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PubMed2004

Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments.

The Onto-Tools suite is composed of an annotation database and five seamlessly integrated web-accessible data mining tools: Onto-Express (OE), Onto-Compare (OC), Onto-Design (OD), Onto-Translate (OT) and Onto-Miner (OM). OM is a new tool that provides a unified access point and an application programming interface for most annotations available. Our database has been enhanced with more than 120 new commercial microarrays and annotations for Rattus norvegicus, Drosophila melanogaster and Carnorhabditis elegans. The Onto-Tools have been redesigned to provide better biological insight, improved performance and user convenience. The new features implemented in OE include support for gene names, LocusLink IDs and Gene Ontology (GO) IDs, ability to specify fold changes for the input genes, links to the KEGG pathway database and detailed output files. OC allows comparisons of the functional bias of more than 170 commercial microarrays. The latest version of OD allows the user to specify keywords if the exact GO term is not known as well as providing more details than the previous version. OE, OC and OD now have an integrated GO browser that allows the user to customize the level of abstraction for each GO category. The Onto-Tools are available online at http://vortex.cs.wayne.edu/Projects.html.

Animals↗

PubMed2000

The Logic and Realism of the Hypothesis of Exploitation Ecosystems.

Hypotheses on trophic dynamics in terrestrial ecosystems fall into two major categories: those in which plants are assumed to be invulnerable to their consumers and those in which the build-up of plant biomass is assumed to require top-down control of folivores. The hypothesis of exploitation ecosystems (EEH) belongs to the latter category and focuses particularly on the consequences of the high energetic costs of maintenance of endotherms. Carnivorous endotherms require relatively high prey densities in order to break even. Moreover, they are dependent on folivorous prey during the limiting season, at least at high latitudes. The endotherm branch of the grazing web is thus predicted to collapse from three-link trophic dynamics (carnivores → folivores → plants → inorganic resources) to two-link dynamics (folivores → plants → inorganic resources) along gradients of decreasing primary productivity. Consequently, the vegetation of cold and unproductive areas is predicted to be under intense winter grazing pressure, which prevents the accumulation of aboveground plant biomass and excludes erect woody plants. In the most extreme habitats (e.g., polar deserts and their high alpine counterparts), even folivorous endotherms are predicted to be absent, and the scanty vegetation is predicted to be structured by preemptive competition. Within temperature-determined productivity gradients, EEH is corroborated by biomass patterns, by patterns in the structure and dynamics of carnivore, folivore, and plant communities, and by experimental results. The general idea of top-down trophic dynamics is supported for other autotroph-based systems, too, but the relevance and sufficiency of the energy constraint in explaining patterns in trophic dynamics appears to be variable. Moreover, critical empirical evidence for or against the capacity of folivorous insects to regulate plant biomass has not yet been obtained. Another open question is the ability of boreal and temperate browsers, evolved in productive environments with intense predation pressure and abundance of forage, to prevent the regeneration of the least palatable tree species. There are, thus, many open questions waiting to be answered and many exciting experiments waiting to be conducted.

herbivory↗

PubMed2005

CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences.

BACKGROUND: With the recent progress made in large-scale genome sequencing projects a vast amount of novel data is becoming available. A comparative sequence analysis, exploiting sequence information from various resources, can be used to uncover hidden information, such as genetic variation. Although there are enormous amounts of SNPs for a wide variety of organisms submitted to NCBI dbSNP and annotated in most genome assembly viewers like Ensembl and the UCSC Genome Browser, these platforms do not easily allow for extensive annotation and incorporation of experimental data supporting the polymorphism. However, such information is very important for selecting the most promising and useful candidate polymorphisms for use in experimental setups. DESCRIPTION: The CASCAD database is designed for presentation and query of candidate SNPs that are retrieved by in silico mining of high-throughput sequencing data. Currently, the database provides collections of laboratory rat (Rattus norvegicus) and zebrafish (Danio rerio) candidate SNPs. The database stores detailed information about raw data supporting the candidate, extensive annotation and links to external databases (e.g. GenBank, Ensembl, UniGene, and LocusLink), verification information, and predictions of a potential effect for non-synonymous polymorphisms in coding regions. The CASCAD website allows search based on an arbitrary combination of 27 different parameters related to characteristics like candidate SNP quality, genomic localization, and sequence data source or strain. In addition, the database can be queried with any custom nucleotide sequences of interest. The interface is crosslinked to other public databases and tightly coupled with primer design and local genome assembly interfaces in order to facilitate experimental verification of candidates. CONCLUSIONS: The CASCAD database discloses detailed information on rat and zebrafish candidate SNPs, including the raw data underlying its discovery. An advanced web-based search interface http://cascad.niob.knaw.nl allows universal access to the database content and allows various queries supporting many types of research utilizing single nucleotide polymorphisms.

Animals↗

PubMed2004

Web-based, virtual course units as a didactic concept for medical teaching.

The objective was to develop a web-based, virtual series of lectures for evidence-based, standardized knowledge transfer independent of location and time with possibilities for interactive participation and a concluding web-based online examination. Within the framework of a research project, specific Intranet and Internet capable course modules were developed together with a concluding examination. The concept of integrating digital and analogue course units supported by sound was based on FlashCam (Nexus Concepts), Flash MX (Macromedia), HTML and JavaScript. A Web server/SGI Indigo Unix server was used as a platform by the course provider. A variety of independent formats (swf, avi, mpeg, DivX, etc.) were integrated in the individual swf modules. An online examination was developed to monitor the learning effect. The examination papers are automatically forwarded by email after completion. The results are also returned to the user automatically after they have been processed by a key program and an evaluation program. The system requirements for the user PC have deliberately been kept low (Internet Explorer 5.0, Flash-Player 6, 56 kbit/s modem, 200 MHz PC). Navigation is intuitive. Users were provided with a technical online introduction and a FAQ list. Eighty-two students of dentistry in their 3rd to 5th years of study completed a questionnaire to assess the course content and the user friendliness (SPSS V11) with grades 1 to 6 (1 = 'excellent' and 6 = 'unsatisfactory'). The course units can be viewed under the URL: http://giga.rrze.uni-erlangen.de/movies/MKG/trailer and URL: http://giga.rrze.uni-erlangen.de/movies/MKG/demo/index. Some 89% of the students gave grades 1 (excellent) and 2 (good) for accessibility independent of time and 83% for access independent of location. Grades 1 and 2 were allocated for an objectivization of the knowledge transfer by 67% of the students and for the use of video sequences for demonstrating surgical techniques by 91% of the students. The course units were used as an optional method of studying by 87% of the students; 76% of the students made use of this facility from home; 83% of the students used Internet Explorer as a browser; 60% used online streaming and 35% downloading as the preferred method for data transfer. The course units contribute to an evidence-based objectivization of multimedia knowledge transfer independent of time and location. Online examinations permit automatic monitoring and evaluation of the learning effect. The modular structure permits easy updating of course contents. Hyperlinks with literature sources facilitate study.

Computer-Assisted Instruction↗