Isolation and characterization of charge-tagged phenylperoxyl radicals in the gas phase : direct evidence for products and pathways in low temperature benzene oxidation

The phenylperoxyl radical has long been accepted as a critical intermediate in the oxidation of benzene and an archetype for arylperoxyl radicals in combustion and atmospheric chemistry. Despite being central to many contemporary mechanisms underpinning these chemistries, reports of the direct detection or isolation of phenylperoxyl radicals are rare and there is little experimental evidence connecting this intermediate with expected product channels. We have prepared and isolated two charge-tagged phenyl radical models in the gas phase [i.e., 4-(N,N,N-trimethylammonium) phenyl radical cation and 4-carboxylatophenyl radical anion] and observed their reactions with dioxygen by ion-trap mass spectrometry. Measured reaction rates show good agreement with prior reports for the neutral system (k(2)[(Me3N+)C6H4 center dot + O-2] = 2.8 x 10(-11) cm(3) molecule(-1) s(-1), Phi = 4.9%; k(2)[(-O2C)C6H4 center dot + O-2] = 5.4 x 10(-1)1 cm(3) molecule(-1) s(-1), Phi = 9.2%) and the resulting mass spectra provide unequivocal evidence for the formation of phenylperoxyl radicals. Collisional activation of isolated phenylperoxyl radicals reveals unimolecular decomposition by three pathways: (i) loss of dioxygen to reform the initial phenyl radical; (ii) loss of atomic oxygen yielding a phenoxyl radical; and (iii) ejection of the formyl radical to give cyclopentadienone. Stable isotope labeling confirms these assignments. Quantum chemical calculations for both charge-tagged and neutral phenylperoxyl radicals confirm that loss of formyl radical is accessible both thermodynamically and entropically and competitive with direct loss of both hydrogen atom and carbon dioxide.

The fragmentation pathways of protonated Amiton in the gas phase : towards the structural characterisation of organophosphorus chemical warfare agents by electrospray ionisation tandem mass spectrometry

Amiton (O,O-diethyl-S-[2-(diethylamino)ethyl]phosphorothiolate), otherwise known as VG, is listed in schedule 2 of the Chemical Weapons Convention (CWC) and has a structure closely related to VX (O-ethyl-S-(2-diisopropylamino)ethylmethylphosphonothiolate). Fragmentation of protonated VG in the gas phase was performed using electrospray ionisation ion trap mass spectrometry (ESI-ITMS) and revealed several characteristic product ions. Quantum chemical calculations provide the most probable structures for these ions as well as the likely unimolecular mechanisms by which they are formed. The decomposition pathways predicted by computation are consistent with deuterium-labeling studies. The combination of experimental and theoretical data suggests that the fragmentation pathways of VG and analogous organophosphorus nerve agents, such as VX and Russian VX, are predictable and thus ESI tandem mass spectrometry is a powerful tool for the verification of unknown compounds listed in the CWC. Copyright (c) 2006 Commonwealth of Australia. Published by John Wiley & Sons, Ltd.

Fragmentation pathways of 2,3-dimethyl-2,3-dinitrobutane cations in the gas phase

2,3-Dimethyl-2,3-dinitrobutane (DMNB) is an explosive taggant added to plastic explosives during manufacture making them more susceptible to vapour-phase detection systems. In this study, the formation and detection of gas-phase \[M+H](+), \[M+Li](+), \[M+NH(4)](+) and \[M+Na](+) adducts of DMNB was achieved using electrospray ionisation on a triple quadrupole mass spectrometer. The \[M+H](+) ion abundance was found to have a strong dependence on ion source temperature, decreasing markedly at source temperatures above 50 degrees C. In contrast, the \[M+Na](+) ion demonstrated increasing ion abundance at source temperatures up to 105 degrees C. The relative susceptibility of DMNB adduct ions toward dissociation was investigated by collision-induced dissociation. Probable structures of product ions and mechanisms for unimolecular dissociation have been inferred based on fragmentation patterns from tandem mass (MS/MS) spectra of source-formed ions of normal and isotopically labelled DMNB, and quantum chemical calculations. Both thermal and collisional activation studies suggest that the \[M+Na](+) adduct ions are significantly more stable toward dissociation than their protonated analogues and, as a consequence, the former provide attractive targets for detection by contemporary rapid screening methods such as desorption electrospray ionisation mass spectrometry. Copyright (C) 2009 Commonwealth of Australia. Published by John Wiley & Sons, Ltd.

Recursive pathways to marginal likelihood estimation with prior-sensitivity analysis

We investigate the utility to computational Bayesian analyses of a particular family of recursive marginal likelihood estimators characterized by the (equivalent) algorithms known as "biased sampling" or "reverse logistic regression" in the statistics literature and "the density of states" in physics. Through a pair of numerical examples (including mixture modeling of the well-known galaxy dataset) we highlight the remarkable diversity of sampling schemes amenable to such recursive normalization, as well as the notable efficiency of the resulting pseudo-mixture distributions for gauging prior-sensitivity in the Bayesian model selection context. Our key theoretical contributions are to introduce a novel heuristic ("thermodynamic integration via importance sampling") for qualifying the role of the bridging sequence in this procedure, and to reveal various connections between these recursive estimators and the nested sampling technique.

EMT and MET in carcinoma : clinical observations, regulatory pathways and new models

The articles collected here in this special edition Epithelial-Mesenchymal (EMT) and Mesenchymal-Epithelial Transitions (MET) in Cancer provide a snapshot of the very rapidly progressing cinemascope of the involvement of these transitions in carcinoma progression. Pubmed analysis of EMT and cancer shows an exponential increase in the last few years in the number of papers and reviews published under these terms (Fig. 1). The last few years have seen these articles appearing in high calibre journals including Nature, Nature Cell Biology, Cancer Cell, PNAS, JNCI, JCI, and Cell, signaling the acceptance and quality of work in this field.

Effect of handling and fixation processes on fluorescence spectroscopy of mouse skeletal muscles under two-photon excitation

We investigated the effects of handling and fixation processes on the two-photon fluorescence spectroscopy of endogenous fluorophors in mouse skeletal muscle. The skeletal muscle was handled in one of two ways: either sectioned without storage or sectioned following storage in a freezer. The two-photon fluorescence spectra measured for different storage or fixation periods show a differential among those samples that were stored in water or were fixed either in formalin or methanol. The spectroscopic results indicate that formalin was the least disruptive fixative, having only a weak effect on the two-photon fluorescence spectroscopy of muscle tissue, whereas methanol had a significant influence on one of the autofluorescence peaks. The two handling processes yielded similar spectral information, indicating no different effects between them.

Coal seam gas water : potential hazards and exposure pathways in Queensland

The extraction of coal seam gas (CSG) produces large volumes of potentially contaminated water. It has raised concerns about the environmental health impacts of the co-produced CSG water. In this paper, we review CSG water contaminants and their potential health effects in the context of exposure pathways in Queensland’s CSG basins. The hazardous substances associated with CSG water in Queensland include fluoride, boron, lead and benzene. The exposure pathways for CSG water are: (1) water used for municipal purposes, (2) recreational water activities in rivers, (3) occupational exposures, (4) water extracted from contaminated aquifers, and; (5) indirect exposure through the food chain. We recommend mapping of exposure pathways into communities in CSG regions to determine the potentially exposed populations in Queensland. Future efforts to monitor chemicals of concern and consolidate them into a central database will build the necessary capability to undertake a much needed environmental health impact assessment.

Fatty acid synthesis and pyruvate metabolism pathways remain active in dihydroartemisinin induced dormant ring stages of Plasmodium falciparum

Artemisinin (ART) based combination therapy (ACT) is used as the first line treatment of uncomplicated falciparum malaria worldwide. However, despite high potency and rapid action there is a high rate of recrudescence associated with ART monotherapy or ACT long before the recent emergence of ART resistance. ART induced ring stage dormancy and recovery has been implicated as possible cause of recrudescence; however, little is known about the characteristics of dormant parasites including whether dormant parasites are metabolically active. We investigated the transcription of 12 genes encoding key enzymes in various metabolic pathways in P. falciparum during dihydroartemisinin (DHA) induced dormancy and recovery. Transcription analysis showed an immediate down regulation for 10 genes following exposure to DHA, but continued transcription of 2 genes encoding apicoplast and mitochondrial proteins. Transcription of several additional genes encoding apicoplast and mitochondrial proteins, particularly genes encoding enzymes in pyruvate metabolism and fatty acid synthesis pathways, were also maintained. Additions of inhibitors for biotin acetyl CoA carbozylase and enoyl-acyl carrier reductase of the fatty acid synthesis pathways delayed the recovery of dormant parasites by 6 and 4 days, respectively following DHA treatment. Our results demonstrate most metabolic pathways are down regulated in DHA induced dormant parasites. In contrast fatty acid and pyruvate metabolic pathways remain active. These findings highlight new targets to interrupt recovery of parasites from ART-induced dormancy and to reduce the rate of recrudescence following ART treatment.

Second-harmonic generation from biological tissues : effect of excitation wavelength

We report on the measurement of second-harmonic signals from hyperplastic parenchyma and stroma in malignant human prostate tissue under femtosecond pulsed illumination in the wavelength range from 730 to 870 nm. In particular, the relationship of the second-harmonic generation to the excitation wavelength is measured. The result in these two regions behaves considerably differently and thus provides a possible indicator for identifying tissue components and malignancy.

Dependence of second-harmonic signals generated in malignant human prostate tissue on excitation wavelength

The dependence of second harmonic generation (SHG) from hyperplastic parenchyma and stroma in maligant human prostate tissue on excitation wavelengths was measured. A femtosecond pulsed laser, a scanning microscope and a spectrograph were used to perform the measurements. The spectra were measured under excitation power of 10 mW at excitation wavelengths of 730 nm, 750 nm, 800 nm, 850 nm and 890 nm. Analysis suggested that the SHG in prostate tissue is highly structured and wavelength dependent signifying its ability to be used as an indicator for recognizing tissue components, ultrastructures, micro-environments and diseases.

Chemotherapeutic compounds targeting the DNA double-strand break repair pathways : the good, the bad, and the promising

The repair of DNA double-strand breaks (DSBs) is a critical cellular mechanism that exists to ensure genomic stability. DNA DSBs are the most deleterious type of insult to a cell’s genetic material and can lead to genomic instability, apoptosis, or senescence. Incorrectly repaired DNA DSBs have the potential to produce chromosomal translocations and genomic instability, potentially leading to cancer. The prevalence of DNA DSBs in cancer due to unregulated growth and errors in repair opens up a potential therapeutic window in the treatment of cancers. The cellular response to DNA DSBs is comprised of two pathways to ensure DNA breaks are repaired: homologous recombination and non-homologous end joining. Identifying chemotherapeutic compounds targeting proteins involved in these DNA repair pathways has shown promise as a cancer therapy for patients, either as a monotherapy or in combination with genotoxic drugs. From the beginning, there have been a number of chemotherapeutic compounds that have yielded successful responses in the clinic, a number that have failed (CGK-733 and iniparib), and a number of promising targets for future studies identified. This review looks in detail at how the cell responds to these DNA DSBs and investigates the chemotherapeutic avenues that have been and are currently being explored to target this repair process.

Enhancement of optical absorption in thin-film solar cells through the excitation of higher-order nanoparticle plasmon modes

Recent research in the rapidly emerging field of plasmonics has shown the potential to significantly enhance light trapping inside thin-film solar cells by using metallic nanoparticles. In this article it is demonstrated the plasmon enhancement of optical absorption in amorphous silicon solar cells by using silver nanoparticles. Based on the analysis of the higher-order surface plasmon modes, it is shown how spectral positions of the surface plasmons affect the plasmonic enhancement of thin-film solar cells. By using the predictive 3D modeling, we investigate the effect of the higher-order modes on that enhancement. Finally, we suggest how to maximize the light trapping and optical absorption in the thin-film cell by optimizing the nanoparticle array parameters, which in turn can be used to fine tune the corresponding surface plasmon modes.

Excitation of surface plasmon-polariton waves at a semiconductor-metal interface

The excitation of surface plasmon-polariton waves propagating across an external magnetic field (Voigt geometry) in a semiconductor-metal structure by means of the attenuated total reflection method is investigated. The phase matching conditions for the surface waves excitation in the Kretchmann configuration are derived and analyzed. The effect of different nonlinearities on the excitation of the surface waves is studied as well.

Bistable regime of surface magnetoplasma waves excitation at a semiconductor-metal interface

The theoretical analysis of the bistability associated with the excitation of surface magnetoplasma waves (SWs) propagating across an external magnetic field at the semiconductor-metal interface by the attenuated total reflection (ATR) method is presented. The Kretschmann-Raether configuration of the ATR method is considered, i.e. a plane electromagnetic wave is incident onto a metal surface through a coupling prism. The third-order nonlinearity of the semiconductor medium is considered in the general form using the formalism of the third-order nonlinear susceptibilities and of the perturbation theory. The examples of the nonlinear mechanisms which influence the SW propagation are given. The analytical and numerical analyses show that the realization of bistable regimes of the SW excitation is possible. The SW amplitude values providing bistability in the structure are evaluated and are reasonably low to provide the experimental observation.