Ecology. Words (and axes) fly over transgenic trees.
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Biotechnology↗
SEARCH · PubMed Health
Results for “ecosystem engineer”
Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.
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Setting moral limits on technology. The Jewish perspective differs in some ways from Catholic and Protestant ones.
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Bioethics↗
Genetics and bioethics: the current state of affairs.
The pursuit of genetic knowledge has such emotional, social, scientific, and financial importance that it has been compared to the divine quest for the Holy Grail, and to the calamity of opening Pandora's Box. Therefore, it comes as no surprise that the recent announcement of a completed blueprint for the human genome has fueled calls for both increased research and increased precautions. This new era, which holds the potential promise of advances in medicine, agriculture and other areas, also requires the careful investigation of a myriad of issues. Those issues such as informed consent, patenting, privacy, and confidentiality, have been explored in at least some detail. Others, such as equity, mutual respect, empowering education, consensus building, and planning for long-term survival, have not been as fully examined, nor have they been as comprehensively integrated into mainstream thinking. To facilitate this, we need to implement an ethical approach that leads us to ask critical questions about the appropriate use of our new tools.
Bioethics↗
Potential opportunities and problems for genetically altered rumen microorganisms.
Rumen microbiologists are beginning to use genetic engineering techniques, and researchers should carefully consider both the potentials and limitations of using this technology to manipulate the rumen microbial ecosystem. Despite encouraging rhetoric, it is difficult to identify specific examples where genetic engineering would enhance ruminal performance. Many practical problems (lactic acidosis, deamination, etc.) might be better served by genetic engineering approaches that delete rather than add genes. The difficulty with this approach is that a highly selective means of preventing wild types from recolonizing the rumen would be needed. The addition of specific genes is confounded by 1) the fact that the rumen microorganisms are already adapted to the rumen, 2) the diversity of species inhabiting the rumen and 3) the complexity of interactions among these species. Aspects such as increased rates of cellulose digestion and changes in amino acid composition of the microflora are particularly sensitive to these biological constraints. Genetic engineering has, however, the potential to alleviate new limitations that humans have imposed on the rumen (detoxification, resistance to low pH, the digestion of novel feed materials, etc). A particular strategy of moving acid-resistant cellulose genes into noncellulytic, but acid-resistant, rumen bacteria is described.
Animals↗
[Effects of different recover and restoration measures on soil quality in Karst Rocky Desertification Region].
The soil quality of karst rocky desertification region were taken as case studies with four different recover and restoration measures for 13 years long-term fixed site harnessing in Guizhou Province, and plant diversity and soil fertility over different measures were investigated. The results showed that the plant diversity was the lowest, soil feritilities and ecosystem environment were the poorest in the control land with no restoration measure. The plant diversity rised evidently and the soil quality restorated to some degree in the measure of changing into a Zanthorylum bungeamum woods (Measure A) and the measure of changing into multispecies woods (Measure B). The diversity of auxiliary community were resumed to the best degree and soil quality were resumed to the best degree in measure of closed forest (Measure C). The plant diversity was higher and soil quality was best in measure of secondary forest (Measure D). Therefore, the proper biological measures and the essential engineering measures are effective to recover the serious degradation ecosystem in Karst mountain of Guizhou Province.
Conservation of Natural Resources↗
OLS4: a new Ontology Lookup Service for a growing interdisciplinary knowledge ecosystem.
SUMMARY: The Ontology Lookup Service (OLS) is an open source search engine for ontologies which is used extensively in the bioinformatics and chemistry communities to annotate biological and biomedical data with ontology terms. Recently, there has been a significant increase in the size and complexity of ontologies due to new scales of biological knowledge, such as spatial transcriptomics, new ontology development methodologies, and curation on an increased scale. Existing Web-based tools for ontology browsing such as BioPortal and OntoBee do not support the full range of definitions used by today's ontologies. In order to support the community going forward, we have developed OLS4, implementing the complete OWL2 specification, internationalization support for multiple languages, and a new user interface with UX enhancements such as links out to external databases. OLS4 has replaced OLS3 in production at EMBL-EBI and has a backward compatible API supporting users of OLS3 to transition. AVAILABILITY AND IMPLEMENTATION: The source code of OLS is available at https://github.com/EBISPOT/ols4 and DOI 10.5281/zenodo.14960290 with Apache 2.0 License. A freely available implementation is accessible at https://www.ebi.ac.uk/ols4.
Biological Ontologies↗
Evaluation of aquatic sediment microcosms and their use in assessing possible effects of introduced microorganisms on ecosystem parameters.
In this paper we describe a sediment microcosm system consisting of 20 undisturbed, layered sediment cores with overlying site water which are incubated under identical conditions of temperature, light, stirring rate of overlying water, and water exchange rate. Ecosystem parameters (nutrient level, photosynthetic potential, community structure of heterotrophic bacteria, thymidine incorporation rate, and oxygen microgradients) of the laboratory microcosms and the source ecosystem were compared and shown to be indistinguishable for the first 2 weeks. In weeks 3 and 4, small differences were detectable in the nutrient level, community structure of heterotrophic bacteria, and thymidine incorporation rate. However, the photosynthetic potential, depth profiles of heterotrophic bacterial community structure, and oxygen microgradients were maintained throughout the incubation period and did not differ between laboratory microcosms and the source ecosystem. The microcosm system described here would thus appear to be a valid model of aquatic sediments for up to 4 weeks; the actual period would depend on the sediment source and incubation temperature. The validated systems were used with Rhine river sediment to assess possible effects on ecosystem parameters of Pseudomonas sp. strain B13 FR1(pFRC20P), a genetically engineered microorganism (GEM) that had been constructed to degrade mixtures of halo- and alkylbenzoates and -phenols. The GEM survived in the surface sediment at densities of 5 x 10(4) to 5 x 10(5)/g (dry weight) for 4 weeks and degraded added chloro- and methylaromatics. The GEM did not measurably influence ecosystem parameters such as photosynthesis, densities of selected heterotrophic bacteria, thymidine incorporation rate, and oxygen microgradients. Thus, the microcosm system described here would seem to be useful for the study of the ecology of biodegradation and the fate and effect of microorganisms introduced into the environment.
Bacteria↗
Ethical debates in genetic engineering: U.S. scientists' attitudes on patenting, germ-line research, food labeling, and agri-biotech issues.
A 1995 survey of 1,257 scientists working in the field of recombinant DNA research indicates wide areas of agreement as well as some noteworthy divisions when it comes to such thorny questions as patenting, germ-line research, food labeling, and biodiversity. In general, the scientists surveyed approve of patenting living organisms that result from rDNA research, but vary significantly on what should be patentable. They advocate human germ-line therapy, yet have reservations about using it for any but serious diseases. They oppose mandatory labeling of biologically engineered food products, but understand that the public has a right to know and advocate openness. Finally, they favor development of threats to biodiversity and maintain that publicly funded researchers should be legally obligated to consider the potential environmental effects of their research. Some clear differences arise between scientists working in industry and those in academia and between men and women.
Access to Information↗
Dimensional approaches to designing better experimental ecosystems: a practitioners guide with examples.
Enclosed, experimental ecosystems ("mesocosms") are now widely used research tools in ecology. However, the small size, short duration and often simplified biological and physical complexity of mesocosm experiments raises questions about extrapolating results from these miniaturized ecosystems to nature. Dimensional analysis, a technique widely used in engineering to create scale models, employs "compensatory distortion" as a means of maintaining functional similarity in properties and relationships of interest. An earlier paper outlined a general approach to applying dimensional analysis to the construction and interpretation of mesocosm experiments (Petersen and Hastings in Am Nat 157:324, 2001). In this paper we use examples, largely drawn from the aquatic literature, to illustrate how dimensional approaches might be used to maintain key ecological properties. Such key properties include effective habitat size, environmental variability, vertical and horizontal gradients, and interactions among habitats. We distinguish both continuous and discrete approaches that can be used to achieve functional similarity through compensatory distortion. In addition to its potential as a tool for improving the realism of experimental ecosystems, the dimensional approach points towards new options for developing, testing and advancing our understanding of scaling relationships in nature.
Body Size↗
Molecular strategies for gene containment in transgenic crops.
The potential of genetically modified (GM) crops to transfer foreign genes through pollen to related plant species has been cited as an environmental concern. Until more is known concerning the environmental impact of novel genes on indigenous crops and weeds, practical and regulatory considerations will likely require the adoption of gene-containment approaches for future generations of GM crops. Most molecular approaches with potential for controlling gene flow among crops and weeds have thus far focused on maternal inheritance, male sterility, and seed sterility. Several other containment strategies may also prove useful in restricting gene flow, including apomixis (vegetative propagation and asexual seed formation), cleistogamy (self-fertilization without opening of the flower), genome incompatibility, chemical induction/deletion of transgenes, fruit-specific excision of transgenes, and transgenic mitigation (transgenes that compromise fitness in the hybrid). As yet, however, no strategy has proved broadly applicable to all crop species, and a combination of approaches may prove most effective for engineering the next generation of GM crops.
Crops, Agricultural↗
Genetic modification and selection of microorganisms for growth on Mars.
Genetic engineering has often been suggested as a mechanism for improving the survival prospects of terrestrial microoganisms when seeded on Mars. The survival characteristics that these pioneer microorganisms could be endowed with and a variety of mechanisms by which this can be achieved are discussed, together with an overview of some of the potential hurdles that must be overcome. Also, a number of biologically useful properties for these microorganisms are presented that could facilitate the initial human colonisation and ultimately the planetary engineering of Mars.
Bacteria, Anaerobic↗
Genetic transformation: a powerful tool for dissection of adaptive traits in trees.
Plant transformation and regeneration systems have become indispensable parts of gene discovery and functional characterization over the last two decades. Adoption of transformation methods in studies of plant adaptation to natural environments has been slow. This is a result of poor genomic knowledge and inefficient transformation systems for species dominating terrestrial ecosystems, and logistical difficulties in conducting field tests of genetically engineered organisms. In trees, where long generation cycles, high background polymorphism, large sizes and outcrossing systems of mating make production of near-isogenic lines and large experiments difficult, transformation is an attractive alternative for establishing direct linkages between genes and adaptively significant phenotypes. Here, we outline the capabilities, challenges, and prospects for transformation to become a significant tool for studying the ecophysiological adaptation of trees to the environment. Focusing on poplars (genus Populus) as model system, we describe how transformation-based approaches can provide insights into the genes that control adaptive traits. The availability of the poplar genome sequence, along with its large expressed sequences tag (EST) databanks, facile transformation and rapid growth, enable reverse genetic approaches to be used to test virtually any hypothesis of gene function.
Adaptation, Physiological↗
Engineering hypervirulence in a mycoherbicidal fungus for efficient weed control.
Agents proposed for biocontrol of major weeds in arable row-crop agriculture have not met expectations because an evolutionary balance has developed between microorganism and weed, even when the mycoherbicide is used inundatively at very high levels (>10(4)spores/cm<(2)). Sufficient virulence can be achieved by transferring genes to the microorganism, tipping the evolutionary balance. Virulence was increased ninefold and was more rapidly effected; furthermore, the requirement for a long duration at high humidity was decreased by introducing NEP1 encoding a phytotoxic protein, to an Abutilon theophrasti-specific, weakly mycoherbicidal strain of Colletotrichum coccodes. The parent strain was at best infective on juvenile cotyledons of this intransigent weed. The transgenic strain was lethal through the three-leaf stage, a sufficient time window to control this asynchronously germinating weed. Strategies of coupling virulence genes with fail-safe mechanisms to prevent spread (due to broadened host range) and to mitigate transgene introgression into crop pathogens could be very useful in the biocontrol of major weeds in row crops.
Agriculture↗
Genetic engineering in plants.
Until now most research, and its funding, has been focused on animal and human health care as well as simple microbiological model systems such as Escherichia coli and yeast. Molecular plant studies have generally lagged behind, often simply adapting discoveries from the animal field to plants. Clearly, good health and the efficient tackling of diseases is crucial for the well-being of humans, and good remedies have a high economic value for the pharmaceutical industry. However, one should not forget that plants are an essential component of the large ecosystem that is our planet. They are not only the basic food producers but they are also necessary for a balanced atmosphere (oxygen production) and stable and viable climates. Especially in this period of demographic explosion and growing environmental deterioration, there is a need to rebuild our agricultural systems. Plants also have a wide variety of 'non-food' uses, for instance as energy sources, construction materials, or cosmetics. Last, but not least, they produce a lot of chemicals that can be used as pharmaceuticals. The growing awareness of the importance of plants has coincided with the development of plant molecular biology. Specific features make them ideally suited for gene engineering and genetic studies in general.
Biotechnology↗
Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.
Emerging spatial multiomics technologies provide an increasingly large amount of information content at multiple scales. However, it remains challenging to efficiently represent and harmonize diverse spatial datasets. Here we present Giotto Suite, a suite of modular packages that provides scalable and extensible end-to-end solutions for multiscale and multiomic data analysis, integration and visualization. At its core, Giotto Suite is centered around an innovative data framework, allowing the representation and integration of spatial omics data in a technology-agnostic manner. Giotto Suite integrates molecular, morphology, spatial and annotated feature information to create a responsive and flexible workflow, as demonstrated by applications to several state-of-the-art spatial technologies. Furthermore, Giotto Suite builds upon interoperable interfaces and data structures that bridge the established fields of genomics and spatial data science in R, thereby enabling independent developers to create custom-engineered pipelines. As such, Giotto Suite creates an immersive and multiscale ecosystem for spatial multiomic data analysis.
Genomics↗
A distinct urban biogeochemistry?
Most of the global human population lives in urban areas where biogeochemical cycles are controlled by complex interactions between society and the environment. Urban ecology is an emerging discipline that seeks to understand these interactions, and one of the grand challenges for urban ecologists is to develop models that encompass the myriad influences of people on biogeochemistry. We suggest here that existing models, developed primarily in unmanaged and agricultural ecosystems, work poorly in urban ecosystems because they do not include human biogeochemical controls such as impervious surface proliferation, engineered aqueous flow paths, landscaping choices, and human demographic trends. Incorporating these human controls into biogeochemical models will advance urban ecology and will require enhanced collaborations with engineers and social scientists.
Biochemical Phenomena↗
Survival of genetically modified Escherichia coli carrying extraneous antibiotic resistance gene through microbial interactions.
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Animals↗
Gene co-ops and the biotrade: translating genetic resource rights into sustainable development.
The 1992 Convention on Biological Diversity marks a basic change in the international status of genetic resources. Prior to the Convention, these resources were considered to be the "heritage of mankind.' Although the intent of this open access regime was to ensure the widespread availability of genetic resources for agriculture and industry, commercial use of the resources provided no additional economic incentive for conservation by source countries. The Biodiversity Convention corrects this policy failure by establishing that states have sovereign rights over their genetic resources, thereby enabling market incentives to complement various multilateral mechanisms that might directly fund biodiversity conservation. A number of obstacles face countries that are translating this broad right to regulate access into specific policies, laws, and regulations designed to meet conservation and development objectives. A review of these obstacles and of trends in technological development suggest that nations and developing country institutions should take a set of actions to develop access legislation and Material Transfer Agreements, establish biodiversity "cooperatives' and intermediary institutions to facilitate information exchange, develop minimum standards for access legislation, and require that prior informed consent of local communities be obtained by all biodiversity collectors.
Animal Population Groups↗