Persistence Problem in Two-Dimensional Fluid Turbulence

We present a natural framework for studying the persistence problem in two-dimensional fluid turbulence by using the Okubo-Weiss parameter Lambda to distinguish between vortical and extensional regions. We then use a direct numerical simulation of the two-dimensional, incompressible Navier-Stokes equation with Ekman friction to study probability distribution functions (PDFs) of the persistence times of vortical and extensional regions by employing both Eulerian and Lagrangian measurements. We find that, in the Eulerian case, the persistence-time PDFs have exponential tails; by contrast, this PDF for Lagrangian particles, in vortical regions, has a power-law tail with an exponent theta = 2.9 +/- 0.2.

Dynamics of zeolite cage and its effect on the diffusion properties of sorbate: persistence of diffusion anomaly in NaA zeolite

Recent computer simulations on zeolites Y and A have found that the diffusion coefficient and the rate of intercage diffusion exhibit, apart from a linear dependence on the reciprocal of the square of the sorbate diameter, an anomalous peak as sorbate diameter approaches the window diameter. Here we report molecular dynamics simulations of zeolite NaA incorporating framework flexibility as a function of sorbate diameter in order to verify the existence of anomalous diffusion. Results suggest persistence of anomalous diffusion or ring effect. This suggests that the anomalous behavior is a general effect characteristic of zeolites Y and A. The barrier for diffusion across the eight-ring window is seen to be negative and is found to decrease with sorbate size. The effect of sorbate on the cage motion has also been investigated. Results suggest that the window expands during intercage migration only if the sorbate size is comparable to the window diameter. Flexible cage simulations yield a higher value for the diffusion coefficient and also the rate of intercage diffusion. This increase has been shown to be due to an increase in the intercage diffusions via the centralized diffusion mode rather than the surface-mediated mode. It is shown that this increase arises from an increase in the single particle density distribution in the region near the cage center.

Additional role for the ccd operon of F-plasmid as a transmissible persistence factor

Toxin-antitoxin (TA) systems are found on both bacterial plasmids and chromosomes, but in most cases their functional role is unclear. Gene knockouts often yield limited insights into functions of individual TA systems because of their redundancy. The well-characterized F-plasmid-based CcdAB TA system is important for F-plasmid maintenance. We have isolated several point mutants of the toxin CcdB that fail to bind to its cellular target, DNA gyrase, but retain binding to the antitoxin, CcdA. Expression of such mutants is shown to result in release of the WT toxin from a functional preexisting TA complex as well as derepression of the TA operon. One such inactive, active-site mutant of CcdB was used to demonstrate the contribution of CcdB to antibiotic persistence. Transient activation of WT CcdB either by coexpression of the mutant or by antibiotic/heat stress was shown to enhance the generation of drug-tolerant persisters in a process dependent on Lon protease and RecA. An F-plasmid containing a ccd locus can, therefore, function as a transmissible persistence factor.

Quorum sensing and pathogenesis: role of small signalling molecules in bacterial persistence

The pathogenesis of Mycobacterium tuberculosis is associated with its ability to survive inside the human host and the bacteria use a variety of mechanism to evade the host's defence. A clearer understanding of the host pathogen interaction is needed to follow the pathogenicity and virulence. Recent advances in the study of inter and intra-cellular communication in bacteria had prompted us to study the role of quorum sensing in bacterial survival and pathogenicity. The cell cell communication in bacteria (quorum sensing) is mediated through the exchange of small molecules called as autoinducers that allow bacteria to modulate their gene expression in response to change in cell-population density. It is a coordinated response that confers multicellularity to a bacterial population in response to stress from external environment. Quorum sensing molecules are the global regulators and regulate a wide range of physiological processes including biofilm formation, motility, cell differentiation, long-term survival and many others. Many bacterial pathogens require quorum sensing to produce the virulence factors in response to host pathogen interaction. Here, we summarize our current understanding on small molecule signalling and their role in the bacterial persistence. New discoveries in these areas have enriched our knowledge on intracellular signalling and their role in the long-term survival of mycobacteria under nutrient starvation.

Effects of initial height on the steady-state persistence probability of linear growth models

The effects of the initial height on the temporal persistence probability of steady-state height fluctuations in up-down symmetric linear models of surface growth are investigated. We study the (1 + 1)-dimensional Family model and the (1 + 1)-and (2 + 1)-dimensional larger curvature (LC) model. Both the Family and LC models have up-down symmetry, so the positive and negative persistence probabilities in the steady state, averaged over all values of the initial height h(0), are equal to each other. However, these two probabilities are not equal if one considers a fixed nonzero value of h(0). Plots of the positive persistence probability for negative initial height versus time exhibit power-law behavior if the magnitude of the initial height is larger than the interface width at saturation. By symmetry, the negative persistence probability for positive initial height also exhibits the same behavior. The persistence exponent that describes this power-law decay decreases as the magnitude of the initial height is increased. The dependence of the persistence probability on the initial height, the system size, and the discrete sampling time is found to exhibit scaling behavior.

Unoccupied electronic states in NiS2-xSex across the metal-insulator transition

We investigate the evolution of the electronic structure across the insulator-metal transition in NiS2-xSex with changing composition, but in the absence of any structural or magnetic changes. A comparison of the inverse photoemission spectra with band-structure calculations establishes the importance of correlation effects in these systems. Systematic changes in the spectral distribution establish the persistence of the upper Hubbard band well into the metallic regime, with the insulator-to-metal transition being driven by a transfer of spectral weight from the Hubbard band to states close to the Fermi energy.

targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis

Background: Tuberculosis still remains one of the largest killer infectious diseases, warranting the identification of newer targets and drugs. Identification and validation of appropriate targets for designing drugs are critical steps in drug discovery, which are at present major bottle-necks. A majority of drugs in current clinical use for many diseases have been designed without the knowledge of the targets, perhaps because standard methodologies to identify such targets in a high-throughput fashion do not really exist. With different kinds of 'omics' data that are now available, computational approaches can be powerful means of obtaining short-lists of possible targets for further experimental validation. Results: We report a comprehensive in silico target identification pipeline, targetTB, for Mycobacterium tuberculosis. The pipeline incorporates a network analysis of the protein-protein interactome, a flux balance analysis of the reactome, experimentally derived phenotype essentiality data, sequence analyses and a structural assessment of targetability, using novel algorithms recently developed by us. Using flux balance analysis and network analysis, proteins critical for survival of M. tuberculosis are first identified, followed by comparative genomics with the host, finally incorporating a novel structural analysis of the binding sites to assess the feasibility of a protein as a target. Further analyses include correlation with expression data and non-similarity to gut flora proteins as well as 'anti-targets' in the host, leading to the identification of 451 high-confidence targets. Through phylogenetic profiling against 228 pathogen genomes, shortlisted targets have been further explored to identify broad-spectrum antibiotic targets, while also identifying those specific to tuberculosis. Targets that address mycobacterial persistence and drug resistance mechanisms are also analysed. Conclusion: The pipeline developed provides rational schema for drug target identification that are likely to have high rates of success, which is expected to save enormous amounts of money, resources and time in the drug discovery process. A thorough comparison with previously suggested targets in the literature demonstrates the usefulness of the integrated approach used in our study, highlighting the importance of systems-level analyses in particular. The method has the potential to be used as a general strategy for target identification and validation and hence significantly impact most drug discovery programmes.

Efficient Output-Sensitive Construction of Reeb Graphs

The Reeb graph tracks topology changes in level sets of a scalar function and finds applications in scientific visualization and geometric modeling. This paper describes a near-optimal two-step algorithm that constructs the Reeb graph of a Morse function defined over manifolds in any dimension. The algorithm first identifies the critical points of the input manifold, and then connects these critical points in the second step to obtain the Reeb graph. A simplification mechanism based on topological persistence aids in the removal of noise and unimportant features. A radial layout scheme results in a feature-directed drawing of the Reeb graph. Experimental results demonstrate the efficiency of the Reeb graph construction in practice and its applications.

pi-conjugation and conformation in a semiconducting polymer: small angle x-ray scattering study

Small angle x-ray scattering (SAXS) in a poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) solution has shown the important role of pi-electron conjugation in controlling the chain conformation and assembly. By increasing the extent of conjugation from 30 to 100%, the persistence length (l(p)) increases from 20 to 66 angstrom. Moreover, a pronounced second peak in the pair distribution function has been observed in a fully conjugated chain, at larger length scales. This feature indicates that the chain segments tend to self-assemble as the conjugation along the chain increases. Xylene enhances the rigidity of the PPV backbone to yield extended structures, while tetrahydrofuran solvates the side groups to form compact coils in which the lp is much shorter.

On the Maximum Cloud Zone and the ITCZ over Indian, Longitudes during the Southwest Monsoon

An investigation is presented of the daily variation of the maximum cloud zone (MCZ) and the 7W mb trough in the Northern Hemisphere over the Indian longitudes 70–90°E during April–October for 1973–77. It is found that during June–September there are two favorable locations for a MCZ over these longitudes–on a majority of days the MCZ is present in the monsoon zone north of 15°N, and often a secondary MCZ occurs in the equatorial region (0–10°N). The monsoon MCZ gets established by northward movement of the MCZ occurring over the equatorial Indian ocean in April and May. The secondary MCZ appears intermittently, and is characterized by long spells of persistence only when the monsoon MCZ is absent. In each of the seasons studied, the MCZ temporarily disappeared from the mean summer monsoon location (15–28°N) about four weeks after it was established near the beginning of July. It is reestablished by the northward movement of the secondary MCZ, which becomes active during the absence of the monsoon MCZ, in a manner strikingly similar to that observed in the spring to summer transition. A break in monsoon conditions prevails just prior to the temporary disappearance of the monsoon MCZ. Thus we conclude that the monsoon MCZ cannot survive for longer than a month without reestablishment by the secondary MCZ. Possible underlying mechanisms are also discussed.

The averaging principle and the diagram technique

Rae and Davidson have found a striking connection between the averaging method generalised by Kruskal and the diagram technique used by the Brussels school in statistical mechanics. They have considered conservative systems whose evolution is governed by the Liouville equation. In this paper we have considered a class of dissipative systems whose evolution is governed not by the Liouville equation but by the last-multiplier equation of Jacobi whose Fourier transform has been shown to be the Hopf equation. The application of the diagram technique to the interaction representation of the Jacobi equation reveals the presence of two kinds of interactions, namely the transition from one mode to another and the persistence of a mode. The first kind occurs in the treatment of conservative systems while the latter type is unique to dissipative fields and is precisely the one that determines the asymptotic Jacobi equation. The dynamical equations of motion equivalent to this limiting Jacobi equation have been shown to be the same as averaged equations.

Functional transfer of Salmonella pathogenicity island 2 to Salmonella bongori and Escherichia coli.

The type III secretion system (T3SS) encoded by the Salmonella pathogenicity island 2 (SPI2) has a central role in systemic infections by Salmonella enterica and for the intracellular phenotype. Intracellular S. enterica uses the SPI2-encoded T3SS to translocate a set of effector proteins into the host cell, which modify host cell functions, enabling intracellular survival and replication of the bacteria. We sought to determine whether specific functions of the SPI2-encoded T3SS can be transferred to heterologous hosts Salmonella bongori and Escherichia coli Mutaflor, species that lack the SPI2 locus and loci encoding effector proteins. The SPI2 virulence locus was cloned and functionally expressed in S. bongori and E. coli. Here, we demonstrate that S. bongori harboring the SPI2 locus is capable of secretion of SPI2 substrate proteins under culture conditions, as well as of translocation of effector proteins under intracellular conditions. An SPI2-mediated cellular phenotype was induced by S. bongori harboring the SPI2 if the sifA locus was cotransferred. An interference with the host cell microtubule cytoskeleton, a novel SPI2-dependent phenotype, was observed in epithelial cells infected with S. bongori harboring SPI2 without additional effector genes. S. bongori harboring SPI2 showed increased intracellular persistence in a cell culture model, but SPI2 transfer was not sufficient to confer to S. bongori systemic pathogenicity in a murine model. Transfer of SPI2 to heterologous hosts offers a new tool for the study of SPI2 functions and the phenotypes of individual effectors.

Context-dependency of a complex fruit-frugivore mutualism: temporal variation in crop size and neighborhood effects

The quantity of fruit consumed by dispersers is highly variable among individuals within plant populations. The outcome Of Such selection operated by firugivores has been examined mostly with respect to changing spatial contexts. The influence of varying temporal contexts on frugivore choice, and their possible demographic and evolutionary consequences is poorly understood. We examined if temporal variation in fruit availability across a hierarchy of nested temporal levels (interannual, intraseasonal, 120 h, 24 h) altered frugivore choice for a complex seed dispersal system in dry tropical forests of southern India. The interactions between Phyllanthus emblica and its primary disperser (ruminants) was mediated by another frugivore (a primate),which made large quantities of fruit available on the ground to ruminants. The direction and strength of crop size and neighborhood effects on this interaction varied with changing temporal contexts.Fruit availability was higher in the first of the two study years, and at the start of the season in both years. Fruit persistence on trees,determined by primate foraging, was influenced by crop size andconspecific neighborhood densities only in the high fruit availability year. Fruit removal by ruminants was influenced by crop size in both years and neighborhood densities only in the high availability year. In both years, these effects were stronger at the start of the season.Intraseasonal reduction in fruit availability diminished inequalities in fruit removal by ruminants and the influence of crop size and fruiting neighborhoods. All trees were not equally attractive to frugivores in a P. emblica population at all points of time. Temporal asymmetry in frugivore-mediated selection could reduce potential for co-evolution between firugivores and plants by diluting selective pressures. Inter-dependencies; formed between disparate animal consumers can add additional levels of complexity to plant-frugivore mutualistic networks and have potential reproductive consequences for specific individuals within populations.

Stress responses in mycobacteria

Mycobacterium tuberculosis is a successful pathogen that overcomes numerous challenges presented by the immune system of the host. This bacterium usually establishes a chronic infection in the host where it may silently persist inside a granuloma until, a failure in host defenses, leads to manifestation of the disease. None of the conventional anti-tuberculosis drugs are able to target these persisting bacilli. Development of drugs against such persisting bacilli is a constant challenge since the physiology of these dormant bacteria is still not understood at the molecular level. Some evidence suggests that the in vivo environment encountered by the persisting bacteria is anoxic and nutritionally starved. Based on these assumptions, anaerobic and starved cultures are used as models to study the molecular basis of dormancy. This review outlines the problem of persistence of M. tuberculosis and the various in vitro models used to study mycobacterial latency. The basis of selecting the nutritional starvation model has been outlined here. Also, the choice of M. smegmatis as a model suitable for studying mycobacterial latency is discussed. Lastly, general issues related to oxidative stress and bacterial responses to it have been elaborated. We have also discussed general control of OxyR-mediated regulation and emphasized the processes which manifest in the absence of functional OxyR in the bacteria. Lastly, a new class of protein called Dps has been reviewed for its important role in protecting DNA under stress.

Studies on the nucleolus -II.The persisting nucleoli of Cicer arietinum Linn.

The behaviour of the nucleoli from mitotic prophase till the end of telophase is illustrated. Since at prophase, the SAT-threads appear embedded in the nucleolar matrix, their orientation in the mass and the rate of dissolution of the latter would determine whether this relationship would continue till meta- or ana-phase. The persistence of the nucleoli-SAT association often till anaphase indicates that the movement of such nucleoli on the spindle is governed by that of the SAT-chromosomes.