生命信息安全控制原理的再探讨

建立生命信息安全控制原理的理论性平台,由该平台的视野分析免疫学所涉及的诸多理论问题,譬如免疫记忆、免疫功能等方面,并针对性进行归纳以及绘制出相关图形,试图将免疫学理论中所呈现的纷繁复杂性的方面以及过于分散的条块更加条理化、清晰化及整体化。由逻辑学的层面讨论免疫学学名的形成,分析结果:免疫学学名应归结为主观是非逻辑意识产物,并主张认识论应回归自然生成逻辑的观点。免疫记忆在本质上是对遗传信息的记忆,离开了遗传信息的识别与分析就不存在免疫记忆。众多学者的系列研究资料表明,CD4+T细胞在CD8+T细胞反应的起始就辅助其发挥作用,并维持其记忆细胞功能,而CD4+T细胞的记忆是由TCR-MHCⅡ信号所决定。X线晶体衍射及三维结构图所显示MHCII类肽结合凹槽内的多肽更能显示出呈递多肽遗传信息的功能,而MHCI类分子肽结合凹槽内的多肽难以与呈递多肽遗传信息的功能联系起来。只有辅助性T细胞是决定与辅助记忆的细胞,其不仅决定B细胞胸腺依赖性抗原的记忆,而且决定CD8+T细胞的记忆性。对生命信息识别从记忆属性层面进行分类,即分为遗传信息密码识别(记忆属性)和非遗传信息密码识别(非记忆属性)2大类。通过危险因素、生命信息感应器、信息识别及应答调控这样4个相连贯环节的分析,绘制出生命信息安全控制原理图。从功能效应层面进行讨论,将生命信息安全控制的功效分类为正面功能效应和负面功能效应2大类,其中将组织修复归结为正面功能效应,创伤引起的无菌性炎症归结为负面功能效应。绘制出生命信息安全控制功效图,并讨论了生命信息安全控制功效图的建立在理论方面的重要意义。     

生命信息安全控制太极经纬图解构

基于前期危险因子与生命机体机制信息相关互动图,探索危险因子与生命机体机制信息间所属功能位置关系和内在联系,将该互动图从二维形式提升到三维形式,构建出生命信息安全控制太极经纬图。该图由5个太极纬平面和1个垂直贯穿太极纬平面的生命信息安全控制轴组成,控制轴与太极纬平面间构成虚与实、经与纬关系,形成“致虚极,守静笃”的动态平衡局面。5个太极纬平面分别代表模式识别受体识别病原体相关分子模式和损伤相关分子模式、NK细胞活化受体识别机制、特异性识别系统机制、正负反馈性调控机制以及黏膜、皮肤与共生微生物相互联系机制。由太极纬平面间内在功能联系分析:第1、2太极纬平面机制处在整个系统最前沿位置,应对危险原发生第一响应,把危险原信息传递给第3太极纬平面;第3太极纬平面接受危险原信息,发生第二响应,处在“后援位置”;第4太极纬平面针对信息应答过度或不足作适时调整,作正、负反馈性功效,在整体系统中处于极其重要效应作用地位;第5太极纬平面机制是整个系统的基盘,特别是黏膜系统,该安全控制系统重点布局集中在此,体现在功能力量对比中巨量共生微生物客观存在决定其重要作用地位。由太极经纬图显示,NK细胞活化受体-配体关系中的配体归入该系统范畴中。首次提出“危险原”概念,涵盖抗原、病原体相关分子模式、损伤相关分子模式和NK细胞活化受体-配体(变应信息)的配体。还推出NK细胞功能效应机制原理假说:以物种整体遗传信息为背景,构筑决定攻击与否防控性配套受体-配体关系,推测细胞基因组中存在表达代表自身身份信息配体的基因家族和表达报告变应信息配体的基因家族。上述构建的太极经纬图显示出生命信息安全控制机制的整体构象。     

真核生物转录因子对DNA序列的识别

真核生物转录因子对ＤＮＡ序列的识别杨岐生（浙江大学生物科学与技术系,杭州３１００２７）关键词真核生物转录因子,蛋白质－ＤＮＡ识别研究蛋白质和ＤＮＡ两类生物大分子的相互作用,以阐明基因表达、调控及信息传递的分子机制,是认识生命活动本质的核心问题。本文介...     

水稻挥发性信息化合物对昆虫的作用

植物挥发性化合物是联系植物、害虫和天敌间3层营养关系的关键信息因子。是害虫防治理论与实践的基础．首先,介绍了水稻挥发性信息化合物的基本化学特征及其在植食性昆虫和天敌昆虫寄主选择中的作用;其次,分析了水稻挥发性信息化合物的产生与作用机制及其生态学功能和水稻挥发性信息化合物研究中存在的问题;最后,展望了水稻挥发性信息化合物的研究前景．对水稻挥发性化合物的更进一步研究有两个方向,一是对存在于水稻体内,启动相关代谢途径的小分子信号物质的生理生化和分子生物学特性进行研究;二是研究捕食性节肢动物对信息化合物的接收、识别和学习等行为及与这些行为相关的生理生化和分子基础．     

糖组学:全面了解生命基础的重要一环

<正>糖类物质是组成生物体的基本物质之一,在各种生命活动中发挥着重要作用.目前还没有一种生命体能离开糖类物质而存在,糖类不仅是细胞能量的主要来源,而且在细胞的构建、细胞的生物合成和细胞生命活动的调控中,均扮演着重要的角色.糖组学是从分析和破解一个生物或一个细胞特定阶段全部糖类物质所含信息的角度入手,研究糖类物质的分子结构、微观不均一性、表达调控、与识别分子的相互作用和功能多样性以及其与疾病之间关     

昆虫对植物次生性物质的适应策略

植物次生性物质是植食性昆虫在取食过程中遇到的主要障碍之一,也是天敌昆虫寻找寄主或猎物的主要信息来源。当今,昆虫学中的一些重要理论问题,如寄主植物的识别,食性的形成,植物求救信号的释放,天敌对寄主或猎物的识别和寻找机制等等,均与植物次生性物质有关。在长期的演化过程中,昆虫适应了植物次生性物质的种种不利作用,改变了这类物质对植物本身的防御作用,使其能充分地利用各分类阶元的植物次生性物质作为寻找寄主植物、昆虫寄主或猎物以及取食的信号。昆虫与植物次生性物质的这种关系是当今协同演化理论得以产生的主要依据之一。关于昆…     

论生物体的信息代谢

生物体的信息代谢是指依托生物体物质和能量代谢、建立在生物体各组织结构层次上的由单源信息的出现到互信息的构建到组合信息的形成到信息网络的整合以及由信息网络到组合信息到互信息到单源信息的逐渐崩解的同期性动态链接过程。信息代谢是生命信息进化的高级表现,也是生命的本质;它蕴育着各种生命活动。     

棉铃虫性信息物质研究进展

半个多世纪以来,众多学者对昆虫性信息物质进行了广泛而深入的研究,自蚕蛾醇的结构被鉴定开始,鳞翅目昆虫的性信息物质一直是研究的热点。棉铃虫Helicoverpa armigera(Hübner)由于危害严重倍受关注。本文综述了棉铃虫性信息物质的提取、鉴定、产生和识别机制,及各组分功能作用等研究现状,为进一步深入研究提供了思路。     

Progress in research on the sex pheromones of Helicoverpa armigera (Hiibner)

半个多世纪以来,众多学者对昆虫性信息物质进行了广泛而深入的研究,自蚕蛾醇的结构被鉴定开始,鳞翅目昆虫的性信息物质一直是研究的热点.棉铃虫Helicoverpa armigera (Hübner)由于危害严重倍受关注.本文综述了棉铃虫性信息物质的提取、鉴定、产生和识别机制,及各组分功能作用等研究现状,为进一步深入研究提供了思路.     

白蚁采食行为中的信息交流

白蚁作为社会性昆虫, 其采食个体间依赖各种信息交流机制进行联系与协作, 其中包括踪迹、 警戒、 食物信息、 同伴识别和助食等。通常的联系信号为挥发性或半挥发性化学物质或者一定频谱和功率的机械振动波。其中踪迹信息素、 蚁源烃类、 警戒信息素、 助食素和机械振动信号等都在白蚁采食过程中起着重要作用。白蚁采食过程中食物定向和食物品质信息的传达主要依靠腹板腺分泌的踪迹信息素, 已发现有十二碳烯醇类、 降碳倍半萜类和大环二萜类。蚁源的机械振动也在食物品质表达方面起到一定作用, 但食物品质的表达机制还不明确。白蚁采食协作的基础是同伴识别, 蚁源烃类（C21~C35）是同伴识别的主要信息物质, 采食个体分泌的助食素则可促成共同取食。警戒信息素传递白蚁采食的安全信息, 通常为一些兵蚁源的萜类物质, 但得到功能鉴定的结构还不多。近来研究还发现特殊的蚁源机械振动也可起到示警作用。已初步证实各种信息交流机制间存在交互作用, 但交互作用的机理有待进一步解析。生物物理因素在白蚁采食行为中的作用值得更多重视。本文以白蚁的采食行为为线索, 评述白蚁采食个体间信息交流机制的研究进展及利用问题, 并对今后的研究提出展望。     

Finding simplicity in complexity: general principles of biological and nonbiological organization

What differentiates the living from the nonliving? What is life? These are perennial questions that have occupied minds since the beginning of cultures. The search for a clear demarcation between animate and inanimate is a reflection of the human tendency to create borders, not only physical but also conceptual. It is obvious that what we call a living creature, either bacteria or organism, has distinct properties from those of the normally called nonliving. However, searching beyond dichotomies and from a global, more abstract, perspective on natural laws, a clear partition of matter into animate and inanimate becomes fuzzy. Based on concepts from a variety of fields of research, the emerging notion is that common principles of biological and nonbiological organization indicate that natural phenomena arise and evolve from a central theme captured by the process of information exchange. Thus, a relatively simple universal logic that rules the evolution of natural phenomena can be unveiled from the apparent complexity of the natural world.     

Life,information theory,and topology

The information content of an organism determines to a large extent its ability to perform the basic vital functions: selection of food, breaking up of the food molecules into appropriate parts, selection of those parts, and their assimilation. The information content needed is very large and requires a sufficiently large complexity of the organism. The information content of an organism is largely determined by the information content of the constituent organic molecules. The information content of the latter is in its turn determined by the number of physically distinguishable atoms or radicals of which the molecule is composed. The different arrangements of atoms in a molecule are represented by the structural formula, which is basically a graph. It is shown that the topology of this graph also determines to a large extent the information content. Different points of a graph may be physically indistinguishable; in general, however, they are different in regard to their topological properties. A study of the relations between the topological properties of graphs and their information content is suggested, and several theorems are demonstrated. A relation between topology and living processes is thus found also on the molecular level.     

生命信息安全控制体系整体结构性构建与分析

在前期生命信息安全控制原理探讨的基础上,基于整体论的思考,旨在构思能表述生命信息安全控制体系实质内涵的几何图形。所作图呈圆台形,自上而下依次为2大部分(内在部分和外延部分),5个层次(特异性识别系统、泛特异性识别系统、皮肤黏膜、共生微生物及外环境开放接触面)。在圆台形生命信息安全控制体系中,圆台形的中心轴为生命信息安全控制轴;特异性识别系统、泛特异性识别系统、皮肤、黏膜和共生微生物组成内在部分;外延部分即外环境开放接触面;内在部分各部间以及与外延部分之间存在物质、能量、信息交流沟通传递的空间界面。特异性识别系统建立在泛特异性识别系统基础上,置于最顶端,寓意着生物进化高级发展的一种客观结局,泛特异性识别系统与特异性识别系统作为一个整体和共生微生物层次联系,其中安插皮肤、黏膜组织层次,符合宏生物与微生物之间存在的完全不可分割的相关关系客观事实。共生微生物层次举足轻重,所占份额最大,主导整个体系的稳定性,成为整个体系的基座。就上述5个层次及其相互关系的解析归纳,证明构建的圆台形几何图能真实客观反映出生命信息安全控制体系各层次之间完全不可分割、相互依存影响的关系。     

我国转基因技术风险交流分析

随着生物技术的迅猛发展,发展转基因产业的战略选择与公众对转基因安全疑虑的矛盾十分突出。通过转基因舆情分析,指出我国转基因风险交流存在的不足主要为风险交流工作缺乏顶层设计,信息公开程度较低,风险交流方式和内容单调,公益机构未能发挥应有作用。在此基础上,提出了加强转基因风险交流的政策建议:(1)明确转基因风险交流的目标;(2)建立转基因风险交流协调框架;(3)建立转基因信息公开平台和信息监测平台;(4)完善管理部门和公益机构的风险交流职能;(5)改革科技项目政策。     

Organisms as Functional Machines: A Connectivity Explanation

Living organisms exist as a complex set of levels of organizationarranged in a pattern of strong ordering with none of theselevels being more important than others for a full understandingof life. Central to biological strong ordering is the organismallevel. Individual organisms are of special interest to biologistsbecause they are relevant to all biological processes regardlessof the operational level of the process. This is especiallytrue for investigations of the morphological-physiological propertiesof organisms. For such studies, living organisms must be consideredas complex machines with all of the sophisticated integrationand multifarious interactions of component parts typical ofcomplex systems. Understanding of the properties of any individualfeature in an organism depends as much, or possibly even more,on an appreciation of its connections and interactions withother features of that organism than on an understanding ofits intrinsic attributes. Learning the connectivity skills,including the modes of thinking, needed to comprehend the integrationof diverse components of any complex system requires a differenttraining than that needed to determine the detailed attributesof individual parts; both are necessary, however, to achieveproper advances in biological knowledge. Case studies of severalvertebrate features will be used to illustrate types of interactionswhich exist between structural/functional attributes, and howtheir recognition can lead to new and interesting questions.This "feeling for the organism" may be the major factor separatingthose biologists who are able to make important discoveriesfrom those who will only provide the subsequent, less excitingdetails of normal science.     

The mathematical logic of life

Protein synthesis can be likened to a particular coded information storage, transmission and execution system. Noise, error or mutations are the essential phenomena to which a living organism is subjected. Genetic coding aims at preserving the integrity of a structure under aggression from the surroundings. It can be shown that the different amino acids translated in the proteins, except the particular case of SER, obey a logical code for optimization of resistance to mutation effects. The study of the structure of this code allows a better comprehension of the logic of life.     

What makes a gene name? Named entity recognition in the biomedical literature

The recognition of biomedical concepts in natural text (named entity recognition, NER) is a key technology for automatic or semi-automatic analysis of textual resources. Precise NER tools are a prerequisite for many applications working on text, such as information retrieval, information extraction or document classification. Over the past years, the problem has achieved considerable attention in the bioinformatics community and experience has shown that NER in the life sciences is a rather difficult problem. Several systems and algorithms have been devised and implemented. In this paper, the problems and resources in NER research are described, the principal algorithms underlying most systems sketched, and the current state-of-the-art in the field surveyed.     

La triade méthodologique: substance, énergie,information — comme fondement de la physiologie théorique

The organism as an open system and the organism as a system with an automatic adjustment, these are the two main contemporary schemes of theoretical physiology. However, these schemes, in spite of being synthetic in comparison to the models formerly proposed, are analytic according to the requirements of biological thinking. Some other schemes have to be integrated as strong heuristic means, for instance, the scheme of circuits generating oscillations of relaxation. The notions of “substance, energy, information” constitute a methodological triad which systematically can be used examining the great problems of life. “Energy” is a mediatory term which was to be recognized as possessing a working function and an informational one (as a signal). We propose to distinguish between structural and operational information on the one hand and between bounded and free (or brought up to date) information on the other hand. The living substance is “impregnated” with information, owing to a constant expense of energy. Adaptation, habituation, homeostasis, evolution — all these notions lend themselves to a more coherent analysis from the proposed point of view, as is demonstrated by examples.     

CHEMO-ORIENTATION

1. A new classification system for chemo-orientation mechanisms is suggested, based on delineating (a) internal and external orientation information available to an organism, (b) mode of information processing, (c) type of motor output pattern, and (d) guidance systems that modulate or direct motor output.
2. Cross-phyletic comparison of chemo-orientation indicates that morphology, to a greater extent than phylogeny, determines the kind of chemo-orientation mechanisms available to an organism. Analogies are drawn between single-celled organisms with surface chemical receptor sites and higher organisms with elaborate chemosensory organs and nervous systems.     

Chemoattractants of Distyostelium discoideum (Protozoa: Sarcomastigophora, Eumycetozoa)

The authors summarize data on interaction of protozoan Dictyostelium discoideum with folia acid and cyclic adenozinmonophosphate as chemoattractants. These substances play role of antagonists in the life cycle of Dictyostelium discoideum: one disperses cells in space and another gathers them into groups forming and organism. Analysis of interaction between Dictyostelium discoideum and environment allows to reveal that Deictyosteliceae has unique mechanism of adaptation of shortage of feeding resource--forming of multicellular organism with functional differentiation of cells. This mechanism could be found at different hierarchical levels of living organisms.