Metabonomics investigation of human urine after ingestion of green tea with gas chromatography/mass spectrometry, liquid chromatography/mass spectrometry and (1)H NMR spectroscopy

A method using gas chromatography/mass spectrometry (GC/MS), liquid chromatography/mass spectrometry (LC/MS) and (1)H NMR with pattern recognition tools such as principle components analysis (PCA) was used to study the human urinary metabolic profiles after the intake of green tea. From the normalized peak areas obtained from GC/MS and LC/MS and peak heights from (1)H NMR, statistical analyses were used in the identification of potential biomarkers. Metabolic profiling by GC/MS provided a different set of quantitative signatures of metabolites that can be used to characterize the molecular changes in human urine samples. A comparison of normalized metabonomics data for selected metabolites in human urine samples in the presence of potential overlapping peaks after tea ingestion from LC/MS and (1)H NMR showed the reliability of the current approach and method of normalization. The close agreements of LC/MS with (1)H NMR data showed that the effects of ion suppression in LC/MS for early eluting metabolites were not significant. Concurrently, the specificity of detecting the stated metabolites by (1)H NMR and LC/MS was demonstrated. Our data showed that a number of metabolites involved in glucose metabolism, citric acid cycle and amino acid metabolism were affected immediately after the intake of green tea. The proposed approach provided a more comprehensive picture of the metabolic changes after intake of green tea in human urine. The multiple analytical approach together with pattern recognition tools is a useful platform to study metabolic profiles after ingestion of botanicals and medicinal plants.     

Translational diffusion of macromolecules and nanoparticles modeled as non-overlapping bead arrays in an effective medium

There are three objectives to the present work. First, starting from a boundary element (BE) formulation of low Reynolds number hydrodynamics, model the translational diffusion of macromolecules modeled as an array of non-overlapping beads, and show how this approach is equivalent to previous formulations of "bead hydrodynamics" and under what conditions. Second, show how this approach can be improved upon by accounting for the variation in forces over the surfaces of individual beads and also extending the approach to a gel modeled as an effective medium, EM. Third, develop a "combined obstruction and hydrodynamic effect" model of the translational diffusion of irregularly shaped macromolecules in a gel. In one of the cases studied, the BE approach is shown to be equivalent to previous "bead model" formulations in which intersubunit hydrodynamic interaction is modeled using the Rotne-Prager tensor. A bead model that accounts for the variation in hydrodynamic stress forces over the individual bead surfaces is shown to be in best agreement with exact results for simple bead arrays made up of 2-4 subunits. The translational diffusion of rods, modeled as strings of from 2 to 100 touching beads in dilute gels is examined. Interpolation formulas valid over a range of gel concentrations and rod lengths are derived for the parallel and perpendicular components of the diffusion tensor as well as the orientationally averaged diffusion tensor. The EM model accounts for the long-range hydrodynamic interaction exerted by the gel support matrix on the diffusing particle of interest but does not account for the reduction in diffusion caused by the direct obstruction of the gel, or steric effect. Both effects are accounted for by writing the translational diffusion in a gel as the product of two terms representing long-range hydrodynamic interaction and steric effects. Finally, the diffusion of a 564 base pair DNA in a 2% agarose gel is examined and model results are compared to experiment (Pluen, A.; Netti, P. A.; Jain, R. K.; Berk, D. A. Biophys. J. 1999, 77, 542-552). For reasonable choices of model parameters, fair agreement between theory and experiment is achieved.     

Recent advances in supramolecular self-assembly and biological applications of luminescent alkynylplatinum(II) polypyridine complexes

Among various transition metal complexes, platinum(II) complexes are among one of the most extensively explored classes of metal complexes for supramolecular assembly, as their square-planar molecular geometry allows axial interactions between adjacent complex molecules and access to the formation of supramolecular assemblies with the aid of noncovalent Pt(II)⋯Pt(II) interactions. In the presence of external stimuli, alkynylplatinum(II) polypyridine complexes can self-assemble with alterations in their spectroscopic and luminescence properties. In light of their inherent advantages, including low-energy photoexcitation, red to near-infrared emission, large Stokes shifts, long phosphorescence lifetimes and high photostability, successful applications of alkynylplatinum(II) polypyridine complexes in the detection of biological analytes have been made possible. In this account, presented in part of the FACS Foundation Lecture, we introduce the basic concepts and our recent advances in the development of detection assays for various biomolecules based on luminescent alkynylplatinum(II) polypyridine complexes with selected examples.     

The development of a comprehensive toolbox based on multi-level,high-throughput screening of MOFs for CO/N2 separations

The separation of CO/N₂ mixtures is a challenging problem in the petrochemical sector due to the very similar physical properties of these two molecules, such as size, molecular weight and boiling point. To solve this and other challenging gas separations, one requires a holistic approach. The complexity of a screening exercise for adsorption-based separations arises from the multitude of existing porous materials, including metal–organic frameworks. Besides, the multivariate nature of the performance criteria that needs to be considered when designing an optimal adsorbent and a separation process – i.e. an optimal material requires fulfillment of several criteria simultaneously – makes the screening challenging. To address this, we have developed a multi-scale approach combining high-throughput molecular simulation screening, data mining and advanced visualization, as well as process system modelling, backed up by experimental validation. We have applied our recent advances in the engineering of porous materials'' morphology to develop advanced monolithic structures. These conformed, shaped monoliths can be used readily in industrial applications, bringing a valuable strategy for the development of advanced materials. This toolbox is flexible enough to be applied to multiple adsorption-based gas separation applications.

The separation of challenging mixtures through adsorption is a multidimensional problem that requires a holistic approach. Our toolbox combines experiments, molecular and process simulations with data visualization to find optimal, porous materials.     

Novel Sulfonamide Derivatives as Inhibitors of Histone Deacetylase

Inhibition of the enzyme histone deacetylase (HDAC) is emerging as a novel approach to the treatment of cancer. A series of novel sulfonamide derivatives were synthesized and evaluated for their ability to inhibit human HDAC. Compounds were identified which are potent enzyme inhibitors, with IC₅₀ values in the low nanomolar range against enzyme obtained from HeLa cell extracts, and with antiproliferative effects in cell culture. Extensive characterization of the structure–activity relationships of this series identified key requirements for activity. These include the direction of the sulfonamide bond and substitution patterns on the central phenyl ring. The alkyl spacer between the aromatic head group and the sulfonamide functionality also influenced the HDAC inhibitory activity. One of these compounds, m 11.1 , also designated PXD101, has entered clinical trials for solid tumors and haematological malignancies.     

Oligonucleotide sequencing using guanine-specific methylation and electrospray ionization ion trap mass spectrometry

This paper describes a novel method to map guanine bases in short oligonucleotides using a simple chemical modification reaction and subsequent analysis by electrospray ionization ion trap mass spectrometry (ITMS). In situ guanine-specific methylation followed by gas-phase fragmentation permits the determination of the positions of all guanine residues. Collision-induced dissociation (CID) of the monomethylated oligonucleotide strand promotes rapid depurination and further collision (MS3) of the apurinic oligonucleotide leads to preferential cleavage of the backbone at the site of depurination. The mass of the resulting complementary product ions verifies the position of each guanine base in the sequence. The utility of this methodology is demonstrated for oligonucleotide sequences up to 10 bases in length. In addition, this technique successfully illustrates the use of selective fragmentation for sequencing oligonucleotides by ITMS.     

Shear layer behavior resulting from shock wave diffraction

All previous studies on shock wave diffraction in shock tubes have spatial and temporal limitations due to the size of the test sections. These limitations result from either the reflection of the expansion wave, generated at the corner, from the top wall and/or of the reflection of the incident diffracted shock from the bottom wall of the test section passing back through the region of interest. This has limited the study of the evolution of the shear layer and its associated vortex, which forms a relatively small region of the flow behind the shock with an extent of only a few centimeters, and yet is a region of significant interest. A special shock tube is used in the current tests which allow evolution of the flow to be examined at a scale about an order of magnitude larger than in previously published results, with shear layer lengths of up to 250 mm being achieved without interference from adjacent walls. Tests are presented for incident shock wave Mach numbers of nominally 1.3–1.5. Studies have been undertaken with wall angles of 10, 20, 30 and 90°. Significant changes are noted as the spatial and temporal scale of the experiment increases. For a given wall angle, the flow behind the incident shock is not self-similar as is usually assumed. Both shear layer instability and the development of turbulent patches become evident, neither of which have been noted in previous tests.