Site-directed mutagenesis and structural modeling of Coq10p indicate the presence of a tunnel for coenzyme Q6 binding

Coq10p is a protein required for coenzyme Q function, but its specific role is still unknown. It is a member of the START domain superfamily that contains a hydrophobic tunnel implicated in the binding of lipophilic molecules. We used site-directed mutagenesis, statistical coupling analysis and molecular modeling to probe structural determinants in the Coq10p putative tunnel. Four point mutations were generated (coq10-K50E, coq10-L96S, coq10-E105K and coq10-K162D) and their biochemical properties analysed, as well as structural consequences. Our results show that all mutations impaired Coq10p function and together with molecular modeling indicate an important role for the Coq10p putative tunnel. (C) 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Aerosol properties, in-canopy gradients, turbulent fluxes and VOC concentrations at a pristine forest site in Amazonia

Aerosol physical and chemical properties were measured in a forest site in central Amazonia (Cuieiras reservation, 2.61S; 60.21W) during the dry season of 2004 (Aug-Oct). Aerosol light scattering and absorption, mass concentration, elemental composition and size distributions were measured at three tower levels (Ground: 2 m; Canopy: 28 m, and Top: 40 m). For the first time, simultaneous eddy covariance fluxes of fine mode particles and volatile organic compounds (VOC) were measured above the Amazonian forest canopy. Aerosol fluxes were measured by eddy covariance using a Condensation Particle Counter (CPC) and a sonic anemometer. VOC fluxes were measured by disjunct eddy covariance using a Proton Transfer Reaction Mass Spectrometer (PTR-MS). At nighttime, a strong vertical gradient of phosphorus and potassium in the aerosol coarse mode was observed, with higher concentrations at Ground level. This suggests a source of primary biogenic particles below the canopy. Equivalent black carbon measurements indicate the presence of light-absorbing aerosols from biogenic origin. Aerosol number size distributions typically consisted of superimposed Aitken (76 nm) and accumulation modes (144 nm), without clear events of new particle formation. Isoprene and monoterpene fluxes reached respectively 7.4 and 0.82 mg m(-2) s(-1) around noon. An average fine particle flux of 0.05 +/- 0.10 10(6) m(-2) s(-1) was calculated, denoting an equilibrium between emission and deposition fluxes of fine mode particles at daytime. No significant correlations were found between VOC and fine mode aerosol concentrations or fluxes. (C) 2009 Elsevier Ltd. All rights reserved.

Aerosol inorganic composition at a tropical site: Discrepancies between filter-based sampling and a semi-continuous method

The concentrations of the water-soluble inorganic aerosol species, ammonium (NH4+), nitrate (NO3-), chloride (Cl-), and sulfate (SO42-), were measured from September to November 2002 at a pasture site in the Amazon Basin (Rondnia, Brazil) (LBA-SMOCC). Measurements were conducted using a semi-continuous technique (Wet-annular denuder/Steam-Jet Aerosol Collector: WAD/SJAC) and three integrating filter-based methods, namely (1) a denuder-filter pack (DFP: Teflon and impregnated Whatman filters), (2) a stacked-filter unit (SFU: polycarbonate filters), and (3) a High Volume dichotomous sampler (HiVol: quartz fiber filters). Measurements covered the late dry season (biomass burning), a transition period, and the onset of the wet season (clean conditions). Analyses of the particles collected on filters were performed using ion chromatography (IC) and Particle-Induced X-ray Emission spectrometry (PIXE). Season-dependent discrepancies were observed between the WAD/SJAC system and the filter-based samplers. During the dry season, when PM2.5 (D-p <= 2.5 mu m) concentrations were similar to 100 mu g m(-3), aerosol NH4+ and SO42- measured by the filter-based samplers were on average two times higher than those determined by the WAD/SJAC. Concentrations of aerosol NO3- and Cl- measured with the HiVol during daytime, and with the DFP during day- and nighttime also exceeded those of the WAD/SJAC by a factor of two. In contrast, aerosol NO3- and Cl- measured with the SFU during the dry season were nearly two times lower than those measured by the WAD/SJAC. These differences declined markedly during the transition period and towards the cleaner conditions during the onset of the wet season (PM2.5 similar to 5 mu g m(-3)); when filter-based samplers measured on average 40-90% less than the WAD/SJAC. The differences were not due to consistent systematic biases of the analytical techniques, but were apparently a result of prevailing environmental conditions and different sampling procedures. For the transition period and wet season, the significance of our results is reduced by a low number of data points. We argue that the observed differences are mainly attributable to (a) positive and negative filter sampling artifacts, (b) presence of organic compounds and organosulfates on filter substrates, and (c) a SJAC sampling efficiency of less than 100%.

Electric field gradients in (111)In-doped (Hf/Zr)(3)Al(2) and (Hf/Zr)(4)Al(3) mixed compounds: ab initio calculations, perturbed angular correlation measurements and site preference

The quadrupolar hyperfine interactions of in-diffused (111)In -> (111)Cd probes in polycrystalline isostructural Zr(4)Al(3) and Hf(4)Al(3) samples containing small admixtures of the phases (Zr/Hf)(3)Al(2) were investigated. A strong preference of (111)In solutes for the contaminant (Zr/Hf)(3)Al(2) minority phases was observed. Detailed calculations of the electric field gradient (EFG) at the Cd nucleus using the full-potential augmented plane wave + local orbital formalism allowed us to assign the observed EFG fractions to the various lattice sites in the (Zr/Hf)(3)Al(2) compounds and to understand the preferential site occupation of the minority phases by the (111)In atoms. The effects of the size of the supercell and relaxation around the oversized In and Cd probe atoms were investigated in detail.

The n-site approximation for the triplet-creation model

The nonequilibrium phase transition of the one-dimensional triplet-creation model is investigated using the n-site approximation scheme. We find that the phase diagram in the space of parameters (gamma, D), where gamma is the particle decay probability and D is the diffusion probability, exhibits a tricritical point for n >= 4. However, the fitting of the tricritical coordinates (gamma(t), D(t)) using data for 4 <= n <= 13 predicts that gamma(t) becomes negative for n >= 26, indicating thus that the phase transition is always continuous in the limit n -> infinity. However, the large discrepancies between the critical parameters obtained in this limit and those obtained by Monte Carlo simulations, as well as a puzzling non-monotonic dependence of these parameters on the order of the approximation n, argue for the inadequacy of the n-site approximation to study the triplet-creation model for computationally feasible values of n.

New insights on the Lewis acidity of diorganolead(IV) compounds: Diphenyllead(IV) complexes with N,O,S-chelating ligands

The reactions of PbPh2(OAC)(2) with alkylglyoxylate thiosemicarbazones (HRGTSC, R = Et, Bu) afforded complexes of the type [PbPh2(GTSC)] center dot H2O, [PbPh2(RGTSC)(2)] and [PbPh2Cl(BUGTSC)]. The structures of HRGTSC (R = Me, Et, Bu), [PbPh2(OAc)(RGTSC)](R = Me, Et, Bu), [PbPh2Cl(BuGTSC)] and [PbPh2(GTSC)] center dot H2O have been studied by X-ray diffraction. [PbPh2(OAc)(RGTSC)] and [PbPh2(GTSC)] center dot H2O have [PbC2NO3S] kernels and the coordination sphere of the metal is pentagonal bipyramidal. [PbPh2Cl(BuGTSC)] has a [PbC2NOSCI] kernel and the coordination geometry around lead is pentagonal bipyramidal with one vacant site. Analysis of the bond distances in [PbPh2(GTSC)] center dot H2O suggests a significant affinity between diphenyllead(IV) and carboxylate donor groups, supporting a borderline acidic character for this organometallic cation. H-1 and C-13 NMR spectra in DMSO-d(6) suggest the partial dissociation of the acetate in [PbPh2(OAc)(RGTSC)] solutions and indicate some differences in the coordination mode of the two RGTSC(-) ligands in [PbPh2(RGTSC)(2)] complexes. (C) 2007 Elsevier Ltd. All rights reserved.

THE PYROCHLORE SUPERGROUP OF MINERALS: NOMENCLATURE

A new scheme of nomenclature for the pyrochlore supergroup, approved by the CNMNC-IMA, is based on the ions at the A, B and Y sites. What has been referred to until now as the pyrochlore group should be referred to as the pyrochlore supergroup, and the subgroups should be changed to groups. Five groups are recommended, based on the atomic proportions of the B atoms Nb, Ta, Sb, Ti, and W. The recommended groups are pyrochlore, microlite, romite, betafite, and elsmoreite, respectively. The new names are composed of two prefixes and one root name (identical to the name of the group). The first prefix refers to the dominant anion (or cation) of the dominant valence [or H(2)O or rectangle] at the Y site. The second prefix refers to the dominant cation of the dominant valence [or H(2)O or rectangle] at the A site. The prefix "" keno-"" represents "" vacancy"". Where the first and second prefixes are equal, then only one prefix is applied. Complete descriptions are missing for the majority of the pyrochlore-supergroup species. Only seven names refer to valid species on the grounds of their complete descriptions: oxycalciopyrochlore, hydropyrochlore, hydroxykenomicrolite, oxystannomicrolite, oxystibiomicrolite, hydroxycalcioromite, and hydrokenoelsmoreite. Fluornatromicrolite is an IMA-approved mineral, but the complete description has not yet been published. The following 20 names refer to minerals that need to be completely described in order to be approved as valid species: hydroxycalciopyrochlore, fluornatropyrochlore, fluorcalciopyrochlore, fluorstrontiopyrochlore, fluorkenopyrochlore, oxynatropyrochlore, oxyplumbopyrochlore, oxyyttropyrochlore-(Y), kenoplumbopyrochlore, fluorcalciomicrolite, oxycalciomicrolite, kenoplumbomicrolite, hydromicrolite, hydrokenomicrolite, oxycalciobetafite, oxyuranobetafite, fluornatroromite, fluorcalcioromte, oxycalcioromite, and oxyplumboromite. For these, there are only chemical or crystalstructure data. Type specimens need to be defined. Potential candidates for several other species exist, but are not sufficiently well characterized to grant them any official status. Ancient chemical data refer to wet-chemical analyses and commonly represent a mixture of minerals. These data were not used here. All data used represent results of electron-microprobe analyses or were obtained by crystal-structure refinement. We also verified the scarcity of crystal-chemical data in the literature. There are crystalstructure determinations published for only nine pyrochlore-supergroup minerals: hydropyrochlore, hydroxykenomicrolite, hydroxycalcioromite, hydrokenoelsmoreite, hydroxycalciopyrochlore, fluorcalciopyrochlore, kenoplumbomicrolite, oxycalciobetafite, and fluornatroromite. The following mineral names are now discarded: alumotungstite, bariomicrolite, bariopyrochlore, bindheimite, bismutomicrolite, bismutopyrochlore, bismutostibiconite, calciobetafite, ceriopyrochlore-(Ce), cesstibtantite, ferritungstite, jixianite, kalipyrochlore, monimolite, natrobistantite, partzite, plumbobetafite, plumbomicrolite, plumbopyrochlore, stannomicrolite, stetefeldtite, stibiconite, stibiobetafite, stibiomicrolite, strontiopyrochlore, uranmicrolite, uranpyrochlore, yttrobetafite-(Y), and yttropyrochlore-(Y).

Correlations between chemical composition and provenance of Justino site ceramics by INAA

Instrumental neutron activation analysis (INAA), have been used for the definition of compositional groups of potteries from Justino site, Brazil, according to the chemical similarities of ceramic paste. The outliers were identified by means of robust Mahalanobis distance. The temper effect in the ceramic paste was studied by means of modified Mahalanobis filter. The results were interpreted by means of cluster, principal components, and discriminant analyses. This work provides contributions for the reconstruction of the prehistory of baixo Sao Francisco region, and for the reconstitution of the Brazilian Northeast ceramist population of general frame.

Tissue-, substrate-, and site-specific characteristics of mitochondrial reactive oxygen species generation

Reactive oxygen species are a by-product of mitochondrial oxidative phosphorylation, derived from a small quantity of superoxide radicals generated during electron transport. We conducted a comprehensive and quantitative study of oxygen consumption, inner membrane potentials, and H(2)O(2) release in mitochondria isolated from rat brain, heart, kidney, liver, and skeletal muscle, using various respiratory substrates (alpha-ketoglutarate, glutamate, succinate, glycerol phosphate, and palmitoyl carnitine). The locations and properties of reactive oxygen species formation were determined using oxidative phosphorylation and the respiratory chain modulators oligomycin, rotenone, myxothiazol, and antimycin A and the Uncoupler CCCP. We found that in mitochondria isolated from most tissues incubated under physiologically relevant conditions, reactive oxygen release accounts for 0.1-0.2% of O(2) consumed. Our findings support an important participation of flavoenzymes and complex III and a substantial role for reverse electron transport to complex I as reactive oxygen species sources. Our results also indicate that succinate is an important substrate for isolated mitochondrial reactive oxygen production in brain, heart, kidney, and skeletal muscle, whereas fatty acids generate significant quantities of oxidants in kidney and liver. Finally, we found that increasing respiratory rates is an effective way to prevent mitochondrial oxidant release under many, but not all, conditions. Altogether, our data uncover and quantify many tissue-, substrate-, and site-specific characteristics of mitochondrial ROS release. (C) 2009 Elsevier Inc. All rights reserved.

A proposed EPR approach to evaluating agonist binding site of a peptide receptor

Angiotensin II (Ang II) and its transmembrane AT(1) receptor were selected in order to test an innovative strategy that might allow the assessment of the agonist binding site in the receptor molecule. With the use of the 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC) paramagnetic probe, a biologically active agonist (TOAC(1)-Ang II), as well as an inactive control (TOAC(4)-Ang II) analogs were mixed in solution with various synthesized AT(1) fragments. Comparative intermolecular interactions, as estimated by analyzing the EPR spectra of solutions, suggested the existence of an agonist binding site containing a sequence composed of portions of the N-terminal (13-17) and the third extracellular loop (266-278) fragments of the AT(1) molecule. Therefore, this combined EPR-TOAC approach shows promise as an alternative for use also in other applications related to specific intermolecular association processes.

The role in the substrate specificity and catalysis of residues forming the substrate aglycone-binding site of a beta-glycosidase

The relative contributions to the specificity and catalysis of aglycone, of residues E190, E194, K201 and M453 that form the aglycone-binding site of a beta-glycosidase from Spodoptera frugiperda (EC 3.2.1.21), were investigated through site-directed mutagenesis and enzyme kinetic experiments. The results showed that E190 favors the binding of the initial portion of alkyl-type aglycones (up to the sixth methylene group) and also the first glucose unit of oligosaccharidic aglycones, whereas a balance between interactions with E194 and K201 determines the preference for glucose units versus alkyl moieties. E194 favors the binding of alkyl moieties, whereas K201 is more relevant for the binding of glucose units, in spite of its favorable interaction with alkyl moieties. The three residues E190, E194 and K201 reduce the affinity for phenyl moieties. In addition, M453 favors the binding of the second glucose unit of oligosaccharidic aglycones and also of the initial portion of alkyl-type aglycones. None of the residues investigated interacted with the terminal portion of alkyl-type aglycones. It was also demonstrated that E190, E194, K201 and M453 similarly contribute to stabilize ES double dagger. Their interactions with aglycone are individually weaker than those formed by residues interacting with glycone, but their joint catalytic effects are similar. Finally, these interactions with aglycone do not influence glycone binding.

PREDICTION OF METAL CATION TOXICITY TO THE BIOLUMINESCENT FUNGUS GERRONEMA VIRIDILUCENS

A correlation between the physicochemical properties of mono- [Li(I), K(I), Na(I)] and divalent [Cd(II), Cu(II), Mn(II), Ni(II), Co(II), Zn(II), Mg(II), Ca(II)] metal cations and their toxicity (evaluated by the free ion median effective concentration. EC50(F)) to the naturally bioluminescent fungus Gerronema viridilucens has been studied using the quantitative ion character activity relationship (QICAR) approach. Among the 11 ionic parameters used in the current study, a univariate model based on the covalent index (X(m)(2)r) proved to be the most adequate for prediction of fungal metal toxicity evaluated by the logarithm of free ion median effective concentration (log EC50(F)): log EC50(F) = 4.243 (+/-0.243) -1.268 (+/-0.125).X(m)(2)r (adj-R(2) = 0.9113, Alkaike information criterion [AIC] = 60.42). Additional two- and three-variable models were also tested and proved less suitable to fit the experimental data. These results indicate that covalent bonding is a good indicator of metal inherent toxicity to bioluminescent fungi. Furthermore, the toxicity of additional metal ions [Ag(I), Cs(I), Sr(II), Ba(II), Fe(II), Hg(II), and Pb(II)] to G. viridilucens was predicted, and Pb was found to be the most toxic metal to this bioluminescent fungus (EC50(F)): Pb(II) > Ag(I) > Hg(I) > Cd(II) > Cu(II) > Co(II) Ni(II) > Mn(II) > Fe(II) approximate to Zn(II) > Mg(II) approximate to Ba(II) approximate to Cs(I) > Li(I) > K(I) approximate to Na(I) approximate to Sr(II)> Ca(II). Environ. Toxicol. Chem. 2010;29:2177-2181. (C) 2010 SETAC

The isatin-Schiff base copper(II) complex Cu(isaepy)(2) acts as delocalized lipophilic cation, yields widespread mitochondrial oxidative damage and induces AMP-activated protein kinase-dependent apoptosis

We previously demonstrated that Bis[(2-oxindol-3-ylimino)-2-(2-aminoethyl) pyridine-N, N`] copper(II) [Cu(isaepy)(2)] was an efficient inducer of the apoptotic mitochondrial pathway. Here, we deeply dissect the mechanisms underlying the ability of Cu(isaepy)(2) to cause mitochondriotoxicity. In particular, we demonstrate that Cu(isaepy)(2) increases NADH-dependent oxygen consumption of isolated mitochondria and that this phenomenon is associated with oxy-radical production and insensitive to adenosine diphosphate. These data indicate that Cu(isaepy)(2) behaves as an uncoupler and this property is also confirmed in cell systems. Particularly, SH-SY5Y cells show: (i) an early loss of mitochondrial transmembrane potential; (ii) a decrease in the expression levels of respiratory complex components and (iii) a significant adenosine triphosphate (ATP) decrement. The causative energetic impairment mediated by Cu(isaepy)(2) in apoptosis is confirmed by experiments carried out with rho(0) cells, or by glucose supplementation, where cell death is significantly inhibited. Moreover, gastric and cervix carcinoma AGS and HeLa cells, which rely most of their ATP production on oxidative phosphorylation, show a marked sensitivity toward Cu(isaepy)(2). Adenosine monophosphate-activated protein kinase (AMPK), which is activated by events increasing the adenosine monophosphate: ATP ratio, is deeply involved in the apoptotic process because the overexpression of its dominant/negative form completely abolishes cell death. Upon glucose supplementation, AMPK is not activated, confirming its role as fuel-sensing enzyme that positively responds to Cu(isaepy)(2)-mediated energetic impairment by committing cells to apoptosis. Overall, data obtained indicate that Cu(isaepy)(2) behaves as delocalized lipophilic cation and induces mitochondrial-sited reactive oxygen species production. This event results in mitochondrial dysfunction and ATP decrease, which in turn triggers AMPK-dependent apoptosis.

On the apparent lack of preferential site occupancy and electrooxidation of CO adsorbed at low coverage onto stepped platinum surfaces

We report time evolution studies of low coverage CO adsorption (surface hydrogen site blocking < 40%) and oxidative stripping on stepped Pt(776) and Pt(554) surfaces. It was observed that there is no preferential site occupancy for CO adsorption on step or terrace. It is proposed that CO adsorption onto these surfaces is a random process, and after CO adsorption there is no appreciable shift from CO-(111) to CO-(110) sites. This implies that after adsorption, CO molecules either have a very long residence time, or that the diffusion coefficient is much lower than previously thought. After CO electrooxidation the sites released included both terrace (111) and step (110) orientations. For surface hydrogen site blocking > 40%, the lateral interactions might play a role in the preferential CO site occupancy. (C) 2011 Elsevier B.V. All rights reserved.

Simple telemedicine for developing regions: Camera phones and paper-based microfluidic devices for real-time, off-site diagnosis

This article describes a prototype system for quantifying bioassays and for exchanging the results of the assays digitally with physicians located off-site. The system uses paper-based microfluidic devices for running multiple assays simultaneously, camera phones or portable scanners for digitizing the intensity of color associated with each colorimetric assay, and established communications infrastructure for transferring the digital information from the assay site to an off-site laboratory for analysis by a trained medical professional; the diagnosis then can be returned directly to the healthcare provider in the field. The microfluidic devices were fabricated in paper using photolithography and were functionalized with reagents for colorimetric assays. The results of the assays were quantified by comparing the intensities of the color developed in each assay with those of calibration curves. An example of this system quantified clinically relevant concentrations of glucose and protein in artificial urine. The combination of patterned paper, a portable method for obtaining digital images, and a method for exchanging results of the assays with off-site diagnosticians offers new opportunities for inexpensive monitoring of health, especially in situations that require physicians to travel to patients (e.g., in the developing world, in emergency management, and during field operations by the military) to obtain diagnostic information that might be obtained more effectively by less valuable personnel.