Characterization of the Core Oligosaccharide and the O‐Antigen Biological Repeating Unit from Halomonas stevensii Lipopolysaccharide: The First Case of O‐Antigen Linked to the Inner Core

A novel core structure among bacterial lipopolysaccharides (LPS) that belong to the genus Halomonas has been characterized. H. stevensii is a moderately halophilic microorganism, as are the majority of the Halomonadaceae. It brought to light the pathogenic potential of this genus. On account of their role in immune system elicitation, elucidation of LPS structure is the mandatory starting point for a deeper understanding of the interaction mechanisms between host and pathogen. In this paper we report the structure of the complete saccharidic portion of the LPS from H. stevensii. In contrast to the finding that the O‐antigen is usually covalently linked to the outer core oligosaccharide, we could demonstrate that the O‐polysaccharide of H. stevensii is linked to the inner core of an LPS. By means of high‐performance anion‐exchange chromatography with pulsed amperometric detection we were able to isolate the core decasaccharide as well as a tridecasaccharide constituted by the core region plus one O‐repeating unit after alkaline degradation of the LPS. The structure was elucidated by one‐ and two‐dimensional NMR spectroscopy, ESI Fourier transform ion cyclotron resonance (FT‐ICR) mass spectrometry, and chemical analysis.     

On the dynamic behaviour of elastic plastic beams simply supported and axially loaded

Summary An elasto-plastic beam-column model withn degrees of freedom statically loaded with an axial compressive force is considered. Its dynamic behaviour in the elasto-plastic range, resulting from the action of a transversal distributed force periodically varying in time in condition of resonance with the structure in the elastic range, is examined. The principal differences with previous results obtained with one degree of freedom model are showed.

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Sommario Si considera un modello adn gradi di libertà di un'asta elasto plastica sollecitata staticamente da una forza assiale di compressione. Se ne esamina la risposta, in campo elasto plastico, ad un carico trasversale distribuito, variabile con legge armonica ed in condizioni di risonanza con la struttura in campo elastico, evidenziando le principali differenze rispetto alle conclusioni tratte in precedenza utilizzando schemi ad un grado di libertà.

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The present investigation has been promoted and financed by the Consiglio Nazionale Ricerche (C.N.R.) at the Istituto di Scienza e Tecnica delle Costruzioni del Politecnico di Milano.     

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson's Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17,004, 68,484, and 273,936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (S(CD)), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.     

Hydrogen atom abstraction selectivity in the reactions of alkylamines with the benzyloxyl and cumyloxyl radicals. The importance of structure and of substrate radical hydrogen bonding

A time-resolved kinetic study on the hydrogen abstraction reactions from a series of primary and secondary amines by the cumyloxyl (CumO(?)) and benzyloxyl (BnO(?)) radicals was carried out. The results were compared with those obtained previously for the corresponding reactions with tertiary amines. Very different hydrogen abstraction rate constants (k(H)) and intermolecular selectivities were observed for the reactions of the two radicals. With CumO(?), k(H) was observed to decrease on going from the tertiary to the secondary and primary amines. The lowest k(H) values were measured for the reactions with 2,2,6,6-tetramethylpiperidine (TMP) and tert-octylamine (TOA), substrates that can only undergo N-H abstraction. The opposite behavior was observed for the reactions of BnO(?), where the k(H) values increased in the order tertiary < secondary < primary. The k(H) values for the reactions of BnO(?) were in all cases significantly higher than those measured for the corresponding reactions of CumO(?), and no significant difference in reactivity was observed between structurally related substrates that could undergo exclusive α-C-H and N-H abstraction. This different behavior is evidenced by the k(H)(BnO(?))/k(H)(CumO(?)) ratios that range from 55-85 and 267-673 for secondary and primary alkylamines up to 1182 and 3388 for TMP and TOA. The reactions of CumO(?) were described in all cases as direct hydrogen atom abstractions. With BnO(?) the results were interpreted in terms of the rate-determining formation of a hydrogen-bonded prereaction complex between the radical α-C-H and the amine lone pair wherein hydrogen abstraction occurs. Steric effects and amine HBA ability play a major role, whereas the strength of the substrate α-C-H and N-H bonds involved appears to be relatively unimportant. The implications of these different mechanistic pictures are discussed.     

Kähler–Einstein submanifolds of the infinite dimensional projective space

This paper consists of two main results. In the first one we describe all Kähler immersions of a bounded symmetric domain into the infinite dimensional complex projective space in terms of the Wallach set of the domain. In the second one we exhibit an example of complete and non-homogeneous Kähler–Einstein metric with negative scalar curvature which admits a Kähler immersion into the infinite dimensional complex projective space.     

Efficient organic monoliths prepared by γ-radiation induced polymerization in the evaluation of histone deacetylase inhibitors by capillary(nano)-high performance liquid chromatography and ion trap mass spectrometry

New monolithic HPLC columns were prepared by γ-radiation-triggered polymerization of hexyl methacrylate and ethylene glycol dimethacrylate monomers in the presence of porogenic solvents. Polymerization was carried out directly within capillary (250-200 μm I.D.) and nano (100-75 μm I.D.) fused-silica tubes yielding highly efficient columns for cap(nano)-LC applications. The columns were applied in the complete separation of core (H2A, H2B, H3, and H4) and linker (H1) histones under gradient elution with UV and/or electrospray ionization (ESI) ion trap mass spectrometry (MS) detections. Large selectivity towards H1, H2A-1, H2A-2, H2B, H3-1, H3-2 and H4 histones and complete separation were obtained within 8 min time windows, using fast gradients and very high linear flow velocities, up to 11 mm/s for high throughput applications. The method developed was the basis of a simple and efficient protocol for the evaluation of post-translational modifications (PTMs) of histones from NCI-H460 human non-small-cell lung cancer (NSCLC) and HCT-116 human colorectal carcinoma cells. The study was extended to monitoring the level of histone acetylation after inhibition of Histone DeACetylase (HDAC) enzymes with suberoylanilide hydroxamic acid (SAHA), the first HDAC inhibitor approved by the FDA for cancer therapy. Attractive features of our cap(nano)-LC/MS approach are the short analysis time, the minute amount of sample required to complete the whole procedure and the stability of the polymethacrylate-based columns. A lab-made software package ClustMass was ad hoc developed and used to elaborate deconvoluted mass spectral data (aligning, averaging, clustering) and calculate the potency of HDAC inhibitors, expressed through a Relative half maximal Inhibitory Concentration parameter, namely R_IC(50) and an averaged acetylation degree.     

Water evaporation from gel beads

Hydrogels are characterized by properties which make them ideal candidates for applications in several fields, such as drug delivery, biomedicine, and functional foods. Molecular diffusion out of a hydrogel matrix depends on their hydrodynamic radii and the mesh sizes within the matrix of the gel. A quantitative experimental and mathematical understanding of interactions, kinetics, and transport phenomena within complex hydrogel systems assists network design by identifying the key parameters and mechanisms that govern the rate and extent of solute release. In this article a calorimetric differential scanning calorimetry (DSC) study reports on the approach to parallel water effusion from a hydrogel matrix to the release of a model protein. The measurement of the water evaporation is taken as the simplest routine determination of a phenomenon that is basically due to a diffusive process through the porous structure of the gel and thermodynamically governed by the difference in the water chemical potential inside and outside of the bead. The analysis of the experimental calorimetric curves is made with the purpose of extracting several numerical parameters characteristic of each curve. The rationale is to develop a simple methodology to understand the release properties of the porous structure of the complex gel matrix by means of DSC.