微孢子虫生物多样性研究的述评

微孢子虫作为一类专营细胞内寄生的低等的原生动物,有着比较悠久的进化历史。微孢子虫是一种既具有真核生物特征又具有原核生物特征的生物,同样具有生物多样性的本质,文章尝试用生物多样性的概念和原理,阐述原始的真核寄生物微孢子虫的物种多样性、遗传多样性和生态系统多样性的研究概况。     

城市生物多样性分布格局研究进展

城市生物多样性分布格局由自然生态环境和城市化过程所决定;其动态和机理与自然生态系统迥然不同.城市生物多样性为城市生态系统提供了诸多生态系统功能和服务,对改善城市环境、维持城市可持续发展有着重要的意义和作用.城市化过程深刻改变了城市的生物多样性分布格局,导致了诸如本地物种多样性降低、外来物种多样性增加、物种同质化等一系列问题.近年来,城市生物多样性受到学界高度关注,大量研究结果既回答了一些关键性问题,又提出了诸多新的论题和挑战.分析了当前城市生物多样性分布格局研究的若干热点问题,总结了影响城市生物多样性格局的主要因素,探讨了城市生物多样性格局研究方法的关键问题,指出了未来城市生物多样性研究的发展方向,特别强调了城市生物多样性的生态系统功能研究在未来城市生物多样性研究中的重要地位.     

Molecular profiling of silkworm biodiversity in India: An overview

Molecular tools opened a new vista to understand natures bio-diversity and its relevance and the same approach was availed of to build-up the foundation work on the bio-diversity of silkworm spp in India. It is well established that the heritage of usage of silk for dress materials in India, Russia, and China dates back to pre-medieval period and in spite of industrial development resulting to de-forestation, India still can claim as the owner of wide bio-diversity, espicially in northern India for silkworm spp. The molecular diversity was assessedamong Antheraea mylitta, A. assama, A. pernyi, A. proylei, A. roylei and Philcosomia cynthia wiht 11 ISSR and 8 non-random primers on agarose gel. Neis statistics as also Euclidean distance matrix was applied to find the genetic diversity between the six species, wherein the closest relationship between A. pernyi and A. proylei is established. With the help of POPGEN statistics, the average genetic heterozygosity appeared as 0.271 while Shanons index is 0.4312 and alleles with segregation ratios of 3:1, 2:1, 1:1, 9:1 (generated with ISSR primers) were identified which can be utilized for future molecular breeding program. Further, and attempt was made to isolate a number of bands generated with 3 ISSR and six non-random primers, specific for different species and 22 such markers have been characterized through sequencing which will be made available through international public domain database.From Genetika, Vol. 40, No. 12, 2004, pp. 1618–1627.Original English Text Copyright © 2004 by Chatterjee, Tanushree.This article was submitted by the authors in English.     

An overview of human protein databases and their application to functional proteomics in health and disease

Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased organs. In recent years, a variety of publicly available bioinformatics databases have been developed to support protein-related information management and biological knowledge discovery. In addition to being used to annotate the proteome, these resources also offer the opportunity to develop global approaches to the study of the functional role of proteins both in health and disease. Here, we present a comprehensive review of the major human protein bioinformatics databases. We conclude this review by discussing a few examples that illustrate the importance of these databases in functional proteomics research.     

An overview of biodiversity and conservation status of steppes of the Anatolian Biogeographical Region

The Anatolian Biogeographical Region is unique in the Palearctic realm, with high plant and butterfly species richness and populations of globally threatened birds, mammals and herptiles (amphibians and reptiles). It is a place of diverse land-use practices, dating back to the earliest farming practices in the world. Among 10,930 species of vascular plants, birds, butterflies, mammals and herptiles distributed in Turkey, we identified 1130 living predominantly in steppic environments and being classified either as threatened, near-threatened or data deficient at the national level, if not globally. A total of 28 effective protected areas were present in the region, covering 1.5 % of the 391,597 km² land area. Only 16.2 % of the threatened and near-threatened species (n = 809) were distributed within the protected area network, ranging from 94.1 % for birds to as low as 12.9 % for vascular plants. The total area of steppe and steppe forest vegetation has been reduced by at least 44 % of its former extent due to diverse habitat destructive activities. The most significant threats arise from unsustainable agricultural activities including overgrazing, conversion to croplands and afforestation. To maintain steppe diversity, we propose a “to-do list”, including mainstreaming biodiversity, effective implementation of Turkey’s Rangeland Act, conducting effective environmental impact assessments, establishing an effective site network for steppe biodiversity conservation and filling gaps in scientific knowledge.     

我国海洋大型底栖生物多样性研究及展望:以黄海为例

本文综述了我国海洋大型底栖生物生态学和生物多样性研究进展,指出在该领域已有的研究中以胶州湾、长江口、福建和浙江沿岸等海域研究较多,其他海域还需要加强.介绍了常规大型底栖生物群落研究(包括种类组成、栖息密度(丰度)、生物量、生物多样性、次级生产力、能量级等)中的研究方法,环境变化、环境污染、海洋工程建设等对大型底栖生物的影响等方面的主要研究成果和进展,并重点以黄海为例,列举了已有的主要调查项目和研究成果.我国已有的研究表明,渤海海域底栖动物区系简单,大型底栖生物共413种,种数在四个海区中最少,优势种主要是低温、广盐暖水种;年总平均生物量为19.83 g/m2,以软体动物占有绝对优势;年总平均栖息密度474个/m2,多毛类和软体动物为主要贡献类群.黄海大型底栖生物共853种,优势种为狭盐性北温带种;北黄海年总平均生物量为99.66 g/m2,以棘皮动物最高;南黄海年总平均生物量为27.69 g/m2,多毛类贡献量最高;北黄海年总平均密度为2,017.40个/m2,而南黄海只有88.67个/m2差异较大;北黄海大型底栖生物的总平均密度和生物量远高于其他海域.南黄海年平均次级生产力为4.98 g(去灰干重)/m2,两个高生产力区位于黄海冷水团两侧.东海共发现大型底栖生物l,300种,主要优势种类有45种,与黄海优势种生物之间有很大差别;东海平均生物量的季节变化不显著,基本趋势为春季＞冬季＞夏季＞秋季;东海各海域的年总平均生物量浙江海域(28.22 g/m2)＞长江口海域(15.55 g/m2)＞台湾海峡(8.98 g/m2);年总平均栖息密度为164个/m2,呈现由北向南逐渐增加的趋势.南海大型底栖生物共发现1,661种,明显高于渤、黄、东海,部分优势种类与东海相同,与黄海、渤海差别较大;年总平均生物量为20.06 g/m2,基本趋势为春季＞冬季＞秋季＞夏季,软体动物和棘皮动物为主要贡献类群;年总平均栖息密度为198个/m2,夏季＞春季＞冬季＞秋季,多毛类生物为主要贡献者.指出随着人类活动和全球气候变化对海洋环境的影响越来越剧烈,对海洋生物资源和生物多样性的保护显得尤为急迫,而对海洋大型底栖生物长期的变化规律、变化机理、未来变化趋势预测的研究,是探究海洋大型底栖生物生态服务功能,提出资源有效保护和合理开发建议,使之永续利用的基础和迫切任务.     

Bioinformatics databases and tools in virology research: an overview

Viruses are major factors of human infectious diseases. Understanding of the structure-function correlation in viruses is important for the identification of potential anti-viral inhibitors and vaccine targets. In virology research, virus-related databases and bioinformatic analysis tools are essential for discerning relationships within complex datasets about viruses and host-virus interactions. Bioinformatic analyses on viruses include the identification of open reading frames, gene prediction, homology searching, sequence alignment, and motif and epitope recognition. The predictions of features such as transmembrane domains, glycosylation sites, and protein secondary and tertiary structure are important for analyzing the structure-function relationship of proteins encoded in viral genomes. Biochemical pathway analysis can help elucidate information at the biological systems level. Microarray analysis provides methods for high throughput screening and gene expression profiling. Virus-related bioinformatics databases include those concerned with viral sequences, taxonomy, homologous protein families, structures, or dedicated to specific viruses such as influenza and herpes simplex virus (HSV). This review provides a guide and overview of computational programs for these analyses as a resource for genomics and proteomics studies in virology research. These resources are useful for understanding viral diseases, as well as for the design and development of anti-viral agents.     

Designing databases to store biological information

The increasing amount of data produced by large-scale biological experiments has highlighted the inadequacies of traditional scientific data management methods such as laboratory notebooks. Databases designed to store biological information are becoming increasingly common, but there is little guidance in the literature about the best practices of biological database design. This paper suggests best practices, and provides examples for the implementation of these practices.     

Maximizing biodiversity, information and sustainability

Numerous global changes—notably anthropogenic extinction—force reconsideration of our management practices and the ways we regulate human influence in today’s world. Here, I define management to maximize biodiversity and illustrate the science that provides information to set goals for such management. Maximizing biodiversity simultaneously achieves sustainability and systemic health by avoiding the abnormal or pathological. The normal or sustainable are determined through the use of empirical integrative patterns to objectively account for the complexity of systems within which we find ourselves as a species. The science that reveals these integrative patterns provides measures of problems that can be solved by maximizing biodiversity—problems heretofore recognized only qualitatively. I use the Shannon-Weiner information index to test, and, with no surprise, reject the null hypothesis that there is no direct anthropogenic effect on biodiversity. The results of this science serve as examples of the kind of information most useful for guiding management and illustrate maximized biodiversity as a standard for management. Reference points based on maximized biodiversity are preferable to statistical parameters in meeting the objective of avoiding the abnormal or pathological in our interactions with other species, ecosystems and the biosphere. Management to maximize biodiversity is implemented by modifying human interactions with other biotic systems to achieve consistency in such interactions by mimicking natural role models of sustainability. Human influence is a significant factor in today’s world and the magnitude of such influence is illustrated by comparing humans with other species.     

生物多样性数据集成模式初探

本文以生物多样性研究发展现状的分析为基础,为生物多样性保护政策的制定提供可靠的数据支持为目标,通过对国内外几个著名的生物多样性数据库建设情况的分析,从相关学者的需求出发,提出了设计一个多层次多角度并带有一定人工智能的生物多样性集成数据库的构想。该系统基于都柏林核心(Dublin Core)的数据规范,并符合基于开放文献预研的元数据互操作协议(The Open Archixles Initiative Protocol for Metadata Hatvesting,OAIPMH)的标准,是一个集文字、图件、图片、声音、影像为一体的,能够在网上和硬件载体(如光盘)上同时进行发布的分布式数据库平台。其网上数据库系统的子系统之间以及子系统和硬件载体之间可以通过元数据获取的开放档案倡议协议互相交换数据。     

An ecological perspective on bacterial biodiversity

Bacteria may be one of the most abundant and species-rich groups of organisms, and they mediate many critical ecosystem processes. Despite the ecological importance of bacteria, past practical and theoretical constraints have limited our ability to document patterns of bacterial diversity and to understand the processes that determine these patterns. However, recent advances in molecular techniques that allow more thorough detection of bacteria in nature have made it possible to examine such patterns and processes. Here, we review recent studies of the distribution of free-living bacterial diversity and compare our current understanding with what is known about patterns in plant and animal diversity. From these recent studies a preliminary picture is emerging: bacterial diversity may exhibit regular patterns, and in some cases these patterns may be qualitatively similar to those observed for plants and animals.     

Appropriate application of information from biodiversity databases is critical when investigating species distributions and diversity: a comment on Dallas et al. ()

Using data from biodiversity informatics resources, Dallas et al. (Ecol. Lett., 20, 2017, 1526–1533) suggested limited relationships between climate and local abundance among several taxonomic groups. Investigation of a subset of these data suggests that their results may be misleading due to inappropriate application of the biodiversity data.     

海洋生物多样性信息资源

海洋生物多样性甚高, 但却饱受人为的破坏及干扰。目前全球最大的含点位数据的在线开放性数据库是海洋生物地理信息系统(OBIS), 共约12万种3,700万笔资料; 另一个较大的数据库世界海洋生物物种登录(WoRMS)已收集全球22万种海洋生物之物种分类信息。除此之外, 以海洋生物为主的单一类群的数据库只有鱼库(FishBase)、藻库(AlgaeBase)及世界六放珊瑚(Hexacorallians of the World)3个。跨类群及跨陆海域的全球性物种数据库则甚多, 如网络生命大百科(EOL)、全球生物物种名录(CoL)、整合分类信息系统(ITIS)、维基物种(Wikispecies)、ETI生物信息(ETI Bioinformatics)、生命条形码(BOL)、基因库(GenBank)、生物多样性历史文献图书馆(BHL)、海洋生物库(SeaLifeBase); 海洋物种鉴定入口网(Marine Species Identification Portal)、FAO渔业及水产养殖概要(FAO Fisheries and Aquaculture Fact Sheets)等可查询以分类或物种解说为主的数据库。全球生物多样性信息网络(GBIF)、发现生命(Discover Life)、水生物图库(AquaMaps)等则是以生态分布数据为主, 且可作地理分布图并提供下载功能, 甚至于可以改变水温、盐度等环境因子的参数值, 利用既定的模式作参数改变后之物种分布预测。谷歌地球(Google Earth)及国家地理(National Geographic)网站中的海洋子网页, 以及珊瑚礁库(ReefBase)等官方机构或非政府组织之网站, 则大多以海洋保育的教育倡导为主, 所提供的信息及素材可谓包罗万象, 令人目不暇给。更令用户感到方便的是上述许多网站或数据库彼此间均已可交互链接及查询。另外, 属于搜索引擎的谷歌图片(Google Images)与谷歌学术(Google Scholar)透过海洋生物数据库所提供的直接链接, 在充实物种生态图片与学术论文上亦发挥极大帮助, 让用户获得丰富多样的信息。为了保育之目的, 生物多样性数据库除了整合与公开分享外, 还应鼓励并推荐大家来使用。本文乃举Rainer Froese在巴黎演讲之内容为例, 介绍如何使用海洋生物多样性之数据来预测气候变迁对鱼类分布的影响。最后就中国大陆与台湾目前海洋生物多样性数据库的现况、两岸的合作及如何与国际接轨作介绍。     

Geospatially structured biodiversity information as a component of a regional biodiversity clearing house

To function effectively, the international biodiversity Clearing HouseMechanism (CHM), based on the Convention on Biological Diversity (CBD), needs tobe rooted at the regional and local levels. This article presents an example ofhow stakeholders of regional data and information can be encouraged to formnetworks linked to national biodiversity focal points (NFPs). We pay specialattention to exploiting the geospatial properties of biodiversity data andinformation, and demonstrate how data and information can best be filtered,classified and labelled to facilitate geographically based information retrievalon the Internet. The geocodability of bibliographic reports proved to be poor,indicating an urgent need to reconsider the geographical properties ofbiodiversity information under production. Also, it is useful to utilisenetworking processes with information from fields other than biodiversity wheninitiating the network. Finally, we present and discuss problems of integrityand interoperability of data, and also the process of biodiversity informationproduction from the point of view of general information theory and innovationsoffered by modern information technology.