元基因组文库分析技术研究进展

随着新的分析技术的不断出现和成熟,促进了微生物分子生态学及相关学科的诞生和迅速发展。其中,元基因组文库分析技术即是近年来微生物分子生态学研究领域兴起的一种新的分析技术。就元基因组分析技术诞生的背景及该技术的原理进行了讨论,着重阐述了元基因组文库分析技术在寻找新基因、开发新的生物活性物质、研究群落中微生物多样性、人类元基因组测序等方面的应用。另外,归纳总结了目前国际上常用的诸如PCR为基础的筛选、荧光原位杂交（fluorescent in situ hybridization,FISH）、底物诱导的基因表达筛选（substrate induced gene expression screening,SIGEX）、基因芯片等元基因组文库筛选方法,并就不同方法的优缺点进行了分析和讨论,指出了目前元基因组文库分析技术存在的主要问题并对今后该技术的发展进行了展望。     

植物DNA条形码研究领域文献计量学及可视化分析

为全面了解植物DNA条形码研究领域的发展和最新动态,探讨中国DNA条形码发展的状态和前景,该文利用Web of Science数据库对该研究领域进行文献计量学统计,并对引用频次、研究热点和研究前沿进行了可视化分析。结果表明:(1)中国、美国、加拿大学者在该领域文献贡献率最大,中国研究机构发文量领先,但美国、加拿大科研机构论文质量较高,影响力较大。(2) 2009年是该领域研究的高峰期,该研究领域的前沿和研究热点主要集中在物种的识别和生物多样性应用、DNA条形码候选序列筛选和鉴定技术的规范化。(3)中国学者在植物DNA条形码领域研究具有领军作用和很高的影响力,国家提倡中药产业的发展也推动了我国DNA条形码蓬勃发展,但论文的质量和影响力与美国、英国、加拿大等发达国家研究还有一定差距,应加大与发达国家科研机构合作,提高研究能力,DNA条形码技术在植物的鉴定、分类和生物多样性的保护起到非常重要的作用。这表明建立一个更全面、通用的全球植物DNA条码库以及开发新的标记并采用新的测序技术是植物DNA条形码研究的未来前景。     

Implications of transgenic, insecticidal plants for insect and plant biodiversity

Genetically modified plants are widely grown predominantly in North America and to a lesser extent in Australia, Argentina and China but their regions of production are expected to spread soon beyond these limited areas also reaching Europe where great controversy over the application of gene technology in agriculture persists. Currently, several cultivars of eight major crop plants are commercially available including canola, corn, cotton, potato, soybean, sugar beet, tobacco and tomato, but many more plants with new and combined multiple traits are close to registration. While currently agronomic traits (herbicide resistance, insect resistance) dominate, traits conferring “quality” traits (altered oil compositions, protein and starch contents) will begin to dominate within the next years. However, economically the most promising future lies in the development and marketing of crop plants expressing pharmaceutical or “nutraceuticals” (functional foods), and plants that express a number of different genes. From this it is clear that future agricultural and, ultimately, also natural ecosystems will be challenged by the large-scale introduction of entirely novel genes and gene products in new combinations at high frequencies all of which will have unknown impacts on their associated complex of non-target organisms, i.e. all organisms that are not targeted by the insecticidal protein. In times of severe global decline of biodiversity, pro-active precaution is necessary and careful consideration of the likely expected effects of transgenic plants on biodiversity of plants and insects is mandatory.In this paper possible implications of non-target effects for insect and plant biodiversity are discussed and a case example of such non-target effects is presented. In a multiple year research project, tritrophic and bitrophic effects of transgenic corn, expressing the gene from Bacillus thuringiensis (Bt-corn) that codes for the high expression of an insecticidal toxin (Cry1Ab), on the natural enemy species, Chrysoperla carnea (the green lacewing), was investigated. In these laboratory trials, we found prey-mediated effects of transgenic Bt-corn causing significantly higher mortality of C. carnea larvae. In further laboratory trials, we confirmed that the route of exposure (fed directly or via a herbivorous prey) and the origin of the Bt (from transgenic plants or incorporated into artificial diet) strongly influenced the degree of mortality. In choice feeding trials where C. carnea could choose between Spodoptera littoralis fed transgenic Bt-corn and S. littoralis fed non-transgenic corn, larger instars showed a significant preference for S. littoralis fed non-transgenic corn while this was not the case when the choice was between Bt- and isogenic corn fed aphids. Field implications of these findings could be multifold but will be difficult to assess because they interfere in very intricate ways with complex ecosystem processes that we still know only very little about. The future challenge in pest management will be to explore how transgenic plants can be incorporated as safe and effective components of IPM systems and what gene technology can contribute to the needs of a modern sustainable agriculture that avoids or reduces adverse impacts on biodiversity? For mainly economically motivated resistance management purposes, constitutive high expression of Bt-toxins in transgenic plants is promoted seeking to kill almost 100% of all susceptible (and if possible heterozygote resistant) target pest insects. However, for pest management this is usually not necessary. Control at or below an established economic injury level is sufficient for most pests and cropping systems. It is proposed that partially or moderately resistant plants expressing quantitative rather than single gene traits and affecting the target pest sub-lethally may provide a more meaningful contribution of agricultural biotechnology to modern sustainable agriculture. Some examples of such plants produced through conventional breeding are presented. Non-target effects may be less severe allowing for better incorporation of these plants into IPM or biological control programs using multiple control strategies, thereby, also reducing selection pressure for pest resistance development.     

Global biodiversity research during 1900–2009: a bibliometric analysis

We performed a bibliometric analysis of published biodiversity research for the period of 1900–2009, based on the Science Citation Index (SCI) database. Our analysis reveals the authorial, institutional, spatiotemporal, and categorical patterns in biodiversity research and provides an alternative demonstration of research advancements, which may serve as a potential guide for future research. The growth of article outputs has exploded since the 1990s, along with an increasing collaboration index, references, and citations. Ecology, environmental sciences, biodiversity conservations, and plant science were most frequently used subject categories in biodiversity studies, and Biological Conservation, Journal of Soil and Water Conservation, Conservation Biology and Biodiversity and Conservation were most active journals in this field. The United States was the largest contributor in global biodiversity research, as the U.S. produced the most single-country and collaborative articles, had the greatest number of top research institutions, and had a central position in collaboration networks. We perceived an increasing number of both internationally collaborative and inter-institutionally collaborative articles, with the latter form of collaboration being more prevalent than the former. A keyword analysis found several interesting terminology preferences, confirmed conservation’s central position as a topic in biodiversity research, revealed the adoption of advanced technologies, and demonstrated keen interest in both the patterns and underlying processes of ecosystems. Our study reveals patterns in scientific outputs and academic collaborations and serves as an alternative and innovative way of revealing global research trends in biodiversity.     

Transgenic plants and biosafety: science, misconceptions and public perceptions

One usually thinks of plant biology as a non-controversial topic, but the concerns raised over the biosafety of genetically modified (GM) plants have reached disproportionate levels relative to the actual risks. While the technology of changing the genome of plants has been gradually refined and increasingly implemented, the commercialization of GM crops has exploded. Today's commercialized transgenic plants have been produced using Agrobacterium tumefaciens-mediated transformation or gene gun-mediated transformation. Recently, incremental improvements of biotechnologies, such as the use of green fluorescent protein (GFP) as a selectable marker, have been developed. Non-transformation genetic modification technologies such as chimeraplasty will be increasingly used to more precisely modify germplasm. In spite of the increasing knowledge about genetic modification of plants, concerns over ecological and food biosafety have escalated beyond scientific rationality. While several risks associated with GM crops and foods have been identified, the popular press, spurred by colorful protest groups, has left the general public with a sense of imminent danger. Reviewed here are the risks that are currently under research. Ecological biosafety research has identified potential risks associated with certain crop/transgene combinations, such as intra- and interspecific transgene flow, persistence and the consequences of transgenes in unintended hosts. Resistance management strategies for insect resistance transgenes and non-target effects of these genes have also been studied. Food biosafety research has focused on transgenic product toxicity and allergenicity. However, an estimated 3.5 x 10(12) transgenic plants have been grown in the U.S. in the past 12 years, with over two trillion being grown in 1999 and 2000 alone. These large numbers and the absence of any negative reports of compromised biosafety indicate that genetic modification by biotechnology poses no immediate or significant risks and that resulting food products from GM crops are as safe as foods from conventional varieties. We are increasingly convinced that scientists have a duty to conduct objective research and to effectively communicate the results--especially those pertaining to the relative risks and potential benefits--to scientists first and then to the public. All stakeholders in the technology need more effective dialogues to better understand risks and benefits of adopting or not adopting agricultural biotechnologies.     

A review of the impact of pipelines and power lines on biodiversity and strategies for mitigation

Linear infrastructure such as pipelines and power lines is ubiquitous and responsible for loss of habitats and disruption of landscape connectivity. We reviewed published research to answer the following questions: (1) Which organisms are commonly used to indicate impacts of pipelines and power lines to biodiversity? (2) How do pipelines and power lines impact biodiversity? and (3) How are these impacts mitigated? Studies of pipelines most often used mammals and plants as bioindicators, whereas studies of power lines focused largely on birds and plants. A myriad of impacts were identified, including the mortality of plants during construction, changes to the structure and composition of plant and animal communities that resulted from construction, the creation of open and shrubby corridors within intact forests, and collisions and electrocutions of birds with power lines. However, in most studies baseline data were not collected, so magnitudes of the impacts are often unknown. Mitigation in many studies was mentioned only in the discussion as a way to reduce impacts, but mitigation techniques were rarely tested directly. We outline considerations when selecting bioindicators—research that takes a community- or ecosystem-level approach will more fully determine the scope of impacts of linear infrastructure than the historical approach of focusing on populations of select bioindicators. Mitigation strategies must ultimately result from appropriate baseline studies, scientific data collection and analyses, and be implemented within an adaptive management strategy.     

生物质能源植物种植对生物多样性的影响

随着化石燃料资源的减少和全球环境问题的加剧, 全球生物质能源的生产增长迅速, 生物质能源植物种植面积不断增长。全球生物质能源植物的大面积种植对生物多样性造成了严重影响: 不但直接或间接侵占了大片自然或半自然生态系统, 造成生物原生栖息地的退化和消失, 而且还易造成生态系统单一并改变生态系统结构与功能, 加剧面源污染, 引起外来种入侵, 甚至增加了转基因生物安全风险。为减少生物质能源植物种植对生物多样性的影响, 政府或相关单位需制订可持续发展的生物质能源生产管理规范, 合理规划以避免在生物多样性丰富或脆弱区种植生物质能源植物, 积极开发新技术并改变生物质能源原料的利用效益, 加强生产方式管理并改变传统种植模式。     

Plant tissue culture. Biotechnology. Milestones

Summary The progress in the development of the technologies of plant tissue and cell culture over the past four decades has been remarkable. This article covers my personal reflections on the various topics and is based on my involvement in the field during that period. There are three fundamental technologies which constitute most of what is referred to as plant in vitro technologies or tissue culture. The origin and some of the key persons involved in the development of each of these procedures will be discussed. The technology that is most common is growing plant tissue on gel-solidified nutrient media. That technology is being used in the most vital procedures, namely the regeneration of plants from cultured cells. The culture of plant cells in liquid suspension was developed very shortly after that, and has become a very effective technology for plant regeneration by somatic embryogenesis. The method of meristem culture arose out of a need for developing plants that were virus-free. In many species the technique is now being used to produce virus-free crop plants. Another important technology is the culture of anthers and microspores for producing haploid and homozygous plants. Included with plant tissue culture is the development of the plant protoplast and cell fusion technologies for the production of new plant hybrids. The final aspect of the development concerns the integration of tissue culture with molecular genetics, which has developed into the rapidly expanding field of biotechnology.     

CRISPR/Cas及其衍生编辑技术在基因治疗中的应用进展

基因治疗是指利用基因编辑技术对细胞基因进行“修饰”而达到治疗的目的。CRISPR/Cas的出现为基因编辑提供了简单、高效和多功能的平台,同时,为克服DNA双链断裂产生的不良影响,基于CRISPR/Cas的新型技术,如碱基编辑器（base editors,BE）、Prime Editors（PE）和Cas13效应器,被相继开发出来。目前,CRISPR/Cas及其衍生编辑技术已被广泛应用于动物细胞模型构建、药物靶点筛查和基因功能研究等领域,在基因治疗领域也展现出广阔的应用前景。基于此,简要介绍了CRISPR/Cas及其衍生编辑技术,综述了其在单基因遗传病、肿瘤和其他疾病的基因治疗中的应用进展,并分析了其当下面临的挑战,以期为基因编辑在单基因遗传病、肿瘤和其他疾病治疗领域提供理论参考。     

Microbial catalysis in bioelectrochemical technologies: status quo, challenges and perspectives

Over the past decade, microbial electrochemical technologies, originally developed from an interesting physiological phenomenon, have evolved from a rush of initiatives for sustainable bioelectricity generation to a multitude of specialized applications in very different areas. Genetic engineering of microbial biocatalysts for target bioelectrochemical applications like biosensing or bioremediation, as well as the discovery of entirely new bioelectrochemical processes such as microbial electrosynthesis of commodity chemicals, open up completely new possibilities. Where stands this technology today? And what are the general and specific challenges it faces not only scientifically but also for transition into commercial applications? This review intends to summarize the recent advances and provides a perspective on future developments.     

Identifying essential genes in Arabidopsis thaliana

Eight years after publication of the Arabidopsis genome sequence and two years before completing the first phase of an international effort to characterize the function of every Arabidopsis gene, plant biologists remain unable to provide a definitive answer to the following basic question: what is the minimal gene set required for normal growth and development? The purpose of this review is to summarize different strategies employed to identify essential genes in Arabidopsis, an important component of the minimal gene set in plants, to present an overview of the datasets and specific genes identified to date, and to discuss the prospects for future saturation of this important class of genes. The long-term goal of this collaborative effort is to facilitate basic research in plant biology and complement ongoing research with other model organisms.     

基因编辑技术及其在中国的研究发展

基因编辑技术是一种能够对生物体的基因组及其转录产物进行定点修饰或者修改的技术,早期基因编辑技术包括归巢内切酶、锌指核酸内切酶和类转录激活因子效应物。近年来,以CRISPR/Cas9系统为代表的新型技术使基因编辑的研究和应用领域得以迅速拓展。本文对基因编辑技术的原理、技术发展及其应用进行了阐述,对我国在基因编辑机制研究及技术发展、基因编辑动植物模型构建、基因治疗等领域的研究进展进行了回顾,并对基因技术的发展前景及趋势进行了展望。     

Engineering plants with increased disease resistance: what are we going to express?

To engineer plants with increased and durable disease resistance using transgenic technologies we must address two questions. First, what gene or genes do we want to express to improve disease resistance, and second, how are we going to express these genes so that crop yields are actually increased? Emerging technologies are providing us with a plethora of candidate genes that might lead to enhanced crop protection through genetic engineering. These genes can come from plants, from pathogens or from other organisms and several strategies for their manipulation show promise. Here, we discuss recent advances and consider future perspectives for producing plants with durable disease resistance.     

Microbial diversity--biotechnological and industrial perspectives

Biodiversity is an addition sum of the studies on genetic, taxonomic commercial and ecosystem aspects of living systems. All the living individuals of a species contain a distinct combination of genes and the intrinsic interaction among the gene pool influences evolution, survival and phenotypic/genotypic changes of the part of the biodiversity i.e. community. The amount of genetic diversity within population varies tremendously and much of modern conservation biology is concerned with the maintenance of genetic diversity within the population of plants, animals and microbes. Germplasm, obtained with the vast biodiversity, provides a major source of biological material for the development of medicines, vaccines, pharmaceutical products, improved crop and animal varieties and for other environmental applications. Industrialized nations, who have the technology and resources to patent and develop commercial biological products, are having the benefits of biodiversity through the collected and conserved germplasm flowing through the international research centers. In fact a particular genetic contribution usually represents only a small percentage of the total value of the eventual products. In addition, the research and development process required to commercialize a particular product requires enormous technical efforts. The principle of patenting genes is the morally or ethically correct is a matter of intense debate. However, geneticists, having conceived of the technologies with vast and immediate therapeutic, food and environmental values must try to bring to the material to market as soon as possible.     

等温扩增技术及其结合CRISPR在微生物快速检测中的研究进展

等温扩增技术因其对仪器依赖性低、核酸扩增高效等优势,非常适合于快速检测,已在微生物快速检测领域得到了广泛应用。本文从核酸提取、等温扩增(以环介导等温扩增技术(Loop-mediated isothermal amplification,LAMP)和重组酶聚合酶扩增技术(Recombinase polymerase amplification,RPA)为例)和产物检测角度,就近年来核酸等温扩增技术的发展及其在病原微生物核酸快速检测领域的应用进行综述,并概述了核酸等温扩增技术与CRISPR(Clustered regularly interspaced short palindromic repeats)基因编辑技术相结合的最新研究成果,为这些新兴技术的研究和未来的发展提供新思路。     

生物多样性国际研究态势分析

生物多样性研究是综合性和高度交叉性的跨学科研究领域,是1997年底Science周刊上预测的1998年及近期的6个重大科学热点之一。检索1986—2008年间SCIE文献数据库中关于生物多样性的研究论文(article,proceedings paper和review),利用Thomson Data Analyzer(TDA)分析工具和Aureka分析平台进行数据挖掘。分析表明,该研究涉及多个学科领域,近年来在生态学领域的论文数量增加最多,而生物多样性保护、进化生物学、生物化学与分子生物学方面的论文增长速度较快。生物多样性研究越来越重视全球变化和人类社会对生物多样性的影响,DNA技术和基因工程等先进技术在生物多样性研究和保护中的作用也更加突出。     

药用植物分子农场研究进展

植物分子农场可以利用植物生产具有药物用途的重组蛋白或者次生代谢化合物,应用广泛。随着对动植物中具有药物用途的代谢途径的深入解析,代谢途径中关键限速酶或调控蛋白的功能不断被明确,如何选择植物分子农场的底盘植物和遗传改造途径等问题,特别是如何协同提高植物制药产量与品质一直是植物分子农场体系建立中面临的关键科学问题。综述了药用的植物分子农场的最新研究进展,着重介绍了底盘植物的选择与药用植物分子农场的构建策略,以期为提高分子农场应用效果提供有力的科技支撑。