Quasi-Hamiltonian structure and Hojman construction

Given a smooth vector field Γ and assuming the knowledge of an infinitesimal symmetry X, Hojman [S. Hojman, The construction of a Poisson structure out of a symmetry and a conservation law of a dynamical system, J. Phys. A Math. Gen. 29 (1996) 667-674] proposed a method for finding both a Poisson tensor and a function H such that Γ is the corresponding Hamiltonian system. In this paper, we approach the problem from geometrical point of view. The geometrization leads to the clarification of several concepts and methods used in Hojman's paper. In particular, the relationship between the nonstandard Hamiltonian structure proposed by Hojman and the degenerate quasi-Hamiltonian structures introduced by Crampin and Sarlet [M. Crampin, W. Sarlet, Bi-quasi-Hamiltonian systems, J. Math. Phys. 43 (2002) 2505-2517] is unveiled in this paper. We also provide some applications of our construction.     

Inorganic Sol-Gel Preparation of Medium Sized Microparticles of Li2TiO3 from TiCl4 as Tritium Breeding Material for Fusion Reactors

Microspheres of Li₂TiO₃ were fabricated by a classical, inorganic sol-gel process from commercially available TiCl₄. Elaborated process consists of the following main steps: (1) dissolving of TiCl₄ in concentrated aqueous HCl and addition of LiOH; (2) formation of sol emulsion in 2-ethylhexanol-1 containing the surfactant SPAN-80 (EH); (3) gelation of emulsion drops by extraction of water with partially dehydrated EH; (4) impregnation of gel to Li:Ti molar ratio MR = 2; (5) thermal treatment at 1200°C in order to receive chloride free product. This temperature can be significantly lowered (to 750°C) by dechlorination starting solution TiCl₄ by chemical treatment of the with nitric acid to form of nitrate-stabilized titania sols. Tritium release from sol-gel made Li₂TiO₃ microspheres were found very close to that observed for other traditional materials, however for the first sample process starts slightly earlier.     

Application of High Pressure-DTA for High Pressure-liquid Phase Epitaxy of Doped Mercury and Thallium HTS Formations

The fabrication method of superconducting thin films of compositions HgBa₂Ca₂Cu₃O_8+δ (Hg-1223) and Tl₂Ba₂CuO_y (2201) on single-crystalline SrTiO₃ and LaAlO₃ substrates is reported. The highest obtained T _c was 134 K and J _c over 10⁶ A cm^–2 at 77 K. High pressure DTA(HP-DTA) was applied to grow mercury- and thallium-based high-temperature superconducting crystals and thin films, to identify melting points of particular phases within these oxide systems and determine suitable processing conditions. The DTA system operates at the: maximum temperature of 1200°C, volume up to 5 cm³, working pressure up to 1.5 GPa and at a working atmosphere — inert gas with up to 25% oxygen. This revised version was published online in August 2006 with corrections to the Cover Date.     

Second-generation mimics of ganglioside GM1 oligosaccharide: a three-dimensional view of their interactions with bacterial enterotoxins by NMR and computational methods

As a step to delineate a strategy of ligand design for cholera toxin (CT), NMR studies were performed on several mimics of the GM1 ganglioside oligosaccharide. The conformation of these analogues was investigated first in solution and then upon binding to cholera toxin by transferred nuclear Overhauser effect (TR-NOE) measurements. It was demonstrated that CT selects a conformation similar to the global minima of the free saccharides from the ensemble of presented conformations. No evidence of major conformational distortions was obtained, but one or two of the available conformers of the hydroxyacid side chain appear to be selected in the bound state. The NMR data were interpreted with the aid of computer models, generated and analyzed by using a combination of different approaches (MacroModels' MC/EM and MC/SD, Autodock, and GRID). Analysis of the NMR data supported by computational studies allowed us to interpret the experimental observations and to derive workable models of the ligand:toxin complexes. These models suggest that the higher affinity of the (R)-lactic acid derivative 3 may stem from lipophilic interactions with a hydrophobic area in the toxin binding site located in the vicinity of the sialic acid side chain binding region of the CT:GM1 complex, and formed by the side chain of Ile-58 and Lys-34. Thus, the models obtained have allowed us to make useful design suggestions for the improvement of ligand affinity.     

Direct zonal liquid chromatographic method for the kinetic study of actinomycin-DNA binding

The binding of an anticancer drug (actinomycin D or ACTD) to double-stranded DNA (dsDNA) was studied by means of high-performance liquid chromatography (HPLC). ACTD is an antitumor antibiotic containing one chromophore group and two pentapeptidic lactone cycles that binds dsDNA. Incubations of ACTD with DNA were performed at physiological pH. The complexed and free ligand concentrations of the mixture were quantified at 440 nm from their separation on a size-exclusion chromatographic (SEC) column using the same buffer for the elution and the sample incubation. The DNA and the ACTD-DNA complexes were eluted at the column exclusion volume while the ligand was retained on the support. An apparent binding curve was obtained by plotting the amount emerging at the exclusion column volume against that eluted at free ACTD retention volume. A dissociating effect was evidenced and the binding parameters were significantly different from those obtained at equilibrium by visible absorbance titration. The equilibrium binding parameters determined by absorption spectroscopy were used as starting data in the numerical simulations of the chromatographic process. The results showed a strong dependency of the apparent binding parameters on the reaction kinetics. Finally the comparison of the apparent binding curve obtained from the HPLC experiments and from the numerical simulations permitted an evaluation of the dissociation rate constant (kd = 0.004 s(-1)).     

Structural basis for recognition of bacterial cell wall teichoic acid by pseudo-symmetric SH3b-like repeats of a viral peptidoglycan hydrolase

Endolysins are bacteriophage-encoded peptidoglycan hydrolases targeting the cell wall of host bacteria via their cell wall-binding domains (CBDs). The molecular basis for selective recognition of surface carbohydrate ligands by CBDs remains elusive. Here, we describe, in atomic detail, the interaction between the Listeria phage endolysin domain CBD500 and its cell wall teichoic acid (WTA) ligands. We show that 3′O-acetylated GlcNAc residues integrated into the WTA polymer chain are the key epitope recognized by a CBD binding cavity located at the interface of tandem copies of beta-barrel, pseudo-symmetric SH3b-like repeats. This cavity consists of multiple aromatic residues making extensive interactions with two GlcNAc acetyl groups via hydrogen bonds and van der Waals contacts, while permitting the docking of the diastereomorphic ligands. Our multidisciplinary approach tackled an extremely challenging protein–glycopolymer complex and delineated a previously unknown recognition mechanism by which a phage endolysin specifically recognizes and targets WTA, suggesting an adaptable model for regulation of endolysin specificity.

Combining genetic, biochemical and computational approaches, we elucidated the molecular mechanisms underlying the recognition of Listeria wall teichoic acid by bacteriophage-encoded SH3b repeats.     

Bead injection for surface enhanced Raman spectroscopy: automated on-line monitoring of substrate generation and application in quantitative analysis

The technique of bead injection has been adapted for surface enhanced Raman scattering (SERS) to substantially improve precision, long term stability and sensitivity of SERS detection in analytical chemistry. For this purpose a fully automated flow system comprising a dedicated flow-cell has been developed and tested. With the developed flow-cell, which contains two inlet and two outlet channels, it is possible to retain, perfuse and discharge minute amounts of polymer beads while monitoring all steps by Raman spectroscopy. First, beads carrying cation exchanger moieties were retained in the flow-cell and subsequently perfused with a silver nitrate and a hydroxylamine solution using one inlet of the flow cell. By this sequence homogeneous SERS active silver layers were formed on the beads. The uniformity of the achieved silver layer was studied by secondary electron microscopy. For measurement, the analyte was then introduced from the second inlet channel such that the interaction between the activated SERS beads and analyte occurred in close proximity and within the focus of the laser excitation beam. Due to the complete computer control of all experimental steps, including bead entrapment, SERS layer generation, sample introduction and final bead removal, highly reproducible conditions for SERS were achieved. The method was developed using 9-aminoacridine as a test molecule. Quantitative studies were carried out for 9-aminoacridine and acridine showing linear calibrations from 1-100 nmol l(-1) and 50-1,000 nmol l(-1), respectively, using a sample volume of 200 microl each. Typical relative standard deviations were 4.7% for 9-aminoacrine and 5.8% for acridine.     

On-line preconcentration and determination of mercury in biological samples by flow injection vapour generation inductively coupled plasma atomic emission spectrometry

An FI-ICP-AES method for the determination of trace levels of mercury in biological samples has been described, which is based on the extraction of the mercury complex with 1,5-bis (di-2-pyridyl)methylene thiocarbonohydrazide (DPTH) on-line into isobuthyl-methyl ketone (IBMK). The organic phase (containing the complex) has been mixed on-line with SnCl₂ in N,N-dimethylformamide. Thus, mercury vapour can be generated directly from the organic phase and separated in a gas-liquid separation device. The detection limit for mercury is 4 ng/ml and the calibration curve is linear at least from 10 to 2500 ng/ml. The relative standard deviation for 10 replicate measurements is ±1% for 100 ng/ml of Hg(II). Results from the analysis of some certified biological reference materials are given.     

Preparation of thin SnO2 layers by inorganic sol-gel process

SnO₂ sols were prepared in the following way: (1) precipitation of metastannic acid with aqueous ammonia from aqueous solutions of SnCl₄, (2) washing the precipitates with NH₄NO₃ solution and water, (3) peptization of precipitates in water, sometimes with an addition of HNO₃, at elevated temperature using mechanical stirring. In those sols, sometimes diluted with water or ethanol, substrates (glass or silica derived wafers) were dipped and withdrawn at various rates. Gel coatings were converted into crystalline SnO₂ by thermal treatment at 600°C. Coatings with thickness between 300–2000 Å were prepared.     

Carbohydrate-based DNA ligands: sugar-oligoamides as a tool to study carbohydrate-nucleic acid interactions

Sugar-oligoamides have been designed and synthesized as structurally simple carbohydrate-based ligands to study carbohydrate-DNA interactions. The general design of the ligands 1-3 has been done as to favor the bound conformation of Distamycin-type gamma-linked covalent dimers which is a hairpin conformation. Indeed, NMR analysis of the sugar-oligoamides in the free state has indicated the presence of a percentage of a hairpin conformation in aqueous solution. The DNA binding activity of compounds 1-3 was confirmed by calf thymus DNA (ct-DNA) NMR titration. Interestingly, the binding of the different sugar-oligoamides seems to be modulated by the sugar configuration. Semiquantitative structural information about the DNA ligand complexes has been derived from NMR data. A competition experiment with Netropsin suggested that the sugar-oligoamide 3 bind to DNA in the minor groove. The NMR titrations of 1-3 with poly(dA-dT) and poly(dG-dC) suggested preferential binding to the ATAT sequence. TR-NOE NMR experiments for the sugar-oligoamide 3-ct-DNA complex both in D(2)O and H(2)O have confirmed the complex formation and given information on the conformation of the ligand in the bound state. The data confirmed that the sugar-oligoamide ligand is a hairpin in the bound state. Even more relevant to our goal, structural information on the conformation around the N-glycosidic linkage has been accessed. Thus, the sugar asymmetric centers pointing to the NH-amide and N-methyl rims of the molecule have been characterized.