Characterization of an N6 adenine methyltransferase from Helicobacter pylori strain 26695 which methylates adjacent adenines on the same strand

Genomic sequences of Helicobacter pylori strains 26695, J99, HPAGI and G27 have revealed an abundance of restriction and modification genes. hp0050, which encodes an N6 adenine DNA methyltransferase, was cloned, overexpressed and purified to near homogeneity. It recognizes the sequence 5'-GRRG-3' (where R is A or G) and, most intriguingly, methylates both adenines when R is A (5'-GAAG-3'). Kinetic analysis suggests a nonprocessive (repeated-hit) mechanism of methylation in which HP0050 methyltransferase methylates one adenine at a time in the sequence 5'-GAAG-3'. This is the first report of an N6 adenine DNA methyltransferase that methylates two adjacent residues on the same strand. Interestingly, HP0050 homologs from two clinical strains of H. pylori (PG227 and 128) methylate only 5'-GAGG-3' compared with 5'-GRRG-3' in strain 26695. HP0050 methyltransferase is highly conserved as it is present in more than 90% of H. pylori strains. Inactivation of hp0050 in strain PG227 resulted in poor growth, suggesting its role in the biology of H. pylori. Collectively, these findings provide impetus for exploring the role(s) of this conserved DNA methyltransferase in the cellular processes of H. pylori.

Metal-ion-mediated tuning of duplex DNA binding by bis(2-(2-pyridyl)-1H-benzimidazole)

Studies of double-stranded-DNA binding have been performed with three isomeric bis)2-(n-pyridyl)-1H-benzimidazole)s (n = 2, 3, 4). Like the well-known Hoechst 33258, which is a bisbenzimidazole compound, these three isomers bind to the minor groove of duplex DNA. DNA binding by the three isomers was investigated in the presence of the divalent metal ions Mg2+, Co2+, Ni2+, Cu2+, and Zn2+. Ligand-DNA interactions were probed with fluorscence and circular dichroism spectroscopy. These studies revealed that the binding of the 2-pyridyl derivative to DNA is dramatically reduced in the presence of Co2+, Ni2+, and Cu2+ ions and is abolished completely at a ligand/metal-cation ratio of 1:1. Control experiments done with the isomeric 3- and 4-pyridyl derivatives showed that their binding to DNA is unaffected by the aforementioned transition-metal ions. The ability of 2-(2-pyridyl)benzimidazole changes of the ligand associated with ion chelation probably ledto such unusual binding results for the ortho isomer. The addition of ethylenediaminetetraacetic acid (EDTA) reversed the effects completely.

A new glucose: Towards conformationally locked flexoses through annulation

A new family of surf ace-modified carbohydrates with locked, axial-rich conformations and bipolarofacial architectures has been developed with the aid of carbocyclic ring annulation. These novel trans-decalin-based carbohydrates have been synthesized, from simple aromatic precursors such as tetralin, through the ozonolysis of an appropriately protected allylic alcohol, followed by a cascade of intramolecular acetalizations to generate the sugar pyran moiety. The stereoselective synthesis of (racemic) cyclohexane-annulated 0-glucopyranoside and a-glucofuranoside from a common annulated trans-cyclohexadiene diol (trans-CHD) precursor under-scores the versatility of our approach. The efficacy of the annulation stratagem in generating carbohydrate diversity has been demonstrated through the synthesis of two regioisomeric annulated gulose derivatives, which differ only in the site of ring annulation on the sugar moiety. The mapping of the MLP surface and solid-state architecture of the new sugar shows that cycloalkane annulation results in surface modification and fine-tuning of sugar hydrophilicity. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005).

Boundary value problems for third-order nonlinear ordinary differential equations

In this paper, we describe how to analyze boundary value problems for third-order nonlinear ordinary differential equations over an infinite interval. Several physical problems of interest are governed by such systems. The seminumerical schemes described here offer some advantages over solutions obtained by using traditional methods such as finite differences, shooting method, etc. These techniques also reveal the analytic structure of the solution function. For illustrative purposes, several physical problems, mainly drawn from fluid mechanics, are considered; they clearly demonstrate the efficiency of the techniques presented here.

Preliminary X-ray crystallographic analysis of 2-methylcitrate synthase from Salmonella typhimurium

Analysis of the genomic sequences of Escherichia coli and Salmonella typhimurium has revealed the presence of several homologues of the well studied citrate synthase (CS). One of these homologues has been shown to code for 2-methylcitrate synthase (2-MCS) activity. 2-MCS catalyzes one of the steps in the 2-methylcitric acid cycle found in these organisms for the degradation of propionate to pyruvate and succinate. In the present work, the gene coding for 2-MCS from S. typhimurium (StPrpC) was cloned in pRSET-C vector and overexpressed in E. coli. The protein was purified to homogeneity using Ni-NTA affinity chromatography. The purified protein was crystallized using the microbatch-under-oil method. The StPrpC crystals diffracted X-rays to 2.4 A resolution and belonged to the triclinic space group P1, with unit-cell parameters a = 92.068, b = 118.159, c = 120.659 A, alpha = 60.84, beta = 67.77, gamma = 81.92 degrees. Computation of rotation functions using the X-ray diffraction data shows that the protein is likely to be a decamer of identical subunits, unlike CSs, which are dimers or hexamers.

Observation of a chiral smectic phase in azobenzene-linked bolaamphiphiles containing free sugars

Amphiphilic sugars exhibit both lyotropic and thermotropic liquid-crystalline behavior. Interestingly, in spite of the abundance of chiral centers in amphiphilic sugars, their liquid-crystalline phases do not exhibit macroscopic chirality. Herein, we report on the first observation of macroscopic chirality in sugar-based bolaamphiphiles containing free hydroxyl groups. The manifestation of the chiral smectic C* phase in these bolaamphiphiles has been observed to be critically dependent on the presence of the azobenzene moiety and the suitable length of the methylene spacer. These results imply that by suitable selection of linker groups, mesogenic bolaamphiphiles possessing macroscopic chirality can be designed using a variety of naturally available sugar derivatives.

Reversible electrochemistry of cytochrome c on recompressed, binderless exfoliated graphite electrodes

The direct electrochemistry of cytochrome c (cyt-c) has been investigated on exfoliated graphite (EG) electrodes. The as-polished and roughened (using SiC emery sheet) EG surfaces are inactive for the direct electron transfer. However, when the EG electrode was sonicated before the experiment, a pair of redox waves were obtained for freely diffusing cyt-c in the solution phase. The formal potential was found to be 0.01 V (vs. SCE) in 0.1 M phosphate buffer at a pH of 7.1. The electrochemical response for the adsorbed cyt-c on sonicated EG electrodes, which is shown to have carbonyl functional groups on its surface, shows nearly reversible voltammograms in the same electrolyte. However, the formal potential in the adsorbed state is more negative than that observed for the solution phase cyt-c. A structure based on an open heme conformation proposed by Hildebrandt and Stockburger is probably present on the EG surface. It is suggested that the electrochemistry at the EG electrode is essentially governed by favourable electrostatic interactions.

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.

Novel peptides of therapeutic promise from Indian Conidae

Highly structured small peptides are the major toxic constituents of the venom of cone snails, a family of widely distributed predatory marine molluscs. These animals use the venom for rapid prey immobilization. The peptide components in the venom target a wide variety of membrane-bound ion channels and receptors. Many have been found to be highly selective for a diverse range of mammalian ion channels and receptors associated with pain-signaling pathways. Their small size, structural stability, and target specificity make them attractive pharmacologic agents. A select number of laboratories mainly from the United States, Europe, Australia, Israel, and China have been engaged in intense drug discovery programs based on peptides from a few snail species. Coastal India has an estimated 20-30% of the known cone species; however, few serious studies have been reported so far. We have begun a comprehensive program for the identification and characterization of peptides from cone snails found in Indian Coastal waters. This presentation reviews our progress over the last 2 years. As expected from the evolutionary history of these venom components, our search has yielded novel peptides of therapeutic promise from the new species that we have studied.

In vitro protection of umbilical cord blood–derived primitive hematopoietic stem progenitor cell pool by mannose-specific lectins via antioxidant mechanisms

BACKGROUND: Earlier we reported that an oral administration of two mannose-specific dietary lectins, banana lectin (BL) and garlic lectin (GL), led to an enhancement of hematopoietic stem and progenitor cell (HSPC) pool in mice. STUDY DESIGN AND METHODS: Cord blood–derived CD34+ HSPCs were incubated with BL, GL, Dolichos lectin (DL), or artocarpin lectin (AL) for various time periods in a serum- and growth factor–free medium and were subjected to various functional assays. Reactive oxygen species (ROS) levels were detected by using DCHFDA method. Cell fractionation was carried out using lectin-coupled paramagnetic beads. RESULTS: CD34+ cells incubated with the lectins for 10 days gave rise to a significantly higher number of colonies compared to the controls, indicating that all four lectins possessed the capacity to protect HSPCs in vitro. Comparative analyses showed that the protective ability of BL and GL was better than AL and DL and, therefore, further experiments were carried out with them. The output of long-term culture-initiating cell (LTC-IC) and extended LTC-IC assays indicated that both BL and GL protected primitive stem cells up to 30 days. The cells incubated with BL or GL showed a substantial reduction in the ROS levels, indicating that these lectins protect the HSPCs via antioxidant mechanisms. The mononuclear cell fraction isolated by lectin-coupled beads got enriched for primitive HSPCs, as reflected in the output of phenotypic and functional assays. CONCLUSION: The data show that both BL and GL protect the primitive HSPCs in vitro and may also serve as cost-effective HSPC enrichment tools.

Slow m=1 instabilities of softened gravity Keplerian discs

We present the simplest model that permits a largely analytical exploration of the m =1 counter-rotating instability in a `hot' nearly Keplerian disc of collisionless self-gravitating matter. The model consists of a two-component softened gravity disc, whose linear modes are analysed using the Wentzel-Kramers-Brillouin approximation. The modes are slow in the sense that their (complex) frequency is smaller than the Keplerian orbital frequency by a factor which is of order the ratio of the disc mass to the mass of the central object. Very simple analytical expressions are derived for the precession frequencies and growth rates of local modes; it is shown that a nearly Keplerian discm must be unrealistically hot to avoid an overstability. Global modes are constructed for the case of zero net rotation.

Design of a compact wideband bandpass filter

This article presents the analysis and design of a compact multi-layer layer, high selectivity wideband bandpass filter using stub loaded and `U' shaped resonators over a slotted bottom ground plane. While the resonators with folded open circuit stub loadings create the desired bandpass characteristics. the IT shaped resonators reduce the size of filter. The slotted bottom ground plane is used to enhance the coupling to achieve the desired bandwidth. The proposed filter has been analyzed using circuit model, and the results were verified through full wave simulations and measurements. The fabricated filter is compact and measures a size of 18 mm x 25 mm x 1.6 MM. (C) 2010 Wiley Periodicals, Inc. Microwave Opt Technol Lett 52: 1387-1389, 2010: Published online in Wiley InterScience (www.interscience.wiley.com).

Manifestation of conical intersections in resonance Raman intensities

This paper deals with the manifestations of conical intersections (CIs), unequivocal spectroscopic signatures of which are still elusive, in the resonance Raman intensities. In particular, the results of our calculations on the `two state-two vibrational mode' and the `two state-three vibrational mode' models are presented. The models comprise two excited states of different spatial symmetry, one bright and one dark, which are coupled by a nontotally symmetric mode while the energy gap between them is tuned by one/two totally symmetric modes. Time dependent theory for vibronically coupled states is employed for the calculation and analysis of Raman excitation profiles (REPs). The manifestation of intersections in REPs is studied by extensive modelm calculations and the results of two specific models are presented. Themfeasibility of using REPs to probe the role of CIs in polyatomic systems is ascertained by multimode calculations on two polyatomic systems viz., pyrazine and trans-azobenzene. The study also notes the importance of the pump excitation wavelength dependence in a femtosecond time-resolved experiment probing the intersection-induced nonadiabatic dynamics. Copyright (C) 2009 John Wiley & Sons, Ltd.

Thermodynamic analysis of three state denaturation of Peanut Agglutinin

Peanut Agglutinin (PNA) is a homotetrameric protein with a very unusual open quaternary structure. During denaturation, it first dissociates into a molten globule like state, which subsequently undergoes complete denaturation. Urea denaturation of PNA at neutral pH has been studied by intrinsic fluorescence spectroscopy and has been fitted to a three state model, A(4) double left right arrow 4I double left right arrow 4U, to get all the relevant thermodynamic parameters. Urea denaturation leads to continuous red shift of wavelength maxima. The molten globule like state is formed in a short range of urea concentration. Refolding of the denatured PNA has been attempted by intrinsic fluorescence study. Refolding by instantaneous dilution shows the occurrence of the formation of an intermediate at a relatively rapid rate, within few seconds. The transition from PNA tetramer to molten globule like state is found to have a Delta G value of similar to 33 kcal/mole while it is similar to 8 kcal/mole for the transition from molten globule like state to a completely denatured state. This in turn indicates that the tetramerization in PNA contributes significantly to the stability of the oligomer.

Supercapacitor studies of electrochemically deposited PEDOT on stainless steel substrate

There has been increasing interest on various properties and applications of electronically conducting polymers. Polyethylenedioxythiophene (PEDOT) is an interesting polymer of this type as it exhibits very high ionic conductivity. In the present study, PEDOT has been electrochemically deposited on stainless steel (SS) substrate for supercapacitor studies. PEDOT/SS electrodes prepared in 0.1M H2SO4 in presence of a surfactant, sodium dodecylsulphate (SDS), have been found to yield higher specific capacitance (SC) than the electrodes prepared from neutral aqueous electrolyte. The effects of concentration of H(2)SO4(,) concentration of SDS, potential of deposition, and nature of supporting electrolytes used for capacitor studies on SC of the PEDOT/SS electrodes have been studied. SC values as high as 250 F/g in 1M oxalic acid have been obtained during the initial stages of cycling. However, there is a rapid decrease in SC on repeated charge-discharge cycling. Spectroscopic data reflect structural changes in PEDOT on extended cycling. (C) 2007 Wiley Periodicals, Inc.