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.     

Engineering microbes with synthetic biology frameworks

Typically, the outcome of biologically engineered unit operations cannot be controlled a priori due to the incorporation of ad hoc design into complex natural systems. To mitigate this problem, synthetic biology presents a systematic approach to standardizing biological components for the purpose of increasing their programmability and robustness when assembled with the aim to achieve novel biological functions. A complex engineered biological system using only standardized biological components is yet to exist. Nevertheless, current attempts to create and to implement modular, standardized biological components pave the way for the future creation of highly predictable artificial biological systems. Although synthetic biology frameworks can be applied to any biological engineering endeavor, this article will focus on providing a brief overview of advances in the field and its recent utilization for the engineering of microbes.     

生命现象研究中的奥秘探索之四个方面

发现生命现象,理清生命现象的脉络,是认识生命本质的基础。在检索相关文献的基础上,对探究生命现象的方法和规律进行了总结和归纳。从试验材料、试验方法、创新技巧和猜想能力四个方面进行了论述,以便为理解生命现象提供一些参考。     

A method of determining the antioxidative activity of biological matter

A procedure is described for determining antioxidation activity of the water-soluble biological material. The procedure is based on the study of kinetics of the reduced 2.6-dichlorophenolindophenol oxidation by air oxygen both with and without the biological material as well as on calculation of the value for the constant of the biological material inhibition of 2.6-dichlorophenolindophenol oxidation as an index of the biological material antioxidation activity.     

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.     

A Conceptual Framework for the Interpretation of Biological Markers for Environmental Exposure Assessment

Human exposure to environmental contaminants occurs via air, water, soil, dust, food, and other environmental media. Given this multitude of sources, environmental exposure assessment is moving away from single route exposure assessment to more integrated measures of exposure. Biological markers are frequently advocated as appropriate exposure assessment tools since they provide a measure of internal dose integrated over all routes of exposure. However, contributing sources may be difficult to identify through use of biological markers, and thus, have had limited utility in the regulatory community. To explore the different perspectives on the use and application of biological markers for exposure assessors, epidemiologists, and regulatory personnel, we have developed a biological marker conceptual framework. This framework is developed as a paradigm for the interpretation of biological markers for environmental exposure assessment linking the exposure assessment and the health effects assessment perspectives regarding biological markers. Further, it incorporates issues of source-specific exposures, aggregate exposure assessment, route-specific contributions, and biological variation in response to exposure. This structure provides an approach to explore the current constraints in using biological markers to evaluate source-specific exposures. This framework is discussed in the context of currently available biological markers for lead, carbon monoxide, and toluene. Biological markers represent a complex tool to assess human exposures to environmental contaminants; the biological marker framework presents a structure for their interpretation recognizing that many of the determinants of exposure, bioavailablity, and toxicokinetics are still being evaluated. The conceptual framework presented here provides another tool for the researcher in assessing the utility of biological markers in exposure assessment and epidemiology.     

Optimal allocation of replicates for measurement evaluation studies

Optimal experimental design is important for the efficient use of modern highthroughput technologies such as microarrays and proteomics. Multiple factors including the reliability of measurement system, which itself must be estimated from prior experimental work, could influence design decisions. In this study, we describe how the optimal number of replicate measures （technical replicates） for each biological sample （biological replicate） can be determined. Different allocations of biological and technical replicates were evaluated by minimizing the variance of the ratio of technical variance （measurement error） to the total variance （sum of sampling error and measurement error）. We demonstrate that if the number of biological replicates and the number of technical replicates per biological sample are variable, while the total number of available measures is fixed, then the optimal allocation of replicates for measurement evaluation experiments requires two technical replicates for each biological replicate. Therefore, it is recommended to use two technical replicates for each biological replicate if the goal is to evaluate the reproducibility of measurements.     

纳米技术与生物学实验的微型化

纳米技术是近年来发展迅速的新技术,有着几乎无限的潜力。一方面生物分子的尺度是纳米与亚纳米级的,纳米技术可以从生物科学学到许多生物分子作用的奥秘;另一方面,纳米技术为生物学的研究提供新材料、新方法,使生物学研究可以多快好省地进行。本文简单介绍几种利用纳米技术开展生物学研究的思路与方法。     

基于设计的生物大分子成药性优化策略研究进展

目前生物药物正处在高速发展阶段,但生物大分子的一些固有特性限制了其成药性,使得很多具有良好治疗潜能的生物大分子 最终不能开发成药物,因而严重制约了生物药物的发展。生物药物开发的瓶颈已从“新分子的产生”转向“如何获得具有优良生理特性 和预期治疗效果的有效药物”。近年来,通过合理设计改造生物大分子高级结构以优化其成药性的研究获得了快速发展。综述基于设计 的生物大分子成药性优化策略研究进展。     

A Missing Link: K-4 Biological Evolution Content Standards

The National Science Education Standards (NSES) is one of the most influential documents in US science education. The NSES has been utilized by local schools and districts, state departments of education, and national curriculum groups to form the backbone for curriculum frameworks, programs, and assessment systems to guide science education. The NSES provides national biological evolution content standards for fifth grade through high school but not for kindergarten through fourth grade. This article presents K-4 biological evolution content standards that can be used in conjunction with the current NSES K-4 life science and earth science content standards, brief examples of integration activities using the K-4 biological evolution content standards, and supplemental teacher information for the K-4 biological evolution content standards. The biological evolution content standards and the additional materials can guide teachers when teaching biological evolution to K-4th grade students.     

Paper-based archiving of mammalian and plant samples for RNA analysis

The ability to archive biological samples for subsequent nucleic acid analysis is essential for tissue specimens and forensic samples. FTA Card is a chemically treated filter paper designed for the collection and room temperature storage of biological samples for subsequent DNA analysis. Its usefulness for the preservation of biological samples for subsequent RNA analysis was tested. Here, we demonstrate that RNA in biological samples stored on FTA Cards is stable and can be used successfully for RT-PCR and northern blot analysis. RNA stability depends on the storage temperature and the type of biological specimen. RNA in mammalian cells stored on FTA Cards is stable for over one year at temperatures at or below -20 degrees C and for two to three months in samples stored at room temperature. For plant leaf, longer storage times (> 5 days) require temperatures at or below -70 degrees C following sample application. FTA Cards may constitute a method not only for convenient collection and storage of biological samples but also for rapid RT-PCR analysis of tissue and cell samples.     

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.     

A dynamic model for functional mapping of biological rhythms

Functional mapping is a statistical method for mapping quantitative trait loci (QTLs) that regulate the dynamic pattern of a biological trait. This method integrates mathematical aspects of biological complexity into a mixture model for genetic mapping and tests the genetic effects of QTLs by comparing genotype-specific curve parameters. As a way of quantitatively specifying the dynamic behavior of a system, differential equations have proven to be powerful for modeling and unraveling the biochemical, molecular, and cellular mechanisms of a biological process, such as biological rhythms. The equipment of functional mapping with biologically meaningful differential equations provides new insights into the genetic control of any dynamic processes. We formulate a new functional mapping framework for a dynamic biological rhythm by incorporating a group of ordinary differential equations (ODE). The Runge-Kutta fourth order algorithm was implemented to estimate the parameters that define the system of ODE. The new model will find its implications for understanding the interplay between gene interactions and developmental pathways in complex biological rhythms.     

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.     

A dynamic model for functional mapping of biological rhythms

Functional mapping is a statistical method for mapping quantitative trait loci (QTLs) that regulate the dynamic pattern of a biological trait. This method integrates mathematical aspects of biological complexity into a mixture model for genetic mapping and tests the genetic effects of QTLs by comparing genotype-specific curve parameters. As a way of quantitatively specifying the dynamic behaviour of a system, differential equations have proved to be powerful for modelling and unravelling the biochemical, molecular, and cellular mechanisms of a biological process, such as biological rhythms. The equipment of functional mapping with biologically meaningful differential equations provides new insights into the genetic control of any dynamic processes. We formulate a new functional mapping framework for a dynamic biological rhythm by incorporating a group of ordinary differential equations (ODE). The Runge–Kutta fourth-order algorithm was implemented to estimate the parameters that define the system of ODE. The new model will find its implications for understanding the interplay between gene interactions and developmental pathways in complex biological rhythms.     

MetNetGE: interactive views of biological networks and ontologies

Background  

Linking high-throughput experimental data with biological networks is a key step for understanding complex biological systems. Currently, visualization tools for large metabolic networks often result in a dense web of connections that is difficult to interpret biologically. The MetNetGE application organizes and visualizes biological networks in a meaningful way to improve performance and biological interpretability.     

Inferring biological structures from super-resolution single molecule images using generative models

Localization-based super resolution imaging is presently limited by sampling requirements for dynamic measurements of biological structures. Generating an image requires serial acquisition of individual molecular positions at sufficient density to define a biological structure, increasing the acquisition time. Efficient analysis of biological structures from sparse localization data could substantially improve the dynamic imaging capabilities of these methods. Using a feature extraction technique called the Hough Transform simple biological structures are identified from both simulated and real localization data. We demonstrate that these generative models can efficiently infer biological structures in the data from far fewer localizations than are required for complete spatial sampling. Analysis at partial data densities revealed efficient recovery of clathrin vesicle size distributions and microtubule orientation angles with as little as 10% of the localization data. This approach significantly increases the temporal resolution for dynamic imaging and provides quantitatively useful biological information.     

Estimation of Human Biological Age Based on the Parameters of Heart Rhythmic Activity

A linear regression model has been constructed for estimating human biological age, with the parameters of heart rhythmic activity being used as biological markers. One of the advantages of using these parameters as biological markers of aging is the possibility to measure a number of parameters for an individual subject in a brief (6–7 min) procedure of rhythmogram recording. This makes the collection of data for a statistically reliable sample much easier, increases the accuracy of the model, and permits its use along with other methods for mass examinations of a population and for control of the effects of drugs and food additives. The model may be extended and supplemented with other biological markers in order to improve the approximation of biological age.