Prediction of retention indices. VI: Isothermal and temperature-programmed retention indices,methylene value,functionality constant,electronic and steric effects

The Kováts retention index system with n-alkanes as reference standards has properties not fully explored when single, isolated or stand-alone analytes are analyzed by isothermal gas chromatography. When a homologous series of analytes are analyzed by either linear or non-linear temperature-programmed gas chromatography, the retention data of the entire series can be treated systematically to produce an I vs. Z plot that is linear, thereby giving insight into the relationship between chemical structure and retention index. Dead time t_M is both instrument and temperature dependent. With no dead time t_M adjustment, the retention indices of analytes calculated from experimental retention times by the method of either linear or logarithmic interpolation give statistically identical values. Linear regression analysis of the data shows the slope as methylene value (A) and intercept as functionality constant or group retention factor (GRF) of the homologous series. The A and (GRF) values vary with chemical structures, intermolecular electronic and steric interactions, and polarity of column liquid phases, and can link gas chromatographic retention index to chemical structure. Examples of the influence of molecular electronic effects and steric effects on retention index are given and discussed.     

Infrared Spectroscopy and Structure of Trigonal Zirconium Orthophosphates with Lanthanides and Actinides

Binary zirconium orthophosphates R_1/3Zr₂(PO₄)₃ and M_1/4Zr₂(PO₄)₃, where R = Y, La, Ce, Pr, Nd, Sm, Eu, Gd, Dy, Ho, Er, Tm, Yb, Lu; M = Th, U, have been synthesized and studied by IR spectroscopy [structural family of NaZr₂(PO₄)₃ (NZP)]. Vibrational analysis for the PO₄ tetrahedron and investigation of symmetry relations among trigonal NZP phases showed that ordering of lanthanide atoms in structures of NaZr₂(PO₄)₃ type with space group R c leads to symmetry reduced to P c. The lanthanide atoms occupy the 2b sites. The phosphorus atoms occupy two independent sites: 6f with C ₂ symmetry and 12g with C ₁ symmetry. Factor group analysis admits that the IR spectrum can contain eight v₃ bands and two v₁ bands of the stretching vibrations of the PO₄ ions. The M atoms of actinides occupy statistical positions in the structure, and space group R c is retained.Original Russian Text Copyright © 2004 by V. S. Kurazhkovskaya, D. M. Bykov, and A. I. Orlova__________Translated from Zhurnal Strukturnoi Khimii, Vol. 45, No. 6, pp. 1013–1019, November–December, 2004.     

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

Chromatographic impulse response technique with curve fitting to measure binary diffusion coefficients and retention factors using polymer-coated capillary columns

The theoretical basis of a Gaussian-like approximate solution was applied to a chromatographic impulse response technique with curve fitting for measuring binary diffusion coefficients and retention factors using a polymer-coated capillary column. The formulae were derived for evaluating both the accuracy of the approximate solution and the sensitivity of the parameters. The validity of the solution also was confirmed experimentally for pulse injection of phenol in acetone into supercritical carbon dioxide flowing at 313.15 K and 11.6-28.6 MPa. Potential sources for experimental errors of the method are discussed.     

Evaluation of the (Allyl alcohol 1,2‐butoxylate‐block‐etoxylate)‐b‐PMMA Copolymers Composition by the Dielectric Measurements

Redox initiated free‐radical polymerization of methyl methacrylate (MMA) with allyl alcohol 1,2‐butoxylate‐block‐etoxylate (AABE) was carried out to yield AABE‐b‐PMMA copolymers at elevated temperatures. The composition of the copolymers depending on the polymerization temperature was qualitatively estimated by the dielectric measurements. It has been seen that AABE segment quantity decreased and PMMA segment quantity increased with increasing the polymerization temperature. The dielectric constant and the dissipation factor of the copolymers were investigated as a function of frequency and temperature. The dielectric constant and the dissipation factor were found to be strongly affected by the polymerization temperature. The highest dielectric constant in all studied temperatures and frequencies was obtained in the case of the copolymer which was prepared at 313 K. The dipolar C‐O and OH groups of the AABE segment have the primary effect on the dielectric constant. The copolymer which was prepared at 323 K, showed the highest dissipation factor near the relaxation temperature of PMMA.     

A high concentration of genistein down-regulates activin A, Smad3 and other TGF-β pathway genes in human uterine leiomyoma cells

Previously, we found that high doses of genistein show an inhibitory effect on uterine leiomyoma (UtLM) cell proliferation. In this study, using microarray analysis and Ingenuity Pathways Analysis™, we identified genes (up- or down-regulated, ≥ 1.5 fold, P ≤ 0.001), functions and signaling pathways that were altered following treatment with an inhibitory concentration of genistein (50 µg/ml) in UtLM cells. Downregulation of TGF-β signaling pathway genes, activin A, activin B, Smad3, TGF-β2 and genes related to cell cycle regulation, with the exception of the upregulation of the CDK inhibitor P15, were identified and validated by real-time RT-PCR studies. Western blot analysis further demonstrated decreased protein expression of activin A and Smad3 in genistein-treated UtLM cells. Moreover, we found that activin A stimulated the growth of UtLM cells, and the inhibitory effect of genistein was partially abrogated in the presence of activin A. Overexpression of activin A and Smad3 were found in tissue samples of leiomyoma compared to matched myometrium, supporting the contribution of activin A and Smad3 in promoting the growth of UtLM cells. Taken together, these results suggest that down-regulation of activin A and Smad3, both members of the TGF-β pathway, may offer a mechanistic explanation for the inhibitory effect of a high-dose of genistein on UtLM cells, and might be potential therapeutic targets for treatment of clinical cases of uterine leiomyomas.     

Proteomic analysis reveals platelet factor 4 and beta-thromboglobulin as prognostic markers in severe acute respiratory syndrome

Previously, we reported that proteomic fingerprints were present in sera of patients with severe acute respiratory syndrome (SARS), and could separate patients into subgroups with different prognoses. In the present study, we examined the prognostic values of the SARS-associated proteomic features by biostatistical analysis, and deciphered the identities of those with prognostic values. Data of 20 SARS-associated serum proteomic features and ten serological variables from 38 SARS adult patients before treatment were subjected to multivariate logistic regression. Proteomic features of m/z 6634, m/z 7769, m/z 8635, and m/z 8865 were identified as independent prognostic markers. After purification by cation-exchange chromatography and gel electrophoresis, proteomic features of m/z 7769 and m/z 8865 were found to be platelet factor 4 (PF4) and beta-thromboglobulin (beta-TG) by tandem mass spectrometry, respectively. The associations of decreased serum PF4 and increased serum beta-TG levels with poor prognosis were confirmed by Western blot. Previous studies suggest that PF4 and beta-TG are involved in the pathogenesis of acute respiratory distress syndrome (ARDS) in a negative and positive way, respectively. Our results suggest that PF4 and beta-TG may also play similar roles in the development of ARDS in SARS patients.     

Stimulation of Microvascular Networks on Sulfonated Polyrotaxane Surfaces with Immobilized Vascular Endothelial Growth Factor

Modulation of material properties and growth factor application are critical in constructing suitable cell culture environments to induce desired cellular functions. Sulfonated polyrotaxane (PRX) surfaces with immobilized vascular endothelial growth factors (VEGFs) are prepared to improve network formation in vascular endothelial cells. Sulfonated PRXs, whereby sulfonated α‐cyclodextrins (α‐CDs) are threaded onto a linear poly(ethylene glycol) chain capped with bulky groups at both terminals, are coated onto surfaces. The molecular mobility of sulfonated PRX surfaces is modulated by tuning the number of threading α‐CDs. VEGF is immobilized onto surfaces with varying mobility. Low mobility and VEGF‐immobilization reinforce cell proliferation, yes‐associated protein activity, and rhoA, pdgf, ang‐1, and pecam‐1 gene expression. Highly mobile surfaces and soluble VEGF weakly affect these cell responses. Network formation is strongly stimulated in vascular endothelial cells only on low‐mobility VEGF‐immobilized surfaces, suggesting that molecular mobility and VEGF immobilization synergistically control cell function.