Multivariate statistical differentiation of renal cell carcinomas based on lipidomic analysis by ambient ionization imaging mass spectrometry

Desorption electrospray ionization (DESI) mass spectrometry (MS) was used in an imaging mode to interrogate the lipid profiles of thin tissue sections of 11 sample pairs of human papillary renal cell carcinoma (RCC) and adjacent normal tissue and nine sample pairs of clear cell RCC and adjacent normal tissue. DESI-MS images showing the spatial distributions of particular glycerophospholipids (GPs) and free fatty acids in the negative ion mode were compared to serial tissue sections stained with hematoxylin and eosin (H&E). Increased absolute intensities as well as changes in relative abundance were seen for particular compounds in the tumor regions of the samples. Multivariate statistical analysis using orthogonal projection to latent structures treated partial least square discriminate analysis (PLS-DA) was used for visualization and classification of the tissue pairs using the full mass spectra as predictors. PLS-DA successfully distinguished tumor from normal tissue for both papillary and clear cell RCC with misclassification rates obtained from the validation set of 14.3% and 7.8%, respectively. It was also used to distinguish papillary and clear cell RCC from each other and from the combined normal tissues with a reasonable misclassification rate of 23%, as determined from the validation set. Overall DESI-MS imaging combined with multivariate statistical analysis shows promise as a molecular pathology technique for diagnosing cancerous and normal tissue on the basis of GP profiles.     

Plasma-induced graft-polymerization of polyethylene glycol acrylate on polypropylene substrates

A detailed study of argon plasma-induced graft-polymerization of polyethylene glycol acrylate (PEGA) on polypropylene (PP) substrates (membranes and films) is presented. The process consists of four steps: (a) plasma pre-activation of the PP substrates; (b) immersion in a PEGA solution; (c) argon plasma-induced graft-polymerization; (d) washing and drying of the samples. Influence of the solution and plasma parameters on the process efficiency evaluated in terms of amount of grafted polymer, coverage uniformity and substrates wettability, are investigated. The plasma-induced graft-polymerization of PEGA is then followed by sample weighting, water droplet adsorption time and contact angle measurements, attenuated total reflection infrared spectroscopy (ATR-IR), X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) analyses. The stability of the obtained thin films was evaluated in water and in phosphate buffer saline (PBS) at 37 °C. Results clearly indicates that plasma-induced graft-polymerization of PEGA is a practical methodology for anti-fouling surface modification of materials.     

"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis

Proton transfers are fundamental to chemical processes in solution and biological systems. Often, the well-known Grotthuss mechanism is assumed where a series of sequential "proton hops" initiates from the donor and combines to produce the net transfer of a positive charge over a long distance. Although direct experimental evidence for the sequential proton hopping has been obtained recently, alternative mechanisms may be possible in complex molecular systems. To understand these events, all accessible protonation states of the mediating groups should be considered. This is exemplified by transfers through water where the individual water molecules can exist in three protonation states (water, hydronium, and hydroxide); as a result, an alternative to the Grotthuss mechanism for a proton transfer through water is to generate a hydroxide by first protonating the acceptor and then transfer the hydroxide toward the donor through water. The latter mechanism can be most generally described as the transfer of a "proton hole" from the acceptor to the donor where the "hole" characterizes the deprotonated state of any mediating molecule. This pathway is distinct and is rarely considered in the discussion of proton-transfer processes. Using a calibrated quantum mechanical/molecular mechanical (QM/MM) model and an effective sampling technique, we study proton transfers in two solution systems and in Carbonic Anhydrase II. Although the relative weight of the "proton hole" and Grotthuss mechanisms in a specific system is difficult to determine precisely using any computational approach, the current study establishes an energetics motivated framework that hinges on the donor/acceptor pKa values and electrostatics due to the environment to argue that the "proton hole" transfer is likely as important as the classical Grotthuss mechanism for proton transport in many complex molecular systems.     

pKa analysis for the zinc-bound water in human carbonic anhydrase II: Benchmark for "multiscale" QM/MM simulations and mechanistic implications

To quantitatively explore the applicability of the generalized solvent boundary potential (GSBP) based QM/MM approach as a "multiscale" framework for studying chemical reactions in biomolecules, the structural and energetic properties of the Human Carbonic Anhydrase II (CAII) are analyzed and compared to those from periodic boundary condition (PBC) simulations and available experimental data. Although the atomic fluctuations from GSBP based simulations are consistently lower compared to those from PBC simulations or crystallographic data, the fluctuations and internal coordinate distributions for residues in the proximity of the active site as well as diffusion constants of active-site water molecules are fairly well described by GSBP simulations. The pKa of the zinc-bound water, calculated with a SCC-DFTB/MM-GSBP based thermodynamic integration approach, agrees well with experiments for the wild type CAII. For the E106Q mutant, however, a 9 pKa unit downward shift relative to the wild type is found in contrast with previous experiments that found little change. This dramatic discrepancy signals a possible change in the mechanism for the interconversion between CO2/HCO3- in the E106Q mutant, which may be similar to the bicarbonate mediated mechanism proposed for the Co2+ substituted CAII (J. Am. Chem. Soc. 2001, 123, 5861).1 The study highlights pKa analyses as a valuable approach for quantitatively validating the computational model for complex biomolecules as well as for revealing energetic properties intimately related to the chemical process of interest.     

Ferroelectric and dielectric behaviour of Bi0.92La0.08FeO3 multiferroic thin films prepared by soft chemistry route

Bi_0.92La_0.08FeO₃ (BLFO) thin films were grown on platine substrates by the soft chemical route. Ferroelectric and dielectric behaviors of BLFO films deposited by spin-coating technique and annealed at 773 K for 2 h in air atmosphere were explained. BLFO thin films obtained presents a rhombohedral structure. The BLFO films present dielectric and ferroelectric behaviors with dielectric permittivity and dielectric loss of approximately 81 and 0.0144 at 1 kHz. The Au/BLFO/Pt capacitor shows a hysteresis loop with remnant polarization of 20.6 μC/cm² and coercive field of 53.88 kV/cm. The polarization switching and the fatigue behavior of the BLFO films were significantly enhanced.     

Characterization of carbon nanotubes exposed to Na or bombarded with Na at room temperature

We report an electron spectroscopy study on low energy Na⁺ ion implantation and Na atom intercalation in single walled and multi walled carbon nanotube mat samples. Our results show that these two different methods yield quite different dopant spatial distribution since implanted sodium atoms remain on the surface while intercalated alkali metal particles readily diffuse in the bulk.