155 3D QSAR and protein–protein interaction studies on neuraminidase against Clostridium perfringens: An approach toward target identification using structure-based drug designing

The rapid onset of resistance to new drugs and emergence of antibiotic resistant bacteria has led to resurgence in life-threatening bacterial infections. These problems have revitalized interest in antibiotics and lead to new research. To gain further insight between structural and biological activity of Clostridium perfringens, a gram-positive anaerobe responsible for food poisoning, mynecrosis in wound infections, and enterotoxemia in humans. We have considered various in silico approaches for developing new drug leads, based on small ligand structure. The importance of neuraminidases in the virulence of C. perfringens makes it a potent target for the studies of drug designing against this microbe. Natural products or their direct derivatives play crucial roles in many diseases. In the present study, 3D QSAR analysis using kNN-MFA method was performed on a series of pterocarpan derivatives as Clostridial neuraminidase inhibitors. Twenty-five compounds using random selection and sphere exclusion method for the division of dataset into training and test set were chosen. kNN-MFA methodology with stepwise, simulated annealing and genetic algorithm was used for model building and four predictive models have been generated. The most significant model has a high internal predictivity of 64.80% (q ²?=?0.6480) and an external predictivity of 95.46% (r ²?=?0.9546). Model showed that electrostatic and steric interactions play important role in determining neuraminidase inhibitory activity. The kNN-MFA plots provide further understanding of the relationship between structural features of substituted pterocarpan derivatives and their activities which were applied for designing new compounds as inhibitors. The drug likeliness of these compounds was checked through ADME property prediction and their interaction with the neuraminidase was checked by molecular docking studies. Moreover, analysis of protein–protein interaction network of NanI in C. perfringens was done.     

Sparse sampling of water density fluctuations near liquid-vapor coexistence

Abstract

The free energetics of water density fluctuations in bulk water, at interfaces, and in hydrophobic confinement inform the hydration of hydrophobic solutes as well as their interactions and assembly. The characterisation of such free energetics is typically performed using enhanced sampling techniques such as umbrella sampling. In umbrella sampling, order parameter distributions obtained from adjacent biased simulations must overlap in order to estimate free energy differences between biased ensembles. Many biased simulations are typically required to ensure such overlap, which exacts a steep computational cost. We recently introduced a sparse sampling method, which circumvents the overlap requirement by using thermodynamic integration to estimate free energy differences between biased ensembles. Here we build upon and generalise sparse sampling for characterising the free energetics of water density fluctuations in systems near liquid-vapor coexistence. We also introduce sensible heuristics for choosing the biasing potential parameters and strategies for adaptively refining them, which facilitate the estimation of such free energetics accurately and efficiently. We illustrate the method by characterising the free energetics of cavitation in a large volume in bulk water. We also use sparse sampling to characterise the free energetics of capillary evaporation for water confined between two hydrophobic plates. In both cases, sparse sampling is nearly two orders of magnitude faster than umbrella sampling. Given its efficiency, the sparse sampling method is particularly well suited for characterising free energy landscapes for systems wherein umbrella sampling is prohibitively expensive.     

Comparative transcriptome mining for terpenoid biosynthetic pathway genes in wild and cultivated species of Plantago

Protoplasma - Plantagos are important economical and medicinal plants that possess several bioactive secondary metabolites, such as phenolics, iridoids, triterpenes, and alkaloids. Triterpenoids...     

Effect of Eu doping on the thermoluminescence of UV and gamma irradiated Mg2B2O5 nanophosphors

This article presents the effect of europium (Eu) doping on the thermoluminescence (TL) of ultraviolet (UV-254 nm) and gamma irradiated triclinic Mg₂B₂O₅ nanophosphors. The diffuse reflectance predicts slight decrease in band gap from 5.18 to 4.99 eV with increasing Eu (1%, 3%, and 5%) content in Mg₂B₂O₅. The TL glow curves of UV irradiated samples comprised of a main peak around 500 K with weak intensity peak/shoulders in low temperature region. Interestingly Eu (3%) doped Mg₂B₂O₅ shows maximum TL intensity with suppression of low temperature shoulder peaks and almost linear UV dose dependent TL response. However, in the case of gamma irradiated Eu (1% and 3% doped) samples, TL glow curve comprises of a main peak around 425–445 K and closely lying peak around 500–515 K with relatively lesser intensity. In case of Eu (5%) doped samples, TL peak around 508 K starts dominating over peak around 425 K. TL of both UV and gamma irradiated samples showed the presence of various deep and shallow defect states within the bandgap of materials having different kinetic parameters, which were determined using TLanal software based on Kiti's general order equation. The present study shows that Eu doped Mg₂B₂O₅ nanophosphors can be tuned for UV and gamma dosimetry.     

Electronic structure and defect-induced luminescence study of phase-stabilized t-ZrO2 nanocrystals

Luminescent tetragonal-ZrO₂ (t-ZrO₂) nanocrystals were synthesized using an optimized combustion method without post-synthesis annealing and characterized using X-ray diffraction, electron microscopy, Raman spectroscopy, X-ray photoelectron spectroscopy, UV–Vis. spectroscopy, photoluminescence spectroscopy, thermoluminescence (TL), and vibrating sample magnetometry. The as-synthesized t-ZrO₂ nanocrystals have a bandgap of 4.65 eV and exhibit defect-assisted blue emission (Commission Internationale de I'Elcairage coordinates 0.2294, 0.1984) when excited at 270 nm. The defect states were qualitatively and quantitatively analyzed using TL after irradiating nanocrystals with γ- and UV radiations at various doses. The TL glow curves show intense emission in the high-temperature region from 523 to 673 K for both UV- and γ-irradiated samples; however, another less-intense TL peak was also observed in the low-temperature region from 333 to 453 K with γ irradiation at higher doses, indicating the formation of shallow trapping states. The activation energies, frequency factor, and order of kinetics were estimated using the computerized glow curve deconvolution method for the shallow and deep traps for γ- and UV-irradiated samples. The present study shows that phase-stabilized t-ZrO₂ nanocrystals are potential candidates for luminescence-based applications.     

Pollination-induced floral senescence in orchids: Status of oxidative stress

The orchid flowers may stay fresh in unpollinated state from few weeks to months but show rapid senescence upon pollination. Metabolic changes related to this phenomenon are less well understood in orchid flowers. Presently, two orchid species, Aerides multiflora Roxb. and Rhynchostylis retusa (L.) Bl., varying in their floral life span were evaluated for their postpollination-induced responses, involving the oxidative stress. The unpollinated flowers of A. multiflora stayed fresh for 17 days and attained senescence in 5 days after pollination (DAP), while those of R. retusa. remained fresh for 24 days and showed senescence in 7 DAP. After pollination, wilting began in 2 to 3 days in A. multiflora and 3 to 4 days in R. retusa. There was a higher electrolyte leakage accompanied by a concomitant increase in the levels of malondialdehyde (MDA) and hydrogen peroxide (H₂O₂), indicators of oxidative damage in all the organs after pollination while ascorbic acid decreased significantly. The flowers of A. multiflora showed a greater electrolyte leakage, MDA and H₂O₂ contents as compared to those of R. retusa. Ascorbic acid content, on the other hand, was lower in A. multiflora than in R. retusa, suggesting a higher oxidative damage to the floral organs in the former species. An application of triiodobenzoic acid ( an auxin inhibitor; 0.25 mM) and silver nitrate (ethylene inhibitor; 0.25 mM) to pollinated flowers partially prevented the oxidative damage and consequently the senescence, suggesting the involvement of these hormones. AgNO₃ was more effective in delaying senescence.     

Effects of complex aural stimuli on mental performance

The objective of this study is to investigate the effect of complex aural stimuli on mental performance. A series of experiments were designed to obtain data for two different analyses. The first analysis is a "Stimulus" versus "No-stimulus" comparison for each of the four dependent variables, i.e. quantitative ability, reasoning ability, spatial ability and memory of an individual, by comparing the control treatment with the rest of the treatments. The second set of analysis is a multi-variant analysis of variance for component level main effects and interactions. The two component factors are tempo of the complex aural stimuli and sound volume level, each administered at three discrete levels for all four dependent variables. Ten experiments were conducted on eleven subjects. It was found that complex aural stimuli influence the quantitative and spatial aspect of the mind, while the reasoning ability was unaffected by the stimuli. Although memory showed a trend to be worse with the presence of complex aural stimuli, the effect was statistically insignificant. Variation in tempo and sound volume level of an aural stimulus did not significantly affect the mental performance of an individual. The results of these experiments can be effectively used in designing work environments.     

Symbiotic characteristics of cysteine and methionine auxotrophs of Sinorhizobium meliloti

Twenty one cysteine and 13 methionine auxotrophs of Sinorhizobium meliloti Rmd201 were obtained by random mutagenesis with transposon Tn5. The cysteine auxotrophs were sulfite reductase mutants and each of these auxotrophs had a mutation in cysI/cysJ gene. The methionine auxotrophs were metA/metZ, metE and metF mutants. One hundred per cent co-transfer of Tn5-induced kanamycin resistance and auxotrophy from each Tn5-induced auxotrophic mutant indicated that each mutant cell most likely had a single Tn5 insertion. However, the presence of more than one Tn5 insertions in the auxotrophs used in our study cannot be ruled out. All cysteine and methionine auxotrophs induced nodules on alfalfa plants. The nodules induced by cysteine auxotrophs were fully effective like those of the parental strain-induced nodules, whereas the nodules induced by methionine auxotrophs were completely ineffective. The supplementation of methionine to the plant nutrient medium completely restored symbiotic effectiveness to the methionine auxotrophs. These results indicated that the alfalfa host provides cysteine but not methionine to rhizobia during symbiosis. Histological studies showed that the defective symbiosis of methionine auxotrophs with alfalfa plants was due to reduced number of infected nodule cells and incomplete transformation of bacteroids.     

Structural and functional analysis of rice genome

Rice is an excellent system for plant genomics as it represents a modest size genome of 430 Mb. It feeds more than half the population of the world. Draft sequences of the rice genome, derived by whole-genome shotgun approach at relatively low coverage (4-6 X), were published and the International Rice Genome Sequencing Project (IRGSP) declared high quality (> 10 X), genetically anchored, phase 2 level sequence in 2002. In addition, phase 3 level finished sequence of chromosomes 1, 4 and 10 (out of 12 chromosomes of rice) has already been reported by scientists from IRGSP consortium. Various estimates of genes in rice place the number at >50,000. Already, over 28,000 full-length cDNAs have been sequenced, most of which map to genetically anchored genome sequence. Such information is very useful in revealing novel features of macroand micro-level synteny of rice genome with other cereals. Microarray analysis is unraveling the identity of rice genes expressing in temporal and spatial manner and should help target candidate genes useful for improving traits of agronomic importance. Simultaneously, functional analysis of rice genome has been initiated by marker-based characterization of useful genes and employing functional knock-outs created by mutation or gene tagging. Integration of this enormous information is expected to catalyze tremendous activity on basic and applied aspects of rice genomics.     

Sequence analysis of the long arm of rice chromosome 11 for rice–wheat synteny

The DNA sequence of 106 BAC/PAC clones in the minimum tiling path (MTP) of the long arm of rice chromosome 11, between map positions 57.3 and 116.2 cM, has been assembled to phase 2 or PLN level. This region has been sequenced to 10× redundancy by the Indian Initiative for Rice Genome Sequencing (IIRGS) and is now publicly available in GenBank. The region, excluding overlaps, has been predicted to contain 2,932 genes using different software. A gene-by-gene BLASTN search of the NCBI wheat EST database of over 420,000 cDNA sequences revealed that 1,143 of the predicted rice genes (38.9%) have significant homology to wheat ESTs (bit score 100). Further BLASTN search of these 1,143 rice genes with the GrainGenes database of sequence contigs containing bin-mapped wheat ESTs allowed 113 of the genes to be placed in bins located on wheat chromosomes of different homoeologous groups. The largest number of genes, about one-third, mapped to the homoeologous group 4 chromosomes of wheat, suggesting a common evolutionary origin. The remaining genes were located on wheat chromosomes of different groups with significantly higher numbers for groups 3 and 5. Location of bin-mapped wheat contigs to chromosomes of all the seven homoeologous groups can be ascribed to movement of genes (transpositions) or chromosome segments (translocations) within rice or the hexaploid wheat genomes. Alternatively, it could be due to ancient duplications in the common ancestral genome of wheat and rice followed by selective elimination of genes in the wheat and rice genomes. While there exists definite conservation of gene sequences and the ancestral chromosomal identity between rice and wheat, there is no obvious conservation of the gene order at this level of resolution. Lack of extensive colinearity between rice and wheat genomes suggests that there have been many insertions, deletions, duplications and translocations that make the synteny comparisons much more complicated than earlier thought. However, enhanced resolution of comparative sequence analysis may reveal smaller conserved regions of colinearity, which will facilitate selection of markers for saturation mapping and sequencing of the gene-rich regions of the wheat genome.