Agent-based spatiotemporal simulation of biomolecular systems within the open source MASON framework

Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the various effects that facilitate biocatalysis. Enzymes may display high specificity for their substrates and this information is crucial to the engineering and optimisation of bioprocesses. Simulation results demonstrate that molecule distributions, reaction rate parameters, and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of realistic cell environments. While higher percentage of collisions with occurrence of reaction increases the affinity of the enzyme to the substrate, a faster reaction (i.e., turnover number) leads to a smaller number of time steps. Slower diffusion rates and molecular crowding (physical hurdles) decrease the collision rate of reactants, hence reducing the reaction rate, as expected. Also, the random distribution of molecules affects the results significantly.The authors thank the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/273). The research leading to these results has received funding from the European Union's Seventh Framework Programme FP7/REGPOT-2012-2013.1 under Grant Agreement no. 316265 (BIOCAPS) and the [14VI05] Contract-Programme from the University of Vigo. This document reflects only the authors' views and the European Union is not liable for any use that may be made of the information contained herein

Partitioning of trace elements in a entrained flow IGCC plant: Influence of selected operational conditions

The partitioning of trace elements and the influence of the feed conditions (50:50 coal/pet-coke feed blend and limestone addition) was investigated in this study. To this end feed fuel, fly ash and slag samples were collected under different operational conditions at the 335 MW Puertollano IGCC power plant (Spain) and subsequently analysed. The partitioning of elements in this IGCC plant may be summarised as follows: (a) high volatile elements (70–>99% in gas phase): Hg, Br, I, Cl and S; (b) moderately volatile elements (up to 40% in gas phase and 60% in fly ash): As, Sb, Se, B, F, Cd, Tl, Zn and Sn; (c) elements with high condensation potential: (>90% in fly ash): Pb, Ge, Ga and Bi; (d) elements enriched similarly in fly ash and slag 30–60% in fly ash: Cu, W, (P), Mo, Ni and Na; and (e) low volatile elements (>70% in slag): Cs, Rb, Co, K, Cr, V, Nb, Be, Hf, Ta, Fe, U, Ti, Al, Si, Y, Sr, Th, Zr, Mg, Ba, Mn, REEs, Ca and Li. The volatility of As, Sb, and Tl and the slagging of S, B, Cl, Cd and low volatile elements are highly influenced by the fuel geochemistry and limestone dosages, respectively

Effectiveness of rosuvastatin plus colchicine, emtricitabine/tenofovir and combinations thereof in hospitalized patients with COVID-19 : a pragmatic, open-label randomized trial

Q1Q1The use of rosuvastatin plus colchicine and emtricitabine/tenofovir in hospitalized patients with SARS- CoV-2 disease (COVID-19) has not been assessed. The objective of this study was to assess the effectiveness and safety of rosuvastatin plus colchicine, emtricitabine/tenofovir, and their combined use in these patients.Revista Internacional - Indexad

Glycoprotein Ib activation by thrombin stimulates the energy metabolism in human platelets

<div><p>Thrombin-induced platelet activation requires substantial amounts of ATP. However, the specific contribution of each ATP-generating pathway <i>i</i>.<i>e</i>., oxidative phosphorylation (OxPhos) versus glycolysis and the biochemical mechanisms involved in the thrombin-induced activation of energy metabolism remain unclear. Here we report an integral analysis on the role of both energy pathways in human platelets activated by several agonists, and the signal transducing mechanisms associated with such activation. We found that thrombin, Trap-6, arachidonic acid, collagen, A23187, epinephrine and ADP significantly increased glycolytic flux (3–38 times <i>vs</i>. non-activated platelets) whereas ristocetin was ineffective. OxPhos (33 times) and mitochondrial transmembrane potential (88%) were increased only by thrombin. OxPhos was the main source of ATP in thrombin-activated platelets, whereas in platelets activated by any of the other agonists, glycolysis was the principal ATP supplier. In order to establish the biochemical mechanisms involved in the thrombin-induced OxPhos activation in platelets, several signaling pathways associated with mitochondrial activation were analyzed. Wortmannin and LY294002 (PI3K/Akt pathway inhibitors), ristocetin and heparin (GPIb inhibitors) as well as resveratrol, ATP (calcium-release inhibitors) and PP1 (Tyr-phosphorylation inhibitor) prevented the thrombin-induced platelet activation. These results suggest that thrombin activates OxPhos and glycolysis through GPIb-dependent signaling involving PI3K and Akt activation, calcium mobilization and protein phosphorylation.</p></div

Effect of β-Glucans in Diets on Growth, Survival, Digestive Enzyme Activity, and Immune System and Intestinal Barrier Gene Expression for Tropical Gar (Atractosteus tropicus) Juveniles

The application of β-1,3/1,6-glucan derived from yeast at five concentrations (0%, 0.5%, 1.0%, 1.5%, and 2.0%) in formulated diets was evaluated in juveniles for its effects on the growth, survival, digestive enzymatic activity, and expression of genes associated with the immune system (interlukin-10 (IL-10), transforming growth factor (TGF), occludin (OCC), mucin2 (MUC2), lysozyme (LYS), and nucleotide-binding and oligomerization domain 2 (NOD2)) in tropical gar (Atractosteus tropicus). For the experiment, three replicates of 30 fish per experimental unit (70 L) were cultivated for 62 days. The growth results showed no statistically significant differences in relation to weight and total length between treatments. The activity of digestive enzymes (alkaline proteases, trypsin, leucine aminopeptidase, and amylase) did not show significant differences between treatments, except for chymotrypsin activity, where fish fed 1.0% and 1.5% of β-glucans showed higher activities compared with the rest of the treatments. On the other hand, the analysis of gene expression did not show significant differences between treatments, although a tendency of increase in the expression of IL-10, TGF, MUC2, and OCC was observed with an addition of 1.5% of the prebiotic, but there was a decrease in the fish fed with 2% of the prebiotic. It is possible to include concentrations of between 0.5% and 1.5% of β-glucans in the diets for A. tropicus, with no detectable adverse effects on growth, survival, digestive enzyme activity, or specific gene expression. β-glucan 1,3/1,6 added at 1.0% and 1.5% in the diet significantly increases chymotrypsin activity.info:eu-repo/semantics/publishedVersio

Sublittoral soft bottom communities and diversity of Mejillones Bay in northern Chile (Humboldt Current upwelling system)

The macrozoobenthos of Mejillones Bay (23°S; Humboldt Current) was quantitatively investigated over a 7-year period from austral summer 1995/1996 to winter 2002. About 78 van Veen grab samples taken at six stations (5, 10, 20 m depth) provided the basis for the analysis of the distribution of 60 species and 28 families of benthic invertebrates, as well as of their abundance and biomass. Mean abundance (2,119 individuals m-2) was in the same order compared to a previous investigation; mean biomass (966 g formalin wet mass m-2), however, exceeded prior estimations mainly due to the dominance of the bivalve Aulacomya ater. About 43% of the taxa inhabited the complete depth range. Mean taxonomic Shannon diversity (H', Log e) was 1.54 ± 0.58 with a maximum at 20 m (1.95 ± 0.33); evenness increased with depth. The fauna was numerically dominated by carnivorous gastropods, polychaetes and crustaceans (48%). About 15% of the species were suspensivorous, 13% sedimentivorous, 11% detritivorous, 7% omnivorous and 6% herbivorous. Cluster analyses showed a significant difference between the shallow and the deeper stations. Gammarid amphipods and the polychaete family Nephtyidae characterized the 5-mzone, the molluscs Aulacomya ater, Mitrella unifasciata and gammarids the intermediate zone, while the gastropod Nassarius gayi and the polychaete family Nereidae were most prominent at the deeper stations. The communities of the three depth zones did not appear to be limited by hypoxia during non-El Niño conditions. Therefore, no typical change in community structure occurred during El Niño 1997–1998, in contrast to what was observed for deeper faunal assemblages and hypoxic bays elsewhere in the coastal Humboldt Current system

SEGURIDAD ALIMENTARIA EN FAMILIAS DE NUEVO LEÓN, MÉXICO

La seguridad alimentaria se puede analizar a partir de información generada para otros objetivos, sin embargo lo deseable es que esa información sea creada con la finalidad de analizar, desarrollar programas y crear políticas alimentarias, en Nuevo León, México, se realizan investigaciones poblacionales pero ninguna de ellas enfoca directamente el aspecto de la seguridad alimentaria de manera que los resultados e inferencias se determinan de otras investigaciones y bases de datos. La seguridad alimentaria es una condición dinámica en  la que se incluyen a los factores sociales, la falta de seguridad alimentaria en general no es un problema de producción sino a la falta de “Derecho alimentario” que significa falta de recursos para adquirirlos. Las fuentes de información que sustentan la seguridad alimentaria nutricional son variadas pero deben permitir el seguimiento de la situación alimentaria, entre otros, la vigilancia nutricional y alimentaria es la más frecuente a través de encuestas cualitativas y cuantitativas. En el análisis de la seguridad alimentaria en Nuevo León se utilizaron los componentes de disponibilidad alimentaria, acceso alimentario y otros indicadores tales como:peso al nacer, estado nutricio en menores de cinco años, patrón de consumo alimentario, índice de marginación, intervenciones en nutrición.Palabras calves: seguridad alimentaria, familias, Nuevo León, México Nourishing security, families, Nuevo León, Méxic