The trajectory of a stiff rod in a curved potential energy trough. An initial result for short nucleosomal rods

The equilibrium trajectory of the axis of a rod subject to an externally imposed curved potential energy trough tends to conform to the shape of the curved trough, but also tends to be straight because of elastic resistance to bending. The actual path of the axis is a balance between the two extremes. We consider a potential energy trough centered along a circular arc of radius R. For a rod of small length compared to R, we show that the axis at equilibrium forms an arc of a circle of radius greater than R. The value of the radius of the axial path depends on the relative values of the Hooke's Law bending constant for the rod and the depth and width of the trough. Motivation for the calculation is provided by nucleosomal DNA, which conforms to the surface of a roughly cylindrical histone core at physiological ionic strength, but is observed to unwind into a partially extended conformation at very low ionic strength. We suggest that the rigidity to bending of short DNA segments becomes sufficiently great at low ionic strength to overcome attractive interactions with the histone surface. Alternately, of course, if during the cell cycle mutually attractive forces between DNA and histone core are weakened at constant ionic strength, the same type of unfolding would be expected to occur as the strength of the DNA-histone contacts drops below the level required to overcome elastic resistance to bending of the DNA rod.     

Curvature-based interaction potential between a micro/nano curved surface body and a particle on the surface of the body

The interaction potential between a curved surface body and a particle located on the surface of the body is studied in this paper. Based on the negative exponential pair potential (1/R ⁿ ) between particles, the interaction potential is proved to be of the curvature-based form, i.e., it can be written as a function of curvatures of the surface. Idealized numerical experiments are designed to test the accuracy of curvature-based potential. Based on the curvature-based potential, propositions below are confirmed: a highly curved surface body will induce driving forces on the particle located on the surface, and curvatures and the gradients of curvatures are essential factors forming the driving forces. In addition, the tangent driving force acting on the particle from the curved surface body is studied. Based on duality, the following rule is proved: for a convex or concave curved body sharing the same curved surface, the curvature-based interaction potential between them and a particle on the surface can make up the potential of a particle in the whole space.     

江苏省能源农业发展的资源现状与发展潜力

在讨论江苏省农村生物质类型和资源总量的基础上,利用已有统计资料和数据,对江苏省能源农业发展的资源基础现状进行定量的估算,并通过对发展能源农业的种质和可利用土地、江苏省农业和畜牧业发展态势的分析研究,对江苏省能源农业的发展潜力进行了预测.研究表明,2006年江苏省农村生物质能总蕴藏量和可利用量折合标准煤分别达到14238.06万t和2311.54万t.到2010年和2015年,江苏省农村生物质能资源量折合标准煤将分别达到5390万t和6109万t.     

Future energy potential of Miscanthus in Europe

European field experiments have demonstrated Miscanthus can produce some of the highest energy yields per hectare of all potential energy crops. Previous modelling studies using MISCANMOD have calculated the potential energy yield for the EU27 from mean historical climate data (1960–1990). In this paper, we have built on the previous studies by further developing a new Miscanthus crop growth model MISCANFOR in order to analyse (i) interannual variation in yields for past and future climates, (ii) genotype-specific parameters on yield in Europe. Under recent climatic conditions (1960–1990) we show that 10% of arable land could produce 1709 PJ and mitigate 30 Tg of carbon dioxide-carbon (CO₂-C) equivalent greenhouse gasses (GHGs) compared with EU27 primary energy consumption of 65 598 PJ, emitting 1048 Tg of CO₂-C equivalent GHGs in 2005. If we continue to use the clone Miscanthus × giganteus , MISCANFOR shows that, as climate change reduces in-season water availability, energy production and carbon mitigation could fall 80% by 2080 for the Intergovernmental Panel on Climate Change A2 scenario. However, because Miscanthus is found in a huge range of climates in Asia, we propose that new hybrids will incorporate genes conferring superior drought and frost tolerance. Using parameters from characterized germplasm, we calculate energy production could increase from present levels by 88% (to 2360 PJ) and mitigate 42 Tg of CO₂-C equivalent using 10% arable land for the 2080 mid-range A2 scenario. This is equivalent to 3.6% of 2005 EU27 primary energy consumption and 4.0% of total CO₂ equivalent C GHG emissions.     

中梁山岩溶槽谷区不同土地利用方式坡地产流规律

坡地产流是造成岩溶区水土流失的主要驱动力,研究典型岩溶槽谷区坡地产流规律,对岩溶区防治水土流失、合理利用地下水资源具有重要理论意义。在重庆市中梁山龙凤和龙车槽谷选取不同土地利用方式的4个标准径流小区,对降水、地表径流、壤中流、裂隙流和土壤含水率进行了同步监测,探讨了坡地产流特征。结果表明:(1)4个不同土地利用方式的径流小区,坡地总产流量从大到小依次为:耕地(3696.9L)果园地(3657.2L)竹林地(2922.9L)林地(2211.1L),总径流系数(3.1%—5.2%)远低于非岩溶区(约20%);(2)4个径流小区的产流形式主要为地表径流,壤中流和裂隙流产生滞后于地表径流;(3)降水因子、前期土壤含水率共同影响地表径流,但降水因子对地表径流的影响远大于前期土壤含水率。降水因子中,15min最大雨强是影响耕地、果园地的地表径流的主要因素,降水量是影响林地、竹林地的地表径流的主要因素;前期土壤含水率对耕地、林地、果园地地表径流影响较大,对竹林地地表径流影响较小。     

The spatiotemporal trajectory of a dengue epidemic in a medium-sized city

Understanding the transmission dynamics of infectious diseases is important to allow for improvements of control measures. To investigate the spatiotemporal pattern of an epidemic dengue occurred at a medium-sized city in the Northeast Region of Brazil in 2009, we conducted an ecological study of the notified dengue cases georeferenced according to epidemiological week (EW) and home address. Kernel density estimation and space-time interaction were analysed using the Knox method. The evolution of the epidemic was analysed using an animated projection technique. The dengue incidence was 6.918.7/100,000 inhabitants; the peak of the epidemic occurred from 8 February-1 March, EWs 6-9 (828.7/100,000 inhabitants). There were cases throughout the city and was identified space-time interaction. Three epicenters were responsible for spreading the disease in an expansion and relocation diffusion pattern. If the health services could detect in real time the epicenters and apply nimbly control measures, may possibly reduce the magnitude of dengue epidemics.     

Adenosine A(2a) receptor-mediated inhibition of rod opsin mRNA expression in tiger salamander

The neuromodulator adenosine mediates dark-adaptive changes in retinal photoreceptors through A(2a) receptors. In cold-blooded vertebrates, opsin mRNA expression is lower at night than during the day. In the present study, we tested whether adenosine could inhibit opsin mRNA expression in cultured rod cells and if endogenous adenosine acts to suppress opsin mRNA in the intact retina at night. Semi-quantitative in situ hybridization showed that treatment with 100 nm of the A(2a)/A(2b) agonist N(6)-[2-(3,5-dimethoxyphenyl)-2-(2-methylphenyl)-ethyl]adenosine (DPMA) reduced opsin mRNA 41% in cultured rod cells. The effect of DPMA was blocked by 10 microm of the A(2a) antagonist 8-(3-chlorostyryl)caffeine (CSC) but not by 10 microm of the A(2b) antagonist alloxazine. One micromolar adenosine alone had no effect on opsin mRNA. However, in the presence of the adenosine deaminase inhibitor erythro-9-(2-hydroxy-3-nonyl)adenine hydrochloride (EHNA), 1 microm adenosine reduced opsin mRNA 61%. EHNA alone reduced opsin mRNA by 26%. Consistent with an A(2a) receptor mechanism, 100 nm forskolin (adenylate cyclase agonist) decreased opsin mRNA 34%. Finally, northern blots showed that intravitreal injection of 10 microm CSC at night increased opsin I mRNA 38%. Thus, endogenous adenosine suppresses rod opsin I mRNA expression at night; in vitro results indicate this reduction occurs through A(2a)-like receptor binding and stimulation of adenylate cyclase activity.     

The elasticity of the potential of emission reduction to energy saving: Definition,measurement, and evidence from China

Based on energy and CO₂ emission efficiencies, this paper proposes a definition of the elasticity of the potential of emission reduction to energy saving (E_peres), and measures the elasticity in China’s 30 provincial regions. Although E_peres is a relative definition, it can be used (1) to measure the amount of reduced CO₂ emissions per unit fossil energy saving, (2) to reflect the effectiveness of fossil energy saving for CO₂ emission reduction in different regions, and (3) to provide decision-making criteria for selecting pathways for emission reductions in different regions. The results show that compared with energy saving, emission reduction is a more serious issue in China. This indicates that energy saving policies have been highly effective since their implementation during the 11th “Five-Year Plan”. With respect to provincial disparities, the emission reductions caused by fossil energy saving are not significant in Beijing, Shanghai, and Guangdong. Fujian province has significant E_peres, indicating that emission reduction causing by fossil energy saving is effective. E_peres has been increasing over time in Hunan and Hubei. Hainan’s E_peres has remained less than 1, indicating that its emission-reduction effect of fossil energy saving is worse than in other provinces. Moreover, the elasticity of Eastern China is greater than that of Central China and Western China. This finding sheds light on pathway selection for energy saving and emission reduction in China: it would be more appropriate to encourage fossil energy saving in Eastern China, and to promote clean energy use (e.g., water electricity and solar energy) in Central China and Western China.     

The molecular mechanics program DUPLEX: Computing structures of carcinogen modified DNA by surveying the potential energy surface

The nucleic acids molecular mechanics program DUPLEX has been designed with useful features for surveying the potential energy surface of polynucleotides, especially ones that are modified by polycyclic aromatic carcinogens. The program features helpful strategies for addressing the multiple minimum problem: (1) the reduced variable domain of torsion angle space; (2) search strategies that emphasize large scale searches for smaller subunits, followed by building to larger units by a variety of strategies; (3) the use of penalty functions to aid the minimizer in locating selected structural types in first stage minimizations; penalty functions are released in terminal minimizations to yield final unrestrained minimum energy conformations. Predictive capability is illustrated by DNA modified by activated benzo[a]pyrenes.     

The relation of proton motive force,adenylate energy charge and phosphorylation potential to the specific growth rate and efficiency of energy transduction inBacillus licheniformis under aerobic growth conditions

The magnitude of the proton motive force (p) and its constituents, the electrical () and chemical potential (-ZpH), were established for chemostat cultures of a protease-producing, relaxed (rel ^–) variant and a not protease-producing, stringent (rel ⁺) variant of an industrial strain ofBacillus licheniformis (respectively referred to as the A- and the B-type). For both types, an inverse relation of p with the specific growth rate was found. The calculated intracellular pH (pH_in) was not constant but inversely related to . This change in pH_in might be related to regulatory functions of metabolism but a regulatory role for pH_in itself could not be envisaged. Measurement of the adenylate energy charge (EC) showed a direct relation with for glucose-limited chemostat cultures; in nitrogen-limited chemostat cultures, the EC showed an approximately constant value at low and an increased value at higher . For both limitations, the ATP/ADP ratio was directly related to .The phosphorylation potential (G'p) was invariant with . From the values for G'p and p, a variable H⁺/ATP-stoichiometry was inferred: H⁺/ATP=1.83+0.52µ, so that at a given H⁺/O-ratio of four (4), the apparent P/O-ratio (inferred from regression analysis) showed a decline of 2.16 to 1.87 for =0 to _max (we discuss how more than half of this decline will be independent of any change in internal cell-volume). We propose that the constancy of G'p and the decrease in the efficiency of energy-conservation (P/O-value) with increasing are a way in which the cells try to cope with an apparent less than perfect coordination between anabolism and catabolism to keep up the highest possible with a minimum loss of growth-efficiency. Protease production in nitrogen-limited cultures as compared to glucose-limited cultures, and the difference between the A- and B-type, could not be explained by a different energy-status of the cells.Abbreviations CCCP carbonylcyanide-p-trichloromethoxyphenylhydrazone - DW dry weight of biomass - F Faraday's constant, 96.6 J/(mV × mol) - Fo chemostat outflow-rate (ml/h) - FCCP carbonylcyanide-p-trifluoromethoxyphenylhydrazone - G'p phosphorylation potential, the Gibbs energy change for ATP-synthesis from ADP and P_i - G'⁰p standard Gibbs energy change at specified conditions - H⁺/ATP number of protons translocated through - ATP synthase in synthesis of one ATP - H⁺/O protons translocated during transfer of 2 electrons from substrate to oxygen - specific growth rate (1/h) - _H+ transmembrane electrochemical proton potential, J/mol - M_b molar weight (147.6 g/mol) of bacteria with general cell formula C_6.0H_10.8O_3.0N_1.2 - pH_out,in extracellular, intracellular pH - P_i (intracellular) inorganic phosphate - p proton motive force, mV - pH transmembrane pH-difference - transmembrane electrical potential, mV - P/O number of ADP phosphorylated to ATP upon reduction of one O^2– to H₂O by two electrons transferred through the electron transfer chain - P/O (H⁺/O) × (H⁺/ATP)^–1 - P/O_F, P/O_N P/O with the two electrons donated by resp. (NADH + H⁺) and FADH - q specific rate of consumption or production (mol/g DW × h) - rel ⁺,rel ^– stringent, relaxed genotype - R universal gas constant, 8.36 J/(mol × degree) - T absolute temperature - TPMP⁺ triphenylmethylphosphonium ion - TPP⁺ tetraphenyl phosphonium ion - Y growth yield, g DW/mol - Z conversion constant=61.8 mV for 310 K (37 °C) - ZpH transmembrane proton potential or chemical potential, mV     

Enhanced sampling of the molecular potential energy surface using mutually orthogonal latin squares: application to peptide structures

The computational identification of the optimal three-dimensional fold of even a small peptide chain from its sequence, without reference to other known structures, is a complex problem. There have been several attempts at solving this by sampling the potential energy surface of the molecule in a systematic manner. Here we present a new method to carry out the sampling, and to identify low energy conformers of the molecule. The method uses mutually orthogonal Latin squares to select (of the order of) n(2) points from the multidimensional conformation space of size m(n), where n is the number of dimensions (i.e., the number of conformational variables), and m specifies the fineness of the search grid. The sampling is accomplished by first calculating the value of the potential energy function at each one of the selected points. This is followed by analysis of these values of the potential energy to obtain the optimal value for each of the n-variables separately. We show that the set of the n-optimal values obtained in this manner specifies a low energy conformation of the molecule. Repeated application of the method identifies other low energy structures. The computational complexity of this algorithm scales as the fourth power of the size of the molecule. We applied this method to several small peptides, such as the neuropeptide enkephalin, and could identify a set of low energy conformations for each. Many of the structures identified by this method have also been previously identified and characterized by experiment and theory. We also compared the best structures obtained for the tripeptide (Ala)(3) by the present method, with those obtained by an exhaustive grid search, and showed that the algorithm is successful in identifying all the low energy conformers of this molecule.     

典型喀斯特山区农业生物质能潜力估算——以贵州省为例

喀斯特山区生态环境脆弱,能源利用模式低值粗放,开展该区域的农业可利用生物质能潜力研究,对喀斯特山区农村能源建设和生态环境保护具有重要意义。以贵州省为例,在考虑土壤生态保留前提下,利用草谷比、土壤生态保留系数、收集系数、折标系数、副产物系数估算农村地区可利用农业生物质能资源总量。结果表明:(1) 2009—2015年间,贵州省年均可利用生物质能资源量达5191.50×10~4t标准煤,地均和人均农业生物质能资源量分别达到295 t标准煤/km~2和1.48 t标准煤/人,其中年均可能源化利用的达到1974.05×10~4t标准煤,占贵州省同期能源消费总量的21.84%。(2)贵州省生物质能储量结构比例分布不均,畜禽粪便资源利用潜力巨大,贡献值高达85%;其中,牛粪资源蕴藏量达年均3009.78×10~4t标准煤,贡献值达到68.39%,是贵州省最重要的农业生物质能资源。(3)从时序变化特征看,2009—2015年间贵州省生物质能资源量呈现U形结构,2011年达到最低值,这与2010年的西南大旱重要事件耦合。最后,针对贵州省农业生物质能现状,论文提出喀斯特山区应该合理布局秸秆电厂和秸秆固化成型燃料生产企业,提高畜禽的规模化养殖水平并加强农业生产防灾减灾工作,农村生活能源推广以沼气、节柴灶与节能秸秆气化炉高效利用相结合的能源利用结构等建议。     

Effect of external electric fields on the potential energy profile of K+ ions in selective filter of the KcsA potassium channel

In this study, the potential energy profile of potassium ions in the selective filter part of a KcsA channel was investigated via the application of the molecular simulation method. For this purpose, using the molecular dynamics simulation, the effect of an applied electric field, either constant or oscillating, was studied on the dynamics of K ions in the filter. It was found that when the channel is exposed to a constant electric field of strength 0.03 V/nm, the ions experience a hopping motion. Furthermore, it was shown that the application of oscillating electric fields of 1 and 2.5 GHz, can increase the rigidity of the filter atomic bonds. By computing the potential energy of K ion in the filter, it was shown that the depth of the potential wells, corresponding to the filter sites, increased when an alternative field was applied. Therefore, exposing the channel to the GHz oscillating electric field could disturb the passing rate of ions through the filter, which in turn may affect the operation of these kinds of channels.     

A population study of a mutation allele associated with cone–rod dystrophy in the standard wire-haired dachshund

Cone–rod dystrophy in the standard wire-haired dachshund (SWHD) is inherited as a simple autosomal recessive trait and the recently discovered mutation is widespread within the SWHD population in Norway and other Scandinavian countries. The gene frequency was estimated to be 4.8%. On the basis of the assumption that the size of the ancestral haplotype around a mutation is inversely correlated with the number of generations since the mutation arose, we have found that the mutation is of a relatively recent origin. The conserved haplotype was found to be 8 Mb in size and therefore we estimate that the mutation arose roughly eight generations (approximately 37 years) ago. This indicates that the mutation arose after breed separation.     

Differential membrane protein phosphorylation in bovine retinal rod outer segment disk membranes as a function of disk age

The outer segment portion of photoreceptor rod cells is composed of a stacked array of disk membranes. Newly formed disks are found at the base of the rod outer segment (ROS) and are relatively high in membrane cholesterol. Older disks are found at the apical tip of the ROS and are low in membrane cholesterol. Disk membranes were separated based on their membrane cholesterol content and the extent of membrane protein phosphorylation determined. Light induced phosphorylation of ROS disk membrane proteins was investigated using magic angle spinning³¹P NMR. When intact rod outer segment preparations were stimulated by light, in the presence of endogenously available kinases, membrane proteins located in disks at the base of the ROS were more heavily phosphorylated than those at the tip. SDS-gel electrophoresis of the phosphorylated disk membranes subpopulations identified a phosphoprotein species with a molecular weight of approximately 68–72 kDa that was more heavily phosphorylated in newly formed disks than in old disks. The identity of this phosphoprotein is presently under investigation. When the phosphorylation reaction was carried out in isolated disk membrane preparations with exogenously added co-factors and kinases, there was no preferential protein phosphorylation. Taken collectively, these results suggest that within the ROS there is a protein phosphorylation gradient that maybe indicative of co-factor or kinase heterogeneity.     

The redox potentials of the b-type cytochromes of higher plant chloroplasts

1. In fresh chloroplasts, three b-type cytochromes exist. These are b-559_HP (λ_max, 559 nm; E_m at pH 7, +370 mV; pH-independent E_m), b-559_LP (λ_max, 559 nm; E_m at pH 7, +20 mV; pH-independent E_m) and b-563 (λ_max, 563 nm; E_m at pH 7, ?110 mV; pH-independent E_m). b-559_HP may be converted to a lower potential form (λ_max, 559 nm; E_m at pH 7, +110 mV; pH-independent E_m).2. In catalytically active b-f particle preparations, three cytochromes exist. These are cytochrome f (λ_max, 554 nm; E_m at pH 7, +375 mV, pK on oxidised cytochrome at pH 9), b-563 (λ_max, 563 nm; E_m at pH 7, ?90 mV, small pH-dependence of E_m) and a b-559 species (λ_max, 559 nm, E_m at pH 7, +85 mV; pH-independent E_m).3. A positive method of demonstration and estimation of b-559_LP in fresh chloroplasts is described which involves the use of menadiol as a selective reductant of b-559_LP.     

Sex-role reversal of a monogamous pipefish without higher potential reproductive rate in females

In monogamous animals, males are usually the predominant competitors for mates. However, a strictly monogamous pipefish Corythoichthys haematopterus exceptionally exhibits a reversed sex role. To understand why its sex role is reversed, we measured the adult sex ratio and the potential reproductive rate (PRR), two principal factors influencing the operational sex ratio (OSR), in a natural population of southern Japan. The adult sex ratio was biased towards females throughout the breeding season, but the PRR, which increased with water temperature, did not show sexual difference. We found that an alternative index of the OSR (Sf/Sm: sex ratio of 'time in') calculated from the monthly data was consistently biased towards females. The female-biased OSR associated with sex-role reversal has been reported in some polyandrous or promiscuous pipefish, but factors biasing the OSR differed between these pipefish and C. haematopterus. We concluded that the similar PRR between the sexes in C. haematopterus does not confer reproductive benefit of polygamous mating on either sex, resulting in strict monogamous mating, and its female-biased adult sex ratio promotes female-female competition for a mate, resulting in sex-role reversal.     

Ocean energy and the law of the sea: The need for a protocol

Although fossil fuels are the overwhelming source of energy for the world, and will continue to be so for the foreseeable future, demographic, environmental, political, and economic factors indicate that interest in alternative, renewable sources of energy will grow. There is a need for both global and national policies on ocean energy management. In particular, coastal states and the energy industry would benefit from guidelines that helped to create a predictable, stable environment in which long‐term, high‐cost research, development, and investment decisions could be made with confidence. Coastal states have jurisdiction over the maritime zones most relevant to energy production, but many lack the expertise and funds to develop this potential source. Industry must operate within the control of coastal states and will not be served well by a plethora of differing legal interpretations and unilaterally imposed restrictions and obligations from state to state. An Ocean Energy Protocol to the 1982 UN Convention on the Law of the Sea would afford governments and industry the opportunity to clarify their respective obligations and address particular interests for mutual benefit.     

The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes

Nucleosomes impede access to DNA. Therefore, nucleosome positioning is fundamental to genome regulation. Nevertheless, the molecular nucleosome positioning mechanisms are poorly understood. This is partly because in vitro reconstitution of in vivo-like nucleosome positions from purified components is mostly lacking, barring biochemical studies. Using a yeast extract in vitro reconstitution system that generates in vivo-like nucleosome patterns at S. cerevisiae loci, we find that the RSC chromatin remodelling enzyme is necessary for nucleosome positioning. This was previously suggested by genome-wide in vivo studies and is confirmed here in vivo for individual loci. Beyond the limitations of conditional mutants, we show biochemically that RSC functions directly, can be sufficient, but mostly relies on other factors to properly position nucleosomes. Strikingly, RSC could not be replaced by either the closely related SWI/SNF or the Isw2 remodelling enzyme. Thus, we pinpoint that nucleosome positioning specifically depends on the unique properties of the RSC complex.