Oxidation of proteins: Basic principles and perspectives for blood proteomics.

Protein oxidation mechanisms result in a wide array of modifications, from backbone cleavage or protein crosslinking to more subtle modifications such as side chain oxidations. Protein oxidation occurs as part of normal regulatory processes, as a defence mechanism against oxidative stress, or as a deleterious processes when antioxidant defences are overcome. Because blood is continually exposed to reactive oxygen and nitrogen species, blood proteomics should inherently adopt redox proteomic strategies. In this review, we recall the biochemical basis of protein oxidation, review the proteomic methodologies applied to analyse redox modifications, and highlight some physiological and in vitro responses to oxidative stress of various blood components.

Practical considerations for improving the productivity of mass spectrometry-based proteomics.

Mass spectrometry (MS) is currently the most sensitive and selective analytical technique for routine peptide and protein structure analysis. Top-down proteomics is based on tandem mass spectrometry (MS/ MS) of intact proteins, where multiply charged precursor ions are fragmented in the gas phase, typically by electron transfer or electron capture dissociation, to yield sequence-specific fragment ions. This approach is primarily used for the study of protein isoforms, including localization of post-translational modifications and identification of splice variants. Bottom-up proteomics is utilized for routine high-throughput protein identification and quantitation from complex biological samples. The proteins are first enzymatically digested into small (usually less than ca. 3 kDa) peptides, these are identified by MS or MS/MS, usually employing collisional activation techniques. To overcome the limitations of these approaches while combining their benefits, middle-down proteomics has recently emerged. Here, the proteins are digested into long (3-15 kDa) peptides via restricted proteolysis followed by the MS/MS analysis of the obtained digest. With advancements of high-resolution MS and allied techniques, routine implementation of the middle-down approach has been made possible. Herein, we present the liquid chromatography (LC)-MS/MS-based experimental design of our middle-down proteomic workflow coupled with post-LC supercharging.

Low-energy electron collisions with glycine

We report cross sections for elastic electron scattering by gas phase glycine (neutral form), obtained with the Schwinger multichannel method. The present results are the first obtained with a new implementation that combines parallelization with OpenMP directives and pseudopotentials. The position of the well known pi* shape resonance ranged from 2.3 eV to 2.8 eV depending on the polarization model and conformer. For the most stable isomer, the present result (2.4 eV) is in fair agreement with electron transmission spectroscopy assignments (1.93 +/- 0.05 eV) and available calculations. Our results also point out a shape resonance around 9.5 eV in the A' symmetry that would be weakly coupled to vibrations of the hydroxyl group. Since electron attachment to a broad and lower lying sigma* orbital located on the OH bond has been suggested the underlying mechanism leading to dissociative electron attachment at low energies, we sought for a shape resonance around similar to 4 eV. Though we obtained cross sections with the target molecule at the equilibrium geometry and with stretched OH bond lengths, least-squares fits to the calculated eigenphase sums did not point out signatures of this anion state (though, in principle, it could be hidden in the large background). The low energy (similar to 1 eV) integral cross section strongly scales as the bond length is stretched, and this could indicate a virtual state pole, since dipole supported bound states are not expected at the geometries addressed here. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3687345]

Electron Interactions with Disulfide Bridges

Because of its electronic properties, sulfur plays a major role in a variety of metabolic processes and, more in general, in the chemistry of life. In particular, S-S bridges between cysteines are present in the amino acid backbone of proteins. Protein disulfur radical anions may decay following different paths through competing intra and intermolecular routes, including bond cleavage, disproportionation, protein-protein cross linking, and electron transfer. Indeed, mass spectrometry ECD (electron capture dissociation massspectroscopy) studies have shown that capture of low-energy (<0.2 eV) electrons by multiply protonated proteins is followed by dissociation of S-S bonds holding two peptide chains together. In view of the importance of organic sulfur chemistry, we report on electron interactions with disulphide bridges. To study these interactions we used as prototypes the molecules dimethyl sulfide [(CH3)2S] and dimethyl disulfide [(H3C)S2(CH3)]. We seek to better understand the electron-induced cleavage of the disulfide bond. To explore dissociative processes we performed electron scattering calculations with the Schwinger Multichannel Method with pseudopotentials (SMCPP), recently parallelized with OpenMP directives and optimized with subroutines for linear algebra (BLAS) and LAPACK routines. Elastic cross sections obtained for different S-S bond lengths indicate stabilization of the anion formed by electron attachment to a σ*SS antibonding orbital, such that dissociation would be expected.

Automated de novo sequencing of proteins by tandem high-resolution mass spectrometry

A de novo sequencing program for proteins is described that uses tandem MS data from electron capture dissociation and collisionally activated dissociation of electrosprayed protein ions. Computer automation is used to convert the fragment ion mass values derived from these spectra into the most probable protein sequence, without distinguishing Leu/Ile. Minimum human input is necessary for the data reduction and interpretation. No extra chemistry is necessary to distinguish N- and C-terminal fragments in the mass spectra, as this is determined from the electron capture dissociation data. With parts-per-million mass accuracy (now available by using higher field Fourier transform MS instruments), the complete sequences of ubiquitin (8.6 kDa) and melittin (2.8 kDa) were predicted correctly by the program. The data available also provided 91% of the cytochrome c (12.4 kDa) sequence (essentially complete except for the tandem MS-resistant region K13–V20 that contains the cyclic heme). Uncorrected mass values from a 6-T instrument still gave 86% of the sequence for ubiquitin, except for distinguishing Gln/Lys. Extensive sequencing of larger proteins should be possible by applying the algorithm to pieces of ≈10-kDa size, such as products of limited proteolysis.

Megalencephalic Leukoencephalopathy With Subcortical Cysts (mlc) - A Case With Clinical And Magnetic Resonance Imaging (mri) Dissociation.

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Evaluation of the maxillary premolar roots dissociation using radiographic holders with conventional and digital radiography

This in vivo study evaluated the dissociation quality of maxillary premolar roots combining variations of vertical and horizontal angulations by using X-ray holders (Rinn -XCP), and made a comparison between two types of intraoral radiography systems - conventional film (Kodak Insight, Rochester, USA) and digital radiography (Kodak RVG 6100, Kodak, Rochester, USA). The study sample was comprised of 20 patients with a total of 20 maxillary premolars that were radiographed, using the paralleling angle technique (GP), with a 20º variation of the horizontal angle (GM) and 25º variation of the horizontal angle combined with 15º vertical angle (GMV). Each image was independently analyzed by two experienced examiners. These examiners assigned a score to the diagnostic capability of root dissociation and the measurement of the distance between the apexes. Statistical data was derived using the Wilcoxon Signed Rank test, Friedman and T test. The means of the measured distances between buccal and lingual root apexes were greater for the GMV, which ranged from 2.3 mm to 3.3 mm. A statistically significant difference was found between GM and GMV when compared to GP with p < 0.01. An established best diagnostic dissociation roots image was found in the GMV. These results support the use of the anterior X-ray holders which offer a better combined deviation (GMV) to dissociate maxillary premolar roots in both radiography systems.

Capture fishery in northern Todos os Santos Bay, tropical southwestern Atlantic, Brazil

Information on marine and estuarine capture fishery activity in northern Todos os Santos Bay, northeastern Brazil, based on daily data collected between September 2003 and June 2005 is presented. Small-scale artisanal fishery in this area includes the use of traditional vessels both nonmotorized and motorized for locomotion, being carried out mainly by canoe or on foot, and involves many different kinds of gear, including gillnet, hook and line, seine nets, and traps. A total of 113 taxa were grouped into 77 resources, including 88 fish, 10 crustaceans, and 15 mollusks. Data on nominal catches of fish, crustaceans and mollusks are presented by month and location. A total of 345.2 tonnes of fishery resources were produced (285.4 tonnes of fish, 39.2 tonnes of fresh invertebrates, and 20.6 tonnes of processed invertebrates). Temporal variation in the fish catch was associated with the life cycle of the species or with the hydrographic conditions. The first-sale value of this catch amounted to around US$ 615,000.00, fishes representing 71.3% of it. A table of the average price of each fishery resource is presented. The results produced in this study may be considered a reference for future monitoring programs of fishery resources in the area.

Mn, Cu, and Zn abundances in barium stars and their correlations with neutron capture elements

Barium stars are optimal sites for studying the correlations between the neutron-capture elements and other species that may be depleted or enhanced, because they act as neutron seeds or poisons during the operation of the s-process. These data are necessary to help constrain the modeling of the neutron-capture paths and explain the s-process abundance curve of the solar system. Chemical abundances for a large number of barium stars with different degrees of s-process excesses, masses, metallicities, and evolutionary states are a crucial step towards this goal. We present abundances of Mn, Cu, Zn, and various light and heavy elements for a sample of barium and normal giant stars, and present correlations between abundances contributed to different degrees by the weak-s, mains, and r-processes of neutron capture, between Fe-peak elements and heavy elements. Data from the literature are also considered in order to better study the abundance pattern of peculiar stars. The stellar spectra were observed with FEROS/ESO. The stellar atmospheric parameters of the eight barium giant stars and six normal giants that we analyzed lie in the range 4300 < T(eff)/K < 5300, -0.7 < [Fe/H] <= 0.12 and 1.5 <= log g < 2.9. Carbon and nitrogen abundances were derived by spectral synthesis of the molecular bands of C(2), CH, and CN. For all other elements we used the atomic lines to perform the spectral synthesis. A very large scatter was found mainly for the Mn abundances when data from the literature were considered. We found that [Zn/Fe] correlates well with the heavy element excesses, its abundance clearly increasing as the heavy element excesses increase, a trend not shown by the [Cu/Fe] and [Mn/Fe] ratios. Also, the ratios involving Mn, Cu, and Zn and heavy elements usually show an increasing trend toward higher metallicities. Our results suggest that a larger fraction of the Zn synthesis than of Cu is owed to massive stars, and that the contribution of the main-s process to the synthesis of both elements is small. We also conclude that Mn is mostly synthesized by SN Ia, and that a non-negligible fraction of the synthesis of Mn, Cu, and Zn is owed to the weak s-process.

Comparative study of the adsorption and dissociation of vinylacetic acid and acrylic acid on silicon (001)

In this work, we employ the state of the art pseudopotential method, within a generalized gradient approximation to the density functional theory, to investigate the adsorption process of acrylic acid (AAc) and vinylacetic acid (VAA) on the silicon surface. Our total energy calculations support the proposed experimental process, as it indicates that the chemisorption of the molecule is as follows: The gas phase VAA (AAc) adsorbs molecularly to the electrophilic surface Si atom and then dissociates into H(2)C = CH - COO and H, bonded to the electrophilic and nucleophilic surface silicon dimer atoms, respectively. The activation energy for both processes correspond to thermal activations that are smaller than the usual growth temperature. In addition, the electronic structure, calculated vibrational modes, and theoretical scanning tunneling microscopy images are discussed, with a view to contribute to further experimental investigations.

A comparative solid state (13)C NMR and thermal study of CO(2) capture by amidines PMDBD and DBN

The present work shows study of the CO(2) capture by amidines DBN and PMDBD using (13)C solid-state NMR and thermal techniques. The solid state (13)C NMR analyses demonstrate the formation of a single PMDBD-CO(2) product which was assigned to stable bicarbonate. In the case of DBN, it is shown that two DBN-CO(2) products are formed, which are suggested to be stable bicarbonate and unstable carbamate. The role of water in the DBN-CO(2) capture as well as the stability of the products to environmental moisture was also investigated. The results suggest that the carbamate formation is favored in dry DBN, but in the presence of water it decompose to form bicarbonate. Thermal analysis shows a good gravimetric CO(2) absorption of DBN. Release of CO(2) was found to be almost quantitative from the PMDBDH(+) bicarbonate about 110 degrees C.

Equivalent Carbon Dioxide Capture and Storage Processes in Offshore Petroleum Production Facilities

The present study approaches the economic and technical evaluation of equivalent carbon dioxide (CO(2) eqv.) capture and storage processes, considered in a proposal case compared to a base case. The base case considers an offshore petroleum production facility, with high CO(2) content (4 vol%) in the composition of the produced gas and both CO(2) and natural gas emissions to the atmosphere, called CO(2) eqv. emissions. The results obtained with this study, by using a Hysys process simulator, showed a CO(2) emission reduction of 65% comparing the proposal case in relation to the base case.

Dissociation of deprotonated microcystin variants by collision-induced dissociation following electrospray ionization

Microcystins (MC) are a family of hepatotoxic cyclic heptapeptides produced by a number of different cyanobacterial species. Considering the recent advances in the characterization of deprotonated peptides by mass spectrometry, the fragmentation behavior of four structurally related microcystin compounds was investigated using collision-induced dissociation (CID) experiments on an orbitrap mass spectrometer. It is demonstrated in this study that significant structural information can be obtained from the CID spectra of deprotonated microcystins. A predominant ring-opening reaction at the isoMeAsp residue, as well as two major complementary fragmentation pathways, was observed, reducing the complexity of the product ion spectra in comparison with spectra observed from protonated species. This proposed fragmentation behavior was applied to characterize [Leu(1)]MC-LR from a cyanobacterial cell extract. In conclusion, CID spectra of microcystins in the negative ion mode provide rich structurally informative mass spectra which greatly enhance confidence in structural assignments, in particular when combined with complementary positive ion CID spectra. Copyright (C) 2011 John Wiley & Sons, Ltd.

Dissociation between skin conductance orienting and secondary task reaction time: Time course with a visual discrimination task

A dissociation between two putative measures of resource allocation skin conductance responding, and secondary task reaction time (RT), has been observed during auditory discrimination tasks. Four experiments investigated the time course of the dissociation effect with a visual discrimination task. participants were presented with circles and ellipses and instructed to count the number of longer-than-usual presentations of one shape (task-relevant) and to ignore presentations of the other shape (task-irrelevant). Concurrent with this task, participants made a speeded motor response to an auditory probe. Experiment 1 showed that skin conductance responses were larger during task-relevant stimuli than during task-irrelevant stimuli, whereas RT to probes presented at 150 ms following shape onset was slower during task-irrelevant stimuli. Experiments 2 to 4 found slower RT during task-irrelevant stimuli at probes presented at 300 ms before shape onset until 150 ms following shape onset. At probes presented 3,000 and 4,000 ms following shape onset probe RT was slower during task-relevant stimuli. The similarities between the observed time course and the so-called psychological refractory period (PRF) effect are discussed.

Prey capture and accommodation in the sandlance, Limnichthyes fasciatus (Creediidae; Teleostei)

The eyes of the sandlance, Limnichthyes fasciatus (Creediidae. Teleostei) move independently and possess a refractive cornea, a convexiclivate fovea and a non-spherical lens giving rise to a wide separation of the nodal point from the axis of rotation of the eye much like that of a chameleon. To investigate this apparent convergence of the visual optics in these phylogenetically disparate species, we examine feeding behaviour and accommodation in the sandlance with special reference to the possibility that sandlances use accommodation as a depth cue to judge strike length. Frame-by-frame analysis of over 2000 strikes show a 100% success rate. Explosive strikes are completed in 50 ms over prey distances of four body lengths. Close-up video confirms that successful strikes can be initiated monocularly (both normally and after monocular occlusion) showing that binocular cues are not necessary to judge the length of a strike. Additional means of judging prey distance may also be derived from parallax information generated by rotation of the eye as suggested for chameleons. Using photorefraction on anaesthetised sandlances, accommodative changes were induced with acetylcholine and found to range between 120 D and 180 D at a speed of 600-720 D s(-1). The large range of accommodation (25% of the total power) is also thought to be mediated by corneal accommodation where the contraction of a unique cornealis muscle acts to change the corneal curvatures.