Magnetic and spin evolution of pulsars

We explore the consequences of the model of spin-down-induced flux expulsion for the magnetic field evolution in solitary as well as in binary neutron stars. The spin evolution of pulsars, allowing for their field evolution according to this model, is shown to be consistent with the existing observational constraints in both low- and high-mass X-ray binary systems. The contribution from pulsars recycled in massive binaries to the observed excess in the number of low-field (10(11)-10(12) G) solitary pulsars is argued to be negligible in comparison with that of normal pulsars undergoing a 'restricted' field decay predicted by the adopted field decay model. Magnetic fields of neutron stars born in close binaries with intermediate- or high-mass main-sequence companions are predicted to decay down to values as low as similar to 10(6) G, which would leave them unobservable as pulsars during most of their lifetimes. The post-recycling evolution of some of these systems can, however, account for the observed binary pulsars having neutron star or massive white dwarf companions. Pulsars recycled in the disc population low-mass binaries are expected to have residual fields greater than or similar to 10(8) G, while for those processed in globular clusters larger residual fields are predicted because of the lower field strength of the neutron star at the epoch of binary formation. A value of tau similar to 1-2 x 10(7) yr for the mean value of the Ohmic decay time-scale in the crusts of neutron stars is suggested, based on the consistency of the model predictions with the observed distribution of periods and magnetic fields in the single and binary pulsars.

Optical studies of SN 2009jf: a Type Ib supernova with an extremely slow decline and aspherical signature

Optical UBVRI photometry and medium-resolution spectroscopy of the Type Ib supernova SN 2009jf, during the period from similar to -15 to +250 d, with respect to the B maximum are reported. The light curves are broad, with an extremely slow decline. The early post-maximum decline rate in the V band is similar to SN 2008D; however, the late-phase decline rate is slower than other Type Ib supernovae studied. With an absolute magnitude of M-V = -17.96 +/- 0.19 at peak, SN 2009jf is a normally bright supernova. The peak bolometric luminosity and the energy deposition rate via the 56Ni -> 56Co chain indicate that similar to 0.17+0.03(-0.03) M-circle dot of 56Ni was ejected during the explosion. The He i 5876 A line is clearly identified in the first spectrum of day similar to -15, at a velocity of similar to 16 000 km s-1. The O i] 6300-6364 A line seen in the nebular spectrum has a multipeaked and asymmetric emission profile, with the blue peak being stronger. The estimated flux in this line implies that greater than or similar to 1.34 M-circle dot oxygen was ejected. The slow evolution of the light curves of SN 2009jf indicates the presence of a massive ejecta. The high expansion velocity in the early phase and broader emission lines during the nebular phase suggest it to be an explosion with a large kinetic energy. A simple qualitative estimate leads to the ejecta mass of M-ej = 4-9 M-circle dot and kinetic energy E-K = 3-8 x 1051 erg. The ejected mass estimate is indicative of an initial main-sequence mass of greater than or similar to 20-25 M-circle dot.

A Suzaku view of IGR J16393-4643

The pulsar IGR J16393-4643 belongs to a class of highly absorbed supergiant high-mass X-ray binaries (HMXBs), characterized by a very high column density of absorbing matter. We present the results of simultaneous broad-band pulsation and spectrum analysis from a 44-ks Suzaku observation of the source. The orbital intensity profile created with the Swift Burst Alert Telescope (Swift-BAT) light curve shows an indication of IGR J16393-4643 being an eclipsing system with a short eclipse semi-angle theta(E) similar to 17 degrees. For a supergiant companion star with a 20-R-circle dot radius, this implies an inclination of the orbital plane in the range 39 degrees-57 degrees, whereas for a main-sequence B star as the companion with a 10-R-circle dot radius, the inclination of the orbital plane is in the range 60 degrees-77 degrees. Pulse profiles created for different energy bands have complex morphology, which shows some energy dependence and increases in pulse fraction with energy. We have also investigated broad-band spectral characteristics, phase-averaged spectra and resolving the pulse phase into peak and trough phases. The phase-averaged spectrum has a very high N-H(similar to 3 x 10(23) cm(-2)) and is described by a power law (Gamma similar to 0.9) with a high-energy cut-off above 20 keV. We find a change in the spectral index in the peak and trough phases, implying an underlying change in the source spectrum.

Structural features of B-DNA dodecamer crystal structures: Influence of crystal packing versus base sequence

We have analyzed the set of inter and intra base pair parameters for each dinucleotide step in single crystal structures of dodecamers, solved at high and medium resolution and all crystallized in P2(1)2(1)2(1) space group. The objective was to identify whether all the structures which have either the Drew-Dickerson (DD) sequence d[CGCGAATTCGCG] with some base modification or related sequence (non-DD), would display the same sequence dependent structural variability about its palindromic sequence, despite the molecule being bent at one end because of similar crystal lattice packing effect. Most of the local doublet parameters for base pairs steps G2-C3 and G10-C11 positions, symmetrically situated about the lateral twofold, were significantly correlated between themselves. In non-DD sequences, significant correlations between these positional parameters were absent. The different range of local step parameter values at each sequence position contributed to the gross feature of smooth helix axis bending in all structures. The base pair parameters in some of the positions, for medium resolution DD sequence, were quite unlike the high-resolution set and encompassed a higher range of values. Twist and slide are the two main parameters that show wider conformational range for the middle region of non-DD sequence structures in comparison to DD sequence structures. On the contrary, the minor and major groove features bear good resemblance between DD and non-DD sequence crystal structure datasets. The sugar-phosphate backbone torsion angles are similar in all structures, in sharp contrast to base pair parameter variation for high and low resolution DD and non-DD sequence structures, consisting of unusual (epsilon =g(-), xi =t) B-II conformation at the 10(th) position of the dodecamer sequence. Thus examining DD and non-DD sequence structures packed in the same crystal lattice arrangement, we infer that inter and intra base pair parameters are as symmetrically equivalent in its value as the symmetry related step for the palindromic DD sequence about lateral two-fold axis. This feature would lead us to agree with the conclusion that DNA conformation is not substantially affected by end-to-end or lateral inter-molecular interaction due to crystal lattice packing effect. Non-DD sequence structures acquire step parameter values which reflect the altered sequence at each of the dodecamer sequence position in the orthorhombic lattice while showing similar gross features of DD sequence structures

A DYNAMO MODEL OF MAGNETIC ACTIVITY IN SOLAR-LIKE STARS WITH DIFFERENT ROTATIONAL VELOCITIES

We attempt to provide a quantitative theoretical explanation for the observations that Ca II H/K emission and X-ray emission from solar-like stars increase with decreasing Rossby number (i.e., with faster rotation). Assuming that these emissions are caused by magnetic cycles similar to the sunspot cycle, we construct flux transport dynamo models of 1M(circle dot) stars rotating with different rotation periods. We first compute the differential rotation and the meridional circulation inside these stars from a mean-field hydrodynamics model. Then these are substituted in our dynamo code to produce periodic solutions. We find that the dimensionless amplitude f(m) of the toroidal flux through the star increases with decreasing rotation period. The observational data can be matched if we assume the emissions to go as the power 3-4 of f(m). Assuming that the Babcock-Leighton mechanism saturates with increasing rotation, we can provide an explanation for the observed saturation of emission at low Rossby numbers. The main failure of our model is that it predicts an increase of the magnetic cycle period with increasing rotation rate, which is the opposite of what is found observationally. Much of our calculations are based on the assumption that the magnetic buoyancy makes the magnetic flux tubes rise radially from the bottom of the convection zone. Taking into account the fact that the Coriolis force diverts the magnetic flux tubes to rise parallel to the rotation axis in rapidly rotating stars, the results do not change qualitatively.

Sequence specific interaction of Mycobacterium smegmatis topoisomerase I with duplex DNA

We have identified strong topoisomerase sites (STS) for Mycobacteruim smegmatis topoisomerase I in double-stranded DNA context using electrophoretic mobility shift assay of enzyme-DNA covalent complexes; Mg2+, an essential component for DNA relaxation activity of the enzyme, is not required for binding to DNA, The enzyme makes single-stranded nicks, with transient covalent interaction at the 5'-end of the broken DNA strand, a characteristic akin to prokaryotic topoisomerases. More importantly, the enzyme binds to duplex DNA having a preferred site with high affinity, a. property similar to the eukaryotic type I topoisomerases, The preferred cleavage site is mapped on a 65 bp duplex DNA and found to be CG/TCTT. Thus, the enzyme resembles other prokaryotic type I topoisomerases in mechanistics of the reaction, but is similar to eukaryotic enzymes in DNA recognition properties.

A New Tetrahydrofurannulation Via Tandem Radical Cyclization Reaction-Reductive Deoxygenation Sequence

Treatment of bromoketals 2, derived from allyl alcohols 1, with tributyltin chloride, sodium cyanoborohydride and AIBN furnishes the tetrahydrofurannulated products 3 via a 5-exo-trig radical cyclisation reaction followed by reductive cleavage of ketal 4.

Homology between jacalin and artocarpin from jackfruit (Artocarpus integrifolia) seeds. Partial sequence and preliminary crystallographic studies of artocarpin

Jacalin and artocarpin, the two lectins from jackfruit (Artocarpus integrifolia) seeds, have different physicochemical properties and carbohydrate-binding specificities. However, comparison of the partial amino-acid sequence of artocarpin with the known sequence of jacalin indicates close to 50% sequence identity. Artocarpin crystallizes in two forms, both monoclinic P2(1), with one and two tetramic molecules, respectively, in the asymmetric units of form I (a = 69.9, b = 73.7, c = 60.6 Angstrom and beta = 95.1 degrees) and form II (a = 87.6, b = 72.2, c = 92.6 Angstrom and beta = 101.1 degrees). Both the crystal structures have been solved by the molecular replacement method using the known structure of jacalin as the search model and ope of them partially refined, confirming that the two lectins are indeed homologous.

Synthesis and properties of main chain discotic liquid crystalline polyethers based on rufigallol

Two series of thermotropic main chain discotic liquid crystalline polyethers, PR4m-n, based on rufigallol were prepared starting from the symmetric tetraethers of rufigallol, R4m; m and n represent the number of carbon atoms in the side chain and spacer segment, respectively. The symmetric tetraethers were in turn readily prepared by selective alkylation of rufigallol under controlled phase-transfer conditions. GPC analysis of the polymers suggested that they were all of moderate molecular weights, with M-n varying between 5400 and 17 000. The length of the spacer segment n in these polyethers was systematically varied, and its effect on the phase transition temperatures and the mesophase structure was examined using DSC, polarized light microscopy, and X-ray diffraction. It is noticed that when the spacer lengths are relatively long(n greater than or equal to 2m), the isotropization temperature (TD-i) decreases as the spacer length n increases, an observation that is in accordance with those previously made. However, when the spacer lengths are relatively small (n < 2m), the dependence of TD-i is quite the opposite; TD-i actually increases with an increase in spacer length. Furthermore, X-ray diffraction studies indicate that, in the discotic columnar mesophases that are formed, the columns pack in a hexagonal manner when n greater than or equal to 2m, while they do so in a rectangular lattice when n < 2m, leading to the formation of Dh and Dr mesophases, respectively. Finally, comparison of the discotic polyethers with their low molar mass analogues confirms the role of polymerization in stabilizing the mesophase; while all the polymers exhibit columnar mesophases, some of their low molar mass analogues are not liquid crystalline.

Structural and Sequence Characteristics of Long alpha Helices in Globular Proteins

Elucidation of the detailed structural features and sequence requirements for iv helices of various lengths could be very important in understanding secondary structure formation in proteins and, hence. in the protein folding mechanism. An algorithm to characterize the geometry of an alpha helix from its C-alpha coordinates has been developed and used to analyze the structures of long cu helices (number of residues greater than or equal to 25) found in globular proteins, the crystal structure coordinates of which are available from the Brookhaven Protein Data Bank, Ail long a helices can be unambiguously characterized as belonging to one of three classes: linear, curved, or kinked, with a majority being curved. Analysis of the sequences of these helices reveals that the long alpha helices have unique sequence characteristics that distinguish them from the short alpha helices in globular proteins, The distribution and statistical propensities of individual amino acids to occur in long alpha heices are different from those found in short alpha helices, with amino acids having longer side chains and/or having a greater number of functional groups occurring more frequently in these helices, The sequences of the long alpha helices can be correlated with their gross structural features, i.e., whether they are curved, linear, or kinked, and in case of the curved helices, with their curvature.

New main group ligands for complexation with transition and inner transition elements

Symmetrical and unsymmetrical diphosphinoamines of the type X(2)PN(R)PX(2) and X(2)PN(R)YY' offer vast scope for the synthesis of a variety of transition metal organometallic complexes. Diphosphinoamines can be converted into their dioxides which are also accessible from appropriate (chloro)phosphane oxide precursors. The diphosphazane dioxides form an interesting series of complexes with lanthanide and actinide elements. Structural and spectroscopic studies have been carried out on a wide range of transition metal complexes incorporating linear P-N-P ligands and judiciously functionalized cyclophosphazanes and cyclo-phosphazenes.

Similarities in the Genomic Sequence and Coat Protein-Structure of Plant Viruses

The genomic sequences of several RNA plant viruses including cucumber mosaic virus, brome mosaic virus, alfalfa mosaic virus and tobacco mosaic virus have become available recently. The former two viruses are icosahedral while the latter two are bullet and rod shaped, respectively in particle morphology. The non-structural 3a proteins of cucumber mosaic virus and brome mosaic virus have an amino acid sequence homology of 35% and hence are evolutionarily related. In contrast, the coat proteins exhibit little homology, although the circular dichroism spectrum of these viruses are similar. The non-coding regions of the genome also exhibit variable but extensive homology. Comparison of the brome mosaic virus and alfalfa mosaic virus sequences reveals that they are probably related although with a much larger evolutionary distance. The polypeptide folds of the coat protein of three biologically distinct isometric plant viruses, tomato bushy stunt virus, southern bean mosaic virus and satellite tobacco necrosis virus have been shown to display a striking resemblance. All of them consist of a topologically similar 8-standard β-barrel. The implications of these studies to the understanding of the evolution of plant viruses will be discussed.

Large cryptic internal sequence repeats in protein structures from Homo sapiens

Amino acid sequences are known to constantly mutate and diverge unless there is a limiting condition that makes such a change deleterious. However, closer examination of the sequence and structure reveals that a few large, cryptic repeats are nevertheless sequentially conserved. This leads to the question of why only certain repeats are conserved at the sequence level. It would be interesting to find out if these sequences maintain their conservation at the three-dimensional structure level. They can play an active role in protein and nucleotide stability, thus not only ensring proper functioning but also potentiating malfunction and disease. Therefore, insights into any aspect of the repeats - be it structure, function or evolution - would prove to be of some importance. This study aims to address the relationship between protein sequence and its three-dimensional structure, by examining if large cryptic sequence repeats have the same structure.

Sequence-dependent conformation of an A-DNA double helix: The crystal structure of the octamer d(G-G-T-A-T-A-C-C)

The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1·8 and 2·25 Å, respectively. The molecules adopt an A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.

Immunological studies on nucleic acids and their components.8.Antibodies specific to a deoxyribotrinucleotide sequence

Bovine serum albumin conjugates of two trinucleotides, dpTpTpA and dTpTpAp, were prepared by linking the trinucleotides through their end phosphates by the ‘carbodiimide method’. Antibodies were raised in rabbits by injecting the trinucleotide-bovine serum albumin conjugates. Analysis by double diffusion in agar gel, quantitative precipitin reaction and its inhibition by haptens showed clearly the presence of antibodies specific to the whole trinucleotide molecule. The titre of antibodies obtained by the trinucleotide-rabbit serum albumin conjugates with their respective antisera was approximately the same, indicating that linking the trinucleotide through either 5′ or 3′ phosphate does not have an appreciable effect on the titre of antibodies. The results also demonstrate that the nucleotide(s) away from the carrier protein is more immunodominant than the one linked directly to the protein.