A thermodynamic perspective on food webs: quantifying entropy production within detrital-based ecosystems

Because ecosystems fit so nicely the framework of a "dissipative system", a better integration of thermodynamic and ecological perspectives could benefit the quantitative analysis of ecosystems. One obstacle is that traditional food web models are solely based upon the principles of mass and energy conservation, while the theory of non-equilibrium thermodynamics principally focuses on the concept of entropy. To properly cast classical food web models within a thermodynamic framework, one requires a proper quantification of the entropy production that accompanies resource processing of the food web. Here we present such a procedure, which emphasizes a rigorous definition of thermodynamic concepts (e.g. thermodynamic gradient, disequilibrium distance, entropy production, physical environment) and their correct translation into ecological terms. Our analysis provides a generic way to assess the thermodynamic operation of a food web: all information on resource processing is condensed into a single resource processing constant. By varying this constant, one can investigate the range of possible food web behavior within a given fixed physical environment. To illustrate the concepts and methods, we apply our analysis to a very simple example ecosystem: the detrital-based food web of marine sediments. We examine whether entropy production maximization has any ecological relevance in terms of food web functioning.     

Menaquinone-7 is specific cofactor in tetraheme quinol dehydrogenase CymA

Little is known about enzymatic quinone-quinol interconversions in the lipid membrane when compared with our knowledge of substrate transformations by globular enzymes. Here, the smallest example of a quinol dehydrogenase in nature, CymA, has been studied. CymA is a monotopic membrane tetraheme c-type cytochrome belonging to the NapC/NirT family and central to anaerobic respiration in Shewanella sp. Using protein-film electrochemistry, it is shown that vesicle-bound menaquinone-7 is not only a substrate for this enzyme but is also required as a cofactor when converting other quinones. Here, we propose that the high concentration of quinones in the membrane negates the evolutionary pressure to create a high affinity active site. However, the instability and reactivity of reaction intermediate, semiquinone, might require a cofactor that functions to minimize damaging side reactions.     

Statistical entropy analysis to evaluate resource efficiency: Phosphorus use in Austria

In a resource efficient economy, entropy generation must be kept low and high-entropy wastes should be transformed into low-entropy recycled products, thus saving natural resources. Based on this idea, statistical entropy analysis (SEA) was put forward as a method to evaluate material flow systems with respect to their ability to concentrate or dilute a substance throughout its life cycle using a single metric, relative statistical entropy (RSE). Whereas its application has so far been restricted to highly aggregated material flow systems or to assessments at plant or process level, in the present study the SEA method was adapted to assess the efficiency of resource use in material flow systems which consist of numerous resource flows and include multiple recycling loops. Phosphorus (P) use in Austria served as a case study to illustrate SEA-based resource efficiency assessment for different scenarios and over time. The evaluation enabled exploiting the outcomes of existing P flow studies in a straightforward way and produced additional insights related to the characteristics of resource use within the system. Changes in P management over time had a significant effect on the resource efficiency of P use. The RSE increased by 40% due to P use in Austria in the year 2000 compared to an increase of 30% in 2010. The generally favorable trend of statistical entropy (lower dissipation) in 2010 could be attributed mainly to lower dissipative emissions, more efficient bio-industry, and increasing P removal rates in waste water treatment, which overcompensated the negative impact of the ban of recycling of meat and bone meal (in 2001) on P use efficiency. Further, the SEA-based assessment applied to a scenario of optimized P management reflected the positive effects of measures to reduce emissions, enhance recycling, and reduce consumption of P on resource efficiency (50% lower RSE increase in the target system compared to the original state). In synthesis, this study shows that the SEA method is able to integrate various dimensions of resource use into a single indicator, which can serve as a basis to assess and improve the resource efficiency of macro-scale material flow systems.     

Under what conditions signal transduction pathways are highly flexible in response to external forcing? A case study on calcium oscillations

Sensitivity and flexibility are typical properties of biological systems. These properties are here investigated in a model for simple and complex intracellular calcium oscillations. In particular, the influence of external periodic forcing is studied. The main point of the study is to compare responses of the system in a chaotic regime with those obtained in a regular periodic regime. We show that the response to external signals in terms of the range of synchronization is not significantly different in regular and chaotic Ca2+ oscillations. However, both types of oscillation are highly flexible in regimes with weak dissipation. Therefore, we conclude that dissipation of free energy is a suitable index characterizing flexibility. For biological systems this appears to be of special importance since for thermodynamic reasons, notably in view of low free energy consumption, dissipation should be minimized.     

Evaluation of HYDRUS-1D and modified PRZM-3 models for tribenuron methyl herbicide transport in soil profile under vetiver cultivation

Abstract

Tribenuron methyl (TBM) is widely used in weed control. Due to its phytotoxicity, concerns on TBM pollution to soil have been raised. In this research, TBM concentration in the soil profile and vetiver grass were measured and simulated using HYDRUS-1D and modified PRZM-3 models. The treatments were two herbicide concentrations to soil with vetiver (C₁V and C₂V) and without vetiver (C₁S and C₂S). In control treatment (C_o) no herbicide was applied to the soil. In general, according to the measured data, TBM soil residues in C₁V and C₂V treatments were 39.8% and 30.1% lower than that obtained in C₁S and C₂S treatments, respectively. The TBM was leached to 90?cm soil depth and it was limited to about 50?cm in the treatments with vetiver grass. The simulated herbicide residue in the soil profile in modified PRZM-3 model was more accurate than the HYDRUS-1D model. The dissipation processes of herbicides in soil and solving method of water movement in soil, considered in the modified PRZM-3 model, are more precise than that obtained in the HYDRUS-1D model. However, the prediction of TBM uptake by vetiver in the HYDRUS-1D model was closer to the measured values than that obtained in the modified PRZM-3 model.     

Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review

Plasma membranes are complex entities common to all living cells. The basic principle of their organization appears very simple, but they are actually of high complexity and represent very dynamic structures. The interactions between bioactive molecules and lipids are important for numerous processes, from drug bioavailability to viral fusion. The cell membrane is a carefully balanced environment and any change inflicted upon its structure by a bioactive molecule must be considered in conjunction with the overall effect that this may have on the function and integrity of the membrane. Conceptually, understanding the molecular mechanisms by which bioactive molecules interact with cell membranes is of fundamental importance.     

Cooperative binding promotes demand-driven recruitment of AnxA8 to cholesterol-containing membranes

The functionality of cellular membranes is critically determined by their lipid composition. Within the endolysosomal system, cholesterol is mainly found in more peripheral compartments. In contrast, cholesterol levels are low in late endosomes/lysosomes (LEL), and the occurrence of enlarged pools of this lipid is commonly linked to endolysosomal dysfunction. Here, we show that Annexin A8 (AnxA8), a member of the annexin family of Ca^2 +-dependent membrane-binding proteins, participates in the endosomal regulation of cholesterol homeostasis. Depletion of AnxA8 caused accumulation of cholesterol in LEL, and pharmacological inhibition of the LEL cholesterol export recruited AnxA8 to the cholesterol-laden LEL. Biophysical analysis revealed that cholesterol enhanced the Ca^2 +-dependent affinity of AnxA8 to lipid bilayers, and induced positive cooperativity of membrane binding. Our findings identify AnxA8 as a regulator of LEL cholesterol balance and point to altered membrane binding cooperativity induced by aberrant lipid composition in the target membrane as a means to control the demand-driven recruitment of this cytosolic regulatory protein.     

Dissipation and maintenance of stable states in an enzymatic system: analysis and simulation

The constraint-based analysis has emerged as a useful tool for analysis of biochemical networks. An essential assumption for constraint-based analysis is the formation of a stable steady state. This work investigates dissipation and maintenance of stable states in a simple reversible enzymatic reaction with substrate inhibition. Under mass-action kinetics, the conditions under which the reaction maintains a stable steady state are analytically derived and numerically confirmed. It is shown that, in order to maintain a steady state in the regulated reaction, maximal enzyme activity must be much higher than input rate. Moreover, it is revealed that requirements for large enzyme activity are due to substrate inhibition. It is suggested that high activities of enzymes may play a vital role in protecting a stable state from its catastrophic collapse, giving an additional explanation to an intriguing problem—why the activities of some enzymes greatly exceed the flux capacity of a pathway. In addition, dissipation of the enzymatic reaction is analysed. It is shown that the collapse of stable states is always associated with a point at which dissipation is the highest. Therefore, in order to maintain a stable state, dissipation of the reaction must be less than a critical value. Moreover, although external forcing may not change net mass flow, it may lead to collapse of stable states. Furthermore, when stable states collapse at a critical forcing amplitude and period, dissipation also reaches a highest value. It is concluded that collapse of stable steady state in the enzyme system with substrate inhibition always corresponds to critical points at which dissipation is highest, regardless if the reaction is forced or not. Therefore, for the substrate inhibited reaction, maintenance of stable states is intrinsically related to level of dissipation.     

缺磷强光下脐橙的过剩能量耗散机制

采用营养液培养的方法,对缺磷强光下脐橙的过剩能量耗散机制进行了研究.结果表明,在强光下,用缺磷营养液处理脐橙后,光合色素含量、净光合速率P_n、光呼吸速率P_r、最大荧光F_m、光化学效率F_v/F_m和电子传递速率ETR下降,初始荧光F_o和光呼吸/光合比P_r/P_n升高.叶绿素荧光的非光化学猝灭的快相qNf下降,中间相qNm和慢相qNs升高.用DTT处理后F_o升高,qNm和qNs下降,qNf无明显变化.缺磷强光胁迫加剧了脐橙光合作用的光抑制,进而启动了多种能量耗散机制.     

Dissipation of phorate in different types of soils

Summary Studies on the dissipation of phorate in different types of soils of Kerala, India, were carried out. The residues of the insecticide persisted most in the forest soil followed by alluvial, red, laterite and sandy soils in the descending order. The half-life periods of the insecticide estimated by chemical and bioassay methods approximated to one another. Correlations of the persistence of the insecticide with the properties of the soil revealed that organic matter played a dominant role in prolonging the persistence of the insecticide in the soils.Part of Ph.D. thesis of Senior author presented to Kerala Agricultural University, Vellanikkara, Trichur District, Kerala State, India.