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。     

Executable cell biology

Computational modeling of biological systems is becoming increasingly important in efforts to better understand complex biological behaviors. In this review, we distinguish between two types of biological models--mathematical and computational--which differ in their representations of biological phenomena. We call the approach of constructing computational models of biological systems 'executable biology', as it focuses on the design of executable computer algorithms that mimic biological phenomena. We survey the main modeling efforts in this direction, emphasize the applicability and benefits of executable models in biological research and highlight some of the challenges that executable biology poses for biology and computer science. We claim that for executable biology to reach its full potential as a mainstream biological technique, formal and algorithmic approaches must be integrated into biological research. This will drive biology toward a more precise engineering discipline.     

The Ties that Undermine

Do biological relations ground responsibilities between biological fathers and their offspring? Few think biological relations ground either necessary or sufficient conditions for responsibility. Nevertheless, many think biological relations ground responsibility at least partially. Various scenarios, such as cases concerning the responsibilities of sperm donors, have been used to argue in favor of biological relations as partially grounding responsibilities. In this article, I seek to undermine the temptation to explain sperm donor scenarios via biological relations by appealing to an overlooked feature of such scenarios. More specifically, I argue that sperm donor scenarios may be better explained by considering the unique abilities of agents involved. Appealing to unique ability does not eliminate the possibility of biological relations providing some explanation for perceived responsibilities on the part of biological fathers. However, since it is unclear exactly why biological relations are supposed to ground responsibility in the first place, and rather clear why unique ability grounds responsibility in those scenarios where it is exhibited, the burden of proof seems shifted to those advocating biological relations as grounds of responsibility to provide an explanation. Since this seems unlikely, I conclude it is best to avoid appealing to biological relations as providing grounds for responsibility.     

杂草生防作用物对本土生物群落的影响

传统生物防治是治理外来入侵杂草危害切实可行的有效策略和途径,近来对传统生物防治的批评主要集注于,引进的生防作用物攻击威胁本土非靶标生物。引进的生防作用物可能对本土非靶标生物产生直接和间接影响,这类影响通过不同营养级生物之间的取食关系,以及通过同一营养级内生物间的竞争关系,而影响本土非靶标生物群落。列举若干杂草生物防治案例对以上影响方式及其发生途径进行了评述。就防范杂草生防作用物对非靶标生物的负面影响,提出了以下对策:(i)把引进天敌防治外来入侵生物作为最后的有效手段;(ii)适当增加对非靶标生物潜在影响的生态学评估;(iii)选择寄主专一性强而且能有效控制靶标杂草的天敌;(iv)加强对杂草传统生物防治的生态学研究。     

The lipidomic correlates of epigenetic aging across the adult lifespan: A population-based study

Lipid signaling is involved in longevity regulation, but which specific lipid molecular species affect human biological aging remains largely unknown. We investigated the relation between complex lipids and DNA methylation-based metrics of biological aging among 4181 participants (mean age 55.1 years (range 30.0–95.0)) from the Rhineland Study, an ongoing population-based cohort study in Bonn, Germany. The absolute concentration of 14 lipid classes, covering 964 molecular species and 267 fatty acid composites, was measured by Metabolon Complex Lipid Panel. DNA methylation-based metrics of biological aging (AgeAccelPheno and AgeAccelGrim) were calculated based on published algorithms. Epigenome-wide association analyses (EWAS) of biological aging-associated lipids and pathway analysis were performed to gain biological insights into the mechanisms underlying the effects of lipidomics on biological aging. We found that higher levels of molecular species belonging to neutral lipids, phosphatidylethanolamines, phosphatidylinositols, and dihydroceramides were associated with faster biological aging, whereas higher levels of lysophosphatidylcholine, hexosylceramide, and lactosylceramide species were associated with slower biological aging. Ceramide, phosphatidylcholine, and lysophosphatidylethanolamine species with odd-numbered fatty acid tail lengths were associated with slower biological aging, whereas those with even-numbered chain lengths were associated with faster biological aging. EWAS combined with functional pathway analysis revealed several complex lipids associated with biological aging as important regulators of known longevity and aging-related pathways.     

生物固氮在我国农业生产中的研究现状及发展对策

简述了生物固氦在我国农业生产中3个热点的研究现状:提高现有固氦生物的固氦能力、化学模拟固氦酶、固氦微生物的生物工程,同时提出了生物固氦在令后生态农业中的发展对策。     

Microevolution in biological control: Mechanisms, patterns, and processes

Microevolution may determine both the safety and efficacy of classical biological control. Despite a growing body of literature, there are several key unanswered questions regarding the role of evolution in biological control: (1) How common is local adaptation of natural enemies to their hosts or the environment in the native range? How critical is it for success of biological control to find locally adapted agents for importation? (2) Does adaptive evolution following introductions play an important role in biological control? (3) Do introductions of biological control agents impose bottlenecks in population size that reduce genetic variation, and is reduced genetic variation associated with low fitness and poor performance? (4) How great is the risk of evolution of host range of biological control agents? (5) What is the risk of target pests evolving resistance to biological control agents? If pests evolve increased resistance, will biological control agents evolve mechanisms to overcome that resistance? Here, we review the four fundamental processes of microevolution, and discuss how they interact in the context of biological control. We discuss our current state of knowledge regarding the outstanding questions, highlight the types of experiments that can address them, and suggest ways to use microevolution to define risks, and enhance efficacy and safety of biological control.     

应用生物完整性指数评价水生态系统健康的研究进展

生物完整性指数(IBI)法是评价水生态系统健康的一种重要且被广泛应用的方法.本文综述了生物完整性指数的指示物种选择原因、构建方法以及在水生态系统健康评价中的应用,并总结了现阶段生态系统评估常用的鱼类完整性指数（F_IBI）、底栖无脊椎动物完整性指数（B_IBI）和着生藻类完整性指数（P_IBI)中候选生物状况参数指标,提出了使用微生物完整性指数(M_IBI)评价水生态系统健康的可行性和必要性.     

生物法处理木质素的研究进展

对生物法处理木质素进行了简要概述,包括微生物降解、生物法酸析提取木质素以及生物法纯化木质素的效果及其研究进展.生物法处理木质素对资源的合理利用、经济的发展以及环境保护具有重要的意义.     

Multimodal Networks: Structure and Operations

A multimodal network (MMN) is a novel graph-theoretic formalism designed to capture the structure of biological networks and to represent relationships derived from multiple biological databases. MMNs generalize the standard notions of graphs and hypergraphs, which are the bases of current diagrammatic representations of biological phenomena and incorporate the concept of mode. Each vertex of an MMN is a biological entity, a biot, while each modal hyperedge is a typed relationship, where the type is given by the mode of the hyperedge. The current paper defines MMNs and concentrates on the structural aspects of MMNs. A companion paper develops MMNs as a representation of the semantics of biological networks and discusses applications of the MMNs in managing complex biological data. The MMN model has been implemented in a database system containing multiple kinds of biological networks.     

聚谷氨酸-明胶生物胶生物学评价

考察了聚谷氨酸-明胶生物胶的生物性能。从细胞毒性、急性毒性、皮肤刺激、溶血、热源、皮肤致敏等试验对其进行生物学检测。结果发现：聚谷氨酸-明胶生物胶的细胞毒性、急性毒性、皮肤刺激、溶血、热源、皮肤致敏试验均为阴性。这些结果表明聚谷氨酸-明胶生物胶具有良好的生物性能。     

On the limitations of standard statistical modeling in biological systems: A full Bayesian approach for biology

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist.     

生物防治利用生物多样性保护生物多样性

本文论述了生物防治与保护生物多样性的关系,提出生物多样性是生防作用物的必要来源,生物防治是保护生物多样性的重要措施。文中分析了自然界和农田生态系统中天敌的多样性和寄主专一性,并从外来种的治理、濒危物种和栖境的保护等几个方面探讨了生物防治对于保护生物多样性的作用。作者还强调应加强国际间天敌资源的交换,建立严格的天敌引种释放法规,以便开展更多的安全有效的生物防治项目。     

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.     

Emphasis of biological research for space radiation]

The paper summarized issues, current status and the recent topics in biological research of space radiation. Researches to estimate a risk associated with space radiation exposure during a long-term manned space flight, such as in the International Space Station, is emphasized because of the large uncertainty of biological effects and a complexity of the radiation environment in space. The Issues addressed are; 1) biological effects and end points in low dose radiation, 2) biological effects under low dose rate and long-term radiation exposure, 3) modification of biological responses to radiation under space environments, 4) various aspects of biological end points vs. cellular and molecular mechanisms, 5) estimation of human risk associated with radiation exposure in space flight, 6) regulations for radiation exposure limits for space workers. The paper also summarized and introduced recent progress in space related radiation researches with various biological systems.     

Trends in biological control: public interest,international networking and research direction

We investigated trends in biological control to both capture its evolution and explore future opportunities. We examined recent changes in public interest, international networking and peer-reviewed research. A Google Trends analysis revealed that the popularity of biological control is decreasing in terms of search hits on the internet. This trend is potentially worrying for the biological control community, given that public interest tends to drive political decisions regarding regulatory processes and governmental funding of research. To examine patterns of international collaboration, we established the list of authors who published their work in the three main biological control journals from the early 1990s to 2016. International co-authorship has intensified and the biological control sector is increasingly characterized by multilateral collaboration. We surveyed papers published in BioControl and Biological Control over the last 25 years to identify research trends with respect to target pests, commodities, biological control agents and biological control approaches. Finally, we report that articles on biological control are published in the broad-based scientific journals Science and Nature on a regular basis. This reflects contributions that biological control research makes to scientific discussions in general. Our analyses revealed a thriving scientific discipline with several major research trends in arthropod, plant pathogen and weed biological control.     

Physical plasma in biological solids: a possible mechanism for resonant interactions between low intensity microwaves and biological systems

Observed semiconductor properties of biological material in vitro indicate possible involvement of semiconduction in biological processes. Since in inorganic semiconductors solid-state plasma occurs, it is hypothesized that in organic semiconductors solid-state plasma similarly occurs. Some results of experimental investigation of resonant effects of microwaves in biological systems are considered in the light of that hypothesis. The conditions necessary for the existence of physical plasma in biological solid structures are discussed, and certain parameters of physical plasma in these structures are evaluated. Its is proposed that microwave radiation may support or damp plasma oscillations, thereby stimulating or suppressing biological functions.     

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.     

Biological Motion Primes the Animate/Inanimate Distinction in Infancy

Given that biological motion is both detected and preferred early in life, we tested the hypothesis that biological motion might be instrumental to infants’ differentiation of animate and inanimate categories. Infants were primed with either point-light displays of realistic biological motion, random motion, or schematic biological motion of an unfamiliar shape. After being habituated to these displays, 12-month-old infants categorized animals and vehicles as well as furniture and vehicles with the sequential touching task. The findings indicated that infants primed with point-light displays of realistic biological motion showed better categorization of animates than those exposed to random or schematic biological motion. These results suggest that human biological motion might be one of the motion cues that provide the building blocks for infants’ concept of animacy.     

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.