Processing of DNA double-stranded breaks and intermediates of recombination and repair by saccharomyces cerevisiae Mre11 and its stimulation by Rad50, Xrs2, and Sae2 proteins

Saccharomyces cerevisiae RAD50, MRE11, and XRS2 genes are essential for telomere length maintenance, cell cycle checkpoint signaling, meiotic recombination, and DNA double-stranded break (DSB) repair via nonhomologous end joining and homologous recombination. The DSB repair pathways that draw upon Mre11-Rad50-Xrs2 subunits are complex, so their mechanistic features remain poorly understood. Moreover, the molecular basis of DSB end resection in yeast mre11-nuclease deficient mutants and Mre11 nuclease-independent activation of ATM in mammals remains unknown and adds a new dimension to many unanswered questions about the mechanism of DSB repair. Here, we demonstrate that S. cerevisiae Mre11 (ScMre11) exhibits higher binding affinity for single-over double-stranded DNA and intermediates of recombination and repair and catalyzes robust unwinding of substrates possessing a 3' single-stranded DNA overhang but not of 5' overhangs or blunt-ended DNA fragments. Additional evidence disclosed that ScMre11 nuclease activity is dispensable for its DNA binding and unwinding activity, thus uncovering the molecular basis underlying DSB end processing in mre11 nuclease deficient mutants. Significantly, Rad50, Xrs2, and Sae2 potentiate the DNA unwinding activity of Mre11, thus underscoring functional interaction among the components of DSB end repair machinery. Our results also show that ScMre11 by itself binds to DSB ends, then promotes end bridging of duplex DNA, and directly interacts with Sae2. We discuss the implications of these results in the context of an alternative mechanism for DSB end processing and the generation of single-stranded DNA for DNA repair and homologous recombination.

Performance improvement of short-length regular low-density parity-check codes with low-complexity post-processing

It is well known that extremely long low-density parity-check (LDPC) codes perform exceptionally well for error correction applications, short-length codes are preferable in practical applications. However, short-length LDPC codes suffer from performance degradation owing to graph-based impairments such as short cycles, trapping sets and stopping sets and so on in the bipartite graph of the LDPC matrix. In particular, performance degradation at moderate to high E-b/N-0 is caused by the oscillations in bit node a posteriori probabilities induced by short cycles and trapping sets in bipartite graphs. In this study, a computationally efficient algorithm is proposed to improve the performance of short-length LDPC codes at moderate to high E-b/N-0. This algorithm makes use of the information generated by the belief propagation (BP) algorithm in previous iterations before a decoding failure occurs. Using this information, a reliability-based estimation is performed on each bit node to supplement the BP algorithm. The proposed algorithm gives an appreciable coding gain as compared with BP decoding for LDPC codes of a code rate equal to or less than 1/2 rate coding. The coding gains are modest to significant in the case of optimised (for bipartite graph conditioning) regular LDPC codes, whereas the coding gains are huge in the case of unoptimised codes. Hence, this algorithm is useful for relaxing some stringent constraints on the graphical structure of the LDPC code and for developing hardware-friendly designs.

Microstructure and texture evolution during sub-transus thermomechanical processing of Ti-6Al-4V-0.1B alloy: part I. hot rolling in (alpha plus beta) phase field

In the current study, the evolution of microstructure and texture has been studied for Ti-6Al-4V-0.1B alloy during sub-transus thermomechanical processing. This part of the work deals with the deformation response of the alloy by rolling in the (alpha + beta) phase field. The (alpha + beta) annealing behavior of the rolled specimen is communicated in part II. Rolled microstructures of the alloys exhibit either kinked or straight alpha colonies depending on their orientations with respect to the principal rolling directions. The Ti-6Al-4V-0.1B alloy shows an improved rolling response compared with the alloy Ti-6Al-4V because of smaller alpha lamellae size, coherency of alpha/beta interfaces, and multiple slip due to orientation factors. Accelerated dynamic globularization for this alloy is similarly caused by the intralamellar transverse boundary formation via multiple slip and strain accumulation at TiB particles. The (0002)(alpha) pole figures of rolled Ti-6Al-4V alloy shows ``TD splitting'' at lower rolling temperatures because of strong initial texture. Substantial beta phase mitigates the effect of starting texture at higher temperature so that ``RD splitting'' characterizes the basal pole figure. Weak starting texture and easy slip transfer for Ti-6Al-4V-0.1B alloy produce simultaneous TD and RD splittings in basal pole figures at all rolling temperatures.

Microstructure and texture evolution during sub-transus thermo-mechanical processing of Ti-6Al-4V-0.1B alloy: part II. static annealing in (alpha plus beta) regime

The first part of this study describes the evolution of microstructure and texture in Ti-6Al-4V-0.1B alloy during sub-transus rolling vis-A -vis the control alloy Ti-6Al-4V. In the second part, the static annealing response of the two alloys at self-same conditions is compared and the principal micromechanisms are analyzed. Faster globularization kinetics has been observed in the Ti-6Al-4V-0.1B alloy for equivalent annealing conditions. This is primarily attributed to the alpha colonies, which leads to easy boundary splitting via multiple slip activation in this alloy. The other mechanisms facilitating lamellar to equiaxed morphological transformations, e.g., termination migration and cylinderization, also start early in the boron-modified alloy due to small alpha colony size, small aspect ratio of the alpha lamellae, and the presence of TiB particles in the microstructure. Both the alloys exhibit weakening of basal fiber (ND||aOE (c) 0001 >) and strengthening of prism fiber (RD||aOE (c) aOE(a)) upon annealing. A close proximity between the orientations of fully globularized primary alpha and secondary alpha phases during alpha -> beta -> alpha transformation has accounted for such a texture modification.

Processing of enriched elemental boron (B-10 similar to 65 at. %)

Procedures were developed for purification and processing of electrodeposited enriched boron powder for control rod application in India's first commercial Proto Type Fast Breeder Reactor (PFBR). Methodology for removal of anionic (F-, Cl-, BF4-) and cationic (Fe2+, Fe3+, Ni2+) impurities was developed. Parameters for grinding boron flakes obtained after electrodeposition were optimized to obtain the boron powder having particle size less than 100 gm. The rate of removal of impurities was studied with respect to time and concentration of the reagents used for purification. Process parameters for grinding and removal of impurities were optimized. A flowsheet was proposed which helps in minimizing the purification time and concentration of the reagent used for the effective removal of impurities. The purification methodology developed in this work could produce boron that meets the technical specifications for control rod application in a fast reactor.

Developments in Biotechnology for Environmentally Benign Iron Ore Beneficiation

Biomineralization and biogenesis of iron ore deposits are illustrated in relation to indigenous microorganisms inhabiting iron ore mines. Aerobic and anaerobic microorganisms indigenous to iron oxide mineralization are analyzed. Microbially-induced flotation and flocculation of iron ore minerals such as hematite, alumina, calcite and quartz are discussed with respect to use of four types of microorganisms, namely, Paenibacillus polymyxa, Bacillus subtilis, Saccharomyces cerevisiae and Desulfovibrio desulfuricans. The role of the above organisms in the removal of silica, alumina, clays and apatite from hematite is illustrated with respect to mineral-specific bioreagents, surface chemical changes and microbe-mineral interaction mechanisms. Silica and alumina removal from real iron ores through biobeneficiation is outlined. Environmental benefits of biobeneficiation are demonstrated with respect to biodegradation of toxic reagents and environmentally-safe waste disposal and processing.

Data acquisition and processing at ocean bottom for a Tsunami warning system

The design and development of a Bottom Pressure Recorder for a Tsunami Early Warning System is described here. The special requirements that it should satisfy for the specific application of deployment at ocean bed and pressure monitoring of the water column above are dealt with. A high-resolution data digitization and low circuit power consumption are typical ones. The implementation details of the data sensing and acquisition part to meet these are also brought out. The data processing part typically encompasses a Tsunami detection algorithm that should detect an event of significance in the background of a variety of periodic and aperiodic noise signals. Such an algorithm and its simulation are presented. Further, the results of sea trials carried out on the system off the Chennai coast are presented. The high quality and fidelity of the data prove that the system design is robust despite its low cost and with suitable augmentations, is ready for a full-fledged deployment at ocean bed. (C) 2013 Elsevier Ltd. All rights reserved.

Microbially induced selective flotation of sphalerite from galena using mineral-adapted strains of Bacillus megaterium

The selective flotation of sphalerite from a sphalerite-galena mineral mixture has been achieved using cells and extracellular secretions of Bacillus megaterium after adaptation to the chosen minerals. The extracellular secretions obtained after thermolysis of bacterial cells adapted to sphalerite yield the highest flotation recovery of sphalerite with a selectivity index value of 24.5, in comparison to the other cellular and extra-cellular bio-reagents studied. The protein profile for the unadapted and mineral-adapted cells has been found to differ distinctly, attesting to variation in the yield and nature of extra-cellular polymeric substances (EPS). The changes induced in the bacterial cell wall components after adaptation to sphalerite or galena with respect to the contents of phosphate, uronic acid and acetylated sugars of B. megaterium have been quantified. The role of the dissolved metal ions from the minerals as well as that of the constituents of extracellular secretions in modulating the surface charge of the bacterial cells as well as the minerals under study has been confirmed using various enzymatic treatments of the bacterial cells. It has been demonstrated that the induction of additional molecular weight protein fractions as well as the higher amount of extracellular proteins and phosphate secreted after adaptation to sphalerite vis-A-vis galena are contributory factors for the selective separation of sphalerite from galena. (C) 2013 Elsevier B.V. All rights reserved.

Basic studies on the role of components of Bacillus megaterium as flotation biocollectors in sulphide mineral separation

Studies were carried out to assess the utility of the cellular and extracellular constituents of Bacillus megaterium for the flotation of sphalerite and galena minerals. Based on the flotation results on the individual minerals, it was observed that sphalerite was preferentially floated compared to galena. A maximum selectivity index (SI) value of 11.7 was achieved in the presence of the soluble fraction of the thermolysed cells, which was higher than that obtained with the intact cells (SI of 6.5) and the insoluble fraction of the thermolysed cells (SI of 9.6). The results of the various enzymatic treatment tests revealed that extracellular DNA played a vital role in the selective flotation of sphalerite. A noteworthy finding was that the single-stranded DNA (ssDNA) had a higher biocollector capacity vis-A -vis the double-stranded DNA (dsDNA), leading to better flotation efficiency. About 95 % recovery of sphalerite could be achieved from the mineral mixture by the combined addition of the ssDNA with the non-DNA components of the bacterial cells, resulting in a maximum SI of 19.1. Calcium and phosphate components of the nutrient media were found to be essential for better selectivity of separation of sphalerite. The mechanisms of microbe-mineral interaction are discussed.

A Communication-Theoretic Framework for 2-DMR Channel Modeling: Performance Evaluation of Coding and Signal Processing Methods

We develop a communication theoretic framework for modeling 2-D magnetic recording channels. Using the model, we define the signal-to-noise ratio (SNR) for the channel considering several physical parameters, such as the channel bit density, code rate, bit aspect ratio, and noise parameters. We analyze the problem of optimizing the bit aspect ratio for maximizing SNR. The read channel architecture comprises a novel 2-D joint self-iterating equalizer and detection system with noise prediction capability. We evaluate the system performance based on our channel model through simulations. The coded performance with the 2-D equalizer detector indicates similar to 5.5 dB of SNR gain over uncoded data.

Semisolid Processing of A380 Al Alloy Using Cooling Slope

This study is aimed toward obtaining near spherical microstructural features of Rheocast A380 aluminum alloy. Cooling slope (CS) technique has been used to generate semisolid slurry from the superheated alloy melt. Spherodization of primary grains is the heart of semisolid processing which improves mechanical properties significantly in the parts cast from semisolid state compared to the conventional casting processes. Keeping in view of the desired microstructural morphology, i.e., rosette or spherical shape of primary alpha-Al phase, successive slurry samples have been collected during melt flow and oil quenched to investigate the microstructure evolution mechanism. Conventionally cast A380 Al alloy sample shows dendritic grains surrounded by large eutectic phase whereas finer, near spherical grains have been observed within the cooling slope processed slurry and also in the solidified castings which confirms the effectiveness of semisolid processing of the alloy following cooling slope technique. Grain refiner addition into the alloy melt is found to have favorable effect which leads to the generation of finer primary grains within the slurry with higher degree of sphericity.

Capacity of Gaussian Channels With Energy Harvesting and Processing Cost

Energy harvesting sensor nodes are gaining popularity due to their ability to improve the network life time and are becoming a preferred choice supporting green communication. In this paper, we focus on communicating reliably over an additive white Gaussian noise channel using such an energy harvesting sensor node. An important part of this paper involves appropriate modeling of energy harvesting, as done via various practical architectures. Our main result is the characterization of the Shannon capacity of the communication system. The key technical challenge involves dealing with the dynamic (and stochastic) nature of the (quadratic) cost of the input to the channel. As a corollary, we find close connections between the capacity achieving energy management policies and the queueing theoretic throughput optimal policies.

Binaural Signal Processing Motivated Generalized Analytic Signal Construction and AM-FM Demodulation

Binaural hearing studies show that the auditory system uses the phase-difference information in the auditory stimuli for localization of a sound source. Motivated by this finding, we present a method for demodulation of amplitude-modulated-frequency-modulated (AM-FM) signals using a ignal and its arbitrary phase-shifted version. The demodulation is achieved using two allpass filters, whose impulse responses are related through the fractional Hilbert transform (FrHT). The allpass filters are obtained by cosine-modulation of a zero-phase flat-top prototype halfband lowpass filter. The outputs of the filters are combined to construct an analytic signal (AS) from which the AM and FM are estimated. We show that, under certain assumptions on the signal and the filter structures, the AM and FM can be obtained exactly. The AM-FM calculations are based on the quasi-eigenfunction approximation. We then extend the concept to the demodulation of multicomponent signals using uniform and non-uniform cosine-modulated filterbank (FB) structures consisting of flat bandpass filters, including the uniform cosine-modulated, equivalent rectangular bandwidth (ERB), and constant-Q filterbanks. We validate the theoretical calculations by considering application on synthesized AM-FM signals and compare the performance in presence of noise with three other multiband demodulation techniques, namely, the Teager-energy-based approach, the Gabor's AS approach, and the linear transduction filter approach. We also show demodulation results for real signals.

Effect of boron addition and processing of Ti-6Al-4V on corrosion behaviour and biocompatibility

Ti-6Al-4V is widely used to prepare biomedical implant for orthopaedic and dental applications, but it is an expensive choice relative to other implant materials such as stainless steels and Co-Cr alloys, in large part due to the high manufacturing cost. Adding boron to refine the as cast microstructure of Ti-6Al-4V can eliminate the need for extensive hot working and thereby reduce processing costs. The effect of 0.1 wt-% boron addition and the choice of processing route (forging or extrusion) was studied in the context of potential biomedical applications. Corrosion tests in simulated body fluid indicated that the presence of boron increased the corrosion rate of Ti-6Al-4V and that the increase was higher for forged alloys than for extruded alloys. Boron addition and processing route were found to have a minimal effect on the viability of osteoblasts on the alloy surfaces. It is concluded that the addition of boron could offer advantages during the processing of Ti-6Al-4V for biomedical applications.

Processing-microstructure-yield strength correlation in a near beta Ti alloy, Ti-5Al-5Mo-5V-3Cr

A combined set of thermo-mechanical steps recommended for high strength beta Ti alloy are homogenization, deformation, recrystallization, annealing and ageing steps in sequence. Recrystallization carried out above or below beta transus temperature generates either beta annealed (lath type morphology of alpha) or bimodal (lath+globular morphology of alpha) microstructure. Through variations in heat treatment parameters at these processing steps, wide ranges of length scales of features have been generated in both types of microstructures in a near beta Ti alloy, Ti-5Al-5Mo-5V-3Cr (Ti-5553). 0.2% Yield strength (YS) has been correlated to various microstructural features and associated heat treatment parameters. Relative importance of microstructural features in influencing YS has been identified. Process parameters at different steps have been identified and recommended for attaining different levels of YS for this near beta Ti alloy. (C) 2014 Elsevier B.V. All rights reserved.