Free energy of biological systems

The generalization of the Gibbs potential to open spatially inhomogeneous systems is given. This generalization is based on the abandonment of the local equilibrium hypothesis and the introduction of the specific parameters of spatial inhomogeneity: thermodynamical forces and the coordinates of useful works. The existence of the potential state function whose decrease determines the algebraic sum of useful (external) and dissipative (internal) works executed by the system was justified. This function presents the difference between the internal energy of the spatial inhomogeneous system and its homogeneous parts and was named (owing to its independence from the pathways of processes in the space of thermostatic variables) the general thermodynamic potential. It was demonstrated that the application of this potential to biological systems permits one to trace their development for each of their intrinsic degrees of freedom, to combine the thermodynamic and kinetic approaches to the problems of their evolution, to find a criterion of maturity of a biological organism and a general measure of the orderliness of the biosystem, to find the driving forces of biological processes, and confirm the possibility of development of biosystems without the equilibrium state.     

Rapid divergence and convergence of life‐history in experimentally evolved Drosophila melanogaster

Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life‐history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought.     

比较图元向量和点的聚类系数对差异网络的研究

差异分析对于揭示生命体的生长、发育和衰老过程及疾病发生具有重大的意义,基于网络的差异分析方法已经成为系统生物学的一个研究热点。网络节点往往通过与局部结构作用实现某种功能,其与局部结构的关系变化,很可能影响其功能。本文利用仿真实验的方法比较了图元向量和点的聚类系数两种局部结构测度的性能,并且利用他们分别设计算法挖掘差异网络中模块化变化的基因簇。应用AGEMAP数据库中小鼠12个组织基因表达数据进行实验,大部分聚类簇都高度显著富集与衰老相关的GO项。     

镜像神经元研究概况述评

镜像神经元是近来国外认知神经科学研究的热点,通过一系列最新的技术,人们确立了人体内存在镜像神经系统的观点。镜像神经系统在语言进化、动作识别与理解、行为模仿等方面都起着重要的作用。本文就镜像神经系统的研究做一概述。     

Study of the genetic code adaptability by means of a genetic algorithm

We used simulated evolution to study the adaptability level of the canonical genetic code. An adapted genetic algorithm (GA) searches for optimal hypothetical codes. Adaptability is measured as the average variation of the hydrophobicity that the encoded amino acids undergo when errors or mutations are present in the codons of the hypothetical codes. Different types of mutations and point mutation rates that depend on codon base number are considered in this study. Previous works have used statistical approaches based on randomly generated alternative codes or have used local search techniques to determine an optimum value. In this work, we emphasize what can be concluded from the use of simulated evolution considering the results of previous works. The GA provides more information about the difficulty of the evolution of codes, without contradicting previous studies using statistical or engineering approaches. The GA also shows that, within the coevolution theory, the third base clearly improves the adaptability of the current genetic code.     

Design of a Calorimeter for the Continuous Study of Heat Production during Anaerobic Microbial Growth

A conduction type calorimeter has been designed to chase microbial growth in batch system. The calorimeter is of a twin structure having thermopile plates as a temperature sensor, The heat evolution during the microbial growth at a required temperature can be observed as an output-voltage generated at thermopile terminals with a sensitivity of 58.5 mV K^?1

A stainless steel cell with a volume of 300 cm³ serves as a culture cell which is capable of being autoclaved prior to the initiation of calorimetric run, taking out from the calorimeter body.

Because of the twin structure, the apparatus works with sufficient stability in detecting small heat evolution for long duration. Its operation has been demonstrated with the growth of Sacch. cerevisiae grown on liquid synthetic medium under anaerobic condition.     

Directed molecular evolution of antibodies

Antibodies play a key role in the immune system, are characterized by a homogeneous overall structure and by their ability to interact with an almost unlimited number of compounds. Encoded by a fixed number of genes, they acquire their specificity and affinity of recognition after a succession of genetic recombination and molecular mutation processes. Since the pioneer works of Kohler and Milstein in 1975 describing the possibility of producing monoclonal antibodies with pre-determined specificity, the use of antibodies in the fields of research, diagnosis and therapy has never stopped increasing. Thus, about twenty monoclonal antibodies have yet been authorized to be used in human immunotherapy. However, a majority of these molecules have been engineered to bring them into line with their clinical use: chimerization, humanization, recombinant expression of single or fused fragments. Furthermore, the recent development of in vitro molecular evolution approaches now make it possible to engineer the affinity, the specificity as well as the stability of monoclonal antibodies. The potential of in vitro molecular evolution of antibodies will be illustrated through the example of the specificity improvement of an anti-progesterone antibody.     

Systems biology: a switch for sex

The yeast pheromone response pathway works in a graded fashion, such that more pheromone leads to more response, but a recent study has shown that small modifications convert it into a bistable switch, with implications for the evolution and engineering of reaction networks.     

Comparative modeling and protein-like features of hydrophobic-polar models on a two-dimensional lattice

Lattice models of proteins have been extensively used to study protein thermodynamics, folding dynamics, and evolution. Our study considers two different hydrophobic-polar (HP) models on the 2D square lattice: the purely HP model and a model where a compactness-favoring term is added. We exhaustively enumerate all the possible structures in our models and perform the study of their corresponding folds, HP arrangements in space and shapes. The two models considered differ greatly in their numbers of structures, folds, arrangements, and shapes. Despite their differences, both lattice models have distinctive protein-like features: (1) Shapes are compact in both models, especially when a compactness-favoring energy term is added. (2) The residue composition is independent of the chain length and is very close to 50% hydrophobic in both models, as we observe in real proteins. (3) Comparative modeling works well in both models, particularly in the more compact one. The fact that our models show protein-like features suggests that lattice models incorporate the fundamental physical principles of proteins. Our study supports the use of lattice models to study questions about proteins that require exactness and extensive calculations, such as protein design and evolution, which are often too complex and computationally demanding to be addressed with more detailed models.     

The evolution of phenotypic integration: How directional selection reshapes covariation in mice

Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection.     

Evolutionary physiology by data of publications for 1965–2005

Evolutionary physiology as independent direction of physiology was formed in the XX century and was rapidly developing in its second half. To evaluate some tendencies of this process, we analyzed publications in Journal of Evolutionary Biochemistry and Physiology, one of the leading specialized periodicals on this problem. Analysis of works published for 4 decades has shown that the majority of papers deals with study of evolution of function of the nervous system (40–60 papers per year), less papers concern study of functions of sensory and visceral systems (20–30 per year). Among the used method, the most widely spread is the comparative-physiological method. By the end of the 1990s the number of works with use of methods of embryophysiology decreased. In the performed studies, predominant are physiological methods. Use of biochemical methods decreased, while of methods of molecular biology increased. The most often used objects of studies were mammals. By the end of the XX—beginning of the XXI century, in the greater number of papers the object of study has become human, while the number of publications in which experiments were performed on amphibians, reptiles, and birds decreased. More than a half of all works were carried out in St. Petersburg (Leningrad); the number of papers submitted from Moscow institutions gradually decreased, but the number of works from regions of Russia rose. Most studies were performed at institutes of the Russian Academy of Sciences and universities, while the number of papers from institutes of the Russian Academy of Medical Sciences decreased. For the last few years, several generalizations on evolution of functions and functional evolution have been formulated; handbooks and monographs on problems of evolutional physiology have been published.     

Fifty years after Enlow and Brown's Comparative histological study of fossil and recent bone tissues (1956–1958): A review of Professor Donald H. Enlow's contribution to palaeohistology and comparative histology of bone

Fifty years after the publication of Enlow and Brown's seminal paper (1956–1958), this historical analysis of Professor Donald H. Enlow's works emphasizes their influence on the evolution of palaeohistology, comparative bone histology, and bone biology in general. Comparative analysis of recent and fossil bone tissues has shown the great variability of bone at the tissue level (histodiversity). Historically, Enlow's works have greatly influenced a shift in the reinterpretation of the causes of bone histodiversity, from phylogenetic to more functional (ontogenetic) explanations. This allows us to consider the issue of complex causalities in evolutionary biology.     

On the Stock Estimation for a Harvested Fish Population

We consider a stage-structured model of a harvested fish population and we are interested in the problem of estimating the unknown stock state for each class. The model used in this work to describe the dynamical evolution of the population is a discrete time system including a nonlinear recruitment relationship. To estimate the stock state, we build an observer for the considered fish model. This observer is an auxiliary dynamical system that uses the catch data over each time interval and gives a dynamical estimate of the stock state for each stage class. The observer works well even if the recruitment function in the considered model is not well known. The same problem for an age-structured model has been addressed in a previous work (Ngom et al., Math. Biosci. Eng. 5(2):337–354, 2008).     

A field guide for teaching evolution in the social sciences

The theory of evolution by natural selection has begun to revolutionize our understanding of perception, cognition, language, social behavior, and cultural practices. Despite the centrality of evolutionary theory to the social sciences, many students, teachers, and even scientists struggle to understand how natural selection works. Our goal is to provide a field guide for social scientists on teaching evolution, based on research in cognitive psychology, developmental psychology, and education. We synthesize what is known about the psychological obstacles to understanding evolution, methods for assessing evolution understanding, and pedagogical strategies for improving evolution understanding. We review what is known about teaching evolution about nonhuman species and then explore implications of these findings for the teaching of evolution about humans. By leveraging our knowledge of how to teach evolution in general, we hope to motivate and equip social scientists to begin teaching evolution in the context of their own field.     

Convergence and coevolution in a mutualism: evidence from a molecular phylogeny of Ficus

Abstract.— The interaction between Ficus (Moraceae) and their pollinating wasps (Chalcidoidea: Agaonidae; more than 700 species-specific couples) is one of the most specialized mutualisms found in nature. Both partners of this interaction show extensive variation in their respective biology. Here we investigate Ficus life-history trait evolution and fig/fig wasp coadaptation in the context of a well-resolved molecular phylogeny. Mapping out variations in Ficus life-history traits on an independently derived phylogeny constructed from ribosomal DNA sequences (external and internal transcribed spacer) reveals several parallel transitions in Ficus growth habit and breeding system. Convergent trait evolution might explain the discrepancies between morphological analyses and our molecular reconstruction of the genus. Morphological characters probably correlate with growth habit and breeding system and could therefore be subject to convergent evolution. Furthermore, we reconstruct the evolution of Ficus inflorescence characters that are considered adaptations to the pollinators. Our phylogeny reveals convergences in ostiole shape, stigma morphology, and stamen:ovule ratio. Statistical tests taking into account the phylogenetic relationship of the species show that transitions in ostiole shape are correlated with variation in wasp pollinator head shape, and evolutionary changes in stigma morphology and stamen:ovule ratio correlate with changes in the pollination behavior of the associated wasp. These correlations provide evidence for reciprocal adaptations of morphological characters between these mutualistic partners that have interacted over a long evolutionary time. In light of previous ecological studies on mutualism, we discuss the adaptive significance of these correlations and what they can tell us about the coevolutionary process occurring between figs and their pollinators.     

草莓DNA分子标记及其应用

综述了限制性长度多态性(RFLP)、随机扩增多态性DNA(RAPD)、扩增片段长度多态性(AFLP)、简单重复序列(SSR)等不同类型分子标记在草莓指纹图谱构建、品种鉴别、遗传多样性、进化、遗传作图以及相关性状的标记等方面的应用,分析了草莓分子标记研究中的关键问题,提出了今后研究方向。     

Theory of V.A. Dogiel on polymerization and oligomerization as a general integration concept

The theory of V.A. Dogiel on the significance of polymerization and oligomerization processes in the evolution of Protozoa and Metazoa is compared with the paper of I.I. Schmalhausen (1972) on factors and steps of aromorph evolution. Dogiel’s theory is considered as a general integration conception. Four steps are distinguished in the evolution of biological systems: (1) formation of morphofunctional system by units of the lower structural level, (2) polymerization of morphofunctional units of a system, (3) oligomerization of morphofunctional units of system by means of their reduction, uniting, or differentiation, (4) integration and stabilization of a system owing to development of morphofunctional connections between its parts.     

The evolution of retrotransposon regulatory regions and its consequences on the Drosophila melanogaster and Homo sapiens host genomes

It has now been established that transposable elements (TEs) make up a variable, but significant proportion of the genomes of all organisms, from Bacteria to Vertebrates. However, in addition to their quantitative importance, there is increasing evidence that TEs also play a functional role within the genome. In particular, TE regulatory regions can be viewed as a large pool of potential promoter sequences for host genes. Studying the evolution of regulatory region of TEs in different genomic contexts is therefore a fundamental aspect of understanding how a genome works. In this paper, we first briefly describe what is currently known about the regulation of TE copy number and activity in genomes, and then focus on TE regulatory regions and their evolution. We restrict ourselves to retrotransposons, which are the most abundant class of eukaryotic TEs, and analyze their evolution and the subsequent consequences for host genomes. Particular attention is paid to much-studied representatives of the Vertebrates and Invertebrates, Homo sapiens and Drosophila melanogaster, respectively, for which high quality sequenced genomes are available.     

Simulation as experiment: a philosophical reassessment for biological modeling

Some scientific modelers suggest that complex simulation models that mimic biological processes should have a limited place in ecological and evolutionary studies. However, complex simulation models can have a role that is different from that of simpler models that are designed to be fit to data. Simulation can be viewed as another kind of experimental system and should be analyzed as such. Here, I argue that current discussions in the philosophy of science and in the physical sciences fields about the use of simulation as an experimental system have important implications for biology, especially complex sciences such as evolution and ecology. Simulation models can be used to mimic complex systems, but unlike nature, can be manipulated in ways that would be impossible, too costly or unethical to do in natural systems. Simulation can add to theory development and testing, can offer hypotheses about the way the world works and can give guidance as to which data are most important to gather experimentally.