Thiazole orange-induced c-di-GMP quadruplex formation facilitates a simple fluorescent detection of this ubiquitous biofilm regulating molecule

Recently, there has been an explosion of research activities in the cyclic dinucleotides field. Cyclic dinucleotides, such as c-di-GMP and c-di-AMP, have been shown to regulate bacterial virulence and biofilm formation. c-di-GMP can exist in different aggregate forms, and it has been demonstrated that the polymorphism of c-di-GMP is influenced by the nature of cation that is present in solution. In previous work, polymorphism of c-di-GMP could only be demonstrated at hundreds of micromolar concentrations of the dinucleotide, and it has been a matter of debate if polymorphism of c-di-GMP exists under in vivo conditions. In this Article, we demonstrate that c-di-GMP can form G-quadruplexes at low micromolar concentrations when aromatic molecules such as thiazole orange template the quadruplex formation. We then use this property of aromatic molecule-induced G-quadruplex formation of c-di-GMP to design a thiazole orange-based fluorescent detection of this important signaling molecule. We determine, using this thiazole orange assay on a crude bacterial cell lysate, that WspR D70E (a constitutively activated diguanylate cyclase) is functional in vivo when overexpressed in E. Coli . The intracellular concentration of c-di-GMP in an E. Coli cell that is overexpressed with WspR D70E is very high and can reach 2.92 mM.     

Photochemical activation of ruthenium(II)-pyridylamine complexes having a pyridine-N-oxide pendant toward oxygenation of organic substrates

Ruthenium(II)-acetonitrile complexes having η(3)-tris(2-pyridylmethyl)amine (TPA) with an uncoordinated pyridine ring and diimine such as 2,2'-bipyridine (bpy) and 2,2'-bipyrimidine (bpm), [Ru(II)(η(3)-TPA)(diimine)(CH(3)CN)](2+), reacted with m-chloroperbenzoic acid to afford corresponding Ru(II)-acetonitrile complexes having an uncoordinated pyridine-N-oxide arm, [Ru(II)(η(3)-TPA-O)(diimine)(CH(3)CN)](2+), with retention of the coordination environment. Photoirradiation of the acetonitrile complexes having diimine and the η(3)-TPA with the uncoordinated pyridine-N-oxide arm afforded a mixture of [Ru(II)(TPA)(diimine)](2+), intermediate-spin (S = 1) Ru(IV)-oxo complex with uncoordinated pyridine arm, and intermediate-spin Ru(IV)-oxo complex with uncoordinated pyridine-N-oxide arm. A Ru(II) complex bearing an oxygen-bound pyridine-N-oxide as a ligand and bpm as a diimine ligand was also obtained, and its crystal structure was determined by X-ray crystallography. Femtosecond laser flash photolysis of the isolated O-coordinated Ru(II)-pyridine-N-oxide complex has been investigated to reveal the photodynamics. The Ru(IV)-oxo complex with an uncoordinated pyridine moiety was alternatively prepared by reaction of the corresponding acetonitrile complex with 2,6-dichloropyridine-N-oxide (Cl(2)py-O) to identify the Ru(IV)-oxo species. The formation of Ru(IV)-oxo complexes was concluded to proceed via intermolecular oxygen atom transfer from the uncoordinated pyridine-N-oxide to a Ru(II) center on the basis of the results of the reaction with Cl(2)py-O and the concentration dependence of the consumption of the starting Ru(II) complexes having the uncoordinated pyridine-N-oxide moiety. Oxygenation reactions of organic substrates by [Ru(II)(η(3)-TPA-O)(diimine)(CH(3)CN)](2+) were examined under irradiation (at 420 ± 5 nm) and showed selective allylic oxygenation of cyclohexene to give cyclohexen-1-ol and cyclohexen-1-one and cumene oxygenation to afford cumyl alcohol and acetophenone.     

Unique inclusion properties of crystalline powder p-tert-butylthiacalix[4]arene toward alcohols and carboxylic acids

Powdery crystals of p-tert-butylthiacalix[4]arene (2) selectively include EtOH from 1:1 mixtures of MeOH-EtOH and EtOH-PrOH, and EtCO(2)H from HCO(2)H-EtCO(2)H. On the other hand, no acid is included from HCO(2)H-MeCO(2)H, even though MeCO(2)H is included from the neat acid. The origins of these phenomena are discussed based on X-ray analysis of inclusion crystals prepared separately by crystallization.     

Ultrafast nonradiative decay of electronically excited States of malachite green: ab initio calculations

We have investigated the nonradiative deactivation process of malachite green in the singlet excited states, S(1) and S(2), by high-level ab initio quantum chemical calculations using the CASPT2//CASCF approach. The deactivation pathways connecting the Franck-Condon region and conical intersection regions are identified. The initial population in the S(1) state is on a flat surface and the relaxation involves a rotation of phenyl rings, which leads the molecule to reach the conical intersection between the S(1) and S(0) states, where it efficiently decays back to the ground state. There exists a small barrier connecting the Franck-Condon and conical intersection regions on the S(1) potential energy surface. The decay mechanism from the S(2) state also involves the twisting motion of phenyl rings. In contrast to the excitation to the S(1) state, the initial population is on a downhill ramp potential and the barrierless relaxation through the rotation of substituted phenyl rings is expected. During the course of relaxation, the molecule switches to the S(1) state at the conical intersection between S(2) and S(1), and then it decays back to the ground state through the intersection between S(1) and S(0). In relaxation from both S(1) and S(2), large distortion of phenyl rings is required for the ultrafast nonradiative decay to the ground state.     

Electric field gradient in Mg and Zn detected by β-emitters,8Li and12x0392;x0392;x0392;

The quadrupole coupling constants of⁸Li and¹²B in hcp Mg and Zn are determined by use of a newly developed nuclear quadrupole resonance technique (NNQR) as ¦eqQ(⁸Li in Mg)/h¦=3.0±0.3 kHz, ¦eqQ(⁸Li in Zn)/h¦=33.5±2 kHz, and ¦eqQ(¹²B in Mg)/h¦=47.0±0.1 kHz. Correspondingly, the electric field gradients at room temperature are deduced: ¦q(⁸Li in Mg)¦=(3.81±0.39)×10¹⁸, ¦q(⁸Li in Zn)¦=(4.25±0.27)×10¹⁹, and ¦q(¹²B in Mg)¦=(1.47±0.03)×10²⁰, all in V/m². The experiments are compared with the results of first-principles super-cell band structure calculations which can treat local lattice relaxations around the impurity nuclei. The calculations show that the most favorable location of these light interstitials in hcp Mg is not the octahedral-like sites which have the biggest interstitial volume, but the basal trigonal sites with a local lattice expansion of as big as 30%. Calculated electric field gradients at the impurity nuclei reproduce the experimental values fairly well.     

Comparisons of CIP,compact and CIP‐CSL2 schemes for reproducing internal solitary waves

Six different models were evaluated for reproducing internal solitary waves which occur and propagate in a stratified flow field with a sharp interface. Three stages were used to compute internal solitary waves in a stratified field: (1) first‐phase computation of momentum equations, (2) second‐phase computation of momentum equations, which corresponds to computing the Poisson's equation, and (3) density computation. The six models discussed in this paper consisted of combinations of four different schemes, a three‐point combined compact difference scheme (CCD), a normal central difference scheme (CDS), a cubic‐polynomial interpolation (CIP), and an exactly conservative semi‐Lagrangian scheme (CIP‐CSL2). The residual cutting method was used to solve the Poisson's equation. Three tests were used to confirm the validity of the computations using KdV theory; i.e. the incremental wave speed and amplitude of internal solitary waves, the maximum horizontal velocity and amplitude, and the wave form. In terms of the shape of an internal solitary wave, using CIP for momentum equations was found to provide better performance than CCD. These results suggest one of the most appropriate scheme for reproducing internal solitary waves may be one in which CIP is used for momentum equations and CCD to solve the Poisson's equation. Copyright © 2005 John Wiley & Sons, Ltd.     

Permeation flux of organic molecules through silica-surfactant nanochannels in a porous alumina membrane.

The permeation fluxes of phenol, benzene sulfonate (BS) and benzene disulfonate (BDS) through a porous anodic alumina membrane with the perpendicularly oriented silica-surfactant nanochannel assembly membrane (NAM) were measured in water-ethanol mixture media. The permeation flux depended on solute charges and on solvent composition. As the ethanol ratio increased, the fluxes of BS and BDS increased and the flux of phenol decreased. The results of extraction/elution experiments also depended on the solute charges and the solvent composition. Chromatographic experiments in n-hexane showed that dipole and hydrophobic interactions affect the retention of solutes. Permeation of the solute across the NAM in water-ethanol mixture is likely to be determined by various factors such as dipole interaction, hydrophobic interaction, solvation, and anion-exchange efficiencies.     

Dependence of aerodynamic characteristics and flow pattern on surface structure of a baseball

In this report, the aerodynamic characteristics, such as lift and drag, of an official rubber baseball are studied experimentally by comparing the characteristics of a sphere having a smooth surface and those of spheres having different surface structures. In addition, the flow velocity distribution is measured quantitatively using the spark tracing method. From the obtained results, the flow patterns for these baseballs and the flow mechanism around a sphere have been clarified.