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.

Direct Writing of Copper Film Patterns by Laser-Induced Decomposition of Copper Acetate

Direct writing of patterns is being widely attempted in the field of microelectronic circuit/device manufacture. Use of this technique eliminates the need for employing photolithographic process. Laser induced direct writing can be achieved by (i) Photochemical reaction [i] , (ii) Evaporation from target material [2], and (iii) decomposition.Micron size features of palladium and copper through decomposition of palladium acetate and copper formate respectively on quartz and silicon using Argon ion laser have been reported [3,4] .In this commuication we report a technique for both single line and large area depositon of copper through decomposition of copper acetate,(CH3COO)2Cu, on alumina substrates.Nd:YAG laser known for its reliability and low maintenance cost as compared to excimer and other gas lasers is used. This technique offers an attractive and economical alternative for manufacture of thin film microcircuits.

Medium access control schemes for local area networks with multiple priority function

This paper deals with the development and performance evaluation of three modified versions of a scheme proposed for medium access control in local area networks. The original scheme implements a collision-free and fair medium arbitration by using a control wire in conjunction with a data bus. The modifications suggested in this paper are intended to realize the multiple priority function in local area networks.

Characterization of a large-area PVDF thin film for electro-mechanical and ultrasonic sensing applications

Large-area PVDF thin films have been prepared and characterized for quasi-static and high frequency dynamic strain sensing applications. These films are prepared using hot press method and the piezoelectric phase (beta-phase) has been achieved by thermo-mechanical treatment and poling under DC field. The fabricated films have been characterized for quasi-static strain sensing and the linear strain-voltage relationship obtained is promising. In order to evaluate the ultrasonic sensing properties, a PZT wafer has been used to launch Lamb waves in a metal beam on which the PVDF film sensor is bonded at a distance. The voltage signals obtained from the PVDF films have been compared with another PZT wafer sensor placed on the opposite surface of the beam as a reference signal. Due to higher stiffness and higher thickness of the PZT wafer sensors, certain resonance patterns significantly degrade the sensor sensitivity curves. Whereas, the present results show that the large-area PVDF sensors can be superior with the signal amplitude comparable to that of PZT sensors and with no resonance-induced effect, which is due to low mechanical impedance, smaller thickness and larger area of the PVDF film. Moreover, the developed PVDF sensors are able to capture both A(0) and S-0 modes of Lamb wave, whereas the PZT sensors captures only A(0) mode in the same scale of voltage output. This shows promises in using large-area PVDF films with various surface patterns on structures for distributed sensing and structural health monitoring under quasi-static, vibration and ultrasonic situations. (C) 2010 Elsevier B.V. All rights reserved.

Source and target enzyme signature in serine protease inhibitor active site sequences

Amino acid sequences of proteinaceous proteinase inhibitors have been extensively analysed for deriving information regarding the molecular evolution and functional relationship of these proteins. These sequences have been grouped into several well defined families. It was found that the phylogeny constructed with the sequences corresponding to the exposed loop responsible for inhibition has several branches that resemble those obtained from comparisons using the entire sequence. The major branches of the unrooted tree corresponded to the families to which the inhibitors belonged. Further branching is related to the enzyme specificity of the inhibitor. Examination of the active site loop sequences of trypsin inhibitors revealed that there are strong preferences for specific amino acids at different positions of the loop. These preferences are inhibitor class specific. Inhibitors active against more than one enzyme occur within a class and confirm to class specific sequence in their loops. Hence, only a few positions in the loop seem to determine the specificity. The ability to inhibit the same enzyme by inhibitors that belong to different classes appears to be a result of convergent evolution

Heat Shock Protein 90 as a Drug Target against Protozoan Infections Biochemical characterization of HSP90 From plasmodium falciparum and trypanosoma evansi and evaluation of its inhibitor as a candidate drug

Using a pharmacological inhibitor of Hsp90 in cultured malarial parasite, we have previously implicated Plasmodium falciparum Hsp90 (PfHsp90) as a drug target against malaria. In this study, we have biochemically characterized PfHsp90 in terms of its ATPase activity and interaction with its inhibitor geldanamycin (GA) and evaluated its potential as a drug target in a preclinical mouse model of malaria. In addition, we have explored the potential of Hsp90 inhibitors as drugs for the treatment of Trypanosoma infection in animals. Our studies with full-length PfHsp90 showed it to have the highest ATPase activity of all known Hsp90s; its ATPase activity was 6 times higher than that of human Hsp90. Also, GA brought about more robust inhibition of PfHsp90 ATPase activity as compared with human Hsp90. Mass spectrometric analysis of PfHsp90 expressed in P. falciparum identified a site of acetylation that overlapped with Aha1 and p23 binding domain, suggesting its role in modulating Hsp90 multichaperone complex assembly. Indeed, treatment of P. falciparum cultures with a histone deacetylase inhibitor resulted in a partial dissociation of PfHsp90 complex. Furthermore, we found a well known, semisynthetic Hsp90 inhibitor, namely 17-(allylamino)-17-demethoxygeldanamycin, to be effective in attenuating parasite growth and prolonging survival in a mouse model of malaria. We also characterized GA binding to Hsp90 from another protozoan parasite, namely Trypanosoma evansi. We found 17-(allylamino)-17-demethoxygeldanamycin to potently inhibit T. evansi growth in a mouse model of trypanosomiasis. In all, our biochemical characterization, drug interaction, and animal studies supported Hsp90 as a drug target and its inhibitor as a potential drug against protozoan diseases.

devovo biosynthesis of heme offers a new chemotherapeutic target in the human malarial parasite

The human malarial parasite, Image , has been found to synthesize heme Image , despite the accumulation of large quantities of polymeric heme derived from the hemoglobin of the red cell host. The parasite δ-aminolevulinate dehydrase level is significantly lower than that of the host and its inhibition by succinylacetone leads to inhibition of parasite protein synthesis and viability.

Determination of rational strategies for players in two-target games

This paper addresses some of the basic issues involved in the determination of rational strategies for players in two-target games. We show that unlike single-target games where the task of role assignment and selection of strategies is conceptually straightforward, in two-target games, many factors like the preference ordering of outcomes by players, the relative configuration of the target sets and secured outcome regions, the uncertainty about the parameters of the game, etc., also influence the rational selection of strategies by players. The importance of these issues is illustrated through appropriate examples.

Model Based Target Tracking in a Wireless Network of Passive Infrared Sensor Nodes

We consider the problem of tracking an intruder in a plane region by using a wireless sensor network comprising motes equipped with passive infrared (PIR) sensors deployed over the region. An input-output model for the PIR sensor and a method to estimate the angular speed of the target from the sensor output are proposed. With the measurement model so obtained, we study the centralized and decentralized tracking performance using the extended Kalman filter.

Enhancement in Bath Mixing and Plume area in a New Degassing Process - A Computational Fluid Dynamic Study

Reaction between the various species in slag and metal phase is usually mass transfer controlled. There have been continuous efforts to increase the reaction efficiency in slag-metal system, especially during decarburization of steel to produce the ultra low carbon steel (ULCS) in secondary steelmaking. It has been found that the surface reaction is a dominant factor in the final stage of decarburization. In the initial stage, the inner site reaction is major factor in the refining process. The mixing of bath affects the later reaction. However, the former reaction (surface reaction) is affected by the plume size area at the top of the metal surface. Therefore, a computational study has been made to understand the fluid dynamics of a new secondary steelmaking process called Revolutionary Degasser Activator (REDA) to study the bath mixing and plume area. REDA process has been considered as it is claimed that this process can reduce the carbon content in steel below 10ppm in a less time than the other existing processes such as RH and Tank degasser. This study shows that both bath mixing and plume area are increased in REDA process facilitating it to give the desired carbon content in less time. Qualitative comments are made on slag-metal reaction system based on this finding.

Cytotoxic T lymphocytes raised against Japanese encephalitis virus: effector cell phenotype, target specificity and in vitro virus clearance.

Several H-2 defined cell lines were examined for their ability to support infection and replication of Japanese encephalitis virus (JEV) before their use in in vitro and in vivo stimulation protocols for generating cytotoxic T lymphocytes (CTLs) against JEV. Among II different cell lines tested, two H-2(d) macrophage tumour lines (P388D1, RAW 264.7), an H-2(d) hybridoma (Sp2/0), an H-2K(k)D(d) neuroblastoma (Neuro 2a), and H-2(k) fibroblast cell line (L929) were found to support JEV infection and replication. These cell lines were used to generate anti-JEV CTLs by using in vivo immunization followed by in vitro stimulation of BALB/c mice. We observed that not only syngeneic and allogeneic infected cells but also JEV-infected xenogeneic cells could prime BALB/c mice for the generation of JEV-specific CTLs upon subsequent in vitro stimulation of splenocytes with JEV-infected syngeneic cells. Although infected xenogeneic cells were used for immunization, the anti-JEV effecters that were generated lysed infected syngeneic targets but not JEV-infected xenogeneic or allogeneic target cells in a 5h Cr-51 release assay. These anti-JEV effecters recognized syngeneic target cells infected with West Nile virus to a lesser extent and were shown to be Lyt-2.2(+) T cells. The results of unlabelled cold target competition studies suggested alterations in the cell surface expression of viral antigenic determinants recognized by these CTLs. We further demonstrate that the JEV-specific CTLs generated could virtually block the release of infectious virus particles from infected P388D1 and Neuro 2a cells in vitro.

Target space of an asymmetric chiral gauged wzw model

It is shown that the asymmetric chiral gauging of the WZW models give rise to consistent string backgrounds. The target space structure of the chiral gauged SL(2,R) WZW model, with the gauging of subgroups SO(1, 1) in the left and U(1) in the right moving sector, is obtained. We then analyze the symmetries of the background and show the presence of a non-trivial isometry in the canonical parametrization of the WZW model. Using these results, the equivalence of the asymmetric models with the symmetric ones is demonstrated.

Sputter deposited LiPON thin films from powder target as electrolyte for thin film battery applications

Lithium phosphorus oxynitride (LiPON) thin films as solid electrolytes were prepared by reactive radio frequency (rf) magnetron sputtering from Li3PO4 powder compact target. High deposition rates and ease of manufacturing powder target compared with conventional ceramic Li3PO4 targets offer flexibility in handling and reduce the cost associated. Rf power density varied from 1.7 Wcm(-2) to 3 Wcm(-2) and N-2 flow from 10 to 30 sccm for a fixed substrate to target distance of 4 cm for best ionic conductivity. The surface chemical analysis done by X-ray photoelectron spectroscopy showed incorporation of nitrogen into the film as both triply, NE and doubly. Nd coordinated form. With increased presence of NE, ionic conductivity of LiPON was found to be increasing. The electrochemical impedance spectroscopy of LiPON films confirmed an ionic conductivity of 1.1 x 10(-6) Scm(-1) for optimum rf power and N-2 flow conditions. (C) 2011 Elsevier B.V. All rights reserved.