Évolution moléculaire : un modèle Markov-modulé pour les processus de substitution

Les processus Markoviens continus en temps sont largement utilisés pour tenter d’expliquer l’évolution des séquences protéiques et nucléotidiques le long des phylogénies. Des modèles probabilistes reposant sur de telles hypothèses sont conçus pour satisfaire la non-homogénéité spatiale des contraintes fonctionnelles et environnementales agissant sur celles-ci. Récemment, des modèles Markov-modulés ont été introduits pour décrire les changements temporels dans les taux d’évolution site-spécifiques (hétérotachie). Des études ont d’autre part démontré que non seulement la force mais également la nature de la contrainte sélective agissant sur un site peut varier à travers le temps. Ici nous proposons de prendre en charge cette réalité évolutive avec un modèle Markov-modulé pour les protéines sous lequel les sites sont autorisés à modifier leurs préférences en acides aminés au cours du temps. L’estimation a posteriori des différents paramètres modulants du noyau stochastique avec les méthodes de Monte Carlo est un défi de taille que nous avons su relever partiellement grâce à la programmation parallèle. Des réglages computationnels sont par ailleurs envisagés pour accélérer la convergence vers l’optimum global de ce paysage multidimensionnel relativement complexe. Qualitativement, notre modèle semble être capable de saisir des signaux d’hétérogénéité temporelle à partir d’un jeu de données dont l’histoire évolutive est reconnue pour être riche en changements de régimes substitutionnels. Des tests de performance suggèrent de plus qu’il serait mieux ajusté aux données qu’un modèle équivalent homogène en temps. Néanmoins, les histoires substitutionnelles tirées de la distribution postérieure sont bruitées et restent difficilement interprétables du point de vue biologique.

Gas phase kinetic and quantum chemical studies of the reactions of silylene with the methylsilanes. Absolute rate constants, temperature dependences, RRKM modelling and potential energy surfaces

Time resolved studies of silylene, SiH2, generated by the 193 nm laser. ash photolysis of phenylsilane, have been carried out to obtain rate coefficients for its bimolecular reactions with methyl-, dimethyl- and trimethyl-silanes in the gas phase. The reactions were studied over the pressure range 3 - 100 Torr with SF6 as bath gas and at five temperatures in the range 300 - 625 K. Only slight pressure dependences were found for SiH2 + MeSiH3 ( 485 and 602 K) and for SiH2 + Me2SiH2 ( 600 K). The high pressure rate constants gave the following Arrhenius parameters: [GRAPHICS] These are consistent with fast, near to collision-controlled, association processes. RRKM modelling calculations are consistent with the observed pressure dependences ( and also the lack of them for SiH2 + Me3SiH). Ab initio calculations at both second order perturbation theory (MP2) and coupled cluster (CCSD(T)) levels, showed the presence of weakly-bound complexes along the reaction pathways. In the case of SiH2 + MeSiH3 two complexes, with different geometries, were obtained consistent with earlier studies of SiH2 + SiH4. These complexes were stabilised by methyl substitution in the substrate silane, but all had exceedingly low barriers to rearrangement to product disilanes. Although methyl groups in the substrate silane enhance the intrinsic SiH2 insertion rates, it is doubtful whether the intermediate complexes have a significant effect on the kinetics. A further calculation on the reaction MeSiH + SiH4 shows that the methyl substitution in the silylene should have a much more significant kinetic effect ( as observed in other studies).

Gas-phase kinetics of chlorosilylene reactions II. ClSiH + C2H4: absolute rate measurements and quantum chemical and RRKM calculations for the prototype pi addition reaction

Time-resolved studies of chlorosilylene, ClSiH, generated by the 193 nm laser flash photolysis of 1-chloro-1-silacyclopent-3-ene, are carried out to obtain rate constants for its bimolecular reaction with ethene, C2H4, in the gas-phase. The reaction is studied over the pressure range 0.13-13.3 kPa (with added SF6) at five temperatures in the range 296-562 K. The second order rate constants, obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equation: log(k(infinity)/cm(3) molecule(-1) s(-1))=(-10.55 +/- 0.10) + (3.86 +/- 0.70) kJ mol(-1)/RT ln10. The Arrhenius parameters correspond to a loose transition state and the rate constant at room temperature is 43% of that for SiH2 + C2H4, showing that the deactivating effect of Cl-for-H substitution in the silylene is not large. Quantum chemical calculations of the potential energy surface for this reaction at the G3MP2//B3LYP level show that, as well as 1-chlorosilirane, ethylchlorosilylene is a viable product. The calculations reveal how the added effect of the Cl atom on the divalent state stabilisation of ClSiH influences the course of this reaction. RRKM calculations of the reaction pressure dependence suggest that ethylchlorosilylene should be the main product. The results are compared and contrasted with those of SiH2 and SiCl2 with C2H4.

Do variations in substitution rates and male mutation bias correlate with life-history traits? A study of 32 mammalian genomes

Life-history traits vary substantially across species, and have been demonstrated to affect substitution rates. We compute genomewide, branch-specific estimates of male mutation bias (the ratio of male-to-female mutation rates) across 32 mammalian genomes and study how these vary with life-history traits (generation time, metabolic rate, and sperm competition). We also investigate the influence of life-history traits on substitution rates at unconstrained sites across a wide phylogenetic range. We observe that increased generation time is the strongest predictor of variation in both substitution rates (for which it is a negative predictor) and male mutation bias (for which it is a positive predictor). Although less significant, we also observe that estimates of metabolic rate, reflecting replication-independent DNA damage and repair mechanisms, correlate negatively with autosomal substitution rates, and positively with male mutation bias. Finally, in contrast to expectations, we find no significant correlation between sperm competition and either autosomal substitution rates or male mutation bias. Our results support the important but frequently opposite effects of some, but not all, life history traits on substitution rates. KEY WORDS: Generation time, genome evolution, metabolic rate, sperm competition.

Aromatic nitro substitution reaction between 4-nitro-N-n-butyl-1,8-naphthalimide and n-heptanethiol in water-methanol binary mixtures

The second-order rate constants of thiolysis by n-heptanethiol on 4-nitro-N-n-butyl-1,8-naphthalimide (4NBN) are strongly affected by the water-methanol binary mixture composition reaching its maximum at around 50% mole fraction. In parallel solvent effects on 4NBN absorption molar extinction coefficient also shows a maximum at this composition region. From the spectroscopic study of reactant and product and the known H-bond capacity of the mixture a rationalization that involves specific solvent H-donor interaction with the nitro group is proposed to explain the kinetic data. Present findings also show a convenient methodology to obtain strongly fluorescent imides, valuable for peptide and analogs labeling as well as for thio-naphthalimide derivatives preparations. Copyright (C) 2008 John Wiley & Sons, Ltd.

Capital flows and monetary control under a domestic currency substitution regime: the recent Brazilian experience

The 90s have witnessed a resumption in capital flows to Latin America. due to the conjugation of low interest rates in the US and economic reforms in most LA countries. In Brazil. however. substantial capital flows have becn induced by the extremely high domestic interest rates practiced by the Central Bank as a measure of last reson given the absence of successful stabilization policies. These very high interest rates were needed to prevent capital flight in a context of a surprisingly stable inflation rate above 20% a month. and keep interest bearing govemment securities preferable to foreign assets as money substitutes. We carefully describe how this domestic currency substitution regime (interest bearing govemment securities are substituted for MIas cash holdings) requires the Central Bank to renounce aoy control over monerary aggregates. In this domestic currency substitution regime. hyperinflation is the most likely outcome of an isolated (i.e.. without fiscal adjusanents) attempt by the Brazilian Central Bank to control money.

Dietary macronutrients and performance and plasma hormone and metabolite levels of broiler chickens fat by carbohydrate substitution

The present experiment was aimed to study the effects of an isocaloric substitution of fat by carbohydrate calories while maintaining the same CP content - on some endocrine parameters and key metabolites of the lipid (L), protein (CP) and carbohydrate (CHO) metabolism and muscle cell membrane integrity of broiler chickens. Ninety male broiler chicks (Cobb) were obtained at 1-day old and raised in an environmentally controlled room. Food and water was provided ad libitum. At day 7, the chicks were provided with the experimental diets: Control diet (CON: 20% CP; 9.1% L; 39.6% CHO), Low lipid diet (LowL: 22% CP; 3.36% L; 59.7% CHO), and low carbohydrate diet (LowCHO: 22% CP; 8.09% L; 46.7% CHO). T e chickens fed the CON manifested the best growth rate feed conversion compared to both other groups. The CO chickens showed the highest plasma T-3 Concentrations at 14 days of age as compared to both LowL and LowCHO chickens. At 35 days of age however, LowL chickens were characterized by the highest plasma T-3 levels. Overall, CON birds had the highest plasma T-4 levels (P < 0.0001) compared to LowL and LowCHO chickens. Plasma corticosterone levels were not affected by diet composition. Glucose levels increased towards the end of the experimental period, but there was no overall effect of diet composition on plasma glucose levels. Chickens fed the CON diet were consistently characterized by the highest plasma uric acid levels compared to LowL and LowCHO chickens. Irrespectively of diet, plasma triglyceride levels were high at 14 days of age, then decreased and finally increased again during the last week. This latter increase was most pronounced for the CON chickens and is congruous with their high fat deposition. At 28 days of age, a significant effect of diet was observed, as CON birds had lower plasma free fatty acid (FFA) levels compared to LowL but not to LowCHO chickens. However there was no overall effect of diet composition on plasma FFA levels. Creatine kinase (CK) activities increased significantly with age and were consistently higher in CON chickens. In conclusion, fast growth in broiler chickens is positively correlated with catabolism of protein from dietary or endogenous origin and (muscle) cell membrane disruption as reflected in high plasma uric acid levels and CK activity, respectively. The currently investigated substitution of fat by CHO had no marked effects on endocrine functioning and intermediary metabolism, but this does not exclude that larger substitutions between both nutrients can have an effect.

Import substitution in Brazil between 1995 and 2000

Includes bibliography

First report on the kinetics of the uncatalyzed esterification of cellulose under homogeneous reaction conditions: a rationale for the effect of carboxylic acid anhydride chain-length on the degree of biopolymer substitution

The kinetics of the homogeneous acylation of microcrystalline cellulose, MCC, with carboxylic acid anhydrides with different acyl chain-length (Nc; ethanoic to hexanoic) in LiCl/N,N-dimethylacetamide have been studied by conductivity measurements from 65 to 85 A degrees C. We have employed cyclohexylmethanol, CHM, and trans-1,2-cyclohexanediol, CHD, as model compounds for the hydroxyl groups of the anhydroglucose unit of cellulose. The ratios of rate constants of acylation of primary (CHM; Prim-OH) and secondary (CHD; Sec-OH) groups have been employed, after correction, in order to split the overall rate constants of the reaction of MCC into contributions from the discrete OH groups. For the model compounds, we have found that k((Prim-OH))/k((Sec-OH)) > 1, akin to reactions of cellulose under heterogeneous conditions; this ratio increases as a function of increasing Nc. The overall, and partial rate constants of the acylation of MCC decrease from ethanoic- to butanoic-anhydride and then increase for pentanoic- and hexanoic anhydride, due to subtle changes in- and compensations of the enthalpy and entropy of activation.

Thermodynamics of Axial Substitution and Kinetics of Reactions with Amino Acids for the Paddlewheel Complex Tetrakis(acetato)chloridodiruthenium(II,III)

The known paddlewheel, tetrakis(acetato)chloridodiruthenium(II,III), offers a versatile synthetic route to a novel class of antitumor diruthenium(II,III) metallo drugs, where the equatorial ligands are nonsteroidal anti-inflammatory carboxylates. This complex was studied here as a soluble starting prototype model for antitumor analogues to elucidate the reactivity of the [Ru-2(CH3COO)(4)](+) framework. Thermodynamic studies on equilibration reactions for axial substitution of water by chloride and kinetic studies on reactions of the diaqua complexes with the amino acids glycine, cysteine, histidine, and tryptophan were performed. The standard thermodynamic reaction parameters Delta H degrees, Delta S degrees, and Delta V degrees were determined and showed that both of the sequential axial substitution reactions are enthalpy driven. Kinetic rate laws and rate constants were determined for the axial substitution reactions of coordinated water by the amino acids that gave the corresponding aqua(amino acid)-Ru-2 substituted species. The results revealed that the [Ru-2(CH3COO)(4)](+) paddlewheel framework remained stable during the axial ligand substitution reactions and was also mostly preserved in the presence of the amino acids.

Bioinspired fabrication of biosilica-based bone substitution materials

Until today, autogenic bone grafts from various donor regions represent the gold standard in the field of bone reconstruction, providing both osteoinductive and osteoconductive characteristics. However, due to low availability and a disequilibrium between supply and demand, the risk of disease transfer and morbidity, usually associated with autogeneic bone grafts, the development of biomimic materials with structural and chemical properties similar to those of natural bone have been extensively studied. So far,rnonly a few synthetic materials, so far, have met these criteria, displaying properties that allow an optimal bone reconstitution. Biosilica is formed enzymatically under physiological-relevant conditions (temperature and pH) via silicatein (silica protein), an enzyme that was isolated from siliceous sponges, cloned, and prepared in a recombinant way, retaining its catalytic activity. It is biocompatible, has some unique mechanical characteristics, and comprises significant osteoinductive activity.rnTo explore the application of biosilica in the fields of regenerative medicine,rnsilicatein was encapsulated, together with its substrate sodium metasilicate, into poly(D,L-lactide)/polyvinylpyrrolidone(PVP)-based microspheres, using w/o/wrnmethodology with solvent casting and termed Poly(D,L-lactide)-silicatein silicacontaining-microspheres [PLASSM]. Both silicatein encapsulation efficiency (40%) and catalytic activity retention upon polymer encapsulation were enhanced by addition of an essential pre-emulsifying step using PVP. Furthermore, the metabolic stability, cytoxicity as well as the kinetics of silicatein release from the PLASSM were studied under biomimetic conditions, using simulated body fluid. As a solid support for PLASSM, a polyvinylpyrrolidone/starch/Na2HPO4-based matrix (termed plastic-like filler matrix containing silicic acid [PMSA]) was developed and its chemical and physical properties determined. Moreover, due to the non-toxicity and bioinactivity of the PMSA, it is suggested that PMSA acts as osteoconductive material. Both components, PLASSM and PMSA, when added together, form arnbifunctional 2-component implant material, that is (i)non-toxic(biocompatible), (ii)moldable, (iii) self-hardening at a controlled and clinically suitable rate to allows a tight insertion into any bone defect (iv) biodegradable, (v)forms a porous material upon exposure to body biomimetic conditions, and (vi)displays both osteoinductive (silicatein)and osteoconductive (PMSA) properties.rnPreliminary in vivo experiments were carried out with rabbit femurs, by creatingrnartificial bone defects that were subsequently treated with the bifunctional 2-component implant material. After 9 weeks of implantation, both computed tomography (CT) and morphological analyses showed complete resorption of the implanted material, concurrent with complete bone regeneration. The given data can be considered as a significant contribution to the successful introduction of biosilica-based implants into the field of bone substitution surgery.

There is a place for radical cystectomy and urinary diversion, including orthotopic bladder substitution, in patients aged 75 and older: Results of a retrospective observational analysis from a high-volume center

INTRODUCTION The incidence of cancer increases with age and owing to the changing demographics we are increasingly confronted with treating bladder cancer in old patients. We report our results in patients>75 years of age who underwent open radical cystectomy (RC) and urinary diversion. MATERIAL AND METHODS From January 2000 to March 2013, a consecutive series of 224 old patients with complete follow-up who underwent RC and urinary diversion (ileal orthotopic bladder substitute [OBS], ileal conduit [IC], and ureterocutaneostomy [UCST]) were included in this retrospective single-center study. End points were the 90-day complication rates (Clavien-Dindo classification), 90-day mortality rates, overall and cancer-specific survival rates, and continence rates (OBS). RESULTS Median age was 79.2 years (range: 75.1-91.6); 35 of the 224 patients (17%) received an OBS, 178 of the 224 patients (78%) an IC, and 11 of the 224 patients (5%) an UCST. The 90-day complication rate was 54.3% in the OBS (major: Clavien grade 3-5: 22.9%, minor: Clavien Grade 1-2: 31.4%), 56.7% in the IC (major: 27%, minor: 29.8%), and 63.6% in the UCST group (major: 36.4%, minor: 27.3%); P = 0.001. The 90-day mortality was 0% in the OBS group, 13% in the IC group, and 10% in the UCST group (P = 0.077). The Glasgow prognostic score was an independent predictor of all survival parameters assessed, including 90-day mortality. Median follow-up was 22 months. Overall and cancer-specific survivals were 90 and 98, 47 and 91, and 11 and 12 months for OBS, IC, and UCST, respectively. In OBS patients, daytime continence was considered as dry in 66% and humid in 20% of patients. Nighttime continence was dry in 46% and humid 26% of patients. CONCLUSION With careful patient selection, oncological and functional outcome after RC can be good in old patients. Old age as the sole criterion should not preclude the indication for RC or the option of OBS. In old patients undergoing OBS, satisfactory continence results can be achieved.

Influence of cement properties in the reaction rate and mechanical behavior of concrete with high fl y ash content

The use of fly ash (FA) as an admixture to concrete is broadly extended for two main reasons: the reduction of costs that supposes the substitution of cement and the micro structural changes motivated by the mineral admixture. Regarding this second point, there is a consensus that considers that the ash generates a more compact concrete and a reduction in the size of the pore. However, the measure in which this contributes to the pozzolanic activity or as filler is not well defined. There is also no justification to the influence of the physical parameters, fineness of the grain and free water, in its behavior. This work studies the use of FA as a partial substitute of the cement in concretes of different workability (dry and wet) and the influence in the reactivity of the ash. The concrete of dry consistency which serves as reference uses a cement dose of 250 Kg/m 3 and the concrete of fluid consistency utilized a dose of cement of 350 Kg/m 3 . Two trademark of Portland Cement Type 1 were used. The first reached the resistant class for its fineness of grain and the second one for its composition. Moreover, three doses of FA have been used, and the water/binder ratio was constant in all the mixtures. We have studied the mechanical properties and the micro-structure of the concretes by means of compressive strength tests, mercury intrusion porosimetry (MIP) and thermal analysis (TA). The results of compressive strength tests allow us to observe that concrete mixtures with cements of the same classification and similar dosage of binder do not present the same mechanical behavior. These results show that the effective water/binder ratio has a major role in the development of the mechanical properties of concrete. The study of different dosages using TA, thermo-gravimetry and differential thermal analysis, revealed that the portlandite content is not restrictive in any of the dosages studied. Again, this proves that the rheology of the material influences the reaction rate and content of hydrated cement products. We conclude that the available free water is determinant in the efficiency of pozzolanic reaction. It is so that in accordance to the availability of free water, the ashes can react as an active admixture or simply change the porous distribution. The MIP shows concretes that do not exhibit significant changes in their mechanical behavior, but have suffered significant variation in their porous structure

Employment rate impacts of charging the Heavy Good Vehicle corridor (Madrid-Sevilla) across Spanish regions: a Random Utility Based Multiregional Input-Output approach

The implementation of a charging policy for heavy goods vehicles in European Union (EU) member countries has been imposed to reflect costs of construction and maintenance of infrastructure as well as externalities such as congestion, accidents and environmental impact. In this context, EU countries approved the Eurovignette directive (1999/62/EC) and its amending directive (2006 /38/EC) which established a legal framework to regulate the system of tolls. Even if that regulation seek s to increase the efficien cy of freight, it will trigger direct and indirect effects on Spain’s regional economies by increasing transport costs. This paper presents the development of a multiregional Input-Output methodology (MRIO) with elastic trade coefficients to predict in terregional trade, using transport attributes integrated in multinomial logit models. This method is highly useful to carry out an ex-ante evaluation of transport policies because it involves road freight transport cost sensitivity, and determine regional distributive and substitution economic effect s of countries like Spain, characterized by socio-demographic and economic attributes, differentiated region by region. It will thus be possible to determine cost-effective strategies, given different policy scenarios. MRIO mode l would then be used to determine the impact on the employment rate of imposing a charge in the Madrid-Sevilla corridor in Spain. This methodology is important for measuring the impact on the employment rate since it is one of the main macroeconomic indicators of Spain’s regional and national economic situation. A previous research developed (DESTINO) using a MRIO method estimated employment impacts of road pricing policy across Spanish regions considering a fuel tax charge (€/liter) in the entire shortest cost path network for freight transport. Actually, it found that the variation in employment is expected to be substantial for some regions, and negligible for others. For example, in this Spanish case study of regional employment has showed reductions between 16.1% (Rioja) and 1.4% (Madrid region). This variation range seems to be related to either the intensity of freight transport in each region or dependency of regions to transport intensive economic sect ors. In fact, regions with freight transport intensive sectors will lose more jobs while regions with a predominantly service economy undergo a fairly insignificant loss of employment. This paper is focused on evaluating a freight transport vehicle-kilometer charge (€/km) in a non-tolled motorway corridor (A-4) between Madrid-Sevilla (517 Km.). The consequences of the road pricing policy implementation show s that the employment reductions are not as high as the diminution stated in the previous research because this corridor does not affect the whole freight transport system of Spain.

Mutation in bone morphogenetic protein receptor-IB is associated with increased ovulation rate in Booroola Mérino ewes

Ewes from the Booroola strain of Australian Mérino sheep are characterized by high ovulation rate and litter size. This phenotype is due to the action of the FecBB allele of a major gene named FecB, as determined by statistical analysis of phenotypic data. By genetic analysis of 31 informative half-sib families from heterozygous sires, we showed that the FecB locus is situated in the region of ovine chromosome 6 corresponding to the human chromosome 4q22–23 that contains the bone morphogenetic protein receptor IB (BMPR-IB) gene encoding a member of the transforming growth factor-β (TGF-β) receptor family. A nonconservative substitution (Q249R) in the BMPR-IB coding sequence was found to be associated fully with the hyperprolificacy phenotype of Booroola ewes. In vitro, ovarian granulosa cells from FecBB/FecBB ewes were less responsive than granulosa cells from FecB+/FecB+ ewes to the inhibitory effect on steroidogenesis of GDF-5 and BMP-4, natural ligands of BMPR-IB. It is suggested that in FecBB/FecBB ewes, BMPR-IB would be inactivated partially, leading to an advanced differentiation of granulosa cells and an advanced maturation of ovulatory follicles.