A distinct physiological role of MutY in mutation prevention in mycobacteria

Oxidative damage to DNA results in the occurrence of 7,8-dihydro-B-oxoguanine (8-oxoG) in the genome. In eubacteria, repair of such damage is initiated by two major base-excision repair enzymes, MutM and MutY. We generated a MutY-deficient strain of Mycobacterium smegmatis to investigate the role of this enzyme in DNA repair. The MutY deficiency in M. smegmatis did not result in either a noteworthy susceptibility to oxidative stress or an increase in the mutation rate. However, rifampicin resistant isolates of the MutY-deficient strain showed distinct mutations in the rifampicin-resistance-determining region of rpoB. Besides the expected C to A (or G to T) mutations, an increase in A to C (or T to G) mutations was also observed. Biochemical characterization of mycobacterial MutY (M. smegmatis and M. tuberculosis) revealed an expected excision of A opposite 8-oxoG in DNA. Additionally, excision of G and T opposite 8-oxoG was detected. MutY formed complexes with DNA containing 8-oxoG: A, 8-oxoG: G or 8-oxoG: T but not 8-oxoG : C pairs. Primer extension reactions in cell-free extracts of M. smegmatis suggested error-prone incorporation of nucleotides into the DNA. Based on these observations, we discuss the physiological role of MutY in specific mutation prevention in mycobacteria.

Novel insertion and deletion mutants of RpoB that render Mycobacterium smegmatis RNA polymerase resistant to rifampicin-mediated inhibition of transcription

The startling increase in the occurrence of rifampicin (Rif) resistance in the clinical isolates of Mycobacterium tuberculosis worldwide is posing a serious concern to tuberculosis management. The majority of Rif resistance in bacteria arises from mutations in the RpoB subunit of the RNA polymerase. We isolated M. smegmatis strains harbouring either an insertion (6 aa) or a deletion (10 aa) in their RpoB proteins. Although these strains showed a compromised fitness for growth in 7H9 Middlebrook medium, their resistance to Rif was remarkably high. The attenuated growth of the strains correlated with decreased specific activities of the RNA polymerases from the mutants. While the RNA polymerases from the parent or a mutant strain (harbouring a frequently occurring mutation, H442Y, in RpoB) were susceptible to Rif-mediated inhibition of transcription from calf thymus DNA, those from the insertion and deletion mutants were essentially refractory to such inhibition. Three-dimensional structure modelling revealed that the RpoB amino acids that interact with Rif are either deleted or unable to interact with Rif due to their unsuitable spatial positioning in these mutants. We discuss possible uses of the RpoB mutants in studying transcriptional regulation in mycobacteria and as potential targets for drug design.

Annealing effect on transport properties of Nd0.67Sr0.33MnO3 thin films

Annealing dependence of the lattice parameter, resistivity, magnetoresistance and thermopower have been studied on Nd0.87Sr0.33MnO3 thin films deposited on LaAlO3 and alumina substrates by pulsed laser ablation. Upon annealing at 800 degrees C and 1000 degrees C the lattice constant of the LaAlO3 film tends toward that of the bulk target due to reduction in oxygen vacancies. This results in a metal-insulator transition at temperatures which increase with progressive annealing along with a decrease in the observed low temperature MR. Using a magnon scattering model we estimate the e(g) bandwidth of the film annealed at 1000 degrees C and show that the magnon contribution to the resistivity is suppressed in a highly oxygen deficient film and gains prominence only upon subsequent annealing. We also show that upon annealing, the polaron concentration and the spin cluster size increases in the paramagnetic phase, using an adiabatic polaron hopping model which takes into account an exchange dependent activation energy above the resistivity peak.

Features of a unique intronless cluster of class I small heat shock protein genes in tandem with box C/D snoRNA genes on chromosome 6 in tomato (Solanum lycopersicum)

Physical clustering of genes has been shown in plants; however, little is known about gene clusters that have different functions, particularly those expressed in the tomato fruit. A class I 17.6 small heat shock protein (Sl17.6 shsp) gene was cloned and used as a probe to screen a tomato (Solanum lycopersicum) genomic library. An 8.3-kb genomic fragment was isolated and its DNA sequence determined. Analysis of the genomic fragment identified intronless open reading frames of three class I shsp genes (Sl17.6, Sl20.0, and Sl20.1), the Sl17.6 gene flanked by Sl20.1 and Sl20.0, with complete 5' and 3' UTRs. Upstream of the Sl20.0 shsp, and within the shsp gene cluster, resides a box C/D snoRNA cluster made of SlsnoR12.1 and SlU24a. Characteristic C and D, and C' and D', boxes are conserved in SlsnoR12.1 and SlU24a while the upstream flanking region of SlsnoR12.1 carries TATA box 1, homol-E and homol-D box-like cis sequences, TM6 promoter, and an uncharacterized tomato EST. Molecular phylogenetic analysis revealed that this particular arrangement of shsps is conserved in tomato genome but is distinct from other species. The intronless genomic sequence is decorated with cis elements previously shown to be responsive to cues from plant hormones, dehydration, cold, heat, and MYC/MYB and WRKY71 transcription factors. Chromosomal mapping localized the tomato genomic sequence on the short arm of chromosome 6 in the introgression line (IL) 6-3. Quantitative polymerase chain reaction analysis of gene cluster members revealed differential expression during ripening of tomato fruit, and relatively different abundances in other plant parts.

The Effects of Nitrogen Bonding on Hardness of AIN/CrN Multilayer Hard Coatings

AIN/CrN multilayer hard coatings with various bilayer thicknesses were fabricated by a reactive sputtering process. The microstructural and mechanical characterizations of multilayer coatings were investigated through transmission electron microscope (TEM) observations and the hardness measurements by nano indentation. In particular, the variation of chemical bonding states of the bilayer nitrides was elucidated by near edge X-ray absorption fine structure (NEXAFS) spectroscopy. Many broken nitrogen bonds were formed by decreasing the bilayer thickness of AIN/CrN multilayer coatings. Existence of optimum AIN/CrN multilayer coatings thickness for maximum hardness could be explained by the competition of softening by the formation of broken nitrogen bonds and strengthening induced by decreasing bilayer thickness.

Hardness and Nitrogen Bonding Structure of A(x)Ti(1-x)N/CrN Multilayer Hard Coating

AlxTi1-xN/CrN multilayer coatings were fabricated by magnetron sputtering and those hardness variations were studied by observing the crack propagation and measuring the chemical bonding state of nitrides by Ti addition. While AlN/CrN multilayer shown stair-like crack propagation, AlxTi1-xN/CrN multilayer illustrated straight crack propagation. Most interestingly, Ti addition induced more broken nitrogen bonds in the nitride multilayers, leading to the reduction of hardness. However, the hardness of Al0.25Ti0.75N/CrN multilayer, having high Ti contents, increased by the formation of many Ti-N bond again instead of Al-N bond. From these results, we found that linear crack propagation behavior was dominated by broken nitrogen bonds in the AlxT1-xN/CrN multilayer coatings.

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.

Mycobacterium tuberculosis mutT1 (Rv2985) and ADPRase (Rv1700) proteins constitute a two-stage mechanism of 8-Oxo-dGTP and 8-Oxo-GTP detoxification and adenosine to cytidine mutation avoidance

Approximately one third of the world population is infected with Mycobacterium tuberculosis, the causative agent of tuberculosis. A better understanding of the pathogen biology is crucial to develop new tools/strategies to tackle its spread and treatment. In the host macrophages, the pathogen is exposed to reactive oxygen species, known to damage dGTP and GTP to 8-oxo-dGTP and 8-oxo-GTP, respectively. Incorporation of the damaged nucleotides in nucleic acids is detrimental to organisms. MutT proteins, belonging to a class of Nudix hydrolases, hydrolyze 8-oxo-G nucleoside triphosphates/diphosphates to the corresponding nucleoside monophosphates and sanitize the nucleotide pool. Mycobacteria possess several MutT proteins. However, a functional homolog of Escherichia coli MutT has not been identified. Here, we characterized MtuMutT1 and Rv1700 proteins of M. tuberculosis. Unlike other MutT proteins, MtuMutT1 converts 8-oxo-dGTP to 8-oxo-dGDP, and 8-oxo-GTP to 8-oxo-GDP. Rv1700 then converts them to the corresponding nucleoside monophosphates. This observation suggests the presence of a two-stage mechanism of 8-oxo-dGTP/8-oxo-GTP detoxification in mycobacteria. MtuMutT1 converts 8-oxo-dGTP to 8-oxo-dGDP with a K-m of similar to 50 mu M and V-max of similar to 0.9 pmol/min per ng of protein, and Rv1700 converts 8-oxo-dGDP to 8-oxo-dGMP with a K-m of similar to 9.5 mu M and V-max of similar to 0.04 pmol/min per ng of protein. Together, MtuMutT1 and Rv1700 offer maximal rescue to E. coli for its MutT deficiency by decreasing A to C mutations (a hallmark of MutT deficiency). We suggest that the concerted action of MtuMutT1 and Rv1700 plays a crucial role in survival of bacteria against oxidative stress.

Scale-dependent relationships between tree species richness and ecosystem function in forests

1. The relationship between species richness and ecosystem function, as measured by productivity or biomass, is of long-standing theoretical and practical interest in ecology. This is especially true for forests, which represent a majority of global biomass, productivity and biodiversity. 2. Here, we conduct an analysis of relationships between tree species richness, biomass and productivity in 25 forest plots of area 8-50ha from across the world. The data were collected using standardized protocols, obviating the need to correct for methodological differences that plague many studies on this topic. 3. We found that at very small spatial grains (0.04ha) species richness was generally positively related to productivity and biomass within plots, with a doubling of species richness corresponding to an average 48% increase in productivity and 53% increase in biomass. At larger spatial grains (0.25ha, 1ha), results were mixed, with negative relationships becoming more common. The results were qualitatively similar but much weaker when we controlled for stem density: at the 0.04ha spatial grain, a doubling of species richness corresponded to a 5% increase in productivity and 7% increase in biomass. Productivity and biomass were themselves almost always positively related at all spatial grains. 4. Synthesis. This is the first cross-site study of the effect of tree species richness on forest biomass and productivity that systematically varies spatial grain within a controlled methodology. The scale-dependent results are consistent with theoretical models in which sampling effects and niche complementarity dominate at small scales, while environmental gradients drive patterns at large scales. Our study shows that the relationship of tree species richness with biomass and productivity changes qualitatively when moving from scales typical of forest surveys (0.04ha) to slightly larger scales (0.25 and 1ha). This needs to be recognized in forest conservation policy and management.

Boron doped defective graphene as a potential anode material for Li-ion batteries

Graphene with large surface area and robust structure has been proposed as a high storage capacity anode material for Li ion batteries. While the inertness of pristine graphene leads to better Li kinetics, poor adsorption leads to Li clustering, significantly affecting the performance of the battery. Here, we show the role of defects and doping in achieving enhanced adsorption without compromising on the high diffusivity of Li. Using first principles density functional theory (DFT) calculations, we carry out a comprehensive study of diffusion kinetics of Li over the plane of the defective structures and calculate the change in the number of Li atoms in the vicinity of defects, with respect to pristine graphene. Our results show that the Li-C interaction, storage capacity and the energy barriers depend sensitively on the type of defects. The un-doped and boron doped mono-vacancy, doped di-vacancy up to two boron, one nitrogen doped di-vacancy, and Stone-Wales defects show low energy barriers that are comparable to pristine graphene. Furthermore, boron doping at mono-vacancy enhances the adsorption of Li. In particular, the two boron doped mono-vacancy graphene shows both a low energy barrier of 0.31 eV and better adsorption, and hence can be considered as a potential candidate for anode material.

Pressure induced manifold enhancement of Li-kinetics in FCC fullerene

The reduction of the diffusion energy barrier for Li in electrodes is one of the required criteria to achieve better performances in Li ion batteries. Using density functional theory based calculations, we report a pressure induced manifold enhancement of Li-kinetics in bulk FCC fullerene. Scanning of the potential energy surface reveals a diffusion path with a low energy barrier of 0.62 eV, which reduces further under the application of hydrostatic pressure. The pressure induced reduction in the diffusion barrier continues till a uniform volume strain of 17.7% is reached. Further enhancement of strain increases the barrier due to the repulsion caused by C-C bond formation between two neighbouring fullerenes. The decrease in the barrier is attributed to the combined effect of charge transfer triggered by the enhanced interaction of Li with the fullerene as well as the change in profile of the local potential, which becomes more attractive for Li. The lowering of the barrier leads to an enhancement of two orders of magnitude in Li diffusivity at room temperature making pressurized bulk fullerene a promising artificial solid electrolyte interface (SEI) for a faster rechargeable battery.

CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change

Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characterizing forest responses to global change. Within very large plots (median size 25ha), all stems 1cm diameter are identified to species, mapped, and regularly recensused according to standardized protocols. CTFS-ForestGEO spans 25 degrees S-61 degrees N latitude, is generally representative of the range of bioclimatic, edaphic, and topographic conditions experienced by forests worldwide, and is the only forest monitoring network that applies a standardized protocol to each of the world's major forest biomes. Supplementary standardized measurements at subsets of the sites provide additional information on plants, animals, and ecosystem and environmental variables. CTFS-ForestGEO sites are experiencing multifaceted anthropogenic global change pressures including warming (average 0.61 degrees C), changes in precipitation (up to +/- 30% change), atmospheric deposition of nitrogen and sulfur compounds (up to 3.8g Nm(-2)yr(-1) and 3.1g Sm(-2)yr(-1)), and forest fragmentation in the surrounding landscape (up to 88% reduced tree cover within 5km). The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics. Ongoing research across the CTFS-ForestGEO network is yielding insights into how and why the forests are changing, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change.

A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily

Uracil DNA glycosylases (UDGs) are an important group of DNA repair enzymes, which pioneer the base excision repair pathway by recognizing and excising uracil from DNA. Based on two short conserved sequences (motifs A and B), UDGs have been classified into six families. Here we report a novel UDG, UdgX, from Mycobacterium smegmatis and other organisms. UdgX specifically recognizes uracil in DNA, forms a tight complex stable to sodium dodecyl sulphate, 2-mercaptoethanol, urea and heat treatment, and shows no detectable uracil excision. UdgX shares highest homology to family 4 UDGs possessing Fe-S cluster. UdgX possesses a conserved sequence, KRRIH, which forms a flexible loop playing an important role in its activity. Mutations of H in the KRRIH sequence to S, G, A or Q lead to gain of uracil excision activity in MsmUdgX, establishing it as a novel member of the UDG superfamily. Our observations suggest that UdgX marks the uracil-DNA for its repair by a RecA dependent process. Finally, we observed that the tight binding activity of UdgX is useful in detecting uracils in the genomes.

Organic-inorganic hybrid PtCo nanoparticle with high electrocatalytic activity and durability for oxygen reduction

In Pt-transition metal (TM) alloy catalysts, the electron transfer from the TM to Pt is retarded owing to the inevitable oxidation of the TM surface by oxygen. In addition, acidic electrolytes such as those employed in fuel cells accelerate the dissolution of the surface TM oxide, which leads to catalyst degradation. Herein, we propose a novel synthesis strategy that selectively modifies the electronic structure of surface Co atoms with N-containing polymers, resulting in highly active and durable PtCo nanoparticle catalysts useful for the oxygen reduction reaction (ORR). The polymer, which is functionalized on carbon black, selectively interacts with the Co precursor, resulting in Co-N bond formation on the PtCo nanoparticle surface. Electron transfer from Co to Pt in the PtCo nanoparticles modified by the polymer is enhanced by the increase in the difference in electronegativity between Pt and Co compared with that in bare PtCo nanoparticles with the TM surface oxides. In addition, the dissolution of Co and Pt is prevented by the selective passivation of surface Co atoms and the decrease in the O-binding energy of surface Pt atoms. As a result, the catalytic activity and durability of PtCo nanoparticles for the ORR are significantly improved by the electronic ensemble effects. The proposed organic/inorganic hybrid concept will provide new insights into the tuning of nanomaterials consisting of heterogeneous metallic elements for various electrochemical and chemical applications.