Enhancement of protein sensitivity for MALDI imaging mass spectrometry after chemical treatment of tissue sections

MALDI imaging mass spectrometry (IMS) has become a valuable tool for the investigation of the content and distribution of molecular species in tissue specimens. Numerous methodological improvements have been made to optimize tissue section preparation and matrix deposition protocols, as well as MS data acquisition and processing. In particular for proteomic analyses, washing the tissue sections before matrix deposition has proven useful to improve spectral qualities by increasing ion yields and the number of signals observed. We systematically explore here the effects of several solvent combinations for washing tissue sections. To minimize experimental variability, all of the measurements were performed on serial sections cut from a single mouse liver tissue block. Several other key steps of the process such as matrix deposition and MS data acquisition and processing have also been automated or standardized. To assess efficacy, after each washing procedure the total ion current and number of peaks were counted from the resulting protein profiles. These results were correlated to on-tissue measurements obtained for lipids. Using similar approaches, several selected washing procedures were also tested for their ability to extend the lifetime as well as revive previously cut tissue sections. The effects of these washes on automated matrix deposition and crystallization behavior as well as their ability to preserve tissue histology were also studied. Finally, in a full-scale IMS study, these washing procedures were tested on a human renal cell carcinoma biopsy.     

Transferable specific scaling factors for interpretation of infrared spectra of biomolecules from density functional theory

A set of transferable local scaling factors is established for assignment of infrared spectra of molecular systems of biological interest experimentally recorded under gas-phase conditions. Each scaling factor is specific for an experimentally observable vibrational mode chosen among those bringing significant structural information. Those factors are provided for harmonic calculations at the DFT B3LYP and DFT B3PW91 levels respectively with 7 and 2 different basis sets. The used training set of neutral molecules comprises nucleobases, aminoacids, peptides, sugars, and neurotransmitters. The proposed specific scaling factors usable for unambiguous conformer assignments lead to typical prediction errors ca. 10 cm(-1) for free and moderately hydrogen-bonded group frequencies with red-shifts up to 200 cm(-1).     

Revisiting the determination of langmuir parameters--application to tetrahydrothiophene adsorption onto activated carbon

The selection of a proper sorbent for a given application is a complex problem. The design and efficiency of adsorption processes require an equilibrium adsorption model. Linear transformation is one of the methods available to estimate the adjustable parameters of isotherm models but possesses limitations compared to nonlinear regressions. A different approach to calculate predicted equilibrium isotherm values leading to an alternative nonlinear regression is presented in this paper and compared with usual regression methods. Adsorption isotherm data of gaseous THT onto three activated carbon materials constitute an experimental basis for the discussion. Assessment of the goodness-of-fit of the Langmuir model is supported by different selected test functions. The new nonlinear approach did not obtain the best results for each test function, but raises questions about the inherent combined error in regression procedures.     

Swelling and contraction of ferrocyanide-containing polyelectrolyte multilayers upon application of an electric potential

We developed a new platform at the interface of polyelectrolyte multilayers (PEMs) and electroactive polymers (EAPs) by combining the easy buildup of PEM thin films and the deformation characteristics of the EAPs. The PEM films were made of poly(L-glutamic acid) (PGA) and poly(allylamine hydrochloride) (PAH). After [Fe(CN)6]4- ions (FCIV) were added, cyclic voltammetry (CV) was performed, resulting in a reversible expansion and contraction of the film. The shape change as well as the film buildup prior to the cycling were monitored in situ using the electrochemical quartz crystal microbalance with dissipation monitoring (EC-QCM-D). Electrochemical atomic force microscopy (EC-AFM) images confirmed the rapid shape deformation. The process takes place in an aqueous environment under mild conditions (maximum potential of 600 mV and no pH change), which makes it a promising tool for biomedical applications. In addition, the electrochemically active films are produced using the layer-by-layer (LbL) method that is already established in biotechnology and biomaterials science; therefore, the presented approach can be readily adapted in these areas, bringing about a new possibility for the nanoscale dynamic control of coating thickness in various applications.     

Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the (1)H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3-(trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating (13)C NMR chemical shifts in solids to the scales used for high-resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice.     

Statistical quantification of the influence of material properties on the oxidation and ignition of activated carbons

The influence of material properties on the reactivities of activated carbon materials have been studied on a laboratory scale. Carbon samples having diversified origin and properties were characterized using a thermogravimetry (TG) coupled with a differential scanning calorimetry (DSC). Reactivity parameters like the Point of Initial Oxidation (PIO) representing the beginning of the oxidation reactions and the Spontaneous Ignition Temperature (SIT) where the bed combustion takes place in a self sustaining manner were experimentally determined. The intrinsic properties of the activated carbons influencing oxidation and ignition were examined qualitatively followed by quantitative statistical correlations. Results from both qualitative and statistical correlations showed that increase in the oxygen content in the form of surface oxygenated groups increased the reactivity of activated carbons. It was by far the single most influential property discriminated from the analysis. The porosity characteristics like the specific surface area and pore volume did show some vague trends but could not be validated like that of the oxygen content. The effects of these individual properties on the oxidation and ignition reactivity are discussed.     

Pore-filling-dependent selectivity effects in the vapor-phase separation of xylene isomers on the metal-organic framework MIL-47

Vapor-phase adsorption and separation of the C8 alkylaromatic components p-xylene, m-xylene, o-xylene, and ethylbenzene on the metal-organic framework MIL-47 have been studied. Low coverage Henry adsorption constants and adsorption enthalpies were determined using the pulse chromatographic technique at temperatures between 230 and 290 degrees C. The four C8 alkylaromatic components have comparable Henry constants and adsorption enthalpies. Adsorption isotherms of the pure components were determined using the gravimetric technique at 70, 110, and 150 degrees C. The adsorption capacity and steepness of the isotherms differs among the components and are strongly temperature dependent. Breakthrough experiments with several binary mixtures were performed at 70-150 degrees C and varying total hydrocarbon pressure from 0.0004 to 0.05 bar. Separation of the different isomers could be achieved. In general, it was found that the adsorption selectivity increases with increasing partial pressure or degree of pore filling. The separation at a high degree of pore filling in the vapor phase is a result of differences in packing modes of the C8 alkylaromatic components in the pores of MIL-47.     

G-quadruplex DNA assemblies: loop length, cation identity, and multimer formation

G-rich DNA sequences are able to fold into structures called G-quadruplexes. To obtain general trends in the influence of loop length on the structure and stability of G-quadruplex structures, we studied oligodeoxynucleotides with random bases in the loops. Sequences studied are dGGGW(i)GGGW(j)GGGW(k)GGG, with W = thymine or adenine with equal probability, and i, j, and k comprised between 1 and 4. All were studied by circular dichroism, native gel electrophoresis, UV-monitored thermal denaturation, and electrospray mass spectrometry, in the presence of 150 mM potassium, sodium, or ammonium cations. Parallel conformations are favored by sequences with short loops, but we also found that sequences with short loops form very stable multimeric quadruplexes, even at low strand concentration. Mass spectrometry reveals the formation of dimers and trimers. When the loop length increases, preferred quadruplex conformations tend to be more intramolecular and antiparallel. The nature of the cation also has an influence on the adopted structures, with K(+) inducing more parallel multimers than NH4(+) and Na(+). Structural possibilities are discussed for the new quadruplex higher-order assemblies.     

N-heterocyclic carbene complexes of Rh: reaction with dioxygen without oxidation

The reaction of oxygen with rhodium complexes containing N-heterocyclic carbenes was found to give dioxygen complexes with rare square planar geometries and unusually short O-O bond lengths. Analysis of the bonding in these complexes by Rh L-edge X-ray absorption spectroscopy (XAS), Raman spectroscopy, and DFT calculations provides evidence for a bonding model in which singlet oxygen is bound to a Rh(I) d8 metal complex, rather than the more common Rh(III) d6 peroxo species with octahedral geometry and O-O bond lengths in the 1.4-1.5 A range.     

Reactivity of an aminopyridine [LMnII]2+ complex with H2O2. Detection of intermediates at low temperature

In the present work we report the reactivity of [LMnII]2+ toward addition of hydrogen peroxide (H2O2) in acetonitrile solution, where L is a pentadentate polypyridine ligand. Formation of peroxo complexes is evidenced by low-temperature UV-visible spectroscopy, ESI-mass spectrometry, and EPR spectroscopy using parallel as well as perpendicular mode detection. The influence of the medium (basicity, water content) on the formation of various species is investigated. In basic nonanhydrous medium the fate of the reaction mixture solution is the formation of the di-mu-oxo mixed-valent Mn(III)Mn(IV) dinuclear complex. In acidic medium the building of the oxo bridges is avoided and the reaction mixture evolves toward oxidation of the ligand L. This reaction route offers new opportunities for the study of oxidation reactivity of Mn (hydro)peroxo complexes.