Nucleotide sequence of the first cosmid from the Mycobacterium leprae genome project: structure and function of the Rif-Str regions

The nucleotide sequence of cosmid B1790, carrying the Rif-Str regions of the Mycobacterium leprae chromosome, has been determined. Twelve open reading frames were identified in the 36716bp sequence, representing 40% of the coding capacity. Five ribosomal proteins, two elongation factors and the β and β'subunits of RNA polymerase have been characterized and two novel genes were found. One of these encodes a member of the so-called ABC family of ATP-binding proteins while the other appears to encode an enzyme involved in repairing genomic lesions caused by free radicals. This finding may well be significant as M. leprae, an intracellular pathogen, lives within macrophages.

Inefficient excision of uracil from loop regions of DNA oligomers by E.coli uracil DNA glycosylase

Kinetic parameters for uracil DNA glycosylase (E.coli)-catalysed excision of uracil from DNA oligomers containing dUMP in different structural contexts were determined. Our results show that single-stranded oligonucleotides (unstructured) are used as somewhat better substrates than the double-stranded oligonucleotides. This is mainly because of the favourable V-max value of the enzyme for single-stranded substrates. More interestingly, however, we found that uracil release from loop regions of DNA hairpins is extremely inefficient. The poor efficiency with which uracil is excised from loop regions is a result of both increased K-m and lowered V-max values. This observation may have significant implications in uracil DNA glycosylase-directed repair of DNA segments that can be extruded as hairpins. In addition, these studies are useful in designing oligonucleotides for various applications in DNA research where the use of uracil DNA glycosylase is sought.

Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks

Structure comparison tools can be used to align related protein structures to identify structurally conserved and variable regions and to infer functional and evolutionary relationships. While the conserved regions often superimpose well, the variable regions appear non superimposable. Differences in homologous protein structures are thought to be due to evolutionary plasticity to accommodate diverged sequences during evolution. One of the kinds of differences between 3-D structures of homologous proteins is rigid body displacement. A glaring example is not well superimposed equivalent regions of homologous proteins corresponding to a-helical conformation with different spatial orientations. In a rigid body superimposition, these regions would appear variable although they may contain local similarity. Also, due to high spatial deviation in the variable region, one-to-one correspondence at the residue level cannot be determined accurately. Another kind of difference is conformational variability and the most common example is topologically equivalent loops of two homologues but with different conformations. In the current study, we present a refined view of the ``structurally variable'' regions which may contain local similarity obscured in global alignment of homologous protein structures. As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of `variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments. Also, through an example, we have demonstrated how the additional information on local backbone structures through protein blocks can aid in comparative modeling of a loop region. In addition, understanding on sequence-structure relationships can be enhanced through our approach. This has been illustrated through examples where the equivalent regions in homologous protein structures share sequence similarity to varied extent but do not preserve local structure.

Star formation in giant extragalactic H II regions

Star formation properties in Giant Extragalactic H II Regions (GEHRs) are investigated using optical photometry and evolutionary population synthesis models. Photometric data in $BVR$ bands and in the emission line of H-alpha are obtained by CCD imaging at Vainu Bappu Observatory, Kavalur. Aperture photometry is performed for 180 GEHRs in galaxies NGC 1365, 1566, 2366, 2903, 2997, 3351, 4303, 4449, 4656 and 5253. Thirty six of these GEHRs having published spectroscopic data are studied for star formation properties. The population synthesis model is constructed based on Maeder's stellar evolutionary and Kurucz stellar atmosphere models, to synthesize observational quantities of embedded clusters in GEHRs. The observed H-alpha luminosity is a measure of the number of massive stars while the contribution to BVR bands is from intermediate mass (5-15 solar mass) stars when the cluster is young and from evolving supergiants when the cluster is old (age >/= 6~Myr). Differential reddening between gas and embedded stars is essential to constrain the dereddened cluster colors within the range of youngest clusters. Obscuring dust closely associated with gas, which is distributed in filaments and clumps, as in the case of 30 Doradus, is the most likely configuration giving rise to net reduction of extinction towards stars. The fraction of the stellar photons escaping the nebula unattenuated is estimated to be 50%. GEHRs are rarely found to be simple systems containing stars from single generation. In the present sample such regions in addition to being older than 3~Myr, have their Lyman continuum luminosity reduced by as much as 60%, compared to the observed $B$ band luminosity for a normal IMF. The missing ionizing photons may be escaping the nebula, leading to the ionization of extra-H II region ionized medium. Co-existence of young (age

Interactions of 3' terminal and 5' terminal regions of physalis mottle virus genomic RNA with its replication complex

Physalis mottle virus (PhMV) belongs to the tymogroup of positive-strand RNA viruses with a genome size of 6 kb. Crude membrane preparations from PhMV-infected Nicotiana glutinosa plants catalyzed the synthesis of PhMV genomic RNA from endogenously bound template. Addition of exogenous genomic RNA enhanced the synthesis which was specifically inhibited by the addition of sense and antisense transcripts corresponding to 3' terminal 242 nucleotides as well as the 5' terminal 458 nucleotides of PhMV genomic RNA while yeast tRNA or ribosomal RNA failed to inhibit the synthesis. This specific inhibition suggested that the 5' and 3' non-coding regions of PhMV RNA might play an important role in viral replication.

Singularity structure and chaotic behavior of the homopolar disk dynamo

We study in great detail a system of three first-order ordinary differential equations describing a homopolar disk dynamo (HDD). This system displays a large variety of behaviors, both regular and chaotic. Existence of periodic solutions is proved for certain ranges of parameters. Stability criteria for periodic solutions are given. The nonintegrability aspects of the HDD system are studied by investigating analytically the singularity structure of the system in the complex domain. Coexisting attractors (including period-doubling sequence) and coexisting strange attractors appear in some parametric regimes. The gluing of strange attractors and the ungluing of a strange attractor are also shown to occur. A period of bifurcation leading to chaos, not observed for other chaotic systems, is shown to characterize the chaotic behavior in some parametric ranges. The limiting case of the Lorenz system is also studied and is related to HDD.

Interfacial Regions Governing Internal Cavities of Dendrimers. Studies of Poly(alkyl aryl ether) Dendrimers Constituted with Linkers of Varying Alkyl Chain Length

This report deals with a study of the properties of internal cavities of dendritic macromolecules that are capable Of encapsulating and mediating photoreactions of guest molecules. The internal cavity structures of dendrimers are determined by the interfacial regions between the aqueous exterior and hydrocarbon like interior constituted by the linkers that connect symmetrically sited branch points constituting the dendrimer and head groups that cap the dendrimers. Phloroglucinol-based poly(alkyl aryl ether) dendrimers constituted with a homologous series of alkyl linkers were undertaken for the current study. Twelve dendrimers within first, second, and third generations, having ethyl, n-propyl, n-butyl, and n-pentyl groups as the linkers and hydroxyl groups at peripheries in each generation, were synthesized. Encapsulation of pyrene and coumarins by aqueous basic solutions of dendrimers were monitored-by UV-vis and fluorescence spectroscopies, which showed that a lower generation dendrimer with an optimal alkyl linker presented better encapsulation abilities than a higher generation dendrimer. Norrish type I photoreaction of dibenzyl ketone was carried out within the above: series of dendrimers to probe their abilities to hold guests and reactive inthermediate radical pairs within themselves. The extent of cage effect from the series of third generation dendrimers was observed to be higher with dendrimers having an n-pentyl group as the linker.

Monte Carlo and molecular dynamics simulation of argon clusters andn-alkanes in the confined regions of zeolites

Geometry and energy of argon clusters confined in zeolite NaCaA are compared with those of free clusters. Results indicate the possible existence of magic numbers among the confined clusters. Spectra obtained from instantaneous normal mode analysis of free and confined clusters give a larger percentage of imaginary frequencies for the latter indicating that the confined cluster atoms populate the saddle points of the potential energy surface significantly. The variation of the percentage of imaginary frequencies with temperature during melting is akin to the variation of other properties. It is shown that confined clusters might exhibit inverse surface melting, unlike medium-to-large-sized free clusters that exhibit surface melting. Configurational-bias Monte Carte (CBMC) simulations of n-alkanes in zeolites Y and A are reported. CBMC method gives reliable estimates of the properties relating to the conformation of molecules. Changes in the conformational properties of n-butane and other longer n-alkanes such as n-hexane and n-heptane when they are confined in different zeolites are presented. The changes in the conformational properties of n-butane and n-hexane with temperature and concentration is discussed. In general, in zeolite Y as well as A, there is significant enhancement of the gauche population as compared to the pure unconfined fluid.

On the integrability and chaotic behavior of an ecological model

A three-species food chain model is studied analytically as well as numerically. Integrability of the model is studied using Painleve analysis while chaotic behavior is studied using numerical techniques, such as calculation of Lyapunov exponents, plotting the bifurcation diagram and phase plots. We correct and critically comment on the wrong results reported recently on this ecological model, in a paper by Rai [1995].

Predictive uncertainty of chaotic daily streamflow using ensemble wavelet networks approach

Perfect or even mediocre weather predictions over a long period are almost impossible because of the ultimate growth of a small initial error into a significant one. Even though the sensitivity of initial conditions limits the predictability in chaotic systems, an ensemble of prediction from different possible initial conditions and also a prediction algorithm capable of resolving the fine structure of the chaotic attractor can reduce the prediction uncertainty to some extent. All of the traditional chaotic prediction methods in hydrology are based on single optimum initial condition local models which can model the sudden divergence of the trajectories with different local functions. Conceptually, global models are ineffective in modeling the highly unstable structure of the chaotic attractor. This paper focuses on an ensemble prediction approach by reconstructing the phase space using different combinations of chaotic parameters, i.e., embedding dimension and delay time to quantify the uncertainty in initial conditions. The ensemble approach is implemented through a local learning wavelet network model with a global feed-forward neural network structure for the phase space prediction of chaotic streamflow series. Quantification of uncertainties in future predictions are done by creating an ensemble of predictions with wavelet network using a range of plausible embedding dimensions and delay times. The ensemble approach is proved to be 50% more efficient than the single prediction for both local approximation and wavelet network approaches. The wavelet network approach has proved to be 30%-50% more superior to the local approximation approach. Compared to the traditional local approximation approach with single initial condition, the total predictive uncertainty in the streamflow is reduced when modeled with ensemble wavelet networks for different lead times. Localization property of wavelets, utilizing different dilation and translation parameters, helps in capturing most of the statistical properties of the observed data. The need for taking into account all plausible initial conditions and also bringing together the characteristics of both local and global approaches to model the unstable yet ordered chaotic attractor of a hydrologic series is clearly demonstrated.

Nonlinear dynamics and chaotic motions in feedback-controlled two- and three-degree-of-freedom robots

The dynamics of a feedback-controlled rigid robot is most commonly described by a set of nonlinear ordinary differential equations. In this paper we analyze these equations, representing the feedback-controlled motion of two- and three-degrees-of-freedom rigid robots with revolute (R) and prismatic (P) joints in the absence of compliance, friction, and potential energy, for the possibility of chaotic motions. We first study the unforced or inertial motions of the robots, and show that when the Gaussian or Riemannian curvature of the configuration space of a robot is negative, the robot equations can exhibit chaos. If the curvature is zero or positive, then the robot equations cannot exhibit chaos. We show that among the two-degrees-of-freedom robots, the PP and the PR robot have zero Gaussian curvature while the RP and RR robots have negative Gaussian curvatures. For the three-degrees-of-freedom robots, we analyze the two well-known RRP and RRR configurations of the Stanford arm and the PUMA manipulator respectively, and derive the conditions for negative curvature and possible chaotic motions. The criteria of negative curvature cannot be used for the forced or feedback-controlled motions. For the forced motion, we resort to the well-known numerical techniques and compute chaos maps, Poincare maps, and bifurcation diagrams. Numerical results are presented for the two-degrees-of-freedom RP and RR robots, and we show that these robot equations can exhibit chaos for low controller gains and for large underestimated models. From the bifurcation diagrams, the route to chaos appears to be through period doubling.

On the large-scale diffuse magnetic field of the sun - II. The contribution of active regions

Dikpati and Choudhuri (1993, 1995) developed a model for the poleward migration of the weak diffuse magnetic field on the Sun's surface. This field was identified with the poloidal component produced by the solar dynamo operating at the base of the convection zone, and its evolution was studied by considering the effects of meridional circulation and turbulent diffusion. The earlier model is extended in this paper by incorporating the flux from, the decay of tilted active regions near the solar surface as an additional source of the poloidal field. This extended model can now explain various low-latitude features in the time-latitude diagram of the weak diffuse fields. These low-latitude features could not be accounted for in the earlier model, which was very successful in modeling the behavior at high latitudes. The time-latitude diagrams show that regions of a particular polarity often have 'tongues' of opposite polarity. Such tongues can be produced in the theoretical model by incorporating fluctuations in the source term arising out of the decaying active regions.

Chaotic and power law states in the Portevin-Le Chatelier effect

Recent studies on the Portevin-Le Chatelier effect report an intriguing crossover phenomenon from low-dimensional chaotic to an infinite-dimensional scale-invariant power law regime in experiments on CuAl single crystals and AlMg polycrystals, as function of strain rate. We devise fully dynamical model which reproduces these results. At low and medium strain rates, the model is chaotic with the structure of the attractor resembling the reconstructed experimental attractor. At high strain rates, power law statistics for the magnitudes and durations of the stress drops emerge as in experiments and concomitantly, the largest Lyapunov exponent is zero.

Multivariate nonlinear ensemble prediction of daily chaotic rainfall with climate inputs

The basic characteristic of a chaotic system is its sensitivity to the infinitesimal changes in its initial conditions. A limit to predictability in chaotic system arises mainly due to this sensitivity and also due to the ineffectiveness of the model to reveal the underlying dynamics of the system. In the present study, an attempt is made to quantify these uncertainties involved and thereby improve the predictability by adopting a multivariate nonlinear ensemble prediction. Daily rainfall data of Malaprabha basin, India for the period 1955-2000 is used for the study. It is found to exhibit a low dimensional chaotic nature with the dimension varying from 5 to 7. A multivariate phase space is generated, considering a climate data set of 16 variables. The chaotic nature of each of these variables is confirmed using false nearest neighbor method. The redundancy, if any, of this atmospheric data set is further removed by employing principal component analysis (PCA) method and thereby reducing it to eight principal components (PCs). This multivariate series (rainfall along with eight PCs) is found to exhibit a low dimensional chaotic nature with dimension 10. Nonlinear prediction employing local approximation method is done using univariate series (rainfall alone) and multivariate series for different combinations of embedding dimensions and delay times. The uncertainty in initial conditions is thus addressed by reconstructing the phase space using different combinations of parameters. The ensembles generated from multivariate predictions are found to be better than those from univariate predictions. The uncertainty in predictions is decreased or in other words predictability is increased by adopting multivariate nonlinear ensemble prediction. The restriction on predictability of a chaotic series can thus be altered by quantifying the uncertainty in the initial conditions and also by including other possible variables, which may influence the system. (C) 2011 Elsevier B.V. All rights reserved.

The orientational relaxation of bipolar active regions

In the mean, bipolar active regions are oriented nearly toroidally, according to Hale's polarity law, with a latitude-dependent tilt known as Joy's Law. The tilt angles of individual active regions deviate from this mean behavior and change over time. It has been found that on average the change is toward the mean angle at a rate characteristic of 4.37 days (Howard, 1996). We show that this orientational relaxation is consistent with the standard model of flux tube emergence from a deep dynamo layer. Under this scenario Joy's law results from the Coriolis effect on the rising flux tube (D'Silva and Choudhuri, 1993), and departures from it result from turbulent buffeting of the tubes (Longcope and Fisher, 1996). We show that relaxation toward Joy's angle occurs because the turbulent perturbations relax on shorter time scales than the perturbations from the Coriolis force. The turbulent perturbations relax more rapidly because they are localized to the topmost portion of the convection zone while the Coriolis perturbations are more widely distributed. If a fully-developed active region remains connected to the strong toroidal magnetic field at the base of the convection zone, its tilt will eventually disappear, leaving it aligned perfectly toroidally. On the other hand, if the flux becomes disconnected from the toroidal field the bipole will assume a tilt indicative of the location of disconnection. We compare models which are connected and disconnected from the toroidal field. Only those disconnected at points very deep in the convection zone a-re consistent with observed time scale of orientational relaxation.