Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 angstrom resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis, for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting beta-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

Relation between sedimentary framework and hydrogeology in the Guarani Aquifer System in Sao Paulo state, Brazil

This paper presents the results of a new investigation of the Guarani Aquifer System (SAG) in Sao Paulo state. New data were acquired about sedimentary framework, flow pattern, and hydrogeochemistry. The flow direction in the north of the state is towards the southwest and not towards the west as expected previously. This is linked to the absence of SAG outcrop in the northeast of Sao Paulo state. Both the underlying Piramboia Formation and the overlying Botucatu Formation possess high porosity (18.9% and 19.5%, respectively), which was not modified significantly by diagenetic changes. Investigation of sediments confirmed a zone of chalcedony cement close to the SAG outcrop and a zone of calcite cement in the deep confined zone. The main events in the SAG post-sedimentary history were: (1) adhesion of ferrugineous coatings on grains, (2) infiltration of clays in eodiagenetic stage, (3) regeneration of coatings with formation of smectites, (4) authigenic overgrowth of quartz and K-feldspar in advanced eodiagenetic stage, (5) bitumen cementation of Piramboia Formation in mesodiagenetic stage, (6) cementation by calcite in mesodiagenetic and telodiagenetic stages in Piramboia Formation, (7) formation of secondary porosity by dissolution of unstable minerals after appearance of hydraulic gradient and penetration of the meteoric water caused by the uplift of the Serra do Mar coastal range in the Late Cretaceous, (8) authigenesis of kaolinite and amorphous silica in unconfined zone of the SAG and cation exchange coupled with the dissolution of calcite at the transition between unconfined and confined zone, and (9) authigenesis of analcime in the confined SAG zone. The last two processes are still under operation. The deep zone of the SAG comprises an alkaline pH, Na-HCO(3) groundwater type with old water and enriched delta(13)C values (<-3.9), which evolved from a neutral pH, Ca-HCO(3) groundwater type with young water and depleted delta(13)C values (>-18.8) close to the SAG outcrop. This is consistent with a conceptual geochemical model of the SAG, suggesting dissolution of calcite driven by cation exchange, which occurs at a relatively narrow front recently moving downgradient at much slower rate compared to groundwater flow. More depleted values of delta(18)O in the deep confined zone close to the Parana River compared to values of relative recent recharged water indicate recharge occur during a period of cold climate. The SAG is a ""storage-dominated"" type of aquifer which has to be managed properly to avoid its overexploitation. (C) 2011 Elsevier Ltd. All rights reserved.

Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts

Schistosoma mansoni is a well-adapted blood-dwelling parasitic helminth, persisting for decades in its human host despite being continually exposed to potential immune attack. Here, we describe in detail micro-exon genes (MEG) in S. mansoni, some present in multiple copies, which represent a novel molecular system for creating protein variation through the alternate splicing of short (<= 36 bp) symmetric exons organized in tandem. Analysis of three closely related copies of one MEG family allowed us to trace several evolutionary events and propose a mechanism for micro-exon generation and diversification. Microarray experiments show that the majority of MEGs are up-regulated in life cycle stages associated with establishment in the mammalian host after skin penetration. Sequencing of RT-PCR products allowed the description of several alternate splice forms of micro-exon genes, highlighting the potential use of these transcripts to generate a complex pool of protein variants. We obtained direct evidence for the existence of such pools by proteomic analysis of secretions from migrating schistosomula and mature eggs. Whole-mount in situ hybridization and immunolocalization showed that MEG transcripts and proteins were restricted to glands or epithelia exposed to the external environment. The ability of schistosomes to produce a complex pool of variant proteins aligns them with the other major groups of blood parasites, but using a completely different mechanism. We believe that our data open a new chapter in the study of immune evasion by schistosomes, and their ability to generate variant proteins could represent a significant obstacle to vaccine development.

A study of slag corrosion of oxides and oxide-carbon refractories during steel refining

The use of ceramic material as refractories in the manufacturing industry is a common practice worldwide. During usage, for example in the production of steel, these materials do experience severe working conditions including high temperatures, low pressures and corrosive environments. This results in lowered service lives and high consumptions of these materials. This, in turn, affects the productivity of the whole steel plant and thereby the cost. In order to investigate how the service life can be improved, studies have been carried out for refractories used in the inner lining of the steel ladles. More specifically, from the slag zone, where the corrosion is most severe. By combining thermodynamic simulations, plant trails and post-mortem studies of the refractories after service, vital information about the behaviour of the slagline refractories during steel refining and the causes of the accelerated wear in this ladle area has been achieved. The results from these studies show that the wear of the slagline refractories of the ladle is initiated at the preheating station, through reduction-oxidation reactions. The degree of the decarburization process is mostly dependent on the preheating fuel or the environment. For refractories without antioxidants, refractory decarburization is slower when coal gas is used in ladle preheating than when a mixture of oil and air is used. In addition, ladle preheating of the refractories without antioxidants leads to direct wear of the slagline refractories. This is due to the total loss of the matrix strength, which results in a sand-like product. Thermal chemical changes that take place in the slagline refractories are due to the MgO-C reaction as well as the formation of liquid phases from impurity oxides. In addition, the decrease in the system pressure during steel refining makes the MgO-C reaction take place at the steel refining temperatures. This reduces the refractory’s resistance to corrosion. This is a serious problem for both the magnesia-carbon and dolomite-carbon refractories. The studies of the reactions between the slagline refractories and the different slag compositions showed that slags rich in iron oxide lead mostly to the oxidation of carbon/graphite in the carbon-containing refractories. This leads to an increased porosity and wettability and therefore an enhanced penetration of slag into the refractory structure. If the slag contains high contents of alumina and or silica (such as the steel refining slag), reactions between the slag components and the dolomite-carbon refractory are promoted. This leads to the formation of low-temperature melting phases such as calcium-aluminates and silicates. The state of these reaction products during steel refining leads to an accelerated wear of the dolomite-carbon refractory. The main products of the reactions between the magnesia-carbon refractory and the steel refining slag are MgAl2O4 spinels, and calcium-aluminates, and silicates. Due to the good refractory properties of MgAl2O4 spinels, the slag corrosion resistance of the magnesiacarbon refractory is promoted.

An Experimental Study of Submerged Entry Nozzles (SEN) Focusing on Decarburization and Clogging

The submerged entry nozzle (SEN) is used to transport the molten steel from a tundish to a mould. The main purpose of its usage is to prevent oxygen and nitrogen pick-up by molten steel from the gas. Furthermore, to achieve the desired flow conditions in the mould. Therefore, the SEN can be considered as a vital factor for a stable casting process and the steel quality. In addition, the steelmaking processes occur at high temperatures around 1873 K, so the interaction between the refractory materials of the SEN and molten steel is unavoidable. Therefore, the knowledge of the SEN behaviors during preheating and casting processes is necessary for the design of the steelmaking processes  The internal surfaces of modern SENs are coated with a glass/silicon powder layer to prevent the SEN graphite oxidation during preheating. The effects of the interaction between the coating layer and the SEN base refractory materials on clogging were studied. A large number of accretion samples formed inside alumina-graphite clogged SENs were examined using FEG-SEM-EDS and Feature analysis. The internal coated SENs were used for continuous casting of stainless steel grades alloyed with Rare Earth Metals (REM). The post-mortem study results clearly revealed the formation of a multi-layer accretion. A harmful effect of the SENs decarburization on the accretion thickness was also indicated. In addition, the results indicated a penetration of the formed alkaline-rich glaze into the alumina-graphite base refractory. More specifically, the alkaline-rich glaze reacts with graphite to form a carbon monoxide gas. Thereafter, dissociation of CO at the interface between SEN and molten metal takes place. This leads to reoxidation of dissolved alloying elements such as REM (Rare Earth Metal). This reoxidation forms the “In Situ” REM oxides at the interface between the SEN and the REM alloyed molten steel. Also, the interaction of the penetrated glaze with alumina in the SEN base refractory materials leads to the formation of a high-viscous alumina-rich glaze during the SEN preheating process. This, in turn, creates a very uneven surface at the SEN internal surface. Furthermore, these uneven areas react with dissolved REM in molten steel to form REM aluminates, REM silicates and REM alumina-silicates. The formation of the large “in-situ” REM oxides and the reaction of the REM alloying elements with the previously mentioned SEN´s uneven areas may provide a large REM-rich surface in contact with the primary inclusions in molten steel. This may facilitate the attraction and agglomeration of the primary REM oxide inclusions on the SEN internal surface and thereafter the clogging. The study revealed the disadvantages of the glass/silicon powder coating applications and the SEN decarburization. The decarburization behaviors of Al2O3-C, ZrO2-C and MgO-C refractory materials from a commercial Submerged Entry Nozzle (SEN), were also investigated for different gas atmospheres consisting of CO2, O2 and Ar. The gas ratio values were kept the same as it is in a propane combustion flue gas at different Air-Fuel-Ratio (AFR) values for both Air-Fuel and Oxygen-Fuel combustion systems. Laboratory experiments were carried out under nonisothermal conditions followed by isothermal heating. The decarburization ratio (α) values of all three refractory types were determined by measuring the real time weight losses of the samples. The results showed the higher decarburization ratio (α) values increasing for MgO-C refractory when changing the Air-Fuel combustion to Oxygen-Fuel combustion at the same AFR value. It substantiates the SEN preheating advantage at higher temperatures for shorter holding times compared to heating at lower temperatures during longer holding times for Al2O3-C samples. Diffusion models were proposed for estimation of the decarburization rate of an Al2O3-C refractory in the SEN. Two different methods were studied to prevent the SEN decarburization during preheating: The effect of an ZrSi2 antioxidant and the coexistence of an antioxidant additive and a (4B2O3 ·BaO) glass powder on carbon oxidation for non-isothermal and isothermal heating conditions in a controlled atmosphere. The coexistence of 8 wt% ZrSi2 and 15 wt% (4B2O3 ·BaO) glass powder of the total alumina-graphite refractory base materials, presented the most effective resistance to carbon oxidation. The 121% volume expansion due to the Zircon formation during heating and filling up the open pores by a (4B2O3 ·BaO) glaze during the green body sintering led to an excellent carbon oxidation resistance. The effects of the plasma spray-PVD coating of the Yttria Stabilized Zirconia (YSZ) powder on the carbon oxidation of the Al2O3-C coated samples were investigated. Trials were performed at non-isothermal heating conditions in a controlled atmosphere. Also, the applied temperature profile for the laboratory trials were defined based on the industrial preheating trials. The controlled atmospheres consisted of CO2, O2 and Ar. The thicknesses of the decarburized layers were measured and examined using light optic microscopy, FEG-SEM and EDS. A 250-290 μm YSZ coating is suggested to be an appropriate coating, as it provides both an even surface as well as prevention of the decarburization even during heating in air. In addition, the interactions between the YSZ coated alumina-graphite refractory base materials in contact with a cerium alloyed molten stainless steel were surveyed. The YSZ coating provided a total prevention of the alumina reduction by cerium. Therefore, the prevention of the first clogging product formed on the surface of the SEN refractory base materials. Therefore, the YSZ plasma-PVD coating can be recommended for coating of the hot surface of the commercial SENs.

Evaluation of a thermally driven heat pump for solar heating and cooling applications

Exploiting solar energy technology for both heating and cooling purposes has the potential of meeting an appreciable portion of the energy demand in buildings throughout the year. By developing an integrated, multi-purpose solar energy system, that can operate all twelve months of the year, a high utilisation factor can be achieved which translates to more economical systems. However, there are still some techno-economic barriers to the general commercialisation and market penetration of such technologies. These are associated with high system and installation costs, significant system complexity, and lack of knowledge of system implementation and expected performance. A sorption heat pump module that can be integrated directly into a solar thermal collector has thus been developed in order to tackle the aforementioned market barriers. This has been designed for the development of cost-effective pre-engineered solar energy system kits that can provide both heating and cooling. This thesis summarises the characterisation studies of the operation of individual sorption modules, sorption module integrated solar collectors and a full solar heating and cooling system employing sorption module integrated collectors. Key performance indicators for the individual sorption modules showed cooling delivery for 6 hours at an average power of 40 W and a temperature lift of 21°C. Upon integration of the sorption modules into a solar collector, measured solar radiation energy to cooling energy conversion efficiencies (solar cooling COP) were between 0.10 and 0.25 with average cooling powers between 90 and 200 W/m2 collector aperture area. Further investigations of the sorption module integrated collectors implementation in a full solar heating and cooling system yielded electrical cooling COP ranging from 1.7 to 12.6 with an average of 10.6 for the test period. Additionally, simulations were performed to determine system energy and cost saving potential for various system sizes over a full year of operation for a 140 m2 single-family dwelling located in Madrid, Spain. Simulations yielded an annual solar fraction of 42% and potential cost savings of €386 per annum for a solar heating and cooling installation employing 20m2 of sorption integrated collectors.

Computer and IT skills of Australian first-year university undergraduate students

The use of computers and information technology is becoming more widespread in chemical education and in the wider community and workforce. Universities are increasing the use of computers and information technology in their teaching and learning programs. The Australian situation, reported here, can be viewed as a microcosm, reflecting a world-wide trend.

The penetration of general IT literacy and ability amongst Australian undergraduate students is rising rapidly. This paper reports surveys of the detailed IT skills of Australian undergraduate students. To the best of our knowledge, apart from our own work, there have been no other published surveys of specific IT skills. Most students have some reasonable computer skills at the start of their university studies, but the level of skill is not uniformly high. In fact, many IT literate students lack a sufficient level of skill to use the new technologies, including full use of web-based flexible learning. There is an urgent need for IT training for university students in order to achieve successful learning outcomes using IT and to satisfy the needs of future employers.

This article, which is the second in a series (1) of investigations on the computer skills of undergraduate students at the start of university, is an expanded version of a paper presented at the World Chemistry Congress held in Brisbane (Australia) during 1-6 July 2001.