Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria

DNA fingerprinting has attracted considerable interest as means for identifying, tracing and preventing the dissemination of infectious agents. Various methods have been developed for typing of pathogenic bacteria, which differ in discriminative power, reproducibility and ease of interpretation. During recent years a typing method, which uses the information provided by whole genome sequencing of bacterial species, has gained increased attention. Short sequence repeat (SSR) motifs are known to undergo frequent variation in the number of repeated units through cellular mechanisms most commonly active during chromosome replication. A class of SSRs, named variable number of tandem repeats (VNTRs), has proven to be a suitable target for assessing genetic polymorphisms within bacterial species. This review attempts to give an overview of bacterial agents where VNTR-based typing, or multiple-locus variant-repeat analysis (MLVA) has been developed for typing purposes, together with addressing advantages and drawbacks associated with the use of tandem repeated DNA motifs as targets for bacterial typing and identification.     

Binding of the bioactive component daphnetin to human serum albumin demonstrated using tryptophan fluorescence quenching

Daphnetin (7,8-dihydroxycoumarin), one of the major bioactive components isolated from Daphne koreane Nakai, has been used in traditional Chinese medicine for the treatment of coagulation disorders. It is also a chelator, an antioxidant and a protein kinase inhibitor. In this paper, a combination of intrinsic fluorescence, Fourier transform infrared (FT-IR) spectroscopy and circular dichroic (CD) spectroscopy has been used to characterize the binding between daphnetin and human serum albumin (HSA) under physiological conditions with drug concentrations of 6.7 x 10(-6) - 2.3 x 10(-5) mol x L(-1), and a HSA concentration of 1.5 x 10(-6) mol x L(-1). Changes in the CD spectra and FT-IR spectra were observed upon ligand binding, and the degree of tryptophan fluorescence quenching did change significantly in the complexes. These data have proved the change in protein secondary structure accompanying ligand binding. The change in tryptophan fluorescence intensity was used to determine the binding constants. The thermodynamic parameters, the enthalpy change (DeltaH) and the entropy change (DeltaS) were calculated to be -12.45 kJ x mol(-1)and 52.48 J x mol(-1) x K(-1) according to the van't Hoff equation, which indicated that hydrophobic and electrostatic interactions played the main role in the binding of daphnetin to HSA, in accordance with the results of calculations performed on a Silicon Graphics Ocatane2 workstation. In addition, the binding distance between daphnetin and HSA was obtained (4.02 nm) based on the Forster energy transfer theory.     

pH-sensitive modulation of the second hydration sphere in lanthanide(III) tetraamide-DOTA complexes: a novel approach to smart MR contrast media

The lanthanide(III) complexes of three tetraamide DOTA bearing pyridyl, phenolic and hydroxypyridyl substituents have been studied by NMR, luminescence and cyclic voltammetry. The relaxivity profiles of the gadolinium complexes of the pyridyl and phenolic ligands were flat and essentially the same between pH 2 and 8. The hydroxypyridyl ligand, however, exhibited two regions of enhanced relaxivity. The small relaxivity enhancement (25 %) at lower pH (pH 2-4) has been attributed to an increase in the prototropic exchange of the coordinated water molecule while the slightly larger enhancement (84 %) at higher pH (pH 6-9) reflects deprotonation of the ligand amide protons. Deprotonation of the amides results in the formation of an intramolecular acid-base pair interaction with the phenolic protons and this, in turn, causes a highly organized second hydration sphere to come into effect, thereby increasing the relaxivity. The water relaxivity of the Gd(3+)-hydroxypyridyl complex is further enhanced upon binding to serum albumin.     

Cationic copolymerization of indene with styrene derivatives: Synthesis of random copolymers of indene with high molecular weight

Random copolymers with high molecular weights of indene and p‐methylstyrene (pMeSt) were synthesized by cationic polymerization with trichloroacetic acid/tin tetrachloride in CH₂Cl₂ at low temperatures. When indene and pMeSt (1:1 v/v), for example, were polymerized at ?40 °C, both monomers were consumed at very similar rates to give a copolymer with high molecular weight [number‐average molecular weight (M_n): 8–9 × 10⁴]. This is indeed quite unexpected behavior for the combination of these two monomers because pMeSt polymerized over 1000 times faster than indene in the homopolymerization under the reaction conditions previously described. The product copolymer of indene and pMeSt had a random monomer sequence in it that was confirmed by NMR analyses and thermal‐property measurements. In sharp contrast with pMeSt, styrene and p‐chlorostyrene, which have no electron‐donating groups on the phenyl ring, led to low molecular weight polymers (M_n < 10,000) in the copolymerization with indene (1:1 v/v). © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2449–2457, 2002     

Electrochemical Studies of Oxidation of Lomefloxacin and Interaction with Calf Thymus DNA at Nano‐SnO2/DHP Modified Electrode

A nanoparticle thin film modified electrode has been constructed using a glassy carbon electrode (GCE) coated with a nano‐tin oxide/dihexadecylphosphate (nano‐SnO₂/DHP). In pH 6.0 phosphate buffer solutions (PBS), lomefloxacin (LMF) appeared as an anodic peak with peak potential of 1.35 V at nano‐SnO₂/DHP modified electrode. In comparison with a bare GCE or a nano‐SnO₂ modified electrode, the nano‐SnO₂/DHP modified electrode exhibited an enhanced effectiveness for the oxidation of LMF. Cyclic voltammetry (CVs) coupled with fluorescence and UV/vis absorbance spectra techniques were used to study the interaction of LMF with Calf thymus DNA (ctDNA) in phosphate buffer solutions (PBS). The interaction of LMF and ctDNA could result in a considerable decrease in the peak currents and positive shift in the peak potential, as well as changes of fluorescence, UV/vis adsorption spectra and gel electrophoresis. All the acquired data showed that the new adduct between LMF and ctDNA was formed. Electrochemistry coupled with spectroscopy techniques could provide a relatively easy way to obtain useful information about the molecular mechanism of LMF‐ctDNA interactions.     

Three New Serratane Triterpenoids from Phlegmariurus squarrosus

Three new serratane triterpenoids, (3α,14α,15α,21α)‐3,14,15,21,29‐pentahydroxyserratan‐24‐oic acid ( 1 ), (3α,21β)‐serrat‐14‐ene‐3,21,24,30‐tetraol ( 2 ), and (3α,21α)‐serrat‐14‐ene‐3,21,24,29‐tetraol ( 3 ), were isolated from Phlegmariurus squarrosus, together with eight known compounds. Their chemical structures were elucidated on the basis of in‐depth spectroscopic analyses.     

Theoretical study of CH…O hydrogen bond in proton transfer reaction of glycine

Density functional theory (DFT) calculations are used to study the strength of the CH…O H‐bond in the proton transfer reaction of glycine. Comparison has been made between four proton transfer reactions (ZW1, ZW2, ZW3, SCRFZW) in glycine. The structural parameters of the zwitterionic, transition, and neutral states of glycine are strongly perturbed when the proton transfer takes place. It has been found that the interaction of water molecule at the side chain of glycine is high in the transition state, whereas it is low in the zwitterionic and neutral states. This strongest multiple hydrogen bond interaction in the transition state reduces the barrier for the proton transfer reaction. The natural bond orbital analysis have also been carried out for the ZW2 reaction path, it has been concluded that the amount of charge transfer between the neighboring atoms will decide the strength of H‐bond. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Similarities and differences in the electron ionization-induced fragmentation of structurally related N-alkoxymethyl lactams and sultams

Unimolecular fragmentation patterns of the molecular ions of selected lactams and sultams bearing alkoxymethyl group at the nitrogen atom were studied. The main common fragmentation reaction observed for all compounds studied in this work is the elimination of an aldehyde molecule. This reaction is considered to proceed via two different mechanisms. For lactams, hydrogen rearrangement within an alkoxymethyl group is observed, which leads to the appropriate N-methyl derivatives. For sultams, transfer of the methyl group to the nitrogen and oxygen atoms, proceeding through an ion-neutral complex, dominates. Another important fragmentation channel characteristic exclusively for lactams is the loss of an alkyl radical. This process takes place within the N-alkoxymethyl moiety, yielding the appropriate protonated ion of N-formyllactams. This process is accompanied by relatively high kinetic energy release.     

Rigid-body dynamics in the isothermal-isobaric ensemble: a test on the accuracy and computational efficiency

We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL.     

Boomerang‐Type Substitution Reaction: Reactivity of Fullerene Epoxides and a Halofullerenol

The C_s‐symmetric fullerene chlorohydrin C₆₀(Cl)(OH)(OOtBu)₄ reacts with 4‐dimethylaminopyridine (DMAP) and 1,4‐diazabicyclo[2.2.2]octane (DABCO) to yield two isomers with the formula C₆₀(O)(OOtBu)₄ in good yields. These isomers differ with respect to the location of the epoxy functionality. The one from DMAP is C_s symmetric, whereas that from DABCO is C₁ symmetric with the epoxy group on the central pentagon. Two different mechanisms are proposed to explain the chemoselectivity of these reactions. The reaction with DMAP involves single‐electron transfer as the key step; DMAP acts as the electron donor. A combination of an oxygen‐atom shift and S_N2′′ processes (boomerang substitution) are responsible for the formation of isomer with DACBO. Various related reactions support the proposed mechanisms. The structures of new fullerene derivatives were determined by spectroscopy, single‐crystal X‐ray analysis, and chemical correlation experiments.