Thermoluminescence: theory

Thermoluminescence (TL) probes the emission of luminescence associated with the de-trapping of a radical pair as the temperature is increased. This technique has proved useful for characterizing the energetic arrangement of cofactors in photosynthetic reaction centers. In the original TL theory, stemming from solid-state physics, the radical pair recombination was considered to coincide with the light-emitting process. In photosynthetic systems, however, recombination takes place through various routes among which the radiative pathway generally represents a relatively minor leak, and the theoretical framework must be modified accordingly. The radiative route is the one with the largest activation energy and is thus (still) more disfavored at low temperature, so that during the heating process, the TL peak tends to lag behind the decay of the radical pair. A consequence is that the integrated luminescence emission increases with the heating rate. In this article, we examine how the characteristics of the TL emission depend on the redox potentials of the cofactors, showing good agreement between theory and experimental studies on Photosystem (PS) II mutants. We also analyze the effect on (thermo-) luminescence of the connectivity of the light-harvesting pigment antenna, and show that while this should affect significantly luminescence kinetics at room temperature, the effect on TL is expected to be small.     

群落构建的中性理论和生态位理论

物种共存和生物多样性维持一直是生态学研究的中心论题。基于物种生态位分化的群落构建理论已经发展了近一个世纪, 但我们对群落构建和生物多样性维持的机理仍然不清楚。近年来, 群落中性理论以其简约性和预测能力成为群落生态学研究的焦点, 但由于其“物种在生态功能上等价”的假设与大量研究结果相悖, 同时对自然群落结构的准确预测也只限于少数的生态系统, 因而饱受质疑。如今, 越来越多的生态学家认为群落构建的生态位理论与中性理论之争的最终归宿应该是二者的整合。 在本文中, 我们在简要回顾生态位理论和群落中性理论发展的基础上, 分析二者之间的主要分歧和互补性, 试图梳理二者整合的途径。我们认为, 尽管中性理论的发展极大地丰富了群落构建理论, 但二者的整合尚处于初级阶段; 群落构建零模型假说、中性—生态位连续体假说、随机生态位假说等都不失为有价值的尝试, 今后需要在其他类型的生态系统中进行实验验证, 以更好地理解确定性过程和随机过程在决定群落构建和生物多样性维持中的作用。     

Neutral theory: a historical perspective

To resolve a panselectionist paradox, the population geneticist Kimura invented a neutral theory, where each gene is equally likely to enter the next generation whatever its allelic type. To learn what could be explained without invoking Darwinian adaptive divergence, Hubbell devised a similar neutral theory for forest ecology, assuming each tree is equally likely to reproduce whatever its species. In both theories, some predictions worked; neither theory proved universally true. Simple assumptions allow neutral theorists to treat many subjects still immune to more realistic theory. Ecologists exploit far fewer of these possibilities than population geneticists, focussing instead on species abundance distributions, where their predictions work best, but most closely match non-neutral predictions. Neutral theory cannot explain adaptive divergence or ecosystem function, which ecologists must understand. By addressing new topics and predicting changes in time, however, ecological neutral theory can provide probing null hypotheses and stimulate more realistic theory.     

Acetylcholinesterase: theory of noncompetitive inhibition

The theory of noncompetitive inhibition of acetylcholinesterase based on the binding of inhibitor to the acetylenzyme and the free enzyme was proven correct by demonstrating that tripropylammonium ion increases the steady-state concentration of acetylenzyme, as predicted by the theory. By contrast, the traditional theory that the inhibitor binds to the enzyme-substrate complex and the free enzyme predicts that the amount of acetylenzyme will be drastically reduced when the inhibition is high. A third theory involving all three types of binding remains possible.     

Lednev's model: theory and experiment

The results of theoretical and experimental investigations of V.V. Lednev on interactions of weak and extremely weak magnetic fields with biosystems have been reviewed. The period since 1989, when the first version of the interference model has been suggested, until now has been considered. Some mathematical expressions, are presented, which have been published earlier in the papers that are now bibliographic rarity. The results of experimental investigations are also summarized that have been performed in this period under the supervision of V.V. Lednev in the laboratory of biophysics of intracellular regulation in the Institute of Theoretical and Experimental Biophysics of the Russian Academy of Sciences.     

Biological staining: mechanisms and theory

New staining techniques continue to be introduced, and older ones continue to be used and improved. Several factors control specificity, selectivity and visibility of the end product in any procedure using dyes, fluorochromes, inorganic reagents or histochemical reactions applied to sections or similar preparations. Local concentration of the tissue target often determines the intensity of the observed color, as does the fine structure within the object being stained, which may facilitate or impede diffusion of dyes and other reagents. Several contributions to affinity control the specificity of staining. These include electrical forces, which result in accumulation of dye ions in regions of oppositely charged tissue polyions. Weaker short-range attractions (hydrogen bonding, van der Waals forces or hydrophobic bonding, depending on the solvent) hold dyes ions and histochemical end products in contact with their macromolecular substrates. Nonionic forces can also increase visibility of stained sites by causing aggregation of dye molecules. Covalent bonds between dye and tissue result in the strongest binding, such as in methods using Schiff's reagent and possibly also some mordant dyes. The rate at which a reagent gains access to or is removed from targets in a section or other specimen affect what is stained, especially when more then one dye is used, together or sequentially. Rate-controlled staining is greatly influenced by the presence and type of embedding medium, such as a resin, that infiltrates the tissue. The rates of chemical reactions are major determinants of outcome in many histochemical techniques. Selective staining of different organelles within living cells is accomplished mainly with fluorochromes and is controlled by mechanisms different from those that apply to fixed tissues. Quantitative structure-activity relations (QSAR) of such reagents can be derived from such molecular properties as hydrophilic-hydrophobic balance, extent of conjugated bond systems, acid-base properties and ionic charge. The QSAR correlates with staining of endoplasmic reticulum, lysosomes, mitochondria, DNA, or the plasma membranes of living cells.     

Transient state isoelectric focusing: theory

Mathematical theory is developed to describe the transient state of isoelectric focusing (pH-gradient electrophoresis) in a linear pH gradient under highly idealized conditions. This theory makes it possible to predict the concentration profile (distribution) for the protein or other amphoteric species of interest as a function of time, when the sample is applied in a zone of infinitesimal thickness at one end of the column, or in a uniform distribution throughout the column. Further, the position of the centroid, and the second moment around the mean, σ², (square of the standard deviation of peak width) are described as a function of time, irrespective of the initial distribution of the protein in the column. Three arbitrary stages of the “focusing” experiment are considered: (1) Focusing, wherein the sample is applied to a preformed pH gradient; (2) Defocusing, which occurs when the electrical field is abolished after an arbitrary time (usually after the concentration profile has begun to approach its steady state) and diffusion is allowed to occur. (3) Refocusing, which occurs after the electrical field is reapplied. Although stages 1 and 3 are conceptually identical aside from the difference in initial conditions, they may differ in several important respects in practice, both with regard to technical problems of measurement, and with regard to the closeness of conditions to the stated assumptions.This theory should make it possible to predict the time necessary to achieve any desired degree of focusing, i.e., approach to the steady-state distribution. Further, this theory and the techniques of analytical scanning isoelectric focusing provide the basis for measurement of the apparent diffusion coefficient (D), the derivative of velocity with respect to position, and if the field strength is known, the slope of the mobility-pH curve at the isoelectric point, {$\text{dM}\text{d(}\text{pH}\text{)}$}.     

Evolutionary theory: The current state

Modern problems for the theory of evolution in Russia are only partly related to domestic realities (a legacy of the 1990s, changing priorities of education, and the clericalization of the society). The main drawback comes from the acceptance of a physicalist paradigm, in which testing evolutionary hypotheses is reduced to testing predictions derived from processes working at lower levels. Hypotheses are no longer tested by direct observation of the real world, which has somehow ceased to be regarded as a source of proof. Instead, hypotheses are thought to be correct if they are supported by more readily understood patterns at lower (molecular or genetic) levels. This substitution may explain the poor support for the epigenetic theory of evolution, although it agrees with observations much better than the currently dominant theoretical concepts.     

生态系统工程师：理论与应用

生物通过非同化--异化过程影响环境的事实普遍存在,生态学家对此也开展了大量的研究,但缺乏相应理论框架的指导,使得这些工作的潜在价值未能得到充分的体现.学者Clive G.Jones等提出的"生态系统工程师"概念,概括了此类生态学现象的一般特征,为认识生物对环境的影响提供了一种新的理论框架.介绍了生态系统工程师概念及相关的理论体系,包括3个术语、2类生态系统工程师、5种生态系统工程概念模型以及工程效应的测定方法.同时,论述了该概念在入侵生态学、保护生物学、恢复生态学等领域的应用前景.最后,讨论了未来的研究方向.可以预料,生态系统工程师概念及相关理论的不断发展将有助于对生态学本质的认识,并为生态系统管理提供新的思路.     

集合种群动态:理论与应用

集合种群是指一相对独立地理区域内各个局域种群的集合,这些局域种群通过一定程度的个体迁移而连结在一起。集合种群理论是生态学最新分支领域——空间生态学的主要研究途径之一;它关注的是局域种群之间个体迁移的动力学后果,以及具有不稳定局域种群物种的区域续存的条件。本文较为全面地介绍了集合种群理论的基本内容,并展望其应用前景。     

Visual perception: A dynamic theory

Perception is generally thought to occur centrally in the nervous system as a result of information which flows unidirectionally through a hierarchy of sensory processors. Such a view is in conflict with recent experimental evidence for a centrifugal control capable of enhancing particular features of the sensory input. Certain phenomena in human perception, resembling order-disorder transitions in physics, also suggest the existence of a positive feedback mechanism in the sensory pathway. A mechanism of perception is proposed in which unstructured feedback can accomplish the desired feature-specific enhancement of the input. The principle used here — the Alopex principle — is one that was devised in this laboratory for the experimental determination of visual receptive fields. The biological requirements for the operation of the principle are discussed, and a possible site in the thalamic relay nuclei is suggested.