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  • Articles  (21,180)
  • Oxford University Press
  • Chemistry and Pharmacology  (20,187)
  • Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics  (993)
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  • 1
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    Calculations of effectiveness factors and the criteria of mass transfer effect for high-temperature methanation (HTM) catalyst (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-16
    Description: Natural gas is an extremely important bridge fuel to a low-carbon energy economy for improving local air quality. Coal to synthetic natural gas (SNG) is an effective way to convert the high-carbon energy (coal) into the low-carbon energy with rich hydrogen (natural gas). For the modern coal to SNG industry, the high-temperature methanation (HTM) catalyst plays an important role, and the advanced evaluation process should necessitate the elimination of mass transfer effect. Some simple but effective model catalysts, such as slab and sphere, can be very helpful in defining the reaction conditions, and thus facilitating the evaluation process for real HTM catalysts. In this work, slab and sphere model catalysts were adopted to derive mass transfer and reaction-coupled equations, the numerical methods were used to solve the coupled equations for the concentration profiles in catalysts, and the effectiveness factors were accordingly calculated. By taking advantage of the Thiele module and the Weisz–Prater module , the criteria for the elimination of mass transfer effect in the HTM catalyst evaluation process were successfully defined. This work also complements the Weisz–Prater criterion by incorporating ‘negative reaction orders’.
    Keywords: Other low-carbon energy technologies
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 2
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    A novel low-carbon space conditioning system incorporating phase-change materials and earth-air heat exchangers (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-16
    Description: The energy expended for conditioning buildings around the world is worryingly large and increasing every year. Currently, almost half of houses around the world use some type of energy-expensive conventional air-conditioning system. These systems are high emitters of gases such as carbon dioxide and so high contributors to climate change. Consequently, alternatives must be considered. Earth–air heat exchangers (EAHEs) and phase-change materials (PCMs) may be options; they have, however, limitations. This paper proposes a novel hybrid space-conditioning system combining EAHEs with PCMs, which uses surfaces as sources of heating or cooling to provide better temperature distribution across a space and comfort enhancement with low energy use. The idea is to use an EAHE to provide cool air to discharge the PCM, consequently helping to overcome most of the limitations of both strategies. Two of a series of experiments undertaken to test the proposed system are reported in this article. The EAHE + PCM system compared with a reference room could decrease temperature swings by up to 47%. The system was proved to work although further work is required to make it commercially viable.
    Keywords: Other low-carbon energy technologies
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 3
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    3D analysis of the incident diffuse irradiance on the building's surfaces in an urban environment (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: The design of a future building with very high-energy efficiency demands from the architect to study the available solar resources in this urban environment. The purpose of the presented methodology is to study the variations in all components of the incident solar radiation daily, monthly and seasonally for all building facades. This is realized in the computer program 3D–SOLARIA. In the focus of the paper is the estimation of the background component of the incident diffuse solar irradiation on a building facade under orthogonally obstructed sky, using anisotropic sky view factors.
    Keywords: Sustainable/low carbon buildings
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 4
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    An integrated approach for sustainable design and assessment of residential building envelope: part I (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: The assessment of building envelope sustainability using existing building performance assessment methods is still a challenge and yet to be fully addressed. This is due to the single-dimensional nature and lack of integration of sustainable performance values. Besides, the issue of sustainability assessment in the building envelope requires considering many factors including life cycle considerations. As such, in an effort to develop an integrated approach that combines relevant sustainable development factors and life cycles, an integrated performance model (IPM) was developed. The IPM is an essential tool developed to aid the sustainable design of the residential building envelope that can reduce carbon emission and whole residential building energy consumption and ensure sustainable performance of the building envelope.
    Keywords: Sustainable/low carbon buildings
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 5
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    Towards the generation of distributed electric power: self-consumption with net balance (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: The results and considerations on one self-consumption photovoltaic installation with net balance in Granada (South of Spain) are presented and discussed in this paper. The use of the building (one faculty) makes it optimal for this kind of consumption. Finally, the potential benefits and problems of self-consumption with net balance are presented.
    Keywords: Solar energy technologies
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 6
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    Numerical investigation of turbulent flow heat transfer and pressure drop of AL2O3/water nanofluid in helically coiled tubes (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-16
    Description: Passive convective heat transfer enhancement can be achieved by improving the thermo-physical properties of the working fluid, changing flow geometry or both. This work presents a numerical study to investigate the combined effect of using helical coils and nanofluids on the heat transfer characteristics and pressure losses in turbulent flow regime. The developed computational fluid dynamics models were validated against published experimental data and empirical correlations. Results have shown that combining the effects of alumina (Al 2 O 3 ) nanoparticles and tube coiling could enhance the heat transfer coefficient by up to 60% compared with that of pure water in straight tube at the same Reynolds number. Also, results showed that the pressure drop in helical coils using Al 2 O 3 nanofluid for volume fraction of 3% was six times that of water in straight tubes (80% of the pressure drop increase is due to nanoparticles addition), while the effect of Reynolds number on the pressure drop penalty factor was found to be insignificant.
    Keywords: Other low-carbon energy technologies
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 7
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    Control strategies for indoor environment quality and energy efficiency--a review (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: The demand for better indoor environment has led to a wide use of heating, ventilating and air conditioning (HVAC) systems. However, this demanding cannot be sustained without a strategy to reduce the energy consumption of HVAC systems. Employing advanced HVAC control is one of the strategies to maintain high-quality indoor thermal comfort with low energy consumption. This paper reviews the development of control technologies for HVAC systems. It summarizes the problems in existing reviews and gives a future perspective on HVAC control systems for occupant comfort and energy efficiency.
    Keywords: Built environment and low-carbon society
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 8
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    Tracer gas technique for measurement of air infiltration and natural ventilation: case studies and new devices for measurement of mechanical air ventilation in ducts (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: In buildings without mechanical ventilation, the fresh air needed by the occupants is supplied only by air infiltration or natural ventilation. Its quantification by analytical methods is difficult, and so experimental methods such as the tracer gas technique are very useful. In this work, several case studies are presented, where one may see the potential of this technique to detect small differences in building air tightness, due to different envelope elements, namely the type of window frames and location of blinds' boxes. The applicability of this technique to other spaces rather than buildings can also be analyzed. When dealing with mechanical ventilation, it is difficult to measure the duct air flow rate precisely, because of the minimum duct length necessary to obtain a good mixing of the tracer gas with the air, when conventional probes are used. Research was carried out with the development of new probes to overcome this situation, and results are also shown. With accurate measurements of air flow rates, it is possible to reduce CO 2 emissions due to air heating or cooling in buildings.
    Keywords: Built environment and low-carbon society
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 9
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    Readdressing working fluid selection with a view to designing a variable geometry ejector (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: A number of factors influence the performance of an ejector, e.g. working fluid, geometry and operating conditions. In the present work, six low-environmental-impact working fluids were evaluated for their use in an ejector cooling system running on low-temperature thermal energy. The numerical analysis was based on a model applying the 1D constant-pressure mixing theory. Ejector performance was assessed for the temperatures of the generator, evaporator and condenser in the range of 80–120°C, 5–15°C and 25–40°C, respectively. The results indicated that owing to its high coefficient of performance and moderate operating pressures throughout the entire ejector cycle, isobutane is a good choice for a refrigerant. The area ratio required for running the ejector in critical mode, under changing operating conditions, varied in a significant range regardless of the selected refrigerant. This clearly indicates the importance of a variable geometry ejector design to strengthen the position of ejector cooling systems among other refrigeration technologies.
    Keywords: Other low-carbon energy technologies
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 10
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    Constructal optimization of a disc-shaped body with cooling channels for specified power pumping (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: The thermal performance of a disc-shaped heat generation body with cooling channels is investigated by using constructal theory based on previous model of heat convection on a disc and previous analytical method of heat conduction on a disc. By taking minimum dimensionless maximum thermal resistance as optimization objective, the optimal aspect ratio of the elemental sector in the radial-pattern disc is obtained for the specified power pumping of the elemental sector; the optimal width ratio of the first-order and elemental cooling channels and the optimal dimensionless radius of the elemental sector are obtained for the specified power pumping of the disc. There exists a critical radius of the disc to determine whether the radial-pattern design and branched-pattern design should be adopted. These conclusions are different from those obtained by Wechsatol et al. 's model, and the essential reason for these differences is that the power pumping is specified in this article, but not the specified flow rate number in Wechsatol et al. 's model. Finally, the assumption about the heat capacity of the coolant and the thermal conductivity of the disc is validated. An analytical method is introduced in this article, which can provide another thought for the constructal optimization of disc with heat convection. The optimal constructs of the discs are obtained for the specified power pumping, which provides some different guidelines for the design of disc with heat convection.
    Keywords: Other low-carbon energy technologies
    Print ISSN: 1748-1317
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 11
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    Theoretical investigation of hot box solar cookers having conventional and finned absorber plates (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: In this paper, solar box cookers with ordinary and finned absorber plates are theoretically investigated in terms of thermodynamic performance parameters. For a typical summer and winter day, temperatures of solar cooker components such as glass cover, internal air, absorber plate, cooking vessel and the liquid are determined theoretically versus time. The analysis is carried out for conventional and finned absorber plates, and accuracy of the results is verified by a previously published experimental work. Energy and exergy efficiencies of box-type solar cookers are plotted versus time for various cases. The methodology presented in this paper enables to make a preliminary evaluation of ordinary and modified solar box cookers with respect to changes in main environmental parameters such as temperature and illumination intensity. Some recommendations are also made to enhance the power outputs of the aforementioned solar cookers.
    Keywords: Solar energy technologies
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 12
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    Design of a celestial vault image capture device for its application in the solar radiation field (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: The sun is the more plentiful source of natural power that we have in the Earth. However, the amount of radiation reaching the Earth's surface depends on astronomical and climatic factors. One of the factors exerting a greater influence is cloudiness. For that reason, it is important to quantify its influence on solar radiation. According to that, in this work, a prototype to capture images of the celestial vault is designed and implemented to be able to measure parameters related to the cloud properties and, later, to determine their influence on solar radiation.
    Keywords: Solar energy technologies
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 13
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    Investigation of concentrating and nonconcentrating evacuated tube solar water heaters using 2D particle imaging velocimetry (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: Under transient climatic conditions, solar water heaters using heat pipes are more effective at capturing incident solar radiation than other equivalent sized solar water heaters. The cost must be reduced to improve uptake of such systems. To investigate two methods were considered by this study: thermosyphon fluid flow and reflective concentrators. A physical reconfigurable laboratory model of the manifold and associated condensers of a heat-pipe-evacuated tube system were fabricated; fluid circulation was via thermosyphonic action, particle imaging velocimetry derived velocity maps and the use of concentrators was simulated. When condenser spacing was doubled, the Nusselt number increased by 43%, the velocity by 55% but the heat transfer efficiency of the model manifold decreased by 9%. Potential annual energy savings of 10 207 GWh could be realized if such systems could be successfully fabricated.
    Keywords: Solar energy technologies
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 14
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    The impact of surface characteristics on ambient temperature at urban micro scale: comparative field study in two climates (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: This paper presents the results of two field studies to examine the differences in ambient temperatures in a micro-scale environment (at distances of 50–200 m between measuring points) in two different climates during typical summer weather conditions at two similar sites in terms of construction and activities. The analysis considered the land use around the measuring locations split into three categories (built, green and open) as well as climatic conditions and studied the effect of these on ambient temperature at each measuring location. It was found that, similarly to macro-scale studies at the urban level, measuring locations with a higher green cover have a lower ambient temperature compared with measuring locations with a higher built and/or open land cover. The results provide measured evidence in two different climates that small green areas distributed within the urban environment can provide a reduction in the ambient temperature thus contributing to the mitigation of urban heat island.
    Keywords: Built environment and low-carbon society
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 15
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    Computational study of a 2D capillary pump evaporator (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: Capillary pump loop (CPL) is a two-phase heat transfer device considered as a useful solution for thermal control applications in spacecrafts, satellites and electronic components. The purpose of this paper is to study various aspects of the working state of the CPL evaporator. A two-dimensional computational model was developed in order to analyze the flow and the phase transformation inside a cylindrical evaporator. At the present analysis, different cases were studied by changing liquid saturation temperature, inclination angle of the evaporator and the length of the porous heated wick. Water, ammonia, acetone and freon-134 were used as working liquids for numerical experiments. Results present the evaporator capability to vaporize each working liquid and find out its possibility of dry-out causing failure. This information is useful in choosing the best working liquid for an evaporator, enabling bigger amounts of heat to be transferred.
    Keywords: Other low-carbon energy technologies
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 16
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    Failure of natural ventilation strategy in a sustainable house in China (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: In recent years, the concept of green building is becoming popular in China. Architects and engineers have the opportunity to actually implement green building practices. This paper reveals the failure of a naturally ventilated LEED-certified townhouse development project in China mentioned in recent research. The house owners made great alterations for the purpose of decoration, which removed or minimized the effectiveness of natural ventilation elements in the original design. The research shows that the houses show ‘International Style’ because the natural ventilation design principles were not fully applied in the design and the localized natural ventilation strategies were not fully considered by means of computational simulation in the design stage. Also, the lack of communication between designers and the owners caused the removal of most natural ventilation elements of these houses during the occupancy period. The authors advocate three criteria to avoid failures of natural ventilation design: localized/ climate adaptive design, relationship among design elements and design intention awareness.
    Keywords: Sustainable/low carbon buildings
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 17
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    Design guideline for application of earth-to-air heat exchanger coupled with solar chimney as a natural heating system (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: In the present paper, design of solar chimney (SC) and earth-to-air heat exchanger (EAHE) to meet the thermal need of flat buildings are studied regarding adaptive thermal comfort criteria. Investigation on the effects of geometric features shows that the design of SC with the air gap and outlet sizes of 0.2 m and also EAHE with the diameter and length of 0.5 and 25.0 m reveals better performance. Thermal comfort analysis shows that the SC is capable to power the underground heating system during few hours of the sunny days even at the ambient temperature as low as 0°C and the heating demand of 1000 W without needing the auxiliary devices. In addition, the required numbers of SCs and the underground air channels are strongly influenced by environmental outdoor conditions and heating demand of building and are approximately calculated by: $$\hbox{ room }\phantom{\rule{0.08em}{0ex}}\hbox{ volume/50 }\phantom{\rule{0.08em}{0ex}}\hbox{ and }\phantom{\rule{0.08em}{0ex}}\hbox{ 2 }\times (\hbox{ room }\phantom{\rule{0.08em}{0ex}}\hbox{ volume/50 })+\hbox{ 1, }$$ respectively.
    Keywords: Other low-carbon energy technologies
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 18
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    Adaptive facade design for the daylighting performance in an office building: the investigation of an opening design strategy with cellular automata (2015)
    Oxford University Press
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    Publication Date: 2015-08-16
    Description: Daylighting has an important role in sustainable architecture as it affects the energy consumption in a building. Especially for an office building, daylight helps not only to reduce the load on artificial lighting but also to promote work efficiency through promoting good human health, well-being and user comfort. The objective of this research is to develop an innovative façade design strategy that comes from the development of digital technology and dynamic daylight performance measuring methods. Thus, the various parameters are studied through the computational process of cellular automata (CA) to generate the several alternative opening patterns on the building façade. Each CA design value was tested under static and dynamic sky condition to analyze the quality and quantity of daylight and visual comfort throughout the year. The results were compared to find an optimum alternative design in terms of the daylighting design criteria, from building code, standard and design guidelines for the office building. Finally, research of an adaptive façade design strategy was concluded with the results from the above hybridization of generative and performative design methodology. This study discovers the architectural design approach from the CA and it will make not only progress in building façade esthetics, but also human comfort with building sustainability.
    Keywords: Sustainable/low carbon buildings
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 19
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    Mutagenesis study to disrupt electrostatic interactions on the twofold symmetry interface of Escherichia coli bacterioferritin (2015)
    Oxford University Press
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    Publication Date: 2015-11-26
    Description: Ferritins and other cage proteins have been utilized as models to understand the fundamentals of protein folding and self-assembly. The bacterioferritin (BFR) from Escherichia coli, a maxi-ferritin made up of 24 subunits, was chosen as the basis for a mutagenesis study to investigate the role of electrostatic intermolecular interactions mediated through charged amino acids. Through structural and computational analyses, three charged amino acids R30, D56 and E60 which involved in an electrostatic interaction network were mutated to the opposite charge. Four mutants, R30D, D56R, E60H and D56R-E60H, were expressed, purified and characterized. All of the mutants fold into α-helical structures. Consistent with the computational prediction, they all show a lowered thermostability; double mutant D56R-E60H was found to be 16°C less stable than the wild type. Except for the mutant E60H, all the other mutations completely shut down the formation of protein cages to favour the dimer state in solution. The mutants, however, retain their ability to form cage-like nanostructures in the dried, surface immobilized conditions of transmission electron microscopy. Our findings confirm that even a single charge-inversion mutation at the 2-fold interface of BFR can affect the quaternary structure of its dimers and their ability to self-assemble into cage structures.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 20
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    Effect of FliG three amino acids deletion in Vibrio polar-flagellar rotation and formation (2015)
    Oxford University Press
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    Publication Date: 2015-11-26
    Description: Most of bacteria can swim by rotating flagella bidirectionally. The C ring, located at the bottom of the flagellum and in the cytoplasmic space, consists of FliG, FliM and FliN, and has an important function in flagellar protein secretion, torque generation and rotational switch of the motor. FliG is the most important part of the C ring that interacts directly with a stator subunit. Here, we introduced a three-amino acids in-frame deletion mutation (PSA) into FliG from Vibrio alginolyticus , whose corresponding mutation in Salmonella confers a switch-locked phenotype, and examined its phenotype. We found that this FliG mutant could not produce flagellar filaments in a fliG null strain but the FliG(PSA) protein could localize at the cell pole as does the wild-type protein. Unexpectedly, when this mutant was expressed in a wild-type strain, cells formed flagella efficiently but the motor could not rotate. We propose that this different phenotype in Vibrio and Salmonella might be due to distinct interactions between FliG mutant and FliM in the C ring between the bacterial species.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 21
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    Sulphation of acetaminophen by the human cytosolic sulfotransferases: a systematic analysis (2015)
    Oxford University Press
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    Publication Date: 2015-11-26
    Description: Sulphation is known to be critically involved in the metabolism of acetaminophen in vivo . This study aimed to systematically identify the major human cytosolic sulfotransferase (SULT) enzyme(s) responsible for the sulphation of acetaminophen. A systematic analysis showed that three of the twelve human SULTs, SULT1A1, SULT1A3 and SULT1C4, displayed the strongest sulphating activity towards acetaminophen. The pH dependence of the sulphation of acetaminophen by each of these three SULTs was examined. Kinetic parameters of these three SULTs in catalysing acetaminophen sulphation were determined. Moreover, sulphation of acetaminophen was shown to occur in HepG2 human hepatoma cells and Caco-2 human intestinal epithelial cells under the metabolic setting. Of the four human organ samples tested, liver and intestine cytosols displayed considerably higher acetaminophen-sulphating activity than those of lung and kidney. Collectively, these results provided useful information concerning the biochemical basis underlying the metabolism of acetaminophen in vivo previously reported.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 22
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    Expression, purification and enzymatic characterization of a recombinant human ubiquitin-specific protease 47 (2015)
    Oxford University Press
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    Publication Date: 2015-11-26
    Description: In this study, the physicochemical and enzymatic properties of recombinant human ubiquitin (Ub)-specific protease (USP) 47, a novel member of the C19 family of de-ubiquitinating enzymes (DUB), were characterized for the first time. Recombinant human USP47 was expressed in a baculovirus expression system and purified to homogeneity. The purified protein was shown to be a monomeric protein with a molecular mass of ~146 kDa on sodium dodecyl sulphate—polyacrylamide gel electrophoresis. USP47 released Ub from Ub-aminoacyl-4-metheylcoumaryl-7-amide and Ub-tagged granzyme B. The substitution of the potential nucleophile Cys109 with Ser severely abrogated the Ub-releasing activity of USP47, indicating that USP47 is indeed a cysteine DUB. An assay using Ub dimer substrates showed that the enzyme cleaved a variety of isopeptide bonds between 2 Ub molecules, including the Lys48- and Lys63-linked isopeptide bonds. USP47 also released a Ub moiety from Lys48- and Lys63-linked polyUb chains. Of the inhibitors tested, N -ethylmaleimide, Zn ion and Ub aldehyde revealed a dose-dependent inhibition of USP47. In this study, clear differences in the enzymatic properties between USP47 and USP7 (the most closely related proteins among DUBs) were also found. Therefore, our results suggest that USP47 may play distinct roles in Ub-mediated cellular processes via DUB activity.
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    In vitro affinity maturation and characterization of anti-P24 antibody for HIV diagnostic assay (2015)
    Oxford University Press
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    Publication Date: 2015-11-26
    Description: P24 antigen is the main structural protein of HIV-1, its detection provide a means to aid the early diagnosis of HIV-1 infection. The aim of this study was to improve the selectivity and sensitivity of the HIV P24 diagnostic assay by developing a cohort of 9E8 affinity-matured antibodies through in vitro phage affinity maturation which was performed by complementarity determining region (CDR)-hot spot mutagenesis strategy. Antibody 9E8-491 had an affinity constant of 5.64 x 10 –11 M, which was 5.7-fold higher than that of the parent antibody (9E8). Furthermore, the affinity, sensitivity and specificity of 9E8-491 were higher than those of 9E8, which indicate that 9E8-491 is a good candidate detection antibody for HIV P24 assay. Structure analysis of matured variants revealed that most hydrogen bonds resided in HCDR3. Among the antibody–antigen predicted binding residues, Tyr 100A/100B was the original conserved residue that was commonly present in HCDR3 of 9E8 and variants. Arg 100 /Asp 100C was the major variant substitution that most likely influenced the binding differences among variants and 9E8 monoclonal antibody. Both efficient library panning and predicted structural data were in agreement that the binding residues were mostly located in HCDR3 and enabled identification of key residues that influence antibody affinity.
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    Dynamic and distinct histone modifications of osteogenic genes during osteogenic differentiation (2015)
    Oxford University Press
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    Publication Date: 2015-11-26
    Description: Many skeletal diseases have common pathological phenotype of defective osteogenesis of bone marrow stromal cells (BMSCs), in which histone modifications play an important role. However, few studies have examined the dynamics of distinct histone modifications during osteogenesis. In this study, we examined the dynamics of H3K9/K14 and H4K12 acetylation; H3K4 mono-, di- and tri-methylation; H3K9 di-methylation and H3K27 tri-methylation in osteogenic genes, runt-related transcription factor 2 (Runx2), osterix (Osx), alkaline phosphatase, bone sialoprotein and osteocalcin, during C3H10T1/2 osteogenesis. H3 and H4 acetylation and H3K4 di-methylation were elevated, and H3K9 di-methylation and H3K27 tri-methylation were reduced in osteogenic genes during C3H10T1/2 osteogenesis. C3H10T1/2 osteogenesis could be modulated by altering the patterns of H3 and H4 acetylation and H3K27 tri-methylation. In a glucocorticoid-induced osteoporosis mouse model, we observed the attenuation of osteogenic potential of osteoporotic BMSCs in parallel with H3 and H4 hypo-acetylation and H3K27 hyper-tri-methylation in Runx2 and Osx genes. When H3 and H4 acetylation was elevated, and H3K27 tri-methylation was reduced, the attenuated osteogenic potential of osteoporotic BMSCs was rescued effectively. These observations provide a deeper insight into the mechanisms of osteogenic differentiation and the pathophysiology of osteoporosis and can be used to design new drugs and develop new therapeutic methods to treat skeletal diseases.
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    In vitro dihydrouridine formation by tRNA dihydrouridine synthase from Thermus thermophilus, an extreme-thermophilic eubacterium (2015)
    Oxford University Press
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    Publication Date: 2015-11-26
    Description: Dihydrouridine (D) is formed by tRNA dihydrouridine synthases (Dus). In mesophiles, multiple Dus enzymes bring about D modifications at several positions in tRNA. The extreme-thermophilic eubacterium Thermus thermophilus , in contrast, has only one dus gene in its genome and only two D modifications (D20 and D20a) in tRNA have been identified. Until now, an in vitro assay system for eubacterial Dus has not been reported. In this study, therefore, we constructed an in vitro assay system using purified Dus. Recombinant T. thermophilus Dus lacking bound tRNA was successfully purified. The in vitro assay revealed that no other factors in living cells were required for D formation. A dus gene disruptant ( dus ) strain of T. thermophilus verified that the two D20 and D20a modifications in tRNA were derived from one Dus protein. The dus strain did not show growth retardation at any temperature. The assay system showed that Dus modified tRNA Phe transcript at 60°C, demonstrating that other modifications in tRNA are not essential for Dus activity. However, a comparison of the formation of D in native tRNA Phe purified from the dus strain and tRNA Phe transcript revealed that other tRNA modifications are required for D formation at high temperatures.
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    Yeast cell-based analysis of human lactate dehydrogenase isoforms (2015)
    Oxford University Press
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    Publication Date: 2015-11-26
    Description: Human lactate dehydrogenase (LDH) has attracted attention as a potential target for cancer therapy and contraception. In this study, we reconstituted human lactic acid fermentation in Saccharomyces cerevisiae , with the goal of constructing a yeast cell-based LDH assay system. pdc null mutant yeast (mutated in the endogenous pyruvate decarboxylase genes) are unable to perform alcoholic fermentation; when grown in the presence of an electron transport chain inhibitor, pdc null strains exhibit a growth defect. We found that introduction of the human gene encoding LDHA complemented the pdc growth defect; this complementation depended on LDHA catalytic activity. Similarly, introduction of the human LDHC complemented the pdc growth defect, even though LDHC did not generate lactate at the levels seen with LDHA. In contrast, the human LDHB did not complement the yeast pdc null mutant, although LDHB did generate lactate in yeast cells. Expression of LDHB as a red fluorescent protein (RFP) fusion yielded blebs in yeast, whereas LDHA-RFP and LDHC-RFP fusion proteins exhibited cytosolic distribution. Thus, LDHB exhibits several unique features when expressed in yeast cells. Because yeast cells are amenable to genetic analysis and cell-based high-throughput screening, our pdc /LDH strains are expected to be of use for versatile analyses of human LDH.
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    Visualization of RelB expression and activation at the single-cell level during dendritic cell maturation in Relb-Venus knock-in mice (2015)
    Oxford University Press
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    Publication Date: 2015-11-26
    Description: RelB is activated by the non-canonical NF-B pathway, which is crucial for immunity by establishing lymphoid organogenesis and B-cell and dendritic cell (DC) maturation. To elucidate the mechanism of the RelB-mediated immune cell maturation, a precise understanding of the relationship between cell maturation and RelB expression and activation at the single-cell level is required. Therefore, we generated knock-in mice expressing a fusion protein between RelB and fluorescent protein (RelB-Venus) from the Relb locus. The Relb Venus / Venus mice developed without any abnormalities observed in the Relb –/– mice, allowing us to monitor RelB-Venus expression and nuclear localization as RelB expression and activation. Relb Venus / Venus DC analyses revealed that DCs consist of RelB – , RelB low and RelB high populations. The RelB high population, which included mature DCs with projections, displayed RelB nuclear localization, whereas RelB in the RelB low population was in the cytoplasm. Although both the RelB low and RelB – populations barely showed projections, MHC II and co-stimulatory molecule expression were higher in the RelB low than in the RelB – splenic conventional DCs. Taken together, our results identify the RelB low population as a possible novel intermediate maturation stage of cDCs and the Relb Venus / Venus mice as a useful tool to analyse the dynamic regulation of the non-canonical NF-B pathway.
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    Molecular and biochemical characterization of bifunctional pyruvate decarboxylases and pyruvate ferredoxin oxidoreductases from Thermotoga maritima and Thermotoga hypogea (2015)
    Oxford University Press
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    Publication Date: 2015-11-26
    Description: Hyperthermophilic bacteria Thermotoga maritima and Thermotoga hypogea produce ethanol as a metabolic end product, which is resulted from acetaldehyde reduction catalysed by an alcohol dehydrogenase (ADH). However, the enzyme that is involved in the production of acetaldehyde from pyruvate is not well characterized. An oxygen sensitive and coenzyme A-dependent pyruvate decarboxylase (PDC) activity was found to be present in cell free extracts of T. maritima and T. hypogea . Both enzymes were purified and found to have pyruvate ferredoxin oxidoreductase (POR) activity, indicating their bifunctionality. Both PDC and POR activities from each of the purified enzymes were characterized in regards to their optimal assay conditions including pH dependency, oxygen sensitivity, thermal stability, temperature dependency and kinetic parameters. The close relatedness of the PORs that was shown by sequence analysis could be an indication of the presence of such bifunctionality in other hyperthermophilic bacteria. This is the first report of a bifunctional PDC/POR enzyme in hyperthermophilic bacteria. The PDC and the previously reported ADHs are most likely the key enzymes catalysing the production of ethanol from pyruvate in bacterial hyperthermophiles.
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    Low pH-driven folding of WW45-SARAH domain leads to stabilization of the WW45-Mst2 complex (2015)
    Oxford University Press
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    Publication Date: 2015-08-30
    Description: The scaffolding protein Salvador (Sav) plays a key role in the Hippo (Hpo) signalling pathway, which controls tissue growth by inhibiting cell proliferation and promoting apoptosis. Dysregulation of the Hippo pathway contributes to cancer development. Since the identification of the first Sav gene in 2002, very little is known regarding the molecular basis of Sav-SARAH mediating interactions due to its insolubility. In this study, refolding of the first Sav (known as WW45)-SARAH provided insight into the biochemical and biophysical properties, indicating that WW45-SARAH exhibits properties of a disordered protein, when the domain was refolded at a neutral pH. Interestingly, WW45-SARAH shows folded and rigid conformations relative to the decrease in pH. Further, diffracting crystals were obtained from protein refolded under acidic pH, suggesting that the refolded WW45 protein at low pH has a homogeneous and stable conformation. A comparative analysis of molecular properties found that the acidic-stable fold of WW45-SARAH enhances a heterotypic interaction with Mst2-SARAH. In addition, using an Mst2 mutation that disrupts homotypic dimerization, we showed that the monomeric Mst2-SARAH domain could form a stable complex of 1:1 stoichiometric ratio with WW45 refolded under acidic pH.
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    Diet-induced hypercholesterolemia imparts structure-function changes to erythrocyte chondroitin sulphate/dermatan sulphate (2015)
    Oxford University Press
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    Publication Date: 2015-08-30
    Description: Hypercholesterolemia is one of the factors contributing to cardiovascular problems. Erythrocytes are known to contribute its cholesterol to atherosclerotic plaque. Our earlier study showed that erythrocytes overexpress chondroitin sulphate/dermatan sulphate (CS/DS), a linear co-polymer, during diabetes which resulted in increased cytoadherence to extracellular matrix (ECM) components. This study was carried out to determine whether diet-induced hypercholesterolemia had any effect on erythrocyte CS/DS and impacted cytoadherence to ECM components. Unlike in diabetes, diet-induced hypercholesterolemia did not show quantitative changes in erythrocyte CS/DS but showed difference in proportion of un-sulphated and 4- O -sulphated disaccharides. Erythrocytes from hypercholesterolemic rats showed increased adhesion to ECM components which was abrogated to various extents when subjected to chondroitinase ABC digestion. However, isolated CS/DS chains showed a different pattern of binding to ECM components indicating that orientation of CS/DS chains could be playing a role in binding.
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    Isolation and characterization of antigen-specific alpaca (Lama pacos) VHH antibodies by biopanning followed by high-throughput sequencing (2015)
    Oxford University Press
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    Publication Date: 2015-08-30
    Description: The antigen-binding domain of camelid dimeric heavy chain antibodies, known as VHH or Nanobody, has much potential in pharmaceutical and industrial applications. To establish the isolation process of antigen-specific VHH, a VHH phage library was constructed with a diversity of 8.4 x 10 7 from cDNA of peripheral blood mononuclear cells of an alpaca ( Lama pacos ) immunized with a fragment of IZUMO1 (IZUMO1 PFF ) as a model antigen. By conventional biopanning, 13 antigen-specific VHHs were isolated. The amino acid sequences of these VHHs, designated as N-group VHHs, were very similar to each other (〉93% identity). To find more diverse antibodies, we performed high-throughput sequencing (HTS) of VHH genes. By comparing the frequencies of each sequence between before and after biopanning, we found the sequences whose frequencies were increased by biopanning. The top 100 sequences of them were supplied for phylogenic tree analysis. In total 75% of them belonged to N-group VHHs, but the other were phylogenically apart from N-group VHHs (Non N-group). Two of three VHHs selected from non N-group VHHs showed sufficient antigen binding ability. These results suggested that biopanning followed by HTS provided a useful method for finding minor and diverse antigen-specific clones that could not be identified by conventional biopanning.
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    The R3 receptor-like protein tyrosine phosphatase subfamily inhibits insulin signalling by dephosphorylating the insulin receptor at specific sites (2015)
    Oxford University Press
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    Publication Date: 2015-08-30
    Description: The autophosphorylation of specific tyrosine residues occurs in the cytoplasmic region of the insulin receptor (IR) upon insulin binding, and this in turn initiates signal transduction. The R3 subfamily (Ptprb, Ptprh, Ptprj and Ptpro) of receptor-like protein tyrosine phosphatases (RPTPs) is characterized by an extracellular region with 6–17 fibronectin type III-like repeats and a cytoplasmic region with a single phosphatase domain. We herein identified the IR as a substrate for R3 RPTPs by using the substrate-trapping mutants of R3 RPTPs. The co-expression of R3 RPTPs with the IR in HEK293T cells suppressed insulin-induced tyrosine phosphorylation of the IR. In vitro assays using synthetic phosphopeptides revealed that R3 RPTPs preferentially dephosphorylated a particular phosphorylation site of the IR: Y960 in the juxtamembrane region and Y1146 in the activation loop. Among four R3 members, only Ptprj was co-expressed with the IR in major insulin target tissues, such as the skeletal muscle, liver and adipose tissue. Importantly, the activation of IR and Akt by insulin was enhanced, and glucose and insulin tolerance was improved in Ptprj -deficient mice. These results demonstrated Ptprj as a physiological enzyme that attenuates insulin signalling in vivo , and indicate that an inhibitor of Ptprj may be an insulin-sensitizing agent.
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    Involvement of thioredoxin on the scaffold activity of NifU in heterocyst cells of the diazotrophic cyanobacterium Anabaena sp. strain PCC 7120 (2015)
    Oxford University Press
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    Publication Date: 2015-08-30
    Description: The diazotrophic cyanobacterium Anabaena sp. strain PCC 7120 (A.7120) differentiates into specialized heterocyst cells that fix nitrogen under nitrogen starvation conditions. Although reducing equivalents are essential for nitrogen fixation, little is known about redox systems in heterocyst cells. In this study, we investigated thioredoxin (Trx) networks in Anabaena using TrxM, and identified 16 and 38 candidate target proteins in heterocysts and vegetative cells, respectively, by Trx affinity chromatography (Motohashi et al. (Comprehensive survey of proteins targeted by chloroplast thioredoxin. Proc Natl Acad Sci USA , 2001; 98 , 11224–11229)). Among these, the Fe–S cluster scaffold protein NifU that facilitates functional expression of nitrogenase in heterocysts was found to be a potential TrxM target. Subsequently, we observed that the scaffold activity of N-terminal catalytic domain of NifU is enhanced in the presence of Trx-system, suggesting that TrxM is involved in the Fe–S cluster biogenesis.
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    Substrate-dependent nitric oxide synthesis by secreted endoplasmic reticulum aminopeptidase 1 in macrophages (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: In this study, we examined the role of aminopeptidases with reference to endoplasmic reticulum aminopeptidase 1 (ERAP1) in nitric oxide (NO) synthesis employing murine macrophage cell line RAW264.7 cells activated by lipopolysaccharide (LPS) and interferon (IFN)- and LPS-activated peritoneal macrophages derived from ERAP1 knockout mouse. When NO synthesis was measured in the presence of peptides having N-terminal Arg, comparative NO synthesis was seen with that measured in the presence of Arg. In the presence of an aminopeptidase inhibitor amastatin, NO synthesis in activated RAW264.7 cells was significantly decreased. These results suggest that aminopeptidases are involved in the NO synthesis in activated RAW264.7 cells. Subsequently, significant reduction of NO synthesis was observed in ERAP1 knockdown cells compared with wild-type cells. This reduction was rescued by exogenously added ERAP1. Furthermore, when peritoneal macrophages prepared from ERAP1 knockout mouse were employed, reduction of NO synthesis in knockout mouse macrophages was also attributable to ERAP1. In the presence of amastatin, further reduction was observed in knockout mouse-derived macrophages. Taken together, these results suggest that several aminopeptidases play important roles in the maximum synthesis of NO in activated macrophages in a substrate peptide-dependent manner and ERAP1 is one of the aminopeptidases involved in the NO synthesis.
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    Properties and functions of the storage sites of glycogen phosphorylase (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: Glycogen phosphorylase (GP) is biologically active as a dimer of identical subunits. Each subunit has two distinct maltooligosaccharide binding sites: a storage site and a catalytic site. Our characterization of the properties of these sites suggested that GP activity consists of two activities: (i) binding to the glycogen molecule and (ii) phosphorolysis of the non-reducing-end glucose residues. Activity (i) is mainly due to the activities of the two storage sites, which depended on the ionic strength of the medium and were directly inhibited by cyclodextrins (CDs). Activity (i) is of benefit to GP because a high concentration of non-reducing-end glucose residues is localized on the surface of the glycogen molecule. Activity (ii), the total activity of the two catalytic sites, exhibited relatively little ionic strength dependence. Because the combined activity of (i) and (ii) is deduced using glycogen as an assay substrate, the sole activity of (ii) must be measured using small maltooligosyl-substrates. By using a very low concentration of pyridylaminated maltohexaose, we demonstrated that the GP catalytic sites are active even in the presence of CDs, and that the actions of the catalytic site and the storage site are independent of each other.
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    A highly effective and adjustable dual plasmid system for O-GlcNAcylated recombinant protein production in E. coli (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: O -GlcNAcylation is a ubiquitous, dynamic and reversible post-translational protein modification in metazoans, and it is catalysed and removed by O -GlcNAc transferase (OGT) and O -GlcNAcase, respectively. Prokaryotes lack endogenous OGT activity. It has been reported that coexpression of mammalian OGT with its target substrates in Escherichia coli produce O -GlcNAcylated recombinant proteins, but the plasmids used were not compatible, and the expression of both OGT and its target protein were induced by the same inducer. Here, we describe a compatible dual plasmid system for coexpression of OGT and its target substrate for O -GlcNAcylated protein production in E. coli . The approach was validated using the CKII and p53 protein as control. This compatible dual plasmid system contains an arabinose-inducible OGT expression vector with a pUC origin and an isopropyl β - d -thiogalactopyranoside-inducible OGT target substrate expression vector bearing a p15A origin. The dual plasmid system produces recombinant proteins with varying O -GlcNAcylation levels by altering the inducer concentration. More importantly, the O -GlcNAcylation efficiency was much higher than the previously reported system. Altogether, we established an adjustable compatible dual plasmid system that can effectively yield O -GlcNAcylated proteins in E. coli .
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    New roles of DNA and SopB in polymerization of SopA of Escherichia coli F plasmid (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: Active equi-paritioning of the F plasmid is achieved by its sopABC gene. SopA binds to the sopAB promoter region and SopB binds to sopC . SopA also polymerizes in the presence of ATP and Mg(II), which is stimulated by SopB. Non-specific DNA is known to inhibit SopA polymerization and disassemble SopA polymer. This study followed kinetics of polymerization and de-polymerization of SopA by turbidity measurement and found new effects by DNA and SopB. Plasmid DNA, at low concentrations, shortened the lag (nucleation) phase of SopA polymerization and also caused an initial ‘burst’ of turbidity. Results with two non-specific 20-bp DNAs indicated sequence/length dependence of these effects. sopAB operator DNA only showed inhibition of SopA polymerization. Results of turbidity decrease of pre-formed SopA polymer in the presence of ethylenediaminetetraacetic acid showed that SopB also accelerates disassembly of the SopA polymer. The steady-state level of turbidity in the presence of SopB and plasmid DNA indicated synergy between SopB and DNA in the disassembly. SopB protein showed no effect on SopA polymerization, when SopB was specifically bound to DNA. This result and others with truncation mutants of SopB suggested that a proper configuration of the domains of SopB is important for SopA-SopB interactions.
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    Preparation of monoPEGylated Cyanovirin-N's derivative and its anti-influenza A virus bioactivity in vitro and in vivo (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: Influenza A virus (IAV) has been raising public health and safety concerns worldwide. Cyanovirin-N (CVN) is a prominent anti-IAV candidate, but both cytotoxicity and immunogenicity have hindered the development of this protein as a viable therapy. In this article, linker-CVN (LCVN) with a flexible and hydrophilic polypeptide at the N-terminus was efficiently produced from the cytoplasm of Escherichia coli at a 〉15-l scale. PEGylation at the N-terminal α-amine of LCVN was also reformed as 20 kDa PEGylated linkered Cyanovirin-N (PEG 20k –LCVN). The 50% effective concentrations of PEG 20k –LCVN were 0.43 ± 0.11 µM for influenza A/HK/8/68 (H3N2) and 0.04 ± 0.02 µM for A/Swan/Hokkaido/51/96 (H5N3), dramatically lower than that of the positive control, Ribavirin (2.88 ± 0.66 x 10 3 µM and 1.79 ± 0.62 x 10 3 µM, respectively). A total of 12.5 µM PEG 20k –LCVN effectively inactivate the propagation of H3N2 in chicken embryos. About 2.0 mg/kg/day PEG 20k –LCVN increased double the survival rate (66.67%, P = 0.0378) of H3N2 infected mice, prolonged the median survival period, downregulated the mRNA level of viral nuclear protein and decreased (attenuated) the pathology lesion in mice lung. A novel PEGylated CVN derivative, PEG 20k –LCVN, exhibited potent and strain-dependent anti-IAV activity in nanomolar concentrations in vitro, as well as in micromolar concentration in vivo .
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    Overproduction and easy recovery of biofuels from engineered cyanobacteria, autolyzing multicellular cells (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: The semi-filamentous multicellular cyanobacterium Limnothrix / Pseudanabaena sp. strain ABRG5-3 undergoes autolysis, which involves the accumulation of polyphosphate compounds and disintegration of thylakoid membranes in cells, as a unique feature that occurs due to growth conditions. In this study, the overexpression and easy recovery of alkane (a saturated hydrocarbon, C 17 H 36 ) as a biofuel were examined in recombinants of the cyanobacteria ABRG5-3 and Synechocystis sp. strain PCC6803. The results obtained indicated that the accumulated mass of alkane accounted for ~50 or 60% of the dry weight of ABRG5-3 or PCC6803 recombinant cells, respectively. Furthermore, cultivating cells in liquid medium BG11 in which the nitrogen resource had been depleted promoted the production of alkane and cell lysis, resulting in the easy recovery of target products from the supernatant.
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    An early endosome regulator, Rab5b, is an LRRK2 kinase substrate (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: Leucine-rich repeat kinase 2 (LRRK2) has been identified as a causative gene for Parkinson’s disease (PD). LRRK2 contains a kinase and a GTPase domain, both of which provide critical intracellular signal-transduction functions. We showed previously that Rab5b, a small GTPase protein that regulates the motility and fusion of early endosomes, interacts with LRRK2 and co-regulates synaptic vesicle endocytosis. Using recombinant proteins, we show here that LRRK2 phosphorylates Rab5b at its Thr6 residue in in vitro kinase assays with mass spectrophotometry analysis. Phosphorylation of Rab5b by LRRK2 on the threonine residue was confirmed by western analysis using cells stably expressing LRRK2 G2019S. The phosphomimetic T6D mutant exhibited stronger GTPase activity than that of the wild-type Rab5b. In addition, phosphorylation of Rab5b by LRRK2 also exhibited GTPase activity stronger than that of the unphosphorylated Rab5b protein. Two assays testing Rab5’s activity, neurite outgrowth analysis and epidermal growth factor receptor degradation assays, showed that Rab5b T6D exhibited phenotypes that were expected to be observed in the inactive Rab5b, including longer neurite length and less degradation of EGFR. These results suggest that LRRK2 kinase activity functions as a Rab5b GTPase activating protein and thus, negatively regulates Rab5b signalling.
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    MicroRNAs as the fine-tuners of Src oncogenic signalling (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: The cellular Src (c-Src) tyrosine kinase is upregulated and believed to play a pivotal role in various human cancers. However, the molecular mechanism underlying c-Src-mediated tumour progression remains elusive. Recent studies have revealed that several microRNAs (miRNAs) function as tumour suppressors by regulating the malignant expression of signalling molecules. Aberrant expression of miRNAs is frequently observed in human cancers and should be exploited to seek related molecular targets. In this review, we focus on miRNAs found to be involved in Src signalling in various cancers. We summarize recent findings on Src-related miRNAs, their target genes, mechanisms behind their interplay and their implications for cancer therapeutics.
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    The emerging role of calcium-modulating cyclophilin ligand in posttranslational insertion of tail-anchored proteins into the endoplasmic reticulum membrane (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: Tail-anchored (TA) proteins, a class of membrane proteins having an N-terminal cytoplasmic region anchored to the membrane by a single C-terminal transmembrane domain, are posttranslationally inserted into the endoplasmic reticulum (ER) membrane. In yeasts, the posttranslational membrane insertion is mediated by the Guided Entry of TA Proteins (GET) complex. Get3, a cytosolic ATPase, targets newly synthesized TA proteins to the ER membrane, where Get2 and Get3 constitute the Get3 receptor driving the membrane insertion. While mammalian cells employ TRC40 and WRB, mammalian homologs of Get3 and Get1, respectively, they lack the gene homologous to Get2. We recently identified calcium-modulating cyclophilin ligand (CAML) as a TRC40 receptor, indicating that CAML was equivalent to Get2 in the context of the membrane insertion. On the other hand, CAML has been well characterized as a signaling molecule that regulates various biological processes, raising the question of how the two distinct actions of CAML, the membrane insertion and the signal transduction, are assembled. In this review, we summarize recent progress of the molecular mechanism of the membrane insertion of TA proteins and discuss the possibility that CAML could sense the various signals at the ER membrane, thereby controlling TA protein biogenesis.
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    Basic and aromatic residues in the C-terminal domain of PriC are involved in ssDNA and SSB binding (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: In bacterial organisms, the oriC -independent primosome plays an essential role in replication restart after dissociation of the replication DNA-protein complex following DNA damage. PriC is a key protein component in the oriC -independent replication restart primosome. Our previous study suggested that PriC was divided into an N-terminal domain and a C-terminal domain, with the latter domain being the major contributor to single-stranded DNA (ssDNA) binding capacity. In this study, we prepared several PriC mutants in which basic and aromatic amino acid residues were mutated to alanine. Five of these residues, Arg107, Lys111, Phe118, Arg121 and Lys165 in the C-terminal domain, were shown to be involved in ssDNA binding. Moreover, we evaluated the binding of the PriC mutants to the ssDNA-binding protein (SSB) complex. Five residues, Phe118, Arg121, Arg129, Tyr152 and Arg155 in the C-terminal domain of PriC, were shown to be involved in SSB binding in the presence of ssDNA. On the basis of these results, we propose a structural model of the C-terminal domain of PriC and discuss how the interactions of PriC with SSB and ssDNA may contribute to the regulation of PriC-dependent replication restart.
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    Recombinant expression, molecular characterization and crystal structure of antitumor enzyme, L-lysine {alpha}-oxidase from Trichoderma viride (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: L -Lysine α-oxidase (LysOX) from Trichoderma viride is a homodimeric 112 kDa flavoenzyme that catalyzes the oxidative deamination of L -lysine to form α-keto--aminocaproate. LysOX severely inhibited growth of cancer cells but showed relatively low cytotoxicity for normal cells. We have determined the cDNA nucleotide sequence encoding LysOX from T. viride. The full-length cDNA consists of 2,119 bp and encodes a possible signal peptide (Met1-Arg77) and the mature protein (Ala78-Ile617). The LysOX gene have been cloned and heterologously expressed in Streptomyces lividans TK24 with the enzyme activity up to 9.8 U/ml. The enzymatic properties of the purified recombinant LysOX, such as substrate specificity and thermal stability, are same as those of native LysOX. The crystal structure of LysOX at 1.9 Å resolution revealed that the overall structure is similar to that of snake venom L -amino acid oxidase (LAAO), and the residues involved in the interaction with the amino or carboxy group of the substrate are structurally conserved. However, the entrance and the inner surface structures of the funnel to the active site, as well as the residues involved in the substrate side-chain recognition, are distinct from LAAOs. These structural differences well explain the unique substrate specificity of LysOX.
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    Structure-based design of a streptavidin mutant specific for an artificial biotin analogue (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: For a multistep pre-targeting method using antibodies, a streptavidin mutant with low immunogenicity, termed low immunogenic streptavidin mutant No. 314 (LISA-314), was produced previously as a drug delivery tool. However, endogenous biotins (BTNs) with high affinity ( K d 〈 10 –10 M) for the binding pocket of LISA-314 prevents access of exogenous BTN-labelled anticancer drugs. In this study, we improve the binding pocket of LISA-314 to abolish its affinity for endogenous BTN species, therefore ensuring that the newly designed LISA-314 binds only artificial BTN analogue. The replacement of three amino acid residues was performed in two steps to develop a mutant termed V212, which selectively binds to 6-(5-((3a S ,4 S ,6a R )-2-iminohexahydro-1 H -thieno[3,4- d ]imidazol-4-yl)pentanamido)hexanoic acid (iminobiotin long tail, IMNtail). Surface plasmon resonance results showed that V212 has a K d value of 5.9 x 10 –7 M towards IMNtail, but no binding affinity for endogenous BTN species. This V212/IMNtail system will be useful as a novel delivery tool for anticancer therapy.
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    G364R mutation of MCM4 detected in human skin cancer cells affects DNA helicase activity of MCM4/6/7 complex (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: A number of gene mutations are detected in cells derived from human cancer tissues, but roles of these mutations in cancer cell development are largely unknown. We examined G364R mutation of MCM4 detected in human skin cancer cells. Formation of MCM4/6/7 complex is not affected by the mutation. Consistent with this notion, the binding to MCM6 is comparable between the mutant MCM4 and wild-type MCM4. Nuclear localization of this mutant MCM4 expressed in HeLa cells supports this conclusion. Purified MCM4/6/7 complex containing the G364R MCM4 exhibited similar levels of single-stranded DNA binding and ATPase activities to the complex containing wild-type MCM4. However, the mutant complex showed only 30–50% of DNA helicase activity of the wild-type complex. When G364R MCM4 was expressed in HeLa cells, it was fractionated into nuclease-sensitive chromatin fraction, similar to wild-type MCM4. These results suggest that this mutation does not affect assembly of MCM2-7 complex on replication origins but it interferes some step at function of MCM2-7 helicase. Thus, this mutation may contribute to cancer cell development by disturbing DNA replication.
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    Importin {alpha}: a key molecule in nuclear transport and non-transport functions (2016)
    Oxford University Press
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    Publication Date: 2016-07-30
    Description: Importin α performs the indispensable role of ferrying proteins from the cytoplasm into the nucleus with a transport carrier, importin β1. Mammalian cells from mouse or human contain either six or seven importin α subtypes, respectively, each with a tightly regulated expression. Therefore, the combination of subtype expression in a cell defines distinct signaling pathways to achieve progressive changes in gene expression essential for cellular events, such as differentiation. Recent studies reveal that, in addition to nucleocytoplasmic transport, importin αs also serve non-transport functions. In this review, we first discuss the physiological significance of importin α as a nuclear transport regulator, and then focus on the functional diversities of importin αs based on their specific subcellular and cellular localizations, such as the nucleus and plasma membrane. These findings enrich our knowledge of how importin αs actively contribute to various cellular events.
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    Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin (2016)
    Oxford University Press
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    Publication Date: 2016-07-30
    Description: The structure of the complex of maize sulfite reductase (SiR) and ferredoxin (Fd) has been determined by X-ray crystallography. Co-crystals of the two proteins prepared under different conditions were subjected to the diffraction analysis and three possible structures of the complex were solved. Although topological relationship of SiR and Fd varied in each of the structures, two characteristics common to all structures were found in the pattern of protein-protein interactions and positional arrangements of redox centres; (i) a few negative residues of Fd contact with a narrow area of SiR with positive electrostatic surface potential and (ii) [2Fe-2S] cluster of Fd and [4Fe-4S] cluster of SiR are in a close proximity with the shortest distance around 12 Å. Mutational analysis of a total of seven basic residues of SiR distributed widely at the interface of the complex showed their importance for supporting an efficient Fd-dependent activity and a strong physical binding to Fd. These combined results suggest that the productive electron transfer complex of SiR and Fd could be formed through multiple processes of the electrostatic intermolecular interaction and this implication is discussed in terms of the multi-functionality of Fd in various redox metabolisms.
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    Suppression of mitochondrial transcription initiation complexes changes the balance of replication intermediates of mitochondrial DNA and reduces 7S DNA in cultured human cells (2016)
    Oxford University Press
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    Publication Date: 2016-06-25
    Description: Analysis of replicating mammalian mitochondrial DNA (mtDNA) suggested that initiation of the replication occurs not only at the specific position, Ori-H but also across a broad zone in mtDNA. We investigated relationship of mitochondrial transcription initiation which takes place upstream of Ori-H and mtDNA replication initiation through analysing the effect of knockdown of mitochondrial transcription factor B2, TFB2M and mitochondrial RNA polymerase, POLRMT, components of the transcription initiation complexes in cultured human cells. Under the conditions where suppression of the transcription initiation complexes was achieved by simultaneous depletion of TFB2M and POLRMT, decrease of replication intermediates of mtDNA RITOLS replication mode accompanied reduction in mtDNA copy number. On the other hand, replication intermediates of coupled leading and lagging strand DNA replication, another proposed replication mode, appeared to be less affected. The findings support the view that the former mode involves transcription from the light strand promoter (LSP), and suggest that initiation of the latter mode is independent from the transcription and has distinct regulation. Further, knockdown of TFB2M alone caused significant decrease of 7S DNA, which implies that transcription initiation complexes formed at the LSP engage 7S DNA synthesis more frequently than the initiation of productive replication and transcription.
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    Two carbohydrate recognizing domains from Cycas revoluta leaf lectin show the distinct sugar-binding specificity--A unique mannooligosaccharide recognition by N-terminal domain (2016)
    Oxford University Press
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    Publication Date: 2016-06-25
    Description: Cycas revoluta leaf lectin (CRLL) of mannose-recognizing jacalin-related lectin (mJRL) has two tandem repeated carbohydrate recognition domains, and shows the characteristic sugar-binding specificity toward high mannose-glycans, compared with other mJRLs. We expressed the N-terminal domain and C-terminal domain (CRLL-N and CRLL-C) separately, to determine the fine sugar-binding specificity of each domain, using frontal affinity chromatography, glycan array and equilibrium dialysis. The specificity of CRLL toward high mannose was basically derived from CRLL-N, whereas CRLL-C had affinity for α1-6 extended mono-antennary complex-type glycans. Notably, the affinity of CRLL-N was most potent to one of three Man 8 glycans and Man 9 glycan, whereas the affinity of CRLL-C decreased with the increase in the number of extended α1-2 linked mannose residue. The recognition of the Man 8 glycans by CRLL-N has not been found for other mannose recognizing lectins. Glycan array reflected these specificities of the two domains. Furthermore, it was revealed by equilibrium dialysis method that the each domain had two sugar-binding sites, similar with Banlec, banana mannose-binding Jacalin-related lectin.
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    Performance analysis of a cascaded solar Organic Rankine Cycle with superheating (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: A cascaded Organic Rankine Cycle (ORC) with scroll expanders is investigated in this paper, the system performances under various configurations are evaluated and the effect of superheating on the system efficiency is clarified. The efficiency of two-stage ORC system is 38.9% higher than that of single-stage system when R245fa is used as the working fluid, while the efficiency of two-stage ORC system is 10% lower than that of single stage when R134a is adopted. The specific work of single-stage ORC system with R245fa increases linearly with the degree of superheat. There is an optimal superheated degree for the system output power and efficiency, which is 35 K for the expansion ratio of 3.5 and 45 K for the expansion ratio of 5.
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    Investigation of the effect of design parameters on power output and thermal efficiency of a Stirling engine by thermodynamic analysis (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: This article demonstrates a study on finite-time thermodynamic assessment and analysis of a Stirling heat engine. Finite-time thermodynamics is performed to specify the net thermal efficiency and power output of the Stirling system with finite-rate heat transfer, regenerative heat loss, conductive thermal bridging loss and finite regeneration process time. The model investigates effects of the inlet temperature of the heat source, the volumetric ratio of the engine, effectiveness of heat exchangers and heat capacitance rates on the net power output and thermal efficiency of the engine. Output power of the Stirling engine is maximized under two optimization scenarios. In the first scenario, the higher working temperature of the Stirling engine is considered as a decision design parameter (decision variable) while in the second scenario, in addition to the higher working temperature, the temperature ratio of the engine is also considered as a design parameter. Furthermore, the thermal efficiency of the cycle corresponding to the magnitude of the maximized power of the engine is evaluated. Finally, sensitivities of results towards shift in the thermal parameters of the engine are studied.
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    Energy saving potential of indirect evaporative cooler under Indian climates (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: Vapour compression refrigeration-based air conditioners are being used for comfort cooling in residences, offices and commercial buildings in many countries throughout the world. These systems consume substantial power and energy and produce harmful effect on environment by damaging ozone layer. This article presents an analytical evaluation of energy saving potential of an indirect evaporative cooler for summer months in Indian climates. Three climates likely to be suitable for indirect evaporative cooling, namely composite, hot and dry and moderate, have been selected for this purpose. The monthly average environmental data for three Indian cities namely Delhi, Jodhpur and Bangalore representing three different climates were used for this study. Summer month—May was selected for the study. It has been found that in order to produce same cooling effect under the same climatic conditions, the power needed by indirect evaporative cooler to be about 55% less than that needed by a conventional air conditioner. The performance of an indirect evaporative cooler in the climates, hot and dry and composite, has been found to be almost similar. Thus, substantial energy can be saved by using this alternative in summer months.
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    Development of a nano-heat transfer fluid carrying direct absorbing receiver for concentrating solar collectors (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: A MATLAB-based computer model to design a novel directly absorbing receiver system (DARS) for concentrating solar collectors employing nanofluid-based solar radiation volumetric absorption is presented. Graphene and aluminum nanosphere-based suspensions in Therminol VP-1 were simulated to identify the optimum thermo-geometric configuration of a DARS comprising a transparent all glass tubular absorber. Several particle concentrations were simulated scrutinizing the optical response of the two colloidal dispersions to yield a minimum supply temperature of 250°C; further investigated are the implications of fluid flow velocity upon system yield. The resulting temperature fields and geometric dimensions of the DARS are predicted. Findings demonstrate that the DARS is able to deliver heat at ~265°C with a receiver tube diameter of 5 mm opposed to commercially available 70-mm diameter metallic absorbers.
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    Mean-line modeling and CFD analysis of a miniature radial turbine for distributed power generation systems (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: Distributed power generation (DPG) based on organic Rankine cycle offers potential in the effective use of energy from low grade heat sources up to 200°C. In this regard, developing an effective expander plays a major role in determining the overall cycle efficiency. In this work mean-line modeling and CFD techniques are employed to develop a small-scale radial turbine for DPG systems with a power output of ~5 kWe. A parametric study is carried out using the mean-line approach to investigate the effects of key input parameters such as operating conditions, velocity ratio, rotational speed and rotor flow angles on the turbine rotor inlet diameter and overall performance. Results from the mean-line approach show that in order to achieve high power output, inlet total temperature, mass flow rate and pressure ratio should be increased. However, for reducing the rotor inlet diameter the velocity ratio should be decreased. CFD technique is then used to assess the flow field and to improve the blade loading by modification of blade angle distribution. CFD is also used to determine the minimum number of rotor blades and the results show that the value suggested by mean-line modeling overestimates this parameter. By using these two approaches a wide range of design configurations are explored and the most effective design is identified to be with specific diameter of 4.83 (rotor inlet diameter of 0.0787 m), specific speed of 0.433 (rotational speed of 55 000 rpm), 10 blades and output power of 4.662 kW.
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    Hybrid hydrogen PEM fuel cell and batteries without DC-DC converter (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: Concerns about greenhouse gases as well as the price and security of oil supply have acted as a spur to sustainable automobile development. The hydrogen fuel cells electric vehicle (HFCEV) is generally recognised by leading automobile manufacturers and scientists as one of the optimum technologies for long-term future low carbon vehicle. In a typical HFCEV power train, a DC–DC converter is required to balance the voltage difference between the fuel cells (FCs) stack and batteries. However, research shows that a considerable amount of energy generated by the hydrogen FCs stack is deplete during this conversion process as heat. This experiment aims to improve the power train efficiency by eliminating the DC–DC converter by finding the best combination of FC stack and batteries, matching the size and capacity of the electrical components.
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    Energy and exergy analysis of passive solar distillation systems (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: In this communication, a comprehensive thermodynamic model for exergy analysis of a passive solar distillation system is presented. Temperatures of basin-liner, saline water body and inner and outer glass cover are estimated theoretically with the help of a computer program using a set of typical design and operating parameters. Energy and exergy analysis of a single-effect, single-slope horizontal passive solar still has been carried out under climatic conditions of India. It has been shown that the passive solar still can produce 4.17 l/m 2 of freshwater daily. Energy and exergy efficiency of the solar still are 30.42 and 4.93%, respectively. Causes, quantity and place of exergy destruction have also been explored for further research and improvement in the design and performance of solar stills. Exergy destruction or irreversibility in the process of each component, i.e. basin-liner, saline water body and glass cover, has been evaluated as 3353, 1633 and 362 W/m 2 , respectively, corresponding to the total solar exergy input of 6958 W/m 2 on a typical day. Their corresponding exergy efficiencies are found to be 3.91, 17.67 and 42.36%. The global exergy efficiency of the solar still is also estimated as 23.14%, taking these exergy destructions into account. The basin-liner is identified as the component around which there is highest possibility of improvement.
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    Experimental study of a capillary pumped loop in comparison with the prediction of a 3D CFD (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: A comparison is presented between experimental and numerical results regarding the operation of a capillary pumped loop evaporator. Two cylindrical evaporators were tested, with different heated porous lengths, 20 and 40 mm, respectively. Both have 22 mm external diameter, 9 mm porous thickness and 80 mm porous length. The working liquid was water. The loop was made from copper tubes and the evaporator from copper porous wick covered with aluminum with grooves formed in the inner surface. All tests took place on a horizontal level using heat load applied to the evaporator surface from an 85-W electric resistance. The experimental measurements were compared with the predictions of a three-dimensional CFD model of the evaporator and were found to be in satisfactory agreement. For the 20-mm wick heated length evaporator CFD model with water initial temperature of 20°C the divergence with the experimental pressure drop mean value was 0 Pa for volume flow rates between 0.4 and 0.6 l/min and 50 Pa for the rest of the values. For 30°C the divergence was 0 Pa 〈0.4 l/min and 50 Pa for larger flow rates. Moreover, for 40°C the difference was up to 50 Pa from 0 to 0.9 l/min. In every case predictions were below the wick capillary limit. The computed outflow temperature presented a maximum difference of 1.5% compared with the experimental data, which is very satisfying. On the other hand, the predictions of the evaporator CFD model with a 40-mm wick heated length were even better.
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    A feasible energy-saving analysis of a new system for CO2 cryogenic capture (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: A new CO 2 cryogenic capture and liquefaction system has been proposed previously in order to separate CO 2 from exhausted gases and make it as a resource for industry. This system combines CO 2 cryogenic capture with N 2 /O 2 separation together. Its energy consumption is lower than the traditional amine solution capture process as theoretical analysis. In this study, the simulation of the proposed system with several improvements was carried out aiming to reduce the energy consumption further. Many heat exchangers were introduced and the heat exchanger arrangements were optimized to recycle the refrigeration capacity from the returned N 2 after the N 2 /O 2 separation. The discharge pressure of mixture gas from the compressor was reduced from 10 to 3.493 MPa. The simulation results showed that the compression work could be greatly reduced and the energy consumption of CO 2 capture in this new system after these improvements reached 2.884 GJ/ton CO 2 . The new system is promising because not only liquid or solid CO 2 could be produced but also N 2 and O 2 could be separated.
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    Spanish photovoltaic learning curve (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: Learning by doing, or learning through market experience, reduces costs for energy production technologies. This phenomenon is modelled by using experience curves which reflect the changes in the cost of the technology as it becomes increasingly used. This article calculates the Spanish photovoltaic (PV) learning curve over the period 2001–12 by using cost data from the PV sector itself (installers, distributors and even engineers) and determines the accuracy of the obtained progress ratio by using both the coefficient of determination R 2 and also the error PR , which is directly determined from fitting the data. The results show a curve with a strong structural change in the speed of cost reduction in October 2009.
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    An innovative psychometric solar-powered water desalination system (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: Important advances have been made in solar water desalination technology but their wide application is restricted by relatively high capital and running costs. Until recently, solar concentrator collectors had usually been employed to distill water in compact desalination systems. Currently, it is possible to replace these collectors by the more efficient evacuated tube collectors, which are now widely available on the market at lower prices. This paper describes the results of experimental and theoretical investigations of the operation of a novel small-scale solar water desalination technology using the psychometric humidification and dehumidification process coupled with a heat pipe evacuated tube solar collector with an aperture area of ~1.73 m 2 . Solar radiation during spring in the Middle East was simulated by an array of halogen floodlights. A synthetic brackish water solution was used for the tests and its total dissolved solids (TDSs) and electrical conductivity were measured. A mathematical model was developed to describe the system's operation. A computer program was written to solve the system of governing equations to perform the theoretical calculations of the humidification and dehumidification processes. The experimental and theoretical values for the total daily distillate output were found to be closely correlated. The test results demonstrate that, at temperatures of 55–60°C, the system produces ~5–6 kg/h of clean water with a high desalination efficiency. Following the experimental calibration of the mathematical model, it was demonstrated that the performance of the system could be improved to produce a considerably higher amount of fresh water.
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Thermal analysis of PCM-filled glass windows in hot summer and cold winter area (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: Phase change material (PCM)-filled glass window was suitable for absorbing or releasing more heat than conventional glass window. Comparisons of thermal performance between PCM-filled glass windows and insulated glass windows (double glass windows filled with dry air and surrounded by sealing strips) were presented in this paper. A 3D unsteady model was built in FLUENT to obtain the internal and external surface temperature fluctuations of these windows in 48 h. Compared with insulated glass windows, thermal performance (especially the thermal regulation effect) of double glass windows filled with Na 2 SO 4 ·10H 2 O was quite satisfactory in sunny days of summer, while double glass windows filled with CaCl 2 ·6H 2 O had a better thermal performance in overcast and rainy days of summer. Because the phase change temperature of these PCM is higher than the ambient temperature in winter, the thermal regulation effects of them were not as good as expected.
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    Simultaneous synthesis of heat exchanger network with the non-isothermal mixing (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: Optimization of heat exchanger network is attributed to improving the process industrial energy utilization ratio. Energy consumption reduction plays an important role in the low-carbon economic development. Several synthesis approaches for heat exchanger network have been proposed and extended during the last three decades. With the evolution of the computer technology, the simultaneous synthesis method via mathematic programming attracts a great deal of attention worldwide. However, some difficulties still need to be overcome, for instance, model simplification and computational complexity. In this work, the simultaneous stage-wise synthesis model without the assumption of isothermal mixing is presented and implemented using effective initialization strategies and a novel two-level algorithm. Three case studies illustrated the better performance of the initialization strategies and two-level algorithm for heat exchanger network synthesis problems, considering non-isothermal mixing.
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    Capturing atmospheric carbon: biological and nonbiological methods (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: Atmospheric carbon dioxide is one of the primary greenhouse gases on earth and its continuous emission by manmade activities is leading to a rise in atmospheric temperature. On the other hand, various natural phenomena exist that contribute to the sequestration of atmospheric carbon dioxide, i.e. its capture and long-term storage. These phenomena include oceanic, geological and chemical processes happening on earth. In addition to the above-mentioned nonbiological methods, various biological methods viz. soil carbon sequestration and phytosequestration have also been contributing to fixation of atmospheric carbon. Phytosequestration is mainly performed by several photosynthetic mechanisms such as C 3 , C 4 and crassulacean acid metabolism (CAM) pathways of plants, carboxysomes of cyanobacteria and pyrenoids of microalgae. For an effective mitigation of global climate change, it is required to stabilize the CO 2 concentration to viable levels. It requires various permutations and combinations of naturally existing and engineering strategies. Although numerous strategies are in commodious use in the present times, the issues of sustainability and long-term stability still exist. We present an overview of the natural and manmade biological and nonbiological processes used today to reduce atmospheric CO 2 levels and discuss the scope and limitations of each of them.
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    Performance of U-tube solar water heater with vertical and inclined panels (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: A conventional natural convection flat plate solar collector needs to be placed at an incline to the horizontal and exposed to the sun in order for the solar hot water heater system to work. This arrangement is satisfactory where there is ample roof top space to locate the collector and storage tank. In a high-rise apartment, space is at a premium and also the hot-water recticulation requires long lengths of piping to distribute the hot water supply to the individual apartment. Most every modern high-rise apartment has a balcony facing outward from the wall structure. Balcony-type solar water heaters (SWHs) are catching up fast in China. Their performance would depend on collector and storage tank designs and sizes, weather conditions (solar radiation intensity and ambient temperature) and direction in which the balconies are facing. This article compares the outdoor performance of two SWH systems incorporating the evacuated glass U-tube solar collectors operating under natural convection. The panels were tested in both the vertical and inclined positions using the same tank but at different times of the year. It was found that the inclined panel system performed better than the system with the vertical panel system.
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    Design and commission a zero-carbon building for hot and humid climate (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: The Construction Industry Council (CIC) Zero-Carbon Building is a net zero-carbon building that was designed for local hot and humid climate of sub-tropical Hong Kong. Over 80 sustainability features of the architecture and building systems have considered the life-cycle carbon emissions, including the embodied carbon of construction materials, emissions associated with the construction process, the 50-years of operation and decommission of the building. The total life-cycle carbon emission was off-set by on-site renewable energy generated by photovoltaics (PV) and bio-diesel combined cooling heating and power (CCHP) system. To optimise the design, a series of climate-responsive strategies on passive architecture were applied to the construction of the building. These include the high-performance facade, effective air tightness and optimised window design that allows the application of natural ventilation and daylighting. Reduction of 20% energy demand was achieved by these passive designs. To further lower the carbon emission on operation, energy-efficient air-conditioning (A/C) systems using desiccant dehumidification, underfloor air supply and radiant cooling have also contributed on achieving an ultralow energy use value. Amalgamated saving of these passive and active systems are over 45% when compared with the design per existing local building energy codes.
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    Affinity maturation of a CDR3-grafted VHH using in silico analysis and surface plasmon resonance (2013)
    Oxford University Press
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    Publication Date: 2013-10-02
    Description: A requirement for advancing antibody-based medicine is the development of proteins that can bind with high affinity to a specific epitope related to a critical protein activity site. As a part of generating such proteins, we have succeeded in creating a binding protein without changing epitope by complementarity-determining region 3 (CDR3) grafting (Inoue et al. , Affinity transfer to a human protein by CDR3 grafting of camelid VHH. Protein Sci. 20, 1971–1981). However, the affinity of the target-binding protein was low. In this manuscript, the affinity maturation of a target-binding protein was examined using CDR3-grafted camelid single domain antibody (VHH) as a model protein. Several amino acids in the CDR1 and CDR2 regions of VHH were mutated to tyrosines and/or serines and screened for affinity-matured proteins by using in silico analysis. The mutation of two amino acids in the CDR2 region to arginine and/or aspartic acid increased the affinity by decreasing the dissociation rate. The affinity of designed mutant increased by ~20-fold over that of the original protein. In the present study, candidate mutants were narrowed down using in silico screening and computational modelling, thus avoiding much in vitro analytical effort. Therefore, the method used in this study is expected to be one of the useful for promoting affinity maturation of antibodies.
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    Topics: Biology , Chemistry and Pharmacology
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    Characterization of deamidation at Asn138 in L-chain of recombinant humanized Fab expressed from Pichia pastoris (2013)
    Oxford University Press
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    Publication Date: 2013-10-02
    Description: A method was previously established for evaluating Asn deamidation by matrix-assisted laser desorption/ionization time of flight-mass spectrometry using endoproteinase Asp-N. In this study, we demonstrated that this method could be applied to the identification of the deamidation site of the humanized fragment antigen-binding (Fab). First, a system for expressing humanized Fab from methylotrophic yeast Pichia pastoris was constructed, resulting in the preparation of ~30 mg of the purified humanized Fab from 1 l culture. Analysis of the L-chain derived from recombinant humanized Fab that was heated at pH 7 and 100°C for 1 h showed the deamidation at Asn138 in the constant region. Then, we prepared L-N138D Fab and L-N138A Fab and examined their properties. The circular dichroism (CD) spectrum of the L-N138D Fab was partially different from that of the wild-type Fab. The measurement of the thermostability showed that L-N138D caused a significant decrease in the thermostability of Fab. On the other hand, the CD spectrum and thermostability of L-N138A Fab showed the same behaviour as the wild-type Fab. Thus, it was suggested that the introduction of a negative charge at position 138 in the L-chain by the deamidation significantly affected the stability of humanized Fab.
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    TRIM proteins as trim tabs for the homoeostasis (2013)
    Oxford University Press
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    Publication Date: 2013-10-02
    Description: The tripartite motif (TRIM) or RBCC proteins are characterized by the TRIM composed of a RING finger, B-box and coiled-coil domains. TRIM proteins often play roles in the post-translational protein modification, including ubiquitylation and other ubiquitin-like modifications. Evidence has accumulated in regard to the contribution of TRIM proteins to diverse cellular processes, including such as cell cycle progression, apoptosis, immunity and transcriptional regulation. In particular, some of the TRIM proteins have been characterized to exert oncogenic or tumour suppressor-like functions depending on the context. A recent report by Inoue and his colleagues has revealed that Terf/TRIM17 stimulates the degradation of a kinetochore protein ZWINT and regulates the proliferation of breast cancer cells. Terf has also been paid attention as a factor promoting neuronal apoptosis, by degrading a Bcl2-like anti-apoptotic protein Mcl-1. Like aircraft trim tabs, TRIM proteins trim the balance of homoeostasis by modulating various biological pathways through protein–protein interactions.
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    Inhibition of DNA binding of MCM2-7 complex by phosphorylation with cyclin-dependent kinases (2013)
    Oxford University Press
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    Publication Date: 2013-10-02
    Description: Cyclin-dependent kinase (CDK) that plays a central role in preventing re-replication of DNA phosphorylates several replication proteins to inactivate them. MCM4 in MCM2-7 and RPA2 in RPA are phosphorylated with CDK in vivo . There are inversed correlations between the phosphorylation of these proteins and their chromatin binding. Here, we examined in vitro phosphorylation of human replication proteins of MCM2-7, RPA, TRESLIN, CDC45 and RECQL4 with CDK2/cyclinE, CDK2/cyclinA, CDK1/cyclinB, CHK1, CHK2 and CDC7/DBF4 kinases. MCM4, RPA2, TRESLIN and RECQL4 were phosphorylated with CDKs. Effect of the phosphorylation by CDK2/cyclinA on DNA-binding abilities of MCM2-7 and RPA was examined by gel-shift analysis. The phosphorylation of RPA did not affect its DNA-binding ability but that of MCM4 inhibited the ability of MCM2-7. Change of six amino acids of serine and threonine to alanines in the amino-terminal region of MCM4 rendered the mutant MCM2-7 insensitive to the inhibition with CDK. These biochemical data suggest that phosphorylation of MCM4 at these sites by CDK plays a direct role in dislodging MCM2-7 from chromatin and/or preventing re-loading of the complex to chromatin.
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    Effects of alcohols on the stability and low-frequency local motions that control the slow changes in structural dynamics of ferrocytochrome c (2013)
    Oxford University Press
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    Publication Date: 2013-10-02
    Description: To determine the effects of alcohols on the low-frequency local motions that control slow changes in structural dynamics of native-like compact states of proteins, we have studied the effects of alcohols on structural fluctuation of M80-containing -loop by measuring the rate of thermally driven CO dissociation from a natively folded carbonmonoxycytochrome c under varying concentrations of alcohols (methanol, ethanol, 1-propanol, 2-propanol, 3°-butanol, 2,2,2-trifluoroethanol). As alcohol is increased, the rate coefficient of CO dissociation ( k diss ) first decreases in subdenaturing region and then increases on going from subdenaturing to denaturing milieu. This decrease in k diss is more for 2,2,2-trifluroethanol and 1-propanol and least for methanol, indicating that the first phase of motional constraint is due to the hydrophobicity of alcohols and intramolecular protein cross-linking effect of alcohols, which results in conformational entropy loss of protein. The thermal denaturation midpoint for ferrocytochrome c decreases with increase in alcohol, indicating that alcohol decrease the global stability of protein. The stabilization free energy ( G ) in alcohols’ solution was calculated from the slope of the Wyman–Tanford plot and water activity. The m -values obtained from the slope of G versus alcohols plot were found to be more negative for longer and linear chain alcohols, indicating destabilization of proteins by alcohols through disturbance of hydrophobic interactions and hydrogen bonding.
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    Linear ubiquitination-mediated NF-{kappa}B regulation and its related disorders (2013)
    Oxford University Press
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    Publication Date: 2013-10-02
    Description: Ubiquitination is a post-translational modification involved in the regulation of a broad variety of cellular functions, such as protein degradation and signal transduction, including nuclear factor-B (NF-B) signalling. NF-B is crucial for inflammatory and immune responses, and aberrant NF-B signalling is implicated in multiple disorders. We found that linear ubiquitin chain assembly complex (LUBAC), composed of HOIL-1L, HOIP and SHARPIN, generates a novel type of Met1 (M1)-linked linear polyubiquitin chain and specifically regulates the canonical NF-B pathway. Moreover, specific deubiquitinases, such as CYLD, A20 (TNFAIP3) and OTULIN/gumby, inhibit LUBAC-induced NF-B activation by different molecular mechanisms, and several M1-linked ubiquitin-specific binding domains have been structurally defined. LUBAC and these linear ubiquitination-regulating factors contribute to immune and inflammatory processes and apoptosis. Functional impairments of these factors are correlated with multiple disorders, including autoinflammation, immunodeficiencies, dermatitis, B-cell lymphomas and Parkinson’s disease. This review summarizes the molecular basis and the pathophysiological implications of the linear ubiquitination-mediated NF-B activation pathway regulation by LUBAC.
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    Different circadian expression of major matrix-related genes in various types of cartilage: modulation by light-dark conditions (2013)
    Oxford University Press
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    Publication Date: 2013-10-02
    Description: We screened circadian-regulated genes in rat cartilage by using a DNA microarray analysis. In rib growth-plate cartilage, numerous genes showed statistically significant circadian mRNA expression under both 12:12 h light–dark and constant darkness conditions. Type II collagen and aggrecan genes—along with several genes essential for post-translational modifications of collagen and aggrecan, including prolyl 4-hydroxylase 1, lysyl oxidase, lysyl oxidase-like 2 and 3'-phosphoadenosine 5'-phosphosulphate synthase 2—showed the same circadian phase. In addition, the mRNA level of SOX9, a master transcription factor for the synthesis of type II collagen and aggrecan, has a similar phase of circadian rhythms. The circadian expression of the matrix-related genes may be critical in the development and the growth of various cartilages, because similar circadian expression of the matrix-related genes was observed in hip joint cartilage. However, the circadian phase of the major matrix-related genes in the rib permanent cartilage was almost the converse of that in the rib growth-plate cartilage under light–dark conditions. We also found that half of the oscillating genes had conserved clock-regulatory elements, indicating contribution of the elements to the clock outputs. These findings suggest that the synthesis of the cartilage matrix macromolecules is controlled by cell-autonomous clocks depending upon the in vivo location of cartilage.
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    Association of epigenetic alterations in the human C7orf24 gene with the aberrant gene expression in malignant cells (2013)
    Oxford University Press
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    Publication Date: 2013-10-02
    Description: Human chromosome 7 open reading frame 24 (C7orf24)/-glutamyl cyclotransferase has been suggested to be a potential diagnostic marker for several cancers, including carcinomas in the bladder urothelium, breast and endometrial epithelium. We here investigated the epigenetic regulation of the human C7orf24 promoter in normal diploid ARPE-19 and IMR-90 cells and in the MCF-7 and HeLa cancer cell lines to understand the transcriptional basis for the malignant-associated high expression of C7orf24. Chromatin immunoprecipitation analysis revealed that histone modifications associated with active chromatin were enriched in the proximal region but not in the distal region of the C7orf24 promoter in HeLa and MCF-7 cells. In contrast, elevated levels of histone modifications leading to transcriptional repression and accumulation of heterochromatin proteins in the C7orf24 promoter were observed in the ARPE-19 and IMR-90 cells, compared to the levels in HeLa and MCF-7 cancer cells. In parallel, the CpG island of the C7orf24 promoter was methylated to a greater extent in the normal cells than in the cancer cells. These results suggest that the transcriptional silencing of the C7orf24 gene in the non-malignant cells is elicited through heterochromatin formation in its promoter region; aberrant expression of C7orf24 associated with malignant alterations results from changes in chromatin dynamics.
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    Identification and characterization of interactions between abscisic acid and human heat shock protein 70 family members (2013)
    Oxford University Press
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    Publication Date: 2013-10-02
    Description: Abscisic acid (ABA) is a stress-inducible plant hormone comprising an inevitable component of the human diet. Recently, stress-induced accumulation of autocrine ABA was shown in humans, as well as ABA-mediated modulation of a number of disease-associated systems. Now, the application of a chemical proteomics approach to gain further insight into ABA mechanisms of action in mammalian cells is reported. An ABA mimetic photoaffinity probe was applied to intact mammalian insulinoma and embryonic cells, leading to the identification of heat shock protein 70 (HSP70) family members, (including GRP78 and HSP70-2) as putative human ABA-binding proteins. In vitro characterization of the ABA–HSP70 interactions yielded K d s in the 20–60 µM range, which decreased several fold in the presence of co-chaperone. However, ABA was found to have only variable- and co-chaperone-independent effects on the ATPase activity of these proteins. The potential implications of these ABA–HSP70 interactions are discussed with respect to the intracellular protein folding and extracellular receptor-like activities of these stress-inducible proteins. While mechanistic and functional relevance remain enigmatic, we conclude that ABA can bind to human HSP70 family members with physiologically relevant affinities and in a co-chaperone-dependent manner.
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    RETRACTION of: Down-regulation of protein tyrosine phosphatase gene expression in lactating mouse mammary gland (2013)
    Oxford University Press
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    Publication Date: 2013-10-02
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    The retrofitting of an old style semi-detached house for energy reduction and carbon savings under the UK climate (2015)
    Oxford University Press
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    Publication Date: 2015-05-13
    Description: The impact of climatic change through greenhouse gas emission is a recognized major global crisis. Energy use in residential and commercial buildings is a major part of the total consumption in European countries and is estimated to be ~40% of the total load. Currently, the concept of building retrofit has become a top priority for the UK government in order to meet the national plans for reducing CO 2 emissions by 80% compared with 1990 levels by 2050. This study presents the simulation results for a case study of energy and CO 2 emission savings of a nineteenth century semi-detached building in the UK. The building was refurbished to high standards of energy efficiency, with four simulation scenarios developed for analysis: As-built, As-built 1965, As-reality and post-retrofit. DesignBuilder software was used to simulate the annual energy consumption and carbon emissions in all cases. In addition to this, thermal imaging and air-tightness tests were conducted and the results were used to validate the models. The post-retrofit results showed there is a significant reduction in energy consumption that exceeded 80% with carbon emissions being reduced above 70%. Economic analysis of each retrofit scenario was then undertaken, and results showed payback varied between 9 and 40 years due to the fluctuation in fuel prices and construction retrofit materials. The models indicate performance of the building post-retrofit can be significantly improved in terms of energy reduction and CO 2 emission savings. Further research is being performed to improve performance through field monitoring and installation of innovative retrofit technologies.
    Keywords: Sustainable/low carbon buildings
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    Numerical analysis of solar-assisted seasonal 'open' thermochemical heat storage (2015)
    Oxford University Press
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    Publication Date: 2015-05-13
    Description: In the last decade, interest in heat storage systems has been increasing. These systems will have increasing importance for utilization of solar energy in domestic heating systems. As solar energy is a diurnal cyclic resource, storing excess solar energy for long- or short-term periods will both increase the utilization of solar energy systems and decrease fossil fuel consumption. The relatively new heat storage method using thermochemical storage has shown some significant advantages such as low heat loss (-〉 zero), high heat storage density and low space requirement. These important properties make thermochemical storage a promising alternative for long-term energy storage. In the present study, a numerical investigation on ‘open’ seasonal thermochemical storage has been undertaken. The simulation results show that the volume/mass of the absorbent, mass flow rate and relative humidity of air have significant importance on the reaction kinetics and system performance during the system discharging process. Conversely, total collector area, solar radiation and mass flow rate of air are important parameters during the charging process. The results conclude that, overall, reactor design is the most important factor for storage performance. In addition, reaction advancement ( X ) has a significant importance on process efficiency.
    Keywords: Other low-carbon energy technologies
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    High-efficiency ventilation and heating systems by means of solar air collectors for industry building refurbishment (2015)
    Oxford University Press
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    Publication Date: 2015-05-13
    Description: For the purpose of energy conservation, modern buildings are becoming more and more air-tight and generally rely on a mechanical ventilation system. According to the literature, solar air heating systems can contribute in a cost-effective way to the heating and ventilation of utility buildings. Especially cost-efficient, unglazed, façade-integrated solar air collectors seem to be an attractive new market for façade renovation. To demonstrate the technical feasibility of generating heating energy on facades, a demonstration plant based on an unglazed solar air collector was installed in 2013 in the façade of a demonstration building and was intensively studied using energy metering.
    Keywords: Sustainable/low carbon buildings
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Solar low-pressure turbo-ejector Maisotsenko cycle-based power system for electricity, heating, cooling and distillation (2015)
    Oxford University Press
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    Publication Date: 2015-05-13
    Description: The article describes the innovative solutions of power, heating and cooling generation utilizing low- or medium-grade heat sources. The proposed technology based on the well-known irreversible Brayton cycle and the revolutionary Maisotsenko cycle (M-cycle) operates at atmospheric or sub-atmospheric pressures. Such energetic systems are simple and reliable and utilize moisture-saturated air as a working fluid. The ejector replacing the mechanical compressor in the Brayton cycle system allows increasing the cycle work by three to five times at the constant airflow. At the same time, the utilized heat serves for simultaneous heating and cooling production that makes the system economically viable and environmentally friendly with the increased integral performance. For system's performance improvement, the schematic and the cycle were upgraded allowing the off-the-shelf components to be employed and replace the electrically driven fan with fluidic jet-fan that served for energy saving of the innovative turbo-ejector system operation.
    Keywords: Solar energy technologies
    Print ISSN: 1748-1317
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Optimization of building-integrated photovoltaic thermal air system combined with thermal storage (2015)
    Oxford University Press
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    Publication Date: 2015-05-13
    Description: Photovoltaic (PV) combined with phase change material (PV/PCM) system is a hybrid solar system that uses a PCM to reduce the PV temperature and to store energy for other applications. This study aims to increase the integrated PV efficiency of buildings by incorporating PCM while utilizing the stored heat in PCM for controlling indoor conditions. Experiments have been carried out on a prototype PV/PCM air system using monocrystalline PV modules. Transient simulations of the system performance have also been performed using a commercial computational fluid dynamics package based on the finite volume method. The results from simulation were validated by comparing it with experimental results. The results indicate that PCM is effective in limiting temperature rise in PV device and the heat from PCM can enhance night ventilation and decrease the building energy consumption to achieve indoor thermal comfort for certain periods of time.
    Keywords: Other low-carbon energy technologies
    Print ISSN: 1748-1317
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Thermal energy storage: the role of the heat pipe in performance enhancement (2015)
    Oxford University Press
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    Publication Date: 2015-05-13
    Description: Heat pipes and thermosyphons—devices of high effective thermal conductivity—have been studied for many years for enhancing the performance of solid, liquid and phase change material (PCM) heat stores. However, as the applications of heat storage widen, from micro-electronics thermal control to concentrated solar heat storage and vehicle thermal management, and even for chemical reactor isothermalization, the challenges facing heat storage increasingly are moving from those associated with the ‘standard’ diurnal storage, in itself a problem for low thermal conductivity materials, to response times measured in a few hours or even minutes. While high thermal conductivity metals such as foams can be impregnated with a PCM, for example, to increase local conductivity, the rapid heat input and removal necessitates a more radical approach—heat pipes, possibly with feedback control, with innovative PCM interfaces. This paper reviews the use of heat pipes in conventional and rapid response PCM and liquid or cold storage applications and introduces some novel concepts that might overcome current limitations.
    Keywords: Other low-carbon energy technologies
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Identifying bottlenecks in charging infrastructure of plug-in hybrid electric vehicles through agent-based traffic simulation (2015)
    Oxford University Press
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    Publication Date: 2015-05-13
    Description: The effect of different charging infrastructure configurations on the electric-driven distance of plug-in hybrid electric vehicles (e-mileage) has been investigated, using an agent-based traffic simulation. Our findings suggest that the same e-mileage can be achieved with fewer charging poles if the poles support charging from several parking slots around them, and the charging cable is switched from one vehicle to the next. We also find that the charging power supported by most Finnish charging stations, 3.7 kW, and the cable switching delay of 1 h seem to be sufficient for effective workplace charging.
    Keywords: Other low-carbon energy technologies
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    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Probe optimization for sequencing by ligation (2015)
    Oxford University Press
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    Publication Date: 2015-04-29
    Description: Sequencing by ligation (SBL) is a straightforward enzymatic method for interrogating DNA sequence, in which the ligation efficiency and specificity of each probe play an essential role. Here, the number of labelled dyes in the probe, probe length and probe constituent were investigated to optimize the ligation efficiency and specificity. First, the performance of double- and single-labelled fluorescent probes in SBL was evaluated. The experimental results showed that double-labelled fluorescent probes could yield a remarkable increase in the fluorescence intensities and avoid higher background compared with single-labelled fluorescent probes. Second, probes between 7- and 9-mers in length were designed to uniform T m difference. We hoped the uniformed probes with smaller T m difference could improve the ligation efficiency. However, 8-mer probes with larger T m difference showed stronger fluorescence intensities. Third, we evaluated whether probes containing deoxyinosines either in the 5' or the 3' end had influence on the ligation efficiency. Consequently, probes containing deoxyinosines at the 5' termini might decrease the ligation efficiency, and the accumulation of 3' terminal deoxyinosines in the sequencing primers was likely to reduce the fluorescence intensity and the ligation efficiency, which was inconsistent with the traditional viewpoint. The optimized probes will improve the ligation efficiency and accuracy in SBL.
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    Topics: Biology , Chemistry and Pharmacology
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    The peroxidase activity of bleomycin-Fe3+ is associated with damage to biological components (2015)
    Oxford University Press
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    Publication Date: 2015-03-28
    Description: In this study, bleomycin-Fe 3+ steadily oxidized tetramethylbenzidine (TMB) in the presence of peroxides. However, the ability of bleomycin-Fe 3+ to function as a peroxidase was extremely low compared with that of other peroxidases. A characteristic property of bleomycin-Fe 3+ different from that observed for other peroxidases is its ability to oxidize TMB at the similar rate at both a pH 5 and 8 in the presence of lipid hydroperoxide (LOOH). In the present experiments, hydroxyl radicals (HO•) were generated only when bleomycin-Fe 3+ was incubated with H 2 O 2 at a pH of 5. No generation of HO• was observed during the incubation of bleomycin-Fe 3+ with LOOH. Meanwhile, bleomycin-Fe 3+ induced the formation of LOOH from linoleic acid and alcohol dehydrogenase was inactivated by bleomycin-Fe 3+ with peroxides. Thiobarbituric acid reactive substances were formed from DNA by bleomycin-Fe 3+ with H 2 O 2 , and strand breaks were caused by bleomycin-Fe 3+ with LOOH. The oxidative substrates for bleomycin-Fe 3+ blocked the damage to biological components induced by bleomycin-Fe 3+ . These results suggest that compound I-like species contribute to the process of damage to biological components induced by bleomycin-Fe 3+ .
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    Ral GTPases: crucial mediators of exocytosis and tumourigenesis (2015)
    Oxford University Press
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    Publication Date: 2015-04-29
    Description: The Ral guanosine triphosphatases (GTPases), RalA and RalB, are members of the Ras superfamily of small GTPases. Research on Ral GTPases and their functions over the past 25 years has revealed the essential involvement of these GTPases in unique and diverse cellular processes including exocyst-mediated exocytosis and related cellular activities. Moreover, it is increasingly appreciated that the aberrant activation of Ral GTPases is one of the major causes of human tumourigenesis induced by oncogenic Ras. Recent evidence suggests that Ral signalling pathways may be potential therapeutic targets for the treatment of human cancers. This review summarizes recent advance in the investigation of Ral GTPases.
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    Identification of diphtheria toxin R domain mutants with enhanced inhibitory activity against HB-EGF (2015)
    Oxford University Press
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    Publication Date: 2015-04-29
    Description: Heparin-binding epidermal growth factor-like growth factor (HB-EGF), a ligand of EGF receptor, is involved in the growth and malignant progression of cancers. Cross-reacting material 197, CRM197, a non-toxic mutant of diphtheria toxin (DT), specifically binds to the EGF-like domain of HB-EGF and inhibits its mitogenic activity, thus CRM197 is currently under evaluation in clinical trials for cancer therapy. To develop more potent DT mutants than CRM197, we screened various mutant proteins of R domain of DT, the binding site for HB-EGF. A variety of R-domain mutant proteins fused with maltose-binding protein were produced and their inhibitory activity was evaluated in vitro . We found four R domain mutants that showed much higher inhibitory activity against HB-EGF than wild-type (WT) R domain. These R domain mutants suppressed HB-EGF-dependent cell proliferation more effectively than WT R domain. Surface plasmon resonance revealed their higher affinity to HB-EGF than WT R domain. CRM197(R460H) carrying the newly identified mutation showed increased cell proliferation inhibitory activity and affinity to HB-EGF. These results suggest that CRM197(R460H) or other recombinant proteins carrying newly identified mutation(s) in the R domain are potential therapeutics targeting HB-EGF.
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    The role of osteoclast differentiation and function in skeletal homeostasis (2016)
    Oxford University Press
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    Publication Date: 2016-01-09
    Description: Osteoclasts are giant multinucleated cells that differentiate from hematopoietic cells in the bone marrow and carry out important physiological functions in the regulation of skeletal homeostasis as well as hematopoiesis. Osteoclast biology shares many features and components with cells of the immune system, including cytokine-receptor interactions (RANKL-RANK), intracellular signalling molecules (TRAF6) and transcription factors (NFATc1). Although the roles of these molecules in osteoclast differentiation are well known, fundamental questions remain unsolved, including the exact location of the RANKL-RANK interaction and the in vivo temporal and spatial information on the transformation of hematopoietic cells into bone-resorbing osteoclasts. This review focuses on the importance of cell-cell contact and metabolic adaptation for differentiation, relatively overlooked aspects of osteoclast biology and biochemistry.
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    Endosomal escape efficiency of fusogenic B18 and B55 peptides fused with anti-EGFR single chain Fv as estimated by nuclear translocation (2016)
    Oxford University Press
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    Publication Date: 2016-01-09
    Description: Although monoclonal antibodies have been used not only as analytical tools but also as biologic therapeutics, they cannot target intracellular proteins due to their large molecular size and low membrane permeability, which limit their applications. During previous attempts to delivery antibodies intracellularly, the low efficiency of escape from endosomes to the cytosol reduced the bioavailability of antibodies or antibody-conjugated effectors. Recently, we found that the fusogenic peptides (FPs) B18 and B55 from bindin, a sea urchin gamete recognition protein, facilitated the endosomal escape of FP-fused enhanced green fluorescent protein (eGFP) and/or of co-administered cargos such as dextrans [Niikura et al. A fusogenic peptide from a sea urchin fertilization protein promotes intracellular delivery of biomacromolecules by facilitating endosomal escape. J. Control. Release 2015;212:85-93]. In this study, we constructed FP-fused anti-epidermal growth factor receptor (EGFR) single-chain Fv (αEGFR[scFv]) proteins and evaluated their endosomal escape efficiency by utilizing a nuclear localization signal). When the FP-fused αEGFR[scFv] proteins were incubated with A431 cells, the estimated endosomal escape efficiency of αEGFR[scFv]-B18 was significantly higher than that of αEGFR[scFv] alone, suggesting that the B18 peptide facilitates endosomal escape of the conjugated scFv in cis . Moreover, αEGFR[scFv]-B55 promoted the intracellular uptake of co-administered eGFP and dextrans in trans . These results imply that B18- and B55-fused antibodies may be useful for the cell-specific intracellular delivery of biomacromolecules.
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    PqqE from Methylobacterium extorquens AM1: a radical S-adenosyl-L-methionine enzyme with an unusual tolerance to oxygen (2016)
    Oxford University Press
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    Publication Date: 2016-01-09
    Description: Methylobacterium extorquens AM1 is an aerobic facultative methylotroph known to secrete pyrroloquinoline quinone (PQQ), a cofactor of a number of bacterial dehydrogenases, into the culture medium. To elucidate the molecular mechanism of PQQ biosynthesis, we are focusing on PqqE which is believed to be the enzyme catalysing the first reaction of the pathway. PqqE belongs to the radical S -adenosyl- l -methionine (SAM) superfamily, in which most, if not all, enzymes are very sensitive to dissolved oxygen and rapidly inactivated under aerobic conditions. We here report that PqqE from M. extorquens AM1 is markedly oxygen-tolerant; it was efficiently expressed in Escherichia coli cells grown aerobically and affinity-purified to near homogeneity. The purified and reconstituted PqqE contained multiple (likely three) iron-sulphur clusters and showed the reductive SAM cleavage activity that was ascribed to the consensus [4Fe-4S] 2+ cluster bound at the N-terminus region. Mössbauer spectrometric analyses of the as-purified and reconstituted enzymes revealed the presence of [4Fe-4S] 2+ and [2Fe-2S] 2+ clusters as the major forms with the former being predominant in the reconstituted enzyme. PqqE from M.extorquens AM1 may serve as a convenient tool for studying the molecular mechanism of PQQ biosynthesis, avoiding the necessity of establishing strictly anaerobic conditions.
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    Functional implication of archaeal homologues of human RNase P protein pair Pop5 and Rpp30 (2016)
    Oxford University Press
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    Publication Date: 2016-01-09
    Description: Pho Pop5 and Pho Rpp30 in the hyperthermophilic archaeon Pyrococcus horikoshii , homologues of human ribonuclease P (RNase P) proteins hPop5 and Rpp30, respectively, fold into a heterotetramer [ Pho Rpp30–( Pho Pop5) 2 – Pho Rpp30], which plays a crucial role in the activation of RNase P RNA ( Pho pRNA). Here, we examined the functional implication of Pho Pop5 and Pho Rpp30 in the tetramer. Surface plasmon resonance (SPR) analysis revealed that the tetramer strongly interacts with an oligonucleotide including the nucleotide sequence of a stem-loop SL3 in Pho pRNA. In contrast, Pho Pop5 had markedly reduced affinity to SL3, whereas Pho Rpp30 had little affinity to SL3. SPR studies of Pho Pop5 mutants further revealed that the C-terminal helix (α4) in Pho Pop5 functions as a molecular recognition element for SL3. Moreover, gel filtration indicated that Pho Rpp30 exists as a monomer, whereas Pho Pop5 is an oligomer in solution, suggesting that Pho Rpp30 assists Pho Pop5 in attaining a functionally active conformation by shielding hydrophobic surfaces of Pho Pop5. These results, together with available data, allow us to generate a structural and mechanistic model for the Pho pRNA activation by Pho Pop5 and Pho Rpp30, in which the two C-terminal helices (α4) of Pho Pop5 in the tetramer whose formation is assisted by Pho Rpp30 act as binding elements and bridge SL3 and SL16 in Pho pRNA.
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    Regulation of bone metabolism by Wnt signals (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: Wnt ligands play a central role in the development and homeostasis of various organs through β-catenin-dependent and -independent signalling. The crucial roles of Wnt/β-catenin signals in bone mass have been established by a large number of studies since the discovery of a causal link between mutations in the low-density lipoprotein receptor-related protein 5 ( Lrp5 ) gene and alternations in human bone mass. The activation of Wnt/β-catenin signalling induces the expression of osterix, a transcription factor, which promotes osteoblast differentiation. Furthermore, this signalling induces the expression of osteoprotegerin, an osteoclast inhibitory factor in osteoblast-lineage cells to prevent bone resorption. Recent studies have also shown that Wnt5a, a typical non-canonical Wnt ligand, enhanced osteoclast formation. In contrast, Wnt16 inhibited osteoclast formation through β-catenin-independent signalling. In this review, we discussed the current understanding of the Wnt signalling molecules involved in bone formation and resorption.
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    Evolutionary well-conserved region in the signal peptide of parathyroid hormone-related protein is critical for its dual localization through the regulation of ER translocation (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: Parathyroid hormone-related protein (PTHrP) has two different targeting signals: an N-terminal signal peptide for the endoplasmic reticulum (ER) targeting and an internal nuclear localization signal. The protein not only functions as a secretory protein, but is also found in the nucleus and/or nucleolus under certain conditions. PTHrP signal peptide is less hydrophobic than most signal peptides mainly due to its evolutionarily well-conserved region (QQWS). The substitution of four tandem leucine residues for this conserved region resulted in a significant inhibition of the signal peptide cleavage. At the same time, proportion of nuclear and/or nucleolar localization decreased, probably due to tethering of the protein to the ER membrane by the uncleaved mutant signal peptide. Almost complete cleavage of the signal peptide accompanied by a lack of nuclear/nucleolar localization was achieved by combining the hydrophobic h-region and an optimized sequence of the cleavage site. In addition, mutational modifications of the distribution of charged residues in and around the signal peptide affect its cleavage and/or nuclear/nucleolar localization of the protein. These results indicate that the well-conserved region in the signal peptide plays an essential role in the dual localization of PTHrP through ER targeting and/or the membrane translocation.
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    Limitation of tuning the antibody-antigen reaction by changing the value of pH and its consequence for hyperthermia (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: Distribution of the isoelectric point (pI) was calculated for the hypervariable regions of Fab fragments of the antibody molecules, which structure is annotated in the structural antibody database SabDab. The distribution is consistent with the universal for all organisms dividing the proteome into two sets of acidic and basic proteins. It shows the additional fine structure in a form of the narrow-sized peaks of pI values. This is an explanation why a small change of the environmental pH can have a strong effect on the antibody-antigen affinity. To show this, a typical enzyme-linked immunospecific assay experiment for testing the reaction of goat anti-human IgA antibodies with human IgA immunoglobulins of saliva as antigens was modified in such a way that Fe 3 O 4 magnetic nanoparticles were added to PBS buffer. The magnetic nanoparticles were remotely heated by the radio frequency magnetic field providing the local change of temperature and pH. It was observed that short times of the heating were significantly increasing the antibody-antigen binding strength while it was not the case for a longer time. The finding discussed in the study can be useful for biopharmaceuticals using antibodies, the immunoassay techniques as well as for control over the use of hyperthermia.
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    5-Aminoimidazole-4-carboxyamide-1-{beta}-D-ribofranoside stimulates the rat enhancer of split- and hairy-related protein-2 gene via atypical protein kinase C lambda (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: The 5'-AMP-activated protein kinase (AMPK) functions as a cellular energy sensor. 5-Aminoimidazole-4-carboxyamide-1-β-D-ribofranoside (AICAR) is a chemical activator of AMPK. In the liver, AICAR suppresses expression of the phosphoenolpyruvate carboxykinase ( PEPCK ) gene. The rat enhancer of split- and hairy-related protein-2 (SHARP-2) is an insulin-inducible transcriptional repressor and its target is the PEPCK gene. In this study, we examined an issue of whether the SHARP-2 gene expression is regulated by AICAR via the AMPK. AICAR increased the level of SHARP-2 mRNA in H4IIE cells. Whereas an AMPK inhibitor, compound-C, had no effects on the AICAR-induction, inhibitors for both phosphoinositide 3-kinase (PI 3-K) and protein kinase C (PKC) completely diminished the effects of AICAR. Western blot analyses showed that AICAR rapidly activated atypical PKC lambda (aPKC). In addition, when a dominant negative form of aPKC was expressed, the induction of SHARP-2 mRNA level by AICAR was inhibited. Calcium ion is not required for the activation of aPKC. A calcium ion-chelating reagent had no effects on the AICAR-induction. Furthermore, the AICAR-induction was inhibited by treatment with an RNA polymerase inhibitor or a protein synthesis inhibitor. Thus, we conclude that the AICAR-induction of the SHARP-2 gene is mediated at transcription level by a PI 3-K/aPKC pathway.
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    Phospho-ubiquitin: upending the PINK-Parkin-ubiquitin cascade (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: Mitochondria with decreased membrane potential are characterized by defects in protein import into the matrix and impairments in high-efficiency synthesis of ATP. These low-quality mitochondria are marked with ubiquitin for selective degradation. Key factors in this mechanism are PTEN-induced putative kinase 1 (PINK1, a mitochondrial kinase) and Parkin (a ubiquitin ligase), disruption of which has been implicated in predisposition to Parkinson’s disease. Previously, the clearance of damaged mitochondria had been thought to be the end result of a simple cascading reaction of PINK1–Parkin–ubiquitin. However, in the past year, several research groups including ours unexpectedly revealed that Parkin regulation is mediated by PINK1-dependent phosphorylation of ubiquitin. These results overturned the simple hierarchy that posited PINK1 and ubiquitin as the upstream and downstream factors of Parkin, respectively. Although ubiquitylation is well-known as a post-translational modification, it has recently become clear that ubiquitin itself can be modified, and that this modification unexpectedly converts ubiquitin to a factor that functions in retrograde signalling.
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    Heterologous expression of peptidyl-Lys metallopeptidase of Armillaria mellea and mutagenic analysis of the recombinant peptidase (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: A method to express, purify and modify the Peptidyl-Lys metallopeptidase (LysN) of Armillaria mellea in Pichia pastoris was developed to enable functional studies of the protease. Based on prior work, we propose a mechanism of action of LysN. Catalytic residues were investigated by site-directed mutagenesis. As anticipated, these mutations resulted in significantly reduced catalytic rates. Additionally, based on molecular modelling eleven mutants were designed to have altered substrate specificity. The S 1 ' binding pocket of LysN is quite narrow and lined with negative charge to specifically accommodate lysine. To allow for arginine specificity in S 1 ', it was proposed to extend the S 1 ' binding pocket by mutagenesis, however the resulting mutant did not show any activity with arginine in P 1 '. Two mutants, A101D and T105D, showed increased specificity towards arginine in subsites S 2 '–S 4 ' compared to the wild type protease. We speculate that the increased specificity to result from the additional negative charge which attract and interact with positively charged residues better than the wild type.
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    Effects of the N terminus of mouse DNA polymerase {kappa} on the bypass of a guanine-benzo[a]pyrenyl adduct (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: DNA polymerase (Pol), one of the typical member of the Y-family DNA polymerases, has been demonstrated to bypass the 10 S (+)- trans-anti -benzo[ a ]pyrene diol epoxide- N 2 -deoxyguanine adducts (BPDE-dG) efficiently and accurately. A large structural gap between the core and little finger as well as an N-clasp domain are essential to its unique translesion capability. However, whether the extreme N-terminus of Pol is required for its activity is unclear. In this work, we constructed two mouse Pol deletions, which have either a catalytic core (mPol 1-516 ) or a core without the first 21-residues (mPol 22-516 ), and tested their activities in the replication of normal and BPDE-DNA. These two Pol deletions are nearly as efficient as the full length protein (Pol 1-852 ) in normal DNA synthesis. However, steady-state kinetics reveals a significant reduction in efficiency of dCTP incorporation opposite the lesion by Pol 22-516 , along with increased frequencies for misinsertion compared with Pol 1-852 . The next nucleotide insertion opposite the template C immediately following the BPDE-dG was also examined, and the bypass differences induced by deletions were highlighted in both insertion and extension step. We conclude that the extreme N-terminal part of Pol is required for the processivity and fidelity of Pol during translesion synthesis of BPDE-dG lesions.
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    Characterization of the 5-flanking region of the human TP53 gene and its response to the natural compound, Resveratrol (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: Tumour suppressor p53, which is encoded by the TP53 gene, is widely known to play an important role in response to DNA damage and various stresses. It has recently been reported that p53 regulates glucose metabolism and that an increase in p53 protein level is induced after serum deprivation or treatments with a natural compound, trans -Resveratrol (Rsv). In this study, we constructed a Luciferase expression vector, pGL4-TP53-551, containing 551 bp of the 5’-upstream region of the human TP53 gene, which was then transfected into HeLa S3 cells. A Luciferase assay showed that Rsv treatment increased the promoter activity of the TP53 gene in comparison to that of PIF1 . Detailed deletion and mutation analyses revealed that Nkx-2.5 and E2F-binding elements are required in addition to duplicated GGAA (TTCC), for the regulation of TP53 promoter activity. In this study, it is suggested that the transient induction of TP53 gene expression by Rsv treatment might be partly involved in its anti-aging effect through maintenance of chromosomal DNAs.
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    Exploring the phosphoproteome profiles during Xenopus egg activation by calcium stimulation using a fully automated phosphopeptide purification system (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: To explore the phosphoproteome profiles during Xenopus egg activation by Ca 2+ -stimulation, an automated phosphopeptide purification system involving a titania column was improved by introducing 4-step elution with phosphate buffers. The number of detected phosphopeptides in the tryptic digest of a Xenopus egg cytosol fraction on mass spectrometry (MS) was increased 1.5-fold and the percentage of multiply phosphorylated peptides increased from 17 to 24% with introduction of the 4-step elution method. Phosphopeptides were purified by the improved method from tryptic digests of cytosol fractions of Xenopus eggs without and with a Ca 2+ -stimulus, and then, analysed by MS. One thousand three hundred and seventy-five and 994 phosphopeptides were reproducibly detected on duplicate MS, respectively. They included 818 and 437 phosphopeptides specific to each digest, respectively. A method involving isobaric tags for relative and absolute quantitation (iTRAQ) was also applied to compare the phosphorylation levels in Xenopus eggs without and with a Ca 2+ -stimulus, the ratios for 112 phosphopeptides in tryptic digests of these egg cytosol fractions being obtained. It was suggested from all the results that the phosphorylation sites and levels change during Xenopus egg activation for many known and unknown sites on structural proteins, signalling related proteins, cell cycle-related proteins and others.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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