Comparison of static immersion and intravenous injection systems for exposure of zebrafish embryos to the natural pathogen Edwardsiella tarda

<p>Abstract</p> <p>Background</p> <p>The zebrafish embryo is an important <it>in vivo </it>model to study the host innate immune response towards microbial infection. In most zebrafish infectious disease models, infection is achieved by micro-injection of bacteria into the embryo. Alternatively, <it>Edwardsiella tarda</it>, a natural fish pathogen, has been used to treat embryos by static immersion. In this study we used transcriptome profiling and quantitative RT-PCR to analyze the immune response induced by <it>E. tarda </it>immersion and injection.</p> <p>Results</p> <p>Mortality rates after static immersion of embryos in <it>E. tarda </it>suspension varied between 25-75%, while intravenous injection of bacteria resulted in 100% mortality. Quantitative RT-PCR analysis on the level of single embryos showed that expression of the proinflammatory marker genes <it>il1b </it>and <it>mmp9 </it>was induced only in some embryos that were exposed to <it>E. tarda </it>in the immersion system, whereas intravenous injection of <it>E. tarda </it>led to <it>il1b </it>and <it>mmp9 </it>induction in all embryos. In addition, microarray expression profiles of embryos subjected to immersion or injection showed little overlap. <it>E. tarda</it>-injected embryos displayed strong induction of inflammatory and defense genes and of regulatory genes of the immune response. <it>E. tarda</it>-immersed embryos showed transient induction of the cytochrome P450 gene <it>cyp1a</it>. This gene was also induced after immersion in <it>Escherichia coli </it>and <it>Pseudomonas aeruginosa </it>suspensions, but, in contrast, was not induced upon intravenous <it>E. tarda </it>injection. One of the rare common responses in the immersion and injection systems was induction of <it>irg1l</it>, a homolog of a murine immunoresponsive gene of unknown function.</p> <p>Conclusions</p> <p>Based on the differences in mortality rates between experiments and gene expression profiles of individual embryos we conclude that zebrafish embryos cannot be reproducibly infected by exposure to <it>E. tarda </it>in the immersion system. Induction of <it>il1b </it>and <it>mmp9 </it>was consistently observed in embryos that had been systemically infected by intravenous injection, while the early transcriptional induction of <it>cyp1a </it>and <it>irg1l </it>in the immersion system may reflect an epithelial or other tissue response towards cell membrane or other molecules that are shed or released by bacteria. Our microarray expression data provide a useful reference for future analysis of signal transduction pathways underlying the systemic innate immune response versus those underlying responses to external bacteria and secreted virulence factors and toxins.</p

Identification of genes related to germination in aged maize seed by screening natural variability

Ageing reduces vigour and viability in maize inbred lines due to non-heritable degenerative changes. Besides non-heritable genetic changes due to chromosome aberrations and damage in the DNA sequence, heritable changes during maize conservation have been reported. Genetic variability among aged seeds of inbred lines could be used for association studies with seed germination. The objective of this study was to identify genes related to germination in aged seeds. The sweet corn inbred line P39 and the field corn inbred line EP44 were used as plant material. Bulks of living and dead seeds after 20 and 22 years of storage were compared by using simple sequence repeats (SSRs) and, when the bulks differed for a marker, the individual grains were genotyped. Differences between dead and living seeds could be explained by residual variability, spontaneous mutation, or ageing. Variability was larger for chromosome 7 than for other chromosomes, and for distal than for proximal markers, suggesting some relationships between position in the genome and viability in aged seed. Polymorphic SSRs between living and dead seeds were found in six known genes, including pathogenesis-related protein 2, superoxide dismutase 4, catalase 3, opaque endosperm 2, and metallothionein1 that were related to germination, along with golden plant 2. In addition, five novel candidate genes have been identified; three of them could be involved in resistance to diseases, one in detoxification of electrophillic compounds, and another in transcription regulation. Therefore, genetic variability among aged seeds of inbreds was useful for preliminary association analysis to identify candidate genes

XDM-Compatible Service Repository for User-Centric Service Creation and Discovery

The key objective of OPUCE system is to enable the participation of end-users in the management of their own services, by providing them with innovative tools which allow an easy creation and delivery of personalized communication and information services. This paper describes the OPUCE service and component repository, which extends the OMA OSPE service model storage approach XDM. By integrating an ebXML registry using the native notification mechanisms of XDM, the search capability of the repository is dramatically improved. Moreover, this repository also exploits semantic Web technology to provide an intuitive visualized browser for convenient service exploring

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection

Animal science

ODS ferritic steels obtained from gas atomized powders through the STARS processing route: Reactive synthesis as an alternative to mechanical alloying

Oxide Dispersion Strengthened Ferritic Stainless Steels (ODS FS) are candidate materials for structural components in fusion reactors. Their ultrafine microstructure and the presence of a very stable dispersion of Y-Ti-O nanoclusters provide reasonable fracture toughness, high mechanical and creep strength, and resistance to radiation damage at the operation temperature, up to about 750 °C. An innovative route to produce ODS FS with composition Fe-14Cr-2W-0.3Ti-0.3Y2O3 (wt.%), named STARS (Surface Treatment of gas Atomized powder followed by Reactive Synthesis), is presented. This route avoids the mechanical alloying (MA) of the elemental or prealloyed powders with yttria to dissolve the yttrium in the ferritic matrix. In this study, starting powders containing Ti and Y are obtained by gas atomization at laboratory and industrial scale. Then, a metastable Cr- and Fe- rich oxide layer is formed on the surface of the powder particles. During consolidation by HIP the metastable oxide layer at Prior Particle Boundaries (PPBs) dissociates, the oxygen diffuses towards saturated solutions or metallic Ti- and Y-rich particles, and Y-Ti-O nano-oxides (mainly Y2TiO5) precipitate in the ferritic matrix. Detailed Microstructural characterization by X-ray Photoelectron Spectroscopy (XPS), X-ray Absorption Spectroscopy (XAS), Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) of powders and consolidated materials is presented and correlated with mechanical behaviour

Robotic injection of zebrafish embryos for high-throughput screening in disease models

The increasing use of zebrafish larvae for biomedical research applications is resulting in versatile models for a variety of human diseases. These models exploit the optical transparency of zebrafish larvae and the availability of a large genetic tool box. Here we present detailed protocols for the robotic injection of zebrafish embryos at very high accuracy with a speed of up to 2000 embryos per hour. These protocols are benchmarked for several applications: (1) the injection of DNA for obtaining transgenic animals, (2) the injection of antisense morpholinos that can be used for gene knock-down, (3) the injection of microbes for studying infectious disease, and (4) the injection of human cancer cells as a model for tumor progression. We show examples of how the injected embryos can be screened at high-throughput level using fluorescence analysis. Our methods open up new avenues for the use of zebrafish larvae for large compound screens in the search for new medicines

The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.

BACKGROUND: The practice and research of medicine generates considerable quantities of data and model resources (DMRs). Although in principle biomedical resources are re-usable, in practice few can currently be shared. In particular, the clinical communities in physiology and pharmacology research, as well as medical education, (i.e. PPME communities) are facing considerable operational and technical obstacles in sharing data and models. FINDINGS: We outline the efforts of the PPME communities to achieve automated semantic interoperability for clinical resource documentation in collaboration with the RICORDO project. Current community practices in resource documentation and knowledge management are overviewed. Furthermore, requirements and improvements sought by the PPME communities to current documentation practices are discussed. The RICORDO plan and effort in creating a representational framework and associated open software toolkit for the automated management of PPME metadata resources is also described. CONCLUSIONS: RICORDO is providing the PPME community with tools to effect, share and reason over clinical resource annotations. This work is contributing to the semantic interoperability of DMRs through ontology-based annotation by (i) supporting more effective navigation and re-use of clinical DMRs, as well as (ii) sustaining interoperability operations based on the criterion of biological similarity. Operations facilitated by RICORDO will range from automated dataset matching to model merging and managing complex simulation workflows. In effect, RICORDO is contributing to community standards for resource sharing and interoperability.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Differences in the Cognitive Skills of Bonobos and Chimpanzees

While bonobos and chimpanzees are both genetically and behaviorally very similar, they also differ in significant ways. Bonobos are more cautious and socially tolerant while chimpanzees are more dependent on extractive foraging, which requires tools. The similarities suggest the two species should be cognitively similar while the behavioral differences predict where the two species should differ cognitively. We compared both species on a wide range of cognitive problems testing their understanding of the physical and social world. Bonobos were more skilled at solving tasks related to theory of mind or an understanding of social causality, while chimpanzees were more skilled at tasks requiring the use of tools and an understanding of physical causality. These species differences support the role of ecological and socio-ecological pressures in shaping cognitive skills over relatively short periods of evolutionary time