Epigenetics: A Historical Overview

Postmigratory mouse primordial germ cells (PGCs) undergo extensive epigenetic remodeling that includes DNA methylation (DM) reprogramming of imprinted genes and, surprisingly, of transposable elements (TEs). Given the danger posed by TEs to the integrity of the germline, even a brief derepression of TEs is counterintuitive and puzzling. In the male fetal gonocytes, a sophisticated repressive mechanism that uses DM and TE-targeting piRNAs has evolved to stably silence TEs. A recent study has further increased the complexity of this problem by revealing that TE silencing is alleviated specifically at the onset of meiosis in testes lacking MAEL, a piRNA pathway protein. These observations and prior work of others are consistent with existence of an additional reprogramming event, transient relaxation of transposon silencing (TRTS), at the onset of both male and female meiosis in mice. In this Point of View we propose that TE expression is inherent to mammalian meiosis and discuss potential functional significance of this phenomenon.     

Plant Neurobiology as a Paradigm Shift Not Only in the Plant Sciences

Plants are complex living beings, extremely sensitive to environmental factors, continuously adapting to the ever changing environment. Emerging research document that plants sense, memorize, and process experiences and use this information for their adaptive behavior and evolution. As any other living and evolving systems, plants act as knowledge accumulating systems. Neuronal informational systems are behind this concept of organisms as knowledge accumulating systems because they allow the most rapid and efficient adaptive responses to changes in environment. Therefore, it should not be surprising that neuronal computation is not limited to animal brains but is used also by bacteria and plants. The journal, Plant Signaling & Behavior, was launched as a platform for exchanging information and fostering research on plant neurobiology in order to allow our understanding of plants in their whole integrated, communicative, and behavioral complexity.

I always go by official statistics because they are very carefully compounded and, even if they are false, we have no others …∼ Jaroslav Hašek, 1911

Key Words: plant neurobiology, sensory biology, behavior, biological complexity, evolution, signal integrationThis quotation of writer and mystificator Jaroslav Hašek is from his electorial speech aimed to get a seat in the Austro-Hungarian parliament for his imaginary political party ‘Moderate Progress within the Limits of the Law’ in 1911. It indicates how statistics can be misused for manipulation of public opinion, sometimes allegedly for general good. This quotation is partially relevant also for recent biology which is passing through a critical cross-road from reductionist-mechanistic concepts and methodologies towards the post-genomic, holistic, systems-based analysis of integrated and communicative hierarchic networks known as life processes.There is a message hidden in this Hašek''s aphorism. All those mathematical models, scientific theories and concepts, however appealing, harmonious and long-standing … but which do not correspond to reality …; inevitably will be ‘killed by ugly’ facts generated by scientific progress, and finally replaced by new models, theories, and concepts.¹Despite the indisputable success of the reductionistic approach in providing many discoveries regarding single cells and their components, it is increasingly clear that promises of ‘mechanistic’ genocentric biology were just chimeras and that living organisms are much more complex than the sum of their constituents. Ernst Mayr, in his final opus, almost a testament published at his age of 100, strongly opposed the belief that the reductionism at the molecular level could help to explain the complexity of life. He stressed that the concept of biological “emergence”, which deals with the occurrence of unexpected features in complex living systems, is not fully accessible using only physical and chemical approaches.²Themes of hierarchy, continuity, and order dominated biology before the turn of the century, but these have in many cases been replaced by images of the workshop. Examples include such terms as ‘machineries’, ‘mechanistic understanding’, ‘mechanistic explanation’, ‘motors’, ‘machines’, ‘clocks’ etc. This shift may well reflect the characteristic style of our age. These concepts, although useful for mining of details, do not reveal the true complexity of life and can be misleading. Even a one-celled organism is made up of ‘millions’ of subcellular parts. Concerning the great complexity of unicellular creatures Ilya Prigogine (1973) wrote: “… but let us have no illusions, our research would still leave us quite unable to grasp the extreme complexity of the simplest of organism.”³ Moreover, eukaryotic cell proved to be, in fact, ‘cells within cell’,^4–8 while there are numerous supracellular situations, the most dramatic one is represented by plants when all cells are interconnected via plasmodesmata into supracellular organism.⁶ All this collectively indicate that the currently valid ‘Cell Theory’ dogma is approaching its replacement with a new updated concept of a basic unit of eukaryotic life.^6–8All those mathematical models, scientific theories and concepts, however appealing, harmonious and long-standing … but which do not correspond to reality …; inevitably will be ‘killed by ugly’ facts generated by scientific progress, and finally replaced by new models, theories, and concepts.Furthermore, genomes are much more complex and dynamic as we ever anticipated.^9,10 They often have as much as 99% of non-coding DNA sequences,¹¹ which is not ‘junk DNA’ but rather DNA which is part of multitask networks integrating coding DNA.¹² In genomes exposed to stress (like mutations), changes are scored preferentially in non-coding sequences which regain a new balance by complex changes in genome composition and activity.^9,10,13,14 There are several definitions regarding what is gene¹¹ and molecular biologists and genetics are learning to be careful not to make strong conclusions from under-expression, knocking-out, or overexpression of any particular gene. It is increasingly clear that mutations in single genes are accompanied with altered expressions of other genes and non-coding DNA sequences too, and even subtle re-arrangements of chromatin structure and genome architecture are possible. The dynamic genome actively regains the lost balance, also via extensive re-shufflings of non-coding DNA.After complete sequencing of numerous genomes, it is clear that our understanding of what constitutes life and what distinguishes living biological systems from non-living chemical - biochemical systems is not much better than our understanding before the start of the genomics era some 60 years ago. Yet, it is also obvious that living systems, whether single cells or whole complex organisms like animals and plants, are not machines and automata which respond to external signals via a limited set of predefined responses and automatic reflexes. While humans and other animals, even insects, are already out of this ‘mechanistic’ trap^15,16 which can be traced back to Descartes,¹⁷ plants are still considered to act only in predetermined automatic fashions, as mechanical devices devoid of any possibility for choice and planning of their activities. In contrast to machines, life systems are based on wet chemistry, being systems of hierarchical and dynamic integration, communication and emergence.^1,18Recently, a critical mass of data has accumulated demanding reconsideration of this mechanistic view of plants.^19,20 Plants are complex living beings, extremely sensitive to environmental factors and continuously adapting to the ever changing environment.²¹ In addition, plants respond to environmental stimuli as integrated organisms. Often, plants make important decisions, such as onset or breakage of dormancy and onset of flowering, which implicate some central or decentralized command center. Moreover, roots and shoots act in an integrated manner allowing dynamic balance of above-ground and below-ground organs. The journal, Plant Signaling & Behavior, was launched as a platform for exchange of information about the integration of discrete processes, including subcellular signalling integrated with higher-level processes. Signal integration and communication results in adaptive behavior of whole supracellular organisms, encompassing also complex, and still elusive, plant-plant, plant-insect, and plant-animal communications. Coordinated behavior based on sensory perception is inherent for neurobiological systems.²² Therefore, plants can be considered for neuronal individuals. Moreover, plants are also able to share knowledge perceived from environment with other plants, communicating both private and public messages.^23,24 This implicates social learning and behavioral inheritance in plants too.After complete sequencing of numerous genomes, it is clear that our understanding of what constitutes life and what distinguishes living biological systems from non-living chemical - biochemical systems is not much better than our understanding before the start of genomics era some 60 years ago.

Behavior

1. An activity of a defined organism: observable activity when measurable in terms of quantitative effects of the environment whether arising from internal or external stimuli.
2. Anything that an organism does that involves action and response to stimulation.

(Webster Third New International Dictionary 1961).Neuronal informational systems allow the most rapid and efficient adaptive responses. Therefore, it should not be surprising that neuronal computation is not limited to animal brains but is used also by bacteria and plants.Some of our colleagues assert that plants do not exhibit any integrated neuronal principles.²⁵ They maintain that plants do not show complex experience- or learning-based behavior. Plants, they aver, act rather as machines manifesting predefined reflexes. Yet recent studies indicate that even prokaryotic bacteria exhibit cognitive behavior^26,27 and posses linguistic communication and rudimentary intelligence.^28–30 Therefore, it should not be too surprising that plants also show features of communication and even plant-specific cognition.^{19,20,31,32–35} As any other living systems, plants act as ‘knowledge accumulating systems’.¹ In fact, in order to adapt, all organisms continuously generate hypotheses about their environment via well formulated ‘questions’ which are solved by an increasing set of possible ‘answers’ in order to adapt.¹ Neuronal informational systems are behind this concept of organisms as ‘knowledge accumulating systems’ because they allow the most rapid and efficient adaptive responses.²² As a consequence, neuronal computation is not limited to animal brains but is used also by bacteria and plants.Reductionistic approaches will continue to “atomize” biological systems. Nevertheless, the avalanche of new data will be in need of functional integration, winning adherents to the idea that plants have integrated signaling and communicative systems that endowed them with complex and adaptive behavior. We trust that Plant Signaling & Behavior, will become an important platform for exchange of these ideas. With progress of sciences, plants show more and more similarities to animals despite obviously plant-specific evolutionary origins, cellular basis, and multicellularity. We can just mention sexuality and sex organs, embryos, stem cells, immunity, circadian rhythms, hormonal and peptide signaling, sensory perception and bioelectricity including action potentials, communication and neurobiological aspects of signal integration. The whole picture strongly suggest that convergent evolution is much more important^36,37 than currently envisioned in evolutionary theories.Reductionistic approaches will continue to “atomize” biological systems. Nevertheless, the avalanche of new data will be in need of functional integration, winning adherents to the idea that plants have integrated signaling and communicative systems that endowed them with complex and adaptive behavior.We have started with Jaroslav Hašek and we close with him as well. His quotation from 1911 is also a warning for future that we should stay open-minded. We should not slip into dogmatic ‘traps’ which have been so characteristic for the mechanistic and genocentric biology. Mathematics and computational biology are important tools, and surely will play decisive role in systems biology in the future. But they can be easily misinterpreted, and even misused. Plant systems biology, and the whole biology in general, must overcome dogmas of mechanistic genocentric biology. We hope that characterizing plants in their whole behavioral and communicative complexity will allow us to better understand what is life and how it emerged from chemical and biochemical complex systems.     

植物数量性状基因定位研究概述

植物重要的性状多为数量性状。长期以来,人类一直寻求解释植物数量性状的遗传规律以便对其进行遗传操纵。现代分子生物技术的发展为植物数量性状基因的定位、分离等研究提供了条件。本文从数量性状基因座(QTL)作图群体类型及其特点,QTL定位方法,植物QTL研究现状,以及QTL精细定位、克隆、利用等方面进行了综述,并对今后植物QTL研究进行了展望。     

Plant Photoreceptors: Phylogenetic Overview

Plants possess photoreceptors to perceive light which controls most aspects of their lives. Three photoreceptor families are well characterized: cryptochromes (crys), phototropins (phots), and phytochromes (phys). Two putative families have been identified more recently: Zeitlupes (ZTLs) and UV-B photoreceptors (ULI). Using Arabidopsis thaliana and Oryza sativa photoreceptor sequences as references, we have searched for photoreceptor encoding genes in the major phyla of plant kingdom. For each photoreceptor family, using a phylogenetic tree based on the alignment of conserved amino acid sequences, we have tried to trace back the evolution and the emergence of the diverse photoreceptor ancestral sequences. The green alga Chlamydomonas contains one cry and one phot sequence, probably close to the corresponding ancestral sequences, and no phy-related sequence. The putative UV-B photoreceptors seem to be restricted to the Brassicacae. Except for mosses and ferns, which contain divergent photoreceptor numbers, the composition of the diverse photoreceptor families is conserved between species. A high conservation of the residues within domains is observed in each photoreceptor family. The complete phylogenic analysis of the photoreceptor families in plants has confirmed the existence of crucial evolutionary nodes between the major phyla. For each photoreceptor class, a major duplication occurred before the separation between Mono- and Eudicotyledons. This allowed postulating on the putative ancestral function of the photoreceptors. [Reviewing Editor: Dr. Rudiger Cerff]     

Adhesion in Development: An Historical Overview

My purpose here is to provide brief historical overviews of three related subjects conceptually fundamental to the broader subject of “cell adhesion in development.” These subjects are (1) the evolution of our present understanding of how animal cells cohere; (2) the question of what principles underlie the ability of embryonic cell populations to organize themselves into anatomically correct structures; and (3) the ongoing effort to understand the origins of the “recognition specificity” evinced in the latter phenomenon. Because this review must be brief, it is not possible to mention all of the significant advances, many of which will be referenced in a recent more detailed review of this subject (Grunwald, 1991). For the same reason, the important work on cell adhesion in nonvertebrate systems is not included.     

Historical Overview of Taenia asiatica in Taiwan

An overview of the epidemiological, biological, and clinical studies of Taenia and taeniasis in Taiwan for the past century is presented. The phenomenal observations that led to the discovery of Taenia asiatica as a new species, which differ from Taenia solium and Taenia saginata, are described. Parasitological surveys of the aborigines in Taiwan revealed a high prevalence of taeniasis, which might be due to the culture of eating raw liver of hunted wild boars. Chemotherapeutic deworming trials involving many patients with taeniasis were discussed. Praziquantel was found to be very effective, but sometimes complete worms could not be recovered from the feces after treatment, probably due to the dissolution of the proglottids. Atabrine, despite some side effects, can still be used, in properly controlled dosages, as the drug of choice for human T. asiatica infection if we need to recover the expelled worms for morphological examinations. Research results on the infection of T. asiatica eggs from Taiwan aborigines in experimental animals were also noted. Since the pig serve as the natural intermediate host of T. asiatica and the predilection site is the liver, a differential comparison of other parasitic pathogens that might cause apparently similar lesions is also presented.     

植物分类学的历史回顾与展望

对植物分类学的研究历史进行了简要的回顾.讨论了不同历史时期植物分类学研究的特点以及该时期代表的分类学家和他们的专著,分析了植物分类学的发展趋势以及我国植物分类学工作者所面临的挑战.     

A Historical Overview of the Ozone Exposure Problem

Ozone can be found in essentially all locations in the troposphere. Too much exposure of vegetation and humans to this potent oxidizing gas can prove toxic. Reports of human toxicity to ozone first appeared in the 1800's from accidental occupational exposures when ozone was first discovered. Ozone was recognized as damaging field vegetation with a report of altered leaf morphology in grapes in the 1950s. Ozone is the major oxidant component in photochemical smog, and is produced by reactions of volatile organic compounds and oxides of nitrogen with sunlight present. Soon after the inception of the U.S. Environmental Protection Agency (US EPA), the Agency set a general “oxidants” standard (which included ozone) in 1971. A primary standard was created to protect human health and a secondary standard to protect against agricultural losses, ecological damage, and other losses. Ozone concentrations have decreased steadily over the last two decades in some areas of the U.S., but have increased in other areas. Several aspects of ozone exposure need further characterization, including better determination of rural concentrations and the relationship of outdoor to indoor concentrations. Ozone is one of the six criteria air pollutants requiring a formal reexamination of the new findings of effects on health and vegetation on a periodic basis, a process that leads to the publication of an US EPA criteria document. As a result of further study concerning ozone effects, significant changes were made to pollution standards in 1979 and 1997. This toxicant has remained a major air pollutant of concern in the U.S. despite regulation and intense study over several decades.     

Ethnographic Studies of Childhood: A Historical Overview

In this article, I briefly survey the ethnographic research literature on childhood in the 20th century, beginning with the social and intellectual contexts for discussions of childhood at the turn of the 20th century. The observations of Bronislaw Malinowski and Margaret Mead in the 1920s were followed by later ethnographers, also describing childhood, some of whom criticized developmental theories; still others were influenced initially by Freudian and other psychoanalytic theories and later by the suggestions of Edward Sapir for research on the child's acquisition of culture. The Six Cultures Study led by John Whiting at midcentury was followed by diverse trends of the period after 1960—including field studies of infancy, the social and cultural ecology of children's activities, and language socialization. Ethnographic evidence on hunting and gathering and agricultural peoples was interpreted in evolutionary as well as cultural and psychological terms. The relationship between ethnography and developmental psychology remained problematic.     

The Neurobiology of Depression: an Integrated Overview from Biological Theories to Clinical Evidence

Depressive disorders are heterogeneous diseases, and the complexity of symptoms has led to the formulation of several aethiopathological hypotheses. This heterogeneity may account for the following open issues about antidepressant therapy: (i) antidepressants show a time lag between pharmacological effects, within hours from acute drug administration, and therapeutic effects, within two-four weeks of subchronic treatment; (ii) this latency interval is critical for the patient because of the possible further mood worsening that may result in suicide attempts for the seemingly ineffective therapy and for the apparent adverse effects; (iii) and only 60–70 % of treated patients successfully respond to therapy. In this review, the complexity of the biological theories that try to explain the molecular mechanisms of these diseases is considered, encompassing (i) the classic “monoaminergic hypothesis” alongside the updated hypothesis according to which long-term therapeutical action of antidepressants is mediated by intracellular signal transduction pathways and (ii) the hypothalamic–pituitary-adrenal axis involvement. Although these models have guided research efforts in the field for decades, they have not generated a compelling and conclusive model either for depression pathophysiology or for antidepressant drugs’ action. So, other emerging theories are discussed: (iii) the alterations of neuroplasticity and neurotrophins in selective vulnerable cerebral areas; (iv) the involvement of inflammatory processes; (v) and the alterations in mitochondrial function and neuronal bioenergetics. The focus is put on the molecular and theoretical links between all these hypotheses, which are not mutually exclusive but otherwise tightly correlated, giving an integrated and comprehensive overview of the neurobiology of depressive disorders.     

影响农杆菌介导遗传转化的植物因子研究进展

农杆菌介导法是植物遗传转化中最常用的一种方法.越来越多的研究表明,植物遗传因子是决定农杆菌遗传转化效率的重要因素,它们至少影响了转化过程的如下5个方面:1)受伤植物释放的酚类物质和糖分子等介导农杆菌的趋化运动和毒性基因vir的诱导表达;2)农杆菌吸附到植物表面;3)T-DNA和毒性蛋白通过由VirB和virD4蛋白组成的Ⅳ型分泌系统从细菌转移到植物细胞质;4)T-复合体利用细胞质ACTIN骨架和输入蛋白进行核定位和核输入;5)T-DNA利用植物的修复装置整合进宿主基因组.就以上5个方面涉及的植物因子研究进展予以综述.     

Long-range Perspectives on Neurobiology and Behavior

This essay is part of the seventh presentation of a yearly educationalproject of the American Society of Zoologists. The purpose isto provide background materials for those who teach the first-yearbiology courses in colleges and universities. The Science asa Way of Knowing project emphasizes the conceptual frameworkof the biological sciences, shows how scientific informationis obtained and validated, and relates science to human concerns.The topic for consideration this year is Neurobiology and Behavior.The introductory essay is concerned mainly with the conceptualframework of neurobiology, as developed over the ages, and afew examples of behavioral studies which can be related to neurobiologyor which are of special interest through links to human considerationsand problems.     

Neurobiology of depression

Current treatments for depression are inadequate for many individuals, and progress in understanding the neurobiology of depression is slow. Several promising hypotheses of depression and antidepressant action have been formulated recently. These hypotheses are based largely on dysregulation of the hypothalamic-pituitary-adrenal axis and hippocampus and implicate corticotropin-releasing factor, glucocorticoids, brain-derived neurotrophic factor, and CREB. Recent work has looked beyond hippocampus to other brain areas that are also likely involved. For example, nucleus accumbens, amygdala, and certain hypothalamic nuclei are critical in regulating motivation, eating, sleeping, energy level, circadian rhythm, and responses to rewarding and aversive stimuli, which are all abnormal in depressed patients. A neurobiologic understanding of depression also requires identification of the genes that make individuals vulnerable or resistant to the syndrome. These advances will fundamentally improve the treatment and prevention of depression.