Theoretical investigations of photophysics and spectroscopic properties in B12 cofactors.

Enzymes incorporating B12 cofactors (cobalamins) are significant biological components as they are involved in the metabolism of every cell of the body. The absorbing riddle, yet unresolved, is the enormous acceleration of the reaction rate that is strictly related to the Co–C bond cleavage initiating every catalytic cycle. Consequently, the realistic explanation of the processes controlled by B12 derivatives demands a profound analysis of their structure coupled with the examination of factors influencing subsequent steps of the reaction as well as properties of the reagents and intermediates. Herein, the photochemical study of cobalamins was presented as it provides a sensitive probe for the investigation of the reactivity of the cobalt-carbon bond in terms of any structural or environmental modification. Theoretical investigations, guided by Density Functional Theory (DFT), Time-Dependent DFT (TD-DFT) and correlated ab initio methods were performed in order to explore the nature of electronically excited states of different vitamin B12 derivatives and the mechanism of events following the photon excitation in vitamin B12. Initially, the most appropriate density functional to study the photochemistry of these complex molecules was determined. Its accuracy was evaluated with respect to both its agreement with available experimental data and higher level ab initio outcomes. Next, the absorption (Abs), circular dichroism (CD) and magnetic CD were calculated for the first time. Based on the examination of certain spectral regions the electronic properties of B12 derivatives were examined. The correlation between the nature of specific electronic transitions and the structure was extensively discussed. In addition, the environmental effect on the character of excited states was investigated as the calculations were performed both in gas phase as well as in water solution modeled via the polarizable continuum model (PCM) or conductor-like screening model (COSMO). In addition, the study of cob(I)alamin, lacking axial ligands, is of significant value especially considering the fact that the complete model of cob(I)alamin was applied as opposed to a majority of previous theoretical efforts. Finally, the lack of photodissociation in CNCbl as opposed to other B12 analogs was investigated in detail. The electronically excited states of CNCbl were examined as a function of two axial ligands calculated at TD-DFT level of theory. By analyzing the shapes of potential energy surfaces (PESs) and the nature of its lowest excited states in different environments, the explanation of subsequent steps following photon excitation of that system was provided

A key for the identification of plant-parasitic nematodes of the genera Longidorus Micoletzky, 1922 and Paralongidorus Siddiqi, Hooper and Khan, 1963 (Nematoda: Longidoridae) occurring in Poland

Plant parasites of the genera Longidorus Micoletzky, 1922 and Paralongidorus Siddiqi, Hooper and Khan, 1963 comprise a group of plant root ectoparasites, some of which are known as pests of economic importance. Their importance is further augmented by the fact that several species are known to be vectors of nepoviruses. To date 16 species from the genus Longidorus and two from Paralongidorus have been recorded in Poland. Despite their economic importance in agriculture currently there is no regional key for species identification. This paper presents such a key. The key has many illustrations and is based mainly on traits which are easily observable even by less experienced users. Thus, it should provide a useful tool for both scientists and specialists working in the field of plant protection, soil ecology and zoology as well as for teaching purposes

TD-DFT insight into photodissociation of the Co-C bond in coenzyme B12

Coenzyme B12 (AdoCbl) is one of the most biologically active forms of vitamin B12, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT) has been applied to investigate the photodissociation of coenzyme B12. To reduce computational cost, while retaining the major spectroscopic features of AdoCbl, a truncated model based on ribosylcobalamin (RibCbl) was used to simulate Co-C photodissociation. Equilibrium geometries of RibCbl were obtained by optimization at the DFT/BP86/TZVP level of theory, and low-lying excited states were calculated by TD-DFT using the same functional and basis set. The calculated singlet states, and absorption spectra were simulated in both the gas phase, and water, using the polarizable continuum model (PCM). Both spectra were in reasonable agreement with experimental data, and potential energy curves based on vertical excitations were plotted to explore the nature of Co-C bond dissociation. It was found that a repulsive 3(σCo-C → σ* Co-C) triplet state became dissociative at large Co-C bond distance, similar to a previous observation for methylcobalamin (MeCbl). Furthermore, potential energy surfaces (PESs) obtained as a function of both Co-CRib and Co-NIm distances, identify the S1 state as a key intermediate generated during photoexcitation of RibCbl, attributed to a mixture of a metal-to-ligand charge transfer (MLCT) and a s bonding-ligand charge transfer (SBLCT) states

Early Effect Markers and Exposure Determinants of Metalworking Fluids Among Metal Industry Workers: Protocol for a Field Study.

Exposure to aerosols from metalworking fluids (MWF) has previously been related to a series of adverse health outcomes (eg, cancer, respiratory diseases). Our present epidemiological study focuses on occupational exposures to MWF and a panel of exposure and effect biomarkers. We hypothesize that these health outcomes are caused by particle exposure that generates oxidative stress, leading to airway inflammation and ultimately to chronic respiratory diseases. We aimed to assess whether MWF exposure, in particular as characterized by its oxidative potential, is associated with biomarkers of oxidative stress and inflammation as well as genotoxic effects. The ultimate goal is to develop exposure reduction strategies based on exposure determinants that best predict MWF-related health outcomes. The following relationships will be explored: (1) exposure determinants and measured exposure; (2) occupational exposure and preclinical and clinical effect markers; (3) exposure biomarkers and biomarkers of effect in both exhaled breath condensate and urine; and (4) biomarkers of effect, genotoxic effects and respiratory symptoms. At least 90 workers from France and Switzerland (30 controls, 30 exposed to straight MWF and 30 to aqueous MWF) were followed over three consecutive days after a nonexposed period of at least two days. The exposure assessment is based on MWF, metal, aldehyde, and ultrafine particle number concentrations, as well as the intrinsic oxidative potential of aerosols. Furthermore, exposure biomarkers such as metals, metabolites of polycyclic aromatic hydrocarbons and nitrosamine are measured in exhaled breath condensate and urine. Oxidative stress biomarkers (malondialdehyde, 8-isoprostane, 8-hydroxy-2'-deoxyguanosine, nitrates, and nitrites) and exhaled nitric oxide, an airway inflammation marker, are repeatedly measured in exhaled breath condensate and urine. Genotoxic effects are assessed using the buccal micronucleus cytome assay. The statistical analyses will include modelling exposure as a function of exposure determinants, modelling the evolution of the biomarkers of exposure and effect as a function of the measured exposure, and modelling respiratory symptoms and genotoxic effects as a function of the assessed long-term exposure. Data collection, which occurred from January 2018 until June 2019, included 20 companies. At the date of writing, the study included 100 subjects and 29 nonoccupationally exposed controls. This study is unique as it comprises human biological samples, questionnaires, and MWF exposure measurement. The biomarkers collected in our study are all noninvasive and are useful in monitoring MWF exposed workers. The aim is to develop preventative strategies based on exposure determinants related to health outcomes. DERR1-10.2196/13744

TRUFA: A user-friendly web server for de novo RNA-seq analysis using cluster computing.

Application of next-generation sequencing (NGS) methods for transcriptome analysis (RNA-seq) has become increasingly accessible in recent years and are of great interest to many biological disciplines including, eg, evolutionary biology, ecology, biomedicine, and computational biology. Although virtually any research group can now obtain RNA-seq data, only a few have the bioinformatics knowledge and computation facilities required for transcriptome analysis. Here, we present TRUFA (TRanscriptome User-Friendly Analysis), an open informatics platform offering a web-based interface that generates the outputs commonly used in de novo RNA-seq analysis and comparative transcriptomics. TRUFA provides a comprehensive service that allows performing dynamically raw read cleaning, transcript assembly, annotation, and expression quantification. Due to the computationally intensive nature of such analyses, TRUFA is highly parallelized and benefits from accessing high-performance computing resources. The complete TRUFA pipeline was validated using four previously published transcriptomic data sets. TRUFA's results for the example datasets showed globally similar results when comparing with the original studies, and performed particularly better when analyzing the green tea dataset. The platform permits analyzing RNA-seq data in a fast, robust, and user-friendly manner. Accounts on TRUFA are provided freely upon request at https://trufa.ifca.es

Electronically Excited States of Vitamin B12: Benchmark Calculations Including Time-Dependent Density Functional Theory and Correlated Ab Initio Methods

Time-dependent density functional theory (TD-DFT) and correlated ab initio methods have been applied to the electronically excited states of vitamin B12 (cyanocobalamin or CNCbl). Different experimental techniques have been used to probe the excited states of CNCbl, revealing many issues that remain poorly understood from an electronic structure point of view. Due to its efficient scaling with size, TD-DFT emerges as one of the most practical tools that can be used to predict the electronic properties of these fairly complex molecules. However, the description of excited states is strongly dependent on the type of functional used in the calculations. In the present contribution, the choice of a proper functional for vitamin B12 was evaluated in terms of its agreement with both experimental results and correlated ab initio calculations. Three different functionals, i.e. B3LYP, BP86, and LC-BLYP, were tested. In addition, the effect of relative contributions of DFT and HF to the exchange-correlation functional was investigated as a function of the range-separation parameter, {\mu}. The issues related to the underestimation of charge transfer (CT) excitation energies by TD-DFT was validated by Tozer's L diagnostic, which measures the spatial overlap between occupied and virtual orbitals involved in the particular excitation. The nature of low-lying excited states was also analyzed based on a comparison of TD-DFT and ab initio results. Based on an extensive comparision against experimental results and ab initio benchmark calculations, the BP86 functional was found to be the most appropriate in describing the electronic properties of CNCbl. Finally, an analysis of electronic transitions and a new re-assignment of some excitations are discussed.Comment: Accepted by the Journal of Chemistry

Method validation of nanoparticle tracking analysis to measure pulmonary nanoparticle content: the size distribution in exhaled breath condensate depends on occupational exposure

A particle exposure assessment based on the dose deposited in the lungs would be the gold standard for the evaluation of any resulting health effects. Measuring particles in exhaled breath condensate (EBC)-a matrix containing water and airway lining fluid-could help to evaluate particle retention in the lungs. This study aimed to (1) validate a nanoparticle tracking analysis (NTA) method for determining the particle number concentration and their hydrodynamic size distribution in EBC, and (2) apply this method to EBC collected from workers exposed to soapstone (n = 55) or quartz dust (n = 12) and controls (n = 11). A standard latex bead solution was used to determine the linear range, limit of detection (LOD), repeatability (coefficient of variation, CV), and bias in spiked EBC. An LM10 NanoSight instrument with NTA version 3.1 software was used for measurement. RTubes(®) were used for field collection of EBC. The repeatability obtained for a D50 size distribution in EBC showed less than 8% variability, with a bias <7%. The particle concentration was linear in the range ≤2.5 × 10(8) particles ml(-1) with a LOD of 4 × 10(6) particles ml(-1). A recovery of 117 ± 20% at 6.2 × 10(7) particles ml(-1) was obtained with a CV <10% and a bias <20%. EBC from workers exposed to quartz, who experienced the largest exposure to silica particles, consistently exhibited a statistically significant (p < 0.01) higher concentration of particles in their EBC, with a size distribution shift towards larger values than the other groups. Results showed that the NTA technique performed well for characterizing the size distribution and concentrations of particles in EBC. The technique needs to be corroborated with a larger population of workers

Does exposure to inflammatory particles modify the pattern of anion in exhaled breath condensate?

Exposure to environmental and occupational particulate matter (PM) induces health effects on the cardio-pulmonary system. In addition, associations between exposure to PM and metabolic syndromes like diabetes mellitus or obesity are now emerging in the literature. Collection of exhaled breath condensate (EBC) is an appealing non-invasive technique to sample pulmonary fluids. This hypothesis-generating study aims to (1) validate an ion chromatography method allowing the robust determination of different metabolism-related molecules (lactate, formate, acetate, propionate, butyrate, pyruvate, nitrite, nitrate) in EBC; (2) apply this method to EBC samples collected from workers exposed to quartz (a known inflammatory particle), to soapstone (a less inflammatory particle than quartz), as well as to controls. A multi-compound standard solution was used to determine the linearity range, detection limit, repeatability and bias from spiked EBC. The biological samples were injected without further treatment into an ion chromatograph with a conductivity detector. RTube <sup>®</sup> were used for field collection of EBC from 11 controls, 55 workers exposed to soapstone and 12 volunteers exposed to quartz dust. The analytical method used proved to be adequate for quantifying eight anions in EBC samples. Its sub-micromolar detection limits and repeatability, combined with a very simple sample preparation, allowed an easy and fast quantification of different glycolysis or nitrosative stress metabolites. Using multivariate discriminant analysis to maximize differences between groups, we observed a different pattern of anions with a higher formate/acetate ratio in the EBC samples for quartz exposed workers compared to the two other groups. We hypothesize that a modification of the metabolic signature could be induced by exposure to inflammatory particles like quartz and might be observed in the EBC via a change in the formate/acetate ratio

Reversible, Opto-Mechanically Induced Spin-Switching in a Nanoribbon-Spiropyran Hybrid Material

It has recently been shown that electronic transport in zigzag graphene nanoribbons becomes spin-polarized upon application of an electric field across the nanoribbon width. However, the electric fields required to experimentally induce this magnetic state are typically large and difficult to apply in practice. Here, using both first-principles density functional theory (DFT) and time-dependent DFT, we show that a new spiropyran-based, mechanochromic polymer noncovalently deposited on a nanoribbon can collectively function as a dual opto-mechanical switch for modulating its own spin-polarization. These calculations demonstrate that upon mechanical stress or photoabsorption, the spiropyran chromophore isomerizes from a closed-configuration ground-state to a zwitterionic excited-state, resulting in a large change in dipole moment that alters the electrostatic environment of the nanoribbon. We show that the electronic spin-distribution in the nanoribbon-spiropyran hybrid material can be reversibly modulated via noninvasive optical and mechanical stimuli without the need for large external electric fields. Our results suggest that the reversible spintronic properties inherent to the nanoribbon-spiropyran material allow the possibility of using this hybrid structure as a resettable, molecular-logic quantum sensor where opto-mechanical stimuli are used as inputs and the spin-polarized current induced in the nanoribbon substrate is the measured output.Comment: Accepted by Nanoscal