Environmental metabolomics: a SWOT analysis (strengths, weaknesses, opportunities, and threats)

Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively explored. This review will use a SWOT analysis model to discuss some of the strengths, weaknesses, opportunities, and threats that are apparent to an investigator venturing into this relatively new field. SWOT has been used extensively in business settings to uncover new outlooks and identify problems that would impede progress. The field of environmental metabolomics provides great opportunities for discovery, and this is recognized by a high level of interest in potential applications. However, understanding the biological consequence of environmental exposures can be confounded by inter- and intra-individual differences. Metabolomic profiles can yield a plethora of data, the interpretation of which is complex and still being evaluated and researched. The development of the field will depend on the availability of technologies for data handling and that permit ready access metabolomic databases. Understanding the relevance of metabolomic endpoints to organism health vs adaptation vs variation is an important step in understanding what constitutes a substantive environmental threat. Metabolomic applications in reproductive research are discussed. Overall, the development of a comprehensive mechanistic-based interpretation of metabolomic changes offers the possibility of providing information that will significantly contribute to the protection of human health and the environment.     

Incorporating costs in LCA

The goal of LCA is to identify the environmental impacts resulting from a product, process, or activity. While LCA is useful for evaluating environmental attributes, it stops short of providing information that business managers routinely utilize for decision-making — i.e., dollars. Thus, decisions regarding the processes used for manufacturing products and the materials comprising those products can be enhanced by weaving cost and environmental information into the decision-making process. Various approaches have been used during the past decade to supplement environmental information with cost information. One of these tools is environmental accounting, the identification, analysis, reporting, and use of environmental information, including environmental cost data. Environmental cost accounting provides information necessary for identifying the true costs of products and processes and for evaluating opportunities to minimize those costs. As demonstrated through two case studies, many companies are incorporating environmental cost information into their accounting systems to prioritize investments in new technologies and products.     

Environmental biotechnology in the postgenomics era

The sequencing of the human genome and many microbial genomes has provided new opportunities to study the environmental impact on life processes, leading to development of new technologies that can be protected by patenting. Development of such new technologies has, however, led in some cases to judicial intervention because of their controversial nature. This article illustrates some of the trends in postgenomics biotechnology development and the attendant legal and ethical considerations.     

Novel and Transgenic Food Crops: Overview of Scientific Versus Public Perception

Recombinant DNA technology offers opportunities to develop new products in many different fields, including agriculture and the agro-food area. Transgenic plants with improved agronomic traits currently grow in field trials and a few varieties have already reached the European market. By and large, new technologies raise both concerns and expectations and modern biotechnology is no exception. Indeed, a voluntary moratorium on experiments involving recombinant DNA molecules was called for in 1974. At the present time, although a majority of academic and industrial scientists agree that transgenic food crops pose no risk for the environment or human health, some others believe that certain applications of modern plant biotechnology are hazardous. In particular, deliberate releases of genetically modified plants are regarded as risky. There is also a disparity between expert and lay perception of r-DNA technology applications to food crops, which makes public information a difficult task. This paper aims at exposing these conflicting points of view on the agricultural applications of modern biotechnology. We also propose some recommendations pertaining to public information in Europe. It appears that consensus conferences might be a good approach to stimulate public information and public debate in Europe, although this approach has to be adapted to the cultural context of each country.     

Carbon nanotube-based environmental technologies: the adopted properties,primary mechanisms,and challenges

Carbon nanotubes (CNTs) show great potential and bright prospect in the field of environment. It is believed that this new kind of material will bring opportunities and benefits to the environmental protection and pollution control. In recent years, a lot of CNT-based environmental technologies have been developed and applied with successful results, but the adequate understanding and large-scale industrial applications of these technologies are lacking. This paper systematically reviews current environmental applications of CNTs, including pollution treatment and environmental remediation, environmental sample analysis, environmental monitoring and sensing, and design of environment-friendly products. The adopted properties of CNTs are introduced. The main roles of CNTs in these technologies are illustrated. Additionally, the main current challenges to realizing their practical applications are analyzed and discussed, involving toxicity and ecological risks, production costs, general applicability, long-term effect, and public acceptance. Further studies should give priority to the toxicity and environmental risk of CNTs when developing new CNT-based technologies. Research on standardizing toxicity testing and risk assessment of CNTs is highly recommended and a large number of toxicity data of CNTs are needed.     

SOD mimics: From the tool box of the chemists to cellular studies

Superoxide dismutases (SODs) are metalloproteins that protect cells against oxidative stress by controlling the concentration of superoxide (O₂⁻) through catalysis of its dismutation. The activity of superoxide dismutases can be mimicked by low-molecular-weight complexes having potential therapeutic applications. This review presents recent strategies for designing efficient SOD mimics, from molecular metal complexes to nanomaterials. Studies of these systems in cells reveal that some SOD mimics, designed to react directly with superoxide, may also indirectly enhance the cellular antioxidant arsenal. Finally, a good understanding of the bioactivity requires information on the cell-penetration, speciation, and subcellular location of the SOD mimics: we will describe recent studies and new techniques that open opportunities for characterizing SOD mimics in biological environments.     

New opportunities revealed by biotechnological explorations of extremophiles

Over the past few decades the extremes at which life thrives has continued to challenge our understanding of biochemistry, biology and evolution. As more new extremophiles are brought into laboratory culture, they have provided a multitude of potential applications for biotechnology. More recently, innovative culturing approaches, environmental genome sequencing and whole genome sequencing have provided new opportunities for the biotechnological exploration of extremophiles.     

A public goods approach to major evolutionary innovations

The history of life is marked by a small number of major transitions, whether viewed from a genetic, ecological, or geological perspective. Specialists from various disciplines have focused on the packaging of information to generate new evolutionary individuals, on the expansion of ecological opportunity, or the abiotic drivers of environmental change to which organisms respond as the major drivers of these episodes. But the critical issue for understanding these major evolutionary transitions (METs) lies in the interactions between environmental, ecologic, and genetic change. Here, I propose that public goods may serve as one currency of such interactions: biological products that are non‐excludable and non‐rivalrous. Such biological public goods may be involved in either the generation of new evolutionary variation, as with genetic sequences that are easily transferred between different microbial lineages, or in the construction of new ecological niches, as with the progressive oxygenation of the oceans and atmosphere. Attention to public goods emphasizes the processes by which organisms actively construct their own evolutionary opportunities. Such public goods may have facilitated some METs.     

Ecology in the age of DNA barcoding: the resource,the promise and the challenges ahead

Ten years after DNA barcoding was initially suggested as a tool to identify species, millions of barcode sequences from more than 1100 species are available in public databases. While several studies have reviewed the methods and potential applications of DNA barcoding, most have focused on species identification and discovery, and relatively few have addressed applications of DNA barcoding data to ecology. These data, and the associated information on the evolutionary histories of taxa that they can provide, offer great opportunities for ecologists to investigate questions that were previously difficult or impossible to address. We present an overview of potential uses of DNA barcoding relevant in the age of ecoinformatics, including applications in community ecology, species invasion, macroevolution, trait evolution, food webs and trophic interactions, metacommunities, and spatial ecology. We also outline some of the challenges and potential advances in DNA barcoding that lie ahead.     

Genetic assignment methods for gaining insight into the management of infectious disease by understanding pathogen, vector, and host movement

For many pathogens with environmental stages, or those carried by vectors or intermediate hosts, disease transmission is strongly influenced by pathogen, host, and vector movements across complex landscapes, and thus quantitative measures of movement rate and direction can reveal new opportunities for disease management and intervention. Genetic assignment methods are a set of powerful statistical approaches useful for establishing population membership of individuals. Recent theoretical improvements allow these techniques to be used to cost-effectively estimate the magnitude and direction of key movements in infectious disease systems, revealing important ecological and environmental features that facilitate or limit transmission. Here, we review the theory, statistical framework, and molecular markers that underlie assignment methods, and we critically examine recent applications of assignment tests in infectious disease epidemiology. Research directions that capitalize on use of the techniques are discussed, focusing on key parameters needing study for improved understanding of patterns of disease.     

Internet-Based Integrated Environmental Assessment Using Ontologies to Share Computational Models

New advances in Internet technologies and computer modeling provide opportunities for collaborative systems to support research and development in the field of industrial ecology. In particular, new information technologies such as semantic search engines based on ontologies could help researchers to link fragments of knowledge generated at research centers from around the world. Using a storyline of four imaginary researchers who hope to find collaborators in order to develop their research findings, we illustrate two levels of a four-level architecture for an Internet-based knowledge integration and collaboration environment for integrated environmental assessment. The foundation of the proposed architecture is a belief that computational models are an effective medium for conveying expert knowledge of various phenomena. Drawing from this premise, the first level of the architecture stands on a base of computational models that in some way represent the expert knowledge of the model builder. At the second level, we provide markup and interface definition tools to describe the type of knowledge contained in each model, together with the types of information services that can be provided.
The results of research at these two levels of an Internet-based knowledge integration environment for integrated environmental assessment in industrial ecology are presented in this article. Our work on the third level of model searching and matching and the fourth level of parametric model integration and solving will be presented in subsequent articles.     

CMEIAS Color Segmentation: An Improved Computing Technology to Process Color Images for Quantitative Microbial Ecology Studies at Single-Cell Resolution

Quantitative microscopy and digital image analysis are underutilized in microbial ecology largely because of the laborious task to segment foreground object pixels from background, especially in complex color micrographs of environmental samples. In this paper, we describe an improved computing technology developed to alleviate this limitation. The system’s uniqueness is its ability to edit digital images accurately when presented with the difficult yet commonplace challenge of removing background pixels whose three-dimensional color space overlaps the range that defines foreground objects. Image segmentation is accomplished by utilizing algorithms that address color and spatial relationships of user-selected foreground object pixels. Performance of the color segmentation algorithm evaluated on 26 complex micrographs at single pixel resolution had an overall pixel classification accuracy of 99+%. Several applications illustrate how this improved computing technology can successfully resolve numerous challenges of complex color segmentation in order to produce images from which quantitative information can be accurately extracted, thereby gain new perspectives on the in situ ecology of microorganisms. Examples include improvements in the quantitative analysis of (1) microbial abundance and phylotype diversity of single cells classified by their discriminating color within heterogeneous communities, (2) cell viability, (3) spatial relationships and intensity of bacterial gene expression involved in cellular communication between individual cells within rhizoplane biofilms, and (4) biofilm ecophysiology based on ribotype-differentiated radioactive substrate utilization. The stand-alone executable file plus user manual and tutorial images for this color segmentation computing application are freely available at . This improved computing technology opens new opportunities of imaging applications where discriminating colors really matter most, thereby strengthening quantitative microscopy-based approaches to advance microbial ecology in situ at individual single-cell resolution.     

Rapid and highly efficient genomic engineering with a novel iEditing device for programming versatile extracellular electron transfer of electroactive bacteria

The advances in synthetic biology bring exciting new opportunities to reprogram microorganisms with novel functionalities for environmental applications. For real-world applications, a genetic tool that enables genetic engineering in a stably genomic inherited manner is greatly desired. In this work, we design a novel genetic device for rapid and efficient genome engineering based on the i ntron-encoded homing-endonuclease empowered genome editing (iEditing). The iEditing device enables rapid and efficient genome engineering in Shewanella oneidensis MR-1, the representative strain of the electroactive bacteria group. Moreover, combining with the Red or RecET recombination system, the genome-editing efficiency was greatly improved, up to approximately 100%. Significantly, the iEditing device itself is eliminated simultaneously when genome editing occurs, thereby requiring no follow-up to remove the encoding system. Then, we develop a new extracellular electron transfer (EET) engineering strategy by programming the parallel EET systems to enhance versatile EET. The engineered strains exhibit sufficiently enhanced electron output and pollutant reduction ability. Furthermore, this device has demonstrated its great potential to be extended for genome editing in other important microbes. This work provides a useful and efficient tool for the rapid generation of synthetic microorganisms for various environmental applications.     

Using Interorganizational Information Systems to Support Environmental Management Efforts at ASG

We examine use of environmental information systems by ASG AB (hereafter ASG), an international logistics and transport firm headquartered in Stockholm, Sweden, as a case study to illustrate the role of information systems in life-cycle-oriented environmental management. This case provides an example of how a firm can use interorganizational information systems (IOISs) to move toward environmentally sustainable business practices. Through the use of IOISs, ASG has been able to improve its environmental performance and that of its suppliers. Further, this improved environmental performance has been a competitive advantage for ASG and enabled it to attract new business. As such, ASG's experiences illustrate how aggressive practices move environmental management beyond compliance and cost control, at which many firms have been successful, to revenue generation. The case also shows how environmentally sustainable business practices can be integrated into a firm's strategy. In addition to illustrating how ASG has used IOISs to improve environmental performance, we compare their use of environmental ISs with the expected evolution of environmental ISs presented in the Shaft and colleagues (1997) framework. Although some of ASG's experiences verify the expected progression of these types of systems, some developments are not as expected. These differences have implications for the framework.     

Prospective sustainability assessment: the case of wood in automotive applications

Purpose

The introduction of renewable materials into automotive applications is perceived as an innovative lightweight solution. Wood-based materials are advantageous in that they have potentially lower environmental impacts as compared with other materials such as steel. However, using wood per se does not automatically ensure more sustainability. Few prospective sustainability assessment methods or studies on the use of wood-based materials in automotive applications have been carried out, although these are needed to reduce unintended, negative sustainability effects and to support sustainable oriented research and innovation. Therefore, this study was conducted to assess the potential sustainability effects and consequences of introducing a wood-based component into an automotive application.

Methods

A combination of methods was used to analyze the potential sustainability effects when introducing wood into automotive applications. This prospective life cycle sustainability analysis solely relied on secondary data. The environmental impacts were analyzed using a simplified environmental life cycle assessment on the product level. A multi-regional input-output-based assessment was conducted to model the country-specific environmental and socioeconomic consequences. The potential shift in social risks and opportunities on a national scale was analyzed by conducting a generic social life cycle assessment. Various aspects of each approach differ, with each providing a specific perspective of the system under study.

Results and discussion

The results indicate that implementing wood into automotive application can have environmental, social, and economic benefits, according to most of the indicators analyzed. Mostly due to the product weight reduction due to the use of a wood-based component, the results show that environmental impacts decrease. Some possible consequences of using wood-based materials are increased value added and increasing the number of jobs in European countries. Similarly, the social risks and opportunities are shifted from countries all over the world to European countries, which perform better than developing countries according to several indicators. However, some indicators, such as migrant acceptance or local supplier quantity, perform better in the current situation.

Conclusions

The presented case study is particularly notable, because the results clearly indicate the advantages of using wood-based materials in automotive applications, although the application of such relatively holistic and complex approaches often may lead to rather indifferent pictures. Policy makers, researchers, and companies can apply this combination of methods that rely solely on generic data to obtain both feasible and informative results. These methods also allow users to link the product level assessment with a regional and social perspective and screen critical topics to support sustainability research and innovation.

     

Gene-based modelling for rice: an opportunity to enhance the simulation of rice growth and development?

Process-based crop simulation models require employment of new knowledge for continuous improvement. To simulate growth and development of different genotypes of a given crop, most models use empirical relationships or parameters defined as genetic coefficients to represent the various cultivar characteristics. Such a loose introduction of different cultivar characteristics can result in bias within a simulation, which could potentially integrate to a high simulation error at the end of the growing season when final yield at maturity is predicted. Recent advances in genetics and biomolecular analysis provide important opportunities for incorporating genetic information into process-based models to improve the accuracy of the simulation of growth and development and ultimately the final yield. This improvement is especially important for complex applications of models. For instance, the effect of the climate change on the crop growth processes in the context of natural climatic and soil variability and a large range of crop management options (e.g., N management) make it difficult to predict the potential impact of the climate change on the crop production. Quantification of the interaction of the environmental variables with the management factors requires fine tuning of the crop models to consider differences among different genotypes. In this paper we present this concept by reviewing the available knowledge of major genes and quantitative trait loci (QTLs) for important traits of rice for improvement of rice growth modelling and further requirements. It is our aim to review the assumption of the adequacy of the available knowledge of rice genes and QTL information to be introduced into the models. Although the rice genome sequence has been completed, the development of gene-based rice models still requires additional information than is currently unavailable. We conclude that a multidiscipline research project would be able to introduce this concept for practical applications.     

Canine embryonic stem cells: State of the art

Embryonic stem cells (ESCs) are permanent cell lines that can be maintained in a pluripotent, undifferentiated state. Appropriate environmental stimuli can cause them to differentiate into cell types of all three germ layers both in vitro and in vivo. Embryonic stem cells bear many opportunities for clinical applications in tissue engineering and regenerative medicine. Whereas most of our knowledge on the biology and technology of ESCs is derived from studies with mouse cells, large animal models mimicking important aspects of human anatomy, physiology, and pathology more closely than mouse models are urgently needed for studies evaluating the safety and efficacy of cell therapies. The dog is an excellent model for studying human diseases, and the availability of canine ESCs would open new possibilities for this model in biomedical research. In addition, canine ESCs could be useful for the development of cell-based approaches for the treatment of dogs. Here, we discuss the features of recently reported canine embryo-derived cells and their potential applications in basic and translational biomedical research.     

牛雄性生殖系干细胞的体外诱导分化

雄性生殖系干细胞(Male germ-line stem cells, mGSCs)是一群具有高度自我更新能力和分化潜能的细胞, 是雄性成体内唯一可复制的二倍体永生细胞。转基因技术与雄性生殖系干细胞异体及异种移植技术相结合, 将会为克隆动物、转基因动物生产及一些人类遗传性疾病的基因治疗提供新的机遇与途径。本试验采用组合酶消化和选择贴壁法, 对5月龄、6月龄牛胎儿及新生牛雄性生殖系干细胞体外培养及分化进行了研究。试验结果显示, 睾丸支持细胞对雄性生殖系干细胞体外增殖、分化所必需的, 同时对数期睾丸支持细胞对雄性生殖系干细胞贴壁、增殖与分化效果明显; 共培养16 d后, 牛雄性生殖系干细胞分化为长形精子细胞, 试验建立了牛雄性生殖系干细胞体外诱导培养分化体系。     

近20年城市遥感研究现状及其发展趋势

随着城市化进程的不断加速,城市遥感研究已成为地理学、生态学、城市规划学等学科领域主要发展方向之一。城市化使人口与经济增长的同时,也使得城市原有的生态环境状况发生改变,从而引起了一系列城市生态环境问题。城市遥感是一门多学科交叉研究领域,近年来已经取得了一系列显著的研究成果。对近年来城市遥感研究涉及的城市地表温度、边界扩张、不透水表面、景观格局以及生态安全5个方面的理论、研究方法、应用动态以及发展方向进行了较为详细的总结与探讨。主要得出如下结论：（1）数据源从单个遥感数据研究走向多源遥感数据融合发展,多源遥感数据尤其是结合高分辨率数据越来越多的被应用到城市研究的各个领域中;（2）城市遥感的研究目标不断扩展、深化和聚焦;（3）城市遥感研究已开始从二维空间向三维空间拓展;（4）城市遥感涉及的研究对象之间相互作用,相互影响在深入解读城市遥感研究理论意义和潜在挑战的基础上,结合最新研究对本文所涉及的主题进行了补充和完善,为城市典型生态环境问题的解决提供新的思路;今后应按照城市形态与构成、城市关键要素、生态环境响应、生态环境评价以及城市扩展与环境预测的体系结构进行综合分析。