Comparative Transcriptomics of H. pylori Strains AM5, SS1 and Their hpyAVIBM Deletion Mutants: Possible Roles of Cytosine Methylation

Helicobacter pylori is an important human pathogen and one of the most successful chronic colonizers of the human body. H. pylori uses diverse mechanisms to modulate its interaction with the host in order to promote chronic infection and overcome host immune response. Restriction-modification genes are a major part of strain-specific genes present in H. pylori. The role of N-6 -adenine methylation in bacterial gene regulation and virulence is well established but not much is known about the effect of C-5 -cytosine methylation on gene expression in prokaryotes. In this study, it was observed by microarray analysis and RT-PCR, that deletion of an orphan C-5 -cytosine methyltransferase, hpyAVIBM in H. pylori strains AM5and SS1 has a significant effect on the expression of number of genes belonging to motility, adhesion and virulence. AM Delta DhpyAVIBM mutant strain has a different LPS profile and is able to induce high IL-8 production compared to wild-type. hpyAVIBM from strain 26695 is able to complement mutant SS1 and AM5 strains. This study highlights a possible significance of cytosine methylation in the physiology of H. pylori.

Carbonization of solvent and capping agent based enhancement in the stabilization of cobalt nanoparticles and their magnetic study

We describe a hybrid synthetic protocol, the solvated metal atom dispersion (SMAD) method, for the synthesis and stabilization of monodisperse amorphous cobalt nanoparticles. By employing an optimized ratio of a weakly coordinating solvent and a capping agent monodisperse colloidal cobalt nanoparticles (2 +/- 0.5 nm) have been prepared by the SMAD method. However, the as-prepared samples were found to be oxidatively unstable which was elucidated by their magnetic studies. Oxidative stability in our case was achieved via a pyrolysis process that led to the decomposition of the organic solvent and the capping agent resulting in the formation of carbon encapsulated cobalt nanoparticles which was confirmed by Raman spectroscopy. Controlled annealing at different temperatures led to the phase transformation of metallic cobalt from the hcp to fcc phase. The magnetic behaviour varies with the phase and the particle size; especially, the coercivity of nanoparticles exhibited strong dependence on the phase transformation of cobalt. The high saturation magnetization close to that of the bulk value was achieved in the case of the annealed samples. In addition to detailed structural and morphological characterization, the results of thermal and magnetic studies are also presented.

Naphthylhydrazone based selective and sensitive chemosensors for Cu2+ and their application in bioimaging

Two new hydroxynaphthyl-hydrazone based fluorogenic chemosensors R-1 and R-2 have been synthesized by Schiff base condensation of Tris(4-formylphenyl)amine with 1-hydroxynaphthalene-2-hydrazide and 1-hydroxynaphthalene-2-carbohydrazone, respectively. They are examined as highly selective and sensitive receptors for Cu2+ ions in aqueous medium. Electronic absorption as well as fluorescence titration studies of receptors R-1 and R-2 with different metal cations in H2O/CH3CN medium showed highly selective and very rapid (< 2 min) binding affinity towards Cu2+ ions even in the presence of other commonly coexisting metal ions such as Na+, K+, Mg2+, Ca2+, Mn2+, Fe2+, Co2+, Ni2+, Zn2+, Cd2+ and Hg2+. Quantification of the fluorescence titration analysis indicated that these newly synthesized receptors (R-1 and R-2) can indicate the presence of Cu2+ ions even at very low concentrations of 598 and 676 ppt, respectively. In addition, the propensity of these receptors as bio-imaging fluorescent probes to detect Cu2+ ions in human cervical HeLa cancer cell lines and their cytotoxicity against HeLa cells have been investigated.

Microwave-assisted, surfactant-free synthesis of air-stable copper nanostructures and their SERS study

A simple, rapid, and surfactant-free synthesis of crystalline copper nanostructures has been carried out through microwave irradiation of a solution of copper acetylacetonate in benzyl alcohol. The structures are found to be stable against oxidation in ambient air for several months. High-resolution electron microscopy (SEM and TEM) reveals that the copper samples comprise nanospheres measuring about 150 nm in diameter, each made of copper nanocrystals similar to 7 nm in extension. The nanocrystals are densely packed into spherical aggregates, the driving force being minimization of surface area and surface energy, and are thus immune to oxidation in ambient air. Such aggregates can also be adherently supported on SiO2 and Al2O3 when these substrates are immersed in the irradiated solution. The air-stable copper nanostructures exhibit surface enhanced Raman scattering, as evidenced by the detection of 4-mercaptobenzoic acid at 10(-6) M concentrations.

How Does the Spacer Length of Cationic Gemini Lipids Influence the Lipoplex Formation with Plasmid DNA? Physicochemical and Biochemical Characterizations and their Relevance in Gene Therapy

Lipoplexes formed by the pEGFP-C3 plasmid DNA (pDNA) and lipid mixtures containing cationic gemini surfactant of the 1,2-bis(hexadecyl dimethyl ammonium) Acmes family referred to as C16CnC16, where n = 2 3, 5, or 12, and the zwitterionic helper lipid, 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine (DOPE) have been studied from a wide variety of physical, chemical, and biological standpoints. The study has been carried out using several experimental methods, such as zeta potential, gel electrophoresis, small-angle X-ray scattering (SAXS), cryo-TEM, gene transfection, cell viability/cytotoxicity, and confocal fluorescence microscopy. As reported recently in a communication (J. Am. Chem. Soc. 2011, 133, 18014), the detailed physicochemical and biological studies confirm that, in the presence of the studied series lipid mixtures, plasmid DNA is compacted with a large number of its associated Na+ counterions. This in turn yields a much lower effective negative charge, q(pDNA)(-), a value that has been experimentally obtained for each mixed lipid mixture. Consequently, the cationic lipid (CL) complexes prepared with pDNA and CL/DOPE mixtures to be used in gene transfection require significantly less amount of CL than the one estimated assuming a value of q(DNA)(-) = -2. This drives to a considerably lower cytotoxicity of the gene vector. Depending on the CL molar composition, alpha, of the lipid mixture, and the effective charge ratio of the lipoplex, rho(eff), the reported SAXS data indicate the presence of two or three structures in the same lipoplex, one in the DOPE-rich region, other in the CL-rich region, and another one present at any CL composition. Cryo-TEM and SAXS studies with C16CnC16/DOPE-pDNA lipoplexes indicate that pDNA is localized between the mixed lipid bilayers of lamellar structures within a monolayer of similar to 2 nm. This is consistent with a highly compacted supercoiled pDNA conformation compared with that of linear DNA. Transfection studies were carried out with HEK293T, HeLa, CHO, U343, and H460 cells. The alpha and rho(eff) values for each lipid mixture were optimized on HEK293T cells for transfection, and using these values, the remaining cells were also transfected in absence (-FBS-FBS) and presence (-FBS+FBS) of serum. The transfection efficiency was higher with the CLs of shorter gemini spacers (n = 2 or 3). Each formulation expressed GFP on pDNA transfection and confocal fluorescence microscopy corroborated the results. C16C2C16/DOPE mixtures were the most efficient toward transfection among all the lipid mixtures and, in presence of serum, even better than the Lipofectamine2000, a commercial transfecting agent Each lipid combination was safe and did not show any significant levels of toxicity. Probably, the presence of two coexisting lamellar structures in lipoplexes synergizes the transfection efficiency of the lipid mixtures which are plentiful in the lipoplexes formed by CLs with short spacer (n = 2, 3) than those with the long spacer (n = 5, 12).

Novel low-temperature growth of SnO2 nanowires and their gas-sensing properties

A simple thermal evaporation method is presented for the growth of crystalline SnO2 nanowires at a low substrate temperature of 450 degrees C via an gold-assisted vapor-liquid-solid mechanism. The as-grown nanowires were characterized by scanning electron microscopy, transmission electron microscopy and X-ray diffraction, and were also tested for methanol vapor sensing. Transmission electron microscopy studies revealed the single-crystalline nature of the each nanowire. The fabricated sensor shows good response to methanol vapor at an operating temperature of 450 degrees C. (C) 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Review of trend detection methods and their application to detect temperature changes in India

Present study performs the spatial and temporal trend analysis of annual, monthly and seasonal maximum and minimum temperatures (t(max), t(min)) in India. Recent trends in annual, monthly, winter, pre-monsoon, monsoon and post-monsoon extreme temperatures (t(max), t(min)) have been analyzed for three time slots viz. 1901-2003,1948-2003 and 1970-2003. For this purpose, time series of extreme temperatures of India as a whole and seven homogeneous regions, viz. Western Himalaya (WH), Northwest (NW), Northeast (NE), North Central (NC), East coast (EC), West coast (WC) and Interior Peninsula (IP) are considered. Rigorous trend detection analysis has been exercised using variety of non-parametric methods which consider the effect of serial correlation during analysis. During the last three decades minimum temperature trend is present in All India as well as in all temperature homogeneous regions of India either at annual or at any seasonal level (winter, pre-monsoon, monsoon, post-monsoon). Results agree with the earlier observation that the trend in minimum temperature is significant in the last three decades over India (Kothawale et al., 2010). Sequential MK test reveals that most of the trend both in maximum and minimum temperature began after 1970 either in annual or seasonal levels. (C) 2012 Elsevier B.V. All rights reserved.

Evaluation of isopentane, R-245fa and their mixtures as working fluids for organic Rankine cycles

Low grade thermal energy from sources such as solar, geothermal and industrial waste heat in the temperature range of 380-425 K can be converted to electrical energy with reasonable efficiency using isopentane and R-245fa. While the former is flammable and the latter has considerable global warming potential, their mixture in 0.7/0.3 mole fraction is shown to obviate these disadvantages and yet retain dominant merits of each fluid. A realistic thermodynamic analysis is carried out wherein the possible sources of irreversibilities such as isentropic efficiencies of the expander and the pump and entropy generation in the regenerator, boiler and condenser are accounted for. The performance of the system in the chosen range of heat source temperatures is evaluated. A technique of identifying the required source temperature for a given output of the plant and the maximum operating temperature of the working fluid is developed. This is based on the pinch point occurrence in the boiler and entropy generation in the boiling and superheating regions of the boiler. It is shown that cycle efficiencies of 10-13% can be obtained in the range investigated at an optimal expansion ratio of 7-10. (C) 2012 Elsevier Ltd. All rights reserved.

Biochemical Properties of MutT2 Proteins from Mycobacterium tuberculosis and M. smegmatis and Their Contrasting Antimutator Roles in Escherichia coli

Mycobacterium tuberculosis, the causative agent of tuberculosis, is at increased risk of accumulating damaged guanine nucleotides such as 8-oxo-dGTP and 8-oxo-GTP because of its residency in the oxidative environment of the host macrophages. By hydrolyzing the oxidized guanine nucleotides before their incorporation into nucleic acids, MutT proteins play a critical role in allowing organisms to avoid their deleterious effects. Mycobacteria possess several MutT proteins. Here, we purified recombinant M. tuberculosis MutT2 (MtuMutT2) and M. smegmatis MutT2 (MsmMutT2) proteins from M. tuberculosis (a slow grower) and M. smegmatis (fast growing model mycobacteria), respectively, for their biochemical characterization. Distinct from the Escherichia coli MutT, which hydrolyzes 8-oxo-dGTP and 8-oxo-GTP, the mycobacterial proteins hydrolyze not only 8-oxo-dGTP and 8-oxo-GTP but also dCTP and 5-methyl-dCTP. Determination of kinetic parameters (K-m and V-max) revealed that while MtuMutT2 hydrolyzes dCTP nearly four times better than it does 8-oxo-dGTP, MsmMutT2 hydrolyzes them nearly equally. Also, MsmMutT2 is about 14 times more efficient than MtuMutT2 in its catalytic activity of hydrolyzing 8-oxo-dGTP. Consistent with these observations, MsmMutT2 but not MtuMutT2 rescues E. coli for MutT deficiency by decreasing both the mutation frequency and A-to-C mutations (a hallmark of MutT deficiency). We discuss these findings in the context of the physiological significance of MutT proteins.

Low temperature growth of SnO2 nanowires by electron beam evaporation and their application in UV light detection

For the first time, high quality tin oxide (SnO2) nanowires have been synthesized at a low substrate temperature of 450 degrees C via vapor-liquid-solid mechanism using an electron beam evaporation technique. The grown nanowires have shown length of 2-4 mu m and diameter of 20-60 nm. High resolution transmission electron microscope studies on the grown nanowires have shown the single crystalline nature of the SnO2 nanowires. We investigated the effect of growth temperature and oxygen partial pressure on SnO2 nanowires growth. Variation of substrate temperature at a constant oxygen partial pressure of 4 x 10(-4) mbar suggested that a temperature equal to or greater than 450 degrees C was the best condition for phase pure SnO2 nanowires growth. The SnO2 nanowires grown on a SiO2 substrate were subjected to UV photo detection. The responsivity and quantum efficiency of SnO2 NWs photo detector (at 10V applied bias) was 12 A/W and 45, respectively, for 12 mu W/cm(2) UV lamp (330 nm) intensity on the photo detector.

Effect of lipopolysaccharide on alteration of phospholipids and their fatty acid composition in spleen and thymus by in vitro metabolic labeling

Lipopolysaccharide (LPS) is an endotoxin, a potent stimulator of immune response and induction of LPS leads to acute lung injury (ALI)/acute respiratory distress syndrome (ARDS). ARDS is a life-threatening disease worldwide with a high mortality rate. The immunological effect of LPS with spleen and thymus is well documented; however the impact on membrane phospholipid during endotoxemia has not yet been studied. Hence we aimed to investigate the influence of LPS on spleen and thymus phospholipid and fatty acid composition by 32P]orthophosphate labeling in rats. The in vitro labeling was carried out with phosphate-free medium (saline). Time course, LPS concentration-dependent, pre- and post-labeling with LPS and fatty acid analysis of phospholipid were performed. Labeling studies showed that 50 mu g LPS specifically altered the major phospholipids, phosphatidylcholine and phosphatidylglycerol in spleen and phosphatidylcholine in thymus. Fatty acid analysis showed a marked alteration of unsaturated fatty acids/saturated fatty acids in spleen and thymus leading to immune impairment via the fatty acid remodeling pathway. Our present in vitro lipid metabolic labeling study could open up new vistas for exploring LPS-induced immune impairment in spleen and thymus, as well as the underlying mechanism.

Cytochrome P450-mediated metabolism in brain: functional roles and their implications

Introduction: Cytochromes P450 (P450) and associated monooxygenases are a family of heme proteins involved in metabolism of endogenous compounds (arachidonic acid, eicosanoids and prostaglandins) as also xenobiotics including drugs and environmental chemicals. Liver is the major organ involved in P450-mediated metabolism and hepatic enzymes have been characterized. Extrahepatic organs, such as lung, kidney and brain have the capability for biotransformation through P450 enzymes. Brain, including human brain, expresses P450 enzymes that metabolize xenobiotics and endogenous compounds. Areas covered: An overview of P450-mediated metabolism in brain is presented focusing on distinct differences seen in expression of P450 enzymes, generation of unique P450 enzymes in brain through alternate splicing and their consequences in terms of metabolism of psychoactive drugs and inflammatory prompts, such as leukotrienes, thus modulating inflammatory response. Expert opinion: The brain possesses unique P450s that metabolize drugs and endogenous compounds through pathways that are markedly different from that seen in liver indicating that extrapolation directly from liver to brain is not appropriate. It is therefore necessary to characterize the unique brain P450s and their ability to metabolize xenobiotics and endogenous compounds to better understand the functions of this important class of enzymes in brain, especially human brain.

Bimetallic core-shell nanocomposites using weak reducing agent and their transformation to alloy nanostructures

An in situ seeding growth methodology towards the preparation of core-shell nanoparticles composed of noble metals has been developed by employing trimethylamine borane (TMAB) as the reducing agent. Being a weak reducing agent, TMAB is able to distinguish the smallest reduction potential window of any two metals which renders selective reduction of metal ions thus affording a core-shell architecture of the nanoparticles. A dramatic effect of solvent was noted during the reduction of Ag+ ions: an immediate reduction took place at room temperature when dry THF was used as solvent however, usage of wet THF (THF used directly from the bottle) brings out the reduction only at reflux conditions. In the case of Au and Pd nanoparticles, preparation was found to be independent of the quality of solvent used. Au nanoparticles are realized at room temperature whereas reflux conditions are required in the case of Pd nanoparticles. This difference in behavior of the monometallic nanoparticles was successfully exploited to construct different noble metal nanoparticles with core-shell architectures such as Au@Ag, Ag@Au, and Ag@Pd. Transformation of these core-shell nanoparticles to their thermodynamically stable alloy counterparts is also demonstrated under very mild conditions reported to date.

Comparison of North American universities with and without medical schools and their technology transfer initiatives

Empirical research available on technology transfer initiatives is either North American or European. Literature over the last two decades shows various research objectives such as identifying the variables to be measured and statistical methods to be used in the context of studying university based technology transfer initiatives. AUTM survey data from years 1996 to 2008 provides insightful patterns about the North American technology transfer initiatives, we use this data in our paper. This paper has three sections namely, a comparison of North American Universities with (n=1129) and without Medical Schools (n=786), an analysis of the top 75th percentile of these samples and a DEA analysis of these samples. We use 20 variables. Researchers have attempted to classify university based technology transfer initiative variables into multi-stages, namely, disclosures, patents and license agreements. Using the same approach, however with minor variations, three stages are defined in this paper. The first stage is to do with inputs from R&D expenditure and outputs namely, invention disclosures. The second stage is to do with invention disclosures being the input and patents issued being the output. The third stage is to do with patents issued as an input and technology transfers as outcomes.

Non-polio enteroviruses and their association with acute diarrhea in children in India

A causative agent in approximately 40% of diarrhea] cases. still remains unidentified. Though many enteroviruses (EVs) are transmitted through fecal-oral route and replicate in the intestinal cells, their association with acute diarrhea has not so far been recognized due to lack of detailed epidemiological investigations. This long-term, detailed molecular epidemiological study aims to conclusively determine the association of non-polio enteroviruses (NPEVs) with acute diarrhea in comaparison with rotavirus (RV) in children. Diarrheal stool specimens from 2161 children aged 0-2 years and 169 children between 2 and 9 years, and 1800 normal stool samples from age-matched healthy children between 0 and 9 years were examined during 2008-2012 for enterovirus (oral polio vaccine strains (OPVs) and NPEVs). Enterovirus serotypes were identified by complete VP1 gene sequence analysis. Enterovirus and rotavirus were detected in 19.01% (380/2330) and 13.82% (322/2330) diarrheal stools. During the study period, annual prevalence of EV- and RV-associated diarrhea ranged between 8% and 22%, but with contrasting seasonal prevalence with RV predominating during winter months and NPEV prevailing in other seasons. NPEVs are associated with epidemics-like outbreaks during which they are detected in up to 50% of diarrheic children, and in non-epidemic seasons in 0-10% of the patients. After subtraction of OPV-positive diarrheal cases (1.81%), while NPEVs are associated with about 17% of acute diarrhea, about 6% of healthy children showed asymptomatic NPEV excretion. Of 37 NPEV serotypes detected in diarrheal children, seven echovirus types 1, 7, 11, 13, 14, 30 and 33 are frequently observed, with Ell being more prevalent followed by E30. In conclusion, NPEVs are significantly associated with acute diarrhea, and NPEVs and rotavirus exhibit contrasting seasonal predominance. This study signifies the need for a new direction of research on enteroviruses involving systematic analysis of their contribution to diarrheal burden. (C) 2013 Elsevier B.V. All rights reserved.