Solution structure of a peptide nucleic acid duplex from NMR data: features and limitations

This paper describes the results of a 1D and 2D NMR spectroscopy study of a palindromic 8-base pair PNA duplex GGCATGCC in H2O and H2O-D2O solutions. The (1)H NMR peaks have been assigned for most of the protons of the six central base pairs, as well as for several amide protons of the backbone. The resulting 36 interbase and base-backbone distance restraints were used together with Watson-Crick restraints to generate the PNA duplex structure in the course of 10 independent simulated annealing runs followed by restrained molecular dynamics (MD) simulations in explicit water. The resulting PNA structures correspond to a P-type helix with helical parameters close to those observed in the crystal structures of PNA. Based on the current limited number of restraints obtained from NMR spectra, alternative structures obtained by MD from starting PNA models based on DNA cannot be ruled out and are also discussed.     

A Sol-Gel Synthesis for Thermally Stable Aniline/Silica Material

Aniline/silica sol-gel material was obtained. The aniline was immobilized on the silica surface using chloropropyltrimethoxysilane as bridge reagent. The base activator NaH was used to produce a fast SN₂ reaction between the base and the alkylorganosilane. The resulting modified silica was characterized by elemental analysis and infrared spectroscopy using an oven cell. The organic coverage on the surface was proportional to the organic precursor concentration. The aniline/silica materials are thermally stable up to 300°C, in high vacuum.     

Human cytokines characterized by dielectric thermal analysis, thermogravimetry, and differential scanning calorimetry

Malaria affects over 500 million people worldwide leading to 1–2 million deaths each year, the majority of whom are children. Four Plasmodium species cause malaria in humans. To properly diagnose, and correctly treat malarial infections, accurate diagnosis of infection is required. Proper diagnosis of infection will result in a reduction of morbidity, mortality, and of drug resistant parasites. However, the current tests for malaria diagnosis do not efficiently identify the appropriate human and parasite biomarkers associated with disease. Detection of specific inflammatory mediators such as cytokines associated with malaria pathogenesis will aid the determination of disease progression, disease prognosis, and the early diagnosis of malaria infection. In this study, we used dielectric thermal analysis (DETA), thermogravimetric analysis, and differential scanning calorimetry (DSC) to characterize five human cytokines (IL-1α, IL-2, IL-4, IL-6, and IL-10), to demonstrate how their thermoanalytical properties can be investigated for sensor design. Analysis for DETA was performed at a frequency range of 0.1–300,000 Hz. Permittivity and loss factor measurements were used to calculate tan δ values. Peak frequencies were used to determine dielectric signatures for each cytokine. The peak frequencies were different for each cytokine analyzed. In addition, activation energies were frequency dependent for IL-2 but frequency independent for the remaining four cytokines. Cytokines were also examined using DSC which established variance in heat of crystallization and heat of fusion of solvent among the five cytokines. A noticeable differentiation was observed with IL-1α among the other four cytokines when analyzed using trend analysis. Detection of unique dielectric signals will aid development of sensitive dielectric sensors capable of detecting cytokines in various human samples.     

H2O nucleation around Au+

First principles electronic structure calculations have been carried out to investigate the ground state geometry, electronic structure, and the binding energy of [Au(H2O)n]+ clusters containing up to 10 H2O molecules. It is shown that the first coordination shell of Au+ contains two H2O molecules forming a H2O-Au+-H2O structure with C2 symmetry. Subsequent H2O molecules bind to the previous H2O molecules forming stable and fairly rigid rings, each composed of 4 H2O molecules, and leading to a dumbbell structure at [Au(H2O)8]+. The 9th and the 10th H2O molecules occupy locations above the Au+ cation mainly bonded to one H2O from each ring, leading to structures where the side rings are partially distorted and forming structures that resemble droplet formation around the Au+ cation. The investigations highlight quantum effects in nucleation at small sizes and provide a microscopic understanding of the observed incremental binding energy deduced from collision induced dissociation that indicates that [Au(H2O)n]+ clusters with 7-10 H2O molecules have comparable binding energy. The charge on the Au+ is shown to migrate to the outside H2O molecules, suggesting an interesting screening phenomenon.     

High‐throughput workflow for identification of phosphorylated peptides by LC‐MALDI‐TOF/TOF‐MS coupled to in situ enrichment on MALDI plates functionalized by ion landing

We report an MS‐based workflow for identification of phosphorylated peptides from trypsinized protein mixtures and cell lysates that is suitable for high‐throughput sample analysis. The workflow is based on an in situ enrichment on matrix‐assisted laser desorption/ionization (MALDI) plates that were functionalized by TiO₂ using automated ion landing apparatus that can operate unsupervised. The MALDI plate can be functionalized by TiO₂ into any array of predefined geometry (here, 96 positions for samples and 24 for mass calibration standards) made compatible with a standard MALDI spotter and coupled with high‐performance liquid chromatography. The in situ MALDI plate enrichment was compared with a standard precolumn‐based separation and achieved comparable or better results than the standard method. The performance of this new workflow was demonstrated on a model mixture of proteins as well as on Jurkat cells lysates. The method showed improved signal‐to‐noise ratio in a single MS spectrum, which resulted in better identification by MS/MS and a subsequent database search. Using the workflow, we also found specific phosphorylations in Jurkat cells that were nonspecifically activated by phorbol 12‐myristate 13‐acetate. These phosphorylations concerned the mitogen‐activated protein kinase/extracellular signal‐regulated kinase signaling pathway and its targets and were in agreement with the current knowledge of this signaling cascade. Control sample of non‐activated cells was devoid of these phosphorylations. Overall, the presented analytical workflow is able to detect dynamic phosphorylation events in minimally processed mammalian cells while using only a short high‐performance liquid chromatography gradient. Copyright © 2015 John Wiley & Sons, Ltd.     

Modification of PP fibres with alkaline copolyamides

Copolyamides with 5.9‐19.7 wt.% of nylon salt ADETA (adipic acid + diethylenetriamine) and 94.1‐80.3 wt.% of ϵ‐caprolactam were synthesized and their properties were estimated. Blended polypropylene/copolyamides fibres containing 5‐15 wt.% of copolyamides were prepared and their properties were evaluated. The electrical properties, hydrophilicity and especially dyeability of modified PP fibres are positively influenced by a higher amount of the copolyamide in the PP and also by a higher amount of the nylon salt ADETA in the copolyamide.     

Matrix-assisted laser desorption/ionization tandem reflectron time-of-flight mass spectrometry of fullerenes

Atandem reflectron time-of-flight mass spectrometer developed in our laboratory provides a unique opportunity to investigate the collision-induced dissociation of fullerene ions formed by matrix-assisted laser desorption/ionization (MALDI). Specifically, this opportunity arises from the ability to utilize high energy collisional activation (normally available only on tandem sector instruments by using continuous ionization techniques) for ions formed by pulsed laser desorption, whereas most MALDI time-of-flight instruments record product ion mass spectra of ions formed by metastable or postsource decay. In this study we investigate the products of mass-selected and collisionally activated C ₆₀ ⁺ and C ₇₀ ⁺ ions by using different target gases over a range of target gas pressures. In general, heavier target gases produce more extensive fragmentation and improve the mass resolution of lower mass ionic products because a greater portion of these ions are formed by single collisions. Additionally, the tandem time-of-flight instrument utilizes a nonlinear (curved-field) reflectron in the second mass analyzer that enables high energy collision-induced dissociation spectra to be recorded without scanning or stepping the reflectron voltage.     

Isolation of Bisphenol A-Tolerating/degrading Shewanella haliotis Strain MH137742 from an Estuarine Environment

Applied Biochemistry and Biotechnology - The human exposure to bisphenol A (BPA) occurs frequently. Once, this compound was one of the highest volume chemicals produced worldwide and used as a...     

Determination of lead in the urine of exposed and unexposed adults by extraction and flow-injection/atomic absorption spectrometry

Lead is extracted from urine with ammonium pyrrolidien dithiocrbamate into methyl isobutyl ketone, and 20 μl of the extract is injected into a water carrier stream in a flow-injection/atomic absorption system. The procedure is simple, quick, accurate and reproducible. Recoveries are 96–105%. The mean urine lead contents of 20 unexposed and 20 printing-press lead exposed workers was found to be 39.0 ± 8.3 and 71.7 ± 26.3 μg Pb l^?1, respectively.     

The adsorption of dyes used in the textile industry on mesoporous materials

An adsorbent material made with a silica lamellar mesoporous material treated with chitosan has been proved to be useful to adsorb both anionic and cationic dyes used in the textile industry. The two tested dyes Tectilon Blue (anionic) and Rhodamine B (cationic) have different adsorption kinetics reflecting a complex mechanism of the phenomenon. Furthermore, the adsorption capacity and interaction strength of Tectilon Blue is higher than those of Rhodamine B. Tectilon Blue molecules are situated with the molecular plane perpendicular to the adsorbent surface, whilst that of the Rhodamine B molecule is flat and parallel to the surface. The differences may be attributed to the different regions of the adsorbent surface on which the dyes are adsorbed because of their different electric charge.