Kinetic Self-Cleavage Models for Permuted Variants of the Antigenomic HDV Ribozyme

The kinetic characteristics have been studied for noncircularly permuted variants of the human hepatitis delta virus antigenomic ribozyme to find out the cause of the two-phase kinetics of the self-cleavage reaction. Different ways of reaction initiation, suboptimal conditions, and jumpwise changes of reaction conditions have been used, and the temperature dependences have been studied. A correlation has been shown between the apparent kinetic constant of the first reaction phase and the portion of the ribozyme molecules that self-cleaved during the first phase. Partial restoration of the initial reaction characteristics has been shown by the reinitiation of reaction being stopped after completing the first phase. On the basis of all the data obtained, a scheme of the self-cleavage reaction has been proposed including: (i) activation of the ribozyme with energy of 40–50 kcal/mol and a characteristic time of several deciminutes under optimal reaction conditions; (ii) fast and reversible reaction of the phosphodiester bond cleavage; (iii) reaction leading to isomerization of the 3",5"-phosphodiester bond to the 2",5" bond in the self-cleavage site with a characteristic activation time of tens of minutes; and (iv) practically irreversible conformational change leading to fixation of the cleavage by immobilization of the 5"-terminal nucleotide of the product in the center of the formed structure and displacement of the 3"-terminal nucleotide to the periphery. The latter process has a characteristic time of tens of minutes and a low activation energy.     

Quantum chemical study of the "catalytic triad" of serine proteases

Using the semi-empirical MNDO/H method several systems simulating the reaction of tetrahedral intermediate formation in the active site of serine proteases have been studied. The role played by elements of the "catalytic triad" in increasing the reactivity of serine hydroxyl has been discussed. The formation of a strong hydrogen bond between His and Asp was shown to be important in lowering the activation energy in the reaction of Ser with substrate. The change in position of the proton located between Ser and His and between His and Asp was analysed. The influence of substrate distortion on the energy of intermediate formation has been considered.     

Evolution of photosystem I and the control of global enthalpy in an oxidizing world

Life on earth is governed by light, chemical reactions, and the second law of thermodynamics, which defines the tendency for increasing entropy as an expression of disorder or randomness. Life is an expression of increasing order, and a constant influx of energy and loss of entropic wastes are required to maintain or increase order in living organisms. Most of the energy for life comes from sunlight and, thus, photosynthesis underlies the survival of all life forms. Oxygenic photosynthesis determines not only the global amount of enthalpy in living systems, but also the composition of the Earth’s atmosphere and surface. Photosynthesis was established on the Earth more than 3.5 billion years ago. The primordial reaction center has been suggested to comprise a homodimeric unit resembling the core complex of the current reaction centers in Chlorobi, Heliobacteria, and Acidobacteria. Here, an evolutionary scenario based on the known structures of the current reaction centers is proposed.     

Life cycle assessment of nanocomposites made of thermally conductive graphite nanoplatelets

Purpose

Polymers typically have intrinsic thermal conductivity much lower than other materials. Enhancement of this property may be obtained by the addition of conductive fillers. Nanofillers are preferred to traditional ones, due to their low percolation threshold resulting from their high aspect ratio. Beyond these considerations, it is imperative that the development of such new fillers takes place in a safe and sustainable manner. A conventional life cycle assessment (LCA) has been conducted on epoxy-based composites, filled with graphite nanoplatelets (GnP). In particular, this study focuses on energy requirements for the production of such composites, in order to stress environmental hot spots and primary energy of GnP production process (nano-wastes and nanoparticles emissions are not included).

Methods

A cradle-to-grave approach has been employed for this assessment, in an attributional modeling perspective. The data for the LCA have been gathered from both laboratory data and bibliographic references. A technical LCA software package, SimaPro (SimaPro 7.3), which contains Ecoinvent (2010) life cycle inventory (LCI) database, has been used for the life cycle impact assessment (LCIA), studying 13 mid-point indicators. Sensitivity and uncertainty analyses have also been performed.

Results and discussion

One kilogram of GnP filler requires 1,879 MJ of primary energy while the preparation of 1 kg of epoxy composite loaded with 0.058 kg of GnP 303 MJ. Besides energy consumption in the filler preparation, it is shown that the thermoset matrix material has also a non-negligible impact on the life cycle despite the use of GnP: the primary energy required to make epoxy resin is 187 MJ, i.e., 62 % of the total energy to make 1 kg of composite.

Conclusions

Raw material extraction and filler and resin preparation phase exhibit the highest environmental impact while the composite production is negligible. Thermosetting resin remains the highest primary energy demand when used as matrix for GnP fillers. The result of the sensitivity analysis carried out on the electricity mix used during the GnP and the composite production processes does not affect the conclusions.     

Challenging the concept of "recycling" as a mechanism for the evolution of homochirality in chemical reactions

The concept that "recycling" of reactants may be key to the spontaneous generation of a homochiral state in closed autocatalytic reaction networks has recently been introduced and has been supported by computer simulations of such reaction networks. It has been suggested that unidirectional cycles maintained away from equilibrium may avoid the inevitable establishment of a racemic state, and under such conditions the explicit reverse reactions dictated by microscopic reversibility may be all be treated as having negligible rates. We show here that because the equilibrium constants in a recycled network are interdependent, it is not valid to neglect all reverse reactions simultaneously; a very low value for the rate constant of one reverse reaction in the network dictates that another reverse reaction in the same network will exhibit a large rate constant. This conclusion is general and applies to any closed mass system where the energy input is subject to microscopic reversibility. Therefore, chemical reversibility cannot be invoked as a mechanism for the evolution of a single chiral molecular state in thermally activated reactions.     

Life cycle assessment of sponge nickel produced by gas atomisation for use in industrial hydrogenation catalysis applications

Purpose

This paper presents a cradle-to-grave comparative life cycle assessment (LCA) of new gas atomised (GA) sponge nickel catalysts and evaluates their performance against the current cast and crush standard currently used in the industrial hydrogenation of butyraldehyde to butanol.

Methods

A comparative LCA has been made, accounting for the energy used and emissions throughout the entire life cycle of sponge nickel catalysts—ranging from the upstream production of materials (mainly aluminium and nickel), to the manufacturing, to the operation and finally to the recycling and disposal. The LCA was performed following ISO14040 principles where possible, and subsequently implemented in the software package GaBi 4.3. The CML2001 impact assessment methodology was used, with primary focus on comparing catalysts for equivalent greenhouse gasses generated over their lifetime and their relative global warming potential and secondary focus on acidification potential. This is justified as the lifetime is dominated by energy use in the operational phase, and acidification is dominated by the production of nickel for which existing ISO14040 collected data has been used. A sensitivity analysis was used to provide a number of scenarios and overall environmental performances of the various sponge nickels considered when compared to the existing industrial standard.

Results and discussion

It was found that the energy and emissions during the operation phase associated with a given catalyst significantly outweigh the primary production, manufacturing and recycling. Primary production of the nickel (and to a lesser extent molybdenum when used as a dopant) also has a significant environmental impact in terms of acidification potential, but this is offset by operational energy savings over the catalysts’ estimated lifetime and end of life recyclability. Finally, the impact of activity improvement and lifetime duration of sponge nickel catalysts was determined as both total life cycle energy for operational use and as a total life cycle global warming potential.

Conclusions

From this assessment, the newly developed, higher activity spongy nickel catalysts produced by gas atomisation could have a significantly lower environmental impact than the current industry standard cast and crush method. Given the potential environmental benefits of such catalysts, applications in other processes that require a catalyst should also be investigated.     

Der Lichteinfluss auf die Haarbildung am Hypokotyl vonSinapis alba L.

Summary In an earlier paper (Mohr 1957) it was described that the formation of anthocyanin and the inhibition of lengthening of the hypocotyl of dark grown seedlings (Sinapis alba) is governed by the action of two photomorphogenic action systems. The one system is the well known reversible red far-red reaction system (low energy reaction), the other one is a high energy reaction system which can be called — in reference to the action peaks in the far-red and in the blue — blue far-red reaction system. The chemical nature of the absorbing pigments is still unknown.In the present paper another photomorphogenic response of the young dark grown seedlings ofSinapis alba, the light dependent formation of unicellular hairs from epidermal cells of the hypocotyl, has been investigated. It has been shown that this response is also governed by these two reaction systems. These systems have been physiologically separated. Experiments have been presented which evaluate the importance of the assumption that the red absorbing pigment of the reversible red far-red pigment system is reformed from a precursor when the pigment present before irradiation is transformed into the far-red absorbing pigment by an irradiation with red.

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Multi-actor multi-criteria sustainability assessment framework for energy and industrial systems in life cycle perspective under uncertainties. Part 2: improved extension theory

Purpose

The concept of sustainability and sustainable development has been widely incorporated in energy and industrial systems. This paper is the second part of a two-paper series dealing with multi-actor multi-criteria sustainability assessment of alternative energy and industrial systems in life cycle perspective under uncertainties.

Methods

The criteria system including four macroscopic aspects (environmental, safety, social and economic aspects) has been developed for sustainability assessment of energy and industrial systems. An improved extension theory which can address interval decision-making matrix has been developed for determining the sustainability degree of the energy and industrial systems.

Results and discussion

The weights of the criteria for sustainability assessment are the first part of the two-paper series. An illustrative case has been studied by the proposed multi-criteria decision-making method, and the sustainability of six alternative options for the production of a 1-t product was investigated. The sustainability degree of these six alternative options can be determined by the proposed method.

Conclusions and perspectives

A methodology for multi-actor multi-criteria sustainability assessment of energy and industrial options has been developed in this study, the traditional extension theory has been modified to deal with the uncertainty problems and the proposed method can rank the alternative energy and industrial systems with the decision-making matrix in which the data of the alternatives with respect to the evaluation criteria are intervals. In the improved extension theory, sustainability has been dived into five grades: excellent, good, satisfied, barely adequate and fail. According to the method for calculating the weights of the criteria for sustainability assessment proposed in part 1, these weights were used to calculate the integrated dependent degree which is a measure of what degree an alternative belongs to the classical fields. An optimal programming model for maximizing the satisfied degree has been developed to rank the sustainability sequence of the alternative options and determine the sustainability degree of each alternative.

     

Life cycle environmental impacts and costs of beer production and consumption in the UK

Purpose

Global beer consumption is growing steadily and has recently reached 187.37 billion litres per year. The UK ranked 8th in the world, with 4.5 billion litres of beer produced annually. This paper considers life cycle environmental impacts and costs of beer production and consumption in the UK which are currently unknown. The analysis is carried out for two functional units: (i) production and consumption of 1 l of beer at home and (ii) annual production and consumption of beer in the UK. The system boundary is from cradle to grave.

Methods

Life cycle impacts have been estimated following the guidelines in ISO 14040/44; the methodology for life cycle costing is congruent with the LCA approach. Primary data have been obtained from a beer manufacturer; secondary data are sourced from the CCaLC, Ecoinvent and GaBi databases. GaBi 4.3 has been used for LCA modelling and the environmental impacts have been estimated according to the CML 2001 method.

Results and discussion

Depending on the type of packaging (glass bottles, aluminium and steel cans), 1 l of beer requires for example 10.3–17.5 MJ of primary energy and 41.2–41.8 l of water, emits 510–842 g of CO₂ eq. and has the life cycle costs of 12.72–14.37 pence. Extrapolating the results to the annual consumption of beer in the UK translates to a primary energy demand of over 49,600 TJ (0.56 % of UK primary energy consumption), water consumption of 1.85 bn hl (5.3 % of UK demand), emissions of 2.16 mt CO₂ eq. (0.85 % of UK emissions) and the life cycle costs of £553 million (3.2 % of UK beer market value). Production of raw materials is the main hotspot, contributing from 47 to 63 % to the impacts and 67 % to the life cycle costs. The packaging adds 19 to 46 % to the impacts and 13 % to the costs.

Conclusions

Beer in steel cans has the lowest impacts for five out of 12 impact categories considered: primary energy demand, depletion of abiotic resources, acidification, marine and freshwater toxicity. Bottled beer is the worst option for nine impact categories, including global warming and primary energy demand, but it has the lowest human toxicity potential. Beer in aluminium cans is the best option for ozone layer depletion and photochemical smog but has the highest human and marine toxicity potentials.

     

Characteristics of the intraspecies interaction of rats with differing zoosocial experience

It has been found that among white outbred rats with different experience of intraspecies contact four types of reaction to the partner are singled out in the "stranger-resident" test: active, neutral passive, highly-aggressive. Belonging to one or another type is determined by the level and correlation of aggression and intraspecies sociability. Among animals isolated in an adult age, all four types of reaction to the partner are represented while in rats kept in isolation since 13--14th day of life only one type is presented--the active one. For animals of the control group the first three types of reaction are typical. It is revealed that only "late" isolation leads to a pathological increase of aggressivity in a part of the animals; an increase of aggression in "early" isolants may be considered as a consequence of sharp rise of intraspecies sociability. Conclusion is made about principal difference in mechanisms of aggression increase in "early" and "late" isolants.     

Psychological status and coping with illness in patients with malignant melanoma

Melanoma patients are subject to different degrees of psychosocial distress. The emotional impact of malignant melanoma can be long lasting and profound, with the most common reactions to melanoma being depression, anxiety and deterioration in quality of life. Coping styles have been shown to have a significant influence on patients' quality of life and their emotional reaction to the illness. The aim of this paper was to investigate the quality of life, emotional status and coping styles in patients with melanoma. 31 patients suffering from malignant melanoma were included in the study. Results of this study show that melanoma has a medium influence on patients' psychological status and quality of life. The most "constructive" coping style--problem focused coping is the mostly used style by the patients, which might be one of the reasons why the illness didn't have a more severe influence on patients' psychological status.     

Oscillations and efficiency in glycolysis

We suggest that temporal oscillations of concentrations of intermediates in biochemical reaction systems may enhance the efficiency of free energy conversion (reduce dissipation) in those reactions. Experiments on glycolysis are used to estimate the Gibbs free energy changes along the glycolysis mechanism, and to postulate a construct for the glycolysis "machine" which involves: the PFK reaction as the primary oscillophor; the GAPDH reaction as a phase-shifting device; and the PK reaction with the property of intrinsic oscillatory response at resonance with the driving frequency. Analysis of a simple reaction mechanism with these postulated properties shows that the conversion of free energy from reactants to products is more efficient in an oscillatory than a steady state operation. The efficiency of free energy conversion in glycolysis from glucose + ADP to products + ATP is estimated to be increased by 5--10% due to oscillations. This may have been relevant for the evolutionary development of oscillations such as in glycolysis, especially in anaerobic cells.     

Mechanism of renaturation of a large protein, aspartokinase-homoserine dehydrogenase

The renaturation of aspartokinase-homoserine dehydrogenase and of some of its smaller fragments has been investigated after complete unfolding by 6 M guanidine hydrochloride. Fluorescence measurements show that a major folding reaction occurs rapidly (in less than a few seconds) after the protein has been transferred to native conditions and results in the shielding of the tryptophan residues from the aqueous solvent; this step also takes place in the fragments and probably corresponds to the independent folding of different segments along the polypeptide chain. The reappearance of the kinase activity, which is an index of the formation of "native" structure within a single chain, is much slower (a few minutes) and has the following properties: it is involved in a kinetic competition with the formation of aggregates; it has an activation energy of 22 +/- 5 kcal/mol; it is not related to a slow reaction in unfolding and thus probably not controlled by the cis-trans isomerization of X-Pro peptide bonds; its rate is inversely proportional to the solvent viscosity. It seems as if this reaction is limited by the mutual arrangement of the regions that have folded rapidly and independently. It is proposed that the mechanism where a fast folding of domains is followed by a slow pairing of folded domains could be generalized to other long chains composed of several domains; such a slow pairing of folded domains would correspond to a rate-limiting process specific to the renaturation of large proteins. The reappearance of the dehydrogenase activity measures the formation of a dimeric species. The dimerization can occur only after each chain has reached its "native" conformation.(ABSTRACT TRUNCATED AT 250 WORDS)     

Energetics and mechanism of proline racemase

The results from the previous six papers are collated so as to allow the construction of the complete free energy profile for the reaction catalyzed by proline racemase. This profile includes the step that involves the isomerization of the two forms of free enzyme, which can become rate limiting at very high substrate levels (in "oversaturation"). The mechanism of the reaction has been defined, the results being best accommodated by a route that involves a transition state or unstable intermediate in which the proline carbanion is flanked by the two catalytic thiols of the enzyme.     

Polymersomes Containing Iron Sulfide (FeS) as Primordial Cell Model

According to Wächtershäuser??s ??Iron-Sulfur-World?? one major requirement for the development of life on the prebiotic Earth is compartmentalization. Vesicles spontaneously formed from amphiphilic components containing a specific set of molecules including sulfide minerals may have lead to the first autotrophic prebiotic units. The iron sulfide minerals may have been formed by geological conversions in the environment of deep-sea volcanos (black smokers), which can be observed even today. Wächtershäuser postulated the evolution of chemical pathways as fundamentals of the origin of life on earth. In contrast to the classical Miller-Urey experiment, depending on external energy sources, the ??Iron-Sulfur-World?? is based on the catalytic and energy reproducing redox system $ FeS + {H_2}S \to FeS{}_2 + {H_2} $ . The energy release out of this redox reaction (?_RG°?=??38 kJ/mol, pH 0) could be the cause for the subsequent synthesis of complex organic molecules and the precondition for the development of more complex units similar to cells known today. Here we show the possibility for precipitating iron sulfide inside vesicles composed of amphiphilic block-copolymers as a model system for a first prebiotic unit. Our findings could be an indication for a chemoautotrophic FeS based origin of life.     

Bridge life cycle assessment with data uncertainty

Purpose

Although life cycle assessment (LCA) has been employed to analyze the environmental impacts of bridges, the uncertainties associated to LCA have not been studied, which have a profound effect on the LCA results. This paper is intended to provide a comprehensive environmental impact assessment of bridge with data uncertainty, by assigning probability distributions on the considered parameters, assessing the variability in the acquisition of inventory and identifying the key parameters with significant environmental impacts.

Methods

A life cycle assessment of a bridge in Shanxi Province of China was conducted in a cradle-to-grave manner, by considering the source of the uncertainty of LCA. A statistical method was applied to quantify the uncertainty of measured inventory data and to calculate the probability distribution of the data. The uncertainty propagation was conducted through using a Monte Carlo simulation. Finally, the factor which is of vital importance to the assessment result was identified by sensitivity analysis.

Results and discussion

For the case of bridge, normal distribution can be adopted to fit environmental substances and environmental impact in steel production. The distributions of the weighted value of human health damage, ecological system damage, and resource and energy consumption can be represented by an approximate similar normal distribution function. The coefficient of variance (COV) of each weighted value is about 40, 30 to 40, and about 6 %, respectively. The COV for the total environmental impact is about 10 % in all stages of the bridge’s life cycle, except the operation stage, which is up to 22.67 %. By conducting sensitivity analysis, PM₁₀, NO_x, and oil consumption was found to have a great influence on the result of human health damage, ecological system damage, and resource and energy consumption, respectively.

Conclusions

The COV for the total environmental impact is 22.67 % in the bridge’s operation stage; it is important to establish a reasonable maintenance strategy to decrease the uncertainty of the bridge’s environmental impact. The COVs of the weighted value for human health damage and resource and energy consumption have a quite modest difference among the four stages of the bridge’s life cycle. However, The COV of the weighted value for ecological system damage shows large difference among the four stages of the bridge’s life cycle; construction stage has the greatest uncertainty. In addition, different values of PM₁₀, NO_x, and oil consumption have a profound influence on the result of human health damage, ecological system damage, and resource and energy consumption, respectively.

     

Unfolding kinetics of tryptophan side chains in the dimerization and hinge regions of HIV-I protease tethered dimer by real time NMR spectroscopy

HIV I protease has been the target of extensive and variety of investigations in recent years because of its importance in the AIDS viral life cycle. We describe here real time NMR studies on the unfolding kinetics of two tryptophans, W6 and W42, which are located in the dimerization and hinge domains of the protein, respectively. Unfolding seems to get initiated in the dimerization domain. The kinetic data at two temperatures, 32 and 42 degrees C, can both be described by two-state models for both the tryptophans, and the final state reached at 42 degrees C does not depend on the path of unfolding. Unfolding free energy changes derived from the kinetic fitting parameters are less than 3 kJ/mol, indicating that the energy landscape is very shallow. The free energy values and the rates for the two tryptophans are different at 32 degrees C, but are nearly the same at 42 degrees C. These are interpreted in the light of the "new view" of protein folding and the relative behaviors of the two tryptophans suggest the existence of cooperative pathways in the unfolding reaction of the protein. These observations would provide valuable insights into protein function, stability, and effects of nonactive site mutations conferring drug resistance.     

Mechanisms on electrical breakdown strength increment of polyethylene by acetophenone and its analogues addition: a theoretical study

A theoretical investigation is completed on the mechanism of electrical breakdown strength increment of polyethylene. It is shown that it is one of the most important factors for increasing electrical breakdown strength of polyethylene through keto-enol isomerization of acetophenone and its analogues at the ground state S₀ and the lowest triplet state T₁. The minimum structures and transition states of the keto- and the enol-tautomer of acetophenone and its analogues at the S₀ and T₁ states are obtained at the B3LYP/6-311+G(d,p) level, as well as the harmonic vibration frequencies of the equilibrium geometries and the minimum energy path (MEP) by the intrinsic reaction coordinate (IRC) theory at the same level. The two C–C bond cleavage reaction channels have been identified in acetophenone. The calculated results show that the energy barriers of keto-enol isomerization of acetophenone and its analogues at S₀ and T₁ states are much smaller than the average C-C bond energy of polyethylene, and the acetophenone doping or bond linked into polyethylene can increase the electrical breakdown strength and inhibit polyethylene electrical tree initiation and aging.

Primeval cells: possible energy-generating and cell-division mechanisms

It is proposed that the first entity capable of adaptive Darwinian evolution consisted of a liposome vesicle formed of abiotically produced phospholipidlike molecules; a very few informational macromolecules; and some abiogenic, lipid-soluble, organic molecule serving as a symporter for phosphate and protons and as a means of high-energy-bond generation. The genetic material had functions that led to the production of phospholipidlike materials (leading to growth and division of the primitive cells) and of the carrier needed for energy transduction. It is suggested that the most primitive exploitable energy source was the donation of 2H+ + 2e- at the external face of the primitive cell. The electrons were transferred (by metal impurities) to internal sinks of organic material, thus creating, via a deficit, a protonmotive force that could drive both the active transport of phosphate and high-energy-bond formation. This model implies that proton translocation in a closed-membrane system preceded photochemical or electron transport mechanisms and that chemically transferable metabolic energy was needed at a much earlier stage in the development of life than has usually been assumed. It provides a plausible mechanism whereby cell division of the earliest protocells could have been a spontaneous process powered by the internal development of phospholipids. The stimulus for developing this evolutionary sequence was the realization that cellular life was essential if Darwinian "survival of the fittest" was to direct evolution toward adaptation to the external environment.     

Life cycle assessment of ocean energy technologies

Purpose

Oceans offer a vast amount of renewable energy. Tidal and wave energy devices are currently the most advanced conduits of ocean energy. To date, only a few life cycle assessments for ocean energy have been carried out for ocean energy. This study analyses ocean energy devices, including all technologies currently being proposed, in order to gain a better understanding of their environmental impacts and explore how they can contribute to a more sustainable energy supply.

Methods

The study followed the methodology of life cycle assessment including all life cycle steps from cradle to grave. The various types of device were assessed, on the basis of a functional unit of 1 kWh of electricity delivered to the grid. The impact categories investigated were based on the ILCD recommendations. The life cycle models were set up using detailed technical information on the components and structure of around 180 ocean energy devices from an in-house database.

Results and discussion

The design of ocean energy devices still varies considerably, and their weight ranges from 190 to 1270 t, depending on device type. Environmental impacts are closely linked to material inputs and are caused mainly by mooring and foundations and structural components, while impacts from assembly, installation and use are insignificant for all device types. Total greenhouse gas emissions of ocean energy devices range from about 15 to 105 g CO₂-eq. kWh^?1. Average global warming potential for all device types is 53?±?29 g CO₂-eq. kWh^?1. The results of this study are comparable with those of other studies and confirm that the environmental impacts of ocean energy devices are comparable with those of other renewable technologies and can contribute to a more sustainable energy supply.

Conclusions

Ocean energy devices are still at an early stage of development compared with other renewable energy technologies. Their environmental impacts can be further reduced by technology improvements already being pursued by developers (e.g. increased efficiency and reliability). Future life cycle assessment studies should assess whole ocean energy arrays or ocean energy farms.