The function of the counting of time as the basis for the individual adaptive activity of the nervous system

An important role of time factor in adaptive process of organisms is shown on the basis of great literary material. The time perception is a result of the interrelationship of the so-called "biological clock" and learning during the whole ontogenesis. The hypothetical mechanisms of time perception are discussed. In own experiments the authors revealed more distinct expressiveness of high-frequency components in electroencephalogram spectrum and less expressiveness of low-frequency components in subjects underestimating time intervals compared with subjects overestimating them. A conception on the role of individual characteristics of nervous system in time perception is developed.     

系统发育研究中“长枝吸引”现象概述

系统发育研究(phylogeny)不仅有助于重建地球所有生物体的进化历史, 而且还可以揭示进化生物学领域中的一些基本问题。清晰了解各生物物种进化历程及不同物种之间的进化关系, 是进一步研究和探索生物学其他学科的基础。但是现今广泛应用的所有系统发育分析方法都存在一定的局限性, 在一定程度上不能有效消除各种误差, 从而不能客观地处理和分析数据, 也就不能成功重建生物进化历程, 真实反映物种进化关系。系统发育研究中, “长枝吸引” (Long-branch Attraction, LBA)假象是最为困扰研究者的问题。文章从“长枝吸引”问题的产生原由、检测方法以及消除策略等多个方面进行详尽概述, 并通过列举典型实例, 阐述了解决“长枝吸引”问题的途径。     

The multifunctionality of regulatory peptides and the rule of "what--where--when" as a principle of their ordered action]

Consistent study of stages and history of discovery of regulatory peptides (RP) as a new class of multifunctional endogenic regulators puts forward some actual problems. A question what new notions on the manner of control of physiological functions have been introduced by RP investigation is considered. Two historical tendencies in the RP studies are estimated. A conception on peptides as multifunctional and colocated factors of neurohumoral regulation of organism was opposed to the idea of "single" substance--a regulator of "unique" function. In this connection a conception of peptide-regulatory continuum is considered and the author postulated the principle "what--where--when" as the main rule of RP well-regulated action. The statement on tissue (regional) specificity of the biogenesis processes of different RP as molecular basis of their regulatory function is grounded.     

The cell theory--history, present state and prospects (on the 150th anniversary of the development of the cell theory)

The main stages of history of this most important biological conception are presented and the state of the modern cell theory and its future prospects are considered. Since 1839, when T. Schwann expounded his conception of the cell, a long pathway in cognition of the cell function and organization has been covered. From the original picture of the complex organism as a "cellular state", made up of relatively independent "elementary organisms", i.e. cells the modern biology has come to the idea of the cell as an integral system either being a part of a complex organism, or living free in the nature (protists). The cell represents certain qualitatively peculiar level in a complex evolutionary established hierarchy of biological systems. Some particular tight relations, existing between cytology, as a fundamental biological science and molecular biology, genetics, ecology and other biological disciplines are considered. The importance of the cell conception is ascertained for practical aims, especially in medicine.     

Life forms of organisms as patterns of organization and spatial ecological factors

Tectological and archaetectonical approaches which are conventionally used in morphology are discussed. The similarity of these approaches to some views on the structure and organization of nature systems was shown. These wiews were originated within the framework of the modern system-cybernetic conception. The morphology particularities of natural object of any rank (from organism to biosphere) allow determination of environment influence character. In some cases intensity of the influence can be determined. This, morphological-geometrical approach of nature investigation acquires high prognostic value. The aspects of "pattern organization" concept and its perspectives are discussed. The patterns of organization of organisms could be characterized only in the context of their interactions with environment. Therefore it is necessary to distinguish new group of ecological factors: spatial or chorological one. It was suggested that spatial ecological factors is predominant if all other physical factors have no extreme values.     

Biostructural theory of the living systems

Eugen Macovschi is among the few scientists who tried, and partly succeeded, to explain the differences between "dead" and "living" in biological sciences. He discovered and characterized the so-called biostructure of the living bodies and worked out a biostructural theory, which is the first supramolecular conception in biology. Nevertheless, complex biological systems are currently considered only from the molecular point of view, although they may be regarded as specific phenomena on highly structured bodies within the four-dimensional Universe. According to Macovschi, the biostructure provides organisms with life properties and controls their life processes and chemical changes. Nevertheless, plant cells or bacterial ones differ much from the animal or human cells. In fact, there are various biostructures which are related with cell properties. Hence, this theory creates confusions and cannot be easily used to explain all the properties of the biosystems. Consequently, it is our goal to highlight the principles, advantages, limitations, and applications of the biostructural theory, which might support new ideas and theories in modern life sciences.     

A novel acyl-CoA beta-transaminase characterized from a metagenome

Background

Bacteria are key components in all ecosystems. However, our knowledge of bacterial metabolism is based solely on the study of cultivated organisms which represent just a tiny fraction of microbial diversity. To access new enzymatic reactions and new or alternative pathways, we investigated bacterial metabolism through analyses of uncultivated bacterial consortia.

Methodology/Principal Findings

We applied the gene context approach to assembled sequences of the metagenome of the anaerobic digester of a municipal wastewater treatment plant, and identified a new gene which may participate in an alternative pathway of lysine fermentation.

Conclusions

We characterized a novel, unique aminotransferase that acts exclusively on Coenzyme A (CoA) esters, and proposed a variant route for lysine fermentation. Results suggest that most of the lysine fermenting organisms use this new pathway in the digester. Its presence in organisms representative of two distinct bacterial divisions indicate that it may also be present in other organisms.     

系统发育基因组学——重建生命之树的一条迷人途径

生物基因组计划的相继启动对系统发育学研究的发展产生了深远影响。将基因组学和系统发育学结合起来的“系统发育基因组学”在这一背景下应运而生, 这门崭新交叉学科的出现成为重建“生命之树”的一条迷人途径。文章重点围绕系统发育基因组学的概念以及分析方法进行扼要介绍, 并探讨了它目前潜在的问题以及将来有待发展和完善的地方。     

Origin of bilateral-symmetrical animals (Bilateria)

The paper is an attempt to attack the old problem of the origin of Bilateria by the methods of evolutionary tetrad (i.e. combination of comparative anatomy, comparative embryology, paleontology, and molecular biology). Three groups of theories of classical comparative anatomy (planulod-turbellarian, archicoelomate, and metameric) are discussed. Comparative embryology brings out clearly that the ventral side of embryo comes from the blastoporal region in all groups of Bilateria (except Chordata, where the blastoporal region corresponds to the dorsal side that is come out of the upside-down morphology of chordates) and mouth and anus comes from the anterior and posterior ends of elongated blastopore. From the point of view of paleontology, some of vendian metazoans demonstrate transitional conditions between the Radiata and Bilateria. Vendian bilaterians are metameric organisms with normal or asymmetric position of segments and could be pictured as "bilateral coelenterates" creeping on the oral surface. In Cnidaria, the expression of homologues of "Brachyury", "goosecoid", and "fork head" genes are revealed in the circular region around the mouth. In Bilateria, these genes are expressed along the elongated blastopore and around the mouth and anus. These results support the old conception on the amphistomic origin of mouth and anus as well as the homology between the oral disc of cnidarians and ventral side of Bilateria. The combination of four mentioned approaches enables us to propose the conception of the origin of Bilateria from vendian bilateral coelenterates with numerous metameric pouches of gastral cavity. Bilaterian ancestors crawled on the oral disc (= ventral side). These ancestors gave rise to both phanerosoic cnidarians and triploblastic bilaterians. Cnidarian ancestors attached to bottom by the aboral pole with the resulting degradation of aboral nerve ganglion. Bilateral symmetry of anthozoans is considered to be primitive feature for cnidarians. In case of triploblastic Bilateria, the elongated blastopore closed in the middle and subdivided into mouth and anus (amphistomy) and gastral pouches separated from the central part of gastral cavity and transformed to metameric coelomic chambers. The primary bilaterians are supposed to be complicated organisms having coelom and segmentation. The complexity of primary Bilateria provides an explanation for the abundance of highly organized organisms (arthropods, mollusks etc.) in Cambrian time. It is postulated that Ctenophora is the only group recent eumetazoans with primary axial symmetry.     

免疫能力与动物种群调节和生活史权衡的关系

在生物医学和动物科学领域,免疫能力是指有机体对疾病的抵抗能力.近年来,对野生动物免疫能力的研究是一个新兴的热点领域,它与生态学结合,产生了生态免疫学.本文从生态学的角度,介绍了免疫能力的概念、影响因素及其与动物种群调节机理的关系,概述了与小型哺乳动物种群密度波动有关的免疫衰退假说、免疫能力选择假说和冬季免疫增强假说,总结了免疫能力与能量代谢和内分泌特征之间的关系,并对免疫能力在生活史权衡研究中的最新进展,即有机体生长与免疫、繁殖与免疫之间的权衡关系等进行了阐述,最后结合国际上本学科研究的发展动态,提出了一些未来的研究方向.     

"Phylogenetic presumptions"--can jurisprudence terms promote comparative biology?

The paper presents the results of a critical analysis of the "phylogenetic presumptions" conception by means of its comparison with the hypothetic-deductive method of the phylogeny reconstruction within the framework of the evolutionary systematics. Rasnitsyn (1988, 2002) suggested this conception by analogy with the presumption of innocence in jurisprudence, where it has only moral grounds. Premises of all twelve the "phylogenetic presumptions" are known for a long time as the criteria of character homology and polarity or as the criteria of relationship between organisms. Many of them are inductive generalizations based on a large body of data and therefore are currently accepted by most of taxonomists as criteria or corresponding rules, but not as presumptions with the imperative "it is true until the contrary is proved". The application of the juristic term "presumption" in phylogenetics introduces neither methodical profits, nor anything to gain a better insight of problems of the phylogenetic reconstruction. Moreover, it gives ill effects as, by analogy with a judicially charged person and his legal defense, it allows a researcher not to prove or substantiate his statements on characters and relationships. Some of Rasnitsyn's presumptions correspond to criteria, which have been recognized as invalid ones on the reason of their non-operationality (presumption "apomorphic state corresponds more effective adaptation") or insufficient ontological grounds (presumptions "are more complex structure is apomorphic", "the most parsimonious cladogram is preferable", and "one should considered every to be inherited").     

Evolution as resistance to entropy. I. Mechanisms of species homeostasis

The idea is discussed that the common output of any evolution is creation of the entities that are increasingly resistant to further evolution. The moving force of evolution is entropy, the tendency to disorder. This general aspiration for chaos is a cause of the mortality of organisms and species, however, being prerequisite for any movement, it creates (by chance) novelties, which may occur (by chance) more resistant to further decay and thus survive. The surviving of those who survive is the most general principle of evolution discovered by Darwin for particular case of biological evolution. The second law of thermodynamics states that our Universe is perishing but its ontology is such that it creates resistance to destruction. The evolution is a history of this resistance. Not only those who die do not survive but also those who evolve. The entities that change (evolve) rapidly disappear rapidly and by this reason they are not observed among both the fossils and now-living organisms. We know only about long-living species. All the existing organisms are endowed with an ability to resist other changing. The following main achievements of the species homeostasis are discussed: high fidelity of DNA replication and effective mechanisms of DNA repair; diploidy; normalizing selection; truncated selection; heterozygote superiority; ability to change phenotype adaptively without changing genotype; parental care and the K-strategy of reproduction; behavior that provides independence of the environment. The global resistance of the living systems to entropy is provided the state that all the essential in biology is determined not by physical-chemical interactions but could semantic rules. A conception of "potential zygotic information" that determines the rules of ontogenesis is proposed. A zygote does not contain this information in explicit form. It is created de novo step by step during ontogenesis and it could not be decoded beforehand. The experimental data on the adaptive mutagenesis and the relevant hypothesis are discussed. It is concluded that the special mechanisms for speeding-up of evolution as created by evolution are impossible conceptually.     

Construction of the bacterial genome--the next goal of genetic engineering

The article deals primarily with literature data on the organization and evolution of bacterial genome. An account of the conception of "current" bacterial evolution consisting of periodical inclusions into a bacterial genome of genes having exogenous origin is given. A hypothesis is proposed that rare inversions going through the oriC or terC chromosomal regions could serve as reparative rearrangements providing balanced distribution of the DNA segments of different origin within the circular genome. It is asserted that the progress in the study of the model microorganism Escherichia coli K-12 as well as in genetical methods give rise to a new experimental challenge--the creation of a "rational" bacterial genome on the basis of E. coli cell. It is proposed that a "rational" bacterial genome could be devoid of many genes which provide the evolutionary formed ecological potential of the species and its capacity for rapid adaptation to new environment.     

The origin of the eukaryotic cell. I. Historical sources and current state of the concept of symbiotic and autogenic origins of the cell

The exogenous (symbiotic) conception of the eukaryotic origin is now widely spread. It is based on the recognition of the principle of combination (addition or enclosing) of diverse prokaryotic organisms; so the complicated unicellular eukaryotic organism (eukaryotic cell) was resulted. the principle of combination takes its historical scientific sources from the ideas of Buffon. With reference to the cell this principle was claimed for the first time. In our time the exogenous conception is characterized as a "symbiotic boom", because it is widely used in attempts to explain the origin of all the main organelles of the cell (right up to the micro-bodies). The autogenetic (endogenous) conception is based on the principle of straight phyliation, on the recognition of a successive evolutionary transformation of prokaryotic forms into eukaryotic ones. In this way all the cell organelles may have an endogenous origin. This principle springing from Lamarck has got a contemporary meaning in the doctrine of Darwin. In the next papers the author will present his own analysis and generation of the present day relevant facts to find out which of these two conceptions based on quite different scientific methodological principles may be correct.     

Darwinian selection leads to Gaia

The Gaia hypothesis, in its strongest form, states that the Earth's atmosphere, oceans, and biota form a tightly coupled system that maintains environmental conditions close to optimal for life. According to Gaia theory, optimal conditions are intrinsic, immutable properties of living organisms. It is assumed that the role of Darwinian selection is to favor organisms that act to stabilize environmental conditions at these optimal levels. In this paper, an alternative form of Gaia theory based on more traditional Darwinian principles is proposed. In the new approach, environmental regulation is a consequence of population dynamics, not Darwinian selection. The role of selection is to favor organisms that are best adapted to prevailing environmental conditions. However, the environment is not a static backdrop for evolution, but is heavily influenced by the presence of living organisms. The resulting co-evolving dynamical process eventually leads to the convergence of equilibrium and optimal conditions. A simple Daisyworld model is used to illustrate this convergence phenomenon. Sensitivity analysis of the Daisyworld model suggests that in stable ecosystems, the convergence of equilibrium and optimal conditions is inevitable, provided there are no externally driven shocks to the system. The end result may appear to be the product of a cooperative venture, but is in fact the outcome of Darwinian selection acting upon "selfish" organisms.     

水生态保护目标制定的理论与应用

我国目前处于生态环境管理的转型期,尚未形成统领水生生物、生物栖息地、水质与水量等要素的水生态保护体系。在总结相关水生态研究成果的基础上,梳理形成了基于水生态系统时空尺度和状态梯度效应理论的水生态保护目标制定构想与方法,分析了淡水生物完整性对自然地理要素、水环境压力、栖息地质量的响应机制,提出以水生态“功能分区-状态评价-问题诊断-目标预设-可达性评估-目标确定”为主线的水生态保护目标制定技术体系,研发了生物完整性评价、水生态保护目标预设和可达性分析等技术方法。以江苏省常州市为典型水生态功能区应用案例,验证了技术体系的适用性与可行性,取得良好的应用效果。水生态保护目标制定理论和方法方面的研究探索可为全国相关工作提供参考依据。     

DNA and the theory of stabilizing selection

A comparison of structural-functional features of genomic DNAs allowed to estimate the role of internal and external factors in evolution of different groups of organisms. The basic difference between higher and lower organisms has been demonstrated. It is reflected in the difference of their reaction on to external factors in accordance with two adaptation types, the openness and autonomization. There is a correlation between structural-functional organization of genomic DNAs of higher and lower organisms and the above mentioned types of adaptation. DNA of lower organisms has been proposed to be characterized as "labile", and that of higher organisms, as "stable". The "DNA lability" means high mutation ability, which characterizes the existence of and evolution of lower organisms (genetic inconstancy of the lower organisms). On the contrary, "DNA stability" means the creation of stable genetic apparatus, reduction of variability in higher organisms (genetic constancy of higher organisms). This suggests the existence of the two principal ways of evolution.     

Ureaplasmas and mycoplasmas in chimpanzees of various breeding capacities

Adult chimpanzees (24 male, 76 female) with low and high rates of conception were examined for ureaplasmas, arginine-metabolizing mycoplasmas and chlamydiae. Ureaplasmas were isolated from the throat of only 1 male and 1 female animal, but from the urethra of 29% of the males and from the vagina of 95% of the females. Mycoplasmas were isolated from the throat more often than were ureaplasmas, but from the genital tract with about the same frequency as ureaplasmas. The numbers of organisms, of either type, isolated from the vagina were larger than the numbers isolated from the male urethra. Chlamydiae were not isolated from any animal. The occurrence of ureaplasmas and mycoplasmas and the numbers of these organisms isolated were similar in animals with low or high rates of conception. Furthermore, no association was noted between the organisms in the lower genital tract and the occurrence of abortion and/or stillbirth.     

Individual and population sex allocation patterns

A variety of sex allocation models is considered in which the reproductive returns on investment in males differ from the returns on investment in females, the amounts of resources available for reproduction vary in the population, the costs of making male and female reproductive structures differ, and the conception sex ratio may be fixed and there may be an initial minimum investment per offspring. Results of these models include quantitative predictions for both individual- and population-level sex allocation, an opportunity to study the magnitude of changes in predicted patterns as key variables change, and therefore an analysis of the robustness of Fisher's equal investment theory. One example is that Fisher's argument is extremely robust for high fecundity organisms, but, in low fecundity organisms, is sensitive to differences between the sexes in reproductive returns on investment per offspring, a situation that occurs in many vertebrates to which Fisher's theory is often applied. A second example is that individual- and population-level patterns often depend strongly on the distribution of resources available for reproduction among individuals in the population.