Perspective: On the active site model in computational catalyst screening

First-principles screening approaches exploiting energy trends in surface adsorption represent an unparalleled success story in recent computational catalysis research. Here we argue that our still limited understanding of the structure of active sites is one of the major bottlenecks towards an ever extended and reliable use of such computational screening for catalyst discovery. For low-index transition metal surfaces, the prevalently chosen high-symmetry (terrace and step) sites offered by the nominal bulk-truncated crystal lattice might be justified. For more complex surfaces and composite catalyst materials, computational screening studies will need to actively embrace a considerable uncertainty with respect to what truly are the active sites. By systematically exploring the space of possible active site motifs, such studies might eventually contribute towards a targeted design of optimized sites in future catalysts

Détermination à l'aide d'un modèle récepteur des zones sources à l'origine des concentrations mesurées dans les précipitations collectées en trois sites du réseau MERA (France)

Ces travaux s'inscrivent dans le cadre du programme national de MEsure des Retombées Atmosphériques (MERA). Ils portent sur la recherche de l'origine des précipitations collectées entre 1997 et 1999 dans trois (Morvan, Iraty, Le Casset) des onze stations du réseau MERA localisées en différents points du territoire français. Deux méthodes statistiques ont été utilisées dans cette étude. Les régions à l'origine des fortes concentrations mesurées au site récepteur ont d'abord été déterminées à l'aide d'un modèle (méthode de Seibert) combinant les mesures réalisées sur site et les rétrotrajectoires de masses d'air puis, dans un second temps les différents profils de transport atmosphérique, leur fréquence et concentrations associées ont été évaluées à l'aide d'une classification par Nuées Dynamiques (méthode K-means/distance Euclidienne simple) des rétrotrajectoires de masses d'air. Le test de Kruskal-Wallis a été utilisé pour vérifier si les médianes des concentrations associées à chaque classe sont statistiquement différentes. L'étude réalisée à Iraty (Pyrénées) et au Casset (Alpes) a montré que ces deux stations sont influencées différemment du Morvan. Plus exactement, ces deux sites ne sont pas, ou pratiquement pas, influencés par les zones d'Europe centrale ou du Nord-Ouest fortement émettrices de SO2, de NOx et de NH3. Seul le pH des précipitations collectées à Iraty semble dépendre des émissions de SO2 et de NOx d'une de ces zones. Iraty et le Casset sont très influencées par les émissions anthropiques et par les poussières d'origine terrestres en provenance d'Afrique du Nord. Néanmoins, les niveaux de concentrations mesurés dans les flux en provenance d'Afrique du Nord sont similaires pour Iraty, le Casset et le Morvan (sauf en ions calcium, pour lequel le Casset et Iraty montrent de fortes concentrations). Une autre région européenne peut influencer les niveaux en composés acidifiants mesurés au Casset, il s'agit de l'Italie et de la zone localisée au niveau de l'ex-Yougoslavie. Mais, les niveaux de concentrations qui en résultent sont faibles par rapport à ceux mesurés dans certains flux arrivant au Morvan.The chemistry of precipitation in France was examined using data from the French atmospheric deposition network (MERA). In order to examine the source-receptor relationships responsible for acid rain at three background sites in France, a receptor-oriented model was applied to the precipitation data collected from 1997 to 1999. This methodology combined precipitation and chemical data with air parcel backward trajectories to establish concentration field maps of likely contributing sources. Then, a clustering technique using partitioning methods (K-means/Euclidian distance) was performed to backward trajectories and the distributions of mixing samples associated with backward trajectories in each cluster were compared. The Kruskal-Wallis test was used to verify that the concentration medians associated with each cluster were statistically significant. The results of this study demonstrated that two stations (Iraty and le Casset) were not influenced by the same sources as Morvan. Specifically, these sites were less influenced by high emissions from Central or Northwestern Europe when compared to Morvan. Only the pH seemed under the influence of SO2 and NOx emissions from one of these areas. Iraty and Le casset are very influenced by anthropogenic emissions and the crustal sources around the Mediterranean Basin and North Africa. Other European areas (e.g. Italy) can influence the concentrations recorded at Le Casset but the levels of concentration are lower than those measured at Morvan.This paper represents a complete statistical analysis of wet-only deposition chemistry data for three stations (Iraty, Le Casset and Morvan). Two statistical methods were used in this study. In order to examine the source-receptor relationships responsible for acid rain at these three background sites in France, a receptor-oriented model was applied to the precipitation data collected from 1997 to 1999. This methodology combined chemical data with air parcel backward trajectories to establish concentration field maps of likely contributing sources. This receptor-oriented model was developed by Seibert and it assumes that if a trajectory endpoint falls in a grid cell (i,j), the air mass is assumed to collect components emitted in this cell and once the components are incorporated, they are transported along the trajectory to the receptor site. This model doesn't take into account the atmospheric diffusion and the removal mechanisms occurring during the trajectory from the sources to the receptor. Finally, a concentration field map for the selected species was calculated taking into account all grid cells. For mapping, the grid cells counting fewer than 10 endpoints were not taken in consideration because the confidence of their results was considered too low. The role of three-dimensional backward trajectories is fundamental, so we used three different information sources: the French Institute of Meteorology, Météo-France; the British Atmospheric Data Centre (BADC); and the Atmospheric Environment Service Long Range Transport model of Air Pollution (AES-LRTAP), Canada. These trajectory models were compared for different chemical species. All data were projected in the EMEP grid (150 x 150 km) for establishment of the concentration field map. A clustering technique by partitioning methods (K-means/Euclidian distance) was performed on backward trajectories and the distributions of mixing samples associated with backward trajectories in each cluster were compared. The Kruskal-Wallis test was used to verify that the median concentrations associated with each cluster were statistically significant.The results of this study for Morvan determined five classes of backward trajectories associated with the precipitation collected at this station located in the centre of France. The fluxes from SW and WSW sectors contribute for 52% of events, while the fluxes of NW and E contribute for 31% of events but are mainly responsible for high concentrations of sulphates, nitrates, ammonium and hydronium ion. Regions found to be responsible for rain events coincide with European regions known for their high anthropogenic emissions of SO2 and NOx (Great Britain, North of France, Belgium, The Netherlands and the North of sea).The results for Iraty (South of France) yielded five classes of backward trajectories associated with the precipitation collected in this station. The fluxes from W sectors (NNW, NW, W and WSW) were responsible for 71% of events, while the flux of S (low wind) was responsible for 29% of events but is mainly responsible for high concentrations of sulphates, nitrates, ammonium and calcium. High concentrations of hydronium ion were identified in the NNW sector.The results for Le Casset (East region and mountainous) gave four classes of backward trajectories associated with the precipitation collected in this station. The fluxes from W and WSW sectors were responsible for 35% of events, while the flux of SSW was responsible for 43% and the flux from the SE was responsible for 22% of events. This last sector was mainly responsible for high concentrations of sulphates, nitrates, ammonium and calcium. The concentrations measured at this station were low. Regions found to be responsible for rain events coincide with southern and eastern areas known for their high anthropogenic emissions of SO2 and NOx (north Africa, northern Italy, Yugoslavia).All these results demonstrate that the Iraty and Le Casset stations were not influenced by the same sources as Morvan. Specifically, these sites were less influenced by the high emissions from central or northwestern Europe than Morvan. Only the measurement of pH seemed to be under the influence of SO2 and NOx emissions of one of these areas. Iraty and Le Casset were very influenced by the anthropogenic emissions and the crustal sources around the Mediterranean Basin and North Africa. Other European areas (e.g., Italy) can influence the concentrations recorded at Le Casset but the levels were lower than those measured at Morvan. A relation between sulphates, nitrates and ammonium was identified for Morvan and Le Casset. This observation suggests that aerosol transport of NH4 HSO4, (NH4)2 SO4 and NH4 NO3 is occurring

Assessment of VOCs Material/Air Exchanges of Building Products Using the DOSEC®-SPME Method

ACTInternational audienceUsing low emissive materials in building is an effective way to reduce indoor concentrations of pollutants such as VOCs. Material emissions are assessed by the ISO 16000-9 standard. This procedure is time-consuming and is not suitable for on-site measurements. This work aimed in assessing an alternative method, DOSEC\textregistered-SPME, for simple measurements. To validate it, emissions of 30 materials were characterized by both ISO 16000-9 and DOSEC\textregistered-SPME. A first correlation was found between the two methods for formaldehyde emissions of raw materials. This encouraging result allows considering the development of new decision making tools for the selection of healthy building materials

Concentration-Dependent Effects of a Dietary Ketone Ester on Components of Energy Balance in Mice

Objectives: Exogenous ketones may provide therapeutic benefit in treatment of obesity. Administration of the ketone ester (KE) R,S-1,3-butanediol acetoacetate diester (BD-AcAc2) decreases body weight in mice, but effects on energy balance have not been extensively characterized. The purpose of this investigation was to explore concentration-dependent effects of BD-AcAc2 on energy intake and expenditure in mice.Methods: Forty-two male C57BL/6J mice were randomly assigned to one of seven isocaloric diets (n = 6 per group): (1) Control (CON, 0% KE by kcals); (2) KE5 (5% KE); (3) KE10 (10% KE); (4) KE15 (15% KE); (5) KE20 (20% KE); (6) KE25 (25% KE); and (7) KE30 (30% KE) for 3 weeks. Energy intake and body weight were measured daily. Fat mass (FM), lean body mass (LBM), and energy expenditure (EE) were measured at completion of the study. Differences among groups were compared to CON using ANOVA and ANCOVA.Results: Mean energy intake was similar between CON and each concentration of KE, except KE30 which was 12% lower than CON (P < 0.01). KE25 and KE30 had lower body weight and FM compared to CON, while only KE30 had lower LBM (P < 0.03). Adjusted resting and total EE were lower in KE30 compared to CON (P < 0.03), but similar for all other groups.Conclusions: A diet comprised of 30% energy from BD-AcAc2 results in lower energy intake, coincident with lower body weight and whole animal adiposity; while KE20 and KE25 have significantly lower body weight and adiposity effects independent of changes in energy intake or expenditure

Endoplasmic Reticulum Stress Links Oxidative Stress to Impaired Pancreatic Beta-Cell Function Caused by Human Oxidized LDL.

Elevated plasma concentration of the pro-atherogenic oxidized low density lipoprotein cholesterol (LDL) triggers adverse effects in pancreatic beta-cells and is associated with type 2 diabetes. Here, we investigated whether the endoplasmic reticulum (ER) stress is a key player coupling oxidative stress to beta-cell dysfunction and death elicited by human oxidized LDL. We found that human oxidized LDL activates ER stress as evidenced by the activation of the inositol requiring 1α, and the elevated expression of both DDIT3 (also called CHOP) and DNAJC3 (also called P58IPK) ER stress markers in isolated human islets and the mouse insulin secreting MIN6 cells. Silencing of Chop and inhibition of ER stress markers by the chemical chaperone phenyl butyric acid (PBA) prevented cell death caused by oxidized LDL. Finally, we found that oxidative stress accounts for activation of ER stress markers induced by oxidized LDL. Induction of Chop/CHOP and p58IPK/P58IPK by oxidized LDL was mimicked by hydrogen peroxide and was blocked by co-treatment with the N-acetylcystein antioxidant. As a conclusion, the harmful effects of oxidized LDL in beta-cells requires ER stress activation in a manner that involves oxidative stress. This mechanism may account for impaired beta-cell function in diabetes and can be reversed by antioxidant treatment

Evidence of the neuron-restrictive silencer factor (NRSF) interaction with Sp3 and its synergic repression to the mu opioid receptor (MOR) gene

Previously, we reported that the neuron-restrictive silencer element (NRSE) of mu opioid receptor (MOR) functions as a critical regulator to repress the MOR transcription in specific neuronal cells, depending on neuron-restriction silence factor (NRSF) expression levels [C.S.Kim, C.K.Hwang, H.S.Choi, K.Y.Song, P.Y.Law, L.N.Wei and H.H.Loh (2004) J. Biol. Chem., 279, 46464–46473]. Herein, we identify a conserved GC sequence next to NRSE region in the mouse MOR gene. The inhibition of Sp family factors binding to this GC box by mithramycin A led to a significant increase in the endogenous MOR transcription. In the co-immunoprecipitation experiment, NRSF interacted with the full-length Sp3 factor, but not with Sp1 or two short Sp3 isoforms. The sequence specific and functional binding by Sp3 at this GC box was confirmed by in vitro gel-shift assays using either in vitro translated proteins or nuclear extract, and by in vivo chromatin immunoprecipitation assays. Transient transfection assays showed that Sp3-binding site of the MOR gene is a functionally synergic repressor element with NRSE in NS20Y cells, but not in the NRSF negative PC12 cells. The results suggest that the synergic interaction between NRSF and Sp3 is required to negatively regulate MOR gene transcription and that transcription of MOR gene would be governed by the context of available transcription factors rather than by a master regulator

Role of Gas6 Receptors in Platelet Signaling during Thrombus Stabilization and Implications for Antithrombotic Therapy

Mechanisms regulating thrombus stabilization remain largely unknown. Here, we report that loss of any 1 of the Gas6 receptors (Gas6-Rs), i.e., Tyro3, Axl, or Mer, or delivery of a soluble extracellular domain of Axl that traps Gas6 protects mice against life-threatening thrombosis. Loss of a Gas6-R does not prevent initial platelet aggregation but impairs subsequent stabilization of platelet aggregates, at least in part by reducing “outside-in” signaling and platelet granule secretion. Gas6, through its receptors, activates PI3K and Akt and stimulates tyrosine phosphorylation of the β3 integrin, thereby amplifying outside-in signaling via αIIbβ3. Blocking the Gas6-R–αIIbβ3 integrin cross-talk might be a novel approach to the reduction of thrombosis

Variability of protein level and phosphorylation status caused by biopsy protocol design in human skeletal muscle analyses

<p>Abstract</p> <p>Background</p> <p>Bergström needle biopsy is widely used to sample skeletal muscle in order to study cell signaling directly in human tissue. Consequences of the biopsy protocol design on muscle protein quantity and quality remain unclear. The aim of the present study was to assess the impact of different events surrounding biopsy protocol on the stability of the Western blot signal of eukaryotic translation initiation factor 4E binding protein 1 (4E-BP1), Akt, glycogen synthase kinase-3β (GSK-3β), muscle RING finger protein 1 (MuRF1) and p70 S6 kinase (p70 S6K). Six healthy subjects underwent four biopsies of the <it>vastus lateralis</it>, distributed into two distinct visits spaced by 48 hrs. At visit 1, a basal biopsy in the right leg was performed in the morning (R1) followed by a second in the left leg in the afternoon (AF). At visit 2, a second basal biopsy (R2) was collected from the right leg. Low intensity mobilization (3 × 20 right leg extensions) was performed and a final biopsy (Mob) was collected using the same incision site as R2.</p> <p>Results</p> <p>Akt and p70 S6K phosphorylation levels were increased by 83% when AF biopsy was compared to R1. Mob condition induced important phosphorylation of p70 S6K when compared to R2. Comparison of R1 and R2 biopsies revealed a relative stability of the signal for both total and phosphorylated proteins.</p> <p>Conclusions</p> <p>This study highlights the importance to standardize muscle biopsy protocols in order to minimize the method-induced variation when analyzing Western blot signals.</p

Identification of Protein Networks Involved in the Disease Course of Experimental Autoimmune Encephalomyelitis, an Animal Model of Multiple Sclerosis

A more detailed insight into disease mechanisms of multiple sclerosis (MS) is crucial for the development of new and more effective therapies. MS is a chronic inflammatory autoimmune disease of the central nervous system. The aim of this study is to identify novel disease associated proteins involved in the development of inflammatory brain lesions, to help unravel underlying disease processes. Brainstem proteins were obtained from rats with MBP induced acute experimental autoimmune encephalomyelitis (EAE), a well characterized disease model of MS. Samples were collected at different time points: just before onset of symptoms, at the top of the disease and following recovery. To analyze changes in the brainstem proteome during the disease course, a quantitative proteomics study was performed using two-dimensional difference in-gel electrophoresis (2D-DIGE) followed by mass spectrometry. We identified 75 unique proteins in 92 spots with a significant abundance difference between the experimental groups. To find disease-related networks, these regulated proteins were mapped to existing biological networks by Ingenuity Pathway Analysis (IPA). The analysis revealed that 70% of these proteins have been described to take part in neurological disease. Furthermore, some focus networks were created by IPA. These networks suggest an integrated regulation of the identified proteins with the addition of some putative regulators. Post-synaptic density protein 95 (DLG4), a key player in neuronal signalling and calcium-activated potassium channel alpha 1 (KCNMA1), involved in neurotransmitter release, are 2 putative regulators connecting 64% of the identified proteins. Functional blocking of the KCNMA1 in macrophages was able to alter myelin phagocytosis, a disease mechanism highly involved in EAE and MS pathology. Quantitative analysis of differentially expressed brainstem proteins in an animal model of MS is a first step to identify disease-associated proteins and networks that warrant further research to study their actual contribution to disease pathology

Neutralising Antibodies against Ricin Toxin

The Centers for Disease Control and Prevention have listed the potential bioweapon ricin as a Category B Agent. Ricin is a so-called A/B toxin produced by plants and is one of the deadliest molecules known. It is easy to prepare and no curative treatment is available. An immunotherapeutic approach could be of interest to attenuate or neutralise the effects of the toxin. We sought to characterise neutralising monoclonal antibodies against ricin and to develop an effective therapy. For this purpose, mouse monoclonal antibodies (mAbs) were produced against the two chains of ricin toxin (RTA and RTB). Seven mAbs were selected for their capacity to neutralise the cytotoxic effects of ricin in vitro. Three of these, two anti-RTB (RB34 and RB37) and one anti-RTA (RA36), when used in combination improved neutralising capacity in vitro with an IC50 of 31 ng/ml. Passive administration of association of these three mixed mAbs (4.7 µg) protected mice from intranasal challenges with ricin (5 LD50). Among those three antibodies, anti-RTB antibodies protected mice more efficiently than the anti-RTA antibody. The combination of the three antibodies protected mice up to 7.5 hours after ricin challenge. The strong in vivo neutralising capacity of this three mAbs combination makes it potentially useful for immunotherapeutic purposes in the case of ricin poisoning or possibly for prevention