Hydrogen Bonds Computing Server (HBCS): an online web server to compute hydrogen-bond interactions and their precision

Hydrogen bonds in biological macromolecules play significant structural and functional roles. They are the key contributors to most of the interactions without which no living system exists. In view of this, a web-based computing server, the Hydrogen Bonds Computing Server (HBCS), has been developed to compute hydrogen-bond interactions and their standard deviations for any given macromolecular structure. The computing server is connected to a locally maintained Protein Data Bank (PDB) archive. Thus, the user can calculate the above parameters for any deposited structure, and options have also been provided for the user to upload a structure in PDB format from the client machine. In addition, the server has been interfaced with the molecular viewers Jmol and JSmol to visualize the hydrogen-bond interactions. The proposed server is freely available and accessible via the World Wide Web at http://bioserver1.physics.iisc.ernet.in/hbcs/.

Kinetics and Force Dependence of P-selectin/PSGL-1 Interactions Measured by AFM

Leukocytes roll along the endothelium of postcapillary venules in response to inflammatory and thrombotic processes. The rolling under hydrodynamic shear forces is a first step in directing leukocytes out of the blood stream into sites of inflammation and is mediated by the selectins, a family of extended, modular, and calcium-dependent lectin receptors. The interactions between P-, E-or L-selectins and their count.

Investigation of biotin-streptavidin binding interactions using microcantilever sensors

We report the investigation of biotin-streptavidin binding interactions using microcantilever sensors. A symmetric cantilever construction is employed to minimize the effects of thermal drift and the control of surface chemistry on the backside of the cantilever is demonstrated to reduce the effects of non-specific binding interactions on the cantilever. Three structurally different biotin modified cantilever surfaces are used as a model system to study the binding interaction with streptavidin. The cantilever response to the binding of streptavidin on these biotin sensing monolayers is compared. The lowest detection limit of streptavidin using biotin-HPDP is found to be between 1 and 10 nM limited by the optical measurement setup. Surface characterization using quartz crystal microbalance (QCM) and high-resolution atomic force microscope (AFM) is used to benchmark the cantilever sensor response. In addition, the QCM and AFM studies reveal that the surface density of bound streptavidin on biotin modified surfaces was low, thereby implying that effects other than steric hindrance are responsible for defining cantilever response. (c) 2006 Elsevier B.V. All rights reserved.

Interactions of CO, HCl, and Sox in Pulverised Coal Flames

The effect of HCl and SO_2 on CO oxidation in pulverised coal flames was investigated experimentally and kinetically in an entrained flow combustion reactor. Two bituminous coals (German 'Goettelborn' and a Polish coal) were used as fuels with a feeding rate of 1 or 1.5 kg/h. HCl or SO_2 is introduced into the reactor premixed with the primary air. Experimental results indicate that HCl addition may inhibit CO oxidation in coal flames and increases CO emission. Reducing temperature in the reactor will enhance the inhibitory effect of HCl on CO oxidation. The measured CO profiles along the reactor height clearly show that the addition of HCl may inhibit CO oxidation. In the experimental range of SO_2 addition. The inhibiting effect of SO_2 on CO oxidation is less significant than HCl. A detailed kinetic mechanism is used to model the reactions. And the controlling reactions are analysed.

An analysis of subgrid-resolved scale interactions with use of results from direct numerical simulations

Subgrid nonlinear interaction and energy transfer are analyzed using direct numerical simulations of isotropic turbulence. Influences of cutoff wave number at different ranges of scale on the energetics and dynamics have been investigated. It is observed that subgrid-subgrid interaction dominates the turbulent dynamics when cut-off wave number locates in the energy-containing range while resolved-subgrid interaction dominates if it is in the dissipation range; By decomposing the subgrid energy transfer and nonlinear interaction into 'forward' and 'backward' groups according to the sign of triadic interaction, we find that individually each group has very large contribution, but the net of them is much smaller, implying that tremendous cancellation happens between these two groups.

Electrostatic Interactions Between Glycosaminoglycan Molecules

The electrostatic interactions between nearest-neighbouring chondroitin sulfate glycosaminoglycan (CS-GAG) molecular chains are obtained on the bottle brush conformation of proteoglycan aggrecan based on an asymptotic solution of the Poisson-Boltzmann equation the CS-GAGs satisfy under the physiological conditions of articular cartilage. The present results show that the interactions are associated intimately with the minimum separation distance and mutual angle between the molecular chains themselves. Further analysis indicates that the electrostatic interactions are not only expressed to be purely exponential in separation distance and decrease with the increasing mutual angle but also dependent sensitively on the saline concentration in the electrolyte solution within the tissue, which is in agreement with the existed relevant conclusions.

Quantifying the Effects of Contact Duration, Loading Rate, and Approach Velocity on P-Selectin-PSGL-1 Interactions Using AFM

Kinetics and its regulation by extrinsic physical factors govern selectin-ligand interactions that mediate tethering and rolling of circulating cells on the vessel wall under hemodynamic forces. While the force regulation of off-rate for dissociation of selectin-ligand bonds has been extensively studied, much less is known about how transport impacts the on-rate for association of these bonds and their stability. We used atomic force microscopy (AFM) to quantify how the contact duration, loading rate, and approach velocity affected kinetic rates and strength of bonds of P-selectin interacting with P-selectin glycoprotein ligand I (PSGL-1). We found a saturable relationship between the contact time and the rupture force, a biphasic relationship between the adhesion probability and the retraction velocity, a piece-wise linear relationship between the rupture force and the logarithm of the loading rate, and a threshold relationship between the approach velocity and the rupture force. These results provide new insights into how physical factors regulate receptor-ligand interactions.

Establecimiento de plan sanitario y profilactico en la Granja Cunicula Artesanal de Nindiri, departamento de Masaya, Nicaragua

Dado que en Nicaragua la producción cunícula se está convirtiendo en una alternativa de consumo para la población, es necesario que en las granjas cunícula se implementen medidas profilácticas para mejorar las condiciones de salud y por ende la calidad de su carne, por lo cual se propuso este trabajo de investigación que lleva por titulo: Establecimiento de Plan Sanitario y Profiláctico en la Granja Cunícula Artesanal de Nindirí, Departamento de Masaya, Nicaragua. Por lo cual se procedió a establecer los siguientes objetivos: Validar la aplicación de minerales y vitaminas en granjas cuniculas de explotación artesanal, validar la aplicación de Coccidiostáticos en los conejos de diferentes categorías, validar la aplicación de desparasitantes externos e internos en los conejos de diferentes categorías. Este estudio se realizó en un período de seis meses mediante laaplicación de cuatro tipos de tratamiento con frecuencia de aplicación TA (Sulfaprin) mensual, TB (Levamisol) cada tres meses, TC (Ivermectina) cada tres meses, TD (Vitaminas AD3E) semanal, en total se estudiaron 80 animales de diferentes categorías. Los tratamientos aplicados demostraron efectividad en el control de las patologías en la granja. Así el plan sanitario permitió mejorar casi en su totalidad patologías predisponentes. En conclusión se puede decir que la aplicación del plan sanitario acompañado de medidas higiénicas, controló en un 95% la presencia de patologías, disminuyó la tasa de mortalidad y los costos de producción, además se obtuvo mejor calidad de la carne.

Kinetic measurements of cell surface E-selectin/carbohydrate ligand interactions

Selectin/ligand interactions initiate the multistep adhesion and signaling cascades in the recruitment of leukocytes from circulation to inflamed tissues and may also play a role in tumor metastasis. Kinetic properties of these interactions are essential determinants governing blood-borne cells' tethering to and rolling on the vessel wall. Extending our recently developed micropipette method, we have measured the kinetic rates of E-selectin/ligand interactions. Red cells coated with an E-selectin construct were allowed to bind HL-60 or Colo-205 cells bearing carbohydrate ligands. Specific adhesions were observed to occur at isolated points, the frequency of which followed a Poisson distribution. These point attachments were formed at the same rate with both the HL-60 and Colo-205 cells (0.14 +/- 0.04 and 0.13 +/- 0.03 mum(2) s(-1) per unit density of E-selectin, respectively) but dissociated from the former at a rate twice as fast as did from the latter (0.92 +/- 0.23 and 0.44 +/- 0.10 s(-1), respectively). The reverse rates agree well with those measured by the flow chamber. The forward rates are orders of magnitude higher than those of Fc gamma receptors interacting with IgG measured under similar conditions, consistent with the rapid kinetics requirement for the function of E-selectin/ligand binding, which is to capture leukocytes on endothelial surfaces from flow.

Estudio de la implementación del plan de bioseguridad en granjas de engorde de cuatro empresas avícolas de Nicaragua

El estudio del plan de bioseguridad de granjas de engorde de las cuatro empresas avícolas de engorde de Nicaragua se realizó con el objetivo de evaluar las medidas de bioseguridad, permitiéndonos: conocer las fortalezas y debilidades, desarrollo tecnológico y distribución de las cuatro empresas por departamento. La información se recopiló en el formato de encuesta de medidas de bioseguridad del MAGFOR, que consiste en un stop de 86 preguntas dirigidas a investigar su cumplimiento, las respuestas se analizaron mediante incorporación de datos en hoja electrónica en Excel y procesadas en Acces para estudiarlas con la formula V/TP x 100; El nivel tecnológico se calculó agregando un valor a cada pregunta con un puntaje de 2 a 5 para dar un peso o ponderación especifica, 2 las de menor tecnología y 5 las de mayor nivel ténológico. Encontrándose que el 78% de la encuestas del plan de bioseguridad es aprobado con rango de 98 a 60% de cumplimiento, estas son consideradas fortalezas para las granjas y el 22% tienen un menor nivel de aceptación considerándose las debilidades de las mismas. En el nivel tecnológico 26 de 44 granjas poseen la categoría alta que es mayor o igual al 80% de tecnología, 13 tienen una categoría media del 60% a 79% y 4 poseen un nivel bajo menor al 59%. Todas ellas ubicadas en los departamentos de Carazo, Estelí, Granada, León, Madríz, Managua. Masaya, Matagalpa y nueva Segovia, siendo Masaya la que presenta mayor cantidad de granjas.

Interactions of Penny-Shaped Cracks in Three-Dimensional Solids

The interaction of arbitrarily distributed penny-shaped cracks in three-dimensional solids is analyzed in this paper. Using oblate spheroidal coordinates and displacement functions, an analytic method is developed in which the opening and the sliding displacements on each crack surface are taken as the basic unknown functions. The basic unknown functions can be expanded in series of Legendre polynomials with unknown coefficients. Based on superposition technique, a set of governing equations for the unknown coefficients are formulated from the traction free conditions on each crack surface. The boundary collocation procedure and the average method for crack-surface tractions are used for solving the governing equations. The solution can be obtained for quite closely located cracks. Numerical examples are given for several crack problems. By comparing the present results with other existing results, one can conclude that the present method provides a direct and efficient approach to deal with three-dimensional solids containing multiple cracks.

Effects of Surface Microtopology and Membrane Stiffness on Kinetics of Selectin/Ligand interactions by a Modified BFP

More and more evidences come out to support that the functionality of adhesion molecules are influenced by the surface microtopology of cell carrier or substrate. Adhesive molecules usually express on the microvilli of a cell, providing a well-defined spatial configuration to mediate the adhesions to the counterpart molecules on the apposed surface.