Interaction of Sesbania Mosaic Virus Movement Protein with VPg and P10: Implication to Specificity of Genome Recognition

Sesbania mosaic virus (SeMV) is a single strand positive-sense RNA plant virus that belongs to the genus Sobemovirus. The mechanism of cell-to-cell movement in sobemoviruses has not been well studied. With a view to identify the viral encoded ancillary proteins of SeMV that may assist in cell-to-cell movement of the virus, all the proteins encoded by SeMV genome were cloned into yeast Matchmaker system 3 and interaction studies were performed. Two proteins namely, viral protein genome linked (VPg) and a 10-kDa protein (P10) c v gft encoded by OFR 2a, were identified as possible interacting partners in addition to the viral coat protein (CP). Further characterization of these interactions revealed that the movement protein (MP) recognizes cognate RNA through interaction with VPg, which is covalently linked to the 59 end of the RNA. Analysis of the deletion mutants delineated the domains of MP involved in the interaction with VPg and P10. This study implicates for the first time that VPg might play an important role in specific recognition of viral genome by MP in SeMV and shed light on the possible role of P10 in the viral movement.

Impact of climate change at species level: a case study of teak in India

In this study, we model the long-term effect of climate change on commercially important teak (Tectona grandis) and its productivity in India. This modelling assessment is based on climate projections of the regional climate model of the Hadley Center (HadRM3) and the dynamic vegetation model, IBIS. According to the model projections, 30% of teak grids in India are vulnerable to climate change under both A2 and B2 SRES scenarios because the future climate may not be optimal for teak at these grids. However, the net primary productivity and biomass are expected to increase because of elevated levels of CO2. Given these directions of likely impacts, it is crucial to further investigate the climate change impacts on teak and incorporate such findings into long-term teak plantation programs. This study also demonstrates the feasibility and limitations of assessing the impact of projected climate change at the species level in the tropics.

Phage Displayed Short Peptides against Cells of Candida albicans Demonstrate Presence of Species, Morphology and Region Specific Carbohydrate Epitopes

Candida albicans is a commensal opportunistic pathogen, which can cause superficial infections as well as systemic infections in immuocompromised hosts. Among nosocomial fungal infections, infections by C. albicans are associated with highest mortality rates even though incidence of infections by other related species is on the rise world over. Since C. albicans and other Candida species differ in their susceptibility to antifungal drug treatment, it is crucial to accurately identify the species for effective drug treatment. Most diagnostic tests that differentiate between C. albicans and other Candida species are time consuming, as they necessarily involve laboratory culturing. Others, which employ highly sensitive PCR based technologies often, yield false positives which is equally dangerous since that leads to unnecessary antifungal treatment. This is the first report of phage display technology based identification of short peptide sequences that can distinguish C. albicans from other closely related species. The peptides also show high degree of specificity towards its different morphological forms. Using fluorescence microscopy, we show that the peptides bind on the surface of these cells and obtained clones that could even specifically bind to only specific regions of cells indicating restricted distribution of the epitopes. What was peculiar and interesting was that the epitopes were carbohydrate in nature. This gives insight into the complexity of the carbohydrate composition of fungal cell walls. In an ELISA format these peptides allow specific detection of relatively small numbers of C. albicans cells. Hence, if used in combination, such a test could help accurate diagnosis and allow physicians to initiate appropriate drug therapy on time.

Growth mechanism of phases by interdiffusion and diffusion of species in the niobium-silicon system

The integrated diffusion coefficient of the phases and the tracer diffusion coefficients of the species are determined in the Nb-Si system by the diffusion couple technique. The diffusion rate of Si is found to be faster than that of Nb in both the NbSi2 and Nb5Si3 phases. The possible atomic mechanism of diffusion is discussed based on the crystal structure and on available details of the defect concentration data. The faster diffusion rate of Si in the Nb5Si3 phase is found to be unusual. The growth mechanism of the phases is also discussed on the basis of the data calculated in this study. (C) 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Planar triazinium cations from VO2+-assisted ring cyclizations: a remarkably efficient thiazole species for nuclear staining, PDT and anaerobic photocleavage of DNA

Planar triazinium cationic species, from VO2+-assisted cyclization of 1-(2-thiazolylazo)-2-naphthol, shows efficient DNA intercalative binding, visible light-induced anaerobic plasmid DNA photocleavage activity and photocytotoxicity in HeLa and MCF-7 cancer cells by an apoptotic pathway with selective localization of the compound in the nucleus as evidenced from the nuclear staining and confocal imaging.

Levitation Effect: Role of Symmetry and Dependence of Diffusivity on the Bond Length of Homonuclear and Heteronuclear Diatomic Species

Molecular dynamics investigation of model diatomic species confined to the alpha-cages of zeolite NaY is reported. The dependence of self-diffusivity on the bond length of the diatomic species has been investigated. Three different sets of runs have been carried out. In the first set, the two atoms of the diatomic molecule interact with the zeolite atoms with equal strength (example, O-2, the symmetric case). In the second and third sets which correspond to asymmetric cases, the two atoms of the diatomic molecule interact with unequal strengths (example, CO). The result for the symmetric case exhibits a well-defined maximum in self-diffusivity for an intermediate bond length. In contrast to this, the intermediate asymmetry leads to a less pronounced maximum. For the large asymmetric case, the maximum is completely absent. These findings are analyzed by computing a number of related properties. These results provide a direct confirmation at the microscopic level of the suggestion by Derouane that the supermobility observed experimentally by Kemball has its origin in the mutual cancellation of forces. The maximum in diffusivity from molecular dynamics is seen at the value predicted by the levitation effect. Further, these findings suggest a role for symmetry in the existence of a diffusivity maximum as a function of diameter of the diffusant often referred to as the levitation effect. The nature of the required symmetry for the existence of anomalous diffusivity is interaction symmetry which is different from that normally encountered in crystallography.

Bile acids in asymmetric synthesis and molecular recognition

This account summarizes the progress made in our laboratory towards the development of new uses of naturally occurring bile acids. Applications in Asymmetric Synthesis (intramolecular coupling, and intermolecular reactions) and Molecular Recognition are described with suitable examples.

Coadsorption of Dioxygen and Water on the Ni(110) Surface: Role of O1--Type Species in the Dissociation of Water

While the adsorption of dioxygen at a clean Ni(110) surface gives rise to two O(1s) features at 531 and 530 eV assigned to O-(a) and O2-(a) type species respectively, coadsorption of dioxygen and water mixtures result in the additional formation of hydroxyl species characterized by an O(1s) peak at 532.3 eV. The latter is attributed to the oxygen induced dissociation of water via a low energy pathway involving the O-(a)-type species. The proportions of the O-(a) and the hydroxyl species are greater for small O-2/H2O ratios and lower temperatures (120 K). With increase in temperature, the relative surface concentrations of the O-(a) and the hydroxyl species decrease while there is an increase in the concentration of the oxidic O2-(a) species. Thus, the surface concentrations of both the hydroxyl and the O2-(a) species depend critically on the presence of O- type species. Above 300K the surface chemistry in the main involves the conversion of O- to O2- species via the hydroxyl species.

Phenology of tree species of tropical moist forest of Uttara Kannada district, Karnataka, India

Phenological observations on tree species in tropical moist forest of Uttara Kannada district (13ℴ55′ to 15ℴ31′ N lat; 74ℴ9′ to 75ℴ10′ E long) during the years 1983–1985 revealed that there exists a strong seasonality for leaf flush, leaf drop and reproduction. Young leaves were produced in the pre-monsoon dry period with a peak in February, followed by the expansion of leaves which was completed in March. Abscission of leaves occurred in the post-monsoon winter period with a peak in December. There were two peaks for flowering (December and March), while fruit ripening had a single peak in May–June, preceding the monsoon rainfall. The duration of maturation of leaves was the shortest, while that of full ripening of fruits was the longest. Mature flowers of evergreen species lasted longer than those of deciduous species; in contrast the phenophase of ripe fruits of deciduous species was longer than that of evergreen species.

Structure of ant assemblages in Western Ghats, India: role of habitat, disturbance and introduced species

1. Habitat fragmentation, anthropogenic disturbance and the introduction of invasive species are factors thought to structure ant assemblages. To understand responses of the ant community to changes in the environment, ants are commonly categorised into functional groups, a scheme developed and based on Australian ants. 2. Behaviourally dominant and aggressive ants of the dominant dolichoderinae functional group have been suggested to structure the ant assemblages in arid and semi-arid habitats of these regions. Given the limited geographical distribution of dominant dolichoderinae, it is crucial to determine the responses of the ant community to changes in the environment in their absence. 3. This study addresses this less studied aspect by considering the associations of ants of Western Ghats, India, with habitat, anthropogenic disturbance and introduced ants. We determined how ant functional groups respond to these factors in this region, where dominant dolichoderines are naturally absent, and whether responses are consistent with predictions derived from the ant functional group scheme. 4. This study provides new information on ant assemblages in a little-studied region. As in other parts of the world, ant assemblages in Western Ghats were strongly influenced by habitat and disturbance, with different functional groups associated with different habitats and levels of disturbance. 5. No functional group showed evidence of being influenced by the abundance of introduced species. In addition, predictions of negative interactions between functional groups were not supported. Our findings suggest that abiotic factors are universal determinants of ant assemblage structure, but that competitive interactions may not be.

Quantitation of spermatogenesis by DNA flow cytometry: Comparative study among six species of mammals

Suspensions of testicular germ cells from six species of mammals were prepared and stained for the DNA content with a fluorochrome (ethidium bromide) adopting a common technique and subjected to DNA flow cytometry. While uniform staining of the germ cells of the mouse, hamster, rat and monkey could be obtained by treating with 0.5% pepsin for 60 min followed by staining with ethidium bromide for 30 min, that of the guinea pig and rabbit required for optimal staining pepsinization for 90 min and treatment with ethidium bromide for 60 min. The procedure adopted here provided a uniform recovery of over 80% of germ cells with each one of the species tested and the cell population distributed itself according to the DNA content (expressed as C values) into 5 major classes-spermatogonia (2C), cells in S-phase, primary spermatocytes (4C), round spermatids (1C), and elongating/elongated spermatids (HC). Comparison of the DNA distribution pattern of the germ cell populations between species revealed little variation in the relative quantities of cells with 2C (8-11%), S-phase (6-9%), and 4C (6-9%) amount of DNA. Though the spermatid cell populations exhibited variations (1C:31-46%, HCI:7-20% and and HC2:11-25%) they represented the bulk of germ cells (70-80%). The overall conversion of 2C to 1C (1C:2C ratio) and meiotic transformation of 4C cells to IC (1C:4C ratio) kinetics were relatively constant between the species studied. The present study clearly demonstrates that DNA flow cytometry can be adopted with ease and assurance to quantify germ cell transformation and as such spermatogenesis by analysing a large number of samples with consistency both within and across the species barrier. Any variation from the norms in germ cell proportions observed following treatment, for e.g. hormonal stimulation or deprivation can then be ascribed due to a specific effect of the hormone/drug on single/multiple steps in germ cell transformation

Fusion of Complementary Online and Offline Strategies for Recognition of Handwritten Kannada Characters

This work describes an online handwritten character recognition system working in combination with an offline recognition system. The online input data is also converted into an offline image, and parallely recognized by both online and offline strategies. Features are proposed for offline recognition and a disambiguation step is employed in the offline system for the samples for which the confidence level of the classifier is low. The outputs are then combined probabilistically resulting in a classifier out-performing both individual systems. Experiments are performed for Kannada, a South Indian Language, over a database of 295 classes. The accuracy of the online recognizer improves by 11% when the combination with offline system is used.

Choice of Classifiers in Hierarchical Recognition of Online Handwritten Kannada and Tamil Aksharas

In this paper, we propose a novel dexterous technique for fast and accurate recognition of online handwritten Kannada and Tamil characters. Based on the primary classifier output and prior knowledge, the best classifier is chosen from set of three classifiers for second stage classification. Prior knowledge is obtained through analysis of the confusion matrix of primary classifier which helped in identifying the multiple sets of confused characters. Further, studies were carried out to check the performance of secondary classifiers in disambiguating among the confusion sets. Using this technique we have achieved an average accuracy of 92.6% for Kannada characters on the MILE lab dataset and 90.2% for Tamil characters on the HP Labs dataset.

DNA recognition by the EcoP15I and EcoPI modification methyltransferases

The DNA-binding properties of the EcoP15I DNA methyltransferase (M . EcoP15I; MTase) were studied using electrophoretic mobility shift assays. We show by molecular size-exclusion chromatography and dimethyl suberimidate crosslinking that M . EcoP15I is a dimer in solution. While M . EcoP15I binds approx. threefold more tightly to its recognition sequence, 5'-CAGCAG-3', than to non-specific sequences in the presence of AdoMet or its analogs, the discrimination between specific and non-specific sequences significantly increases in presence of ATP. These results suggest for the first time a role for ATP in DNA recognition by type-III restriction-modification enzymes. Furthermore, we show that although c2 EcoPI mutant MTases are defective in AdoMet binding, they are still able to bind DNA in a sequence-specific manner.