Diversity of DNA methyltransferases that recognize asymmetric target sequences

DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases usually recognize palindromic DNA sequences and add a methyl group to the target base (either adenine or cytosine) on both strands. However, there are a number of MTases that recognize asymmetric target sequences and differ in their subunit organization. In a bacterial cell, after each round of replication, the substrate for any MTase is hemimethylated DNA, and it therefore needs only a single methylation event to restore the fully methylated state. This is in consistent with the fact that most of the DNA MTases studied exist as monomers in solution. Multiple lines of evidence suggest that some DNA MTases function as dimers. Further, functional analysis of many restriction-modification systems showed the presence of more than one or fused MTase genes. It was proposed that presence of two MTases responsible for the recognition and methylation of asymmetric sequences would protect the nascent strands generated during DNA replication from cognate restriction endonuclease. In this review, MTases recognizing asymmetric sequences have been grouped into different subgroups based on their unique properties. Detailed characterization of these unusual MTases would help in better understanding of their specific biological roles and mechanisms of action. The rapid progress made by the genome sequencing of bacteria and archaea may accelerate the identification and study of species- and strain-specific MTases of host-adapted bacteria and their roles in pathogenic mechanisms.

Starburst in the ultraluminous galaxy Arp 220: Constraints from observations of radio recombination lines and continuum

We present observations of radio recombination lines (RRL) from the starburst galaxy Arp 220 at 8.1 GHz (H92 alpha) and 1.4 GHz (H167 alpha and H165 alpha) and at 84 GHz (H42 alpha), 96 GHz (H40 alpha) and 207 GHz (H31 alpha) using the Very Large Array and the IRAM 30 m telescope, respectively. RRLs were detected at all the frequencies except 1.4 GHz, where a sensitive upper limit was obtained. We also present continuum flux measurements at these frequencies as well as at 327 MHz made with the VLA. The continuum spectrum, which has a spectral index alpha similar to -0.6 (S-nu proportional to nu(alpha)) between 5 and 10 GHz, shows a break near 1.5 GHz, a prominent turnover below 500 MHz, and a flatter spectral index above 50 GHz. We show that a model with three components of ionized gas with different densities and area covering factors can consistently explain both RRL and continuum data. The total mass of ionized gas in the three components is 3.2 x 10(7) M., requiring 3 x 10(5) O5 stars with a total Lyman continuum production rate N-Lyc similar to 1.3 x 10(55) photons s(-1). The ratio of the expected to observed Br alpha and Br gamma fluxes implies a dust extinction A(V) similar to 45 mag. The derived Lyman continuum photon production rate implies a continuous star formation rate (SFR) averaged over the lifetime of OB stars of similar to 240 M yr(-1). The Lyman continuum photon Production rate of similar to 3% associated with the high-density H II regions implies a similar SFR at recent epochs (t < 10(5) yr). An alternative model of high-density gas, which cannot be excluded on the basis of the available data, predicts 10 times higher SFR at recent epochs. If confirmed, this model implies that star formation in Arp 220 consists of multiple starbursts of very high SFR (few times 10(3) M. yr(-1)) and short duration (similar to 10(5) yr). The similarity of IR excess, L-IR/L-Ly alpha similar to 24, in Arp 220 to values observed in starburst galaxies shows that most of the high luminosity of Arp 220 is due to the ongoing starburst rather than to a hidden active galactic nucleus (AGN). A comparison of the IR excesses in Arp 220, the Galaxy, and M33 indicates that the starburst in Arp 220 has an initial mass function that is similar to that in normal galaxies and has a duration longer than 107 yr. If there was no infall of gas during this period, then the star formation efficiency (SFE) in Arp 220 is similar to 50%. The high SFR and SFE in Arp 220 is consistent with their known dependences on mass and density of gas in star-forming regions of normal galaxies.

Concepts of Static Var System Control For Enhancing Power Transfer in Long Transmission Lines

This paper is concerned with the influence of different levels of complexity in modelling various constituent subsystems on the dynamic stability of power systems compensated by static var systems (SVS) operating on pure voltage control. The system components investigated include thyristor controlled reactor (TCR) transients, SVS delays, network transients, the synchronous generator and automatic voltage regulator (AVR). An overall model is proposed which adequately describes the system performance for small signal perturbations. The SVS performance is validated through detailed nonlinear simulation on a physical simulator.

Armchair or Zigzag? A tool for characterizing graphene edge

Electronic, magnetic, and structural properties of graphene flakes depend sensitively upon the type of edge atoms. We present a simple software tool for determining the type of edge atoms in a honeycomb lattice. The algorithm is based on nearest neighbor counting. Whether an edge atom is of armchair or zigzag type is decided by the unique pattern of its nearest neighbors. Particular attention is paid to the practical aspects of using the tool, as additional features such as extracting out the edges from the lattice could help in analyzing images from transmission microscopy or other experimental probes. Ultimately, the tool in combination with density-functional theory or tight-binding method can also be helpful in correlating the properties of graphene flakes with the different armchair-to-zigzag ratios. Program summary Program title: edgecount Catalogue identifier: AEIA_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEIA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 66685 No. of bytes in distributed program, including test data, etc.: 485 381 Distribution format: tar.gz Programming language: FORTRAN 90/95 Computer: Most UNIX-based platforms Operating system: Linux, Mac OS Classification: 16.1, 7.8 Nature of problem: Detection and classification of edge atoms in a finite patch of honeycomb lattice. Solution method: Build nearest neighbor (NN) list; assign types to edge atoms on the basis of their NN pattern. Running time: Typically similar to second(s) for all examples. (C) 2010 Elsevier B.V. All rights reserved.

Analyzing Cache Performance Bottlenecks of STM Applications and addressing them with Compiler's help

Software transactional memory (STM) is a promising programming paradigm for shared memory multithreaded programs as an alternative to traditional lock based synchronization. However adoption of STM in mainstream software has been quite low due to its considerable overheads and its poor cache/memory performance. In this paper, we perform a detailed study of the cache behavior of STM applications and quantify the impact of different STM factors on the cache misses experienced by the applications. Based on our analysis, we propose a compiler driven Lock-Data Colocation (LDC), targeted at reducing the cache overheads on STM. We show that LDC is effective in improving the cache behavior of STM applications by reducing the dcache miss latency and improving execution time performance.

High Rydberg state carbon recombination lines toward Cassiopeia A: 332 MHz VLA observations and comparison with H I and molecular lines

We present observations of the C270alpha carbon recombination line, 21 cm neutral hydrogen line and (CO)-C-12 (J = 1 --> 0) molecular line toward Cas A. A comparison of the distribution of recombination line optical depths over the face of Cas A with that of H I optical depths and molecular line emission favors the association of C270alpha regions with H I rather than molecular clouds. The association makes it possible to self-consistently determine several physical parameters of the clouds by combining the recombination line and 21 cm H I measurements.

Tie lines and activities in the system NiO-MgO-SiO2 at 1373 K

The isothermal section of the phase diagram for the system NiO-MgO-SiO2 at 1373 K is established, The tie lines between (NiXMg1-X)O solid solution with rock salt structure and orthosilicate solid solution (NiYMg1-Y)Si0.5O2 and between orthosilicate and metasilicate (NiZMg1-Z)SiO3 crystalline solutions are determined using electron probe microanalysis (EPMA) and lattice parameter measurement on equilibrated samples, Although the monoxides and orthosilicates of Ni and Mg form a continuous range of solid solutions, the metasilicate phase exists only for 0 < Z < 0.096, The activity of NiO in the rock salt solid solution is determined as a function of composition and temperature in the range of 1023 to 1377 K using a solid state galvanic cell, The Gibbs energy of mixing of the monoxide solid solution can be expressed by a pseudo-subregular solution model: Delta G(ex) = X(1 - X)[(-2430 + 0.925T)X + (-5390 + 1.758T)(1 - X)] J/mol, The thermodynamic data for the rock salt phase are combined with information on interphase partitioning of Ni and Mg to generate the mixing properties for the orthosilicate and the metasilicate solid solutions, The regular solution model describes the orthosilicate and the metasilicate solid solutions at 1373 K within experimental uncertainties, The regular solution parameter Delta G(ex)/Y(1 - Y) is -820 (+/-70) J/mol for the orthosilicate solid solution, The corresponding value for the metasilicate solid solution is -220 (+/-150) J/mol, The derived activities for the orthosilicate solid solution are discussed in relation to the intracrystalline ion exchange equilibrium between M1 and M2 sites. The tie line information, in conjunction with the activity data for orthosilicate and metasilicate solid solutions, is used to calculate the Gibbs energy changes for the intercrystalline ion exchange reactions, Combining this with the known data for NiSi0.5O2, Gibbs energies of formation of MgSi0.5O2, MgSiO3, and metastable NiSiO3 are calculated, The Gibbs energy of formation of NiSiO3, from its component oxides, is equal to 7.67 (+/-0.6) kJ/mol at 1373 K.

Vilsmeier-Haack reaction of 1-methyl-34-dihydroisoquino lines-unexpected formation of 2,3-bisdimethylamino-5,6-dihydropyrrolo [2,1-Image]isoquinolines

Novel pyrroloisoquinolines 4 are obtained from 1-methyl-3,4-dihydroisoquinolines 1 by the action of POCl3 and DMF, along with the expected mono- and dialdehydes 2 and 3 respectively and also directly from N-acetyl-2-phenethylamines.

Japanese encephalitis virus infection of mouse cell lines: ability to prime mice for generation of virus specific cytotoxic T lymphocytes and differences in CTL recognisable viral determinants

Ten different mouse cell lines were examined for Japanese encephalitis virus (JEV) infection in vitro and then tested for their ability to generate virus specific cytotoxic T lymphocytes (CTL). Among all cell lines examined, Neuro La (a neuroblastoma) was readily infected with JEV as examined by immunofluorescence and viral replication. Among other cells, P388D1, RAW 264.7 (Macrophage origin), Sp2/0 (B-cell Hybridoma), YAC-1 (T-cell lymphoma), and L929 (Fibroblast) were semipermissive to JEV infection. The cytopathic effects caused by progressive JEV infection varied from cell line to cell line. In the case of YAC-1 cells long-term viral antigen expression was observed without significant alterations in cell viability. Intermediate degrees of cytopathicity are seen in RAW 264.7 and L929 cells while infection of PS, Neuro 2a, P388D1 and Sp2/0 caused major viability losses. All infected cell lines were able to prime adult BALB/c (H-2(d)) mice for the generation of secondary JEV specific CTL. In contrast to YAC-1, the permissive neuroblastoma cell line Neuro 2a (H-2K(k)D(d)) was found to be least efficient in its ability to stimulate anti-viral CTL generation. Cold target competition studies demonstrated that both Neuro 2a and YAC-1 (H-2K(k)D(d)) cells expressed similar viral determinants that are recognised by CTL, suggesting that the reason for the lower ability of Neuro 2a to stimulate anti-viral CTL was not due to lack of viral CTL determinants. These findings demonstrate that a variety of mouse cell lines can be infected with Japanese encephalitis virus, and that these infected cells could be utilised to generate virus specific CTL in BALB/c mice.

Carbon recombination lines between 34.5 and 770 MHz toward Cassiopeia A

We present observations of low-frequency recombination lines of carbon toward Cas A near 34.5 MHz (n similar to 575) using the Gauribidanur radio telescope and near 560 MHz (n similar to 225) and 770 MHz (n similar to 205) using the NRAO 140 foot (43 m) telescope in Greenbank. We also present high angular resolution (1') observations of the C270 alpha line near 332 MHz using the Very Large Array in B-configuration. A high signal-to-noise ratio spectrum is obtained at 34.5 MHz, which clearly shows a Voigt profile with distinct Lorentzian wings, resulting from significant pressure and radiation broadening at such high quantum numbers. The emission lines detected near 332, 550, and 770 MHz, on the other hand, are narrow and essentially Doppler-broadened. The measured Lorentzian width at 34.5 MHz constrains the allowed combinations of radiation temperature, electron density, and electron temperature in the line-forming region. Radiation broadening at 34.5 MHz places a lower limit of 115 pc on the separation between Cas A and the line-forming clouds. Modeling the variation in the integrated line-to-continuum ratio with frequency indicates that the region is likely to be associated with the cold atomic hydrogen component of the interstellar medium, and the physical properties of this region are likely to be T-e = 75 K, n(e) = 0.02 cm(-3), T-R100 = 3200 K, and n(H) T-e = 10,000 cm(-3) K. Comparison of the distribution of the C270 alpha recombination line emission across Cas A with that of (CO)-C-12 and H I also supports the above conclusion.

Performance issues of distance relays for shunt FACTS compensated transmission lines

In this paper, the performance of distance relays when applied to transmission system equipped with shunt FACTS device, Static Synchronous Compensator (STATCOM) is described. The aim of the proposed study is to evaluate the performance of distance relays when STATCOM is incorporated at the mid point of transmission lines for voltage control. A detailed model of STATCOM and its control strategy is presented. The presence of these devices significantly affects apparent impedance seen by the distance relays due to their rapid response to different power system configurations. The distance relay is evaluated for different loading conditions and for different fault locations. The faults are created during various pre-fault loading conditions. The studies are performed on 400KV and 132KV systems and the results are presented. Simulation studies are carried out using transient simulation software, PSCAD/EMTDC.

A differential-geometric analysis of singularities of point trajectories of serial and parallel manipulators

In this paper, we present a differential-geometric approach to analyze the singularities of task space point trajectories of two and three-degree-of-freedom serial and parallel manipulators. At non-singular configurations, the first-order, local properties are characterized by metric coefficients, and, geometrically, by the shape and size of a velocity ellipse or an ellipsoid. At singular configurations, the determinant of the matrix of metric coefficients is zero and the velocity ellipsoid degenerates to an ellipse, a line or a point, and the area or the volume of the velocity ellipse or ellipsoid becomes zero. The degeneracies of the velocity ellipsoid or ellipse gives a simple geometric picture of the possible task space velocities at a singular configuration. To study the second-order properties at a singularity, we use the derivatives of the metric coefficients and the rate of change of area or volume. The derivatives are shown to be related to the possible task space accelerations at a singular configuration. In the case of parallel manipulators, singularities may lead to either loss or gain of one or more degrees-of-freedom. For loss of one or more degrees-of-freedom, ther possible velocities and accelerations are again obtained from a modified metric and derivatives of the metric coefficients. In the case of a gain of one or more degrees-of-freedom, the possible task space velocities can be pictured as growth to lines, ellipses, and ellipsoids. The theoretical results are illustrated with the help of a general spatial 2R manipulator and a three-degree-of-freedom RPSSPR-SPR parallel manipulator.

Very large array detection of radio recombination lines from the radio nucleus of NGC 253: Ionization by a weak active galactic nucleus, an obscured super star cluster, or a compact supernova remnant?

We have imaged the H92alpha and H75alpha radio recombination line (RRL) emissions from the starburst galaxy NGC 253 with a resolution of similar to4 pc. The peak of the RRL emission at both frequencies coincides with the unresolved radio nucleus. Both lines observed toward the nucleus are extremely wide, with FWHMs of similar to200 km s(-1). Modeling the RRL and radio continuum data for the radio nucleus shows that the lines arise in gas whose density is similar to10(4) cm(-3) and mass is a few thousand M., which requires an ionizing flux of (6-20) x 10(51) photons s(-1). We consider a supernova remnant (SNR) expanding in a dense medium, a star cluster, and also an active galactic nucleus (AGN) as potential ionizing sources. Based on dynamical arguments, we rule out an SNR as a viable ionizing source. A star cluster model is considered, and the dynamics of the ionized gas in a stellar-wind driven structure are investigated. Such a model is only consistent with the properties of the ionized gas for a cluster younger than similar to10(5) yr. The existence of such a young cluster at the nucleus seems improbable. The third model assumes the ionizing source to be an AGN at the nucleus. In this model, it is shown that the observed X-ray flux is too weak to account for the required ionizing photon flux. However, the ionization requirement can be explained if the accretion disk is assumed to have a big blue bump in its spectrum. Hence, we favor an AGN at the nucleus as the source responsible for ionizing the observed RRLs. A hybrid model consisting of an inner advection-dominated accretion flow disk and an outer thin disk is suggested, which could explain the radio, UV, and X-ray luminosities of the nucleus.