Experimental investigation of taxon-specific response of alkaline phosphatase activity in natural freshwater phytoplankton

It is widely accepted that alkaline phosphatase activity (APA) is an efficient indicator of phosphate limitation in freshwater phytoplankton communities. In this study, we investigated whether the response in APA to phosphate limitation differs among the taxa in a mixed phytoplankton assemblage. We used the new enzyme-labeled fluorescence (ELF) technique, which allows microscopic detection of phosphate limitation in individual cells of multiple species. The most prominent findings of this study were that alkaline phosphatase (AP) was induced in many, but not all taxa and that different taxa, as well as different cells within a single taxon, experienced different degrees of phosphate stress under the same environmental conditions. Our approach was to manipulate the limiting nutrient in a natural freshwater phytoplankton community by incubating lake water in the laboratory. We induced nitrogen (N) or phosphate limitation through additions of inorganic nutrients. Both the ELF assay and bulk APA indicated that the lake phytoplankton were not phosphate limited at the start of the experiment. During the experiment, several chlorophyte taxa (e.g., Eudorina and an unidentified solitary spiny coccoid) were driven to phosphate limitation when inorganic N was added, as evidenced by a higher percentage of ELF-labeled cells relative to controls, whereas other chlorophyte taxa such as Actinastrum and Dicryosphaerium were not phosphate stressed under these conditions. In the phosphate-limited treatments, little or no ELF labeling was observed in any cyanobacterial taxa. Furthermore, all taxa observed after the ELF labeling procedure (>10-mum fraction) were labeled with ELF at least on one occasion, demonstrating the wide applicability of the ELF method. By using ELF labeling in tandem with bulk APA, the resolution and analysis of phosphate limitation was increased, allowing the identification of specific phosphate-stressed taxa

Importance of Suspended Particulates in Riverine Delivery of Bioavailable Nitrogen to Coastal Zones

Total nitrogen (TN) loadings in riverine sediments and their coastal depocenters were compared for Il river systems worldwide to assess the potential impact of riverine particulates on coastal nitrogen budgets. Strong relationships between sediment specific surface area and TN allow these impacts to be estimated without the intense sampling normally required to achieve such budgets. About half of the systems showed higher nitrogen loadings in the riverine sediments than those from the coastal depocenter. In spite of uncertainties, these comparisons indicate that large, turbid rivers, such as the Amazon, Huanghe, and the Mississippi, deliver sediments that in turn release significant or major fractions of the total riverine nitrogen delivery. Riverine particulates must therefore be considered an essential factor in watershed nutrient loading to coastal ecosystems and may affect delivered nutrient ratios as well as total nutrient loading. The relative importance of particulate versus dissolved delivery has decreased over recent decades in the Mississippi as a result of damming and fertilizer use in the watershed

The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future

OntoFox: web-based support for ontology reuse

<p>Abstract</p> <p>Background</p> <p>Ontology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, the OBO Foundry principles require that these ontologies be open and non-redundant, avoiding duplication of terms through the re-use of existing resources. As current options to do so present various difficulties, a new approach, MIREOT, allows specifying import of single terms. Initial implementations allow for controlled import of selected annotations and certain classes of related terms.</p> <p>Findings</p> <p>OntoFox <url>http://ontofox.hegroup.org/</url> is a web-based system that allows users to input terms, fetch selected properties, annotations, and certain classes of related terms from the source ontologies and save the results using the RDF/XML serialization of the Web Ontology Language (OWL). Compared to an initial implementation of MIREOT, OntoFox allows additional and more easily configurable options for selecting and rewriting annotation properties, and for inclusion of all or a computed subset of terms between low and top level terms. Additional methods for including related classes include a SPARQL-based ontology term retrieval algorithm that extracts terms related to a given set of signature terms and an option to extract the hierarchy rooted at a specified ontology term. OntoFox's output can be directly imported into a developer's ontology. OntoFox currently supports term retrieval from a selection of 15 ontologies accessible via SPARQL endpoints and allows users to extend this by specifying additional endpoints. An OntoFox application in the development of the Vaccine Ontology (VO) is demonstrated.</p> <p>Conclusions</p> <p>OntoFox provides a timely publicly available service, providing different options for users to collect terms from external ontologies, making them available for reuse by import into client OWL ontologies.</p

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Assessing Coral Reef Fish Population and Community Changes in Response to Marine Reserves in the Dry Tortugas, Florida, USA

The efficacy of no-take marine reserves (NTMRs) to enhance and sustain regional coral reef fisheries was assessed in Dry Tortugas, Florida, through 9 annual fishery-independent research surveys spanning 2 years before and 10 years after NTMR implementation. A probabilistic sampling design produced precise estimates of population metrics of more than 250 exploited and non-target reef fishes. During the survey period more than 8100 research dives utilizing SCUBA Nitrox were optimally allocated using stratified random sampling. The survey domain covered 326 km2, comprised of eight reef habitats in four management areas that offered different levels of resource protection: the Tortugas North Ecological Reserve (a NTMR), Dry Tortugas National Park (recreational angling only), Dry Tortugas National Park Research Natural Area (a NTMR), and southern Tortugas Bank (open to all types of fishing). Surveys detected significant changes in population occupancy, density, and abundance within management zones for a suite of exploited and non-target species. Increases in size, adult abundance, and occupancy rates were detected for many principal exploited species in protected areas, which harbored a disproportionately greater number of adult spawning fishes. In contrast, density and occupancy rates for aquaria and non-target reef fishes fluctuated above and below baseline levels in each management zone. Observed decreases in density of exploited species below baseline levels only occurred at the Tortugas Bank area open to all fishing. Our findings indicate that these NTMRs, in conjunction with traditional fishery management control strategies, are helping to build sustainable fisheries while protecting the fundamental ecological dynamics of the Florida Keys coral-reef ecosystem

RDFScape: Semantic Web meets Systems Biology

<p>Abstract</p> <p>Background</p> <p>The recent availability of high-throughput data in molecular biology has increased the need for a formal representation of this knowledge domain. New ontologies are being developed to formalize knowledge, e.g. about the functions of proteins. As the Semantic Web is being introduced into the Life Sciences, the basis for a distributed knowledge-base that can foster biological data analysis is laid. However, there still is a dichotomy, in tools and methodologies, between the use of ontologies in biological investigation, that is, in relation to experimental observations, and their use as a knowledge-base.</p> <p>Results</p> <p>RDFScape is a plugin that has been developed to extend a software oriented to biological analysis with support for reasoning on ontologies in the semantic web framework. We show with this plugin how the use of ontological knowledge in biological analysis can be extended through the use of inference. In particular, we present two examples relative to ontologies representing biological pathways: we demonstrate how these can be abstracted and visualized as interaction networks, and how reasoning on causal dependencies within elements of pathways can be implemented.</p> <p>Conclusions</p> <p>The use of ontologies for the interpretation of high-throughput biological data can be improved through the use of inference. This allows the use of ontologies not only as annotations, but as a knowledge-base from which new information relevant for specific analysis can be derived.</p

The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain

<p>Abstract</p> <p>Background</p> <p>Skeletal dysplasias are a rare and heterogeneous group of genetic disorders affecting skeletal development. Patients with skeletal dysplasias suffer from many complex medical issues including degenerative joint disease and neurological complications. Because the data and expertise associated with this field is both sparse and disparate, significant benefits will potentially accrue from the availability of an ontology that provides a shared conceptualisation of the domain knowledge and enables data integration, cross-referencing and advanced reasoning across the relevant but distributed data sources.</p> <p>Results</p> <p>We introduce the design considerations and implementation details of the Bone Dysplasia Ontology. We also describe the different components of the ontology, including a comprehensive and formal representation of the skeletal dysplasia domain as well as the related genotypes and phenotypes. We then briefly describe SKELETOME, a community-driven knowledge curation platform that is underpinned by the Bone Dysplasia Ontology. SKELETOME enables domain experts to use, refine and extend and apply the ontology without any prior ontology engineering experience--to advance the body of knowledge in the skeletal dysplasia field.</p> <p>Conclusions</p> <p>The Bone Dysplasia Ontology represents the most comprehensive structured knowledge source for the skeletal dysplasias domain. It provides the means for integrating and annotating clinical and research data, not only at the generic domain knowledge level, but also at the level of individual patient case studies. It enables links between individual cases and publicly available genotype and phenotype resources based on a community-driven curation process that ensures a shared conceptualisation of the domain knowledge and its continuous incremental evolution.</p