Distinct mechanisms of DNA repair in mycobacteria and their implications in attenuation of the pathogen growth

About a third of the human population is estimated to be infected with Mycobacterium tuberculosis. Emergence of drug resistant strains and the protracted treatment strategies have compelled the scientific community to identify newer drug targets, and to develop newer vaccines. In the host macrophages, the bacterium survives within an environment rich in reactive nitrogen and oxygen species capable of damaging its genome. Therefore, for its successful persistence in the host, the pathogen must need robust DNA repair mechanisms. Analysis of M. tuberculosis genome sequence revealed that it lacks mismatch repair pathway suggesting a greater role for other DNA repair pathways such as the nucleotide excision repair, and base excision repair pathways. In this article, we summarize the outcome of research involving these two repair pathways in mycobacteria focusing primarily on our own efforts. Our findings, using Mycobacterium smegmatis model, suggest that deficiency of various DNA repair functions in single or in combinations severely compromises their DNA repair capacity and attenuates their growth under conditions typically encountered in macrophages. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

Study on important diffusion parameters of binary Ni3Sn4 phase

Important diffusion parameters, such as-parabolic growth constant, integrated diffusivity, ratio of intrinsic diffusivities of species Ni and Sn, Kirkendall marker velocity and the activation energy for diffusion kinetics of binary Ni3Sn4 phase have been investigated with the help of incremental diffusion couple technique (Sn/Ni0.57Sn0.43) in the temperature range 200-150 degrees C. Low activation energy extracted from Arrhenius plot indicates grain boundary controlled diffusion process. The species Sn is three times faster than Ni at 200 degrees C. Further, the activation energy of Sn tracer diffusivity is greater than that of Ni.

Microstructure-Wear Resistance Correlation and Wear Mechanisms of Spark Plasma Sintered Cu-Pb Nanocomposites

The dispersion of a softer phase in a metallic matrix reduces the coefficient of friction (COF), often at the expense of an increased wear rate at the tribological contact. To address this issue, unlubricated fretting wear tests were performed on spark plasma sintered Cu-Pb nanocomposites against bearing steel. The sintering temperature and the Pb content as well as the fretting parameters were judiciously selected and varied to investigate the role of microstructure (grain size, second-phase content) on the wear resistance properties of Cu-Pb nanocomposites. A combination of the lowest wear rate (similar to 1.5 x 10(-6) mm(3)/Nm) and a modest COF (similar to 0.4) was achieved for Cu-15 wt pct Pb nanocomposites. The lower wear rate of Cu-Pb nanocomposites with respect to unreinforced Cu is attributed to high hardness (similar to 2 to 3.5 GPa) of the matrix, Cu2O/Fe2O3-rich oxide layer formation at tribological interface, and exuding of softer Pb particles. The wear properties are discussed in reference to the characteristics of transfer layer on worn surface as well as subsurface damage probed using focused ion beam microscopy. Interestingly, the flash temperature has been found to have insignificant effect on the observed oxidative wear, and alternative mechanisms are proposed. Importantly, the wear resistance properties of the nanocomposites reveal a weak Hall-Petch-like relationship with grain size of nanocrystalline Cu. (C) The Minerals, Metals & Materials Society and ASM International 2013

In vitro/In vivo assessment and mechanisms of toxicity of bioceramic materials and its wear particulates

With the progress in modern technological research, novel biomaterials are being largely developed for various biomedical applications. Over the past two decades, most of the research focuses on the development of a new generation of bioceramics as substitutes for hard tissue replacement. In reference to their application in different anatomical locations of a patient, newly developed bioceramic materials can potentially induce a toxic/harmful effect to the host tissues. Therefore, prior to clinical testing, relevant biochemical screening assays are to be performed at the cellular and molecular level, to address the issues of biocompatibility and long term performance of the implants. Along with testing strategies in the bulk material toxicity, a detailed evaluation should also be conducted to determine the toxicity of the wear products of the potential bioceramics. This is important as the bioceramics are intended to be implanted in patients with longer life expectancy and notwithstanding, the material will eventually release finer (mostly nanosized) sized debris particles due to continuous wear at articulating surfaces in the hostile corrosive environment of the human body. The wear particulates generated from a biocompatible bioceramic may act in a different way, inducing early/late aseptic loosening at the implant site, resulting in osteolysis and inflammation. Hence, a study on the chronic effects of the wear particulates, in terms of local and systemic toxicity becomes the major criteria in the toxicity evaluation of implantable bioceramics. In this broad perspective, this article summarizes some of the currently used techniques and knowledge in assessing the in vitro and in vivo cytotoxicity and genotoxicity of bioceramic implant materials. It also addresses the need to conduct a broad evaluation before claiming the biocompatibility and clinical feasibility of any new biomaterial. This review also emphasizes some of the case studies based on the experimental designs that are currently followed and its importance in the context of clinical applications.

Wallner lines, crack velocity and mechanisms of crack nucleation and growth in a brittle bulk metallic glass

Mode I fracture experiments were conducted on brittle bulk metallic glass (BMG) samples and the fracture surface features were analyzed in detail to understand the underlying physical processes. Wollner lines, which result from the interaction between the propagating crack front and shear waves emanating from a secondary source, were observed on the fracture surface and geometric analysis of them indicates that the maximum crack velocity is similar to 800 m s(-1), which corresponds to similar to 0.32 times the shear wave speed. Fractography reveals that the sharp crack nucleation at the notch tip occurs at the mid-section of the specimens with the observation of flat and half-penny-shaped cracks. On this basis, we conclude that the crack initiation in brittle BMGs is stress-controlled and occurs through hydrostatic stress-assisted cavity nucleation ahead of the notch tip. High magnification scanning electron and atomic force microscopies of the dynamic crack growth regions reveal highly organized, nanoscale periodic patterns with a spacing of similar to 79 nm. Juxtaposition of the crack velocity with this spacing suggests that the crack takes similar to 10(-10) s for peak-to-peak propagation. This, and the estimated adiabatic temperature rise ahead of the propagating crack tip that suggests local softening, is utilized to critically discuss possible causes for the nanocorrugation formation. Taylor's fluid meniscus instability is unequivocally ruled out. Then, two other possible mechanisms, viz. (a) crack tip blunting and resharpening through nanovoid nucleation and growth ahead of the crack tip and eventual coalescence, and (b) dynamic oscillation of the crack in a thin slab of softened zone ahead of the crack-tip, are critically discussed. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Electronically nonadiabatic decomposition mechanisms of clusters of zinc and dimethylnitramine

Electronically nonadiabatic decomposition mechanisms of dimethylnitramine (DMNA) in presence of zinc metal clusters are explored. Complete active space self-consistent field (CASSCF) calculation is employed for DMNA-Zn and ONIOM (Our own N-layered integrated molecular orbital and molecular mechanics) methodology is coupled with CASSCF methodology for DMNA-Zn-10 cluster. Present computational results show that DMNA-Zn clusters undergo electronically nonadiabatic reactions, rendering nitro-nitrite isomerization followed by NO elimination. The overall reactions are also found to be highly exothermic in nature. This is the first report on electronically nonadiabatic decomposition pathways of DMNA-Zn-n neutral clusters. (C) 2014 Elsevier B.V. All rights reserved.

Excited electronic state decomposition mechanisms of clusters of dimethylnitramine and aluminum

In this report, electronically non-adiabatic decomposition pathways of clusters of dimethylnitramine and aluminum (DMNA-Al and DMNA-Al-2) are discussed in comparison to isolated dimethylnitramine (DMNA). Electronically excited state processes of DMNA-Al and DMNA-Al-2 are explored using the complete active space self-consistent field (CASSCF) and the restricted active space self-consistent field (RASSCF) theories, respectively. Similar to the nitro-nitrite isomerization reaction pathway of DMNA, DMNA-Al-n clusters also exhibit isomerization pathway. However, it involves several other steps, such as, first Al-O bond dissociation, then N-N bond dissociation followed by isomerization and finally NO elimination. Furthermore, DMNA-Al-n clusters exhibit overall exothermic decomposition reaction pathway and isolated DMNA shows overall endothermic reaction channel.

Multifarious facets of sugar-derived molecular gels: molecular features, mechanisms of self-assembly and emerging applications

The remarkable capability of nature to design and create excellent self-assembled nano-structures, especially in the biological world, has motivated chemists to mimic such systems with synthetic molecular and supramolecular systems. The hierarchically organized self-assembly of low molecular weight gelators (LMWGs) based on non-covalent interactions has been proven to be a useful tool in the development of well-defined nanostructures. Among these, the self-assembly of sugar-derived LMWGs has received immense attention because of their propensity to furnish biocompatible, hierarchical, supramolecular architectures that are macroscopically expressed in gel formation. This review sheds light on various aspects of sugar-derived LMWGs, uncovering their mechanisms of gelation, structural analysis, and tailorable properties, and their diverse applications such as stimuli-responsiveness, sensing, self-healing, environmental problems, and nano and biomaterials synthesis.

Coupled Mechanisms of Precipitation and Atomization in Burning Nanofluid Fuel Droplets

Understanding the combustion characteristics of fuel droplets laden with energetic nanoparticles (NP) is pivotal for lowering ignition delay, reducing pollutant emissions and increasing the combustion efficiency in next generation combustors. In this study, first we elucidate the feedback coupling between two key interacting mechanisms, namely, secondary atomization and particle agglomeration; that govern the effective mass fraction of NPs within the droplet. Second, we show how the initial NP concentration modulates their relative dominance leading to a masterslave configuration. Secondary atomization of novel nanofuels is a crucial process since it enables an effective transport of dispersed NPs to the flame (a pre-requisite condition for NPs to burn). Contrarily, NP agglomeration at the droplet surface leads to shell formation thereby retaining NPs inside the droplet. In particular, we show that at dense concentrations shell formation (master process) dominates over secondary atomization (slave) while at dilute particle loading it is the high frequency bubble ejections (master) that disrupt shell formation (slave) through its rupture and continuous outflux of NPs. This results in distinct combustion residues at dilute and dense concentrations, thereby providing a method of manufacturing flame synthesized microstructures with distinct morphologies.

Mycobacterium tuberculosis RecG Protein but Not RuvAB or RecA Protein Is Efficient at Remodeling the Stalled Replication Forks IMPLICATIONS FOR MULTIPLE MECHANISMS OF REPLICATION RESTART IN MYCOBACTERIA

Aberrant DNA replication, defects in the protection, and restart of stalled replication forks are major causes of genome instability in all organisms. Replication fork reversal is emerging as an evolutionarily conserved physiological response for restart of stalled forks. Escherichia coli RecG, RuvAB, and RecA proteins have been shown to reverse the model replication fork structures in vitro. However, the pathways and the mechanisms by which Mycobacterium tuberculosis, a slow growing human pathogen, responds to different types of replication stress and DNA damage are unclear. Here, we show that M. tuberculosis RecG rescues E. coli Delta recG cells from replicative stress. The purified M. tuberculosis RecG (MtRecG) and RuvAB(MtRuvAB) proteins catalyze fork reversal of model replication fork structures with and without a leading strand single-stranded DNA gap. Interestingly, single-stranded DNA-binding protein suppresses the MtRecG- and MtRuvAB-mediated fork reversal with substrates that contain lagging strand gap. Notably, our comparative studies with fork structures containing template damage and template switching mechanism of lesion bypass reveal that MtRecG but not MtRuvAB or MtRecA is proficient in driving the fork reversal. Finally, unlike MtRuvAB, we find that MtRecG drives efficient reversal of forks when fork structures are tightly bound by protein. These results provide direct evidence and valuable insights into the underlying mechanism of MtRecG-catalyzed replication fork remodeling and restart pathways in vivo.

Prediction of electronically nonadiabatic decomposition mechanisms of isolated gas phase nitrogen-rich energetic salt: Guanidium-triazolate

Electronically nonadiabatic decomposition pathways of guanidium triazolate are explored theoretically. Nonadiabatically coupled potential energy surfaces are explored at the complete active space self-consistent field (CASSCF) level of theory. For better estimation of energies complete active space second order perturbation theories (CASPT2 and CASMP2) are also employed. Density functional theory (DFT) with B3LYP functional and MP2 level of theory are used to explore subsequent ground state decomposition pathways. In comparison with all possible stable decomposition products (such as, N-2, NH3, HNC, HCN, NH2CN and CH3NC), only NH3 (with NH2CN) and N-2 are predicted to be energetically most accessible initial decomposition products. Furthermore, different conical intersections between the S-1 and S-0 surfaces, which are computed at the CASSCF(14,10)/6-31G(d) level of theory, are found to play an essential role in the excited state deactivation process of guanidium triazolate. This is the first report on the electronically nonadiabatic decomposition mechanisms of isolated guanidium triazolate salt. (C) 2015 Elsevier B.V. All rights reserved.

A comparative phase 1 clinical trial to identify anti-infective mechanisms of vitamin D in people with HIV infection

Objectives:To determine if there is a biological mechanism that explains the association between HIV disease progression and increased mortality with low circulating vitamin D levels; specifically, to determine if restoring vitamin D levels induced T-cell functional changes important for antiviral immunity.Design:This was a pilot, open-label, three-arm prospective phase 1 study.Methods:We recruited 28 patients with low plasma vitamin D (<50nmol/l 25-hydroxyvitamin D3), comprising 17 HIV+ patients (11 on HAART, six treatment-naive) and 11 healthy controls, who received a single dose of 200000IU oral cholecalciferol. Advanced T-cell flow cytometry methods measured CD4(+) T-cell function associated with viral control in blood samples at baseline and 1-month after vitamin D supplementation.Results:One month of vitamin D supplementation restored plasma levels to sufficiency (>75nmol/l) in 27 of 28 patients, with no safety issues. The most striking change was in HIV+ HAART+ patients, where increased frequencies of antigen-specific T cells expressing macrophage inflammatory protein (MIP)-1 - an important anti-HIV blocking chemokine - were observed, with a concomitant increase in plasma MIP-1, both of which correlated significantly with vitamin D levels. In addition, plasma cathelicidin - a vitamin D response gene with broad antimicrobial activity - was enhanced.Conclusion:Vitamin D supplementation modulates disease-relevant T-cell functions in HIV-infected patients, and may represent a useful adjunct to HAART therapy. Copyright (C) 2015 Wolters Kluwer Health, Inc. All rights reserved.

Diffusion mechanisms in the Fe3ASi

In this paper, the possible reasons for the high thermal vacancy concentration and the low migration barriers for the Fe atom diffusion in the DO3 structure Fe3Si have been discussed.

Impact response and failure mechanisms of ultrahigh modulus polyethylene fiber composites and polyethylene fiber-carbon fiber hybrid composites

The impact response and failure mechanisms of ultrahigh modulus polyethylene (UHMPE) fiber composites and UHMPE fiber-carbon fiber hybrid composites have been investigated. Charpy impact, drop weight impact and high strain rate impact experiments have been performed in order to study the impact resistance, notch sensitivity, strain rate sensitivity and hybrid effects. Results obtained from dynamic and quasi-static measurements have been compared. Because of the ductility of UHMPE fibers, the impact energy absorption of UHMPE fiber composites is very high, thereby leading to excellent damage tolerance. By hybridizing with UHMPE fibers, the impact properties of carbon fiber composites can be greatly improved. The impact and shock failure mechanisms of these composites are discussed.