High fluoride in groundwater and associated non-carcinogenic risks at Tiruvannamalai region in Tamil Nadu, India.

The present investigation in the Tiruvannamalai region is about high fluoride contamination of groundwater samples from bore wells and open wells. About 75% of groundwater samples were found predominantly containing the fluoride content greater than the acceptable limit of 1.5 mg/L in the ranges 1.51 - 2.00 mg/L (23%), 2.01 - 3.00 mg/L (36%) and greater than or equal to 3.01 mg/L (16%) as per WHO. The other water quality parameters were found within the permissible limit of WHO. Taking the groundwater sources into consideration, the non - carcinogenic risk due to high fluoride concentration in groundwater sources revealed that teen - aged (98%), Children (92%) and Infant (98%) categories were at greater risk than those under Men (50%) and Women (69%) categories. The mapping was done on the spatial distribution of fluoride concentration in groundwater and the associated health risk by Ordinary Kriging. The correlation coefficients among the parameters witnessed that the hydro-chemical facies are interdependent. Box - Whisker plots illustrated the dispersion of various water quality parameters. The WQI data represented the quality of groundwater in view of potable nature due to dissolved ions. The Gibbs, bivariate mixing and the scatter plots ascribed the dissolution of carbonate and silicate minerals which dominate the groundwater chemistry. The factor analysis detailed the extracted loadings of different parameters of groundwater sources and differentiated the percentage variance values between bore well and open well sources.

Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass.

AIMS: The aim of this work was to isolate novel lignin-degrading organisms. METHODS AND RESULTS: Several pure cultures of bacteria that degrade lignin were isolated from bacterial consortia developed from decaying biomass. Among the isolates, Rhizobium sp. strain YS-1r (closest relative of Rhizobium petrolearium strain SL-1) was explored for its lignin-degrading ability. Microcosm studies showed that strain YS-1r was able to degrade a variety of lignin monomers, dimers and also native lignin in switchgrass and alfalfa. The isolate demonstrated lignin peroxidase (LiP) activity when grown on alkali lignin, p-anisoin, switchgrass or alfalfa, and only negligible activity was measured in glucose-grown cells suggesting inducible nature of the LiP activity. Analysis of the strain YS-1r genome revealed the presence of a variety of genes that code for various lignin-oxidizing, H2 O2 -producing as well as polysaccharide-hydrolysing enzymes. CONCLUSIONS: This study shows both the genomic and physiological capability of bacteria in the genus Rhizobium to metabolize lignin and lignin-like compounds. This is the first detailed report on the lignocellulose-degrading ability of a Rhizobium species and thus this study expands the role of alpha-proteobacteria in the degradation of lignin. SIGNIFICANCE AND IMPACT OF THE STUDY: The organism's ability to degrade lignin is significant since Rhizobia are widespread in soil, water and plant rhizospheres and some fix atmospheric nitrogen and also have the ability to degrade aromatic hydrocarbons.

Micro-plastic pollution along the Bay of Bengal coastal stretch of Tamil Nadu, South India.

In the present-day context, micro-plastic particles in a marine environment are increasingly ubiquitous and of considerable persistence. In line with the micro-plastic pollution, the present contribution is devoted to the investigation of micro-plastic particles (MPs) along the urban sandy beach called Marina, the renowned longest beach in India. Along the sea coast of about 5 km, the quantification of micro-plastic particles using optical microscope evidenced the granular, filamentous, filmy and tubular fragments in a total of 72 marine samples including those filtered in the marine water column (WAT; 24 samples), those found in wet sediment (WET; 24 samples) and those found in dry sand (DSS; 24 samples). The filamentous-typed plastics of 79%, 57% and 52%, respectively in WET, WAT and DSS dominated over the other granular and tubular types. The micro-plastic particles were in the range of 60-820 items per m3, 60-1620 items per kg and 20-1540 items per kg for WAT, WET and DSS, respectively. The standard deviation for the microplastics abundance were 193.1, 396.6 and 364.6 for WAT, WET and DSS respectively. Upon visual inspection, the micro particles were observed in eight different colors and most of the samples were found to contain two different fragment types. Apart from the optical microscopic examination, the micro-plastics particles were studied by scanning electron microscope (SEM) coupled with elemental analysis by energy dispersive spectroscopy (EDS). The energy spectral graphs displayed that the micro-filaments and micro-tubular particles contained polyesters and fluoro-polymers. The presence of few micro-filaments of polypropylene and polyethylene was also evidenced from their atomic percentage values of carbon of about 88% and 93%, respectively. The presence of fluoro-polymers and polyesters was also confirmed by Fourier Transform Infra-Red (FTIR). Excepting the fluoro-polymers, the micro-plastics particles contained elements arising from sea water (Na, Cl, S, Mg, Ca, K). Heavy metals such as Cu, Mn, Mo, Ru and Rh were observed in micro-tubular fragments. Fe and Ti elements were detected with the highest atomic percentage of 17.19 and 19.84 in micro-tubular fragments. All the observations and analyses give a photography of the nature and the spatial distribution of MPs along this Indian beach.

Phenylalanine transfer RNA: molecular dynamics simulation.

Yeast phenylalanine transfer RNA was subjected to a 12-picosecond molecular dynamics simulation. The principal features of the x-ray crystallographic analysis are reproduced, and the amplitudes of atomic displacements appear to be determined by the degree of exposure of the atoms. An analysis of the hydrogen bonds shows a correlation between the average length of a bond and the fluctuation in that length and reveals a rocking motion of bases in Watson-Crick guanine X cytosine base pairs. The in-plane motions of the bases are generally of larger amplitude than the out-of-plane motions, and there are correlations in the motions of adjacent bases.

Exploring electron transfer between heme proteins of cytochrome C super family in biosensors: a molecular mechanics study.

Electron transfer between heme proteins with mediators plays an important role in the fabrication of sensitive bio-nano sensors. Heme protein Cytochrome c (pdb code - 1HRC) was chosen as the mediator with Cytochrome c' (pdb code - 1A7V) as the probe protein for our investigation on the electron transfer process. We used the software GRAMM, HEX, and MACRODOX to build the protein complex with further evaluation by GROMACS potential. After molecular mechanics refinement by GROMACS the protein complexes were evaluated in terms of the following criteria: Hydrophobic packing, proximity of the hemes, hydrogen bonds, enthalpy and entropy of binding. The free energy was calculated for each complex to derive the feasible stable models. The combined electron transport of the chosen geometric models was evaluated to choose the possible models. Electrostatic potential was calculated using the program APBS around the heme in the presence and absence of other proteins. From our studies, we derived multiple feasible models and possible electronic path. These studies helped us to understand the relay mechanism between the two proteins and to design mutant proteins by rational site directed mutagenesis to enhance the redox potential and thereby improving the signal to noise ratio in amperometric bionano sensors.

Modeling of neuropeptide receptors Y1, Y4, Y5, and docking studies with neuropeptide antagonist.

Neuropeptide Y (NPY), receptors belong to the G-protein coupled receptor superfamily. NPY mediates several physiological responses, such as blood pressure, food intake, sedation. These actions of NPY are mediated by six receptor subtypes denoted as Y1-Y5 and y6. Modeling of receptor subtypes and binding site identification is an important step in developing new therapeutic agents. We have attempted to model the three NPY receptor types, Y1, Y4, and Y5 using homology modeling and threading methods. The models are consistent with previously reported experimental evidence. To understand the interaction and selectivity of NPY analogues with different neuropeptide receptors, docking studies of two neuropeptide analogues (BVD10 and BVD15) with receptors Y1 and Y4 were carried out. Results of the docking studies indicated that the interaction of ligands BVD10 and BVD15 with Y1 and Y4 receptors are different. These results were evaluated for selectivity of peptide analogues BVD10 and BVD15 towards the receptors.

Electrospinning of PLGA/gum tragacanth nanofibers containing tetracycline hydrochloride for periodontal regeneration.

Controlled drug release is a process in which a predetermined amount of drug is released for longer period of time, ranging from days to months, in a controlled manner. In this study, novel drug delivery devices were fabricated via blend electrospinning and coaxial electrospinning using poly lactic glycolic acid (PLGA), gum tragacanth (GT) and tetracycline hydrochloride (TCH) as a hydrophilic model drug in different compositions and their performance as a drug carrier scaffold was evaluated. Scanning electron microscopy (SEM) results showed that fabricated PLGA, blend PLGA/GT and core shell PLGA/GT nanofibers had a smooth and bead-less morphology with the diameter ranging from 180 to 460 nm. Drug release studies showed that both the fraction of GT within blend nanofibers and the core-shell structure can effectively control TCH release rate from the nanofibrous membranes. By incorporation of TCH into core-shell nanofibers, drug release was sustained for 75 days with only 19% of burst release within the first 2h. The prolonged drug release, together with proven biocompatibility, antibacterial and mechanical properties of drug loaded core shell nanofibers make them a promising candidate to be used as drug delivery system for periodontal diseases.

Factors associated with internet addiction among school-going adolescents in Vadodara.

INTRODUCTION: The internet is an important modern means of obtaining information and communicating with others which has converted the world into a global village. At the same time, increasing internet use among adolescents is also likely to pose a major public health concern that is internet addiction (IA). The aim was to assess the prevalence of IA among school-going adolescents and factors associated with IA. METHODS: A cross-sectional study was designed to survey adolescents studying in 8th to 11th standard of five schools of Vadodara. Information regarding sociodemography and various patterns of internet use were obtained using survey forms. IA test (IAT) was used to screen for IA. Descriptive analysis, univariate analysis, and logistic regression were done to analyze the data. RESULTS: Seven hundred and twenty-four participants that completed IAT were analyzed. Internet use prevalence was 98.9%. Prevalence of IA was 8.7%. Male gender, owning a personal device, hours of internet use/day, use of smartphones, permanent login status, use of internet for chatting, making online friends, shopping, watching movies, online gaming, searching information online and instant messaging were found to be associated significantly with IA in univariate analysis. Internet use for online friendships was found to be a significant predictor of IA (odds ratio [OR] =2.4), and internet use for searching information was found to be protective (OR = 0.20) against IA on logistic regression. CONCLUSIONS: IA is prevalent in the adolescent population and requires awareness and intervention. Characteristics of internet usage found to be associated with IA needs to be considered while developing strategies for interventions.

Hydrophobic packing and spatial arrangement of amino acid residues in globular proteins.

Amino acid residues acquire characteristic hydrophobic environments in globular proteins. Using the crystal data on 21 proteins, a new scale of hydrophobic indices for the residues is set up. This scale provides valuable information with regard to hydrophobic domains, nucleation sites, surface domains, loop sites and the spatial positions of residues in protein molecules.

Location of potential binding sites on deoxy hemoglobin for the design of antigelling agents.

The binding sites of indole-based gelation inhibitors with sickle cell hemoglobin were investigated by two parallel theoretical approaches. A geometric approach originated by Kuntz and co-workers uses a spatial buildup scheme to locate potential binding regions, while a hybrid grid/geometric search method searches for specific indole ring binding pockets over the hemoglobin surface. The binding sites derived from these calculations were tested for their ability to accommodate indole rings by means of accessibility calculations with probes of various radii. These sites were further scanned for van der Waals' overlap and electrostatic interactions. A full 5BrTrp residue was built in each indole ring binding site, and its conformational energy of association with sickle hemoglobin was calculated at that site. Our theoretical results predict a total of 14 potential binding regions, including all of the sites observed from X-ray crystallography, and sites that are consistent with solution nuclear magnetic resonance studies.

Interspecies hybrid HbS: complete neutralization of Val6(beta)-dependent polymerization of human beta-chain by pig alpha-chains.

Interspecies hybrid HbS (alpha(2)(P)beta(2)(S)), has been assembled in vitro from pig alpha-globin and human beta(S)-chain. The alpha(2)(P)beta(2)(S) retains normal tetrameric structure (alpha(2)beta(2)) of human Hb and an O(2) affinity comparable to that of HbS in 50 mM Hepes buffer; but, its O(2) affinity is slightly higher than that of HbS in the presence of allosteric effectors (chloride, DPG and phosphate). The (1)H-NMR spectroscopy detected distinct differences between the heme environments and alpha(1)beta(1) interfaces of pig Hb and HbS, while their alpha(1)beta(2) interfaces appear very similar. The interspecies hybrid alpha(2)(H)beta(2)(P) resembles pig Hb; the pig beta-chain dictated the conformation of the heme environment of the human alpha-subunit, and to the alpha(1)beta(1) interfaces of the hybrid. In the alpha(2)(P)beta(2)(S) hybrid, beta(S)-chain dictated the conformation of human heme environment to the pig alpha-chain in the hybrid; but the conformation of alpha(1)beta(1) interface of this hybrid is close to, but not identical to that of HbS. On the other hand, the alpha(1)beta(2) interface conformation is identical to that of HbS. More important, the alpha(2)(P)beta(2)(S) does not polymerize when deoxygenated; pig alpha-chain completely neutralizes the beta(S)-chain dependent polymerization. The polymerization inhibitory propensity of pig alpha-chain is higher when it is present in the cis alpha(P)beta(S) dimer relative to that in a trans alpha(P)beta(A) dimer. The semisynthetically generated chimeric pig-human and human-pig alpha-chains by exchanging the alpha(1-30) segments of human and pig alpha-chains have established that the sequence differences of pig alpha(31-141) segment can also completely neutralize the polymerization. Comparison of the electrostatic potential energy landscape of the alpha-chain surfaces of HbS and alpha(2)(P)beta(2)(S) suggests that the differences in electrostatic potential energy surfaces on the alpha-chain of alpha(2)(P)beta(2)(S) relative to that in HbS, particularly the ones involving CD region, E-helix and EF-corner of pig alpha-chain are responsible for the polymerization neutralization activity. The pig and human-pig chimeric alpha-chains can serve as blueprints for the design of a new generation of variants of alpha-chain(s) suitable for the gene therapy of sickle cell disease.

[D-TRP32]neuropeptide Y: a competitive antagonist of NPY in rat hypothalamus.

Neuropeptide Y (NPY) is a potent orexigenic peptide. Structure-activity studies have revealed that nearly the entire sequence of NPY is required to elicit feeding responses. Therefore, in order to develop antagonistic peptides for NPY-induced feeding, we synthesized full-length analogs of NPY, substituting D-Trp in the C-terminal receptor binding region, and screened their activity in rat hypothalamus. Although [D-Trp36]NPY and [D-Trp34]NPY inhibited isoproterenol-stimulated hypothalamic membrane adenylate cyclase activity, [D-Trp32]NPY exhibited no intrinsic activity. Furthermore, [D-Trp32]NPY inhibited [125I]NPY binding to rat hypothalamic membranes with a potency comparable to that of NPY. The presence of 30 and 300 nM concentrations of [D-Trp32]NPY shifted the inhibitory dose-response curve of NPY on isoproterenol-stimulated hypothalamic membrane adenylate cyclase activity parallel to the right with comparable KB values. Moreover, in vivo experiments in rats revealed that [D-Trp32]NPY (10 micrograms) significantly attenuated the 1-h feeding response induced by NPY (1 microgram). Several other substitutions at position 32 including 2-D-Nal resulted in agonist activity, suggesting that there are strict structural requirements to induce the antagonistic property in NPY. These findings confirm that [D-Trp32]NPY is a competitive antagonist of NPY in both in vitro and in vivo systems. Analogs based on [D-Trp32]NPY may have potential clinical application, since NPY has been implicated in the pathophysiology of a number of feeding disorders including obesity, anorexia, and bulimia.

Mass spectrometric investigations on Conus peptides.

Molecular masses and primary structure determination of Conus peptides, such as alpha-, mu- and omega-conotoxins, conantokins and conopressins, were accurately measured by state-of-the-art mass spectrometric techniques using only 1-2 pmole quantities. Soft ionization of Conus peptides under electrospray, matrix-assisted laser desorption and continuous flow frit-FAB conditions produced their corresponding singly and multiply charged molecular ions which can be detected by mass spectrometric analysis. The molecular masses of Conus peptides were obtained by the deconvolution of the multiply charged pseudo-molecular ions. Mixture analysis without chromatographic separation can be accomplished by this approach. The ions formed during collision-induced dissociation of either singly or multiply charged ions of any reduced and derivatized peptide provided the corresponding sequences of the amino acids. Preliminary investigations indicate that the developed techniques and procedures could be applied in order to characterize the peptides present in unknown Conus venoms from the Bay of Bengal region.

A new spatial representation of amino acid residues in globular proteins.

For the globular proteins with known three-dimensional structures, an ellipsoid model of each protein was constructed with least volume and its dimensions were derived. The spatial arrangements were made for the C alpha and side chain atoms of that protein within that ellipsoid. This new spatial representation shows the residue position from the centroid, as well as the depth from the surface. The average spatial parameters were then calculated. The correlations between these new spatial parameters and the existing parameters of the amino acid residues were then derived.

Secondary structure prediction for the spectrin 106-amino acid segment, and a proposed model for tertiary structure.

A collective secondary structure prediction for the human erythrocyte spectrin 106-residue repeat segment is developed, based on the sequences of nine segments that have been reported in the literature, utilizing a consensus of several secondary structure prediction methods for locating turn regions. The analysis predicts a five-fold structure, with three alpha-helices and two beta-strand regions, and differs from previous models on the lengths of the helices and the existence of beta-strand structure. We also demonstrate that this structural motif can be folded into tertiary structures that satisfy the experimental spectrin data and several general principles of protein organization.

Internal packing conditions and fluctuations of amino acid residues in globular proteins.

In order to investigate the environmental conditions of amino acid residues in protein molecules, four kinds of packing studies (atomic, geometric, hydrophobic and hydration) were formulated and tested on two proteins; bovine pancreatic trypsin inhibitor (BPTI) and bovine pancreatic ribonuclease S (RNase S). The inter-relationship of these packings on the fluctuations of amino acid residues was analysed by comparing the packing results with the dynamical studies, such as the root-mean-square-deviation values of atomic displacements obtained from the trajectories of molecular dynamics simulation, temperature factor information from crystal structures and residue fluctuations in proteins from continuum model. These analyses yield information about the most fluctuating and most stabilizing residue sites. Comparison of the results obtained by these methods indicate a good agreement, specifying an inverse correlation between the residue packing and fluctuations. This kind of study is helpful in identifying the specific residue sites such as nucleation, receptor binding and antigenic determining sites which in a way indirectly correlates with the functional residues in protein molecules.

Molecular dynamics of phenylalanine transfer RNA.

The atomic motions of yeast phenylalanine transfer RNA have been simulated using the molecular dynamics algorithm. Two simulations were carried out for a period of 12 picoseconds, one with a normal Van der Waals potential and the other with a modified Van der Waals potential intended to mimic the effect of solvent. An analysis of large scale motions, surface exposure, root mean square displacements, helical oscillations and relaxation mechanisms reveals the maintenance of stability in the simulated structures and the general similarity of the various dynamic features of the two simulations. The regions of conformational flexibility and rigidity for tRNA(Phe) have been shown in a quantitative measure through this approach.