Efficiency of electron transport processes

Efficiency of electron transport along the linear chain of molecules was investigated from a dynamic viewpoint. It was proposed that two kinds of efficiency are important for electron transport; one is energy efficiency, the other quantum efficiency. In this paper, these two efficiencies are defined for a linear chain system and the correlation between these quantities and the arrangement of various electron transfers is investigated. The optimization of energy and quantum efficiency is found to set different conditions on the arrangement of the rate constants of electron transfer, and there is strong correlation between neighboring electron transfers. In order to maximize both efficiencies, the rate constants of forward and backward transfers of electrons should be bounded by one another in a limited range. In particular, when there are some bypass reactions on the linear chain, as is the case for photosynthesis and respiration, the rate of the backward transfer should be the same order of magnitude as that of the next forward transfer. The present results are applied to some biological processes. In the early stage of photosynthetic electron transfer it seems that quantum efficiency is more important than energy efficiency. The quantum efficiency is close to unity, whereas a considerable part of the free energy is wasted as heat during the primary electron transfers. On the other hand, in the slower electron transfer processes in photosynthesis and respiration, which take place mostly near equilibrium, the energy efficiency seems to be more important than the quantum efficiency. The relation of these properties to biological function is discussed.     

Theoretical study of the effect of several reverse reaction on the kinetics of the primary processes of photosynthesis

A theoretical model of energy migration and electron transport in photosynthesis of higher plants was considered. The set of different equations describing these processes takes into consideration the states of 4 components of electron transport chain and back reactions of electron transfer from the reduced acceptors to the oxidized reaction centres. The numerical integration of these equations was made for various kinetics parameters characterizing the electron transport chain.     

Spatial club convergence of regional energy efficiency in China

This paper adopts data envelopment analysis method to calculate the regional energy efficiency from the perspective of total-factor energy efficiency. The Markov chain and spatial Markov chain are the common methods to test the club convergence of regional energy efficiency in China. Results indicate that the regional energy efficiency in China has been globally characterized by “club convergence” since 1999, and the energy efficiency transitions in China are closely connected with regional characteristics. A high level of energy efficiency has a positive influence on a region, whereas a low level of energy efficiency has a negative influence. This empirical analysis provides a spatial explanation to the “convergence clubs” of regional energy efficiency in China.     

"蒲公英-蝌蚪-鳝鱼"食物链的物流与能流分析

本文对食物链“蒲公英—蝌蚪—鳝鱼”的物质流和能量流作了定量分析。结果表明：该食物链经济产品的物质、能量转化效率较低,生物量转化效率为1.1％,能量转化效率为0．8％,N、P转化效率分别为3．1％、1．5％。但该食物链刺激鳝鱼食欲,有利于鳝鱼繁殖。     

A value chain approach to improve biomass policy formation

Biomass value chains for energy, fuels and bio‐based products involve complex, cross sector interactions between their upstream and downstream stages. Overarching policymaking to date has included the use of biomass to deliver sector specific aims (e.g. climate change, energy, etc.) however, this is mostly planned without adjusting support across the most challenging stages of biomass value chains and exploiting specific advantages related to their geographic settings (e.g. domestic feedstocks, local markets, etc.). Policies to date have, therefore, resulted in fragmented, suboptimal biomass use and debates for sustainability and resource efficiency. This opinion paper arose from the project Strategic Initiative for Resource Efficient Biomass Policies Funded by the EU Commission. It discusses the development of a dedicated Biomass Policy Framework which applies the principles of value chain analysis in policy design to enable the market uptake of sustainable, domestic, resource efficient biomass solutions. Firstly, it explains how to provide context by identifying value chains which can offer competitive advantages for biomass mobilization, market infrastructures, rural and economic development within their geographic setting. Then the work builds on the context and prioritized value chains and further rationalizes policy needs and aims within individual value chain stages. This is done by identifying policy‐related challenges and gaps that constrain sustainable and resource efficient deployment of the selected value chains. Also, it suggests policy interventions that will overcome challenges, resolve gaps and as a result mobilize local biomass and improve market uptake. Finally, it discusses the contrasting paradigms for biomass policy formation within single sector target setting and the value chain approach of the Biomass Policy Framework and uses the case of low carbon biomass heat to illustrate the strengths of the suggested approach. The paper concludes with remarks for the concept of biomass value chain analysis in policy.     

Wild skylarks seasonally modulate energy budgets but maintain energetically costly inflammatory immune responses throughout the annual cycle

A central hypothesis of ecological immunology is that immune defences are traded off against competing physiological and behavioural processes. During energetically demanding periods, birds are predicted to switch from expensive inflammatory responses to less costly immune responses. Acute phase responses (APRs) are a particularly costly form of immune defence, and, hence, seasonal modulations in APRs are expected. Yet, hypotheses about APR modulation remain untested in free-living organisms throughout a complete annual cycle. We studied seasonal modulations in the APRs and in the energy budgets of skylarks Alauda arvensis, a partial migrant bird from temperate zones that experiences substantial ecological changes during its annual cycle. We characterized throughout the annual cycle changes in their energy budgets by measuring basal metabolic rate (BMR) and body mass. We quantified APRs by measuring the effects of a lipopolysaccharide injection on metabolic rate, body mass, body temperature, and concentrations of glucose and ketone. Body mass and BMR were lowest during breeding, highest during winter and intermediate during spring migration, moult and autumn migration. Despite this variation in energy budgets, the magnitude of the APR, as measured by all variables, was similar in all annual cycle stages. Thus, while we find evidence that some annual cycle stages are relatively more energetically constrained, we find no support for the hypothesis that during these annual cycle stages birds compromise an immune defence that is itself energetically costly. We suggest that the ability to mount an APR may be so essential to survival in every annual cycle stage that skylarks do not trade off this costly form of defence with other annual cycle demands.     

Luminescence resonance energy transfer measurements in myosin.

Myosin is thought to generate force by a rotation between the relative orientations of two domains. Direct measurements of distances between the domains could potentially confirm and quantify these conformational changes, but efforts have been hampered by the large distances involved. Here we show that luminescence resonance energy transfer (LRET), which uses a luminescent lanthanide as the energy-transfer donor, is capable of measuring these long distances. Specifically, we measure distances between the catalytic domain (Cys707) and regulatory light chain domain (Cys108) of the myosin head. An energy transfer efficiency of 21.2 +/- 1.9% is measured in the myosin complex without nucleotide or actin, corresponding to a distance of 73 A, consistent with the crystal structure of Rayment et al. Upon binding to actin, the energy transfer efficiency decreases by 4.5 +/- 1.0%, indicating a conformational change in myosin that involves a relative rotation and/or translation of Cys707 relative to the light chain domain. Addition of ADP also alters the energy transfer efficiency, likely through a rotation of the probe attached to Cys707. These results demonstrate that LRET is capable of making accurate measurements on the relatively large actomyosin complex, and is capable of detecting conformational changes between the catalytic and light chain domains of myosin.     

The chondroitin sulfate form of invariant chain trimerizes with conventional invariant chain and these complexes are rapidly transported from the trans-Golgi network to the cell surface

Targeting of MHCII-invariant chain complexes from the trans-Golgi network to endosomes is mediated by two di-leucine-based signals present in the cytosolic domain of invariant chain. Generation of this endosomal targeting signal is also dependent on multimerization of the invariant chain cytosolic domain sequences, mediated through assembly of invariant chain into homotrimers. A small subset of invariant chain is modified by the addition of chondroitin sulfate and is expressed on the cell surface in association with MHCII. In the present study, we have followed the biosynthetic pathway and route of intracellular transport of this proteoglycan form of invariant chain. We found that the efficiency of chondroitin sulfate modification can be increased by altering the invariant chain amino acid sequence around Ser-201 to the xylosylation consensus sequence. Our results also indicate that, following sulfation, the proteoglycan form is transported rapidly from the trans-Golgi network to the cell surface and is degraded following internalization into an endocytic compartment. Invariant chain-chondroitin sulfate is present in invariant chain trimers that also include conventional non-proteoglycan forms of invariant chain. These data indicate that invariant chain-chondroitin sulfate-containing complexes are transported rapidly from the trans-Golgi network to the cell surface in spite of the presence of an intact endosomal localization signal. Furthermore, these results suggest that invariant chain-chondroitin sulfate may play an important role in the generation of cell-surface pools of invariant chain that can serve as receptors for CD44 and macrophage migration inhibitory factor.     

Differentiation of chloroplast lamellae: Light harvesting efficiency and grana development

Incomplete development of chloroplast lamellae occurred when etiolated pea plants were greened under cycles of 2 min light, 118 min dark. Although the plastids had full photochemical activities, they were nearly agranal. They were also characterized by a high quantum requirement for whole chain electron transport in low light; this is thought to be the result of unequal light absorption by incompletely developed light-harvesting assemblies of photosystem I and II and a lack of regulation of excitation energy distribution between the two photosystems. Continuous illumination induced the final stages of membrane differentiation. These stages were primarily characterized by the appearance of grana stacking and an increase in photosynthetic unit size. A biphasic decrease in quantum requirement for whole chain electron transport correlated directly with the appearance of grana during the final steps of membrane assembly. Structural organization of the membrane may be related to the light-harvesting efficiency of the membrane.     

基于能源代谢分析的南昌市能源消费碳排放综合生态效率研究

有关能源消费的代谢机理及生态效率研究是当前生态经济研究领域中的重点和难点,也是政府决策部门、相关行业及人群关注的热点。基于能源代谢分析理念,构建了基于相对变量的城市能源消费碳排放综合生态效率度量模型,对2000—2013年南昌市能源消费结构、碳排放量及其生态效率进行了测算与分析。结果表明:(1)南昌市在2000—2013年,能源消费量和碳排放量整体上呈"N"型曲线上升的一致性变化特征,主要经历了快速增长、短暂下降、恢复平稳增长3个阶段,且煤炭是南昌市能源消费和碳排放的主要来源,短时期内难以改变;(2)南昌市的能源消费效率和碳排放效率整体上在不断优化;(3)南昌市能源消费碳排放综合生态效率经历了较大的波动变化,整体上的生态效率分值并不高;仍需要加大节能减排力度,全面优化南昌市能源消费结构。     

Digestive tract function in the long-distance migratory garden warbler,Sylvia borin

Digestive tract morphology and function of captive garden warblers (Sylvia borin) were measured during four stages of their endogenous circannual rhythm: before, during and after their autumn fattening prior to migration to wintering grounds in Africa, and after a partially simulated migratory flight. Food intake increased by 33% during fattening, utilization efficiency of dry matter tended to increase, and that of energy increased significantly (P0.01). This was because digestive tract capacity (measured as dry tissue mass) increased, so that mean retention time of food remained constant before, during and after fattening (80–84 min). After a 48-h period of starvation of fattened birds to partially simulate a migratory flight, food intake was lower on the first day of refeeding than on the next 4 days, and utilization efficiency was higher on that day, at least partly because of a longer mean retention time (111 min versus 78 min on the third day). Digestive tract dry tissue mass fell by 50% during starvation, and that of the small intestine by 63%. It is concluded that the garden warbler adapts to long-distance migration without feeding by rapidly reducing the size of its digestive tract, an expensive tissue to maintain, during migration in order to save weight and energy, and possibly also to supply part of the fuel and protein required for the flight. The cost of this strategy appears to be the time taken to rebuild the gut at stopover sites with food, but the low probability of finding such a site in the Sahara Desert means that this strategy is probably optimal for garden warblers.     

Analysis of glycogen structure in rat hepatocytes using cytochemical and FRET methods

Using cytochemical and FRET (Forster, Resonance Energy Transfer) methods, the glycogen structure in rat hepatocytes was investigated during fasting and at different time intervals after per os glucose administration to animals. Hepatocytes on slides were stained with fluorescent PAS-reaction. Staining the slides with ethidium bromide-SO2 (EtBr-SO2) for 40 min revealed a labile glycogen fraction (LE), and the subsequent staining the same samples with auramine-SO2 (Au-SO2) for 50 min showed a stable glycogen fraction (SF) in the cells. The total glycogen content (LF and SF) in the hepatocytes at different stages of refeeding was determined by means of cytofluorimetry, and then efficiency of FRET was measured in the same cells. Registration of FRET in several areas of the cells was carried out on a laser scanning confocal microscope Leica TCS SP5 with application of FRET AB (Acceptor Photobleaching) procedure. In this procedure, auramine served as a donor (D) and ethidium bromide was an acceptor (A). It was shown that the efficiency of FRET varied from 10 to 14 % during refeeding, while the glycogen structure had a marked influence on the value of this parameter. FRET efficiency was shown to correlate with the ratio A/D in the cells of hungry rats and at the early stages after glucose administration to animals, which reflected the degree of filling of the external tiers of glycogen molecules of glucose residues. At later stages, this correlation was either less pronounced or absent. It was found that the FRET efficiency can vary by 3-4 times at the same value of A/D. Since the probability of energy transfer from D to A is proportional to 1/R6, where R is a distance between D and A, such variations of the FRET efficiency indicate that the glycogen molecules possess a labile structure in which the chain of glucose residues can deviate from its axis by a distance of about half their diameter.     

Collective aspects of conformons and the electron transfer chain

A set of interacting harmonic oscillators is used as a model to define a low frequency collective mode in protein molecules. Such a mode may arise from electron-phonon interactions in second order perturbation theory. The mathematical scheme is analogous to those used in the theory of carcadian rhythms and in the theory of superconductivity. This collective mode may receive energy from electrons in the electron transfer chain (conformon) and pass the energy on to other similar modes. The low frequency of the mode leads to slow reactions, in agreement with experimental data. The model is compatible with some general characteristics of the electron transfer chain and its constituents: high thermodynamic efficiency, redox pools, redox switches, entatic states and conformational free energy transfer.     

Photoinduced electron transfer through the hydrocarbon zone of membranes at low temperatures

The photoinduced electron transfer at low temperatures in phospholipide membranes (liposomes) containing chlorophyll and 3 X 10-docsilpalmitate has been investigated. The reduction of 3 X 10-docsilpalmitate was estimated by ESR spectrometry. When diffusion movement of the molecules in membranes was blocked by low temperatures the photoinduced electron transfer has been found. The mechanism of these phenomena were analyzed on the base of donor-acceptor interaction through sigma bonds in hydrocarbon bridged donor-acceptor complexes. The separation of charges in these complexes is regarded as occurs by the migration of a hole along the hydrocarbon system. An approximate estimate of the charge mobility in the saturated hydrocarbon side chain of chlorophyll and activation energy of these movement was obtained.     

ROCK signaling mediates the adoption of different modes of migration and invasion in human mammary epithelial tumor cells

For the invasive migration of tumor cells, at least two mechanisms are currently discussed: (1) the mesenchymal mode depending on extracellular proteolysis and (2) the proteolysis-independent amoeboid mode depending on the activity of the Rho kinase ROCK. The ability of tumor cells to switch between different modes of motility has been shown to limit the efficiency of agents aimed to reduce invasion. Here we show by combining 2D and 3D migration assays that human mammary tumor cells exhibited a strongly reduced migration velocity as compared to their normal counterparts indicating that high invasiveness is not necessarily correlated with high migratory capacity in 2D assays. This reduced migration was apparently due to significant differences in actin organization, decreased persistence of lamellipodia by 50% and increased cell substrate adhesion. These differences resulted from a 2.5-fold higher activity of ROCK and were mediated by its downstream effectors myosin light chain kinase and cofilin. Thus, inhibition of ROCK activity caused a marked increase in 2D migration efficiency by 40%, without, however, affecting 3D invasion. A massive reduction of invasion by 60% was achieved by the simultaneous inhibition of the ROCK-dependent amoeboid and the extracellular proteolysis-dependent mesenchymal mode. These results may point to a new efficient strategy for blocking tumor cell invasion in vivo.     

Effect of Single-Strand Break on Branch Migration and Folding Dynamics of Holliday Junctions

The Holliday junction (HJ), or four-way junction, is a central intermediate state of DNA for homologous genetic recombination and other genetic processes such as replication and repair. Branch migration is the process by which the exchange of homologous DNA regions occurs, and it can be spontaneous or driven by proteins. Unfolding of the HJ is required for branch migration. Our previous single-molecule fluorescence studies led to a model according to which branch migration is a stepwise process consisting of consecutive migration and folding steps. Folding of the HJ in one of the folded conformations terminates the branch migration phase. At the same time, in the unfolded state HJ rapidly migrates over entire homology region of the HJ in one hop. This process can be affected by irregularities in the DNA double helical structure, so mismatches almost terminate a spontaneous branch migration. Single-stranded breaks or nicks are the most ubiquitous defects in the DNA helix; however, to date, their effect on the HJ branch migration has not been studied. In addition, although nicked HJs are specific substrates for a number of enzymes involved in DNA recombination and repair, the role of this substrate specificity remains unclear. Our main goal in this work was to study the effect of nicks on the efficiency of HJ branch migration and the dynamics of the HJ. To accomplish this goal, we applied two single-molecule methods: atomic force microscopy and fluorescence resonance energy transfer. The atomic force microscopy data show that the nick does not prevent branch migration, but it does decrease the probability that the HJ will pass the DNA lesion. The single-molecule fluorescence resonance energy transfer approaches were instrumental in detailing the effects of nicks. These studies reveal a dramatic change of the HJ dynamics. The nick changes the structure and conformational dynamics of the junctions, leading to conformations with geometries that are different from those for the intact HJ. On the basis of these data, we propose a model of branch migration in which the propensity of the junction to unfold decreases the lifetimes of folded states, thereby increasing the frequency of junction fluctuations between the folded states.     

Reversible metabolic depression in lamprey hepatocytes during prespawning migration: dynamics of mitochondrial membrane potential

The lamprey (Lampetra fluviatilis L.) is an extant representative of the ancient vertebrate group of Agnathans. During the prespawning migration (the river period of life from autumn until spring) lamprey hepatocytes exhibit widely different energy states: a high-energy state in autumn and spring, corresponding to a normal physiological standard, and a low-energy state in winter, which is provoked by prolonged starvation and profound metabolic arrest. In spring the restoration of energy status (return to an active state) is associated with hormonally induced lipolysis of the lipid droplets stored in the cells. Lamprey hepatocytes demonstrate an aerobic metabolism based on oxidation of free fatty acids. The dynamics of mitochondrial membrane potential (MMP) were measured throughout the prespawning migration. Pharmacological inhibition of the electron transport chain decreased the MMP and caused extensive depletion of cellular ATP without loss of cell viability. The potential molecular mechanisms responsible for winter metabolic depression in lamprey hepatocytes are discussed.     

Regulation of the primary photosynthesis processes

The mechanisms of primary processes of photosynthesis and macromolecular conformational changes that control the efficiency of primary energy transformation in photosynthesis are discussed. Special attention is focused on the analysis of chlorophyll fluorescence as an integrated parameter indicative of the efficiency and dynamics of primary steps of photosynthesis. Sharp changes in environmental conditions and other unfavorable factors may lead to the distortions of the coupling between consecutive electron transfer steps. As a result, an excess of electrons and/or electronic excitation energy may form at some sites of the electron transport chain. This may lead to the generation of reactive oxygen species responsible for the subsequent oxidative stress. The results of the application of these data in the areas of biotechnology and ecology are demonstrated.     

Relaxation folding and the principle of the minimum rate of energy dissipation for conformational motions in a viscous medium

A numerical simulation of the folding of a model polymer chain of 50 units with valence bonds of a fixed length and fixed valence angle values has been performed using the strong friction approximation. The rate of energy dissipation in the system has been analyzed for conformational motions along a trajectory determined by the equations of mechanics and the trajectories characterized by random and variable deviations from the mechanical path. The validity of the principle of the minimum average rate of the energy dissipation for the conformational relaxation of a macromolecule in a viscous medium has been demonstrated. A profile of the relaxation energy funnel for the folding of a macromolecular chain has been constructed. Slow and rapid stages of folding could be distinguished in the energy funnel profile; the final state was separated from the nearest conformations of the folded chain by an energy gap.     

Modeling negative ion defect migration through the gramicidin A channel

The results of potential of mean force (PMF) calculations for the distinct stages of proton conduction through the gramicidin A channel, including proton migration, reorientation of the water file and negative ion defect migration, are presented. The negative ion defect migration mechanism was hypothesized in experimental studies but was not considered previously in molecular dynamics simulations. The model system consisted of the peptide chains constructed on the base of the structure PDBID:1JNO, the inner file of nine water molecules and external clusters of water molecules placed at both ends of the channel. Potential energy functions were computed with the CHARMM/PM6/TIP3P parameters. The results obtained for proton migration and water file reorientation are basically consistent with those reported previously by Pómès and Roux (Biophys J 82:2304, 2002) within the similar approach. For the newly considered mechanism of negative ion defect migration from the channel center to the end of the water file we obtain the energy 3.8 kcal mol⁻¹ which is not considerably different from the activation energy of water reorientation, 5.4 kcal mol⁻¹. Therefore this mechanism may principally compete for the rate-limiting step in proton conduction in gramicidin.