Two modes of host–enemy coevolution

The process of coevolution between host and enemy has traditionally been viewed as an evolutionary arms race between resistance and counterresistance. The arms-race metaphor of coevolution is widely accepted because it explains the evolution of many characters in species involved in host–enemy interactions. However, molecular work in plant–pathogen systems suggests a coevolutionary interplay between plant recognition of an attacking pathogen and pathogen evasion from recognition. We refer to this process as information coevolution, and contrast this with arms race coevolution to show that these two processes result in very different patterns of host resistance and enemy virulence at the population level. First, information coevolution results in a lower proportion of hosts that are susceptible to enemy attack within a population. Second, information coevolution produces a pattern of local maladaptation of enemy on host, a naturally occurring phenomenon that is difficult to explain under arms race coevolution. We then conduct a literature review to survey the empirical support for either mode of coevolution using the predicted patterns of host resistance and enemy virulence. Evidence supports both modes of coevolution in plant–enemy interactions, whereas no support is found for information coevolution in vertebrate–parasite and invertebrate–parasite systems.     

Just the right size: cell counting in Dictyostelium

The regulation of tissue and organism size plays an essential, but poorly understood, role in multicellular development. Genes have been identified that affect body and organ size in a number of animals. Two recently identified genes, smlA and countin, are required for the proper function of a cell-counting mechanism that regulates organism size in the eukaryotic microorganism Dictyostelium discoideum. The discovery of this process now allows the study of size regulation in a simple multicellular system.     

Chromatin as an expansive canvas for chemical biology

Chromatin is extensively chemically modified and thereby acts as a dynamic signaling platform controlling gene function. Chromatin regulation is integral to cell differentiation, lineage commitment and organism development, whereas chromatin dysregulation can lead to age-related and neurodegenerative disorders as well as cancer. Investigating chromatin biology presents a unique challenge, as the issue spans many disciplines, including cell and systems biology, biochemistry and molecular biophysics. In recent years, the application of chemical biology methods for investigating chromatin processes has gained considerable traction. Indeed, chemical biologists now have at their disposal powerful chemical tools that allow chromatin biology to be scrutinized at the level of the cell all the way down to the single chromatin fiber. Here we present recent examples of how this rapidly expanding palette of chemical tools is being used to paint a detailed picture of chromatin function in organism development and disease.     

SmpB蛋白结构与功能研究进展

SmpB是一类普遍存在于细菌中的小RNA结合蛋白。研究表明SmpB除了在反式翻译中起着辅助tmRNA分子拯救滞留核糖体的作用,其也可以作为RNA分子伴侣调节体内RpoS的表达,以及具有直接调控RNase R及双组份系统的功能。SmpB参与的调控作用对于细菌蛋白质合成质量控制、致病菌中毒力系统调控、维持机体正常生长及发育等过程具有关键作用。本综述主要从SmpB蛋白结构及其对RNA、蛋白质调控功能等方面进行论述,以期对发掘细菌性疾病治疗靶点,研发新型抗生素,提供新的方向和思路。     

Environs: The Superniches of Ecosystems

Evolution proceeds by natural selection of heritable variationsof individual organisms based on direct influences of environment.However, indirect effects probably vastly outweigh direct onesin ecosystems. Therefore, why is evolution based on direct effectsonly? The ecological niche represents the point of direct contactbetween organisms and their environments. To encompass indirectinfluences, niches are extended to new structures, environs,which are units of organism-environment coevolution. The motiveforce for coevolution is closure of outputs back upon inputsof the organism members of ecosystems. Closure is achieved bybiogeochemical cycling and feedback interactions, direct andindirect, between organisms. To the extent that closure doesnot occur, there is no imperative for organism-environment coevolution.Coevolution at the system level based on indirect effects iscompatible with normal evolution at the individual organismlevel based on direct effects. The organism is the unit of thelatter, but environs are the unit of coevolution.     

Increased synaptic microtubules and altered synapse development inDrosophila sec8 mutants

Background  

Sec8 is highly expressed in mammalian nervous systems and has been proposed to play a role in several aspects of neural development and function, including neurite outgrowth, calcium-dependent neurotransmitter secretion, trafficking of ionotropic glutamate receptors and regulation of neuronal microtubule assembly. However, these models have never been testedin vivo. Nervous system development and function have not been described after mutation ofsec8 in any organism.     

Genetic-evolutionary basis of symbiosis doctrine

The author presents the current notion of symbiosis as one of the main adaptation of an organism to changeable environment. Symbiosis is considered as a super organism genetic system within which there are different interactions (including mutualism and antagonism). Genetic integration of symbiotic partners can be realized as cross regulation of their genes, exchange of gene products (proteins, RNA), gene amplification and sometimes gene transfer between organisms. On the phenotypic level these processes result in signal interactions, integration of partner metabolic systems and development of symbiotic organs. Co-evolution is considered as an assemblage of micro- and macroevolution processes basing on pre-adaptations and proceeding under influence of different forms of natural selection (individual, frequency-depended and kin selection). Symbiosis can be compared with sexual process since both are the forms of organism integration characterized by different genetic mechanisms and evolutionary consequences. The genome evolution in symbiotic microorganisms can proceed by: 1) simplification of genome in obligate symbiosis (loss of genes that are necessary for independent existence, transfer of some genes to the host organism); 2) complication of genome in facultative symbiosis (increase in genome plasticity, structural and functional differentiation of genome into systems controlling free-living and symbiotic parts of life cycle). Most of symbiotic interactions are correlated to an increase in genetic plasticity of an organism that can lead to evolutionary saltations and origin of new forms of life.     

Legionella metaeffector exploits host proteasome to temporally regulate cognate effector

Pathogen-associated secretion systems translocate numerous effector proteins into eukaryotic host cells to coordinate cellular processes important for infection. Spatiotemporal regulation is therefore important for modulating distinct activities of effectors at different stages of infection. Here we provide the first evidence of "metaeffector," a designation for an effector protein that regulates the function of another effector within the host cell. Legionella LubX protein functions as an E3 ubiquitin ligase that hijacks the host proteasome to specifically target the bacterial effector protein SidH for degradation. Delayed delivery of LubX to the host cytoplasm leads to the shutdown of SidH within the host cells at later stages of infection. This demonstrates a sophisticated level of coevolution between eukaryotic cells and L. pneumophila involving an effector that functions as a key regulator to temporally coordinate the function of a cognate effector protein.     

Detecting sexually antagonistic coevolution with population crosses

The result of population crosses on traits such as mating rate, oviposition rate and survivorship are increasingly used to distinguish between modes of coevolution between the sexes. Two key hypotheses, erected from a verbal theory of sexually antagonistic coevolution, have been the subject of several recent tests. First, statistical interactions arising in population crosses are suggested to be indicative of a complex signal/receiver system. In the case of oviposition rates, an interaction between populations (x, y and z) would be indicated by the rank order of female oviposition rates achieved by x, y and z males changing depending upon the female (x, y or z) with which they mated. Second, under sexually antagonistic coevolution females will do 'best' when mated with their own males, where best is defined by the weakest response to the signal and the highest fitness. We test these hypotheses by crossing strains generated from a formal model of sexually antagonistic coevolution. Strains differ in the strength of natural selection acting on male and female traits. In our model, we assume sexually antagonistic coevolution of a single male signal and female receptor. The female receptor is treated as a preference function where both the slope and intercept of the function can evolve. Our results suggest that neither prediction is consistently supported. Interactions are not diagnostic of complex signal-receiver systems, and even under sexually antagonistic coevolution, females may do better mating with males of strains other than their own. These results suggest a reinterpretation of several recent experiments and have important implications for developing theories of speciation when sexually antagonistic coevolution is involved.     

HD-Zip III转录因子家族与植物细胞分化

细胞分化是生物生长发育的重要过程, 受到一系列信号的精确调控。植物特有的转录因子HD-Zip III在细胞分化中发挥了重要作用。该文对HD-Zip III基因类型和结构特点进行了简要介绍, 重点论述了HD-Zip III在胚胎形态发生、顶端分生组织形成、叶极性建立和维管组织分化等发育过程中的作用, 系统总结了HD-Zip III基因在不同层次受到的调控, 探讨了该家族基因与陆生维管植物进化的关系。     

Reorganization of Functional Systems in Ontogeny

This paper presents data that many mechanisms functioning at a certain stage of development are eliminated from the systemic organization at the subsequent stage of ontogeny. A new point of view on the principles of function formation in ontogeny is proposed. It is based on the fact that in the process of development (embryonic period, early postnatal period, transition to an independent existence, etc.) the subjective structure of the external world changes, therefore adaptation at a certain stage of ontogeny implies creation of another system of function regulation, which provides survival of the organism under new conditions. This becomes possible owing to a reorganization of the functional systems of the organism, including formation of new mechanisms and elimination of everything from the behavioral repertoire, which had lost its adaptive importance at the given stage of ontogeny. Such reorganization is comparable with formation of a new species in the process of evolution (a transition to another ecological niche). To characterize principles of the transition from one stage of ontogeny to another and to emphasize certain common features of the evolutionary and ontogenetic processes, it is suggested to use the term ontogenetic niche.     

昆虫共生细菌研究进展

昆虫体内定殖着大量微生物,经过漫长协同进化,昆虫与这些微生物构建了共生体系,这些昆虫共生微生物参与整个生态过程,对于生态系统中物质转化与交换、能量流动与利用、信息传递与调控等均发挥着重要作用。昆虫共生细菌具有丰富的物种多样性;昆虫与其共生细菌之间通过化学机制、生理机制、生态学机制和遗传学机制构建复杂的共生体系;昆虫为细菌提供稳定的生境并共享特定的代谢途径,共生细菌则协助宿主营养代谢,提供食物中缺乏的养分,促进昆虫生长和繁殖;通过分泌抗菌肽、毒素等,细菌能增强昆虫对寄生物的防御能力和抗病性,并通过调节昆虫对非生物因子的抗逆性和耐药性,扩大昆虫的生态位。昆虫共生细菌在农林牧渔业可持续安全生产与医药研发等领域具有应用潜力和广阔的发展前景。     

Compensatory reactions of the oxygen-transport systems of the body with hemic hypoxia (studies on a mathematical model]

The mathematical model suggested by the authors and results of experiments have been used to study the significance of basic oxygen-transport systems in regulation of oxygen conditions of the organism with acute and chronic hemic hypoxia of different seriousness, to determine a relative contribution of each of them to compensation of this hypoxic state, to estimate specific weight of proper "hypoxic" (induced by the effect on oxygen-transport blood function) and "toxic" (caused by the total toxic effect) action of sodium nitrite in the development of hemic hypoxia.     

Persistence of selfish genetic elements: population structure and conflict

Selfish genetic elements are vertically transmitted factors that spread by obtaining a transmission advantage relative to the rest of the genome of their host organism, often with a cost to overall host fitness. In many cases, conventional population genetics theory predicts them spreading through populations, reaching fixation and becoming undetectable or sometimes driving the population extinct. However, in several well studied systems, these genetic elements are known to persist at relatively low, stable frequencies. Recent research suggests that several processes might explain these observations, including population structure, intragenomic conflict and coevolution.     

Complexity and Transition Management

This article presents a framework, transition management, for managing complex societal systems. The principal contribution of this article is to articulate the relationship between transition management and complex systems theory. A better understanding of the dynamics of complex, adaptive systems provides insight into the opportunities, limitations, and conditions under which it is possible to influence such systems. Transition management is based on key notions of complex systems theory, such as variation and selection, emergence, coevolution, and self-organization. It involves a cyclical process of phases at various scale levels: stimulating niche development at the micro level, finding new attractors at the macro level by developing a sustainability vision, creating diversity by setting out experiments, and selecting successful experiments that can be scaled up.     

MicroRNAs-29a/b/c regulate early growth response 2 (Egr2) by mPer1

The circadian rhythm is one of the basic systems in an organism. It helps the organism maintain harmony with the daily changes of the external environment to ensure proper physiological activities. Previous studies from our laboratory have indicated that the miR-29a/b/c can bind to the circadian clock gene hPer1 at the 3 ′UTR region and regulate its mRNA and protein expression, affecting various organismal physiological processes. Meanwhile, it has been reported that the circadian gene Per plays a role in the regulation of the early growth response gene Egr2, which plays an important role during midbrain development. Here, we confirmed that miR-29a/b/c regulates Egr2 function through mPer1 binding, which elucidates a novel connection between mPer1 and Egr2.     

Predicting protein domain interactions from coevolution of conserved regions

The knowledge of protein and domain interactions provide crucial insights into their function within a cell. Several computational methods have been proposed to detect interactions between proteins and their constitutive domains. In this work, we focus on approaches based on correlated evolution (coevolution) of sequences of interacting proteins. In this type of approach, often referred to as the mirrortree method, a high correlation of evolutionary histories of two proteins is used as an indicator to predict protein interactions. Recently, it has been observed that subtracting the underlying speciation process by separating coevolution due to common speciation divergence from that due to common function of interacting pairs greatly improves the predictive power of the mirrortree approach. In this article, we investigate possible improvements and limitations of this method. In particular, we demonstrate that the performance of the mirrortree method that can be further improved by restricting the coevolution analysis to the relatively conserved regions in the protein domain sequences (disregarding highly divergent regions). We provide a theoretical validation of our results leading to new insights into the interplay between coevolution and speciation of interacting proteins.     

蜜蜂肠道菌群结构功能研究进展

在长期的共同进化中,肠道菌群与其宿主形成了紧密的联系,为宿主提供了许多有益的作用。作为一种社会性昆虫,蜜蜂的生活习性为其肠道菌群提供了良好而稳定的传播途径,因此,蜜蜂与其肠道菌群形成了一种紧密的互惠互利共生关系。近年来,随着对蜜蜂肠道菌群了解的不断加深,对蜜蜂肠道菌群功能的研究也不断深入,大量研究表明蜜蜂的肠道菌群在宿主食物的消化代谢、宿主免疫的激活和抵抗致病菌、调节宿主生理等方面都有着重要的作用,同时破坏肠道菌群的稳定对蜜蜂的健康有着明显的负面影响。本文对近年来西方蜜蜂肠道菌群功能研究进行了总结,旨在为进一步深入探索蜜蜂肠道菌群与其宿主的相互作用及在养蜂生产上应用肠道菌群防控疾病提供参考。