Characterization of the restriction enzyme-like endonuclease encoded by the Entamoeba histolytica non-long terminal repeat retrotransposon EhLINE1

The genome of the human pathogen Entamoeba histolytica, a primitive protist, contains non-long terminal repeat retrotransposable elements called EhLINEs. These encode reverse transcriptase and endonuclease required for retrotransposition. The endonuclease shows sequence similarity with bacterial restriction endonucleases. Here we report the salient enzymatic features of one such endonuclease. The kinetics of an EhLINE1-encoded endonuclease catalyzed reaction, determined under steady-state and single-turnover conditions, revealed a significant burst phase followed by a slower steady-state phase, indicating that release of product could be the slower step in this reaction. For circular supercoiled DNA the K-m was 2.6 x 10-8 m and the k(cat) was 1.6 x 10-2 sec-1. For linear E. histolytica DNA substrate the K-m and k(cat) values were 1.3 x 10-8 m and 2.2 x 10-4 sec-1 respectively. Single-turnover reaction kinetics suggested a noncooperative mode of hydrolysis. The enzyme behaved as a monomer. While Mg2+ was required for activity, 60% activity was seen with Mn2+ and none with other divalent metal ions. Substitution of PDX12-14D (a metal-binding motif) with PAX(12-14)D caused local conformational change in the protein tertiary structure, which could contribute to reduced enzyme activity in the mutated protein. The protein underwent conformational change upon the addition of DNA, which is consistent with the known behavior of restriction endonucleases. The similarities with bacterial restriction endonucleases suggest that the EhLINE1-encoded endonuclease was possibly acquired from bacteria through horizontal gene transfer. The loss of strict sequence specificity for nicking may have been subsequently selected to facilitate spread of the retrotransposon to intergenic regions of the E. histolytica genome.

The effect of lignin content and lignin modification on Norway spruce wood properties and decay resistance

Three different Norway spruce cutting clones growing in three environments with different soil and climatic conditions were studied. The purpose was to follow variation in the radial growth rate, wood properties and lignin content and to modify wood lignin with a natural monolignol, coniferyl alcohol, by making use of inherent wood peroxidases. In addition, the incorporation of chlorinated anilines into lignin was studied with synthetic model compounds and synthetic lignin preparations to show whether unnatural compounds originating from pesticides could be bound in the lignin polymer. The lignin content of heartwood, sapwood and earlywood was determined by applying Fourier transform infrared (FTIR) spectroscopy and a principal component regression (PCR) technique. Wood blocks were treated with coniferyl alcohol by using a vacuum impregnation method. The effect of impregnation was assessed by FTIR and by a fungal decay test. Trees from a fertile site showed the highest growth rate and sapwood lignin content and the lowest latewood proportion, weight density and modulus of rupture (MOR). Trees from a medium fertile site had the lowest growth rate and the highest latewood proportion, weight density, modulus of elasticity (MOE) and MOR. The most rapidly growing clone showed the lowest latewood proportion, weight density, MOE and MOR. The slowest growing clone had the lowest sapwood lignin content and the highest latewood proportion, weight density, MOE and MOR. Differences between the sites and clones were small, while fairly large variation was found between the individual trees and growing seasons. The cutting clones maintained clone-dependent wood properties in the different growing sites although variation between trees was high and climatic factors affected growth. The coniferyl alcohol impregnation increased the content of different lignin-type phenolic compounds in the wood as well as wood decay resistance against a white-rot fungus, Coriolus versicolor. During the synthetic lignin preparation 3,4-dichloroaniline became bound by a benzylamine bond to β-O-4 structures in the polymer and it could not be released by mild acid hydrolysis. The natural monolignol, coniferyl alcohol, and chlorinated anilines could be incorporated into the lignin polymer in vivo and in vitro, respectively.

Interaction of substrate uridyl 3',5'-adenosine with ribonuclease A:a molecular dynamics study

A wealth of information available from x-ray crystallographic structures of enzyme-ligand complexes makes it possible to study interactions at the molecular level. However, further investigation is needed when i) the binding of the natural substrate must be characterized, because ligands in the stable enzyme-ligand complexes are generally inhibitors or the analogs of substrate and transition state, and when ii) ligand binding is in part poorly characterized. We have investigated these aspects i? the binding of substrate uridyl 3',5'-adenosine (UpA) to ribonuclease A (RNase A). Based on the systematically docked RNase A-UpA complex resulting from our previous study, we have undertaken a molecular dynamics simulation of the complex with solvent molecules. The molecular dynamics trajectories of this complex are analyzed to provide structural explanations for varied experimental observations on the ligand binding at the B2 subsite of ribonuclease A. The present study suggests that B2 subsite stabilization can be effected by different active site groups, depending on the substrate conformation. Thus when adenosine ribose pucker is O4'-endo, Gln69 and Glu111 form hydrogen-bonding contacts with adenine base, and when it is C2'-endo, Asn71 is the only amino acid residue in direct contact with this base. The latter observation is in support of previous mutagenesis and kinetics studies. Possible roles for the solvent molecules in the binding subsites are described. Furthermore, the substrate conformation is also examined along the simulation pathway to see if any conformer has the properties of a transition state. This study has also helped us to recognize that small but concerted changes in the conformation of the substrate can result in substrate geometry favorable for 2',3' cyclization. The identified geometry is suitable for intraligand proton transfer between 2'-hydroxyl and phosphate oxygen atom. The possibility of intraligand proton transfer as suggested previously and the mode of transfer before the formation of cyclic intermediate during transphosphorylation are discussed.

Adsorption-desorption and photocatalytic properties of inorganic-organic hybrid cadmium thiosulfate compounds

Three inorganic-organic hybrid framework cadmium thiosulfate phases have been investigated for adsorption and photodegradation of organic dye molecules. Different classes of organic dyes, viz., triaryl methane, azo, xanthene, anthraquinone, have been studied. The anionic dyes with sulfonate groups appear to readily adsorb on the cadmium thiosulfate compounds in an aqueous medium. The adsorption of the dye molecules, however, does not create any structural changes on the cadmium thiosulfate compounds, though weak electronic interactions have been observed. The adsorbed dyes have been desorbed partially in an alcoholic medium, suggesting possible applications in scavenging specific anionic dyes from the aqueous solutions. Langmuir adsorption/desorption isotherms have been used to model this behavior. UV-assisted (lambda(max) = 365 nm) photocatalytic decomposition studies on the cationic dyes indicate reasonable activity comparable with that of Degussa P-25 (TiO2) catalyst. Sunlight assisted photocatalyti studies have been carried out in detail employing hybrid framework compounds. The Langmuir-Hinshelwood kinetics model, employed to follow the degradation profile of the organic dyes, indicates that the photocatalytic degradation follows the order: triaryl methane > azo > xanthene.

Polypyrrole based amperometric glucose biosensors

Biosensors have gained immense acceptance in the field of medical diagnostics, besides environmental, food safety and biodefence applications due to its attributes of real-time and rapid response. This synergistic combination of biotechnology and microelectronics comprises a biological recognition element coupled with a compatible transducer device. Diabetes is a disease of major concern since the ratio of world population suffering from it is increasing at an alarming rate and therefore the need for development of accurate and stable glucose biosensors is evident. There are many commercial glucose biosensors available yet some limitations need attention. This review presents a detailed account of the polypyrrole based amperometric glucose biosensors. The polymer polypyrrole is used extensively as a matrix for immobilization of glucose oxidase enzyme owing to its favourable features such as stability under ambient conditions, conductivity that allows it to be used as an electron relay, ability to be polymerized under neutral and aqueous mild conditions, and more. The simple one-step electrodeposition on the electrode surface allows easy entrapment of the enzyme. The review is structured into three categories (a) the first-stage biosensors: which report the studies from the inception of use of polypyrrole in glucose biosensors during which time the role of the polymer and the use of mediators was established. This period saw extensive work by two separate groups of Schuhmann and Koopal who contributed a great deal in understanding the electron transfer pathways in polypyrrole based glucose biosensors, (b) the second-stage biosensors: which highlight the shift of polypyrrole from a conventional matrix to composite matrices with extensive use of mediators focused at improving the selectivity of response, and (c) third-stage biosensors: the remarkable properties of nanoparticles and carbon nanotubes and their outstanding ability to mediate electrontransfers have seen their indispensable use in conjugation with polypyrrole for development of glucose biosensors with improved sensitivity and stability characteristics which is accounted in the review, which thus traces the evolution of polypyrrole from a conventional matrix, to composites and thence to the form of nanotube arrays, with the objective of addressing the vital issue of diabetes management through the development of stable and reliable glucose biosensors.

Field Emission Properties of Carbon Nanotube Arrays with Defects and Impurities

It has been found experimentally that the results related to the collective field emission performance of carbon nanotube (CNT) arrays show variability. The emission performance depends on the electronic structure of CNTs (especially their tips). Due to limitations in the synthesis process, production of highly pure and defect free CNTs is very difficult. The presence of defects and impurities affects the electronic structure of CNTs. Therefore, it is essential to analyze the effect of defects on the electronic structure, and hence, the field emission current. In this paper, we develop a modeling approach for evaluating the effect of defects and impurities on the overall field emission performance of a CNT array. We employ a concept of effective stiffness degradation for segments of CNTs, which is due to structural defects. Then, we incorporate the vacancy defects and charge impurity effects in our Green's function based approach. Simulation results indicate decrease in average current due to the presence of such defects and impurities.

Bi4Ti3O12-5BiFeO(3) Aurivillius intergrowth: Structural and ferroelectric properties

Aurivillus intergrowth Bi4Ti3O12-5BiFeO(3) was demonstrated to be ferroelectric that evoked the possibility of achieving high temperature magnetoelectric property in this family of compounds. X-ray diffraction studies confirmed its structure to be orthorhombic [Fmm2; a=5.5061(11) A degrees, b=5.4857(7) A degrees, c=65.742(12) A degrees]. However, transmission electron microscopy established the random incidence of intergrowth at nanoscale corresponding to n=6 and n=7 members of the Aurivillius family. Diffuse ferroelectric orthorhombic to paraelectric tetragonal phase transition around 857 K was confirmed by dielectric and high temperature x-ray diffraction studies. Polarization versus electric field hysteresis loops associated with 2P(r) of 5.2 mu C/cm(2) and coercive field of 42 kV/cm were obtained at 300 K.

A study on the variations of optical and physical properties of aerosols over a tropical semi-arid station during grassland fire

The present paper records the results of a case study on the impact of an extensive grassland fire on the physical and optical properties of aerosols at a semi-arid station in southern India for the first time from ground based measurements using a MICROTOPS-II sunphotometer, an aethalometer and a quartz crystal microbalance impactor (QCM). Observations revealed a substantial increase in aerosol optical depth (AOD) at all wavelengths during burning days compared to normal days. High AOD values observed at shorter wavelengths suggest the dominance of accumulation mode particle loading over the study area. Daily mean aerosol size spectra shows, most of the time, power-law distribution. To characterize AOD, the Angstrom parameters (i.e., alpha and beta) were used. Wavelength exponent (1.38) and turbidity coefficient (0.21) are high during burning days compared to normal days, thereby suggesting an increase in accumulation mode particle loading. Aerosol size distribution suggested dominance of accumulation mode particle loading during burning days compared to normal days. A significant positive correlation was observed between AOD at 500 mn and water vapour and negative correlation between AOD at 500 nm and wind speed for burning and non-burning days. Diurnal variations of black carbon (BC) aerosol mass concentrations increased by a factor of similar to 2 in the morning and afternoon hours during burning period compared to normal days.

Temperature dependent structural properties of nanocrystalline SnS structures

This letter explores the structural behavior of nanocrystalline tin mono sulfide (SnS) structures with respect to temperature (100-600 K). These studies emphasize that the structural properties of SnS nanocrystalline structures depend on the surrounding temperature. The lattice parameters of SnS nanocrystals slightly varied like their microstructures with the increase of temperature. These changes strongly influence the optical properties of SnS nanostructures. On the other hand, the structures exhibited higher strain (similar to 0.44%) than that of microstructured (0.3%) and bulk (0.12%) counterparts. The observed results are discussed under the light of existing concepts and reported.

Synthesis, Structure, and Properties of Boron- and Nitrogen-Doped Graphene

Boron- and nitrogen-doped graphenes are are prepared by the arc discharge between carbon electrodes or by the transformation of nanodiamond under appropriate atmospheres. Using a combination of experiment and theories based on first principles, systematic changes in the carrier-concentration and electronic structure of the doped graphenes are demonstrated. Stiffening of the G-band mode and intensification of the defect-related D-band in the Raman spectra are also observed.

Spatial and vertical heterogeneities in aerosol properties over oceanic regions around India: Implications for radiative forcing

The influence of atmospheric aerosols on Earth's radiation budget and hence climate, though well recognized and extensively investigated in recent years, remains largely uncertain mainly because of the large spatio-temporal heterogeneity and the lack of data with adequate resolution. To characterize this diversity, a major multi-platform field campaign ICARB (Integrated Campaign for Aerosols, gases and Radiation Budget) was carried out during the pre-monsoon period of 2006 over the Indian landmass and surrounding oceans, which was the biggest such campaign ever conducted over this region. Based on the extensive and concurrent measurements of the optical and physical properties of atmospheric aerosols during ICARB, the spatial distribution of aerosol radiative forcing was estimated over the entire Bay of Bengal (BoB), northern Indian Ocean and Arabian Sea (AS) as well as large spatial variations within these regions. Besides being considerably lower than the mean values reported earlier for this region, our studies have revealed large differences in the forcing components between the BoB and the AS. While the regionally averaged aerosol-induced atmospheric forcing efficiency was 31 +/- 6 W m(-2) tau(-1) for the BoB, it was only similar to 18 +/- 7 W m(-2) tau(-1) for the AS. Airborne measurements revealed the presence of strong, elevated aerosol layers even over the oceans, leading to vertical structures in the atmospheric forcing, resulting in significant warming in the lower troposphere. These observations suggest serious climate implications and raise issues ranging from the impact of aerosols on vertical thermal structure of the atmospheric and hence cloud formation processes to monsoon circulation.

Substrate specificity plays an important role in uncoupling the catalytic and scaffolding activities of rat testis DNA topoisomerase IIalpha

Topoisomerase II (topo II) is a dyadic enzyme found in all eukaryotic cells. Topo II is involved in a number of cellular processes related to DNA metabolism, including DNA replication, recombination and the maintenance of genomic stability. We discovered a correlation between the development of postnatal testis and increased binding of topo IIalpha to the chromatin fraction. We used this observation to characterize DNA-binding specificity and catalytic properties of purified testis topo IIalpha. The results indicate that topo IIalpha binds a substrate containing the preferred site with greater affinity and, consequently, catalyzes the conversion of form I to form IV DNA more efficiently in contrast to substrates lacking such a site. Interestingly, topo IIalpha displayed high-affinity and cooperativity in binding to the scaffold associated region. In contrast to the preferred site, however, high-affinity binding of topo IIalpha to the scaffold-associated region failed to result in enhanced catalytic activity. Intriguingly, competition assays involving scaffold-associated region revealed an additional DNA-binding site within the dyadic topo IIalpha. These results implicate a dual role for topo IIalpha in vivo consistent with the notion that its sequestration to the chromatin might play a role in chromosome condensation and decondensation during spermatogenesis.