生物数据标准化研究进展

随着生物测序技术的快速发展,积累了海量的生物数据。生物数据资源作为生物分析研究及应用的核心和源头,为保证数据的正确性、可用性和安全性,对生物数据资源进行标准化的管理非常重要和迫切。本文综述了目前国内外生物数据标准化研制进展,目前国内外对生物数据缺少一个总体的规划,生物数据语义存在大量的不兼容性,数据格式多种多样,在生物数据收集、处理、存储和共享等方面缺乏统一的标准。国内外生物数据标准化处于起步阶段,但各国生物专家都在努力进行标准研制工作。文章最后从生物数据术语、生物数据资源收集、处理和交换、存储、生物数据库建设和生物数据伦理规范等方面出发,对标准研制工作进行一一探讨,期望能为生物数据标准制定提供一定的参考和依据。     

Risk and ethics in biological control

All introduced natural enemies present a degree of risk to nontarget species. Since most biological control programs use relatively host-specific natural enemies, the risk to nontarget species is generally very low, particularly from biological control of weeds, which uses extensively tested and validated host-specificity testing procedures to predict risk. However, many of the published comments about risks of biological control are superficial or misleading, often inappropriately lumping risk from all taxa of agents as “the risk of biological control,” and ignore the potential benefits, rather than dealing with species-by-species risk and benefits. Particularly confounding accurate predictions is the common mixing of parameters of hazard and exposure in discussions of risk. In this paper, traditional risk analysis techniques are discussed and adapted for biological control. How people perceive risk is the key to understanding their attitude to risk. Some of the criticisms of biological control relating to inadequate post-release monitoring are valid and the ethical responsibilities of biological control scientists in this area are also discussed. Biological control scientists should address objectively the criticisms of biological control, continue to review and adjust current host-specificity testing procedures and make appropriate changes. This process will result in better science, ultimately delivering more focused programs, and altering the perception of risk from biological control agents by objective observers.     

Risk and ethics in biological control

All introduced natural enemies present a degree of risk to nontarget species. Since most biological control programs use relatively host-specific natural enemies, the risk to nontarget species is generally very low, particularly from biological control of weeds, which uses extensively tested and validated host-specificity testing procedures to predict risk. However, many of the published comments about risks of biological control are superficial or misleading, often inappropriately lumping risk from all taxa of agents as “the risk of biological control,” and ignore the potential benefits, rather than dealing with species-by-species risk and benefits. Particularly confounding accurate predictions is the common mixing of parameters of hazard and exposure in discussions of risk. In this paper, traditional risk analysis techniques are discussed and adapted for biological control. How people perceive risk is the key to understanding their attitude to risk. Some of the criticisms of biological control relating to inadequate post-release monitoring are valid and the ethical responsibilities of biological control scientists in this area are also discussed. Biological control scientists should address objectively the criticisms of biological control, continue to review and adjust current host-specificity testing procedures and make appropriate changes. This process will result in better science, ultimately delivering more focused programs, and altering the perception of risk from biological control agents by objective observers.     

Biological coupling process for treatment of toxic and refractory compounds in coal gasification wastewater

Coal gasification wastewater (CGW) contains a large number of toxic and refractory compounds, such as phenolic compounds and polycyclic and heterocyclic aromatic compounds. These toxic and refractory compounds are difficult to degrade if biological methods are the only ones used. In recent years, several novel biological coupling processes are used to treat CGW. In the study, this review attempts to offer a comprehensive summary regarding the biological coupling treatment technologies of CGW, including conventional biological processing arts, the combination of adsorption and biotechnology, biological enhancement technologies, co-metabolism technologies and the combination of advanced oxidation and biotechnology. Meanwhile, the treatment efficiency of different biological coupling processes was compared with each other. Co-metabolism and advanced oxidation with biotechnology are both highly effective and promising technologies for degrading toxic and refractory compounds. More research should be conducted on these two aspects in the future.     

Causal Regularities in the Biological World of Contingent Distributions

Former discussions of biological generalizations have focused on the question of whether there are universal laws of biology. These discussions typically analyzed generalizations out of their investigative and explanatory contexts and concluded that whatever biological generalizations are, they are not universal laws. The aim of this paper is to explain what biological generalizations are by shifting attention towards the contexts in which they are drawn. I argue that within the context of any particular biological explanation or investigation, biologists employ two types of generations. One type identifies causal regularities exhibited by particular kinds of biological entities. The other type identifies how these entities are distributed in the biological world.     

Indirect nontarget effects of host-specific biological control agents: Implications for biological control

Classical biological control of weeds currently operates under the assumption that biological control agents are safe (i.e., low risk) if they do not directly attack nontarget species. However, recent studies indicate that even highly host-specific biological control agents can impact nontarget species through indirect effects. This finding has profound implications for biological control. To better understand the causes of these interactions and their implications, we evaluate recent case studies of indirect nontarget effects of biological control agents in the context of theoretical work in community ecology. We find that although particular indirect nontarget effects are extremely difficult to predict, all indirect nontarget effects of host specific biological control agents derive from the nature and strength of the interaction between the biological control agent and the pest. Additionally, recent theoretical work suggests that the degree of impact of a biological control agent on nontarget species is proportional to the agent’s abundance, which will be highest for moderately successful control agents. Therefore, the key to safeguarding against indirect nontarget effects of host-specific biological control agents is to ensure the biological control agents are not only host specific, but also efficacious. Biological control agents that greatly reduce their target species while remaining host-specific will reduce their own populations through density-dependent feedbacks that minimize risks to nontarget species.     

海洋生境修复和生物资源养护原理与技术研究进展及展望

由于人类活动导致的海洋生境、生态系统以及生物资源的衰退已经引起了全球的高度重视。以生态修复的原理为基础,综述了海洋生境修复和生物资源养护的关键设施、关键技术、监测与效果评价以及综合管理的国内外研究进展,并对海洋生境修复与生物资源养护的研究热点和重点进行了展望,以期为我国海洋生境修复和生物资源养护提供参考。     

Physical anthropology,peace and justice: Some observations

Human biological well being is a concern of physical anthropology. Genetic determinants and also sociocultural factors, which operate through biological bases, affect human biological quality. Several populations from different parts of the globe have been identified where varieties of detrimental genes occur in considerable numbers influencing health and some other related biological aspects of human life. Injustice will be done to those populations if necessary measures are not undertaken to improve their biological qualities. Peace cannot prevail in an atmosphere where people are deprived of the basic amenities for survival and maintenance of good health.     

Stochastic models for X chromosome inactivation

Summary A multivariate Gaussian model for mammalian development is presented with the associated biological and mathematical assumptions. Many biological investigations use the female mammal X chromosome to test hypotheses and to estimate parameters of the developmental system. In particular, Lyon's (1961) hypotheses are used as a basis of the mathematical model. Experimental mouse data and three sets of human experimental data are analyzed using the hypothesized Gaussian model. The estimated biological parameters are consistent with some current biological theories.     

Timing‐Mechanismen in der Natur: Biologische Uhren

Increasingly timing mechanisms are detected on all levels of organisation which control the temporal order and coordination of biological processes. The respective mechanisms are designated as „biological clocks”︁. They are based on two principles: oscillations and unidirectional processes (hour‐glass). Oscillating biological clocks such as circadian,clunar or annual clocks coordinate biological events with respect to certain time points (phases)of external daily, lunar or annual hanges in the environment, while hourglass mechanisms mainly determine the duration of steps in development or aging.Complex biological timing mechanisms may comprise endogenous clocks and hourglass processes as well as external signals. Timing of biological events is often coupled with reaching defined thresholds within the underlying clock mechanism.     

Membrane stability

Rupture and buckling of artificial and biological membranes is an important part of many biological processes. In this review, we present some of the main experimental facts and their analysis. Recent theoretical work, in particular thin film models and nucleation mechanisms of membrane instability, are discussed in detail. Possible applications to membrane adhesion and fusion are pointed out. Attempts are made to explain biological phenomena and experimental results for biological membranes based on a rigorous physicochemical approach developed previously for thin films in colloid systems.     

Indirect nontarget effects of host-specific biological control agents: Implications for biological control

Classical biological control of weeds currently operates under the assumption that biological control agents are safe (i.e., low risk) if they do not directly attack nontarget species. However, recent studies indicate that even highly host-specific biological control agents can impact nontarget species through indirect effects. This finding has profound implications for biological control. To better understand the causes of these interactions and their implications, we evaluate recent case studies of indirect nontarget effects of biological control agents in the context of theoretical work in community ecology. We find that although particular indirect nontarget effects are extremely difficult to predict, all indirect nontarget effects of host specific biological control agents derive from the nature and strength of the interaction between the biological control agent and the pest. Additionally, recent theoretical work suggests that the degree of impact of a biological control agent on nontarget species is proportional to the agent’s abundance, which will be highest for moderately successful control agents. Therefore, the key to safeguarding against indirect nontarget effects of host-specific biological control agents is to ensure the biological control agents are not only host specific, but also efficacious. Biological control agents that greatly reduce their target species while remaining host-specific will reduce their own populations through density-dependent feedbacks that minimize risks to nontarget species.     

Zoetic polymers

Conditions mediating the formation of biological polymers in situ are reviewed, and terminology suggested to differentiate polymers found in living cells from synthetic materials and polymers derived from biological sources that are modified or studied in a way that obscures their biological function. Methods currently used to characterize the mechanical properties of biopolymer networks in cells are briefly discussed.     

GOChase: correcting errors from Gene Ontology-based annotations for gene products

SUMMARY: The Gene Ontology (GO) is a controlled biological vocabulary that provides three structured networks of terms to describe biological processes, cellular components and molecular functions. Many databases of gene products are annotated using the GO vocabularies. We found that some GO-updating operations are not easily traceable by the current biological databases and GO browsers. Consequently, numerous annotation errors arise and are propagated throughout biological databases and GO-based high-level analyses. GOChase is a set of web-based utilities to detect and correct the errors in GO-based annotations.     

Digital and biological computing in organizations.

Michael Conrad unveiled many of the fundamental characteristics of biological computing. Underlying the behavioral variability and the adaptability of biological systems are these characteristics, including the ability of biological information processing to exploit quantum features at the atomic level, the powerful 3-D pattern recognition capabilities of macromolecules, the computational efficiency, and the ability to support biological function. Among many other things, Conrad formalized and explicated the underlying principles of biological adaptability, characterized the differences between biological and digital computing in terms of a fundamental tradeoff between adaptability and programmability of information processing, and discussed the challenges of interfacing digital computers and human society. This paper is about the encounter of biological and digital computing. The focus is on the nature of the biological information processing infrastructure of organizations and how it can be extended effectively with digital computing. In order to achieve this goal effectively, however, we need to embed properly digital computing into the information processing aspects of human and social behavior and intelligence, which are fundamentally biological. Conrad's legacy provides a firm, strong, and inspiring foundation for this endeavor.     

A realist approach to biological events

In this paper, I aim to show that the multiple realisability and the causal efficacy of biological events can best be explained by construing biological events as determinables of more determinate physical events. The determination relation itself is spelled out in terms of inclusive essence. In order to secure actual causation for biological events (in contrast to causal influence), two conditions are introduced such that for some events, biological events qualify as their cause. Finally, certain consequences of the presented theory are discussed, such as the question of how the biological token event can retain its identity across modal modifications of its realiser, and such as how the presented solution bears on the classical problem of biological causation.     

生物运动识别的信息加工机制

识别其他生物体的运动对于个体的生存和社会交互都有极为重要的意义.本文首先基于生物运动识别的行为学、心理物理学、脑损伤和精神障碍研究介绍了生物运动识别的一些特性和影响因素;然后基于神经影像学、脑损伤和神经电生理学研究从视觉系统背腹侧双通路加工的角度,梳理了其信息加工机制的进展;最后对生物运动识别信息加工神经机制的研究方向提出了一点建议,并指出研究过程中需要注意的问题.     

Low gravity on earth by magnetic levitation of biological material

The use of a magnetic field gradient levitation apparatus as a tool for investigating gravisensing mechanisms in biological systems and as a low gravity simulator for biological systems is described. The basic principles are described. Differences between its application to pure materials and the heterogeneous materials of biological materials are emphasized.     

Molecular simulations of protein dynamics: new windows on mechanisms in biology

Recent advances in computer hardware and software have led to the development of increasingly successful molecular simulations of protein structural dynamics that are intrinsic to biological processes. These simulations have resulted in models that increasingly agree with experimental observations, suggest new experiments and provide insights into biological mechanisms. Used in combination with data obtained with sophisticated experimental techniques, simulations are helping us to understand biological complexity at the atomic and molecular levels and are giving promising insights into the genetic, thermodynamic and functional/mechanistic behaviour of biological processes. Here, we highlight some examples of such approaches that illustrate the current state and potential of the field of molecular simulation.