Xenbase: Facilitating the Use of Xenopus to Model Human Disease.

At a fundamental level most genes, signaling pathways, biological functions and organ systems are highly conserved between man and all vertebrate species. Leveraging this conservation, researchers are increasingly using the experimental advantages of the amphibian Xenopus to model human disease. The online Xenopus resource, Xenbase, enables human disease modeling by curating the Xenopus literature published in PubMed and integrating these Xenopus data with orthologous human genes, anatomy, and more recently with links to the Online Mendelian Inheritance in Man resource (OMIM) and the Human Disease Ontology (DO). Here we review how Xenbase supports disease modeling and report on a meta-analysis of the published Xenopus research providing an overview of the different types of diseases being modeled in Xenopus and the variety of experimental approaches being used. Text mining of over 50,000 Xenopus research articles imported into Xenbase from PubMed identified approximately 1,000 putative disease- modeling articles. These articles were manually assessed and annotated with disease ontologies, which were then used to classify papers based on disease type. We found that Xenopus is being used to study a diverse array of disease with three main experimental approaches: cell-free egg extracts to study fundamental aspects of cellular and molecular biology, oocytes to study ion transport and channel physiology and embryo experiments focused on congenital diseases. We integrated these data into Xenbase Disease Pages to allow easy navigation to disease information on external databases. Results of this analysis will equip Xenopus researchers with a suite of experimental approaches available to model or dissect a pathological process. Ideally clinicians and basic researchers will use this information to foster collaborations necessary to interrogate the development and treatment of human diseases.

Xenbase: a genomic, epigenomic and transcriptomic model organism database.

Xenbase (www.xenbase.org) is an online resource for researchers utilizing Xenopus laevis and Xenopus tropicalis, and for biomedical scientists seeking access to data generated with these model systems. Content is aggregated from a variety of external resources and also generated by in-house curation of scientific literature and bioinformatic analyses. Over the past two years many new types of content have been added along with new tools and functionalities to reflect the impact of high-throughput sequencing. These include new genomes for both supported species (each with chromosome scale assemblies), new genome annotations, genome segmentation, dynamic and interactive visualization for RNA-Seq data, updated ChIP-Seq mapping, GO terms, protein interaction data, ORFeome support, and improved connectivity to other biomedical and bioinformatic resources.

Periodically poled self-frequency-doubling green laser fabricated from Nd:Mg:LiNbO3 single crystal.

Although a breakthrough in the fabrication of green laser diodes has occurred, the high costs associated with the difficulty of manufacture still present a great obstacle for its practical application. Another approach for producing a green laser, by combining a laser device and a nonlinear crystal, entails the fabrication of complex structures and exhibits unstable performance due to interface contact defects, thus limiting its application. In this work, we report the fabrication by domain engineering of high quality periodically poled LiNbO3, co-doped with Nd³âº and Mg²âº, which combines a laser medium and a high efficiency second harmonic conversion crystal into a single system that is designed to overcome the above problems. An 80 mW self-frequency doubling green laser was constructed for the first time from a periodically poled Nd:Mg:LiNbO3 crystal of 16 mm in length. This crystal can be used for developing compact, stable, highly efficient mini-solid-state-lasers, which promise to have many applications in portable laser-based spectroscopy, photo-communications, terahertz wave generation, and laser displays.