Anionic metabolic profiling of urine from antibiotic-treated rats by capillary electrophoresis–mass spectrometry

A recently developed capillary electrophoresis (CE)-negative-ionisation mass spectrometry (MS) method was used to profile anionic metabolites in a microbial-host co-metabolism study. Urine samples from rats receiving antibiotics (penicillin G and streptomycin sulfate) for 0, 4, or 8 days were analysed. A quality control sample was measured repeatedly to monitor the performance of the applied CE-MS method. After peak alignment, relative standard deviations (RSDs) for migration time of five representative compounds were below 0.4 %, whereas RSDs for peak area were 7.9–13.5 %. Using univariate and principal component analysis of obtained urinary metabolic profiles, groups of rats receiving different antibiotic treatment could be distinguished based on 17 discriminatory compounds, of which 15 were downregulated and 2 were upregulated upon treatment. Eleven compounds remained down- or upregulated after discontinuation of the antibiotics administration, whereas a recovery effect was observed for others. Based on accurate mass, nine compounds were putatively identified; these included the microbial-mammalian co-metabolites hippuric acid and indoxyl sulfate. Some discriminatory compounds were also observed by other analytical techniques, but CE-MS uniquely revealed ten metabolites modulated by antibiotic exposure, including aconitic acid and an oxocholic acid. This clearly demonstrates the added value of CE-MS for nontargeted profiling of small anionic metabolites in biological samples.

Are superhumps good measures of the mass ratio for AM CVn systems?

We extend recent work that included the effect of pressure forces to derive the precession rate of eccentric accretion discs in cataclysmic variables to the case of double degenerate systems. We find that the logical scaling of the pressure force in such systems results in predictions of unrealistically high primary masses. Using the prototype AM CVn as a calibrator for the magnitude of the effect, we find that there is no scaling that applies consistently to all the systems in the class. We discuss the reasons for the lack of a superhump period to mass ratio relationship analogous to that known for SU UMa systems and suggest that this is because these secondaries do not have a single valued mass-radius relationship. We highlight the unreliability of mass-ratios derived by applying the SU UMa expression to the AM CVn binaries.

Atmospheric chemistry and physics in the atmosphere of a developed megacity (London): an overview of the REPARTEE experiment and its conclusions

The REgents PARk and Tower Environmental Experiment (REPARTEE) comprised two campaigns in London in October 2006 and October/November 2007. The experiment design involved measurements at a heavily trafficked roadside site, two urban background sites and an elevated site at 160–190 m above ground on the BT Tower, supplemented in the second campaign by Doppler lidar measurements of atmospheric vertical structure. A wide range of measurements of airborne particle physical metrics and chemical composition were made as well as measurements of a considerable range of gas phase species and the fluxes of both particulate and gas phase substances. Significant findings include (a) demonstration of the evaporation of traffic-generated nanoparticles during both horizontal and vertical atmospheric transport; (b) generation of a large base of information on the fluxes of nanoparticles, accumulation mode particles and specific chemical components of the aerosol and a range of gas phase species, as well as the elucidation of key processes and comparison with emissions inventories; (c) quantification of vertical gradients in selected aerosol and trace gas species which has demonstrated the important role of regional transport in influencing concentrations of sulphate, nitrate and secondary organic compounds within the atmosphere of London; (d) generation of new data on the atmospheric structure and turbulence above London, including the estimation of mixed layer depths; (e) provision of new data on trace gas dispersion in the urban atmosphere through the release of purposeful tracers; (f) the determination of spatial differences in aerosol particle size distributions and their interpretation in terms of sources and physico-chemical transformations; (g) studies of the nocturnal oxidation of nitrogen oxides and of the diurnal behaviour of nitrate aerosol in the urban atmosphere, and (h) new information on the chemical composition and source apportionment of particulate matter size fractions in the atmosphere of London derived both from bulk chemical analysis and aerosol mass spectrometry with two instrument types.

The partial oxidation of methane over Pd/Al2O3 catalyst nanoparticles studied in-situ by near ambient-pressure x-ray photoelectron spectroscopy

Near ambient-pressure X-ray photoelectron spectroscopy (NAP-XPS) is used to study the chemical state of methane oxidation catalysts in-situ. Al2O3{supported Pd catalysts are prepared with different particle sizes ranging from 4 nm to 10 nm. These catalysts were exposed to conditions similar to those used in the partial oxidation of methane (POM) to syn-gas and simultaneously monitored by NAP-XPS and mass spectrometry. NAP-XPS data show changes in the oxidation state of the palladium as the temperature in- creases, from metallic Pd0 to PdO, and back to Pd0. Mass spectrometry shows an increase in CO production whilst the Pd is in the oxide phase, and the metal is reduced back under presence of newly formed H2. A particle size effect is observed, such that CH4 conversion starts at lower temperatures with larger sized particles from 6 nm to 10 nm. We find that all nanoparticles begin CH4 conversion at lower temperatures than polycrystalline Pd foil.

Multiprobabilistic prediction in early medical diagnoses

This paper describes the methodology of providing multiprobability predictions for proteomic mass spectrometry data. The methodology is based on a newly developed machine learning framework called Venn machines. Is allows to output a valid probability interval. The methodology is designed for mass spectrometry data. For demonstrative purposes, we applied this methodology to MALDI-TOF data sets in order to predict the diagnosis of heart disease and early diagnoses of ovarian cancer and breast cancer. The experiments showed that probability intervals are narrow, that is, the output of the multiprobability predictor is similar to a single probability distribution. In addition, probability intervals produced for heart disease and ovarian cancer data were more accurate than the output of corresponding probability predictor. When Venn machines were forced to make point predictions, the accuracy of such predictions is for the most data better than the accuracy of the underlying algorithm that outputs single probability distribution of a label. Application of this methodology to MALDI-TOF data sets empirically demonstrates the validity. The accuracy of the proposed method on ovarian cancer data rises from 66.7 % 11 months in advance of the moment of diagnosis to up to 90.2 % at the moment of diagnosis. The same approach has been applied to heart disease data without time dependency, although the achieved accuracy was not as high (up to 69.9 %). The methodology allowed us to confirm mass spectrometry peaks previously identified as carrying statistically significant information for discrimination between controls and cases.

Long-range ozone transport and its impact on respiratory and cardiovascular health in the north of Portugal

Ozone dynamics depend on meteorological characteristics such as wind, radiation, sunshine, air temperature and precipitation. The aim of this study was to determine ozone trajectories along the northern coast of Portugal during the summer months of 2005, when there was a spate of forest fires in the region, evaluating their impact on respiratory and cardiovascular health in the greater metropolitan area of Porto. We investigated the following diseases, as coded in the ninth revision of the International Classification of Diseases: hypertensive disease (codes 401-405); ischemic heart disease (codes 410-414); other cardiac diseases, including heart failure (codes 426-428); chronic obstructive pulmonary disease and allied conditions, including bronchitis and asthma (codes 490-496); and pneumoconiosis and other lung diseases due to external agents (codes 500-507). We evaluated ozone data from air quality monitoring stations in the study area, together with data collected through HYbrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model analysis of air mass circulation and synoptic-scale zonal wind from National Centers for Environmental Prediction data. High ozone levels in rural areas were attributed to the dispersion of pollutants induced by local circulation, as well as by mesoscale and synoptic scale processes. The fires of 2005 increased the levels of pollutants resulting from the direct emission of gases and particles into the atmosphere, especially when there were incoming frontal systems. For the meteorological case studies analyzed, peaks in ozone concentration were positively associated with higher rates of hospital admissions for cardiovascular diseases, although there were no significant associations between ozone peaks and admissions for respiratory diseases.

Morphometrical, biochemical and molecular tools for assessing biodiversity. An example in Plebeia remota (Holmberg, 1903) (Apidae, Meliponini)

We see today many efforts to quantify biodiversity in different biomes. It is very important then to develop and to apply other methodologies that allow us to assess biodiversity. Here we present an example of application of three tools with this goal. We analyzed two populations of Plebeia remota from two distinct biomes that already showed several differences in morphology and behavior. Based on these differences, it has been suggested that the populations of Cunha and Prudentopolis do not represent a single species. In order to verify the existence or absence of gene flow between these two groups, we characterized the patterns of mtDNA through RFLP, the patterns of wing venation through geometric morphometry, and the cuticular hydrocarbons through gas chromatography-mass spectrometry. We used bees collected in these two locations and also from colonies which have being kept for around 9 years at Sao Paulo University. We found six different haplotypes in these specimens, of which three of them occurred exclusively in the population of Cunha and three only in the Prudentopolis population. The fact that the populations do not share haplotypes suggests no maternal gene flow between them. The two populations were differentiated by the pattern of the wing veins. They also had different mixtures of cuticle hydrocarbons. Furthermore it was shown that the colonies kept at the university did not hybridize. These two groups may constitute different species. We also show here the importance of using other methodologies than traditional taxonomy to assess and understand biodiversity, especially in bees.

Role of glutaredoxin 2 and cytosolic thioredoxins in cysteinyl-based redox modification of the 20S proteasome

The yeast 20S proteasome is subject to sulfhydryl redox alterations, such as the oxidation of cysteine residues (Cys-SH) into cysteine sulfenic acid (Cys-SOH), followed by S-glutathionylation (Cys-S-SG). Proteasome S-glutathionylation promotes partial loss of chymotrypsin-like activity and post-acidic cleavage without alteration of the trypsin-like proteasomal activity. Here we show that the 20S proteasome purified from stationary-phase cells was natively S-glutathionylated. Moreover, recombinant glutaredoxin 2 removes glutathione from natively or in vitro S-glutathionylated 20S proteasome, allowing the recovery of chymotrypsin-like activity and post-acidic cleavage. Glutaredoxin 2 deglutathionylase activity was dependent on its entry into the core particle, as demonstrated by stimulating S-glutathionylated proteasome opening. Under these conditions, deglutathionylation of the 20S proteasome and glutaredoxin 2 degradation were increased when compared to non-stimulated samples. Glutaredoxin 2 fragmentation by the 20S proteasome was evaluated by SDS-PAGE and mass spectrometry, and S-glutathionylation was evaluated by either western blot analyses with anti-glutathione IgG or by spectrophotometry with the thiol reactant 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole. It was also observed in vivo that glutaredoxin 2 was ubiquitinated in cellular extracts of yeast cells grown in glucose-containing medium. Other cytoplasmic oxido-reductases, namely thioredoxins 1 and 2, were also active in 20S proteasome deglutathionylation by a similar mechanism. These results indicate for the first time that 20S proteasome cysteinyl redox modification is a regulated mechanism coupled to enzymatic deglutathionylase activity.

Mass spectrometric investigation of the DNA-binding properties of an anthracycline with two trisaccharide chains

Cosmomycin D (CosD) is an anthracycline that has two trisaccharide chains linked to its ring system. Gel electrophoresis showed that CosD formed stable complexes with plasmid DNA under conditions where daunorubicin (Dn) and doxorubicin (Dx) dissociated to some extent during the experiments. The footprint and stability of CosD complexed with 10- and 16 trier DNA was investigated using several applications of electrospray ionisation mass spectrometry (ESI-MS). ESI-MS binding profiles showed that fewer CosD molecules bound to the sequences than Dn or Dx. In agreement with this, ESI-MS analysis of nuclease digestion products of the complexes showed that CosD protected the DNA to a greater extent than Dn or Dx. In tandem MS experiments, all CosD-DNA complexes were more stable than Dn- and Dx-DNA complexes. These results Support that CosD binds more tightly to DNA and exerts a larger footprint than ESI-MS investigations of the binding properties of CosD Could be carried out rapidly and using only small amounts of sample. (C) 2008 Elsevier Inc. All rights reserved.

Within-canopy sesquiterpene ozonolysis in Amazonia

Through rapid reactions with ozone, which can initiate the formation of secondary organic aerosols, the emission of sesquiterpenes from vegetation in Amazonia may have significant impacts on tropospheric chemistry and climate. Little is known, however, about sesquiterpene emissions, transport, and chemistry within plant canopies owing to analytical difficulties stemming from very low ambient concentrations, high reactivities, and sampling losses. Here, we present ambient sesquiterpene concentration measurements obtained during the 2010 dry season within and above a primary tropical forest canopy in Amazonia. We show that by peaking at night instead of during the day, and near the ground instead of within the canopy, sesquiterpene concentrations followed a pattern different from that of monoterpenes, suggesting that unlike monoterpene emissions, which are mainly light dependent, sesquiterpene emissions are mainly temperature dependent. In addition, we observed that sesquiterpene concentrations were inversely related with ozone (with respect to time of day and vertical concentration), suggesting that ambient concentrations are highly sensitive to ozone. These conclusions are supported by experiments in a tropical rain forest mesocosm, where little atmospheric oxidation occurs and sesquiterpene and monoterpene concentrations followed similar diurnal patterns. We estimate that the daytime dry season ozone flux of -0.6 to -1.5 nmol m(-2) s(-1) due to in-canopy sesquiterpene reactivity could account for 7%-28% of the net ozone flux. Our study provides experimental evidence that a large fraction of total plant sesquiterpene emissions (46%-61% by mass) undergo within-canopy ozonolysis, which may benefit plants by reducing ozone uptake and its associated oxidative damage.

Analysis and risk estimates to workers of Brazilian granitic industries and sandblasters exposed to respirable crystalline silica and natural radionuclides

Occupational exposure to respirable crystalline silica and to radiation emitted by natural radionuclides present both in rocks and sands was studied in the Brazilian extractive process and granite product manufacture. Respirable airborne dust samples were collected in working environments, where workers perform different tasks with distinct commercial granites types, and also in places where sandblasters work with sands from different origins. The free crystalline silica contents were determined using X-ray diffraction of the respirable particulate fraction of each sample. Dust samples from granite cutting and sandblasting ambient had the natural radionuclides concentrations measured by gamma spectrometry. Dust concentrations in the workplaces were quite variable, reaching values up to 10 times higher than the respirable particle mass threshold limit value (TLV) set by the American Conference for Governmental Industrial Hygienists of 3 mg m(-3). Also the free crystalline silica concentrations were high. reaching values up to 48 times the TLV of 0.025 mg m(-3). Additionally, our results suggest that the risk of radiation-induced cancer in the granite or marble industries is negligible. However, the combined exposure to dust, gamma radiation, and radon daughter products could result in the enhancement of lung cancer risks associated to sandblasting activities. (C) 2010 Elsevier Ltd. All rights reserved.

Purification, and Biochemical and Biophysical Characterization of Cellobiohydrolase I from Trichoderma harzianum IOC 3844

Because of its elevated cellulolytic activity, the filamentous fungus Trichoderma harzianum has a considerable potential in biomass hydrolysis applications. Trichoderma harzianum cellobiohydrolase I (ThCBHI), an exoglucanase, is an important enzyme in the process of cellulose degradation. Here, we report an easy single-step ion-exchange chromatographic method for purification of ThCBHI and its initial biophysical and biochemical characterization. The ThCBHI produced by induction with microcrystalline cellulose under submerged fermentation was purified on DEAE-Sephadex A-50 media and its identity was confirmed by mass spectrometry. The ThCBHI biochemical characterization showed that the protein has a molecular mass of 66 kDa and pi of 5.23. As confirmed by small-angle X-ray scattering (SAXS), both full-length ThCBHI and its catalytic core domain (CCD) obtained by digestion with papain are monomeric in solution. Secondary structure analysis of ThCBHI by circular dichroism revealed alpha-helices and beta-strands contents in the 28% and 38% range, respectively. The intrinsic fluorescence emission maximum of 337 nm was accounted for as different degrees of exposure of ThCBHI tryptophan residues to water. Moreover, ThCBHI displayed maximum activity at pH 5.0 and temperature of 50 degrees C with specific activities against Avicel and p-nitrophenyl-beta-D-cellobioside of 1.25 U/mg and 1.53 U/mg, respectively.

U-Pb-Hf-trace element systematics and geochronology of zircon from a granulite-facies metamorphosed mafic-ultramafic layered complex in Central Brazil

Zircon recrystallization is a common process during high-grade metamorphism and promotes partial or complete resetting of the original isotopic and chemical characteristics of the mineral and thus complicates U-Pb geochronological interpretation. In Central Brazil, this complexity may be illustrated by three composite mafic-ultramafic intrusions metamorphosed under amphibolite-to-granulite conditions. Their ages of emplacement and metamorphic ages have been a matter of controversy for the last thirty years. The Serra da Malacacheta and Barro Alto complexes make up the southernmost of these layered bodies and four samples from distinct rock types were investigated in order to verify the consequences of metamorphic alteration of zircon for U-Pb dating. Cathodoluminescent imaging reveals internal features which are typical of concomitant dissolution-reprecipitation processes, such as convolute zoning and inward-moving recrystallization fronts, even in samples in which partially preserved igneous textures are observed. Due to this extensive alteration, LA-ICPMS U-Pb isotopic analysis yielded inconclusive data. However, in situ Hf isotopic and trace-element analyses help to clarify the real meaning of the geochronological data. Low Lu/Hf (<0.004) and homogeneous (176)Hf/(177)Hf(t) values imply that the zircon populations within individual samples have crystallized in a single episode, despite the observed variations in age values. Trace element signatures of zircon grains from garnet-bearing samples reveal that they were unreactive to the development of the peak metamorphism mineral assemblage and, thus, the main chemical feature in such grains is attributed to a coupled dissolution-reprecipitation process. However, in the Cafelandia amphibolite an additional alteration process is identified, probably related to the influx of late-stage fluids. Combined isotopic and geochemical investigation on zircon grains allowed the distinction of two magmatic events. The first corresponds to the crystallization of the Serra da Malacacheta Complex and characterizes a juvenile magmatism at similar to 1.3 Ga. The younger episode, recognized in the Barro Alto Complex, is dated at ca. 800 Ma and is represented by mafic and ultramafic rocks showing intense contamination with continental crust, implying that the emplacement took place, most likely, in a continental back-arc setting. Altered zircon domains as well as titanite grains date the metamorphic event at ca. 760-750 Ma. (C) 2011 Elsevier B.V. All rights reserved.

Dating coeval mafic magmatism and ultrahigh temperature metamorphism in the Anapolis-Itaucu Complex, Central Brazil

Dating granulites has always been of great interest because they represent one of the most extreme settings of an orogen. Owing to the resilience of zircon, even in such severe environments, the link between P-T conditions and geological time is possible. However, a challenge to geochronologists is to define whether the growth of new zircon is related to pre- or post-P-T peak conditions and which processes might affect the (re) crystallization. In this context, the Anapolis-Itaucu Complex, a high-grade complex in central Brazil with ultrahigh temperature (UHT) granulites, may provide valuable information within this topic. The Anapolis-Itaucu Complex (AIC) includes ortho- and paragranulites, locally presenting UHT mineral assemblages, with igneous zircon ages varying between 760 and 650 Ma and metamorphic overgrowths dated at around 650-640 Ma. Also common in the Anapolis-Itaucu Complex are layered mafic-ultramafic complexes metamorphosed under high-grade conditions. This article presents the first geological and geochronological constraints of three of these layered complexes within the AIC, the Damolandia, Taquaral and Goianira-Trindade complexes. U-Pb (LA-MC-ICPMS, SHRIMP and ID-TIMS) zircon analyses reveal a spread of concordant ages spanning within an age interval of similar to 80 Ma with an ""upper"" intercept age of similar to 670 Ma. Under cathodoluminescence imaging, these crystals show partially preserved primary sector zoning, as well as internal textures typical of alteration during high-grade metamorphism, such as inward-moving boundaries. Zircon grains reveal homogeneous initial (176)Hf/(177)Hf values in distinct crystal-scale domains in all samples. Moreover. Hf isotopic ratios show correlation neither with U-Pb ages nor with Th/U ratios, suggesting that zircon grains crystallized during a single growth event. It is suggested, therefore, that the observed spread of concordant U-Pb ages may be related to a memory effect due to coupled dissolution-reprecipitation process during high grade metamorphism. Therefore, understanding the emplacement and metamorphism of this voluminous mafic magmatism is crucial as it may represent an additional heat source for the development of the ultrahigh temperature paragenesis recorded in the paragranulites. (C) 2010 Elsevier B.V. All rights reserved.

A ditryptophan cross-link is responsible for the covalent dimerization of human superoxide dismutase 1 during its bicarbonate-dependent peroxidase activity

Unlike intermolecular disulfide bonds, other protein cross-links arising from oxidative modifications cannot be reversed and are presumably more toxic to cells because they may accumulate and induce protein aggregation. However, most of these irreversible protein cross-links remain poorly characterized. For instance, the antioxidant enzyme human superoxide dismutase 1 (hSod1) has been reported to undergo non-disulfide covalent dimerization and further oligomerization during its bicarbonate-dependent peroxidase activity. The dimerization was shown to be dependent on the oxidation of the single, solvent-exposed TrP(32) residue of hSod1, but the covalent dimer was not isolated nor was its structure determined. In this work, the hSod1 covalent dimer was isolated, digested with trypsin in H(2)O and H(2)(18)O, and analyzed by UV-Vis spectroscopy and mass spectrometry (MS). The results demonstrate that the covalent dimer consists of two hSod1 subunits cross-linked by a ditryptophan, which contains a bond between C3 and N1 of the respective Trp(32) residues. We further demonstrate that the cross-link cleaves under usual MS/MS conditions leading to apparently unmodified Trp(32), partially hinders proteolysis, and provides a mechanism to explain the formation of hSod1 covalent trimers and tetramers. This characterization of the covalent hSod1 dimer identifies a novel oxidative modification of protein Trp residues and provides clues for studying its occurrence in vivo. (C) 2010 Elsevier Inc. All rights reserved.