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.

Tuning of dielectric properties and magnetism of SrTiO(3) by site-specific doping of Mn

Combining experiments with first-principles calculations, we show that site-specific doping of Mn into SrTiO(3) has a decisive influence on the dielectric properties of these doped systems. We find that phonon contributions to the dielectric constant invariably decrease sharply on doping at any site. However, a sizable, random dipolar contribution only for Mn at the Sr site arises from a strong off-centric displacement of Mn in spite of Mn being in a non-d(0) state; this leads to a large dielectric constant at higher temperatures and gives rise to a relaxor ferroelectric behavior at lower temperatures. We also investigate magnetic properties in detail and critically reevaluate the possibility of a true multiglass state in such systems.

Endonuclease Active Site Plasticity Allows DNA Cleavage with Diverse Alkaline Earth and Transition Metal Ions

A majority of enzymes show a high degree of specificity toward a particular metal ion in their catalytic reaction. However, Type II restriction endonuclease (REase) R.KpnI, which is the first member of the HNH superfamily of REases, exhibits extraordinary diversity in metal ion dependent DNA cleavage. Several alkaline earth and transition group metal ions induce high fidelity and promiscuous cleavage or inhibition depending upon their concentration. The metal ions having different ionic radii and co-ordination geometries readily replace each other from the enzyme's active site, revealing its plasticity. Ability of R KpnI to cleave DNA with both alkaline earth and transition group metal ions having varied ionic radii could imply utilization of different catalytic site(s). However, mutation of the invariant His residue of the HNH motif caused abolition of the enzyme activity with all of the cofactors, indicating that the enzyme follows a single metal ion catalytic mechanism for DNA cleavage. Indispensability of His in nucleophile activation together with broad cofactor tolerance of the enzyme indicates electrostatic stabilization function of metal ions during catalysis. Nevertheless, a second metal ion is recruited at higher concentrations to either induce promiscuity or inhibit the DNA cleavage. Regulation of the endonuclease activity and fidelity by a second metal ion binding is a unique feature of R.KpnI among REases and HNH nucleases. The active site plasticity of R.KpnI opens up avenues for redesigning cofactor specificities and generation of mutants specific to a particular metal ion.

Remote detection and distinction of ants using nest-site specific LISS-derived Normalised Difference Vegetation Index

This study in Western Ghats, India, investigates the relation between nesting sites of ants and a single remotely sensed variable: the Normalised Difference Vegetation Index (NDVI). We carried out sampling in 60 plots each measuring 30 x 30 m and recorded nest sites of 13 ant species. We found that NDVI values at the nesting sites varied considerably between individual species and also between the six functional groups the ants belong to. The functional groups Cryptic Species, Tropical Climate Specialists and Specialist Predators were present in regions with high NDVI whereas Hot Climate Specialists and Opportunists were found in sites with low NDVI. As expected we found that low NDVI values were associated with scrub jungles and high NDVI values with evergreen forests. Interestingly, we found that Pachycondyla rufipes, an ant species found only in deciduous and evergreen forests, established nests only in sites with low NDVI (range = 0.015 - 0.1779). Our results show that these low NDVI values in deciduous and evergreen forests correspond to canopy gaps in otherwise closed deciduous and evergreen forests. Subsequent fieldwork confirmed the observed high prevalence of P. rufipes in these NDVI-constrained areas. We discuss the value of using NDVI for the remote detection and distinction of ant nest sites.

Three-Dimensional Site Characterization Model Using Artificial Neural Networks

This research is designed to develop a new technique for site characterization in a three-dimensional domain. Site characterization is a fundamental task in geotechnical engineering practice, as well as a very challenging process, with the ultimate goal of estimating soil properties based on limited tests at any half-space subsurface point in a site.In this research, the sandy site at the Texas A&M University's National Geotechnical Experimentation Site is selected as an example to develop the new technique for site characterization, which is based on Artificial Neural Networks (ANN) technology. In this study, a sequential approach is used to demonstrate the applicability of ANN to site characterization. To verify its robustness, the proposed new technique is compared with other commonly used approaches for site characterization. In addition, an artificial site is created, wherein soil property values at any half-space point are assumed, and thus the predicted values can compare directly with their corresponding actual values, as a means of validation. Since the three-dimensional model has the capability of estimating the soil property at any location in a site, it could have many potential applications, especially in such case, wherein the soil properties within a zone are of interest rather than at a single point. Examples of soil properties of zonal interest include soil type classification and liquefaction potential evaluation. In this regard, the present study also addresses this type of applications based on a site located in Taiwan, which experienced liquefaction during the 1999 Chi-Chi, Taiwan, Earthquake.

Allosteric Communication in Cysteinyl tRNA Synthetase A NETWORK OF DIRECT AND INDIRECT READOUT

Protein structure networks are constructed for the identification of long-range signaling pathways in cysteinyl tRNA synthetase (CysRS). Molecular dynamics simulation trajectory of CysRS-ligand complexes were used to determine conformational ensembles in order to gain insight into the allosteric signaling paths. Communication paths between the anticodon binding region and the aminoacylation region have been identified. Extensive interaction between the helix bundle domain and the anticodon binding domain, resulting in structural rigidity in the presence of tRNA, has been detected. Based on the predicted model, six residues along the communication paths have been examined by mutations (single and double) and shown to mediate a coordinated coupling between anticodon recognition and activation of amino acid at the active site. This study on CysRS clearly shows that specific key residues, which are involved in communication between distal sites in allosteric proteins but may be elusive in direct structure analysis, can be identified from dynamics of protein structure networks.

Structure-function relationship in serine hydroxymethyltransferase

Serine hydroxymethyltransferase (SHMT), a pyridoxal-5V-phosphate (PLP)-dependent enzyme catalyzes thetetrahydrofolate (H4-folate)- dependent retro-aldol cleavage of serine to form 5,10-methylene H4-folate and glycine. The structure–function relationship of SHMT wasstudied in our laboratory initially by mutation of residues that are conserved in all SHMTs and later by structure-based mutagenesis of residues located in the active site. The analysis of mutants showed that K71, Y72, R80, D89, W110, S202, C203, H304, H306 and H356 residues are involved in maintenance of the oligomeric structure. The mutation of D227, a residue involved in charge relay system, led to the formation of inactive dimers, indicating that this residue has a role in maintaining the tetrameric structure and catalysis. E74, a residue appropriately positioned in the structure of the enzyme to carry out proton abstraction, was shown by characterization of E74Q and E74K mutants to be involved in conversion of the enzyme from an ‘open’ to ‘closed’ conformation rather than proton abstraction from the hydroxylgroup of serine. K256, the residue involved in the formation of Schiffs base with PLP, also plays a crucial role in the maintenance of the tetrameric structure. Mutation of R262 residue established the importance of distal interactions in facilitating catalysis and Y82 is not involved in the formaldehyde transfer via the postulated hemiacetal intermediate but plays a role in stabilizing the quinonoid intermediate.The mutational analysis of scSHMT along with the structure of recombinant Bacillus stearothermophilus SHMT and its substrate(s)complexes was used to provide evidence for a direct transfer mechanism rather than retro-aldol cleavage for the reaction catalyzed by SHMT.

Dimethyl sulfoxide induced structural transformations and non-monotonic concentration dependence of conformational fluctuation around active site of lysozyme

Experimental studies have observed significant changes in both structure and function of lysozyme (and other proteins) on addition of a small amount of dimethyl sulfoxide (DMSO) in aqueous solution. Our atomistic molecular dynamic simulations of lysozyme in water-DMSO reveal the following sequence of changes on increasing DMSO concentration. (i) At the initial stage (around 5% DMSO concentration) protein's conformational flexibility gets markedly suppressed. From study of radial distribution functions, we attribute this to the preferential solvation of exposed protein hydrophobic residues by the methyl groups of DMSO. (ii) In the next stage (10-15% DMSO concentration range), lysozome partially unfolds accompanied by an increase both in fluctuation and in exposed protein surface area. (iii) Between 15-20% concentration ranges, both conformational fluctuation and solvent accessible protein surface area suddenly decrease again indicating the formation of an intermediate collapse state. These results are in good agreement with near-UV circular dichroism (CD) and fluorescence studies. We explain this apparently surprising behavior in terms of a structural transformation which involves clustering among the methyl groups of DMSO. (iv) Beyond 20% concentration of DMSO, the protein starts its final sojourn towards the unfolding state with further increase in conformational fluctuation and loss in native contacts. Most importantly, analysis of contact map and fluctuation near the active site reveal that both partial unfolding and conformational fluctuations are centered mostly on the hydrophobic core of active site of lysozyme. Our results could offer a general explanation and universal picture of the anomalous behavior of protein structure-function observed in the presence of cosolvents (DMSO, ethanol, tertiary butyl alcohol, dioxane) at their low concentrations. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3694268]

PocketAnnotate: towards site-based function annotation

A computational pipeline PocketAnnotate for functional annotation of proteins at the level of binding sites has been proposed in this study. The pipeline integrates three in-house algorithms for site-based function annotation: PocketDepth, for prediction of binding sites in protein structures; PocketMatch, for rapid comparison of binding sites and PocketAlign, to obtain detailed alignment between pair of binding sites. A novel scheme has been developed to rapidly generate a database of non-redundant binding sites. For a given input protein structure, putative ligand-binding sites are identified, matched in real time against the database and the query substructure aligned with the promising hits, to obtain a set of possible ligands that the given protein could bind to. The input can be either whole protein structures or merely the substructures corresponding to possible binding sites. Structure-based function annotation at the level of binding sites thus achieved could prove very useful for cases where no obvious functional inference can be obtained based purely on sequence or fold-level analyses. An attempt has also been made to analyse proteins of no known function from Protein Data Bank. PocketAnnotate would be a valuable tool for the scientific community and contribute towards structure-based functional inference. The web server can be freely accessed at http://proline.biochem.iisc.ernet.in/pocketannotate/.

Synthesis of a mixed-metal spinel, NiMn2O4, through site-selective substitution in MOF, (NiMn2){C6H3(COO)(3)}(2)]: synthesis, structure and magnetic studies

A mixed-metal metal-organic framework (MOF) compound NiMn2{C6H3(COO)(3)}(2)], I, is prepared hydrothermally by replacing one of the octahedral Mn2+ ions in Mn-3{C6H3(COO)(3)}(2)] by Ni2+ ions. Magnetic studies on I suggest antiferromagnetic interactions with weak canted antiferromagnetism below 8 K. On heating in flowing air I transforms to NiMn2O4 spinel at low temperature (T < 400 degrees C). The thermal decomposition of I at different temperatures results in NiMn2O4 with particle sizes in the nano regime. The nanoparticle nature of NiMn2O4 was confirmed using PXRD and TEM studies. Magnetic studies on the nanoparticles of NiMn2O4 indicate ferrimagnetism. The transition temperature of NiMn2O4 nanoparticles exhibits a direct correlation with the particle size. This study highlights the usefulness of MOF compound as a single-source precursor for the preparation of important ceramic oxides with better control on the stoichiometry and particle size.

Site-specific N-Linked Glycosylation of Receptor Guanylyl Cyclase C Regulates Ligand Binding, Ligand-mediated Activation and Interaction with Vesicular Integral Membrane Protein 36, VIP36

Guanylyl cyclase C (GC-C) is a multidomain, membrane-associated receptor guanylyl cyclase. GC-C is primarily expressed in the gastrointestinal tract, where it mediates fluid-ion homeostasis, intestinal inflammation, and cell proliferation in a cGMP-dependent manner, following activation by its ligands guanylin, uroguanylin, or the heat-stable enterotoxin peptide (ST). GC-C is also expressed in neurons, where it plays a role in satiation and attention deficiency/hyperactive behavior. GC-C is glycosylated in the extracellular domain, and differentially glycosylated forms that are resident in the endoplasmic reticulum (130 kDa) and the plasma membrane (145 kDa) bind the ST peptide with equal affinity. When glycosylation of human GC-C was prevented, either by pharmacological intervention or by mutation of all of the 10 predicted glycosylation sites, ST binding and surface localization was abolished. Systematic mutagenesis of each of the 10 sites of glycosylation in GC-C, either singly or in combination, identified two sites that were critical for ligand binding and two that regulated ST-mediated activation. We also show that GC-C is the first identified receptor client of the lectin chaperone vesicular integral membrane protein, VIP36. Interaction with VIP36 is dependent on glycosylation at the same sites that allow GC-C to fold and bind ligand. Because glycosylation of proteins is altered in many diseases and in a tissue-dependent manner, the activity and/or glycan-mediated interactions of GC-C may have a crucial role to play in its functions in different cell types.

Isolation of a High Affinity Neutralizing Monoclonal Antibody against 2009 Pandemic H1N1 Virus That Binds at the `Sa' Antigenic Site

Influenza virus evades host immunity through antigenic drift and shift, and continues to circulate in the human population causing periodic outbreaks including the recent 2009 pandemic. A large segment of the population was potentially susceptible to this novel strain of virus. Historically, monoclonal antibodies (MAbs) have been fundamental tools for diagnosis and epitope mapping of influenza viruses and their importance as an alternate treatment option is also being realized. The current study describes isolation of a high affinity (K-D = 2.1 +/- 0.4 pM) murine MAb, MA2077 that binds specifically to the hemagglutinin (HA) surface glycoprotein of the pandemic virus. The antibody neutralized the 2009 pandemic H1N1 virus in an in vitro microneutralization assay (IC50 = 0.08 mu g/ml). MA2077 also showed hemagglutination inhibition activity (HI titre of 0.50 mu g/ml) against the pandemic virus. In a competition ELISA, MA2077 competed with the binding site of the human MAb, 2D1 (isolated from a survivor of the 1918 Spanish flu pandemic) on pandemic H1N1 HA. Epitope mapping studies using yeast cell-surface display of a stable HA1 fragment, wherein `Sa' and `Sb' sites were independently mutated, localized the binding site of MA2077 within the `Sa' antigenic site. These studies will facilitate our understanding of antigen antibody interaction in the context of neutralization of the pandemic influenza virus.