Progressive structure-based alignment of homologous proteins: Adopting sequence comparison strategies

Comparison of multiple protein structures has a broad range of applications in the analysis of protein structure, function and evolution. Multiple structure alignment tools (MSTAs) are necessary to obtain a simultaneous comparison of a family of related folds. In this study, we have developed a method for multiple structure comparison largely based on sequence alignment techniques. A widely used Structural Alphabet named Protein Blocks (PBs) was used to transform the information on 3D protein backbone conformation as a ID sequence string. A progressive alignment strategy similar to CLUSTALW was adopted for multiple PB sequence alignment (mulPBA). Highly similar stretches identified by the pairwise alignments are given higher weights during the alignment. The residue equivalences from PB based alignments are used to obtain a three dimensional fit of the structures followed by an iterative refinement of the structural superposition. Systematic comparisons using benchmark datasets of MSTAs underlines that the alignment quality is better than MULTIPROT, MUSTANG and the alignments in HOMSTRAD, in more than 85% of the cases. Comparison with other rigid-body and flexible MSTAs also indicate that mulPBA alignments are superior to most of the rigid-body MSTAs and highly comparable to the flexible alignment methods. (C) 2012 Elsevier Masson SAS. All rights reserved.

Reproductive queue without overt conflict in the primitively eusocial wasp Ropalidia marginata

Colonies of the primitively eusocial wasp Ropalidia marginata consist of a single egg layer (queen) and a number of non-egg-laying workers. Although the queen is a docile individual, not at the top of the behavioral dominance hierarchy of the colony, she maintains complete reproductive monopoly. If the queen is lost or removed, one and only one of the workers potential queen (PQ)] becomes hyperaggressive and will become the next queen of the colony. The PQ is almost never challenged because she first becomes hyperaggressive and then gradually loses her aggression, develops her ovaries, and starts laying eggs. Although we are unable to identify the PQ when the queen is present, she appears to be a ``cryptic heir designate.'' Here, we show that there is not just one heir designate but a long reproductive queue and that PQs take over the role of egg-laying, successively, without overt conflict, as the queen or previous PQs are removed. The dominance rank of an individual is not a significant predictor of its position in the succession hierarchy. The age of an individual is a significant predictor, but it is not a perfect predictor because PQs often bypass older individuals to become successors. We suggest that such a predesignated reproductive queue that is implemented without overt conflict is adaptive in the tropics, where conspecific usurpers from outside the colony, which can take advantage of the anarchy prevailing in a queenless colony and invade it, are likely to be present throughout the year.

Decentralised carbon footprint analysis for opting climate change mitigation strategies in India

Carbon footprint (CF) refers to the total amount of carbon dioxide and its equivalents emitted due to various anthropogenic activities. Carbon emission and sequestration inventories have been reviewed sector-wise for all federal states in India to identify the sectors and regions responsible for carbon imbalances. This would help in implementing appropriate climate change mitigation and management strategies at disaggregated levels. Major sectors of carbon emissions in India are through electricity generation, transport, domestic energy consumption, industries and agriculture. A majority of carbon storage occurs in forest biomass and soil. This paper focuses on the statewise carbon emissions (CO2. CO and CH4), using region specific emission factors and statewise carbon sequestration capacity. The estimate shows that CO2, CO and CH4 emissions from India are 965.9, 22.5 and 16.9 Tg per year, respectively. Electricity generation contributes 35.5% of total CO2 emission, which is followed by the contribution from transport. Vehicular transport exclusively contributes 25.5% of total emission. The analysis shows that Maharashtra emits higher CO2, followed by Andhra Pradesh, Uttar Pradesh, Gujarat, Tamil Nadu and West Bengal. The carbon status, which is the ratio of annual carbon storage against carbon emission, for each federal state is computed. This shows that small states and union territories (UT) like Arunachal Pradesh, Mizoram and Andaman and Nicobar Islands, where carbon sequestration is higher due to good vegetation cover, have carbon status > 1. Annually, 7.35% of total carbon emissions get stored either in forest biomass or soil, out of which 34% is in Arunachal Pradesh, Madhya Pradesh, Chhattisgarh and Orissa. (C) 2012 Elsevier Ltd. All rights reserved.

Strategies for the Synthesis of Graphene, Graphene Nanoribbons, Nanoscrolls and Related Materials

Single-layer graphene (SLG), the 3.4 angstrom thick two-dimensional sheet of sp(2) carbon atoms, was first prepared in 2004 by mechanical exfoliation of graphite crystals using the scotch tape technique. Since then, SLG has been prepared by other physical methods such as laser irradiation or ultrasonication of graphite in liquid media. Chemical methods of synthesis of SLG are more commonly used; the most popular involves preparation of single-layer graphene oxide followed by reduction with a stable reagent, often assisted by microwave heating. This method yields single-layer reduced graphene oxide. Other methods for preparing SLG include chemical vapour deposition over surfaces of transition metals such as Ni and Cu. Large-area SLG has also been prepared by epitaxial growth over SIC. Few-layer graphene (FLG) is prepared by several methods; arc discharge of graphite in hydrogen atmosphere being the most convenient. Several other methods for preparing FLG include exfoliation of graphite oxide by rapid heating, ultrasonication or laser irradiation of graphite in liquid media, reduction of few-layer graphene oxide, alkali metal intercalation followed by exfoliation. Graphene nanoribbons, which are rectangular strips of graphene, are best prepared by the unzipping of carbon nanotubes by chemical oxidation or laser irradiation. Many graphene analogues of inorganic materials such as MoS2, MoSe2 and BN have been prepared by mechanical exfoliation, ultrasonication and by chemical methods involving high-temperature or hydrothermal reactions and intercalation of alkali metals followed by exfoliation. Scrolls of graphene are prepared by potassium intercalation in graphite or by microwave irradiation of graphite immersed in liquid nitrogen.

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.

Performance of a class of multi-robot deploy and search strategies based on centroidal voronoi configurations

This article considers a class of deploy and search strategies for multi-robot systems and evaluates their performance. The application framework used is deployment of a system of autonomous mobile robots equipped with required sensors in a search space to gather information. The lack of information about the search space is modelled as an uncertainty density distribution. The agents are deployed to maximise single-step search effectiveness. The centroidal Voronoi configuration, which achieves a locally optimal deployment, forms the basis for sequential deploy and search (SDS) and combined deploy and search (CDS) strategies. Completeness results are provided for both search strategies. The deployment strategy is analysed in the presence of constraints on robot speed and limit on sensor range for the convergence of trajectories with corresponding control laws responsible for the motion of robots. SDS and CDS strategies are compared with standard greedy and random search strategies on the basis of time taken to achieve reduction in the uncertainty density below a desired level. The simulation experiments reveal several important issues related to the dependence of the relative performances of the search strategies on parameters such as the number of robots, speed of robots and their sensor range limits.

Simplified implementation of space vector PWM strategies for a three level inverter

Space vector based PWM strategies for three-level inverters have a broader choice of switching sequences to generate the required reference vector than triangle comparison based PWM techniques. However, space vector based PWM involves numerous steps which are computationally intensive. A simplified algorithm is proposed here, which is shown to reduce the computation time significantly. The developed algorithm is used to implement synchronous and asynchronous conventional space vector PWM, synchronized modified space vector PWM and an asynchronous advanced bus-clamping PWM technique on a low-cost dsPIC digital controller. Experimental results are presented for a comparative evaluation of the performance of different PWM methods.

When good neighbors don't need fences: temporal landscape partitioning among baboon social groups

Intraspecific competition is a key factor shaping space-use strategies and movement decisions in many species, yet how and when neighbors utilize shared areas while exhibiting active avoidance of one another is largely unknown. Here, we investigated temporal landscape partitioning in a population of wild baboons (Papio cynocephalus). We used global positioning system (GPS) collars to synchronously record the hourly locations of five baboon social groups for similar to 900 days, and we used behavioral, demographic, and life history data to measure factors affecting use of overlap areas. Annual home ranges of neighboring groups overlapped substantially, as predicted (baboons are considered non-territorial), but home ranges overlapped less when space use was assessed over shorter time scales. Moreover, neighboring groups were in close spatial proximity to one another on fewer days than predicted by a null model, suggesting an avoidance-based spacing pattern. At all time scales examined (monthly, biweekly, and weekly), time spent in overlap areas was greater during time periods when groups fed on evenly dispersed, low-quality foods. The percent of fertile females in social groups was negatively correlated with time spent in overlap areas only during weekly time intervals. This suggests that broad temporal changes in ecological resources are a major predictor of how intensively overlap areas are used, and groups modify these ecologically driven spacing patterns at short time scales based on female reproductive status. Together, these findings offer insight into the economics of territoriality by highlighting the dynamics of spacing patterns at differing time scales.

Antelope mating strategies facilitate invasion of grasslands by a woody weed

Intra and interspecific variation in frugivore behaviour can have important consequences for seed dispersal outcomes. However, most information comes from among-species comparisons, and within-species variation is relatively poorly understood. We examined how large intraspecific differences in the behaviour of a native disperser, blackbuck antelope Antilope cervicapra, influence dispersal of a woody invasive, Prosopis juliflora, in a grassland ecosystem. Blackbuck disperse P. juliflora seeds through their dung. In lekking blackbuck populations, males defend clustered or dispersed mating territories. Territorial male movement is restricted, and within their territories males defecate on dung-piles. In contrast, mixed-sex herds range over large areas and do not create dung-piles. We expected territorial males to shape seed dispersal patterns, and seed deposition and seedling recruitment to be spatially localized. Territorial males had a disproportionately large influence on seed dispersal. Adult males removed twice as much fruit as females, and seed arrival was disproportionately high on territories. Also, because lek-territories are clustered, seed arrival was spatially highly concentrated. Seedling recruitment was also substantially higher on territories compared with random sites, indicating that the local concentration of seeds created by territorial males continued into high local recruitment of seedlings. Territorial male behaviour may, thus, result in a distinct spatial pattern of invasion of grasslands by the woody P. juliflora. An ex situ experiment showed no beneficial effect of dung and a negative effect of light on seed germination. We conclude that large intraspecific behavioural differences within frugivore populations can result in significant variation in their effectiveness as seed dispersers. Mating strategies in a disperser could shape seed dispersal, seedling recruitment and potentially plant distribution patterns. These mating strategies may aid in the spread of invasives, such as P. juliflora, which could, in turn, negatively influence the behaviour and ecology of native dispersers.

Optimal incentive timing strategies for product marketing on social networks

We consider the problem of devising incentive strategies for viral marketing of a product. In particular, we assume that the seller can influence penetration of the product by offering two incentive programs: a) direct incentives to potential buyers (influence) and b) referral rewards for customers who influence potential buyers to make the purchase (exploit connections). The problem is to determine the optimal timing of these programs over a finite time horizon. In contrast to algorithmic perspective popular in the literature, we take a mean-field approach and formulate the problem as a continuous-time deterministic optimal control problem. We show that the optimal strategy for the seller has a simple structure and can take both forms, namely, influence-and-exploit and exploit-and-influence. We also show that in some cases it may optimal for the seller to deploy incentive programs mostly for low degree nodes. We support our theoretical results through numerical studies and provide practical insights by analyzing various scenarios.

Estimating the fraction of progeny virions that must incorporate APOBEC3G for suppression of productive HIV-1 infection

The contest between the host factor APOBEC3G (A3G) and the HIV-1 protein Vif presents an attractive target of intervention. The extent to which the A3G-Vif interaction must be suppressed to tilt the balance in favor of A3G remains unknown. We employed stochastic simulations and mathematical modeling of the within-host dynamics and evolution of HIV-1 to estimate the fraction of progeny virions that must incorporate A3G to render productive infection unsustainable. Using three different approaches, we found consistently that a transition from sustained infection to suppression of productive infection occurred when the latter fraction exceeded similar to 0.8. The transition was triggered by A3G-induced hypermutations that led to premature stop codons compromising viral production and was consistent with driving the basic reproductive number, R-o, below unity. The fraction identified may serve as a quantitative guideline for strategies targeting the A3G-Vif axis. (C) 2013 Elsevier Inc. All rights reserved.

Strategies for high efficiency and stability in biogas-fuelled small engines

This work assesses the performance of small biogas-fuelled engines and explores high-efficiency strategies for power generation in the very low power range of less than 1000 W. Experiments were performed on a small 95-cc, single-cylinder, four-stroke spark-ignition engine operating on biogas. The engine was operated in two modes, i.e., `premixed' and `fuel injection' modes, using both single and dual spark plug configurations. Measurements of in-cylinder pressure, crank angle, brake power, air and fuel flow rates, and exhaust emissions were conducted. Cycle-to-cycle variations in engine in-cylinder pressure and power were also studied and assessed quantitatively for various loading conditions. Results suggest that biogas combustion can be fairly sensitive to the ignition strategies thereby affecting the power output and efficiency. Further, results indicate that continuous fuel injection shows superior performance compared to the premixed case especially at low loads owing to possible charge stratification in the engine cylinder. Overall, this study has demonstrated for the first time that a combination of technologies such as lean burn, fuel injection, and dual spark plug ignition can provide highly efficient and stable operation in a biogas-fuelled small S.I. engine, especially in the low power range of 450-1000W. (C) 2014 Elsevier Inc. All rights reserved.