BOLD--a biological O-linked glycan database

Glycans can be O-linked to proteins via the hydroxyl group of serine, threonine, tyrosine, hydroxylysine or hydroxyproline. Sometimes the glycan is O-linked to the hydroxyl group via a phosphodiester bond. The core monosaccharide residue may be N-acetylgalactosamine, N-acetylglucosamine, galactose, glucose, fucose, mannose, xylose or arabinose. These O-linked glycans can remain as a monosaccharide, but often a complex structure is built up by stepwise addition of monosaccharides. Monosaccharides known to be added include galactose, N-acetylglucosamine, fucose, N-acetylneuraminic acid, N-glycolylneuraminic acid and 2-keto-3-deoxynonulosonic acid. O-linked glycans can also contain sulfate and phosphate residues. This leads to the possibility of the existence of numerous O-glycan structures. The biological O-linked database (BOLD) is a relational database that contains information on O-linked glycan structures, their biological sources (with a link to the SWISS-PROT protein database), the references in which the glycan was described (with a link to MEDLINE), and the methods used to determine the glycan structure. The database provides a valuable resource for glycobiology researchers interested in O-linked oligosaccharide structures that have been previously described on proteins from different species and tissues.     

Capillary electrophoretic chiral separations using cyclodextrin additives: III. Peak resolution surfaces for ibuprofen and homatropine as a function of the pH and the concentration of β-cyclodextrin

Our recent extended peak resolution equation of capillary electrophoresis has been combined with the multiple equilibria-based electrophoretic mobility model of chiral separations to describe peak resolution as a function of the composition of the background electrolyte (pH and the β-cyclodextrin concentration) and a function of the operating variables (effective portion of the applied potential, dimensionless electroosmotic flow coefficient). Using the previously determined model parameters, the resolution surfaces were calculated for a Type I chiral separation (ibuprofen), and a Type III chiral separation (homatropine). In Type I separations resolution can be obtained only over a narrow pH range in the vicinity of the pK_a value, and above a minimum value, the concentration of β-cyclodextrin plays a lesser role. In Type III separations, the pH- and β-cyclodextrin concentration-dependent resolution surface has two lobes, on which the migration order of the enantiomers is opposite. This can be an advantage in trace component analysis. In both Type I and Type III separations, peak resolution varies strongly with the dimensionless electroosmotic flow coefficient when its value is changed in the − 1 to 1 range. The loci of the pH-dependent and the β-cyclodextrin concentration-dependent resolution maxima do not shift significantly when the dimensionless electroosmotic flow coefficient is changed. This fact provides the analyst with an additional resolution enhancement tool that does not alter the selectivity of the separation. The utility of the model and its theoretical predictions has been demonstrated by comparing measured and calculated R_s values for ibuprofen and homatropine.     

Preparation and Swelling Properties of Poly(NIPAM) "Minigel" Particles Prepared by Inverse Suspension Polymerization

The characterization of temperature- and pH-sensitive poly-N-isopropylacrylamide (poly-NIPAM) microgel particles, produced by surfactant-free emulsion polymerization, has been extensively reported. In the work described here poly(NIPAM) gel particles, cross-linked with N-N'-methylenebisacrylamide (BA), have been produced using inverse suspension polymerization. These particles have been termed "minigels" here since they are somewhat larger than conventional microgels. Results suggest that minigel particles are formed as a dilute suspension, within the aqueous dispersed (droplet) phase. The hydrodynamic diameter of the minigel particles produced in this work is 相似文献   

Chemistry of the phenoxathiins. III. Synthesis of benzo[1″,2″:5,6:5″,4″:5′,6′]bis[1,4]oxathiino[3,2-b:3′,2′-b']dipyridine

As a result of studies dealing with the synthesis of 1-azaphenoxathiins, the synthesis of benzo[1″,2″:5,6:5″,4″:5′,6′]bis[1,4]oxathiino[3,2-b:3′,2′-b']dipyridine was examined. Unique evidence of solvent participation in the synthesis of these compounds by the structure elucidation of a novel minor by-product formed during the synthesis of the title compound is also reported.     

Determination of capsaicinoids in salsa by liquid chromatography and enzyme immunoassay

Two simple and rapid methods were developed to monitor pungency of salsa in production. Capsaicin (C) and dihydrocapsaicin (DHC) were quantitated in 17 commercially available tomato-based salsas by enzyme immunoassay (EIA) and liquid chromatography (LC) with fluorescent detection. Samples were extracted with methanol and the extracts were subjected to solid-phase extraction (SPE) using polystyrene-divinylbenzene columns. Analysis of SPE eluates showed good correlation (r2 = 0.953) between LC and EIA, with a slightly high bias for EIA. Salsa fortified with C and DHC from 0.118 to 103.2 microg/g resulted in recoveries of 90-112% (C) and 76-97% (DHC). Limits of detection by LC were 0.1 microg/g for each capsaicinoid and 0.1 microg/g by EIA for total capsaicinoids. The LC on-column response was linear from 0.2 to 100 ng for both C and DHC, whereas the working range for EIA was 0.1-2.0 ppm. Pungency varied between different salsa brands labeled mild, medium, and hot.     

Analysis of a mixture of polychlorinated biphenyls and chlorinated pesticides in human serum by column fractionation and dual-column capillary gas chromatography with electron capture detection

An analytical method is presented for precise identification and quantitation of 29 specific polychlorinated biphenyl (PCB) congeners and 15 chlorinated pesticides in human serum. Analyte surrogates PCB 30, PCB 204, 2,2',4,4',5,5'-hexabromo-biphenyl, perthane, alpha-hexachlorocyclohexane, and dichlorobenzophenone were added to each sample. The serum was extracted with an organic solvent and separated by adsorption chromatography into 3 elution fractions for high-resolution gas chromatographic analysis. Each fraction was analyzed by dual-column capillary chromatography followed by electron capture detection. Two capillary columns, DB-5 and DB-1701, with different polarities were used to increase selectivity for each analyte. Quantitation was performed by selecting 2 sets of calibration standard mixtures and 1,2-dichloronaphthalene as an internal standard. Mean recoveries ranged from 39 to 126% for selected analytes and from 31 to 88% for surrogates. Detection limits for specific congeners and pesticides are reported. Typical chromatographic profiles of calibration standard mixtures, as well as a human sample, are illustrated. Verification of each analyte is assessed, and results of analyses of selected human samples and quality control criteria used to ensure data validity also are presented.     

Binding energies of protonated betaine complexes: a probe of zwitterion structure in the gas phase

The dissociation kinetics of proton-bound dimers of betaine with molecules of comparable gas-phase basicity were investigated using blackbody infrared radiative dissociation (BIRD). Threshold dissociation energies were obtained from these data using master equation modeling. For bases that have comparable or higher gas-phase basicity, the binding energy of the protonated base.betaine complex is ~1.4 eV. For molecules that are ~2 kcal/mol or more less basic, the dissociation energy of the complexes is ~1.2 eV. The higher binding energy of the former is attributed to an ion-zwitterion structure which has a much larger ion-dipole interaction. The lower binding energy for molecules that are ~2 kcal/mol or more less basic indicates that an ion-molecule structure is more favored. Semiempirical calculations at both the AM1 and PM3 levels indicate the most stable ion-molecule structure is one in which the base interacts with the charged quaternary ammonium end of betaine. These results indicate that the measurement of binding energies of neutral molecules to biological ions could provide a useful probe for the presence of zwitterions and salt bridges in the gas phase. From the BIRD data, the gas-phase basicity of betaine obtained from the kinetic method is found to be 239.2 +/- 1.0 kcal/mol. This value is in excellent agreement with the value of 239.3 kcal/mol (298 K) from ab initio calculations at the MP2/6-31+g** level. The measured value is slightly higher than those reported previously. This difference is attributed to entropy effects. The lower ion internal energy and longer time frame of BIRD experiments should provide values closer to those at standard temperature.     

Micellar bile salt mobile phases for the liquid chromatographic separation of routine compounds and optical, geometrical, and structural isomers

Aqueous solutions of bile salts, i.e. sodium cholate (NaC), sodium deoxycholate (NaDC), and sodium taurocholate (NaTC), are characterized and evaluated as reversed-phase liquid chromatographic (RPLC) mobile phases. The separation of the ASTM-recommended RPLC test mix in addition to more than 50 other compounds on a C18 column demonstrates the viability of these bile salts as HPLC mobile phases. The Armstrong-Nome theory was applied and found to adequately describe the partitioning behavior of solutes eluted with these bile salts at low surfactant concentrations. The effect of alcohol additives on chromatographic retention and efficiency was also assessed. Not only are the bile salt molecules rigid and chiral, but they form helical micellar aggregates as well. Consequently, many isomeric compounds can be easily resolved with this mobile phase additive. The base-line resolution of some binaphthyl-type enantiomers with a standard C18 column and the bile salt micellar mobile phases is also demonstrated. In addition, these bile salt mobile phases may be preferable to conventional hydroorganic mobile phase systems for the separation of many classes of routine compounds. A brief prospectus on the future utilization of bile salts in liquid chromatography is presented.     

Ab initio studies of structural features not easily amenable to experiment: Part 20. Structural aspects of ethyl groups

The molecular structures of a number of stable conformations of ethanol, ethylamine, methylethyl ether, methylethylamine and of the ethyl anion have been determined by ab initio geometry optimizations using Pulay's Force method on the 4–21G level. The calculated geometries characterize the extent to which structural groups in a molecule are sensitive to asymmetries in their environment. Characteristic structural trends are consistently found for the CH bond distances and CCH angles in the C₂H₅ groups of trans-ethanol, trans-methylethyl ether and in the ethyl anion. They differ from those previously found for C₂H₅ groups in hydrocarbons. There is qualitative disagreement between the trends calculated for CH bond distances in trans-ethanol and trans-methylethyl ether and those found in the microwave substitution structures of these compounds. Since the substitution parameters are unresolved because of relatively large experimental or model uncertainties, it is presently impossible to decide whether this discrepancy is the result of computational or experimental deficiency. The methyl groups in methylethyl ether and methylethylamine exhibit the characteristic structural distortions which are usually found for CH₃ groups adjacent to electron lone pairs. The CC bond distances in C₂H₅ in the systems studied here are sensitive to the conformational arrangement of ethyl relative to the rest of a system in a way which can be rationalized by orbital interactions involving antibonding orbitals on sp³-hybridized carbon atoms. The calculated conformational stabilities agree qualitatively with experimental trends, except in the case of ethanol where the trans — gauche energy difference is small (about 0.1 kcal mol^?1) and within the uncertainties of the calculations. Our conformational energies for CH₃CH₂NH₂ are in disagreement with a previous ab initio investigation based on a comparison of unoptimized standard geometries. In general, the agreement between calculated structural parameters and corresponding reliable experimental values is very good in all comparable cases.     

The left-definite Legendre type boundary problem

The left-definite Legendre type boundary problem concerns the study of a fourth-order singular differential expressionM _k [–] in a weighted Sobolev spaceH generated by a Dirichlet inner product. The fourth-order differential equation