活植物信息数据库中的植物编码系统

本文概述了南京中山植物园活植物信息数据库中的植物编码系统,重点介绍了植物编码的生成方法。该系统通过将关系数据库ORACLE与Microsoft C所提供的完备的计算模型与关系查询语言的强功能管理手段结合起来,弥补了现行商用数据库的不足,获得了较高的时空效率。     

Climate change and the outdoor regional living plant collections: an example from mainland Portugal

Climate change threatens not only plant species occurring naturally, but also impacts on regional living plant collections, which play an important role in ex situ conservation strategies. In the last few years, several global circulation models have been used to predict different global climate change scenarios. Due to their coarse resolutions, and while more detailed regional approaches are not available, downscaling techniques have been proposed, as a very simple first approach to increase detail. We analysed seven sites on mainland Portugal with potential for species conservation (four botanic gardens and three universities), in the light of downscaled climate change scenarios, using an environmental envelope approach and a predefined bioclimatic neighbourhood for each site. Thresholds for the bioclimatic neighbourhood were based on Rivas-Martínez’s Bioclimatic Classification of the Earth. For each site, the expected geographical shift of its original bioclimatic neighbourhood (1950–2000) was mapped for 2020, 2050 and 2080. Analysing those shifts enabled us to delineate knowledge-transfer paths between sites, according to the analysed scenarios. We concluded that, according to the Intergovernmental Panel on Climate Change A2 scenario, all considered sites will be outside the predefined bioclimatic neighbourhood by 2080, while according to the B2 scenario all of them will be inside that neighbourhood, although sometimes marginally so. Therefore, the implementation of global sustainability measures as considered in the B2 scenario family can be of great importance in order to delay significantly the impacts of climate change, giving extra time for the adaptation of the outdoor regional living plant collections.     

植物园活植物信息管理计算机化的现状及前景

植物园活植物信息管理系统是植物园适应时代和自身发展需要,首先在西方发展起来的一种新的植物园活植物信息管理手段,本文综述了植物园活植物信息管理系统发展的基础和国内外发展的现状,分析了活植物信息计算机化过程中存在的问题及发展前景     

An evaluation of Ficoll density gradient centrifugation as a method for eliminating microbial contamination and purifying plant protoplasts

Ficoll density gradient centrifugation was used to generate sterile protoplasts from non-sterile Pteridium cultures. The method was found to drastically reduce levels of fungal and bacterial contamination introduced prior to centrifugation whilst concentrating and purifying protoplasts.     

The present status of higher plant bioassays for the detection of environmental mutagens

Higher plants provide valuable genetic assay systems for screening and monitoring environmental pollutants. They are now recognized as excellent indicators of cytogenetic and mutagenic effects of environmental chemicals and are applicable for the detection of environmental mutagens both indoor and outdoor. Comparisons between plant and nonplant genetic assay systems indicate that higher plant genetic assays have a high sensitivity (i.e. few false negatives). Two assays which are considered ideal for in situ monitoring and testing of airborne and aqueous mutagenic agents are the Tradescantia stamen hair assay for mutations and the Tradescantia micronucleus assay for chromosome aberrations. Both assays can be used for in vivo and in vitro testing. Other higher plant gentoxicity assys which have a large number of genetic markers and/or data base and are also highly suitable for testing for genotoxic agents include Arabidopsis thaliana, Allium cepa, Hordeum vulgare, Vicia faba, and Zea mays. Since higher plant systems are now recognized as excellent indicators of the cytotoxic, cytogenetic, and mutagenic effects of environmental chemicals and have unique advantages for in situ monitoring and screening it is recommended that higher plant systems be accepted by regulatory authorities as an alternative first-tier assay system for the detection of possible genetic damage resulting from pollution or the use of environmental chemicals. The results from higher platn genetic assays could meke a significant contribution in protecting the public from agents that can cause mutation and cancer. The advantages possessed by higher plant genetic assays, which are inexpensive and easy to handle, make them ideal for use by scientists in developing countries.     

Genomics, environmental genomics and the issue of microbial species

A microbial species concept is crucial for interpreting the variation detected by genomics and environmental genomics among cultivated microorganisms and within natural microbial populations. Comparative genomic analyses of prokaryotic species as they are presently described and named have led to the provocative idea that prokaryotes may not form species as we think about them for plants and animals. There are good reasons to doubt whether presently recognized prokaryotic species are truly species. To achieve a better understanding of microbial species, we believe it is necessary to (i) re-evaluate traditional approaches in light of evolutionary and ecological theory, (ii) consider that different microbial species may have evolved in different ways and (iii) integrate genomic, metagenomic and genome-wide expression approaches with ecological and evolutionary theory. Here, we outline how we are using genomic methods to (i) identify ecologically distinct populations (ecotypes) predicted by theory to be species-like fundamental units of microbial communities, and (ii) test their species-like character through in situ distribution and gene expression studies. By comparing metagenomic sequences obtained from well-studied hot spring cyanobacterial mats with genomic sequences of two cultivated cyanobacterial ecotypes, closely related to predominant native populations, we can conduct in situ population genetics studies that identify putative ecotypes and functional genes that determine the ecotypes' ecological distinctness. If individuals within microbial communities are found to be grouped into ecologically distinct, species-like populations, knowing about such populations should guide us to a better understanding of how genomic variation is linked to community function.     

Modification of a freshwater sampler using evacuated tubes for microbial collections

The modification of a freshwater sampler utilizing three evacuated tubes for the collection of microbial samples is described. To avoid contamination sterile hypodermic needles covered with rubber sleeves are inserted into the evacuated tubes prior to lowering the sampler. At the requisite depth each sleeve is pushed down over the end of the needle so that the tubes fill with water.     

How to evaluate the environmental safety of microbial plant protection products: A proposal

Plant protection products with active micro-organisms are allegedly less hazardous to the environment and wildlife than synthetic chemical pesticides. Nevertheless, they need a proper pre-marketing environmental safety evaluation because of their potential toxicity and pathogenicity. Scientific and technical guidance on such a safety evaluation for regulatory purposes is scarce. Therefore, a risk decision tree is proposed to provide such guidance and to discern the acceptable from the unacceptable environmental risks. The decision tree is based on the risk criteria of the European Union. It takes integrally into account the characterisation, identification and efficacy and also emission, exposure, environmental effects and, finally, the environmental risk assessment. Case by case expert judgement remains necessary in view of limited knowledge of microbial ecology, limited experience with regulatory test protocols and taxonomic difficulties in relation to the indigenousness of active micro-organisms. The decision tree offers regulatory guidance on the environmental safety evaluation of microbial plant protection products.     

An environmental signature for 323 microbial genomes based on codon adaptation indices

Background

Codon adaptation indices (CAIs) represent an evolutionary strategy to modulate gene expression and have widely been used to predict potentially highly expressed genes within microbial genomes. Here, we evaluate and compare two very different methods for estimating CAI values, one corresponding to translational codon usage bias and the second obtained mathematically by searching for the most dominant codon bias.

Results

The level of correlation between these two CAI methods is a simple and intuitive measure of the degree of translational bias in an organism, and from this we confirm that fast replicating bacteria are more likely to have a dominant translational codon usage bias than are slow replicating bacteria, and that this translational codon usage bias may be used for prediction of highly expressed genes. By analyzing more than 300 bacterial genomes, as well as five fungal genomes, we show that codon usage preference provides an environmental signature by which it is possible to group bacteria according to their lifestyle, for instance soil bacteria and soil symbionts, spore formers, enteric bacteria, aquatic bacteria, and intercellular and extracellular pathogens.

Conclusion

The results and the approach described here may be used to acquire new knowledge regarding species lifestyle and to elucidate relationships between organisms that are far apart evolutionarily.     

An environmental signature for 323 microbial genomes based on codon adaptation indices

Background  

Codon adaptation indices (CAIs) represent an evolutionary strategy to modulate gene expression and have widely been used to predict potentially highly expressed genes within microbial genomes. Here, we evaluate and compare two very different methods for estimating CAI values, one corresponding to translational codon usage bias and the second obtained mathematically by searching for the most dominant codon bias.     

The role of microbial metal resistance and detoxification mechanisms in environmental bioassay research

Hydrobiologia - Numerous biological methods and bioassays have been developed for assessing toxicants in both environmental and laboratory samples. In many bioassays, microorganisms are used...     

Accessing microbial diversity for bioremediation and environmental restoration

Biological methods for decontamination promise an improved substitute for ineffective and costly physico-chemical remediation methods, although so far only a fraction of the total microbial diversity (i.e. the culturable fraction with metabolic potential) has been harnessed for this purpose. Exploring and exploiting the "overlooked" genetic resource might ameliorate concerns associated with the degradation of recalcitrant and xenobiotic pollutants that are not degraded or only poorly degraded by known culturable bacteria. Recent advances in the molecular genetics of biodegradation and in knowledge-based methods of rational protein modification provide insight into the development of "designer biocatalysts" for environmental restoration. The application of such genetically engineered microorganisms (GEMs) in the environment has been limited, however, owing to the risks associated with uncontrolled growth and proliferation of the introduced biocatalyst and horizontal gene transfer. Programming rapid death of the biocatalyst soon after the depletion of the pollutant could minimize the risks in developing these technologies for successful bioremediation.     

Targeting transgene expression in research,agricultural, and environmental applications: Promoters used in plant transformation

Summary Plant genetic engineering has contributed substantially to the understanding of gene regulation and plant development, in the generation of transgenic organisms for widespread usage in agriculture, and has increased the potential uses of crops for industrial and pharmaceutical purposes. As the application of geneticallly engineered plants has widened, so has the need to develop methods to fine-tune control of transgene expression. The availability of a broad spectrum of promoters that differ in their ability to regulate the temporal and spatial expression patterns of the transgene can dramatically increase the successful application of transgenic technology. Indeed, a variety of promoters in necessary at all levels of genetic engineering in plants, from basic research discoveries, concepts and question to development of economically viable crops and plant commodities, to addressing legitimate concerns raised about the safety and containment of transgenic plants in the environment. This review covers the characterization and usage of a broad range of promoters employed in plant genetic engineering, including the widespread use of plant promoters with viral and plant origin that drive constitutive expression. Also covered are selected tissue-specific promoters from fruit, seed and grain, tubers, flowers, pistils, anther and pollen, roots and root nodules, and leaves and green tissue. Topics also include organellar promoters, and those found in specific cell types, as well as the development and evaluation of inducible (endogenous and exogenous origin) and synthetic plant promoter systems. Discussions on the relevance and potential pitfalls within specific applications are included.     

Rhizosphere microbial community structure in relation to root location and plant iron nutritional status

Root exudate composition and quantity vary in relation to plant nutritional status, but the impact of the differences on rhizosphere microbial communities is not known. To examine this question, we performed an experiment with barley (Hordeum vulgare) plants under iron-limiting and iron-sufficient growth conditions. Plants were grown in an iron-limiting soil in root box microcosms. One-half of the plants were treated with foliar iron every day to inhibit phytosiderophore production and to alter root exudate composition. After 30 days, the bacterial communities associated with different root zones, including the primary root tips, nonelongating secondary root tips, sites of lateral root emergence, and older roots distal from the tip, were characterized by using 16S ribosomal DNA (rDNA) fingerprints generated by PCR-denaturing gradient gel electrophoresis (DGGE). Our results showed that the microbial communities associated with the different root locations produced many common 16S rDNA bands but that the communities could be distinguished by using correspondence analysis. Approximately 40% of the variation between communities could be attributed to plant iron nutritional status. A sequence analysis of clones generated from a single 16S rDNA band obtained at all of the root locations revealed that there were taxonomically different species in the same band, suggesting that the resolving power of DGGE for characterization of community structure at the species level is limited. Our results suggest that the bacterial communities in the rhizosphere are substantially different in different root zones and that a rhizosphere community may be altered by changes in root exudate composition caused by changes in plant iron nutritional status.     

Natural history collections and the future legacy of ecological research

Oecologia - Natural history collections are now being championed as key to broad ecological studies, especially those involving human impacts in the Anthropocene. However, collections are going...