Improved Detection of Remote Homologues Using Cascade PSI-BLAST: Influence of Neighbouring Protein Families on Sequence Coverage

Background: Development of sensitive sequence search procedures for the detection of distant relationships between proteins at superfamily/fold level is still a big challenge. The intermediate sequence search approach is the most frequently employed manner of identifying remote homologues effectively. In this study, examination of serine proteases of prolyl oligopeptidase, rhomboid and subtilisin protein families were carried out using plant serine proteases as queries from two genomes including A. thaliana and O. sativa and 13 other families of unrelated folds to identify the distant homologues which could not be obtained using PSI-BLAST. Methodology/Principal Findings: We have proposed to start with multiple queries of classical serine protease members to identify remote homologues in families, using a rigorous approach like Cascade PSI-BLAST. We found that classical sequence based approaches, like PSI-BLAST, showed very low sequence coverage in identifying plant serine proteases. The algorithm was applied on enriched sequence database of homologous domains and we obtained overall average coverage of 88% at family, 77% at superfamily or fold level along with specificity of similar to 100% and Mathew's correlation coefficient of 0.91. Similar approach was also implemented on 13 other protein families representing every structural class in SCOP database. Further investigation with statistical tests, like jackknifing, helped us to better understand the influence of neighbouring protein families. Conclusions/Significance: Our study suggests that employment of multiple queries of a family for the Cascade PSI-BLAST searches is useful for predicting distant relationships effectively even at superfamily level. We have proposed a generalized strategy to cover all the distant members of a particular family using multiple query sequences. Our findings reveal that prior selection of sequences as query and the presence of neighbouring families can be important for covering the search space effectively in minimal computational time. This study also provides an understanding of the `bridging' role of related families.

Micro-blast waves using detonation transmission tubing

Micro-blast waves emerging from the open end of a detonation transmission tube were experimentally visualized in this study. A commercially available detonation transmission tube was used (Nonel tube, M/s Dyno Nobel, Sweden), which is a small diameter tube coated with a thin layer of explosive mixture (HMX traces of Al) on its inner side. The typical explosive loading for this tube is of the order of 18 mg/m of tube length. The blast wave was visualized using a high speed digital camera (frame rate 1 MHz) to acquire time-resolved schlieren images of the resulting flow field. The visualization studies were complemented by computational fluid dynamic simulations. An analysis of the schlieren images showed that although the blast wave appears to be spherical, it propagates faster along the tube axis than along a direction perpendicular to the tube axis. Additionally, CFD analysis revealed the presence of a barrel shock and Mach disc, showing structures that are typical of an underexpanded jet. A theory in use for centered large-scale explosions of intermediate strength gave good agreement with the blast trajectory along the tube axis. The energy of these micro-blast waves was found to be J and the average TNT equivalent was found to be . The repeatability in generating these micro-blast waves using the Nonel tube was very good and this opens up the possibility of using this device for studying some of the phenomena associated with muzzle blasts in the near future.

Modelling of metal-slag emulsion

Many industrial processes involve reaction between the two immiscible liquid systems. It is very important to increase the efficiency and productivity of such reactions. One of the important processes that involve such reactions is the metal-slag system. To increase the reaction rate or efficiency, one must increase the contact surface area of one of the phases. This is either done by emulsifying the slag into the metal phase or the metal into the slag phase. The latter is preferred from the stability viewpoint. Recently, we have proposed a simple and elegant mathematical model to describe metal emulsification in the presence of bottom gas bubbling. The same model is being extended here. The effect of slag and metal phase viscosity, density and metal droplet size on the metal droplet velocity in the slag phase is discussed for the above mentioned metal emulsification process. The models results have been compared with experimental data.

Some implications of the volcanic theophany of YHWH on his primeval identity

Abstract: YHWH’s theophany and mode of action are frequently evoked in the Bible as a volcanic event. It is shown here that this representation, of central importance in the story of the Sinai Covenant, is probably not anchored in any specific volcanic eruption experienced by the Israelites in the past. In Antiquity, volcanic activity was specifically associated with the gods who patronized metallurgy, given the homology between lava flowing from a volcano and slag released from a furnace at smelting. Evidence towards such a link is also identified in the Bible. Accordingly, rather than being simply a literary artifice imaging the outstanding powers of YHWH, volcanism may reflect the existence of metallurgical roots in Israelite theology. This contention is supported by Biblical evidences associating YHWH with metal production: (i) his primeval dominion in mining areas, (ii) his special worship by metalworkers, (iii) the representation of his celestial universe as a giant furnace. It is concluded that the volcanic representation of YHWH’s theophany and mode of action reveal a surprising level of preservation of the metallurgic religious traditions in the ancient Israelite theology.

Optimization of Air Staging In A 1 Mw Tangentially Fired Pulverized Coal Furnace

This paper deals with an experimental study of air staging in a 1 MW (heat input power) tangentially fired pulverized coal furnace. The influences of several variables associated with air staging on NOx reduction efficiency and unburned carbon in fly ash were investigated, and these variables included the air stoichiometric ratio of primary combustion zone (SR1), the locations of over-fire air nozzles along furnace height, and the ratio of coal concentration of the fuel-rich stream to that of the fuel-lean one (RRL) in primary air nozzle. The experimental results indicate that SR1 and RRL have optimum values for NOx reduction, and the two optimum values are 0.85 and 3:1, respectively. NO, reduction efficiency monotonically increases with the increase of OFA nozzle location along furnace height. On the optimized operating conditions of air staging, NOx reduction efficiency can attain 47%. Although air staging can effectively reduce NOx emission, the increase of unburned carbon in fly ash should be noticed. (C) 2008 Elsevier B.V. All rights reserved.

Effect of coal-over-coal reburn on furnace temperature and heat flux distributions in 1 MW tangentially fired furnace

The furnace temperature and heat flux distributions of 1 MW tangentially fired furnace were studied during coal-over-coal reburn, and the influences of the position of reburn nozzle and reburn fuel fraction on furnace temperature and heat flux distributions were investigated. Compared with the baseline, the flue gas temperature is 70–90 C lower in primary combustion and 130–150 C higher at furnace exit, and the variations of the flue gas temperature distributions along furnace height are slower. The temperature distribution along the width of furnace wall decreases with the increase of the relative furnace height. In the primary combustion zone and the reburn zone, the temperature and heat flux distributions of furnace wall are much non-uniform and asymmetric along the width of furnace wall, those of furnace wall in the burnout zone are relatively uniform, and the temperature non-uniformity coefficients of the primary combustion zone, the reburn zone and the burnout zone are 0.290, 0.100 and 0.031, respectively.

The formation mechanism of low leaching glassy slag during plasma arc vitrification treatment of fly ash

In this paper, the glass formation theory is applied to study the formation mechanism of the low leaching glassy slag during the process of plasma waste treatment. The research shows that SiO2 acts as network former to form a 3-dimensional Si-O tetrahedral network in which heavy metals are bonded or encapsulated, so the Si-O tetrahedron protect heavy metals against leaching from the vitrified slag or acid corrosion. For given chemical compositions of waste, the formation ability of the vitrified slag can be represented by the ratio of the whole oxygen ions to the whole network former ions in glass (O/Si) which is appropriate in the range of 2~3. A plasma arc reactor is used to conduct the vitrification experiments of two kinds of fly ashes with additives in which effects of various parameters including arc power, cooling speed, treatment temperature are studied. The chemical compositions of fly ashes are analyzed by X-ray fluorescence (XRF) spectrometry. The experimental results show that both cooling speed and O/Si have important influence on the formation of the vitrified slag, which is qualitatively in accordance with the predictions of the glass formation theory.

THE FORMATION MECHANISM OF THE VITRIFIED SLAG IN A PLASMA ARC REACTOR FOR HAZARDOUS WASTE TREATMENT

Various hazardous wastes with additives have been vitrified to investigate the formation mechanism of the glassy slag by a 30 kW DC plasma-arc reactor developed by the Institute of Mechanics, Chinese Academy of Sciences. The average temperature in the reaction area is controlled at 1500°C. The chemical compositions of three sorts of fly ashes are analyzed by XRF (X-Ray Fluorescence). Fly ashes with vitrifying additives can be vitrified to form glassy slag, which show that the ratio of the whole oxygen ions to the whole network former ions in glass (R) is appropriate in the range of 2~3 to form durable vitrified slag. In this experiment, the arc power is controlled below 5 kW to inhibit waste evaporation. To enhance the effects of heat transfer to wastes, ferrous powder has been added into the graphite crucible, which aggregates as ingot below the molten silicate after vitrification. The slag fails to form glass if the quenching rate is less than 1 K/min. Therefore, the slag will break into small chips due to the sharp quenching rate, which is more than 100 K/sec.

Reutilización de escoria negra de acería como soporte en biofiltros para la eliminación de H2S del biogás.

[EN]Due to the limitations associated with fossil fuels it is necessary to promote energy sources that are renewable as well as eco-friendly, such as biogas generated in anaerobic digesters. The biogas, composed principally of methane and CO2, is the result of the biodegradation of organic matter under anaerobic conditions. Its use as fuel is limited by the presence of minority compounds such as hydrogen sulphide (H2S); therefore, its pre-treatment is necessary. Currently there are various technologies for the removal of H2S from a gas stream, but most of them are based on physic-chemical treatments which have a number of drawbacks as reactive consumption, generation of secondary flows, etc. Biofiltration has been used as an efficient and low cost alternative to conventional purification processes, and excellent results for the degradation of H2S have been obtained. However process can be limited due to the progressive ageing of the support material, along with the loss of nutrients and other specific characteristics necessary for the good development of biomass. The purpose of this project is to develop a mixed support consisting of a mixture of an organic material and an inorganic support for its application in the removal of the H2S from biogas. This support material helps to optimize the characteristics of the bed and extend its lifespan. The development of such material will contribute to the implementation of biofiltration for treating biogas from anaerobic digesters for its use as biofuel. The inorganic material used is electric arc furnace (EAF) black slag, a by-product generated in large quantities in the production of steel in the Basque Country. Although traditionally the slag has been used in civil engineering, its physicochemical characteristics make it suitable for reuse as a filter medium in biofiltration. The main conclusion drawn from the experimental results is that EAF black slag is a suitable co-packing material in organic biofilters treating H2S-polluted gaseous streams. High pollutant removal rates have been achieved during the whole experimental period. The removal capacity recorded in biofilters with less inorganic material was higher than in those with higher slag portion. Nevertheless, all the biofilters have shown a satisfactory response even at high inlet loads (48 g·m-3·h-1), where the RE has not decreased over 82%.