Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model.

Microsatellites make up ∼3% of the human genome, and there is increasing evidence that some microsatellites can have important functions and can be conserved by selection. To investigate this conservation, we performed a genome-wide analysis of human microsatellites and measured their conservation using a binary character birth--death model on a mammalian phylogeny. Using a maximum likelihood method to estimate birth and death rates for different types of microsatellites, we show that the rates at which microsatellites are gained and lost in mammals depend on their sequence composition, length, and position in the genome. Additionally, we use a mixture model to account for unequal death rates among microsatellites across the human genome. We use this model to assign a probability-based conservation score to each microsatellite. We found that microsatellites near the transcription start sites of genes are often highly conserved, and that distance from a microsatellite to the nearest transcription start site is a good predictor of the microsatellite conservation score. An analysis of gene ontology terms for genes that contain microsatellites near their transcription start site reveals that regulatory genes involved in growth and development are highly enriched with conserved microsatellites

Modelos, parámetros farmacocinéticos y penetración en leche de Ceftazidima administrada por vía endovenosa en bovinos lecheros en producción

Penetration of ceftazidime in milk and pharmacokinetic parameters and models were determined. Five healthy lactating dairy cows producing 10 ± 2 liters per day were injected intravenously with a bolus administration of a dosage of 10 mg/kg body weight. Blood and milk samples were collected during 24 hours after ceftazidime administration. Concentration of ceftazidime in serum and milk were quantified by HPLC. The pharmacokinetic parameters calculated were: percentage of penetration in milk (47.7 ± 38.2%), volume of distibution in steady state (489.8 ±136.9 ml.kg-1), area under the curve far serum and milk (261.3 ± 124.1 and 115.3 ± 74.4 µg.ml.h-1, respectively) and blood clearance (72.5 ± 18.1 m1.h-1.kg-1. The coefficient of correlation of serum concentrations (CC) and the Akaike information criteria (AIC) were used to discriminate the pharmacokinetic model better adapted to describe the curve of ceftazidime conceniration over time. The hicompartimental model (CC=0,998 and AIC = 34.3) was the most appropriate to obtain the best fitted curve to describe the serum concentration of ceftazidime over time after intravenous administration in lactating dairy cows.En el presente trabajo se determinaron, en bovinos lecheros en lactancia, los modelos y parámetros farmacocinéticos y la penetración en leche de ceftazidima. Se utilizaron 5 bovinos lecheros sanos, con una producción diaria de 10 ± 2 litros. Todos los animales recibieron una monodosis de ceftazidima (10 mg/kg de peso) vía endovenosa y se les tomaron muestras sanguíneas y lácteas durante las 24 horas posteriores a la administración del antibiótico. Las concentraciones séricas y lácteas de la droga fueron cuantificadas por HPLC. Se calcularon los siguientes parámetros farmacocinéticos: porcentaje de penetración en leche (47,7 ± 38,2), volumen de distribución en estado estacionario (489,8 ± 136,9 ml.kg-1), área bajo la curva sérica y láctea (261,3 ± 124,1 y 115,3 ± 74,4 µg.ml-1.h, respectivamente) y aclaramiento sanguíneo (72,5 ± 18,1 ml.h-1.kg-1). Para la discriminación del modelo farmacocinético que mejor se adapte a la descripción de la curva concentración-tiempo de la ceftazidima se utilizó el coeficiente de correlación (CC) de las concentraciones séricas y el criterio de medida Akaike (AIC), pudiendo observarse que el modelo tricompartimental (CC = 0,998 y AIC = 34 ) es el más apropiado para realizar el ajuste de datos séricos de concentración-tiempo de ceftazidima luego de administrada por vía endovenosa a bovinos en lactancia.Trabajo presentado en el I Congreso de la Federación Farmacéutica Sudamericana y II Congreso de Ciencias Farmacéuticas del Cono Sur (Montevideo, 1993)

Effect of temporal resolution of wind data on wind erosion prediction with the Revised Wind Erosion Equation (RWEQ)

In wind erosion modelling and assessment, wind speed is a crucial variable. Available records for large regions of the world generally show relatively low temporal resolution. The effect of using wind data of different temporal resolutions in RWEQ discrete and continuous versions was assessed. Wind erosion was measured during 82 high-wind events occurring between 2005 and 2008. Simulated and measured erosion values were compared. For wind erosion simulation during discrete periods, the model was loaded with wind speeds averaged in 5 minutes and 1 hour- intervals. For continuous simulation, a weather file for RWEQ/ 97 was developed and Weibull factors were calculated using both hourly and daily wind speeds. When the discrete version of RWEQ was used with hourly wind speeds instead of five-minute averages, the total simulated soil loss was reduced by 44%. The model efficiency was not significantly affected by wind speed data resolution. RWEQ continuous version, loaded with monthly Weibull parameters using hourly wind speeds, calculated zero erosion. Monthly Weibull distribution scale factors calculated using daily wind speeds were reduced by 32% on average with respect to hourly data. Increasing the Weibull scale parameter by up to 50% slightly improved the monthly simulated erosion rates. Using low resolution wind speed data reduces the model outputs. This may be corrected but a large amount of field information is needed.Fil: Panebianco, Juan Esteban. Consejo Nacional de Invest.cientif.y Tecnicas. Instituto D/cs D/l/tierra y Ambientales D/l/pampa; Argentina;Fil: Buschiazzo, Daniel Eduardo. Consejo Nacional de Invest.cientif.y Tecnicas. Instituto D/cs D/l/tierra y Ambientales D/l/pampa; Argentina

Desing of a portable wind tunnel for the wind erosion study

La erosión eólica (EE) es un proceso de degradación irreversible de suelos de regiones áridas y semiáridas. Con el uso de túneles de viento portátiles es posible simular la EE controlando variables críticas como la velocidad y dirección del viento, la duración de los eventos erosivos; además de parámetros del suelo en condiciones naturales como los niveles de humedad, rugosidad y cobertura. Los objetivos de este trabajo fueron: 1) describir los principales aspectos del diseño y la operación de un túnel de viento portátil para estudios de erosión eólica, y 2) Calibrar el túnel para cumplir con los criterios aerodinámicos relacionados con el desarrollo de un perfil vertical de viento y de distribución de material erosionado similares a las condiciones naturales. Los principales componentes del túnel son: chasis, motor, hélice, sección curva, placa cribada y las secciones del túnel propiamente dicho. Cada una de estas secciones tiene 2 m de largo; 0,5 m de ancho y 1 m de alto. El túnel fue calibrado en un Haplustol Éntico con una superficie lisa y sin cobertura vegetal. La velocidad máxima alcanzada medida a 0,6 m fue de 22,5 m s-1. Esto significa que el túnel permite simular velocidades consideradas erosivas a campo. El perfil vertical de viento y la distribución de material erosionado son similares a los producidos en condiciones naturales. El túnel de viento desarrollado cumple con las condiciones de diseño para la simulación de eventos de erosión eólica a campo. El uso del mismo mejorará el estudio de procesos básicos y el desarrollo de tecnología para el control de la erosión eólica en suelos de Argentina, además de ser una fuente de consulta para la construcción de futuros túneles de viento para el estudio de la erosión eólica.Wind erosion (WE) is an irreversible soil degradation process of arid and semiarid regions. With portable wind tunnels it is possible to simulate WE controlling critical variables such as wind speed and direction, duration of erosive events; and soil surface parameters under natural conditions as moisture, roughness and cover level. The objectives of this study were: 1) to describe the main aspects of the design and operation of a portable wind tunnel to study WE, and 2) to calibrate the wind tunnel to fit the aerodynamics criterions related to the development of a vertical wind profile and an eroded material distribution similar to natural conditions. The main components of wind tunnel are chassis, engine, wind fan, s-shaped section, honeycomb diffusor, the stabilization section and the working sections. These sections have 2 m length; 0.5 m width and 1 m height. The wind tunnel was calibrated in an Entic Haplustoll in a bare and flat surface. The maximum measured velocity reached at 0.6 m was 22.5 m s-1, implying that the wind tunnel allows simulating field erosive wind velocities. The vertical wind profile and eroded material distribution are similar to those produced under natural field conditions. The use of this wind tunnel will improve the study of basic processes and technology for wind erosion control of soils of Argentina, also it will serve as a guide for future wind tunnel developments to study wind erosion.Fil: Colazo, Juan Cruz. Instituto Nacional de Tecnología Agropecuaria. Centro Regional La Pampa-San Luis. Estación Experimental Agropecuaria San Luis; ArgentinaFil: Mendez, Mariano Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: de Oro, Laura Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: Avecilla, Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: Panebianco, Juan Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; ArgentinaFil: Buschiazzo, Daniel Eduardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Ciencias de la Tierra y Ambientales de La Pampa. Universidad Nacional de La Pampa. Facultad de Ciencias Exactas y Naturales. Instituto de Ciencias de la Tierra y Ambientales de La Pampa; Argentin

Bayesian estimation of nonsynonymous/synonymous rate ratios for pairwise sequence comparisons.

The nonsynonymous/synonymous rate ratio (ω = d(N)/d(S)) is an important measure of the mode and strength of natural selection acting on nonsynonymous mutations in protein-coding genes. The simplest such analysis is the estimation of the d(N)/d(S) ratio using two sequences. Both heuristic counting methods and the maximum-likelihood (ML) method based on a codon substitution model are widely used for such analysis. However, these methods do not have nice statistical properties, as the estimates can be zero or infinity in some data sets, so that their means and variances are infinite. In large genome-scale comparisons, such extreme estimates (either 0 or ∞) of ω and sequence distance (t) are common. Here, we implement a Bayesian method to estimate ω and t in pairwise sequence comparisons. Using a combination of computer simulation and real data analysis, we show that the Bayesian estimates have better statistical properties than the ML estimates, because the prior on ω and t shrinks the posterior of those parameters away from extreme values. We also calculate the posterior probability for ω > 1 as a Bayesian alternative to the likelihood ratio test. The new method is computationally efficient and may be useful for genome-scale comparisons of protein-coding gene sequences

Allosteric Activation of Bacterial Response Regulators: the Role of the Cognate Histidine Kinase Beyond Phosphorylation

Response regulators are proteins that undergo transient phosphorylation, connecting specific signals to adaptive responses. Remarkably, the molecular mechanism of response regulator activation remains elusive, largely because of the scarcity of structural data on multidomain response regulators and histidine kinase/response regulator complexes. We now address this question by using a combination of crystallographic data and functional analyses in vitro and in vivo, studying DesR and its cognate sensor kinase DesK, a two-component system that controls membrane fluidity in Bacillus subtilis. We establish that phosphorylation of the receiver domain of DesR is allosterically coupled to two distinct exposed surfaces of the protein, controlling noncanonical dimerization/tetramerization, cooperative activation, and DesK binding. One of these surfaces is critical for both homodimerization- and kinase-triggered allosteric activations. Moreover, DesK induces a phosphorylation-independent activation of DesR in vivo, uncovering a novel and stringent level of specificity among kinases and regulators. Our results support a model that helps to explain how response regulators restrict phosphorylation by small-molecule phosphoryl donors, as well as cross talk with noncognate sensors.Fil: Trajtenberg, Felipe. Instituto Pasteur de Montevideo; UruguayFil: Albanesi, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; Argentina. Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Ruetalo, Natalia. Instituto Pasteur de Montevideo; UruguayFil: Botti, Horacio. Instituto Pasteur de Montevideo; UruguayFil: Mechaly, Ariel. Instituto Pasteur de Montevideo; Uruguay. Institut Pasteur, Unité de Microbiologie Structurale, Paris; FranciaFil: Nieves, Marcos. Instituto Pasteur de Montevideo, Laboratorio de Biología Celular de Membranas, Montevideo; UruguayFil: Aguilar, Pablo Sebastián. Instituto Pasteur de Montevideo, Laboratorio de Biología Celular de Membranas, Montevideo; UruguayFil: Cybulski, Larisa Estefania. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; Argentina. Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Larrieux, Nicole. Instituto Pasteur de Montevideo; UruguayFil: de Mendoza, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Rosario. Instituto de Biología Molecular y Celular de Rosario; Argentina. Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas; ArgentinaFil: Buschiazzo, Alejandro. Instituto Pasteur de Montevideo; Uruguay. Institut Pasteur, Département de Biologie Structurale et Chimie, Paris; Franci

Solution structure of a repeated unit of the ABA-1 nematode polyprotein allergen of ascaris reveals a novel fold and two discrete lipid-binding sites

Parasitic nematode worms cause serious health problems in humans and other animals. They can induce allergic-type immune responses, which can be harmful but may at the same time protect against the infections. Allergens are proteins that trigger allergic reactions and these parasites produce a type that is confined to nematodes, the nematode polyprotein allergens (NPAs). These are synthesized as large precursor proteins comprising repeating units of similar amino acid sequence that are subsequently cleaved into multiple copies of the allergen protein. NPAs bind small lipids such as fatty acids and retinol (Vitamin A) and probably transport these sensitive and insoluble compounds between the tissues of the worms. Nematodes cannot synthesize these lipids, so NPAs may also be crucial for extracting nutrients from their hosts. They may also be involved in altering immune responses by controlling the lipids by which the immune and inflammatory cells communicate. We describe the molecular structure of one unit of an NPA, the well-known ABA-1 allergen of Ascaris and find its structure to be of a type not previously found for lipid-binding proteins, and we describe the unusual sites where lipids bind within this structur

Rational Design of a New Trypanosoma rangeli Trans-Sialidase for Efficient Sialylation of Glycans

This paper reports rational engineering of Trypanosoma rangeli sialidase to develop an effective enzyme for a potentially important type of reactivity: production of sialylated prebiotic glycans. The Trypanosoma cruzi trans-sialidase and the homologous T. rangeli sialidase has previously been used to investigate the structural requirements for trans-sialidase activity. We observed that the T. cruzi trans-sialidase has a seven-amino-acid motif (197-203) at the border of the substrate binding cleft. The motif differs substantially in chemical properties and substitution probability from the homologous sialidase, and we hypothesised that this motif is important for trans-sialidase activity. The 197-203 motif is strongly positively charged with a marked change in hydrogen bond donor capacity as compared to the sialidase. To investigate the role of this motif, we expressed and characterised a T. rangeli sialidase mutant, Tr13. Conditions for efficient trans-sialylation were determined, and Tr13's acceptor specificity demonstrated promiscuity with respect to the acceptor molecule enabling sialylation of glycans containing terminal galactose and glucose and even monomers of glucose and fucose. Sialic acid is important in association with human milk oligosaccharides, and Tr13 was shown to sialylate a number of established and potential prebiotics. Initial evaluation of prebiotic potential using pure cultures demonstrated, albeit not selectively, growth of Bifidobacteria. Since the 197-203 motif stands out in the native trans-sialidase, is markedly different from the wild-type sialidase compared to previous mutants, and is shown here to confer efficient and broad trans-sialidase activity, we suggest that this motif can serve as a framework for future optimization of trans-sialylation towards prebiotic production

Perspectives on the Trypanosoma cruzi-host cell receptor interaction

Chagas disease is caused by the parasite Trypanosoma cruzi. The critical initial event is the interaction of the trypomastigote form of the parasite with host receptors. This review highlights recent observations concerning these interactions. Some of the key receptors considered are those for thromboxane, bradykinin, and for the nerve growth factor TrKA. Other important receptors such as galectin-3, thrombospondin, and laminin are also discussed. Investigation into the molecular biology and cell biology of host receptors for T. cruzi may provide novel therapeutic targets

The pharmacokinetics of ceftazidime in lactating and non-lactating cows

The pharmacokinetics of ceftazidime (CAZ) were studied in lactating (LTG) and non-lactating (NLTG) cows. Two groups (LTG and NLTG) of 5 healthy dairy cows were given ceftazidime (10 mg/ kg body weight) intravenously (i.v.) and intramuscularly (i.m.). Serum and milk (LTG) and serum samples (NLTG) were collected over a 24-h period post-administration. CAZ concentrations in serum and milk were determined by high-performance liquid chromatography, and an interactive and weighted-non-linear least-squares regression analysis was used to perform the pharmacokinetic analysis. The pharmacokinetic profiles in LTG and NLTG cows which had received CAZ i.v. fitted a three-compartment model and a two-compartment model, respectively. The CAZ concentration-time curves in serum and the area under the curve were greater and more sustained (p<0.05) in the LTG cows by both routes, while the serum clearance (Cls=72.5±18.1 ml/h per kg) was lower (p<0.05) than that in the NLTG cows (Cls=185.9±44.2 ml/h per kg). CAZ given i.v. exhibited a relatively long half-life of elimination (t; 1/2 β (LTG)=1.1±0.2 h; t; 1/2 β (NLTG)=1.4±0.3 h). Compared with other cephalosporins, CAZ had good penetration into the mammary gland (47.7±38.2% for CAZ i.v.; 51.1±39.0% for CAZ i.m.). Finally, the bioavailability of CAZ (F(LTG)=98.9±36.8%; F(NLTG)=77.1±25.3%) was suitable for its use by the i.m. route in lactating and non-lactating cows.Facultad de Ciencias MédicasComisión de Investigaciones Científicas de la provincia de Buenos Aire