Functional correlation of bacterial LuxS with their quaternary associations: interface analysis of the structure networks

Background The genome of a wide variety of prokaryotes contains the luxS gene homologue, which encodes for the protein S-ribosylhomocysteinelyase (LuxS). This protein is responsible for the production of the quorum sensing molecule, AI-2 and has been implicated in a variety of functions such as flagellar motility, metabolic regulation, toxin production and even in pathogenicity. A high structural similarity is present in the LuxS structures determined from a few species. In this study, we have modelled the structures from several other species and have investigated their dimer interfaces. We have attempted to correlate the interface features of LuxS with the phenotypic nature of the organisms. Results The protein structure networks (PSN) are constructed and graph theoretical analysis is performed on the structures obtained from X-ray crystallography and on the modelled ones. The interfaces, which are known to contain the active site, are characterized from the PSNs of these homodimeric proteins. The key features presented by the protein interfaces are investigated for the classification of the proteins in relation to their function. From our analysis, structural interface motifs are identified for each class in our dataset, which showed distinctly different pattern at the interface of LuxS for the probiotics and some extremophiles. Our analysis also reveals potential sites of mutation and geometric patterns at the interface that was not evident from conventional sequence alignment studies. Conclusion The structure network approach employed in this study for the analysis of dimeric interfaces in LuxS has brought out certain structural details at the side-chain interaction level, which were elusive from the conventional structure comparison methods. The results from this study provide a better understanding of the relation between the luxS gene and its functional role in the prokaryotes. This study also makes it possible to explore the potential direction towards the design of inhibitors of LuxS and thus towards a wide range of antimicrobials.

A versatile AC mutual inductance bridge

We report a versatile but easy to make AC mutual inductance bridge. The bridge has been used over the temperature range 4-300 K and with applied magnetic fields up to 7 T. Representative data obtained on various types of magnetic systems are shown.

Shrewd alliances: mixed foraging associations between treeshrews,greater racket-tailed drongos and sparrowhawks on Great Nicobar Island, India

Mixed-species foraging associations may form to enhance feeding success or to avoid predators. We report the costs and consequences of an unusual foraging association between an endemic foliage gleaning tupaid (Nicobar treeshrew Tupaia nicobarica) and two species of birds; one an insectivorous commensal (greater racket-tailed drongo Dicrurus paradiseus) and the other a diurnal raptor and potential predator (Accipiter sp.). In an alliance driven, and perhaps engineered, by drongos, these species formed cohesive groups with predictable relationships. Treeshrew breeding pairs were found more frequently than solitary individuals with sparrowhawks and were more likely to tolerate sparrowhawks in the presence of drongos. Treeshrews maintained greater distances from sparrowhawks than drongos, and permitted the raptors to come closer when drongos were present. Treeshrew foraging rates declined in the presence of drongos; however, the latter may provide them predator avoidance benefits. The choice of the raptor to join the association is intriguing; particular environmental resource states may drive the evolution of such behavioural strategies. Although foraging benefits seem to be the primary driver of this association, predator avoidance also influences interactions, suggesting that strategies driving the formation of flocks may be complex and context dependent with varying benefits for different actors.

A modified least squares algorithm to treat associations in liquid alloys

The associated model for binary systems has been modified to include volume effects and excess entropy arising from preferential interactions between the associate and the free atoms or between the free atoms. Equations for thermodynamic mixing functions have been derived. An optimization procedure using a modified conjugate gradient method has been used to evaluate the enthalpy and entropy interaction energies, the free energy of dissociation of the complex, its temperature dependance and the size of the associate. An expression for the concentration—concentration structure factor [Scc (0)] has been deduced from the modified associated solution model. The analysis has been applied to the thermodynamic mixing functions of liquid Ga-Te alloys at 1120 K, believed to contain Ga2Te3 associates. It is observed that the modified associated solution model incorporating volume effects and terms for the temperature dependance of interaction energies, describes the thermodynamic properties of Ga-Te system satisfactorily.

The condensed nearest neighbor rule using the concept of mutual nearest neighborhood (Corresp.)

A two-stage iterative algorithm for selecting a subset of a training set of samples for use in a condensed nearest neighbor (CNN) decision rule is introduced. The proposed method uses the concept of mutual nearest neighborhood for selecting samples close to the decision line. The efficacy of the algorithm is brought out by means of an example.

Temporal associations in fig-wasp-ant interactions: diel and phenological patterns

In a complex multitrophic plant-animal interaction system in which there are direct and indirect interactions between species, comprehending the dynamics of these multiple partners is very important for an understanding of how the system is structured. We investigated the plant Ficus racemosa L. (Moraceae) and its community of obligatory mutualistic and parasitic fig wasps (Hymenoptera: Chalcidoidea) that develop within the fig inflorescence or syconium, as well as their interaction with opportunistic ants. We focused on temporal resource partitioning among members of the fig wasp community over the development cycle of the fig syconia during which wasp oviposition and development occur and we studied the activity rhythm of the ants associated with this community. We found that the seven members of the wasp community partitioned their oviposition across fig syconium development phenology and showed interspecific variation in activity across the day-night cycle. The wasps presented a distinct sequence in their arrival at fig syconia for oviposition, with the parasitoid wasps following the galling wasps. Although fig wasps are known to be largely diurnal, we documented night oviposition in several fig wasp species for the first time. Ant activity on the fig syconia was correlated with wasp activity and was dependent on whether the ants were predatory or trophobiont-tending species; only numbers of predatory ants increased during peak arrivals of the wasps.

Volume effects and associations in liquid alloys

The regular associated solution model for binary systems has been modified by incorporating the size of the complex as an explicit variable. The thermodynamic properties of the liquid alloy and the interactions between theA ?B type of complex and the unassociated atoms in anA-B binary have been evaluated as a function of relative size of the complex using the activity coefficients at infinite dilution and activity data at one other composition in the binary. The computational procedure adopted for determining the concentration of clusters and interaction energies in the associated liquid is similar to that proposed by Lele and Rao. The analysis has been applied to the thermodynamic mixing functions of liquid Al-Ca alloys believed to contain Al2Ca associates. It is found that the size of the cluster significantly affects the interaction energies between the complex and the unassociated atoms, while the equilibrium constant and enthalpy change for the association reaction exhibit only minor variation, when the equations are fitted to experimental data. The interaction energy between unassociated free atoms remains virtually unaltered as the size of the complex is varied between extreme values. Accurate data on free energy, enthalpy, and volume of mixing at the same temperature on alloy systems with compound forming tendency would permit a rigorous test of the proposed model.

Agglomerative clustering using the concept of mutual nearest neighbourhood

A method for determining the mutual nearest neighbours (MNN) and mutual neighbourhood value (mnv) of a sample point, using the conventional nearest neighbours, is suggested. A nonparametric, hierarchical, agglomerative clustering algorithm is developed using the above concepts. The algorithm is simple, deterministic, noniterative, requires low storage and is able to discern spherical and nonspherical clusters. The method is applicable to a wide class of data of arbitrary shape, large size and high dimensionality. The algorithm can discern mutually homogenous clusters. Strong or weak patterns can be discerned by properly choosing the neighbourhood width.

Disaggregative Clustering Using the Concept of Mutual Nearest Neighborhood

A nonparametric, hierarchical, disaggregative clustering algorithm is developed using a novel similarity measure, called the mutual neighborhood value (MNV), which takes into account the conventional nearest neighbor ranks of two samples with respect to each other. The algorithm is simple, noniterative, requires low storage, and needs no specification of the expected number of clusters. The algorithm appears very versatile as it is capable of discerning spherical and nonspherical clusters, linearly nonseparable clusters, clusters with unequal populations, and clusters with lowdensity bridges. Changing of the neighborhood size enables discernment of strong or weak patterns.

Mutual diffusion coefficients of some binary liquid systems: benzene-n-alkyl alcohol

The mutual diffusion coefficients for binary liquid systems of benzene-n-alkyl alcohol at various compositions have been determined by the diaphragm cell method at 28-degrees-C. The alcohols used were the members of n-paraffinic alcohols ranging from C1 to C8. The maximum possible experimental error is 14%. The data were fitted with a generalized correlation, giving the deviation from the experimental data to within 2.75%, on average.

A geodesic constant method for computing high-frequency mutual coupling between antennas on general quadric cylinders

A Geodesic Constant Method (GCM) is outlined which provides a common approach to ray tracing on quadric cylinders in general, and yields all the surface ray-geometric parameters required in the UTD mutual coupling analysis of conformal antenna arrays in the closed form. The approach permits the incorporation of a shaping parameter which permits the modeling of quadric cylindrical surfaces of desired sharpness/flatness with a common set of equations. The mutual admittance between the slots on a general parabolic cylinder is obtained as an illustration of the applicability of the GCM.

Surface-ray tracing on hybrid surfaces of revolution for UTD mutual coupling analysis

An angle invariance property based on Hertz's principle of particle dynamics is employed to facilitate the surface-ray tracing on nondevelopable hybrid quadric surfaces of revolution (h-QUASOR's). This property, when used in conjunction with a Geodesic Constant Method, yields analytical expressions for all the ray-parameters required in the UTD formulation. Differential geometrical considerations require that some of the ray-parameters (defined heuristically in the UTD for the canonical convex surfaces) be modified before the UTD can be applied to such hybrid surfaces. Mutual coupling results for finite-dimensional slots have been presented as an example on a satellite launch vehicle modeled by general paraboloid of revolution and right circular cylinder.

Surface-ray tracing solution of ellipsoid of revolution for UTD mutual coupling applications

An analytical surface-ray tracing has been carried out for the prolate ellipsoid of revolution using a novel geodesic constant method. This method yields closed form expressions for all the ray-geometric parameters required for the UTD mutual coupling calculations for the antennas located arbitrarily in three dimensions, on the ellipsoid of revolution.

Mutual inhibition and capacity sharing during parallel preparation of serial eye movements

Many common activities, like reading, scanning scenes, or searching for an inconspicuous item in a cluttered environment, entail serial movements of the eyes that shift the gaze from one object to another. Previous studies have shown that the primate brain is capable of programming sequential saccadic eye movements in parallel. Given that the onset of saccades directed to a target are unpredictable in individual trials, what prevents a saccade during parallel programming from being executed in the direction of the second target before execution of another saccade in the direction of the first target remains unclear. Using a computational model, here we demonstrate that sequential saccades inhibit each other and share the brain's limited processing resources (capacity) so that the planning of a saccade in the direction of the first target always finishes first. In this framework, the latency of a saccade increases linearly with the fraction of capacity allocated to the other saccade in the sequence, and exponentially with the duration of capacity sharing. Our study establishes a link between the dual-task paradigm and the ramp-to-threshold model of response time to identify a physiologically viable mechanism that preserves the serial order of saccades without compromising the speed of performance.

Exploiting coherence for the simultaneous discovery of latent facets and associated sentiments

Facet-based sentiment analysis involves discovering the latent facets, sentiments and their associations. Traditional facet-based sentiment analysis algorithms typically perform the various tasks in sequence, and fail to take advantage of the mutual reinforcement of the tasks. Additionally,inferring sentiment levels typically requires domain knowledge or human intervention. In this paper, we propose aseries of probabilistic models that jointly discover latent facets and sentiment topics, and also order the sentiment topics with respect to a multi-point scale, in a language and domain independent manner. This is achieved by simultaneously capturing both short-range syntactic structure and long range semantic dependencies between the sentiment and facet words. The models further incorporate coherence in reviews, where reviewers dwell on one facet or sentiment level before moving on, for more accurate facet and sentiment discovery. For reviews which are supplemented with ratings, our models automatically order the latent sentiment topics, without requiring seed-words or domain-knowledge. To the best of our knowledge, our work is the first attempt to combine the notions of syntactic and semantic dependencies in the domain of review mining. Further, the concept of facet and sentiment coherence has not been explored earlier either. Extensive experimental results on real world review data show that the proposed models outperform various state of the art baselines for facet-based sentiment analysis.