Functional Analysis of DNA Replication Fork Reversal Catalyzed by Mycobacterium tuberculosis RuvAB Proteins

Initially discovered in Escherichia coli, RuvAB proteins are ubiquitous in bacteria and play a dual role as molecular motor proteins responsible for branch migration of the Holliday junction(s) and reversal of stalled replication forks. Despite mounting genetic evidence for a crucial role of RuvA and RuvB proteins in reversal of stalled replication forks, the mechanistic aspects of this process are still not fully understood. Here, we elucidate the ability of Mycobacterium tuberculosis RuvAB (MtRuvAB) complex to catalyze the reversal of replication forks using a range of DNA replication fork substrates. Our studies show that MtRuvAB, unlike E. coli RuvAB, is able to drive replication fork reversal via the formation of Holliday junction intermediates, suggesting that RuvAB-catalyzed fork reversal involves concerted unwinding and annealing of nascent leading and lagging strands. We also demonstrate the reversal of replication forks carrying hemi-replicated DNA, indicating that MtRuvAB complex-catalyzed fork reversal is independent of symmetry at the fork junction. The fork reversal reaction catalyzed by MtRuvAB is coupled to ATP hydrolysis, is processive, and culminates in the formation of an extended reverse DNA arm. Notably, we found that sequence heterology failed to impede the fork reversal activity of MtRuvAB. We discuss the implications of these results in the context of recognition and processing of varied types of replication fork structures by RuvAB proteins.

Distributed Storage Codes With Repair-by-Transfer and Nonachievability of Interior Points on the Storage-Bandwidth Tradeoff

Regenerating codes are a class of recently developed codes for distributed storage that, like Reed-Solomon codes, permit data recovery from any subset of k nodes within the n-node network. However, regenerating codes possess in addition, the ability to repair a failed node by connecting to an arbitrary subset of d nodes. It has been shown that for the case of functional repair, there is a tradeoff between the amount of data stored per node and the bandwidth required to repair a failed node. A special case of functional repair is exact repair where the replacement node is required to store data identical to that in the failed node. Exact repair is of interest as it greatly simplifies system implementation. The first result of this paper is an explicit, exact-repair code for the point on the storage-bandwidth tradeoff corresponding to the minimum possible repair bandwidth, for the case when d = n-1. This code has a particularly simple graphical description, and most interestingly has the ability to carry out exact repair without any need to perform arithmetic operations. We term this ability of the code to perform repair through mere transfer of data as repair by transfer. The second result of this paper shows that the interior points on the storage-bandwidth tradeoff cannot be achieved under exact repair, thus pointing to the existence of a separate tradeoff under exact repair. Specifically, we identify a set of scenarios which we term as ``helper node pooling,'' and show that it is the necessity to satisfy such scenarios that overconstrains the system.

Curcumin-Arteether Combination Therapy of Plasmodium berghei-Infected Mice Prevents Recrudescence Through Immunomodulation

Earlier studies in this laboratory have shown the potential of artemisinin-curcumin combination therapy in experimental malaria. In a parasite recrudescence model in mice infected with Plasmodium berghei (ANKA), a single dose of alpha, beta-arteether (ART) with three oral doses of curcumin prevented recrudescence, providing almost 95% protection. The parasites were completely cleared in blood with ART-alone (AE) or ART+curcumin (AC) treatments in the short-term, although the clearance was faster in the latter case involving increased ROS generation. But, parasites in liver and spleen were not cleared in AE or AC treatments, perhaps, serving as a reservoir for recrudescence. Parasitemia in blood reached up to 60% in AE-treated mice during the recrudescence phase, leading to death of animals. A transient increase of up to 2-3% parasitemia was observed in AC-treatment, leading to protection and reversal of splenomegaly. A striking increase in spleen mRNA levels for TLR2, IL-10 and IgG-subclass antibodies but a decrease in those for INF gamma and IL-12 was observed in AC-treatment. There was a striking increase in IL-10 and IgG subclass antibody levels but a decrease in INF gamma levels in sera leading to protection against recrudescence. AC-treatment failed to protect against recrudescence in TLR2(-/-) and IL-10(-/-) animals. IL-10 injection to AE-treated wild type mice and AC-treated TLR22/2 mice was able to prolong survival. Blood from the recrudescence phase in AE-treatment, but not from AC-treatment, was able to reinfect and kill naive animals. Sera from the recrudescence phase of AC-treated animals reacted with several parasite proteins compared to that from AE-treated animals. It is proposed that activation of TLR2-mediated innate immune response leading to enhanced IL-10 production and generation of anti-parasite antibodies contribute to protective immunity in AC-treated mice. These results indicate a potential for curcumin-based combination therapy to be tested for prevention of recrudescence in falciparum and relapse in vivax malaria.

Interference Alignment in Regenerating Codes for Distributed Storage: Necessity and Code Constructions

Regenerating codes are a class of recently developed codes for distributed storage that, like Reed-Solomon codes, permit data recovery from any arbitrary of nodes. However regenerating codes possess in addition, the ability to repair a failed node by connecting to any arbitrary nodes and downloading an amount of data that is typically far less than the size of the data file. This amount of download is termed the repair bandwidth. Minimum storage regenerating (MSR) codes are a subclass of regenerating codes that require the least amount of network storage; every such code is a maximum distance separable (MDS) code. Further, when a replacement node stores data identical to that in the failed node, the repair is termed as exact. The four principal results of the paper are (a) the explicit construction of a class of MDS codes for d = n - 1 >= 2k - 1 termed the MISER code, that achieves the cut-set bound on the repair bandwidth for the exact repair of systematic nodes, (b) proof of the necessity of interference alignment in exact-repair MSR codes, (c) a proof showing the impossibility of constructing linear, exact-repair MSR codes for d < 2k - 3 in the absence of symbol extension, and (d) the construction, also explicit, of high-rate MSR codes for d = k+1. Interference alignment (IA) is a theme that runs throughout the paper: the MISER code is built on the principles of IA and IA is also a crucial component to the nonexistence proof for d < 2k - 3. To the best of our knowledge, the constructions presented in this paper are the first explicit constructions of regenerating codes that achieve the cut-set bound.

Theoretical-experimental study of shock wave-assisted metal forming process using a diaphragmless shock tube

The use of high-velocity sheet-forming techniques where the strain rates are in excess of 10(2)/s can help us solve many problems that are difficult to overcome with traditional metal-forming techniques. In this investigation, thin metallic plates/foils were subjected to shock wave loading in the newly developed diaphragmless shock tube. The conventional shock tube used in the aerodynamic applications uses a metal diaphragm for generating shock waves. This method of operation has its own disadvantages including the problems associated with repeatable and reliable generation of shock waves. Moreover, in industrial scenario, changing metal diaphragms after every shot is not desirable. Hence, a diaphragmless shock tube is calibrated and used in this study. Shock Mach numbers up to 3 can be generated with a high degree of repeatability (+/- 4 per cent) for the pressure jumps across the primary shock wave. The shock Mach number scatter is within +/- 1.5 per cent. Copper, brass, and aluminium plates of diameter 60 mm and thickness varying from 0.1 to 1 mm are used. The plate peak over-pressures ranging from 1 to 10 bar are used. The midpoint deflection, circumferential, radial, and thickness strains are measured and using these, the Von Mises strain is also calculated. The experimental results are compared with the numerical values obtained using finite element analysis. The experimental results match well with the numerical values. The plastic hinge effect was also observed in the finite element simulations. Analysis of the failed specimens shows that aluminium plates had mode I failure, whereas copper plates had mode II failure.

Ovarian developmental variation in the primitively eusocial wasp Ropalidia marginata suggests a gateway to worker ontogeny and the evolution of sociality

Social insects are characterized by reproductive caste differentiation of colony members into one or a small number of fertile queens and a large number of sterile workers. The evolutionary origin and maintenance of such sterile workers remains an enduring puzzle in insect sociobiology. Here, we studied ovarian development in over 600 freshly eclosed, isolated, virgin female Ropalidia marginata wasps, maintained in the laboratory. The wasps differed greatly both in the time taken to develop their ovaries and in the magnitude of ovarian development despite having similar access to resources. All females started with no ovarian development at day zero, and the percentage of individuals with at least one oocyte at any stage of development increased gradually across age, reached 100% at 100. days and decreased slightly thereafter. Approximately 40% of the females failed to develop ovaries within the average ecological lifespan of the species. Age, body size and adult feeding rate, when considered together, were the most important factors governing ovarian development. We suggest that such flexibility and variation in the potential and timing of reproductive development may physiologically predispose females to accept worker roles and thus provide a gateway to worker ontogeny and the evolution of sociality.

Electrothermal Ageing of Epoxy Nanocomposites

Constant stress accelerated ageing experiments were conducted on unfilled epoxy and epoxy alumina nanocomposites with different filler loadings of 0.1, 1 and 5 wt%. Electrical (6 kV/mm), thermal (60 degrees C) and combined electrothermal (6 kV/mm and 60 degrees C) ageing experiments were performed for a duration of 250 h. The leakage current through the samples were continuously monitored and the variation in the tan delta values with ageing duration was also monitored. It was observed that the increase in the tan delta value with ageing duration was less for the epoxy alumina nanocomposites as compared to the unfilled epoxy. Dielectric spectroscopy measurements were performed on the samples before and after the ageing in the frequency range of 10(-2) to 10(6) Hz. The permittivity and tan delta values were found to increase in the low frequency range. The volume resistivity of unfilled epoxy and epoxy alumina nanocomposites were also measured before and after the ageing. The volume resistivity improved marginally for the thermally aged samples, but reduced for the electrically aged and the electrothermally aged samples. The decrease in the value of volume resistivity was more for the multistress aged unfilled epoxy samples as compared to the multistress aged epoxy alumina nanocomposites. It was also observed that the unfilled epoxy samples having a higher value of tan delta failed first. The time to failure of the samples showed an increasing trend with an increase in the nano filler loading of epoxy alumina nanocomposites.

NMR studies of preimplantation embryo metabolism in human assisted reproductive techniques: a new biomarker for assessment of embryo implantation potential

There has been growing interest in understanding energy metabolism in human embryos generated using assisted reproductive techniques (ART) for improving the overall success rate of the method. Using NMR spectroscopy as a noninvasive tool, we studied human embryo metabolism to identify specific biomarkers to assess the quality of embryos for their implantation potential. The study was based on estimation of pyruvate, lactate and alanine levels in the growth medium, ISM1, used in the culture of embryos. An NMR study involving 127 embryos from 48 couples revealed that embryos transferred on Day 3 (after 72 h in vitro culture) with successful implantation (pregnancy) exhibited significantly (p < 10(-5)) lower pyruvate/alanine ratios compared to those that failed to implant. Lactate levels in media were similar for all embryos. This implies that in addition to lactate production, successfully implanted embryos use pyruvate to produce alanine and other cellular functions. While pyruvate and alanine individually have been used as biomarkers, the present study highlights the potential of combining them to provide a single parameter that correlates strongly with implantation potential. Copyright (C) 2012 John Wiley & Sons, Ltd.

Enabling node repair in any erasure code for distributed storage

Erasure codes are an efficient means of storing data across a network in comparison to data replication, as they tend to reduce the amount of data stored in the network and offer increased resilience in the presence of node failures. The codes perform poorly though, when repair of a failed node is called for, as they typically require the entire file to be downloaded to repair a failed node. A new class of erasure codes, termed as regenerating codes were recently introduced, that do much better in this respect. However, given the variety of efficient erasure codes available in the literature, there is considerable interest in the construction of coding schemes that would enable traditional erasure codes to be used, while retaining the feature that only a fraction of the data need be downloaded for node repair. In this paper, we present a simple, yet powerful, framework that does precisely this. Under this framework, the nodes are partitioned into two types and encoded using two codes in a manner that reduces the problem of node-repair to that of erasure-decoding of the constituent codes. Depending upon the choice of the two codes, the framework can be used to avail one or more of the following advantages: simultaneous minimization of storage space and repair-bandwidth, low complexity of operation, fewer disk reads at helper nodes during repair, and error detection and correction.

Enabling node repair in any erasure code for distributed storage

Erasure codes are an efficient means of storing data across a network in comparison to data replication, as they tend to reduce the amount of data stored in the network and offer increased resilience in the presence of node failures. The codes perform poorly though, when repair of a failed node is called for, as they typically require the entire file to be downloaded to repair a failed node. A new class of erasure codes, termed as regenerating codes were recently introduced, that do much better in this respect. However, given the variety of efficient erasure codes available in the literature, there is considerable interest in the construction of coding schemes that would enable traditional erasure codes to be used, while retaining the feature that only a fraction of the data need be downloaded for node repair. In this paper, we present a simple, yet powerful, framework that does precisely this. Under this framework, the nodes are partitioned into two types and encoded using two codes in a manner that reduces the problem of node-repair to that of erasure-decoding of the constituent codes. Depending upon the choice of the two codes, the framework can be used to avail one or more of the following advantages: simultaneous minimization of storage space and repair-bandwidth, low complexity of operation, fewer disk reads at helper nodes during repair, and error detection and correction.

Correlation between enhanced lattice polarizability and high piezoelectric response in BiScO3-PbTiO3

Piezoelectric and ex situ electric-field induced structural studies were carried out on closely spaced compositions in the morphotropic phase boundary region of (1 - x) PbTiO3-(x)BiScO3. While the common approach of zero field structural analysis failed to provide a unique relationship between the anomalous piezoresponse of x = 0.3725 and structural factor(s), ex situ study of electric-field induced structural changes revealed that the composition exhibiting the highest piezoelectric response is the one which also exhibits significantly enhanced polarizability of the lattices of both coexisting (monoclinic and tetragonal) phases. The enhanced lattice polarizability manifests as a significant fraction of the monoclinic phase transforming irreversibly to the tetragonal phase after electric poling. DOI: 10.1103/PhysRevB.87.064106

Clinical phenotype and the lack of mutations in the CHRNG, CHRND, and CHRNA1 genes in two Indian families with Escobar syndrome

The objective of this study was to report the clinical phenotype and genetic analysis of two Indian families with Escobar syndrome (ES). The diagnosis of ES in both families was made on the basis of published clinical features. Blood samples were collected from members of both families and used in genomic DNA isolation. The entire coding regions and intron-exon junctions of the ES gene CHRNG (cholinergic receptor, nicotinic, gamma), and two other related genes, CHRND and CHRNA1, were amplified and sequenced to search for mutations in both families. Both families show a typical form of ES. Sequencing of the entire coding regions including the intron-exon junctions of the three genes did not yield any mutations in these families. In conclusion, it is possible that the mutations in these genes are located in the promoter or deep intronic regions that we failed to identify or the ES in these families is caused by mutations in a different gene. The lack of mutations in CHRNG has also been reported in several families, suggesting the possibility of at least one more gene for this syndrome. Clin Dysmorphol 22:54-58 (C) 2013 Wolters Kluwer Health vertical bar Lippincott Williams & Wilkins.

Accelerated multistress aging of polymer nanocomposites and its condition monitoring

In recent years, the time dependant maintenance of expensive high voltage power equipments is getting replaced by condition based maintenance so as to detect apriori an impending failure of the equipment. For condition based maintenance, most monitoring systems concentrate on the electrical quantities such as measurement and evaluation of partial discharges, tan delta, tip-up test, dielectric strength, insulation resistance, polarization and depolarization current. However, in the case of equipments being developed with novel nanodielectric insulating materials, the variation in these parameters before an impending failure is not available. Hence in this work, accelerated electrothermal aging studies have been conducted on unfilled epoxy as well as epoxy nanocomposite samples of 5 wt% filler loading, and the tan d values were continuously monitored to obtain the condition of the samples under study. It was observed that those samples whose tan d increased at a rapid rate failed first.

Synthesis and characterisation of novel alkoxycyanobiphenyl-substituted rufigallols

Microwave-assisted synthesis of novel alkoxycyanobiphenyl-substituted rufigallols are reported by systematically replacing one, two, four, five or six cyanobiphenyl-tethered alkoxy chains. The synthesis of the target compounds was challenging since classical reactions failed to produce these hybrids. Chemical structures of the hybrids were determined by H-1 nuclear magnetic resonance (NMR), C-13 NMR, infrared, ultraviolet spectroscopy and elemental analysis. The thermotropic liquid crystalline properties of the new compounds were investigated by polarising optical microscopy, differential scanning calorimetry and X-ray diffractometry.

N-Terminal disordered domain of saccharomyces cerevisiae Hop1 protein Is dispensable for DNA binding, bridging, and synapsis of double-stranded DNA molecules but is ecessary for spore formation

The cytological architecture of the synaptonemal complex (SC), a meiosis-specific proteinaceous structure, is evolutionarily conserved among eukaryotes. However, little is known about the biochemical properties of SC components or the mechanisms underlying their roles in meiotic chromosome synapsis and recombination. Functional analysis of Saccharomyces cerevisiae Hop1, a key structural component of SC, has begun to reveal important insights into its function in interhomolog recombination. Previously, we showed that Hop1 is a structure-specific DNA-binding protein, exhibits higher binding affinity for the Holliday junction, and induces structural distortion at the core of the junction. Furthermore, Hop1 promotes DNA condensation and intra- and intermolecular synapsis between duplex DNA molecules. Here, we show that Hop1 possesses a modular domain organization, consisting of an intrinsically disordered N-terminal domain and a protease-resistant C-terminal domain (Hop1CTD). Furthermore, we found that Hop1CTD exhibits strong homotypic as well as heterotypic protein protein interactions, and its biochemical activities were similar to those of the full-length Hop1 protein. However, Hop1CTD failed to complement the meiotic recombination defects of the Delta hop1 strain, indicating that both N- and C-terminal domains of Hop1 are essential for meiosis and spore formation. Altogether, our findings reveal novel insights into the structure-function relationships of Hop1 and help to further our understanding of its role in meiotic chromosome synapsis and recombination.