Mass Spectrometric Identification of [4Fe–4S](NO)x Intermediates of Nitric Oxide Sensing by Regulatory Iron–Sulfur Cluster Proteins

Nitric oxide (NO) can function as both a cytotoxin and a signalling molecule. In both cases, reaction with iron–sulfur (Fe–S) cluster proteins plays an important role because Fe–S clusters are reactive towards NO and so are a primary site of general NO-induced damage (toxicity). This sensitivity to nitrosylation is harnessed in the growing group of regulatory proteins that function in sensing of NO via an Fe–S cluster. Although information about the products of cluster nitrosylation is now emerging, detection and identification of intermediates remains a major challenge, due to their transient nature and the difficulty in distinguishing spectroscopically similar iron-NO species. Here we report studies of the NO-sensing Fe–S cluster regulators NsrR and WhiD using non-denaturing mass spectrometry, in which non-covalent interactions between the protein and Fe/S/NO species are preserved. The data provide remarkable insight into the nitrosylation reactions, permitting identification, for the first time, of protein-bound mono-, di- and tetranitrosyl [4Fe–4S] cluster complexes ([4Fe–4S](NO), [4Fe–4S])(NO)₂ and [4Fe–4S](NO)₄) as intermediates along pathways to formation of product Roussin's red ester (RRE) and Roussin's black salt (RBS)-like species. The data allow the nitrosylation mechanisms of NsrR and WhiD to be elucidated and clearly distinguished.     

Pesticide residues analysis in honey using ethyl acetate extraction method: validation and pilot survey in real samples

This paper presents a cost-effective and validated multi residue confirmatory method for the determination of 167 chemically different pesticides and a survey study on Cyprus honey samples. This method uses ethyl acetate for the extraction of pesticides from honey and the determination is performed with liquid chromatography (LC) coupled to mass spectrometry (MS) operating in tandem mode (MS/MS) and with GC–ECD (gas chromatography with electron capture detector) analysis. The LC-MS/MS analytical system is especially important in the analysis of polar and non-volatile pesticides. For the validation of the method, blank honey samples were spiked with 146 pesticides (organophosphorous, carbamates, triazoles, amides, neonicodinoids, strobilurines, phenylureas, bendimidazoles and others) for the LC-MS/MS analysis at three levels: 0.01, 0.05 and 0.1 mg kg^?1 and with 21 pesticides for the GC-ECD analysis at two levels: 0.01 and 0.05 mg kg^?1for organochlorines and 0.05 and 0.2 mg kg^?1for the pyrethroids. As blank sample, a sample of honey which did not contain detectable levels of the analytes sought was used. The validation study was in accordance to the DG SANCO guidelines. The scope of validation included recovery, linearity, limits of quantification and precision. Linearity is demonstrated all along the range of concentration that was investigated with correlation coefficients ≥0.98. Recoveries of the majority of compounds were in the 70%–120% range and were characterised by precision lower or equal to 20%. The validated method was used for a survey of 36 samples of honey produced in different areas of Cyprus and this is the first work on Cypriot honey samples investigating a broad range of pesticides. Only coumaphos was detected at concentrations higher than 0.01 mg kg^?1 in the 58.6% of the honey samples analysed for Coumaphos. The results were evaluated in accordance to the provisions of the Commission Regulation (EU) No 37/2010 on pharmacologically active substances and their classification regarding maximum residue limits (MRLs) in foodstuffs of animal origin. The concentrations of coumaphos in all positive samples were at levels much lower than the MRL.     

Structure Elucidation and Activity of Kolossin A,the D‐/L‐Pentadecapeptide Product of a Giant Nonribosomal Peptide Synthetase

The largest continuous bacterial nonribosomal peptide synthetase discovered so far is described. It consists of 15 consecutive modules arising from an uninterrupted, fully functional gene in the entomopathogenic bacterium Photorhabdus luminescens. The identification of its cryptic biosynthesis product was achieved by using a combination of genome analysis, promoter exchange, isotopic labeling experiments, and total synthesis of a focused collection of peptide candidates. Although it belongs to the growing class of D ‐/ L ‐peptide natural products, the encoded metabolite kolossin A was found to be largely devoid of antibiotic activity and is likely involved in interspecies communication. A stereoisomer of this peculiar natural product displayed high activity against Trypanosoma brucei rhodesiense, a recalcitrant parasite that causes the deadly disease African sleeping sickness.     

Symmetry calculation for molecules and transition states

The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three‐dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label‐stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules. © 2014 Wiley Periodicals, Inc.     

Damaging Effects of Ultraviolet Radiation on the Cornea

The cornea sits at the anterior aspect of the eye and, like the skin, is highly exposed to ultraviolet radiation (UVR). The cornea blocks a significant proportion of UVB from reaching the posterior structures of the eye. However, UVA can penetrate the full thickness of the cornea, even reaching the anterior portion of the lens. Epidemiological data indicate that UVR is a contributing factor for a multitude of diseases of the cornea including pterygium, photokeratitis, climatic droplet keratopathy and ocular surface squamous neoplasia (OSSN), although the pathogenic mechanisms of each require further elucidation. UVR is a well‐known genotoxic agent, and its effects have been well characterized in organs such as the skin. However, we are only beginning to identify its effects on the cornea, such as the UVR signature C → T and CC → TT transversions identified by sequencing and increased proliferative and shedding rates in response to UVR exposure. Alarmingly, a single low‐dose exposure of UVR to the cornea is sufficient to elicit genetic, molecular and cellular changes, supporting the consideration of using protective measures, such as wearing sunglasses when outdoors. The aim of this review was to describe the adverse effects of UVR on the cornea.     

On the Stability of Pt-Based Catalysts in HBr/Br2 Solution

Stability studies on supported metal nanoparticles are essential for gaining insight into the design and optimization of high-performance materials. In this work, the dissolutions of Pt-based catalysts in HBr/Br₂ mixture of various concentration regimes were studied and correlated with material structural properties. The dissolution of metal nanoparticles was enhanced by adding Br₂ to the HBr solution. Comparing with commercial Pt/C catalyst, the well-alloyed PtIr/C catalyst was observed to exhibit high resistance towards dissolution. In addition, regulating the accessibility of the metal sites to dissolution-inducing species contributed to the marked stability of the nanoparticles in HBr/Br₂ solutions, as shown for the surface-modified PtIr/C catalysts with organic diamine molecules.     

Quantum Bayesian computation

Quantum Bayesian computation is an emerging field that levers the computational gains available from quantum computers. They promise to provide an exponential speed-up in Bayesian computation. Our article adds to the literature in three ways. First, we describe how quantum von Neumann measurement provides quantum versions of popular machine learning algorithms such as Markov chain Monte Carlo and deep learning that are fundamental to Bayesian learning. Second, we describe quantum data encoding methods needed to implement quantum machine learning including the counterparts to traditional feature extraction and kernel embeddings methods. Third, we show how quantum algorithms naturally calculate Bayesian quantities of interest such as posterior distributions and marginal likelihoods. Our goal then is to show how quantum algorithms solve statistical machine learning problems. On the theoretical side, we provide quantum versions of high dimensional regression, Gaussian processes and stochastic gradient descent. On the empirical side, we apply a quantum FFT algorithm to Chicago house price data. Finally, we conclude with directions for future research.     

EEG Fractal Analysis Reflects Brain Impairment after Stroke

Stroke is the commonest cause of disability. Novel treatments require an improved understanding of the underlying mechanisms of recovery. Fractal approaches have demonstrated that a single metric can describe the complexity of seemingly random fluctuations of physiological signals. We hypothesize that fractal algorithms applied to electroencephalographic (EEG) signals may track brain impairment after stroke. Sixteen stroke survivors were studied in the hyperacute (<48 h) and in the acute phase (∼1 week after stroke), and 35 stroke survivors during the early subacute phase (from 8 days to 32 days and after ∼2 months after stroke): We compared resting-state EEG fractal changes using fractal measures (i.e., Higuchi Index, Tortuosity) with 11 healthy controls. Both Higuchi index and Tortuosity values were significantly lower after a stroke throughout the acute and early subacute stage compared to healthy subjects, reflecting a brain activity which is significantly less complex. These indices may be promising metrics to track behavioral changes in the very early stage after stroke. Our findings might contribute to the neurorehabilitation quest in identifying reliable biomarkers for a better tailoring of rehabilitation pathways.     

CanSAS‐IV

A two-day workshop on beamline integration and data formatting (HDF5/NeXus) of the EIGER detector was held in Baden, Switzerland, January 24–25, 2013. Its aim was to discuss the technical challenges inherent with the next generation of high-frame-rate, high-resolution X-ray imaging detectors, and specifically with the EIGER detector. EIGER is a photon-counting hybrid pixel detector developed at the Paul Scherrer Institute (PSI) and DECTRIS Ltd. With even higher spatial resolution and frame rates than its predecessor, the PILATUS detector, it will be able to continuously produce up to 3000 images per second. The corresponding extreme data rates generated by this and future detectors present a significant challenge for beamline integration of the detectors, for data handling by the users, and for data processing software. Efficient data flow, storage, and processing must be achieved to handle the huge data sets that will be produced in seconds by these devices.