A theoretical approach to the interpretation of the transient data in scanning laser ablation inductively coupled plasma mass spectrometry: Consideration of the geometry of the scanning area

This paper represents a further development of the theoretical basis for the interpretation of transient data obtained by scanning laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to overcome the non-linear distortion of the transient signal as well as to improve spatial resolution. The reconstruction of the relative concentration profile from transient data is suggested in terms of simple models of analytical information gathering for extreme cases of depth distribution of the analyte. The main attention is focused on the geometry of the overlap between the laser spot and the concentration profile, the consideration of which allows defining explicitly the response function necessary for the deconvolution procedure. The profile of the transient signal simulated according the proposed model for a real system (copper conductor lines in polymer matrix) is in good agreement with the measured data. The feasibility of the deconvolution procedure to reconstruct the relative concentration profile for a model system is demonstrated. The suggested analytical framework is intended to overcome certain limitations of scanning LA-ICP-MS which are caused by the measuring process independently from the optimization of hardware and experimental conditions.     

Biofunctionalization of aqueous dispersed, alumina membrane-templated polymer nanorods for use in enzymatic chemiluminescence assays

The noncovalent immobilization of alkaline phosphatase (ALP) onto aqueous dispersed nylon 6 nanorods ( approximately 310 nm mean diameter; approximately 6 microm mean length) prepared by anodic aluminum oxide (AAO) membrane templating was studied. Using multi-stacked layer-by-layer (LBL) assembly with the cationic quaternary ammonium polymer Sapphire II , the amount of ALP enzyme loaded onto the polymer nanostructures was found to be 115+/-7 microg mg(-1) nanorod. The biofunctionalized nanorods were also characterized for their chemiluminescent activity with the dioxetane substrate, CSPD . The results indicate that the kinetic parameters, K(m) and V(max), for the catalytic activity of the nanostructure-bound ALP enzyme are different from those of soluble ('free') ALP. While the K(m) value was measured to be 156 microM for free ALP, the apparent K(m) value determined for the LBL-immobilized ALP is approximately 20% lower (122 microM). Furthermore, despite the relatively high enzyme loading capacity of the nanorods, the specific activity of the bound ALP enzyme was found to be almost nine times lower than that measured for free ALP. Finally, additional experiments revealed that the catalytic activities of both free ALP and nanorod-conjugated ALP are affected similarly by changes in pH, with optimal performance levels occurring under conditions of pH 9.5. To the best of our knowledge, this study represents the first report examining the preparation of aqueous dispersed, AAO-templated polymer nanorods for potential application as enzyme scaffolds in chemiluminescent-based assay systems.     

DNA binding by a new metallointercalator that contains a proflavine group bearing a hanging chelating unit

The new bifunctional molecule 3,6-diamine-9-[6,6-bis(2-aminoethyl)-1,6-diaminohexyl]acridine (D), which is characterised by both an aromatic moiety and a separate metal-complexing polyamine centre, has been synthesised. The characteristics of D and its ZnII complex ([ZnD]) (protonation and metal-complexing constants, optical properties and self-aggregation phenomena) have been analysed by means of NMR spectroscopy, potentiometric, spectrophotometric and spectrofluorimetric techniques. The equilibria and kinetics of the binding process of D and [ZnD] to calf thymus DNA have been investigated at I=0.11 M (NaCl) and 298.1 K by using spectroscopic methods and the stopped-flow technique. Static measurements show biphasic behaviour for both D-DNA and [ZnD]-DNA systems; this reveals the occurrence of two different binding processes depending on the polymer-to-dye molar ratio (P/D). The binding mode that occurs at low P/D values is interpreted in terms of external binding with a notable contribution from the polyamine residue. The binding mode at high P/D values corresponds to intercalation of the proflavine residue. Stopped-flow, circular dichroism and supercoiled-DNA unwinding experiments corroborate the proposed mechanism. Molecular-modelling studies support the intercalative process and evidence the influence of NH+...O interactions between the protonated acridine nitrogen atom and the oxygen atoms of the polyanion; these interactions play a key role in determining the conformation of DNA adducts.     

Effect of sonication on the particle size of montmorillonite clays

This paper reports on the effect of sonication on SAz-1 and SWy-1 montmorillonite suspensions. Changes in the size of the particles of these materials and modifications of their properties have been investigated. The variation of the particle size has been analyzed by DLS (dynamic light scattering). In all cases the clay particles show a bimodal distribution. Sonication resulted in a decrease of the larger modal diameter, as well as a reduction of its volume percentage. Simultaneously, the proportion of the smallest particles increases. After 60 min of sonication, SAz-1 presented a very broad particle size distribution with a modal diameter of 283 nm. On the other hand, the SWy-1 sonicated for 60 min presents a bimodal distribution of particles at 140 and 454 nm. Changes in the properties of the clay suspensions due to sonication were evaluated spectroscopically from dye-clay interactions, using Methylene Blue. The acidic sites present in the interlamellar region, which are responsible for dye protonation, disappeared after sonication of the clay. The changes in the size of the scattering particles and the lack of acidic sites after sonication suggest that sonication induces delamination of the clay particles.     

Unusual cycloartane glycosides from Astragalus eremophilus

Eleven new cycloartane-type glycosides, named eremophilosides A-K have been isolated from the aerial parts of Astragalus eremophilus. Their structures were elucidated by MS and NMR experiments and the relative configurational analysis of eremophilosides C and D was carried out on the basis of the recently reported J-based method. Additionally, the cytotoxic activity of these compounds in MCF7 and U937 cell lines was evaluated. All tested compounds, except eremophilosides B, C, and J were found to inhibit slightly the growth (controlling the cell cycle) and/or to induce death processes in U937 cell line, the most susceptible cell line. Eremophilosides A and K resulted the most effective to induce cell death, the first by necrosis while the latter by apoptosis.     

Protein extraction for proteome analysis from cacao leaves and meristems, organs infected by Moniliophthora perniciosa, the causal agent of the witches' broom disease

Preparation of high-quality proteins from cacao vegetative organs is difficult due to very high endogenous levels of polysaccharides and polyphenols. In order to establish a routine procedure for the application of proteomic and biochemical analysis to cacao tissues, three new protocols were developed; one for apoplastic washing fluid (AWF) extraction, and two for protein extraction--under denaturing and nondenaturing conditions. The first described method allows a quick and easy collection of AWF--using infiltration-centrifugation procedure--that is representative of its composition in intact leaves according to the smaller symplastic contamination detected by the use of the hexose phosphate isomerase marker. Protein extraction under denaturing conditions for 2-DE was remarkably improved by the combination of chemically and physically modified processes including phenol, SDS dense buffer and sonication steps. With this protocol, high-quality proteins from cacao leaves and meristems were isolated, and for the first time well-resolved 1-DE and 2-DE protein patterns of cacao vegetative organs are shown. It also appears that sonication associated with polysaccharide precipitation using tert-butanol was a crucial step for the nondenaturing protein extraction and subsequent enzymatic activity detection. It is expected that the protocols described here could help to develop high-level proteomic and biochemical studies in cacao also being applicable to other recalcitrant plant tissues.     

Infinite Classes of Dihedral Snarks

Flower snarks and Goldberg snarks are two infinite families of cyclically 5–edge–connected cubic graphs with girth at least five and chromatic index four. For any odd integer k, k > 3, there is a Flower snark, say J _k , of order 4k and a Goldberg snark, say B _k , of order 8k. We determine the automorphism groups of J _k and B _k for every k and prove that they are isomorphic to the dihedral group D _4k of order 4k. Research performed within the activity of INdAM–GNSAGA with the financial support of the Italian Ministry MIUR, project “Strutture Geometriche, Combinatoria e loro Applicazioni”.     

Infrared Multiphoton Dissociation Enables Top-Down Characterization of Membrane Protein Complexes and G Protein-Coupled Receptors

Membrane proteins are challenging to analyze by native mass spectrometry (MS) as their hydrophobic nature typically requires stabilization in detergent micelles that are removed prior to analysis via collisional activation. There is however a practical limit to the amount of energy which can be applied, which often precludes subsequent characterization by top-down MS. To overcome this barrier, we have applied a modified Orbitrap Eclipse Tribrid mass spectrometer coupled to an infrared laser within a high-pressure linear ion trap. We show how tuning the intensity and time of incident photons enables liberation of membrane proteins from detergent micelles. Specifically, we relate the ease of micelle removal to the infrared absorption of detergents in both condensed and gas phases. Top-down MS via infrared multiphoton dissociation (IRMPD), results in good sequence coverage enabling unambiguous identification of membrane proteins and their complexes. By contrasting and comparing the fragmentation patterns of the ammonia channel with two class A GPCRs, we identify successive cleavage of adjacent amino acids within transmembrane domains. Using gas-phase molecular dynamics simulations, we show that areas prone to fragmentation maintain aspects of protein structure at increasing temperatures. Altogether, we propose a rationale to explain why and where in the protein fragment ions are generated.     

Bilayer-Coating Strategy for Hydrophobic Nanoparticles Providing Colloidal Stability,Functionality, and Surface Protection in Biological Media

The surface chemistry of nanoparticles is a key step on the pathway from particle design towards applications in biologically relevant environments. Here, a bilayer-based strategy for the surface modification of hydrophobic nanoparticles is introduced that leads to excellent colloidal stability in aqueous environments and good protection against disintegration, while permitting surface functionalization via simple carbodiimide chemistry. We have demonstrated the excellent potential of this strategy using upconversion nanoparticles (UCNPs), initially coated with oleate and therefore dispersible only in organic solvents. The hydrophobic oleate capping is maintained and a bilayer is formed upon addition of excess oleate. The bilayer approach renders protection towards luminescence loss by water quenching, while the incorporation of additional molecules containing amino functions yields colloidal stability and facilitates the introduction of functionality. The biological relevance of the approach was confirmed with the use of two model dyes, a photosensitizer and a nitric oxide (NO) probe that, when attached to the surface of the UCNPs, retained their functionality to produce singlet oxygen and detect intracellular NO, respectively. We present a simple and fast strategy to protect and functionalize inorganic nanoparticles in biological media, which is important for controlled surface engineering of nanosized materials for theranostic applications.     

Effects of soft X‐ray radiation damage on paraffin‐embedded rat tissues supported on ultralene: a chemical perspective

Radiation damage is an important aspect to be considered when analysing biological samples with X‐ray techniques as it can induce chemical and structural changes in the specimens. This work aims to provide new insights into the soft X‐ray induced radiation damage of the complete sample, including not only the biological tissue itself but also the substrate and embedding medium, and the tissue fixation procedure. Sample preparation and handling involves an unavoidable interaction with the sample matrix and could play an important role in the radiation‐damage mechanism. To understand the influence of sample preparation and handling on radiation damage, the effects of soft X‐ray exposure at different doses on ultralene, paraffin and on paraffin‐embedded rat tissues were studied using Fourier‐transform infrared (FTIR) microspectroscopy and X‐ray microscopy. Tissues were preserved with three different commonly used fixatives: formalin, glutaraldehyde and Karnovsky. FTIR results showed that ultralene and paraffin undergo a dose‐dependent degradation of their vibrational profiles, consistent with radiation‐induced oxidative damage. In addition, formalin fixative has been shown to improve the preservation of the secondary structure of proteins in tissues compared with both glutaraldehyde and Karnovsky fixation. However, conclusive considerations cannot be drawn on the optimal fixation protocol because of the interference introduced by both substrate and embedding medium in the spectral regions specific to tissue lipids, nucleic acids and carbohydrates. Notably, despite the detected alterations affecting the chemical architecture of the sample as a whole, composed of tissue, substrate and embedding medium, the structural morphology of the tissues at the micrometre scale is essentially preserved even at the highest exposure dose.