作物组学数据库的比较和应用

组学研究是生命科学研究的重要组成部分,是从整体角度研究全部组分及其相互关系的学科。组学数据库收集整理了与组学研究相关的所有信息,为组学研究提供了全面的数据基础。其中,作物组学数据库主要是以作物为对象建立的组学数据库,尤其是几大主要粮食作物的组学测序及信息挖掘,提升了作物科学的基础研发和生产水平,使我国粮食储备迈上一个新的台阶。本文以水稻、玉米和小麦为代表,通过搜集它们在组学研究中常用的数据库,概述了作物基因组学、转录组学、蛋白质组学、代谢组学及表型组学的主要研究内容,阐述了作物组学数据库在作物科学研究中的发展现状,揭示了在高通量信息时代下多种组学数据库的交叉及综合利用已经成为作物科学研究发展的重要方向和手段。     

关于组学大数据背景下《微生物学》教材框架的思考

微生物学是生物学的重要内容,是全国高等院校生物学专业或相关专业的本科生必修的一门核心基础课,其主要任务是给学生提供基础的、系统的、前沿的微生物学知识和理论。随着高通量测序、质谱、芯片等高通量技术的快速发展,生命科学领域快速进入了以海量多元组学(基因组学、转录组学、蛋白质组学、免疫组学、代谢组学等)数据为特征的大数据时代,而这势必会对微生物学教材已有的内容产生冲击和补充。本文对如何在组学大数据背景下对国内经典的微生物学教材进行改革,将目前最具突破性的组学成果整合到已有的教材框架中或革新现有教材框架进行了初步探讨。     

Data integration in the era of omics: current and future challenges

To integrate heterogeneous and large omics data constitutes not only a conceptual challenge but a practical hurdle in the daily analysis of omics data. With the rise of novel omics technologies and through large-scale consortia projects, biological systems are being further investigated at an unprecedented scale generating heterogeneous and often large data sets. These data-sets encourage researchers to develop novel data integration methodologies. In this introduction we review the definition and characterize current efforts on data integration in the life sciences. We have used a web-survey to assess current research projects on data-integration to tap into the views, needs and challenges as currently perceived by parts of the research community.     

生物多样性信息学研究进展

生物多样性信息学是一门蓬勃发展的新学科。它将现代的信息技术带入生物多样性及其相关学科的研究领域。它在生物多样性基础数据的数字化、模型工具和各种工具软件的开发、数据整合, 以及全球、地区和国家尺度生物多样性信息网络等多个方面的发展, 向我们展示了未来在全球范围内自由、免费共享生物多样性数据和信息, 以及人们行动起来共同关注、调查与监测野外生物多样性的前景。目前, 已有大量数字化的物种编目、标本馆标本、多媒体影像、研究文献等生物多样性基础信息可以通过互联网检索和利用。其中, 最值得关注的是一些成功的国际性研究项目, 如物种2000、全球生物多样性信息网络、生命条形码以及网络生命大百科全书。这些项目的成功不仅体现在对大量基础信息和数据的发布, 而且它们通过与生物多样性信息标准TDWG(Biodiversity Information Standards: TDWG)的合作, 推动了达尔文核心标准(Darwin Core)等一些重要的生物多样性信息标准的应用, 以及地区和国家性生物多样性信息节点的建立, 这些都为将来全球范围生物多样性信息的共享和数据交换奠定了重要基础。在数字化信息的基础上, 研究人员也开发了一些在特定研究领域应用的数据挖掘和模型工具, 例如基于数字化标本的地理分布预测工具MAXENT, 分类学专家知识管理的LifeDesk。公民科学理念的发展则向我们展示了公众和科学爱好者广泛参与以互联网为基础的生物多样性信息学研究活动。因此, 生物多样性信息学的发展前景广阔, 它将为我们实现全球保护战略目标, 应对生物多样性危机, 解决全球气候变化条件下生物多样性资源管理和利用建立坚实的信息基础。     

Herbgenomics: A stepping stone for research into herbal medicine

From the prehistoric era until the publishing of the Compendium of Materia Medica and the first scientific Nobel Prize in the Chinese mainland for Tu's discovery on anti-malarial tablets, each milestone and stepping stone in the developmental history of herbal medicine involved intrepid exploration, bold hypothesis formulation, and cautious verification. After thousands of years of discovery and development, herbal research has entered a new era—the era of herbgenomics. Herbgenomics combines herbal and genomic research, bridging the gap between traditional herbal medicine and cutting-edge omics studies. Therefore, it provides a general picture of the genetic background of traditional herbs, enabling researchers to investigate the mechanisms underlying the prevention and treatment of human diseases from an omics perspective.     

Life sciences and biotechnology in China

Life science and biotechnology have become a top priority in research and development in many countries as the world marches into the new century. China as a developing country with a 1.3 billion population and booming economy is actively meeting the challenge of a new era in this area of research. Owing to support from the government and the scientific community, and reform to improve the infrastructure, recent years have witnessed a rapid progress in some important fields of life science and biotechnology in China, such as genomics and protein sciences, neuroscience, systematics, super-hybrid rice research, stem cell and cloning technology, gene therapy and drug/vaccine development. The planned expansion and development of innovation in related sectors and the area of bioethics are described and discussed.     

Systems biology in animal sciences

Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes and animal traits are not yet frequently used. This paper aims to explain what systems biology is and which areas of animal sciences could benefit from systems biology approaches. Systems biology aims to understand whole biological systems working as a unit, rather than investigating their individual components. Therefore, systems biology can be considered a holistic approach, as opposed to reductionism. The recently developed 'omics' technologies enable biological sciences to characterize the molecular components of life with ever increasing speed, yielding vast amounts of data. However, biological functions do not follow from the simple addition of the properties of system components, but rather arise from the dynamic interactions of these components. Systems biology combines statistics, bioinformatics and mathematical modeling to integrate and analyze large amounts of data in order to extract a better understanding of the biology from these huge data sets and to predict the behavior of biological systems. A 'system' approach and mathematical modeling in biological sciences are not new in itself, as they were used in biochemistry, physiology and genetics long before the name systems biology was coined. However, the present combination of mass biological data and of computational and modeling tools is unprecedented and truly represents a major paradigm shift in biology. Significant advances have been made using systems biology approaches, especially in the field of bacterial and eukaryotic cells and in human medicine. Similarly, progress is being made with 'system approaches' in animal sciences, providing exciting opportunities to predict and modulate animal traits.     

Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology

Over the past 2 decades, there have been revolutionary developments in life science technologies characterized by high throughput, high efficiency, and rapid computation. Nutritionists now have the advanced methodologies for the analysis of DNA, RNA, protein, low-molecular-weight metabolites, as well as access to bioinformatics databases. Statistics, which can be defined as the process of making scientific inferences from data that contain variability, has historically played an integral role in advancing nutritional sciences. Currently, in the era of systems biology, statistics has become an increasingly important tool to quantitatively analyze information about biological macromolecules. This article describes general terms used in statistical analysis of large, complex experimental data. These terms include experimental design, power analysis, sample size calculation, and experimental errors (Type I and II errors) for nutritional studies at population, tissue, cellular, and molecular levels. In addition, we highlighted various sources of experimental variations in studies involving microarray gene expression, real-time polymerase chain reaction, proteomics, and other bioinformatics technologies. Moreover, we provided guidelines for nutritionists and other biomedical scientists to plan and conduct studies and to analyze the complex data. Appropriate statistical analyses are expected to make an important contribution to solving major nutrition-associated problems in humans and animals (including obesity, diabetes, cardiovascular disease, cancer, ageing, and intrauterine growth retardation).     

生物多样性信息学:一个正在兴起的新方向及其关键技术

生物多样性科学和生物信息学是生命科学中两个极为重要也是十分活跃的交叉学科,生物多样性信息学则是目前正在兴起的一个新方向,基发展必将进一步深化信息技术在生物多样性研究中的应用。本文简要介绍了国内外该领域的主要目标与进展,讨论了有关的关键技术（如数据库间的互操作与数字图书馆）,并列出了两个原型系统（Ｓｐｅｃｉｅｓ２０００和ＧＢＩＦ）和其他相关系统的网址。     

整合分析多组学数据筛选疾病靶点的精准医学策略

随着高通量测序技术的不断发展与完善,对于不同层次和类型的生物组学数据的获取及分析方法也日趋成熟与完善。基于单组学数据的疾病研究已经发现了诸多新的疾病相关因子,而整合多组学数据研究疾病靶点的工作方兴未艾。生命体是一个复杂的调控系统,疾病的发生与发展涉及基因变异、表观遗传改变、基因表达异常以及信号通路紊乱等诸多层次的复杂调控机制,利用单一组学数据分析致病因子的局限性愈发显著。通过对多种层次和来源的高通量组学数据的整合分析,系统地研究临床发病机理、确定最佳疾病靶点已经成为精准医学研究的重要发展方向,将为疾病研究提供新的思路,并对疾病的早期诊断、个体化治疗和指导用药等提供新的理论依据。本文详细介绍了基因组、转录组和表观组等系统组学研究在疾病靶点筛选方面出现的新技术手段和研究进展,并对它们之间的整合分析新策略和优势进行了讨论。     

Proteomics and systems biology to tackle biological complexity: Yeast as a case study

In this note we discuss how, by using budding yeast as model organism (as has been done in the past for biochemical, genetics and genomic studies), the integration of "omics" sciences and more specifically of proteomics with systems biology offers a very profitable approach to elucidating regulatory circuits of complex biological functions.     

Accessing data from the International Mouse Phenotyping Consortium: state of the art and future plans

The International Mouse Phenotyping Consortium (IMPC) (http://www.mousephenotype.org) will reveal the pleiotropic functions of every gene in the mouse genome and uncover the wider role of genetic loci within diverse biological systems. Comprehensive informatics solutions are vital to ensuring that this vast array of data is captured in a standardised manner and made accessible to the scientific community for interrogation and analysis. Here we review the existing EuroPhenome and WTSI phenotype informatics systems and the IKMC portal, and present plans for extending these systems and lessons learned to the development of a robust IMPC informatics infrastructure.     

Towards a bioinformatics network for Latin America and the Caribbean (LACBioNet)

Bioinformatics is increasingly recognised as a crucial field for research and development in the biological sciences, and forms an integral part of genomics, proteomics and modern biotechnology. Worldwide participation is important, and scientists in developing countries can contribute to this field. Regional networks for bioinformatics are highly beneficial for capacity strengthening and cooperation, and for establishing productive interactions between scientists in the fields of biological and informatics sciences. Such a network (LACBioNet) is being organised for Latin America and the Caribbean. Its immediate goals include the organisation and extension of nodes and services, information and communication, research and development in different specialty fields of bioinformatics, and training and human resource development.     

多组学技术及其在生命科学研究中应用概述

随着新一代测序技术、高分辨质谱技术、多组学整合分析方法及数据库的发展,组学技术正从传统的单一组学向多组学技术发展。以多组学驱动的系统生物学研究将带来生命科学研究的新范式。本文简要概述了基因组学、表观基因组学、转录组学,蛋白质组学及代谢组学的进展,重点介绍多组学技术平台的组成和功能,多组学技术的应用现状及在合成生物学及生物医学等领域的应用前景。     

Abiogenic synthesis of oligopeptides in the open space

Exobiology is a relatively new field of sciences, which was established in connection with the development of the space technology, expanding the range of biological studies beyond the Earth. The major task of exobiology is the study of processes that give rise to the life, biological evolution, and distribution of living creatures in the universe. The term exobiology was introduced by the Dutch researcher Lederberg (1960). During fifty years of progressive development, it turned into a wide interdisciplinary field of sciences, including a number of disciplines, such as astrophysics, organic and analytical chemistry, geology, geochemistry, and other planet sciences not to mention various biological disciplines. Exobiology has become an inherent part of national and international space programs (Carle et al., 1992; Morrison, 2001).     

An omics evolutionary perspective on phytophagous insect–host plant interactions in Anastrepha obliqua: a review

Phytophagous insects have a close relationship with their host plants. For this reason, their interactions can lead to important changes in insect population dynamics and evolutionary trajectories. Next generation sequencing (NGS) has provided an opportunity to analyze omics data on a large scale, facilitating the change from a classical genetics approach to a more holistic understanding of the underlying molecular mechanisms of host plant use by insects. Most studies have been carried out on model species in Holarctic and temperate zones. In tropical zones, however, the effects of use of various host plants on evolutionary insect history is less understood. In the current review, we describe how omics methodologies help us to understand phytophagous insect–host plant interactions from an evolutionary perspective, using as example the Neotropical phytophagous insect West Indian fruit fly, Anastrepha obliqua (Macquart) (Diptera: Tephritidae), an economically important fruit crop pest in the Americas. Anastrepha obliqua could adopt a generalist or a specialist lifestyle. We first review the adaptive molecular mechanisms of phytophagous insects to host plants, and then describe the main tools to study phytophagous insect–host plant interactions in the era of omics sciences. The omics approaches will advance the understanding of insect molecular mechanisms and their influence on diversification and evolution. Finally, we discuss the importance of a multidisciplinary approach that integrates the use of omics tools and other, more classical methodologies in evolutionary studies.