Relating Species and Community Dynamics in an Heavily Exploited Marine Fish Community

We examined the dynamics of fish species and how they relate to species assemblage coherence in the heavily exploited Georges Bank fish community. Coherence is defined as reduced temporal variability of total assemblage biomass. We assumed that a higher degree of compensation hence coherence occurs within competitively coupled species assemblages; therefore, fisheries may directly alter the dynamics of certain targeted species sizes but assemblage structure will be relatively more stable owing to compensatory interactions. Species-sizes were grouped, based on negative covariance coupling in biomass time series from survey data. Assemblages representing benthic feeders were clearly identified by this method; furthermore, the most heavily exploited species-sizes were decoupled from other species-sizes suggesting that fisheries have diminished their potential to compensate or to be compensated for by competitive interactions. Biomass of species-sizes within known trophic guilds strongly compensated other guild-member biomass fluctuations if the diet of guild members was more specialized. This is an indication that more competitive conditions (more specialization) foster greater compensatory responses between competitors biomass fluctuations.     

Regulation of the distribution of excitation energy in Ochromonas danica,an organism containing a chlorophyll-A/C/carotenoid light harvesting antenna

A chlorophyll a, c-fucoxanthin pigment-protein complex8 functions as the major light harvesting antenna in the Chrysophyte Ochromonas danica. The regulated distribution of excitation energy between the two photosystems was investigated in these organisms and was shown to be strongly wavelength dependent. A light state transition was induced by pre-illumination of cells using light 2 (640 nm) and light 1 (700 nm) of equal absorbed intensity, and detected by reversible changes in the 77 K chlorophyll fluorescence emission spectra. Peaks at 690 nm and 720 nm in the low temperature spectra are most likely associated with PS2 and PS1 respectively. A room temperature fluorescence emission at 680 nm induced by modulated light 2 (500 nm) was strongly quenched in the presence of background light 1 (720 nm). Removal of light 1 led to an increase in fluorescence followed by a slow quenching. The room temperature fluorescence changes were directly correlated with changes in the 77 K emission spectra that indicated a change in the distribution of excitation energy between the two photosystems. It was established that DCMU (1 mol) prevented the state 2. The conversion to state 1 followed a simple photochemical dose dependence and had a half-time of 20 s-1.5 min at 6 W m^-2. In contrast, the conversion to state 2 was independent of light intensity. These data indicate that O. danica undergoes a light state transition in response to the preferential excitation of PS2 or PS1.Abbreviations PS2 photosystem 2 - PS1 photosystem 1 - LHC light harvesting chlorophyll a/b protein - fx fucoxanthin - PQ plastoquinone - DCMU 3-(3,4-dichlorophenyl)-1,1-dimethyl urea     

Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin

Serine proteinases and their protein inhibitors belong to one of the most comprehensively studied models of protein-protein interactions. It is well established that the narrow trypsin specificity is caused by the presence of a negatively charged aspartate at the specificity pocket. X-ray crystallography as well as association measurements revealed, surprisingly, that BPTI with glutamatic acid as the primary binding (P1) residue was able to bind to trypsin. Previous free energy calculations showed that there was a substantially unfavorable binding free energy associated with accommodation of ionized P1 Glu at the S1-site of trypsin. In this study, the binding of P1 Glu to trypsin has been systematically investigated in terms of the protonation states of P1 Glu and Asp189, the orientation of Gln192, as well as the possible presence of counterions using the linear interaction energy (LIE) approach and the free energy perturbation (FEP) method. Twenty-four conceivable binding arrangements were evaluated and quantitative agreement with experiments is obtained when the P1 Glu binds in its protonated from. The results suggest that P1 Glu is one of the variants of BPTI that inhibit trypsin strongest at low pH, contrary to the specificity profile of trypsin, suggesting a new regulation mechanism of trypsin-like enzymes.     

Improving Energy Efficiency by Five Percent and More per Year?

Reduction of specific energy consumption by 1% to 2% per year is typically what is considered feasible for end-use energy applications. This article tries to answer the question of whether much higher rates, for example 5% and more, are feasible for new equipment, installations, and buildings.
After examining some end-use functions in industry, buildings, and the transport sector, it is concluded that for the foreseeable future—that is, not more than 10 to 20 years into the future—such high rates of reduction of specific energy consumption are indeed possible. For the longer term, no definitive proof is available, but there are also no indications that such high rates could not be maintained.
The effect of the reduction of specific energy consumption on total energy use depends on the growth of energy-using activities and on the replacement rates of capital stock. Taking these into account, it is estimated that for industrialized countries a reduction of absolute total energy use by 50% in 50 years compared with the current levels is possible.
Such a reduction requires a huge effort in innovation; however, the possibilities for stimulating innovation seem not to be exhausted yet.     

Allocation of energy use in petroleum refineries to petroleum products

Aim, Scope, and Background  Studies to evaluate the energy and emission impacts of vehicle/fuel systems have to address allocation of the energy use and emissions associated with petroleum refineries to various petroleum products because refineries produce multiple products. The allocation is needed in evaluating energy and emission effects of individual transportation fuels. Allocation methods used so far for petroleum-based fuels (e.g., gasoline, diesel, and liquefied petroleum gas [LPG]) are based primarily on mass, energy content, or market value shares of individual fuels from a given refinery. The aggregate approach at the refinery level is unable to account for the energy use and emission differences associated with producing individual fuels at the next sub-level: individual refining processes within a refinery. The approach ignores the fact that different refinery products go through different processes within a refinery. Allocation at the subprocess level (i.e., the refining process level) instead of at the aggregate process level (i.e., the refinery level) is advocated by the International Standard Organization. In this study, we seek a means of allocating total refinery energy use among various refinery products at the level of individual refinery processes. Main Features  We present a petroleum refinery-process-based approach to allocating energy use in a petroleum refinery to petroleum refinery products according to mass, energy content, and market value share of final and intermediate petroleum products as they flow through refining processes within a refinery. The approach is based on energy and mass balance among refining processes within a petroleum refinery. By using published energy and mass balance data for a simplified U.S. refinery, we developed a methodology and used it to allocate total energy use within a refinery to various petroleum products. The approach accounts for energy use during individual refining processes by tracking product stream mass and energy use within a refinery. The energy use associated with an individual refining process is then distributed to product streams by using the mass, energy content, or market value share of each product stream as the weighting factors. Results  The results from this study reveal that product-specific energy use based on the refinery process-level allocation differs considerably from that based on the refinery-level allocation. We calculated well-to-pump total energy use and greenhouse gas (GHG) emissions for gasoline, diesel, LPG, and naphtha with the refinery process-based allocation approach. For gasoline, the efficiency estimated from the refinery-level allocation underestimates gasoline energy use, relative to the process-level based gasoline efficiency. For diesel fuel, the well-to-pump energy use for the process-level allocations with the mass- and energy-content-based weighting factors is smaller than that predicted with the refinery-level allocations. However, the process-level allocation with the market-value-based weighting factors has results very close to those obtained by using the refinery-level allocations. For LPG, the refinery-level allocation significantly overestimates LPG energy use. For naphtha, the refinery-level allocation overestimates naphtha energy use. The GHG emission patterns for each of the fuels are similar to those of energy use. Conclusions  We presented a refining-process-level-based method that can be used to allocate energy use of individual refining processes to refinery products. The process-level-based method captures process-dependent characteristics of fuel production within a petroleum refinery. The method starts with the mass and energy flow chart of a refinery, tracks energy use by individual refining processes, and distributes energy use of a given refining process to products from the process. In allocating energy use to refinery products, the allocation method could rely on product mass, product energy contents, or product market values as weighting factors. While the mass- and energy-content-based allocation methods provide an engineering perspective of energy allocation within a refinery, the market-value-based allocation method provides an economic perspective. The results from this study show that energy allocations at the aggregate refinery level and at the refining process level could make a difference in evaluating the energy use and emissions associated with individual petroleum products. Furthermore, for the refining-process-level allocation method, use of mass — energy content- or market value share-based weighting factors could lead to different results for diesel fuels, LPG, and naphtha. We suggest that, when possible, energy use allocations should be made at the lowest subprocess level — a confirmation of the recommendation by the International Standard Organization for life cycle analyses. Outlook  The allocation of energy use in petroleum refineries at the refining process level in this study follows the recommendation of ISO 14041 that allocations should be accomplished at the subprocess level when possible. We developed a method in this study that can be readily adapted for refineries in which process-level energy and mass balance data are available. The process-level allocation helps reveal some additional energy and emission burdens associated with certain refinery products that are otherwise overlooked with the refinery-level allocation. When possible, process-level allocation should be used in life-cycle analyses.     

Solvation Energy and Thermal Stability of Hydrophilization-Modified α-Chymotrypsin

As reported in the literature [Mozhaev et al. (1988), Eur. J. Biochem. 173, 147–154], when a series of modifiers, especially the cyclic anhydrides of pyromellitic and mellitic acids, are introduced into each lysine located in the -chymotrypsin (CT) surface, a substantial hydrophilization of the enzyme surface can occur and remarkable stabilization effects of modified enzymes can be obtained. In this paper, four models are applied to calculate the solvation energy of native and the modified CT based on their tertiary structures, which can be built by the CVFF force field. Analyzing the relationship between the solvation energy and the thermal stability in detail, we find that the results of three solvation energy models (Ooi model, WE-1 model, and WE-2 model) can be used to illustrate the relative stability among these enzymes qualitatively. The present study should be of practical value as well as of some theoretical interest.     

Use of thermography for quantitative studies of spatial and temporal variation of stomatal conductance over leaf surfaces

This paper describes a new approach to the calibration of thermal infrared measurements of leaf temperature for the estimation of stomatal conductance and illustrates its application to thermal imaging of plant leaves. The approach is based on a simple reformulation of the leaf energy balance equation that makes use of temperature measurements on reference surfaces of known conductance to water vapour. The use of reference surfaces is an alternative to the accurate measurement of all components of the leaf energy balance and is of potentially wide application in studies of stomatal behaviour. The resolution of the technique when applied to thermal images is evaluated and some results of using the approach in the laboratory for the study of stomatal behaviour in leaves of Phaseolus vulgaris L. are presented. Conductances calculated from infrared measurements were well correlated with estimates obtained using a diffusion porometer.     

NaCl胁迫对PSII光能利用和耗散的影响

用荧光动力学的方法研究了不同浓度的ＮａＣｌ 处理对ＰＳＩＩ光能利用和耗散的影响。结果表明,在较低的光强下,与对照、１００ｍ ｍｏｌ／Ｌ 和２００ｍ ｍｏｌ／Ｌ ＮａＣｌ 处理相比,经３００ｍ ｍｏｌ／Ｌ 和４００ｍ ｍｏｌ／Ｌ ＮａＣｌ 处理的小麦,其荧光光化学淬灭效率较低,荧光非光化学淬灭效率较高,Ｆｏ 淬灭系数较大,ＱＢ － 非还原性ＰＳＩＩ反应中心含量较大; 而在较高光强下, 其荧光非光化学淬灭效率和Ｆｏ 淬灭系数则相对较低。     

Protein translocation through a tunnel induces changes in folding kinetics: a lattice model study

Compaction of a nascent polypeptide chain inside the ribosomal exit tunnel, before it leaves the ribosome, has been proposed to accelerate the folding of newly synthesized proteins following their release from the ribosome. Thus, we used Kinetic Monte Carlo simulations of a minimalist on-lattice model to explore the effect that polypeptide translocation through a variety of channels has on protein folding kinetics. Our results demonstrate that tunnel confinement promotes faster folding of a well-designed protein relative to its folding in free space by displacing the unfolded state towards more compact structures that are closer to the transition state. Since the tunnel only forbids rarely visited, extended configurations, it has little effect on a "poorly designed" protein whose unfolded state is largely composed of low-energy, compact, misfolded configurations. The beneficial effect of the tunnel depends on its width; for example, a too-narrow tunnel enforces unfolded states with limited or no access to the transition state, while a too-wide tunnel has no effect on the unfolded state entropy. We speculate that such effects are likely to play an important role in the folding of some proteins or protein domains in the cellular environment and might dictate whether a protein folds co-translationally or post-translationally.     

植物种群自疏过程中构件生物量与密度的关系

不论是在对植物种群自疏规律还是在对能量守衡法则的研究中,个体大小(M)大多针对植物地上部分生物量,地下部分和构件生物量及其动态十分重要又多被忽视。以1年生植物荞麦为材料研究了自疏种群地下部分生物量、包括地下部分的个体总生物量以及各构件生物量与密度的关系。结果表明:平均地上生物量和个体总生物量与密度的异速关系指数(γabove-ground和γindividual)分别为-1.293和-1.253,与-4/3无显著性差异(P>0.05),为-4/3自疏法则提供了有力证据;平均根生物量-密度异速指数γroot(-1.128)与-1无显著性差异(P>0.05),与最终产量恒定法则一致;平均茎生物量-密度异速指数γstem(-1.263)接近-4/3(P>0.05),平均叶生物量-密度异速指数γleaf(-1.524)接近-3/2(P>0.05),分别符合-4/3自疏法则与-3/2自疏法则;而繁殖生物量与密度的异速关系指数γreproductive(-2.005)显著小于-3/2、-4/3或-1(P<0.001)。因此,不存在一个对植物不同构件普适的生物量-密度之间的关系。光合产物在地上和地下构件的生物量分配格局以及构件生物量与地上生物量之间特异的异速生长关系导致不同构件具有不同的自疏指数。无论对于地上生物量还是个体总生物量,荞麦种群能量均守衡,而对于地下生物量,荞麦种群能量不守衡。