Estimating the Threshold Surface Density of Gp120-CCR5 Complexes Necessary for HIV-1 Envelope-Mediated Cell-Cell Fusion

Reduced expression of CCR5 on target CD4(+) cells lowers their susceptibility to infection by R5-tropic HIV-1, potentially preventing transmission of infection and delaying disease progression. Binding of the HIV-1 envelope (Env) protein gp120 with CCR5 is essential for the entry of R5 viruses into target cells. The threshold surface density of gp120-CCR5 complexes that enables HIV-1 entry remains poorly estimated. We constructed a mathematical model that mimics Env-mediated cell-cell fusion assays, where target CD4(+)CCR5(+) cells are exposed to effector cells expressing Env in the presence of a coreceptor antagonist and the fraction of target cells fused with effector cells is measured. Our model employs a reaction network-based approach to describe protein interactions that precede viral entry coupled with the ternary complex model to quantify the allosteric interactions of the coreceptor antagonist and predicts the fraction of target cells fused. By fitting model predictions to published data of cell-cell fusion in the presence of the CCR5 antagonist vicriviroc, we estimated the threshold surface density of gp120-CCR5 complexes for cell-cell fusion as similar to 20 mu m(-2). Model predictions with this threshold captured data from independent cell-cell fusion assays in the presence of vicriviroc and rapamycin, a drug that modulates CCR5 expression, as well as assays in the presence of maraviroc, another CCR5 antagonist, using sixteen different Env clones derived from transmitted or early founder viruses. Our estimate of the threshold surface density of gp120-CCR5 complexes necessary for HIV-1 entry thus appears robust and may have implications for optimizing treatment with coreceptor antagonists, understanding the non-pathogenic infection of non-human primates, and designing vaccines that suppress the availability of target CD4(+)CCR5(+) cells.

Probing the role of the fully conserved Cys126 in triosephosphate isomerase by site-specific mutagenesis - distal effects on dimer stability

DatabaseStructural data are available in the Protein Data Bank under the accession numbers 3PVF, 3PY2, and 3PWA. Structured digital abstract Tim binds to Tim by x-ray crystallography (View interaction).

Relative performances of textural models in estimating soil moisture characteristic

The soil moisture characteristic (SMC) forms an important input to mathematical models of water and solute transport in the unsaturated-soil zone. Owing to their simplicity and ease of use, texture-based regression models are commonly used to estimate the SMC from basic soil properties. In this study, the performances of six such regression models were evaluated on three soils. Moisture characteristics generated by the regression models were statistically compared with the characteristics developed independently from laboratory and in-situ retention data of the soil profiles. Results of the statistical performance evaluation, while providing useful information on the errors involved in estimating the SMC, also highlighted the importance of the nature of the data set underlying the regression models. Among the models evaluated, the one possessing an underlying data set of in-situ measurements was found to be the best estimator of the in-situ SMC for all the soils. Considerable errors arose when a textural model based on laboratory data was used to estimate the field retention characteristics of unsaturated soils.

The nature of charge ordering in rare earth manganates and its strong dependence on the size of the A-site cations

Charge ordering in rare earth manganates of the type Ln(0.5)A(0.5)MnO(3) (Ln = rare earth, A = alkaline earth) is highly sensitive to the average radius of the A-site cations, [r(A)]. Tn the small [r(A)] regime (e.g., Y0.5Ca0.5MnO3), charge ordering occurs in the paramagnetic state, the transformation to an antiferromagnetic state occurring at still lower temperatures. At moderate [r(A)] values (e.g., Nd0.5Sr0.5MnO3), a ferromagnetic metallic state transforms to a charge-ordered antiferromagnetic state with cooling. These two distinct types of charge ordering and associated properties are explained in terms of the variation of the exchange couplings J(FM) and J(AFM) with [r(A)] and the invariance of the single-ion Jahn-Teller energy with [r(A)]. A qualitative temperature-[r(A)] phase diagram, consistent with the experimental observations, has been constructed to describe the properties of the manganates in the different [r(A)] regimes. (C) 1997 Academic Press.

Statistical thermodynamics of lattice models in zeolites: Implications of local versus global mean field interactions

The statistical thermodynamics of adsorption in caged zeolites is developed by treating the zeolite as an ensemble of M identical cages or subsystems. Within each cage adsorption is assumed to occur onto a lattice of n identical sites. Expressions for the average occupancy per cage are obtained by minimizing the Helmholtz free energy in the canonical ensemble subject to the constraints of constant M and constant number of adsorbates N. Adsorbate-adsorbate interactions in the Brag-Williams or mean field approximation are treated in two ways. The local mean field approximation (LMFA) is based on the local cage occupancy and the global mean field approximation (GMFA) is based on the average coverage of the ensemble. The GMFA is shown to be equivalent in formulation to treating the zeolite as a collection of interacting single site subsystems. In contrast, the treatment in the LMFA retains the description of the zeolite as an ensemble of identical cages, whose thermodynamic properties are conveniently derived in the grand canonical ensemble. For a z coordinated lattice within the zeolite cage, with epsilon(aa) as the adsorbate-adsorbate interaction parameter, the comparisons for different values of epsilon(aa)(*)=epsilon(aa)z/2kT, and number of sites per cage, n, illustrate that for -1 0. We compare the isotherms predicted with the LMFA with previous GMFA predictions [K. G. Ayappa, C. R. Kamala, and T. A. Abinandanan, J. Chem. Phys. 110, 8714 (1999)] (which incorporates both the site volume reduction and a coverage-dependent epsilon(aa)) for xenon and methane in zeolite NaA. In all cases the predicted isotherms are very similar, with the exception of a small steplike feature present in the LMFA for xenon at higher coverages. (C) 1999 American Institute of Physics. [S0021-9606(99)70333-8].

Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A(2)

Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A(2) have been determined at around 1.9 Angstrom resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P2(1)2(1)2(1), The H48Q and the calcium-loop mutant D49E are isomorphous to the trigonal recombinant enzyme, space group P3(1)21, The two active-site mutants show no major structural perturbations. The structural water is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the second water found in native His48 is absent. In the calcium-loop mutant D49E, the two water molecules forming the pentagonal bipyramid around calcium are absent and only one O atom of the Glu49 carboxylate group is coordinated to calcium, resulting in only four ligands.

Aerosol radiative forcing due to enhanced black carbon at an urban site in India

[1] During a comprehensive aerosol field campaign, simultaneous measurements were made of aerosol spectral optical depths, black carbon mass concentration (M-b), total (M-t) and size segregated aerosol mass concentrations over an urban continental location, Bangalore (13 degreesN, 77 degreesE, 960 m msl), in India. Large amounts of BC were observed; both in absolute terms and fraction of total mass (similar to11%) and submicron mass (similar to23%) implying a significantly low single scatter albedo. The aerosol visible optical depth (tau(p)) was in the range 0.24 to 0.45. Estimated surface forcing is as high as -23 W m(-2) and top of the atmosphere (TOA) forcing is +5 Wm(-2) during relatively cleaner periods (tau(p) similar to 0.24). The net atmospheric absorption translates to an atmospheric heating of similar to0.8 K day(-1) for cleaner periods and similar to1.5 K day(-1) for less cleaner periods (tau(p) similar to 0.45). Our observations raise several issues, which may have impacts to regional climate and monsoon.

Glasslike ordering and spatial inhomogeneity of magnetic structure in Ba3FeRu2O9: Role of Fe/Ru site disorder

Several doped 6H hexagonal ruthenates, having the general formula Ba3MRu2O9, have been studied over a significant period of time to understand the unusual magnetism of ruthenium metal. However, among them, the M = Fe compound appears different since it is observed that unlike others, the 3d Fe ions and 4d Ru ions can easily exchange their crystallographic positions, and as a result many possible magnetic interactions become realizable. The present study involving several experimental methods on this compound establishes that the magnetic structure of Ba3FeRu2O9 is indeed very different from all other 6H ruthenates. Local structural study reveals that the possible Fe/Ru site disorder further extends to create local chemical inhomogeneity, affecting the high-temperature magnetism of this material. There is a gradual decrease of Fe-57 Mossbauer spectral intensity with decreasing temperature (below 100 K), which reveals that there is a large spread in the magnetic ordering temperatures, corresponding to many spatially inhomogeneous regions. However, finally at about 25 K, the whole compound is found to take up a global glasslike magnetic ordering.

Structural model for the Cu-B site of dopamine beta-hydroxylase: Crystal structure of a copper(II) complex showing N3OS coordination with an axial sulfur ligation

A copper(II) complex containing a NSO-donor Schiff base and NN-donor 2,2'-bipyridine has been prepared and structurally characterized. The square pyramidal complex with an axial sulfur ligation is a structural model for the CUB site of dopamine-hydroxylase in its oxidized form. The copper(II) complex is catalytically active in the oxidation of ascorbic acid by dioxygen mediated by a copper(I) species which is proposed to have a four-coordinate structure with a N3S coordination geometry.

A gradient PCR-based screen for use in site-directed mutagenesis

Site-directed mutagenesis is widely used to study protein and nucleic acid structure and function. Despite recent advancements in the efficiency of procedures for site-directed mutagenesis, the fraction of site-directed mutants by most procedures rarely exceeds 50% on a routine basis and is never 100%. Hence it is typically necessary to sequence two or three clones each time a site-directed mutant is constructed. We describe a simple and robust gradient-PCR-based screen for distinguishing site-directed mutants from the starting, unmutated plasmid. The procedure can use either purified plasmid DNA or colony PCR, starting from a single colony. The screen utilizes the primer used for mutagenesis and a common outside primer that can be used for all other mutants constructed with the same template. Over 30 site-specific mutants in a variety of templates were successfully screened and all of the mutations detected were subsequently confirmed by DNA sequencing. A single base pair mismatch could be detected in an oligonucleotide of 36 bases. Detection efficiency was relatively independent of starting template concentration and the nature of the outside primer used. (C) 2003 Elsevier Science (USA). All rights reserved.

Seismic Microzonation: Principles,Practices and Experiments

This paper presents an overview of the seismic microzonation and the grade/level based study along with methods used for estimating hazard. The principles of seismic microzonation along with some current practices are discussed. Summary of seismic microzonation experiments carried out in India is presented. A detailed work of seismic microzonation of Bangalore has been presented as a case study. In this case study, a seismotectonic map for microzonation area has been developed covering 350 km radius around Bangalore, India using seismicity and seismotectonic parameters of the region. For seismic microzonation Bangalore Mahanagar Palike (BMP) area of 220 km2 has been selected as the study area. Seismic hazard analysis has been carried out using deterministic as well as probabilistic approaches. Synthetic ground motion at 653 locations, recurrence relation and peak ground acceleration maps at rock level have been generated. A detailed site characterization has been carried out using borehole with standard penetration test (SPT) ―N‖ values and geophysical data. The base map and 3-dimensional sub surface borehole model has been generated for study area using geographical information system (GIS). Multichannel analysis of surface wave (MASW)method has been used to generate one-dimensional shear wave velocity profile at 58 locations and two- dimensional profile at 20 locations. These shear wave velocities are used to estimate equivalent shear wave velocity in the study area at every 5m intervals up to a depth of 30m. Because of wider variation in the rock depth, equivalent shear for the soil overburden thickness alone has been estimated and mapped using ArcGIS 9.2. Based on equivalent shear wave velocity of soil overburden thickness, the study area is classified as ―site class D‖. Site response study has been carried out using geotechnical properties and synthetic ground motions with program SHAKE2000.The soil in the study area is classified as soil with moderate amplification potential. Site response results obtained using standard penetration test (SPT) ―N‖ values and shear wave velocity are compared, it is found that the results based on shear wave velocity is lower than the results based on SPT ―N‖ values. Further, predominant frequency of soil column has been estimated based on ambient noise survey measurements using instruments of L4-3D short period sensors equipped with Reftek 24 bit digital acquisition systems. Predominant frequency obtained from site response study is compared with ambient noise survey. In general, predominant frequencies in the study area vary from 3Hz to 12Hz. Due to flat terrain in the study area, the induced effect of land slide possibility is considered to be remote. However, induced effect of liquefaction hazard has been estimated and mapped. Finally, by integrating the above hazard parameters two hazard index maps have been developed using Analytic Hierarchy Process (AHP) on GIS platform. One map is based on deterministic hazard analysis and other map is based on probabilistic hazard analysis. Finally, a general guideline is proposed by bringing out the advantages and disadvantages of different approaches.

Seismic Microzonation of Bangalore - Preliminary Maps

This paper presents an overview of the seismic microzonation and the grade/level based study along with methods used for estimating hazard. The principles of seismic microzonation along with some current practices are discussed. Summary of seismic microzonation experiments carried out in India is presented. A detailed work of seismic microzonation of Bangalore has been presented as a case study. In this case study, a seismotectonic map for microzonation area has been developed covering 350 km radius around Bangalore, India using seismicity and seismotectonic parameters of the region. For seismic microzonation Bangalore Mahanagar Palike (BMP) area of 220 km2 has been selected as the study area. Seismic hazard analysis has been carried out using deterministic as well as probabilistic approaches. Synthetic ground motion at 653 locations, recurrence relation and peak ground acceleration maps at rock level have been generated. A detailed site characterization has been carried out using borehole with standard penetration test (SPT) ―N‖ values and geophysical data. The base map and 3-dimensional sub surface borehole model has been generated for study area using geographical information system (GIS). Multichannel analysis of surface wave (MASW)method has been used to generate one-dimensional shear wave velocity profile at 58 locations and two- dimensional profile at 20 locations. These shear wave velocities are used to estimate equivalent shear wave velocity in the study area at every 5m intervals up to a depth of 30m. Because of wider variation in the rock depth, equivalent shear for the soil overburden thickness alone has been estimated and mapped using ArcGIS 9.2. Based on equivalent shear wave velocity of soil overburden thickness, the study area is classified as ―site class D‖. Site response study has been carried out using geotechnical properties and synthetic ground motions with program SHAKE2000.The soil in the study area is classified as soil with moderate amplification potential. Site response results obtained using standard penetration test (SPT) ―N‖ values and shear wave velocity are compared, it is found that the results based on shear wave velocity is lower than the results based on SPT ―N‖ values. Further, predominant frequency of soil column has been estimated based on ambient noise survey measurements using instruments of L4-3D short period sensors equipped with Reftek 24 bit digital acquisition systems. Predominant frequency obtained from site response study is compared with ambient noise survey. In general, predominant frequencies in the study area vary from 3Hz to 12Hz. Due to flat terrain in the study area, the induced effect of land slide possibility is considered to be remote. However, induced effect of liquefaction hazard has been estimated and mapped. Finally, by integrating the above hazard parameters two hazard index maps have been developed using Analytic Hierarchy Process (AHP) on GIS platform. One map is based on deterministic hazard analysis and other map is based on probabilistic hazard analysis. Finally, a general guideline is proposed by bringing out the advantages and disadvantages of different approaches.

Site Characterization of Bangalore using Geophysical Method

A number of geophysical methods have been proposed for near-surface site characterization and measurement of shear wave velocity by using a great variety of testing configurations, processing techniques,and inversion algorithms. In particular, two widely-used techniques are SASW (Spectral Analysis of SurfaceWaves) and MASW (Multichannel Analysis of SurfaceWaves). MASW is increasingly being applied to earthquake geotechnical engineering for the local site characterization, microzonation and site response studies.A MASW is a geophysical method, which generates a shear-wave velocity (Vs) profile (i.e., Vs versus depth)by analyzing Raleigh-type surface waves on a multichannel record. MASW system consisting of 24 channels Geode seismograph with 24 geophones of 4.5 Hz frequency have been used in this investigation. For the site characterization program, the MASW field experiments consisting of 58 one-dimensional shear wave velocity tests and 20 two-dimensional shear wave tests have been carried out. The survey points have been selected in such a way that the results supposedly represent the whole metropolitan Bangalore having an area of 220 km2.The average shear wave velocity of Bangalore soils have been evaluated for depths of 5m, 10m, 15m, 20m, 25m and 30 m. The subsoil site classification has been made for seismic local site effect evaluation based on average shear wave velocity of 30m depth (Vs30) of sites using National Earthquake Hazards Reduction Program (NEHRP) and International Building Code (IBC) classification. Soil average shearwave velocity estimated based on overburden thickness from the borehole information is also presented. Mapping clearly indicates that the depth of soil obtained from MASW is closely matching with the soil layers in bore logs. Among total 55 locations of MASW survey carried out, 34 locations were very close to the SPT borehole locations and these are used to generate correlation between Vs and corrected “N” values. The SPT field “N” values are corrected by applying the NEHRP recommended corrections.