O donor set. The Pd(II) and Pt(II) complexes have a square planar geometry, whereas the geometry of the Ni(II) complex is tetrahedral. The ligand showed antibacterial and antifungal activity, which was enhanced upon complexation.     

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.     

Liquid chromatographic analysis of vitamin B6 in reconstituted infant formula: collaborative study

A liquid chromatographic (LC) method was validated for the determination of total vitamin B6 in infant formula. Total vitamin B6 was quantified by converting the phosphorylated and free vitamers into pyridoxine. Pyridoxine was determined by ion pair reversed-phase LC with fluorescence detection. The method was subjected to an AOAC collaborative study involving a factory-manufactured, milk- and soy-based infant formula. Each was spiked at 3 concentrations in the range of 0-1 microg/g and sent as blind duplicate to participant laboratories. Nine laboratories returned valid data which were statistically analyzed for outliers and precision parameters. The repeatability relative standard deviation (RSD(r)) ranges were 2.0-4.0 and 3.5-5.9% for fortified milk- and soy-based formulas, respectively. The reproducibility relative standard deviation (RSD(R)) ranges were 8.2-8.4 and 6.7-11.2% for fortified milk- and soy-based formulas, respectively. HORRAT values ranged from 0.42 to 0.53, indicating that the precision of the method is acceptable. The mean RSD(r):RSD(R) values were 0.60 and 0.55 for milk- and soy-based formulas, respectively. As expected, RSDs for the unfortified samples were higher, but their HORRAT values (0.81 and 2.06) helped define a realistic limit of quantitation as 0.05 microg/g. Recovery data were quantitative and varied between 81.4 and 98.0% (mean = 89.8%) for each of 6 spiked materials.     

Polyketide double bond biosynthesis. Mechanistic analysis of the dehydratase-containing module 2 of the picromycin/methymycin polyketide synthase

Picromycin/methymycin synthase (PICS) is a modular polyketide synthase (PKS) that is responsible for the biosynthesis of both 10-deoxymethynolide (1) and narbonolide (2), the parent 12- and 14-membered aglycone precursors of the macrolide antibiotics methymycin and picromycin, respectively. PICS module 2 is a dehydratase (DH)-containing module that catalyzes the formation of the unsaturated triketide intermediate using malonyl-CoA as the chain extension substrate. Recombinant PICS module 2+TE, with the PICS thioesterase domain appended to the C-terminus to allow release of polyketide products, was expressed in Escherichia coli. Purified PICS module 2+TE converted malonyl-CoA and 4, the N-acetylcysteamine thioester of (2S,3R)-2-methyl-3-hydroxypentanoic acid, to a 1:2 mixture of the triketide acid (4S,5R)-4-methyl-5-hydroxy-2-heptenoic acid (5) and (3S,4S,5R)-3,5-dihydroxy-4-methyl-n-heptanoic acid-delta-lactone (10) with a combined kcat of 0.6 min(-1). The triketide lactone 10 is formed by thioesterase-catalyzed cyclization of the corresponding d-3-hydroxyacyl-SACP intermediate, a reaction which competes with dehydration catalyzed by the dehydratase domain. PICS module 2+TE showed a strong preference for the syn-diketide-SNAC 4, with a 20-fold greater kcat/K(m) than the anti-(2S,3S)-diketide-SNAC 14, and a 40-fold advantage over the syn-(2R,3S)-diketide-SNAC 13. PICS module 2(DH(0))+TE, with an inactivated DH domain, produced exclusively 10, while three PICS module 2(KR(0))+TE mutants, with inactivated KR domains, produced exclusively or predominantly the unreduced triketide ketolactone, (4S,5R)-3-oxo-4-methyl-5-hydroxy-n-heptanoic acid-delta-lactone (7). These studies establish for the first time the structure and stereochemistry of the intermediates of a polyketide chain elongation cycle catalyzed by a DH-containing module, while confirming the importance of key active site residues in both KR and DH domains.     

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.     

An Extensive Assessment of Network Embedding in PPI Network Alignment

Network alignment is a fundamental task in network analysis. In the biological field, where the protein–protein interaction (PPI) is represented as a graph, network alignment allowed the discovery of underlying biological knowledge such as conserved evolutionary pathways and functionally conserved proteins throughout different species. A recent trend in network science concerns network embedding, i.e., the modelling of nodes in a network as a low-dimensional feature vector. In this survey, we present an overview of current PPI network embedding alignment methods, a comparison among them, and a comparison to classical PPI network alignment algorithms. The results of this comparison highlight that: (i) only five network embeddings for network alignment algorithms have been applied in the biological context, whereas the literature presents several classical network alignment algorithms; (ii) there is a need for developing an evaluation framework that may enable a unified comparison between different algorithms; (iii) the majority of the proposed algorithms perform network embedding through matrix factorization-based techniques; (iv) three out of five algorithms leverage external biological resources, while the remaining two are designed for domain agnostic network alignment and tested on PPI networks; (v) two algorithms out of three are stated to perform multi-network alignment, while the remaining perform pairwise network alignment.